Вы находитесь на странице: 1из 19

PERSPECTIVES

have focused largely on a limited region of


OPINION
chemical space that is defined by established
molecular frameworks.
Expanding the medicinal chemistry This raises the question of the potential
impact of synthetic chemistry biases and
synthetic toolbox limitations on the chemical and structural
characteristics of compounds explored
so far in medicinal chemistry efforts. A
Jonas Boström, Dean G. Brown, Robert J. Young and György M. Keserü pioneering investigation of this issue was
reported in 2008 by Roughley and Jordan12.
Abstract | The key objectives of medicinal chemistry are to efficiently design and Analysing a relatively small data set of
synthesize bioactive compounds that have the potential to become safe and published structure–activity relationship
efficacious drugs. Most medicinal chemistry programmes rely on screening (SAR) studies from AstraZeneca,
compound collections populated by a range of molecules derived from a set of GlaxoSmithKline and Pfizer, they found that
known and robust chemistry reactions. Analysis of the role of synthetic organic medicinal chemistry programmes are based
on a limited number of reactions. This
chemistry in subsequent hit and lead optimization efforts suggests that only a few
finding was recently reinforced on a larger
reactions dominate. Thus, the uptake of new synthetic methodologies in drug data set 13, based on a literature analysis at
discovery is limited. Starting from the known limitations of reaction parameters, two points (1984 and 2014). Brown and
synthesis design tools, synthetic strategies and innovative chemistries, here we Boström confirmed that a few reactions
highlight opportunities for the expansion of the medicinal chemists’ synthetic dominate contemporary practice and,
toolbox. More intense crosstalk between synthetic and medicinal chemists in more importantly, that new synthetic
discoveries have a very slow uptake. Five
industry and academia should enable enhanced impact of new methodologies in major reactions are the most dominant and
future drug discovery. most frequently used13 (FIG. 1a) and represent
more than 80% of reactions used for drug
Medicinal chemistry encompasses the these characteristics by 2010; the top 50 discovery purposes12.
design and synthesis of novel bioactive frameworks still covered half (48–52%) It should be noted that most analyses of
compounds that have the potential to of approved and experimental drugs7. this type will show power-law distributions.
become drugs. It typically involves cycles Furthermore, Taylor and colleagues found Thus, a relatively small number of reactions
of iterative optimization of compounds that the 1,175 drugs marketed before 2013 dominate the lists, with long tails of
to enhance their efficacy, safety and contained 351 unique ring systems8, which infrequently used synthetic reactions.
pharmacokinetic characteristics, leading represent 2% of the possible combinations Nonetheless, the most frequently used
to the selection of a candidate drug that of known monocyclic and bicyclic ring reactions (as well as the top frameworks and
ultimately will need to be manufactured systems9. This study also revealed that four ring systems in drugs derived from these
on a large scale if it progresses towards out of five (83%) of the most frequently reaction types) in medicinal chemistry have
regulatory approval. used ring systems were first used in drugs not changed much over time. A similar
An astronomical number of developed before 1983 and, on average, six conclusion was drawn by Schneider and
small-molecule compounds are purportedly new ring systems appear each year, found in colleagues, who analysed a comprehensive
synthetically feasible1,2,3, so although less than one-third of the new drugs. set of 1.15 million unique reactions in the
the number of reported molecules has A similar conclusion was drawn by Pitt and pharmaceutical patent literature14. The
reached 135 million, this still represents colleagues10, who showed that very few authors concluded that the medicinal
only a tiny proportion of the feasible (7%) of the 24,000 reasonable monocyclic chemistry toolkit is biased towards a small
drug-like compounds4. In a pioneering and bicyclic ring systems collected in the set of standard reaction types, in particular
investigation into the characteristics of the VEHICLe database had been synthesized. to amide bond formations and Suzuki–
kind of compounds that have so far been More importantly, they also concluded that Miyaura couplings; 123 different reaction
developed as drugs in 1996, Bemis and the rate of publication of novel examples types accounted for 95% of the reactions,
Murcko reported that half of the 5,120 drug was 5−10 per year. More recently, Reymond which increased to 159 (27%) over 35 years,
molecules analysed could be described by and co‑workers enumerated the chemical but this growth has stagnated over the
only 32 of the most frequently occurring universe of ring systems and found that the past 10 years. Alkylation and acylation
molecular frameworks5. They also found known structures cover a fraction (1.4%) reactions plus protective group chemistry
that the top 20 side chains represent 73% of the chemically feasible ring systems11. are other common transformations
of the total used in marketed drugs6. Wang Overall, the message from these studies used in the discovery phase (FIG. 1b). The
and Hou found no significant change in is that medicinal chemistry efforts so far formation of new carbon–carbon bonds,

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 1


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

the transformation of functional groups because the functional group tolerance of and thereby supporting the synthesis of
and reductions represented over 5% of the the reactions limits the scope of SAR the right compound at the right time more
reactions analysed, while oxidations and the studies. Furthermore, focusing only on effectively.
formation of heterocycles are rare. Similar known robust reactions may undermine the
trends were observed in process chemistry innovative spirit and personal creativity of Why is the toolbox limited?
applications15,16. researchers and delay the implementation Early drug discovery is viewed and practised
The use of a limited set of reactions in of new scientific and technological by many as a numbers game, in which the
most medicinal chemistry efforts potentially achievements. In this Perspective, we briefly more compounds made and tested, the
compromises the quality of drug candidates overview current practice and then discuss greater the chance for success. Although
or the opportunity to identify viable opportunities and challenges in extending alternative drug discovery strategies based
leads for challenging targets; for example, the synthetic toolbox of medicinal chemists on the screening of smaller libraries of

a
Other reaction types
Amide formation
O
O R2
HN R2
+ R1 N
Electrophilic reactions of amines 19% R1 OH R3
32% R3
R1 O R1 R3
N H + N
R2 H R3 R2
8%

9%

Amine Boc-deprotections 19%


13%
R1 O R1
N N H
R2 O R2 Suzuki–Miyaura reaction R2

B(OR)2 X
R1 + R2 R1
Aromatic nucleophilic substitution reaction (SNAr)
R2 X = Cl, Br, I, OTf
R2 N
HN R3
R1 N + R1 N
R3

b 45

40 Library synthesis (577 reactions) 2005–2009


Lead optimization (12,115 reactions) 2005–2009
35
Process chemistry (1,693 reactions) 1997–2005
Reaction frequency (%)

30

25

20

15

10

0
n ) g ps n n n n ic er
tio es in io io tio io all th
la id m ou rs at c at et
lky am fo
r gr nv
e
xid du rm m
O
n g Re fo
A fo nd in co O no
sul bo ect ter c le rg
a
s/ C ot in cy O
id
e C– Pr up
te
ro
(a
m g ro He
io
n n al
y lat ct
io
Ac n
Fu
Figure 1 | Common chemical reactions in drug discovery and develop- compounds in drug discovery programmes are given (data sourced from
ment. a | The uptake of new chemical reactions is slow, and a few have REF.13). b | Reaction types used in library synthesis (GlaxoSmithKline
Nature Reviews (GSK):
| Drug Discovery
consistently dominated the past decades. The percentages of the five most 2005–2009)189, lead optimization (AstraZeneca, GSK and Pfizer: 2005–
frequently used reaction types (amide formation, Suzuki–Miyaura reaction, 2009)12 and process chemistry for the synthesis of candidate drugs
aromatic nucleophilic substitutions, amine Boc-deprotection and electro- (AstraZeneca, GSK and Pfizer: 1997–2005)15,16. The most common reactions
philic reactions with amines) along with all other reaction types to produce show similar popularity in discovery and development settings.

2 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

carefully selected fragment compounds17,18 The third criterion is broad functional the remainder of this Perspective highlights
or virtual screening efforts19,20 relying group tolerance in reagents (for example, strategies to expand the toolbox with the
on low-throughput assays have achieved more diverse building blocks can be used aim of enabling more effective exploration
success, numbers-oriented thinking still in the reactions). It should be noted that of chemical space. These strategies can be
provides the basis for large-scale screening. publications disclosing new synthetic divided into four broad types, which may
Thus, a compound collection of structurally transformations are often from academic also be integrated: technologies that enable
diverse molecules is considered to be crucial groups intent on achieving high yields with accurate predictions of synthetic routes to
for the success of drug discovery efforts in some structural variations, rather than using target compounds; technologies that enable
most companies pursuing novel molecular a diversity of functionalities, and often use a greater automation of compound synthesis
drug targets21. limited set of examples that are less complex using a wider range of reaction conditions
Nevertheless, current screening collections and functionally similar 22,29. Furthermore, and reaction types; application of novel
are mostly populated by compounds made polar functionalities are usually sampled less chemical transformations; and application of
from a limited set of reactions, frequently often because available work‑up/purification broad synthetic strategies and platforms.
using commercially available building blocks. procedures favour more lipophilic
Although these reactions may be ideal for molecules30, which may be less desirable for Predicting synthetic routes
the synthesis of large numbers of compounds medicinal chemistry purposes. Based on How to best synthesize the designed
for screening, one analysis has shown that these data, chemists often cannot discern compounds is a key question in all medicinal
the reliance of these reaction types may whether more complex compounds with a chemistry projects. Unless there is an obvious
lead to an overpopulation of certain types differing physicochemical make‑up (typically route to the target compounds, the first
of molecular frameworks, such as biaryls13. equipped with polar functionalities30) will attempt to predict synthetic feasibility is
Furthermore, the chemistry embedded in the successfully undergo the same reaction often to perform an exact structure search
initial hit structures sets the stage for the type without time-consuming optimization for synthetic precedence, followed by a
of chemistry pursued through to the clinical or different protection strategies. This is substructure search if the exact compound
candidate22,23,24,25. relevant to the final criterion — management is not found. Contemporary tools such as
The limited set of reaction types used in and cultural reasons, such as the common SciFinder and Reaxys provide easy access
medicinal chemistry can be rationalized by focus on rapid cycle times in industry (linked to chemical databases with reaction data
the use of several criteria in their selection. to performance metrics, deadlines and extracted and curated from the scientific and
The first criterion is the availability of bonuses), as well as structural conservatism, patent literature and are thus often used for
starting materials and reagents. The second variable training 31 and experience. this purpose. In many cases, synthetic routes
is the ease of synthesis (such as short reaction Most importantly, synthetic technologies to compounds that are sufficiently similar to
times, moderate temperatures and high should fulfil the objectives of medicinal be useful are found.
yields with limited by‑products). Indeed, chemists, delivering the right compound In this context, synthesis planning can be
analysis of the synthetic methodologies at the right time, and so constraints in considered to be a pattern recognition process
used over the past 240 years in more than resources, time and budget can strongly in which substructures are identified and
6.5 million organic reactions26 indicated affect the synthesis of new compounds. subsequently associated with retrosynthetic
that key parameters, such as reaction time, Indeed, a recent analysis of the synthetic routes. Intuitive retrosynthetic disconnections
temperature, pressure and solvent, are biased aspects of medicinal chemistry 32 concluded are influenced by past education, knowledge
by anthropogenic factors. For example, that medicinal chemists are inevitably biased and experience. To create improved ideas and
half of the reactions were complete within towards robust reactions — essentially, to diminish personal biases, a collaborative
<3 hours, and >90% of reactions were run chemical transformations that are applicable approach to solve issues is for groups of
at atmospheric pressure, typically between to structurally diverse substrates, that tolerate chemists to discuss synthetic routes. To make
−80 °C and +200 °C. Furthermore, medicinal a range of functionalities and that can be this process even broader and more efficient,
chemists are often reluctant to make realized on simple equipment in a reasonable computational tools developed for the design
difficult-­to-synthesize molecules without time frame. Hartenfeller and colleagues and automated assessment of synthetic routes
compelling precedence or predictions, and suggested similar soft criteria33 after provide an extension covering current organic
the strength of computer-aided design is still considering reactions that yielded products chemistry knowledge. Although the current
largely geared towards prioritizing lists of structurally relevant for drug discovery from use of in silico synthesis prediction tools is
compounds and designing libraries rather readily available starting materials with broad scattered, this is likely to change because this
than predicting a single optimal compound. applicability and functional group tolerance. field is undergoing rapid progress34.
Consequently, chemists may prefer to focus Finally, it has become standard practice Synthesis design tools can be grouped
on simple reactions that can efficiently for companies to outsource synthetic into two major categories: retrosynthesis and
cover a lot of ground27 and, indeed, this chemistry to contract research organizations forward synthesis methods. In retrosynthesis,
is what is observed when analysing what (CROs). Paying CROs on a per-compound the design process starts from the desired end
is actually made in medicinal chemistry basis has been common procedure in the product and goes backwards, constructing the
laboratories12,13,28. Access to highly efficient past, and this has also created a bias towards synthesis tree of alternative pathways to the
purification technologies also has an impact the use of robust reactions. product while also identifying feasible routes
on synthetic choices. For example, chiral to known intermediates or available building
syntheses are often avoided in favour of How could the toolbox be expanded? blocks. By contrast, forward synthesis
chiral separations where needed, owing to Based on an understanding of the nature of methods predict chemical reactions between
the increased cost and complexity of (chiral) the limitations of the medicinal chemistry available building blocks and the reaction
reagents and timelines. toolbox and the underlying factors above, conditions needed.

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 3


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

The performance of retrosynthesis Electronic laboratory notebooks tools39. These methods use expert-based
and forward synthesis tools are both (ELNs), which are routinely used in or automatically extracted reaction rules
heavily dependent on the size and the pharma companies, could be considered (for example, REFS40,41) or machine-­learning
quality of the underlying chemical as alternative sources of reaction data approaches (for example, REFS42,43). Although
reaction data source and their underlying that potentially give more confidence in rule-based approaches are relatively well
computational methods. A current reliability, reproducibility and relevance, established, non-rule-based approaches
challenge in developing new improved and could also alleviate the issue of the lack are emerging. Considering the increasing
synthesis design tools is the lack of large of negative synthesis data in the literature. amount of available reaction data, the
high-quality data sets. In general, the AstraZeneca and Roche have reported latter is expected to dominate future
extensive SciFinder or Reaxys data sets extracting their ELN content to internal developments.
are not available for developers. Hence, reaction databases36, and NextMove14 Retrosynthesis tools are mainly
in most cases, the reaction data used in and EBI37 provide solutions to create and rule-based. They can consider the number
the development of in silico tools are maintain reaction databases from ELN of steps, the availability of starting materials,
manually or automatically extracted from systems. That said, the standardization and the types of building blocks and the ease
the primary scientific and patent literature, curation of ELN data are major efforts (for of incorporating them40. Although these
which has several limitations. Reactions example, there are many reasons for a yield methods support the automatic evaluation
that do not work are rarely reported, and of 0%, from the chemist not starting the of possible synthetic paths, they cannot yet
negative data are important for developing reaction to the reaction not working at all fully evaluate synthetic feasibility objectively,
a predictive tool. Moreover, literature for unknown reasons) and have historically and their use has so far been limited.
protocols include a large number of not been prioritized. A recently developed This drawback has been compensated
reactant–reaction combinations that are data exchange format aims to facilitate the by methodologies for quantitatively
neither reproducible nor reliable35, and precompetitive exchange of reaction data36. predicting the synthetic accessibility by
many synthetic transformations identified In the future, data collected from automatic the cheminformatics analysis of structural
this way may be challenging to implement synthesis robots will lead to more reliable descriptors. Software such as ChemPlanner
owing to issues such as high technical data owing to the systematic manner in (Wiley), ICSynth (Infochem) and Chematica
expertise, expensive or custom catalysts, which they are generated and recorded38. (Merck KGaA) can assist medicinal chemists
high functional group sensitivity and toxic This in turn can be used to improve the with retrosynthetic analyses, as highlighted
reagents or intermediates. predictive power of synthesis design in published studies. In a study comparing

Glossary
Chemical space techniques (such as X‑ray crystallography, NMR Robust reactions
Chemical space is a nebulous term used in various ways, spectroscopy and surface plasmon resonance) to identify Reproducible chemical transformations applicable to
but pertinent to drug discovery, it is the classification of inherently weak binders that can be elaborated into lead structurally diverse substrates, tolerating a range of
molecules in terms of their physicochemical make-up, such compounds. functionality and able to be realized on simple equipment
as size, shape, lipophilicity, charge and hydrogen-bonding in a reasonable time period. Factors for robust reactions for
potential, which together can be used to describe the Functional group tolerance medicinal chemistry include the following:
chemical space occupied. The range of organic functionalities that do not react with
• Provide structures relevant for drug discovery
or impede the reagents and/or catalysts involved in a
• Technically straightforward (no special equipment needed)
Design–make–test–analyse (DMTA) cycle transformation. As drug molecules are predisposed to
contain charged or hydrogen-bonding motifs to, for • Moderately sensitive to reaction parameters
The iterative central process in lead optimization, involving
a cycle of four steps: design (a hypothesis is constructed to example, achieve potency and selectivity, this can often • Broad applicability (also with polar substrates)
improve the profile of the lead molecule); make cause issues and interfere with catalysts, ligands and • Broad availability of starting materials and reagents
(compounds exemplifying the design are synthesized); test reactive partners. • Broad functional group tolerance, including polar
(synthesized compounds of confirmed structure and purity functionalities
are tested in one or more carefully constructed and Lead-like • Time for delivery of the target compounds is reasonably
controlled assays); and analyse (the experimental data are Lead-likeness is a term that describes an aspirational short (<1 month ideally)
analysed, and the results are used to amend a design profile for a screening collection of molecules that have
• Simple operational procedure (minimal training and
hypothesis for the next cycle). physicochemical properties, together with predicted
support needed)
safety, pharmacokinetic and pharmacodynamic data
• Low-risk reagents to comply with often onerous local
Drug-like compounds and complexity, that bridge fragment space and
safety rules
Drug-likeness is another term that is used in various ways, drug-like space, as well as appropriate chemical
often to describe the possession of physicochemical functionalities that can be used in the optimization of A full-size poster depicting the set of most popular robust
properties that are typical of orally absorbed the molecules into candidate drugs. reactions (available online for downloading; see
small-molecule drugs. Lipinski’s rule of five (Ro5) is one Supplementary Fig. 1) illustrates their impact on drug
common metric; if no more than one of the following Quality of drug candidates discovery. Our hope is that displaying this poster in offices
criteria is exceeded, then there should be a reasonable Like chemical space, the notion of compound quality is and laboratories could highlight the importance of
chance of oral bioavailability: molecular mass <500 Da, used in various ways, but physicochemical parameters expanding the medicinal chemistry synthetic toolbox and
cLogP <5, number of hydrogen-bond donors <5 and can predict the likely quality of a compound, in stimulate debate.
number of hydrogen-bond acceptors <10. More recently, conjunction with pharmacokinetic and
it has been demonstrated that oral activity is feasible pharmacodynamic data, giving confidence in probable Structurally diverse substrates
beyond Ro5, and these programmes follow specific exposure, efficacy and safety. This should not be The breadth of diversity of a given reaction type is
principles that contribute to the oral bioavailability. prescriptive, but more optimal properties indicate a dependent on the accessibility and intrinsic reactivity of
higher likelihood of success. Note that the actual set of the substrates and/or building blocks involved in the
Fragment physicochemical parameters is dependent on the target, reactions. A reaction that can use a number of different
A simple, small and relatively polar molecule with ~8–17 the compartment where the target is engaged and the reactive groups can be advantageous to medicinal
heavy atoms, often screened using sensitive biophysical route of administration. chemists, as it will allow access to more analogues.

4 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

the routes predicted by ChemPlanner to from ChemPass is a fully expert-trained demonstrate that combining synthetic
that developed by a chemist for a highly system that considers long-range functional methods with the appropriate reactivity,
complex triazole44, the software identified group effects and has built‑in combinatorial selectivity and functional group tolerance
the same route as the chemist and also found explosion management to assist medicinal information into a computational multistep
more feasible alternative routes, one of chemists in idea generation for scaffolds and forward synthesis tool is a viable approach to
which shortened the synthesis of the target analogues. new and structurally diverse compound sets.
compound. In a study at AstraZeneca on five The major disadvantage of these methods These approaches could benefit from recent
target compounds, including synthetically is their limited scalability, as decoding the building block initiatives49,50,51 that increase
challenging drug intermediates45, ICSynth entire organic chemistry reaction knowledge the number of accessible products, ‘design of
identified new, non-intuitive solutions to into complete and reliable transform rules is experiment’ approaches that are increasingly
synthetic problems compared with groups non-trivial. In forward reaction prediction, employed in the optimization of reaction
of medicinal chemists under controlled one of the most challenging tasks is the conditions52,53 and large-scale automated
conditions, and novel disconnection prediction of selectivity in a given reaction. reaction testing 39 that helps to define the
strategies and non-trivial reaction The selectivity problem can be broken down parameter range of the reactions applied in
sequences were subsequently used for into groups: chemoselectivity, regioselectiv- forward synthesis programmes.
the development of new synthetic routes. ity and stereoselectivity. For chemoselectiv- Automated methods that harness the
Finally, in a study in which Chematica was ity, the question is which of many functional power of artificial intelligence and machine
used to design routes for the synthesis of groups present will react most rapidly with learning are expected to play a key role
eight bioactive compounds46, the routes a given reagent. An example would be a in the faster adoption of new synthesis
enabled the efficient preparation of the simple carbonyl reduction, in which one methods and in facilitating the synthesis of
target compounds with improved yields and type of reagent (for example, NaBH4) will previously difficult-to-make compounds54.
provided new or more feasible alternatives to selectively reduce a ketone in the presence The progress that has recently been made
known procedures. of an amide, whereas another reagent such with these approaches by various groups
Although machine learning is used less as BH3 will display the opposite selectivity. using several different techniques strongly
frequently in retrosynthetic predictions, Maintaining a set of rules for each reagent indicates that synthetic chemistry can
Segler and colleagues reported34 a new would be an alternative but can also become be taught to machines using large and
approach combining Monte Carlo tree cumbersome. high-quality data sets34,41,55,56,57,58,59. Thus far,
search and symbolic artificial intelligence. For regioselectivity, the challenge is to most of the publications have disclosed early
An expansion policy neural network accurately predict which of several possible validation results, with 50–80% success rates
was used to guide the search, and the functional groups present will react. This in predicting single-step reaction products,
most promising solutions were selected is probably most prominent in reactions with training sets machine-extracted from
by a filter network to preselect the most of C–H bonds, which are important in the large databases such as Reaxys or a patent
promising retrosynthetic steps. Training recently popularized late-stage function- transform set 14. However, so far, no major
the neural nets on the Reaxys database alization strategies (see further discussion study has been published for real-life
enabled this approach to provide feasible below). An example is electrophilic multiple syntheses, preventing in-depth
synthetic routes for more molecules much aromatic substitution — for example, validation by organic and medicinal
faster than rule-based methodologies. aryl bromination — for which in silico chemists. Nevertheless, this is an emerging
The results were comparable to reported methods frequently suggest substitutions and rapidly evolving area (BOX 1), and these
literature syntheses. that do not correspond to real observations, techniques have the potential to cover a
Forward synthesis tools use both especially for complex heterocyclic significant fraction of relevant reactions
rule-based and machine-learning systems. Mechanistic approaches, such as because they can be based on very large
algorithms. Rule-based approaches require the recently published RegioSQM47, have unbiased databases of reactions (for example,
transformation of the available reaction begun to address these issues, although the from company electronic laboratory
knowledge to reactivity, selectivity (transform approaches are computationally demanding. notebooks and automated synthesis
rules) and functional group tolerance rules. Finally, predicting the stereoselectivity machines). In addition, we see the potential
This determines which reagents can generate of reactions is also challenging. Such to predict new synthetic methods41,58. The
products and which product structures selectivities are frequently determined by high generality of the approach, however,
can be obtained from the available list of through-space interactions with remote means that it could be particularly important
in silico reactions. Most disclosed methods substituents and are likely to require 3D to incorporate practical considerations (see
apply forward-­reaction-based technology information. Although very accurate BOX 2) in reaction planning, ranking and
for only a single in silico step, but ICFRP predictions can be made48, these protocols selection schemes.
from Infochem and SynSpace by ChemPass are time consuming and not general yet. Overall, such tools will enable the more
(the only commercialized software packages The development of new synthetic effective generation of better results, thereby
available to date) can handle multistep methods (see discussion below) and aiding chemists, who struggle to find time
in silico forward synthesis. ICFRP is a computational retrosynthesis or forward to exhaustively search the literature for
general literature-­trained tool that can be synthesis tools in combination can be optimal routes outside of their previous
used for compound design in the forward especially powerful for increasing the experience. In addition, the tools can also
direction and requires human intervention structural diversity of synthetically feasible provide value in evaluating safety, cost
to deal with the potential combinatorial compounds. A number of recent initiatives and operational issues when prioritizing
explosion of possible reaction products (such as EVOSpace by Evotec, ULTIMATE potential synthetic routes. Although the
arising in multistep sequences. SynSpace by Mcule and REAL by Enamine) implementation of synthesis planning tools

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 5


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

often requires substantial investment, some It should not be forgotten that synthetic Expanding reaction conditions
vendors have incorporated pay-for-service chemistry requires planning and creativity, The outcomes of chemical reactions
options and different collaboration models and this is something at which machines are heavily influenced by the reaction
that make the tools accessible for smaller still do not excel. Empowering chemists parameters. Enabling technologies such as
commercial organizations. More recently, with the appropriate in silico tools will be microwave-heated reactors, microreactor
non-commercial tools have also become more effective and efficient than trying to and microfluidic devices, flash reactors
available59. develop one-stop-shop machines, at least and high-pressure/high-temperature
However, there are many idiosyncrasies in the foreseeable future. Paraphrasing autoclaves widen the opportunities for
and poorly predictable practical hurdles Brynjolfsson and Mitchel60, we believe that changing conditions relative to conventional
(such as work‑up and product separation) “AI won’t replace chemists, but chemists who batch processes26,62.
that hinder fully automated processes. use AI will replace those that do not”61. Expanding the range of conditions
can lead to more efficient and/or quicker
synthetic routes and, more importantly,
Box 1 | Example of the impact of automated compound synthesis and testing can provide opportunities for the discovery
of new chemistries, enabling the synthesis
Automation can be particularly beneficial for repetitive and tedious tasks. A recent paper by Cernak of novel compounds (TABLE 1). Microwave
and colleagues highlights the potential impact of emerging technologies in automatically
heating is widely used in both discovery and
synthesizing and testing compounds in a drug discovery setting186. High-throughput nanomole-scale
synthesis (consuming less than 0.05 mg of substrate per reaction) was coupled with an
development phases to improve reaction
affinity-selection mass spectrometry (ASMS) binding affinity assay. Robust chemical reactions were rates and often results in higher yields or
used; 20 reactions were performed using amide formations, Suzuki couplings or Buchwald–Hartwig cleaner reaction profiles. For example,
carbon–nitrogen (C–N) couplings. A single reaction condition was enough for the amide couplings, the microwave-assisted multicomponent
whereas several conditions were surveyed for the other two reactions; although, it should be noted reaction of aldehydes, amines and alkynes
that a large number of reactions did not produce an observable product. The ASMS bioassay was (A3‑coupling) in water affords secondary
used to rank the affinity of the products by titrating the concentration of protein while maintaining a propargylamines as the precursor of
constant concentration of the compound. Synthesis (without the need for time-consuming nitrogen-containing heterocycles (such as
purification steps) and testing were performed rapidly with minimal consumption of starting pyrrolidines, pyrroles, oxazolidinones and
materials (120 mg), and potent inhibitors for three kinase targets (mitogen-activated protein kinase 1
aminoindolizines) and intermediates of
(MAPK1), MAP kinase-activated protein kinase 2 (MK2) and CHEK1) were identified (see figure).
This approach successfully demonstrated reductions in timelines and resource demands and is an
biologically active scaffolds (β‑lactams and
initial indication of what may be possible as efforts progress to include machine-learning algorithms peptidomimetics)63. Chemical reactions
and other artificial intelligence approaches to predict and select which compounds to make (for performed at high reaction temperature and
example, REF.187). Nevertheless, there are many hurdles to address, such as enabling the use of new high pressure might be used for the synthesis
chemical reactions and accurate multiparameter optimization, including functional assays. of novel scaffolds. Djuric and colleagues
Ki, inhibition constant; rt, room temperature.
showed that high-pressure and high-­
temperature chemistry makes substituted
fused pyrimidinone and quinolone
H O
H O R1 = H derivatives accessible with high yields64. The
N N
R1 HO technology also enabled the fast and efficient
N N R1
N
OH H R2 N synthesis and scale‑up of other challenging
R2 R2 =
HN HN heterocyclic scaffolds.
HATU, DIPEA, rt, 20 h
19 reactions Advantages of microfluidics–microreactor
flow chemistry include enhanced mixing,
49% yield
Cl MAPK1 Ki = 35 nM improved heat transfer and wide temperature
Cl
and pressure ranges. A novel synthesis
Br
R NH technology developed by the Ley group
N OH
N O is an elegant example of the reaction
B safety and automation benefits of the flow
R OH R=
technology. The flow synthesis of hazardous
Catalyst, base, rt, 20 h unstable aryl and vinyl diazo compounds
HN HN O
O 144 reactions from the corresponding hydrazones and
NH
89% yield their subsequent reaction with boronic
NH MK2 Ki = 59 nM acids resulted in a new, convenient and
metal-free sp2–sp3 cross-coupling strategy 65.
NH
NH The sequential addition of different diazo
OH R1 H
or N HN compounds to suitable boronic acids
N N
B N
R OH H R2 N provided a strategy for the synthesis of
NH Catalyst, base, rt, 20 h NH R1=H, R2 = structurally complex molecules66. Flow
170 reactions microreactors have also been used for
O
S
O
S flash chemistry, performing extremely fast
N N OMe reactions in a highly controlled way to obtain
Br
85% yield products that are challenging or practically
Nu
CHEK1 Ki = 23 nM
inaccessible in batch conditions67. A recent

Nature Reviews | Drug Discovery


6 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd
©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

example reporting the chemoselective Hartwig and Troshin also demonstrated75 handling and maintaining screening
functionalization of ortho-lithiated the concept of reaction mining, which collections of 1 to 3 million compounds
aryl carbamates shows that even rapid couples automated synthesis and a from commercial sources. Automated77 and
transformations, such as the anionic Fries deconvolution method based on mass integrated synthesis platforms with in‑line
rearrangement, can be outpaced with spectral informatics to identify unknown purification are emerging for make–analyse–
sub-millisecond microfluidic mixing 68. reaction types as one solution to help expand format–bioassay systems78,79, but these often
Attempts are being made across industry the chemist’s toolbox in these types of have rudimentary purification steps and
to automate and integrate many of the automated platforms. Finally, it should be rely on prosaic chemical methodologies.
routine aspects of the design–make–test– noted that many reported automation efforts Developments in affinity-based assay
analyse (DMTA) cycle69. Automation requires typically involve the use of robust chemical systems may circumvent some impurity
robustness, and as the synthetic toolbox reactions, such as the top five most popular issues, but, ultimately, highly pure
advances, an increasing number of chemical reaction types cited above, and readily compounds will be required to qualify hits
reactions may be suitable for automation available reagents. Thus, expanding the and properly interpret data.
and robotic synthesis. The most ambitious scope of the types of reaction used on these Methods to purify compounds are
vision would integrate machine-­learning platforms should also expand the uptake and typically variations on chromatographic
algorithms coupled to an automated application of the technology 13. methods, frequently HPLC platforms,
synthesis and testing module. A continuous A major issue in hit identification is which are often automated, based on
loop of newly designed and synthesized test the provenance and purity of samples, mass-directed or UV‑triggered collection.
molecules informed by real-time screening contributing to false results that waste A major drawback of HPLC purification is
data could be driven by computer and considerable time and effort76. The reliable the need to liquid-load samples, which can
robotics equipment. production of pure compounds remains an cause ‘surfing’ of products on this solvent
Although this bold ambition has yet issue, especially given the cost of populating, front. Purification is fundamentally a
to be fully realized, several groups have
made important in‑roads into this area.
Burke and colleagues have demonstrated70 Box 2 | Example of the impact of continuous-flow technologies
an automated synthesis system that can
Researchers at Eli Lilly recently published a pioneering example of the kilogram-scale manufacture
handle a variety of organic transformations of an active pharmaceutical ingredient — the investigational anticancer drug prexasertib — in
and purifications, built on the versatility a continuous-flow system188 (see figure). The flow process allows greater flexibility of mixing and
and scope of the recently discovered conditions, thus making the process more controllable and reproducible; additionally, reactor design
N‑methyliminodiacetic acid (MIDA) enables novel manipulations such as photochemistry, more controlled use of heterogeneous
boronate reagents. Djuric and colleagues at catalysts or ozone generation. In this example, the continuous process enabled the production of
AbbVie reported an integrated automated 3 kg per day of current good manufacturing practice (CGMP) material in standard laboratory fume
platform that incorporates synthesis, hoods, thus avoiding the need for substantial capital investment in a plant while allaying many safety
purification and testing to complete the issues owing to the small volume of hazardous mixing at any given time. Other processes remain
DMTA cycle within hours (compared unpublished, and the potential for the technique is vast, not least because of rapid progress with the
scale‑up reactions, reproducibility and accessibility of non-standard conditions.
with days using the traditional model),
using amide and Buchwald libraries as two
O O N
illustrative examples69,71. Eli Lilly has also
O O
described a large-scale automated drug DMF-DMA, alkylate,
discovery platform that has been reported to H2NOH·HCl KOH, H2NNH2
O O
be capable of performing >16,000 reactions
OH
on the 100 mg scale per year on a diversity N O
H
of reaction types such as organometallic
cross-coupling reactions, alkylation N
reactions, reductive aminations and NH2 CN
HN
multicomponent synthesis reactions72. O N N
N O
The concept of using self-optimized N
Cl CN N
synthesis techniques is an exciting extension H N N
H
that could be used on these platforms and O O
O O
was recently described and demonstrated N O
by Buchwald and Jensen. In this model, a H N O
H
design of experiment (DoE)-based algorithm
was coupled to online high-performance N
CN
liquid chromatography (HPLC) analysis to HN
N
optimize reaction yields in a Suzuki–Miyaura Deprotection, O
reaction73. A comprehensive review of the N
salt manipulation
N
history and state of the art of automated H
synthesis platforms was recently published by O
Burke and Trobe and provides historical and
NH2 .mesylate or lactate
modern perspectives on the advances and
Prexasertib
challenges of automated synthesis74.

NATURE REVIEWS | DRUG DISCOVERY Nature Reviews


ADVANCE ONLINE| Drug Discovery| 7
PUBLICATION
©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

partitioning process based on lipophilicity, technologies have potential applications valuable, and some progress has been made
which presents issues for compounds with in improving access to novel and diverse with tandem CYP-mediated hydroxylation–
drug-like properties80. Practical tricks, reaction intermediates or in late-stage fluorination93 (FIG. 2d).
such as dry loading of medium pressure, functionalization strategies. The impact
readily scalable ‘flash’ systems and new of such small changes can be profound in Photoredox chemistry. Photoredox
techniques such as hydrophilic interaction optimization programmes83,84. chemistry is a relatively old field94 but
liquid chromatography (HILIC)81 and has been limited in practice owing to a
supercritical fluid methods82 can provide Biocatalytic methods. Biocatalysts (and lack of specific catalysts that can be used
improved performance in relevant particularly their directed evolution) hold across a diversity of reaction conditions
lipophilicity ranges. Supercritical fluid promise for the synthesis of structurally and chemical functional groups. Notable
chromatography with chiral columns diverse molecules under ambient and recent discoveries have identified
has made separating and accessing chiral environmentally benign conditions. The multiple catalysts, ligands and reaction
compounds more routine. However, the concept of mutating specific enzymes conditions that enable important chemical
current practice often involves testing to do unnatural reactions more typical transformations that previously proved
racemates first as a practical measure, and of a traditional synthesis is becoming difficult (for example, often requiring
then if activity is found, a chiral separation more general and practical. For example, multiple steps and/or protecting group
follows. As the technology expands and engineered enzymes can perform manipulation).
becomes even more routine, this strategy carbon–carbon (C–C) bond-forming The basis of photoredox chemistry is
will change and enable all compounds to be reactions of carbenes derived from diazo the activation of a photoredox catalyst
separated into chiral stereoisomers in the compounds, carbon–nitrogen (C–N) by light, which can then potentiate single
absence of initial biological data on bond-forming reactions, carbon–silicon electron transfer between two partner
a racemate. (C–Si) bond-forming reactions and carbon– molecules, causing them to react94. As one
boron (C–B) bond-forming reactions85,86,87 specific example, photoredox chemistry has
Novel reaction technologies (TABLE 2, entries 1–4). been used to make C–N bonds95 (TABLE 2,
Improvements in reaction technologies Enzymes can also be valuable in entry 5), a key transformation for medicinal
have the potential to enable more late-stage functionalization, for example, chemists13. One advantage of the photoredox
effective exploration of novel compounds by cytochrome P450 (CYP) preparations85, method for C–N bond formation is that
in medicinal chemistry programmes. microsomes87 or microbial broths. These it is mechanistically different from the
Here, we focus in particular on rapidly have found application in the generation Buchwald–Hartwig reaction, which is one
emerging new technologies that could of metabolite standards88 (FIG. 2a,b) but can of the few new reaction methodologies
enable reactions that are likely to be also deliver more hydrophilic compounds among the top 20 most used reactions in
valuable in medicinal chemistry but are (FIG. 2c) through directed hydroxylation89. the medicinal chemists’ toolbox identified
under-represented in current practice, Given the impact that methylation90 and in the Brown and Boström analysis13. Thus,
such as biocatalytic methods, photoredox fluorination91,92 can have on bioactivity, the photoredox method can expand the
chemistry, electrochemical methods enzymes that could enable such scope of this important transformation
and C–H bond activation. All these transformations at a late stage would be by providing alternative procedures when

Table 1 | Examples of the impact of enabling technologies


Entry Example Technology Impact Refs

1 R1 Microwave Fast and versatile 63


NH reaction
10 mol% CuCl /10 mol% CuCl2
R1 NH2 + R2 + R3 CHO R
H2O, microwave, 110 °C (100 W), 3
25 min R2
21 examples, 41–89%

2 Y N
High New heterocycles 64
H 390°C, 100 bar temperature
N R
CO2Et THF N and pressure
R Y
N
O
Y = CO2Et, CN, COMe 9 examples, 77–96%

3 N2 R1 N2 R1
Flow New synthesis 65,66

technology
B(OH)2 B(OH)2
R1 H B(OH)2 R2 H
R2

4 I E Flash Chemoselective 68

O R
functionalization
O R 1. PhLi
8 examples, 71–98%
O 2. E
+
O

8 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

Table 2 | Examples of emerging synthetic technologies applied to fragments and lead-like molecules
Entry Example Technology Bond formation Refs
1 R1 Biocatalysis C–C 86
O Bacillus subtilis truncated globin
F F
R1 + Y25L T45A Q49A EtO2C
OEt
N2 F R1 = H F

2 O O
Biocatalysis C–Si 86

R1 Si Rma cyt c variant


OEt + H Si
EtO
N2
R1
R1 = Me

3 Biocatalysis C–B 85

_
N N
BH
3
- + BH2
O +
OEt
R1 Escherichia coli expressing R1
OEt
Rma cyt c O
N2
R1= Me

4 NHTs Biocatalysis C–N (also an 87


TsN3 example of C–H
Me
Me activation)
Cytochrome P411CHA
MeO Whole cells MeO

5 5 mol% NiCl2 ·glyme Photocatalysis C–N 95


Br NBoc
+ NBoc
N
HN 0.02 mol% photocatalyst
F3C DABCO, DMA, rt
Blue LED F3C

6 1 mol% photocatalyst Photocatalysis C–C 96


O
+ 10 mol% NiCl2 ·glyme
N
N CO2H 15 mol% dtbbpy, Cs2CO3
Boc O
Boc Br DMF, 23°C
Blue LEDs

7 NBoc Photocatalysis C–C 97

HO Br 1. Oxalyl chloride
+ 2. 5 mol% Ni catalyst
NBoc N
1 mol% photocatalyst N
F 5:1 dioxane:THP
F
DMSO, 70°C
8 OCF3 Photocatalysis C–N and C–C 96
Photoredox N OCF3
couplings O
Cl NH
N
N
N
Q203, anti-TB clinical candidate
NH2C

9 Ar Ar Photocatalysis C–C, enhanced 99

366 nm, sp3 character


Ph2CO, 2+2 H H

O N
n n = 1,2 O N n

Ph Ph
10 Electrochemistry C–N 101
10 mol% NiCl2 .glyme
+ CF3
10 mol% di-tBupy, rt CF3

LiBr (4 equiv), DMA (0.1 M)


N Br N
H H (+)RVC/(–)Ni
Undivided cell H
I = 4 mA, 4.5 h

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 9


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

Table 2 (cont.) | Examples of emerging synthetic technologies applied to fragments and lead-like molecules
Entry Example Technology Bond formation Refs
11 N Electrochemistry C–N 104

O
S
O 1. Anodic oxidation N
+ N
1.0 M LiClO4, CH3CN
N
2. Piperidine

12 F Electrochemistry C–N 105

NH F RVC(+)-Pt(–), N
I = 5 mA
N
N
Et4PF6, MeOH, THF

13 O Electrochemistry C–O 106

Me
Anodic oxidation CO2H
O
N AcOH, NaOAc N
N
H
O OBn O OBn

14 Electrochemistry C–N (also an 107

example of C–H
BDD anode
OH activation)
HFIP
+ Me

OH Undivided cell
OH
OMe OH
OMe

BDD, boron-doped diamond electrode; DABCO, 1,4‑diazobicyclo[2.2.2]octane; I, current; LED, light-emitting diode; MW, microwave heating; Rma cyt
c, Rhodothermus marinus cytochrome c; rt, room temperature; RVC, reticulated vitreous carbon; TB, tuberculosis.

traditional methods fail and thereby provide the α‑carbon and that a new bond can be such as methyl, ethyl and cyclopropyl to
more opportunities to explore diverse areas formed to an aromatic ring in one step96 drugs (such as loratidine) and drug-like
of chemical space. (TABLE 2, entry 6). Another variant of this scaffolds has been reported100. Such
Photoredox techniques have recently chemistry (TABLE 2, entry 7) utilizes alcohols late-stage functionalization is likely to allow
been applied to a drug discovery platform as substrates for photoredox catalysis instead for more versatility in synthetic planning
with microscale chemistry to produce of carboxylic acids, thus expanding the scope and access to potential test molecules that
‘informer libraries’ across a broad range of of this transformation97. This technology previously would have each required their
substrates (78% reaction success rate), thus has been applied to the efficient synthesis of own de novo synthesis.
illustrating the potential robustness of this Q203, a drug candidate in clinical trials for
reaction type38. The concept of a microscale tuberculosis96 (TABLE 2, entry 8). Electrochemical methods. The
informer library is that one can arrange a Another recent example of photoredox implementation of electrochemical reaction
large matrix of reaction conditions on the catalysis from Suero and co-workers98 protocols is gaining broader utility in
desired medicinal scaffold of interest on a involved the generation of carbynes by organic chemistry and the production of
small scale (for example, <1 mg). Subsequent photocatalysis and their application to medicinal-chemistry-relevant scaffolds101,102.
analysis can then inform the scientist on create chiral centres from three different The increased adoption of this technology
not only one set of conditions but a range fragments by assembly-point functionali- is largely due to improvements in practical
of conditions that can be immediately zation. The usefulness of the methodology methods of electrochemical synthesis. For
employed to produce large libraries of target was demonstrated by the chiral func- example, previously, an ‘electroauxillary’
compounds. This concept of informer tionalization of known drugs and also by functional group, such as arylthio, α‑silyl
libraries is not only applicable to the illustrating a procedure whereby a chiral and organostannane, often needed to be
identification of optimal reaction conditions centre can be directly attached to an installed on one reaction partner to control
but also highly relevant to the previous aromatic ring in a one-step reaction. This the electron transfer event with the other
discussion on automated platform synthesis. type of chemistry should, in principle, reaction partner 103. However, these types
Innovations in photoredox chemistry allow medicinal chemists to access a of groups are not common reagents to a
have also recently been applied to broader and more diverse part of chemical medicinal chemist, and building them
the generation of C–C bonds, where space. The photochemical synthesis of into the reaction partner is a disincentive
N‑protected amino acids can react to replace 3‑azabicyclo[3.2.0]heptanes represents a because it requires substantial scoping and
the carboxylic acid by a functionalized good example of new building blocks with optimization for each target compound.
aromatic ring (sp3–sp2 cross coupling), a enhanced sp3 character 99 (TABLE 2, entry 9). By contrast, the recent examples reported
process that previously would have required Finally, photoredox chemistry has also for C–N bond synthesis shown in TABLE 2
multistep synthetic procedures. MacMillan been used to facilitate the late-stage func- (examples 10, 11 and 12) illustrate very
and colleagues showed that protected amino tionalization of heterocycles. For example, common building blocks that require no
acids can be reductively decarboxylated at the direct addition of simple alkyl groups special electroauxillary to be attached

10 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

to the reagent 104,105. C–O bonds can new ways to form C–C bonds using setting for reaction and library scoping
also be formed under electrochemical electrochemical protocols have also been but can also be scaled up for chemical
reaction conditions with applicability in reported107 (TABLE 2, example 14). process applications108. Advances in the
medicinal chemistry, such as the novel Electrochemical methods are adaptable commercial accessibility and ease of use of
γ‑aminobutyric acid uptake inhibitors106 to flow chemistry, which has applications electrochemical reactors hold promise for
shown in TABLE 2 (example 13). Finally, in automated synthesis in the research this to become a routine methodology 109.
Commercial equipment suppliers play
a HO
a key role in the widespread use of new
OH approaches, especially when the equipment
O
O OH HO2C can simplify the set‑up and execution of
H2N S N OH
N UGTIA9 O normally complex reactions; flow reactors,
H NH NH O
O O which can be used from discovery through to
H2N S N production, are a good example.
N N N
O Br H NH NH

F C–H bond activation and other novel


N N
Epacadostat O Br reaction technologies. There is currently
substantial investment in both academia
F
Gut All metabolites were also isolated from and industry to develop late-stage func-
microbiota Hypha biotransformation panel tionalization methods, spurred by major
O recent discoveries. Late-stage functional-
O HN
H2N S HN ization through targeting specific reactive
N H2N NH
H NH NH CYP3A4/2C19/1A2 C–H bonds for substitution reactions is
N N
particularly desirable in medicinal chemistry,
Br
N N
Br
O as it can eliminate the requirements for
O
F
costly and, at times, cumbersome functional
F group manipulation early in the synthesis
b scheme. An excellent example of this type
Kd 53 nM OH
Kd 2.6 nM
LogD7.4 2.6 of limitation is the popular Suzuki–Miyaura
LogD7.4 3.9
LLE 3.4 LLE 6.0 reaction illustrated in FIG. 1, which typically
N Hypha microbial panel N
relies on boronic acids and halogenated
N N
coupling partners, each with the designed
R
NH
R
NH substitution patterns.
Cernak and colleagues comprehensively
c N N reviewed110 and classified late-stage func-
N Liver microsomes N
tionalization strategies, which can be broadly
N N divided into innate reactions (that is, those
N N not requiring a directing group111 (FIG. 3a))
N CF3 N CF3
HN HN and guided reactions (for example, using
O PDE2 IC50 0.6 nM O OH
PDE2 IC50 0.4 nM directing groups, steric effects or molecular
LipMetE 1.9 LipMetE 2.4 recognition95 (FIG. 3b)). Innate reactions such
LipE 5.9 LipE 7.4
as those illustrated in FIG. 3a can install groups
d O such as CF3 in the last step of the synthesis
O O of highly functionalized molecules95,111. Such
O N
O N H O N techniques can be leveraged in medicinal
H H
HO chemistry to potentially improve potency
CYP2C9 DAST F
but also potentially block reactive/metabolic
Ramelteon 2-(S)-hydroxyramelteon 2-(R)-fluororamelteon sites in these compounds without having to
design new synthetic schemes from scratch112.
Figure 2 | Examples of bioprocessing and natural product chemistry applied to bioactive or drug A compelling example of the directing group
molecules. a | Microbial biotransformations can be used to easily generate metabolic markers, such technology is shown in FIG. 3b (REF.113), in
as those from epacadostat, in good yield, avoiding often complex or capricious
Nature conventional
Reviews synthe-
| Drug Discovery which a celecoxib analogue can be readily
sis88. b | Microbial biotransformation can be used to generate useful structure–activity relationships converted to a diverse array of substituted
and property improvements from a lipophilic lead molecule; the kinase inhibitor shown that was pro- analogues, in this case driven by the
duced by using Hypha’s proprietary technology had reduced lipophilicity (logD7.4) and improved activ- coordination of a Pd catalyst to the pendant
ity and lipophilic efficiency88. c | Late-stage functionalization using liver microsomes can give similar sulfonamide and resultant insertion to a
outcomes to microbial oxidations in facilitating hydroxylations at sites difficult to access syntheti-
proximal ortho-C–H bond. The large-scale
cally89. d | Late-stage functionalization of the drug ramelteon using a combination of cytochrome
preparation and deoxyfluorination enables hydroxylation at particular sites and the introduction of synthesis of clinical candidates is also an area
fluorine, which can modulate properties and add conformational restraint93. CYP, cytochrome P450; of impact, as shown in FIG. 3c (REF.114).
DAST, diethylaminosulfur trifluoride; IC50, half-maximal inhibitory concentration; Kd, dissociation con- The practical uptake of C–H activation
stant; LipE, lipophilic efficiency; LipMetE, lipophilic metabolism efficiency; LLE, ligand lipophilicity chemistry by medicinal chemists will be
efficiency; PDE2, phosphodiesterase 2; UGT1A9, UDP-glucuronosyltransferase 1–9. enhanced when computational models

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 11


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

a
Pd(OAc)2 (10 mol%)
O O Cl H Cl CF3
AgOAc (3 equiv)
H HFIP or CHCl3 CO2Et NaSO2CF3 (3 equiv)
CO2Et N N
+
3,5-bis(trifluoromethyl)- N N t
BuOOH (5 equiv) N N
O O H H
pyridin-2-ol (30 mol%) DCM:H2O (2.5:1)

b O O O O
C6F5 S C6F5 S
N N
H Pd(OAc)2-catalysed methods H
N N
H N R N
CF3 CF3
R = CO2H, Me,
Ph, I, others

MeO MeO

c N
N N N N H
X 1. BnBr Enantioselective
hydrogenation and
N N
elaboration to final
N 2. Pd(dppf)Cl2, Bn candidate
X = I or Br DBU, DMF O
11-β-HSD1 clinical candidate
(multikilogram synthesis)

d
Ph i
Pr O O O Ph i
Pr O O
NH NH
NiCl-catalysed methods R
N OH N
O O

From atorvastatin R = N, O and C bond formation


F F

e f Ts
Ts N I N
O Me
Me Fe(acac)3 (20 mol%) O
+ N
20% NiBr2·diglyme
PhSiH3 (1.5 equiv)
30% 4,4ʹ-di-tert-butyl-2,2ʹ-bipyridine
DCE:(CH2OH)2 (5:1) OTMS
2 equiv DEMS
60°C N N
2 equiv Na2CO3
OTMS
N

g h
H 1. iPrMgCl Br OMe
OMe Suzuki–Miyaura
N N
2. hydrogenation
Cl Cl HO
N B 55 examples, enhanced
Ts sp3 character
Cl Cl OH
Stock solution
Sertraline in Et2O ‘Propellerized’ sertraline N

Ts

Figure 3 | Examples of emerging synthetic methodologies applied to chemistry114. d | Late-stage functionalization provides
Nature novel
Reviews analogues
| Drug and
Discovery
fragments and lead-like scaffolds. a | Illustrations of innate carbon– diversification of approved drug scaffolds115. e | Reductive olefin coupling
hydrogen (C–H) bond activation, where drug-like scaffolds can be substi- as a new and diverse method to make carbon–carbon (C–C) bonds116.
tuted with various functional groups in the last step of a synthetic f | Reductive olefin hydrocarbonation of known drug scaffolds leads to
sequence95,111,113. b | An example of guided C–H bond activation where a novel and diverse analogues117. g | Strain-releasing agents react with
functional group is attached by direction of a neighbouring group113. nucleophiles under mild conditions to introduce complex ring systems118.
c | C–H arylation as used in the synthesis of a clinical candidate, thus h | Cross coupling/hydrogenation to impart enhanced sp3 character com-
demonstrating the suitability of this large-scale and high-yielding pared with typical Suzuki–Miyaura reactions119,120.

12 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

can generate enhanced regiochemical of strain-released heteroatom functional- preparation13, they increasingly also need
predictions. In the conventional ization118 (FIG. 3 g). Strain-releasing agents to make chemogenomic tool compounds in
methodology, a chemist installs a functional can be thought of as high-energy complex order to investigate target biology, and click
group knowing precisely where the species that are spring-loaded to react with chemistry can be valuable here. As a recent
chemistry will occur, but with C–H bond amines under controlled reaction conditions example, click chemistry has been used to
activation, the site of reactivity may be to install small, complex ring systems. In investigate the gene regulatory function
less certain. Cernak and colleagues110 also essence, the complexity of the synthesis has of bromodomain inhibitors by studying
described high-throughput experimental already been addressed in the strain-release the localization of ‘click-able’ inhibitors
methods to help identify suitable late-stage agents, which are becoming commercially both within the cell and within tissue
functionalization strategies and outlined available (for example, FIG. 3 g). compartments124.
decision-making strategies for determining Finally, in addition to entirely new
the likelihood of success. reactions, innovations can also improve the Multicomponent reactions.
Beyond C–H activation, a recent most frequently used reactions. For example, Multicomponent reactions (for example,
reaction development relevant to late-stage even for the widely adopted Suzuki–Miyaura Ugi reactions (FIG. 4b)) can generate many
functionalization — and also with cross-coupling reactions, the recent report of thousands of compounds through a single
strong potential to expand the medicinal the formation of highly desirable quaternary reaction scheme125,126,127. Recently, Zarganes-
chemistry toolbox in general — allows C–C bonds119,120 could substantially expand Tzitzikas and Dömling 128 reviewed the
the direct conversion of carboxylic acids their impact (FIG. 3 h). application of this technology as applied
to boronic acids. Baran and colleagues Although the impact remains to be to the synthesis of telaprevir, a complex
demonstrated that this novel reaction seen for these highlighted emerging molecule for which the number of synthetic
can be used to perform late-stage func- methodologies, we believe that they will steps could be halved by using two
tionalization of approved drugs such as enable access to more sp3-like chemical multicomponent reactions. Although these
atorvastatin (FIG. 3d) and vancomycin and space, which can address perceived techniques have been around for many
to enable improvements in synthesizing limitations of polyaromatic compounds121 years, with the potential increased use of
drugs (for example, bortezomib), as well as and provide other potential advantages automated synthesis platforms as well as the
in the synthesis of a library of compounds (see discussion below). Furthermore, use of DNA-encoded libraries (discussed
that was used to identify potent inhibitors companies that adopt these newer below), multicomponent reactions will
of human neutrophil elastase115. methodologies could gain the advantage probably gain in utility.
Furthermore, access to boron-substituted of structural differentiation of their
compounds is important for the widely drug candidates from those of the many DNA-encoded libraries. DNA-encoded
used Suzuki–Miyaura reaction mentioned companies using established chemistry libraries enable the rapid affinity-based
previously. and commercial building blocks, screening of billions to trillions of
Another example of potentially trans- and this differentiation can provide compounds, based on the construction
formational chemistry is the iron-catalysed important intellectual property benefits in of split-and-mix combinatorial libraries
radical reaction discovered by Baran and crowded areas, such as kinase targets. tagged with specific DNA sequences
colleagues116 to form sp3–sp3 C–C bonds by that allow identification of hits by
reductive coupling of two olefins (FIG. 3e). Synthetic strategies and platforms PCR sequencing 129. These libraries
In this procedure, C–C bonds can be Finally, we briefly highlight some broad pose chemistry challenges, given the
formed from relatively common reagents synthetic strategies and platforms developed requirement for conditions that ensure the
and mild conditions to provide complex over the past two decades that are already stability and integrity of the encoding DNA
scaffolds. A related new reaction, reductive valuable tools for medicinal chemists and element of the molecule. Thus, near neutral
olefin hydrocarbonation using Ni catalysis, chemical biologists and may also have aqueous environments are necessary, for
also has strong potential to affect drug considerable further potential. The breadth which an ever-growing toolbox of reactions
design because it can establish sp3–sp3 C–C of these strategies is far too wide to allow is being exploited130,131. Surprisingly, given
bonds from halogenated alkyl groups and anything more than a brief overview of the aqueous environment and that a DNA
a corresponding alkene117 (FIG. 3f). Such them in a single article, but they are polymerase is used to encode the library,
reactions are interesting for medicinal important to note in the context of the enzyme catalysis has been exemplified
chemists, given the ability to construct discussion here and so are highlighted by synthetically only in the construction of
novel and diverse molecules via C–C bond providing at least one illustrative example on‑DNA glycans132.
formation using common building blocks of each approach, with references to Several success stories with this
and mild conditions. comprehensive reviews on each. technology have recently been published133,
As mentioned previously, the uptake of exemplified in BOX 3 by the discovery
new reactions that can be used to install Click chemistry. Click chemistry (FIG. 4a) of the potent RIPK1 clinical candidate
atypical groups or create novel scaffolds — a concept proposed by Sharpless by GlaxoSmithKline (GSK)134,135, interesting
in drug discovery can be hindered by and colleagues in 2001 that involves a hits for tuberculosis target InhA136 and
the concern of the potentially excessive high-yielding mild reaction — has been potential covalent kinase inhibitors137. As the
time and resources spent on optimizing a extensively used to create probes and tools methodology matures, further applications
procedure for a particular compound. One that operate under bioorthogonal conditions are emerging, such as selections against
major advancement that can help address for chemoproteomic interrogations122,123. multiple targets in parallel as a means
this issue has also come from Baran and Although medicinal chemists may not often of both identifying hits and assessing
colleagues, who introduced the concept use click chemistry in standard compound ligandability 138.

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 13


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

a b
OBn HO CHO CO2H
Click HO O N N OH
MeOH O
N +
OBn HO N
OH OH NH2 EtO2C N
H
OBn EtO2C NC O
OH

c O OH
[Si]O
NHNs O
O MeO
Natural-product-like library, H
HO by macrocyclization N N
O N O

Ar O OMe
O N O
OAc H

NsHN O
Mycobacterium bovis MIC 11 μM

d Androgen receptor agonists


O
H O
Ar
N Ar O
N O
H
OH EC50 860 nM
EC50 7.3 nM O

O F3C N O
H
Ar
N O O
NC N2
H [Rh2(esp)2]
EC50 4.7 nM (1 mol%), EtOAc

O O
O
H
Ar Ar O
N NC N
H N

EC50 3.8 nM EC50 730 nM

e
Li Li Me Me
O O
H Me N N
TIBO TIBO Li Cl Li Li
Me H
Cl H
Si H Si Cl
[Si] [Si]
O Iterative stereocontrolled homologation R1 Bpin
Br
R1 O

O
N
N OH OH OH
1. Bpin R2
2. Oxidation
S HO2C
(+)-Kalkitoxin Post-FGI O
H H
OH

C15H31 OH OH
HO2C
R1 R2
OH
(+)-Hydroxyphthioceranic acid (+)-Zincophorin

f OMe
Ir/chiral phosphine OMe O
Chiral amine OMe
R,R + other 3 variants H
O H
C5H11 OMe H
H C5H11 OMe
+ C5H11 O

Stereodivergent use of (–) Δ9-trans-tetrahydrocannabinol


enantiomeric pairs of catalysts (and 3 isomers from chiral intermediates)

14 | ADVANCE ONLINE PUBLICATION


Nature Reviews | Drug Discovery
www.nature.com/nrd
©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

◀ Figure 4 | Broad synthetic strategies and platforms applied to lead and drug-like scaffolds. bioactive compounds emerge from rounds
a | Click chemistry has become a routine reaction, as exemplified by the synthesis of aldose reductase of synthesis, deliberately chosen to have
inhibitors123. b | Multicomponent reactions can generate diverse scaffolds in large numbers under mild multiple potential outcomes, as exemplified
conditions126. c | Natural-product-inspired macrocycle synthesis leads to compounds with anti-­ by the identification of androgen receptor
tuberculosis activity164. d | Activity-directed synthesis results in the identification of androgen receptor
agonists by synthetic expansion from a
agonists166. e | Generic scheme outlining the iterative ‘machine’ synthesis of polyketide linkages pio-
neered by the Aggarwal group, showing the building blocks and examples of synthetic targets known fragment 166 (FIG. 4d).
accessed pursuing the methodology170. f | Stereodivergent total synthesis of all four trans/cis diaster- Approaches inspired by natural
eomers of Δ9-tetrahydrocannabinol from common reagents and catalysts171. EC50, effective concen- product biosynthesis, such as automated
tration for half-maximum response; FGI, functional-group interconversion; MIC, minimal inhibitory assembly-line synthesis167 of polypropion-
concentration. ate-containing molecules168 or biomimetic
cascades169 (FIG. 4e), also have exciting
potential170. For example, this approach
Fragment-based drug discovery. Various active site or engineered cysteine residues is illustrated by recent work by Carriera’s
fragment-based strategies, which were have been used to aid in initial fragment group171 to make all four diastereomers
pioneered more than two decades ago, tethering 148. More recently, however, Cravatt of Δ9-tetrahydrocannabinols from
are now well established and are often and colleagues equipped fragments with common reagents and catalysts (FIG. 4f).
particularly attractive for challenging targets. photoactivatable moieties (for example, Complementary to wholly synthetic
The first drugs identified by fragment-based diazerene-to-carbene transformation) and strategies, opportunities are now arising for
strategies — vemurafenib139 and venetoclax 140 established a more generic chemical biology harnessing ‘directed evolution’. The notion of
— have been approved, erdafitinib has approach to target discovery 149 based on exploiting natural sources as feedstocks for
breakthrough designation141, and other covalent fragments for isolated proteins and chemical manipulation of drug molecules is
compounds are progressing in the clinic18. even for whole-cell screening 150. attractive as a greener and sustainable source
Such strategies screen libraries of fragments of complex molecules. The idea of targeted
— compounds with roughly 10–17 heavy Natural products as inspiration. Given evolution of source plants or microbial
atoms (~130–250 Da) — using various the long and successful history of natural agents as factories for drug production could
biophysical techniques (particularly X‑ray products in drug discovery, various be a viable future strategy, and opportunities
crystallography and NMR spectroscopy) groups have proposed that populating with directed evolution strategies have
to detect weak interactions with biological screening libraries with molecules that recently been reviewed172.
targets. Hits are then expanded and optimized have natural-product-like characteristics
preferably using structural knowledge of their (such as higher content of sp3-hydridized Outlook
interaction with the target. carbons151,152) could be valuable, particularly Discovering new drugs is a formidable
Here, we briefly highlight some points for novel targets153. Various strategies, such challenge. Biology is amazingly complex,
related to the synthesis of the types of as diversity-oriented synthesis154, have been and ultimately, it is the target biology
compounds included in fragment libraries, developed to achieve these goals by using that will largely determine whether a
which require their own particular reaction pathways designed to efficiently drug discovery project succeeds or fails.
characteristics to improve the likelihood synthesize libraries of such compounds155. Nevertheless, synthetic chemistry is often
of finding hits. The ideal fragment Progress in the development of new a rate-limiting step in the process of
should be soluble (given necessarily synthetic methodologies and applications identifying molecules that have the potential
high concentrations of stock solutions towards molecules with lead-like and/or to become safe and efficacious drugs.
for biophysical screening of their likely less planar character has been achieved Importantly, this can particularly be the
low-affinity binding) and relatively through the funding of European academic case when the biological validation for the
uncomplex 142,143. A case has been made groups in partnership with industry in target is compelling but it falls into a class
for increased three‑­dimensionality in the establishment of a European Lead of targets that have proved challenging to
fragments144 and also for populating Factory 156. This consortium, with close modulate, such as KRAS or c‑Myc in cancer.
screening collections with the motifs of consultation with industry, has focused on Although some novel targets may eventually
fragmented natural products145. However, molecular shape and property guidelines157 prove routinely tractable with platforms
analysis of Astex data indicated that and has been proactive in questioning such as antisense technologies173 or protein
less complex and flatter fragments have the status quo in terms of contemporary degradation technologies174, expanding the
higher hit rates, although effective growth practice in academic synthesis and drug medicinal chemistry toolbox as reviewed
often requires more functionalized discovery 158,159. As their work has progressed, here is also an important strategy.
and/or asymmetric chemistry to yield the consortium has charted progress in When considering how to achieve this, an
candidate-quality structures146. The achieving chemical space expansion160,161, important factor is that the role of medicinal
structure-based design inherent to realizing the goals of lead-oriented chemistry has changed considerably since
fragment-based drug discovery leads synthesis162 and assessing potential its inception. There are many examples from
to optimal binding and ligand-efficient applicability to central nervous system the past when key biological discoveries
molecules, but discipline with properties147 targets163. Interesting screening data are and therapeutic advances were made
is still necessary to ensure the best emerging, such as natural-product-inspired through synthetic chemists exploring
developability characteristics25. macrocycles with anti-tuberculosis activity 164 various chemical routes and SARs in
Another interesting development involves (FIG. 4c). An intriguing concept developed drug classes such as benzodiazepines175,
covalently binding fragments. Electrophilic by the Nelson group in this consortium penicillins, tetracyclines176 and taxanes177,178.
fragments that react with an enzyme is activity-directed synthesis165, whereby Unfortunately, synthetic chemistry is now

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 15


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

often considered a bottleneck in DMTA entities (SMEs) and big pharma together to the most versatile and robust reactions
cycles, which can put considerable pressure with academic researchers — as exemplified (highlighted in BOX 1). Recent contributions
on medicinal chemists to deliver molecules by the European Innovative Medicines from the Burke group70 realized this concept
in a specific time frame for the planned Initiative (IMI) and the Joint European and provided a viable synthesis option for
screening cascades. Reward systems and Compound Library (JECL)180 at the more than ten compound families. Further
pressure on delivery have pushed medicinal European Lead Factory — may be one work in this direction could result in robust
chemists to meet metric-based goals within a way to help address this barrier. Initiatives reactions for automated synthesis that cover
progression-seeking R&D culture179. In these aiming to synthesize novel building a considerable percentage of the relevant
circumstances, a numbers-game attitude and blocks and develop relevant synthetic bioactive chemotypes. Recent advances
a focus on easy‑to‑make compounds can transformations are also important 49,50 in testing the functional group tolerances
often divert medicinal chemists from design and provide an excellent opportunity for of reactions and the stability of specific
principles, and the potential impact of extending industry–academia partnerships29. chemical motifs under reaction conditions181
more complex and/or challenging synthetic Collaborations and incubators could also — together with a larger set of available
strategies is likely to be lost. In addition, help smaller biotech firms and university building blocks — may help to extend the
the way CROs have been used for synthetic start-ups capitalize on their novel chemistry scope of robust reactions.
chemistry has affected what has been made, in drug discovery settings. The predictive power of computational
undeniably tilting towards robust chemistry. Focusing on the technological issues, tools for both designing synthetic routes
With this in mind, we see two academic groups have reported notable and identifying promising molecules to
complementary approaches to enabling achievements in automated syntheses62,74. synthesize depends on the amount and
medicinal chemists to make fuller use of the Given the diversity of reaction types quality of underlying experimental data.
tools discussed above. The first approach is and conditions used in drug discovery The future will bring more data with better
to reduce some of the technical barriers to programmes, however, optimization of all quality, more data-processing power and
using such tools. Precompetitive consortia the useful reactions may not be possible. An hopefully better computational methods,
consisting of small and medium-sized alternative approach is to limit these efforts including those using deep-learning
technologies and artificial intelligence182,183.
This could provide greater confidence in the
Box 3 | Example of the impact of new synthesis strategies: DNA-encoded libraries
value of synthetically challenging molecules
Rapid affinity-based screening of billions to trillions of compounds can be achieved with and help move away from ‘more shots on
DNA-encoded libraries, for which hits can be identified by PCR of specific DNA sequences that are goal’ approaches using the easiest chemistry
linked to each library member. The figure shows an overview of the process from a DNA-encoded available. Furthermore, the technologies
library134 to GSK772, a clinical candidate that targets receptor-interacting protein kinase 1 (RIPK1)135. discussed above may also enable the
Affinity screening of a ~7.7 billion-membered three‑cycle capped amino acid library, encoded by
synthesis of more lead-like molecules.
DNA, identified a key feature through PCR of bound compounds, leading to the off-DNA synthesis of
the 1.3 nM hit compound. This was optimized to the clinical candidate with minimal but important
For example, biocatalytic methods
structural changes. Replacement of the isoxazole heterocycle improved the developability profile of work in aqueous media and favour the
this series. The 3‑benzyl‑1,2,4‑triazole isomer showed the optimal combination of in vitro potency, incorporation of hydrophilic functionalities,
lipophilicity, kinetic aqueous solubility and rat oral exposure. GSK772 is currently in phase IIa clinical and late-stage functionalization methods
studies for psoriasis, rheumatoid arthritis and ulcerative colitis. can address metabolic ‘soft spots’ with the
pIC50, negative logarithmic value of the half-maximal inhibitory concentration. introduction of F or CF3 groups116. Another
important feature of some of these emerging
technologies is the ability to introduce
R1 O R1 O
higher sp3 content in the lead molecules.
O
H
N
H
N
H
N N The second approach is to address
N
H
R3 N
H NH
the cultural barriers that have limited the
O R2 O
R3 uptake of newer approaches. These barriers
O
O can be identified at both the management
Component of library, Selection, PCR and analysis and bench chemistry levels. From a
~7.7×109 compounds identified this structure
management perspective, replacement of
the numbers-game attitude with value-based
O strategies is needed. Projects could benefit
O
Off-DNA synthesis O from multiple values, such as a more
NH N
feasible synthesis, a new catalyst or a new
N chemotype, that require more time and
O
effort than raw synthesis schemes with
RIPK1 pIC50 1.3 nM
robust reactions. These values should be
acknowledged in improved reward schemes.
O N Establishing new types of partnerships
O
Lead optimization NH and collaborations with academia could
NH N
further facilitate the implementation of
N
O new technologies. Industry–academia
relationships should move beyond CRO-type
GSK772
contributions that are not matched with the

Nature Reviews | Drug Discovery


16 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd
©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

academic goals of discovering and publishing 4. Virshup, A. M., Contreras-García, J., Wipf, P., Yang, W. 29. Blakemore, D. C. et al. Organic synthesis provides
& Beratan, D. N. Stochastic voyages into uncharted opportunities to transform drug discovery. Nat. Chem.
new science. First, they should help academic chemical space produce a representative library of all 10, 383–394 (2018).
scientists to understand the true challenges possible drug-like compounds. J. Am. Chem. Soc. 135, 30. Hann, M. M. & Keserü, G. M. Finding the sweet spot:
7296–7303 (2013). the role of nature and nurture in medicinal chemistry.
and needs of medicinal chemistry. Second, 5. Bemis, G. W. & Murcko, M. A. The properties of known Nat. Rev. Drug Discov. 11, 355–365 (2012).
the new chemistries and technologies that drugs. 1. Molecular frameworks. J. Med. Chem. 39, 31. Rafferty, M. F. No denying it: medicinal chemistry
2887–2893 (1996). training is in big trouble. J. Med. Chem. 59,
medicinal chemists in industry have access to 6. Bemis, G. W. & Murcko, M. A. Properties of known 10859–10864 (2016).
could be further improved by incorporating drugs. 2. Side chains. J. Med. Chem. 42, 5095–5099 32. Campbell, I. B., Macdonald, S. J. F. & Procopiou, P. A.
(1999). Medicinal chemistry in drug discovery in big pharma:
technology from academic researchers 7. Wang, J. & Hou, T. Drug and drug candidate building past, present and future. Drug Discov. Today 23,
and SMEs. Third, training schemes with block analysis. J. Chem. Inf. Model. 50, 55–67 (2010). 219–234 (2018).
8. Taylor, R. D., MacCoss, M. & Lawson, A. D. Rings in 33. Hartenfeller, M. et al. A collection of robust organic
industry participation (such as GSK with the drugs. J. Med. Chem. 57, 5845–5859 (2014). synthesis reactions for in silico molecule design.
University of Nottingham)184, new types of 9. Taylor, R. D., MacCoss, M. & Lawson, A. D. Combining J. Chem. Inf. Model. 51, 3093–3098 (2011).
molecular scaffolds from FDA approved drugs: 34. Segler, M. H. S., Preuss, M. & Waller, M. P. Planning
PhD courses developed through initiatives application to drug discovery. J. Med. Chem. 60, chemical syntheses with deep neural networks and
such as the Marie Sklodowska Curie Action 1638–1647 (2017). symbolic AI. Nature 555, 604–610 (2018).
10. Pitt, W. R., Parry, D. M., Perry, B. G. & Groom, C. R. 35. Bergman, R. G. & Danheiser, R. L. Reproducibility in
(MSCA) Innovative Training Networks, Heteroaromatic rings of the future. J. Med. Chem. 52, chemical research. Angew. Chem. Int. Ed. Engl. 55,
internships and postdoctoral programmes 2952–2963 (2009).
 12548–12549 (2016).
11. Visini, R., Arús-Pous, J., Awale, M. & Reymond, J. L. 36. Engkvist, O. et al. Computational prediction of
at industry partners may also improve the Virtual exploration of the ring systems chemical chemical reactions: current status and outlook.
background knowledge and creativity of the universe. J. Chem. Inf. Model. 57, 2707–2718 (2017). Drug Discov. Today 23, 1203–1218 (2018).
12. Roughley, S. D. & Jordan, A. M. The medicinal 37. Rahman, S. A. et al. Reaction decoder tool (RDT):
next generation of medicinal chemists. chemist’s toolbox: an analysis of reactions used in the extracting features from chemical reactions.
Finally, it is noteworthy that pursuit of drug candidates. J. Med. Chem. 54, Bioinformatics 32, 2065–2066 (2016).
3451–3479 (2011). 38. Buitrago Santanilla, A. et al. Organic chemistry.
small-molecule drugs currently constitute 13. Brown, D. G. & Boström, J. Analysis of past and Nanomole-scale high-throughput chemistry for the
a smaller proportion of the top echelon of present synthetic methodologies on medicinal synthesis of complex molecules. Science 347, 49–53
chemistry: where have all the new reactions gone? (2015).
drug revenues by sales than ever before185. J. Med. Chem. 59, 4443–4458 (2016). 39. Perera, D. et al. A platform for automated nanomole-
This could be a catalyst for the practitioners 14. Schneider, N., Lowe, D. M., Sayle, R. A., Tarselli, M. A. scale reaction screening and micromole-scale
& Landrum, G. A. Big data from pharmaceutical synthesis in flow. Science 359, 429–434 (2018).
of small-molecule drug discovery to patents: a computational analysis of medicinal 40. Szymkuc´, S. et al. Computer-assisted synthetic
better define the key problems that need chemists’ bread and butter. J. Med. Chem. 59, planning: The end of the beginning. Angew. Chem. Int.
4385–4402 (2016). Ed. Engl. 55, 5904–5937 (2016).
to be addressed and the areas in which 15. Carey, J. S., Laffan, D., Thomson, C. & Williams, M. T. 41. Segler, M. H. S. & Waller, M. P. Modelling chemical
small-molecule drug discovery has the Analysis of the reactions used for the preparation of reasoning to predict and invent reactions. Chem. Eur.
drug candidate molecules. Org. Biomol. Chem. 4, J. 23, 6118–6128 (2017).
greatest potential to provide major advances 2337–2347 (2006). 42. Kayala, M. A. & Baldi, P. ReactionPredictor: prediction
compared with alternative platforms. We 16. Dugger, R. W., Ragan, J. A. & Brown Ripin, D. H. of complex chemical reactions at the mechanistic level
Survey of GMP bulk reactions run in a research facility using machine learning. J. Chem. Inf. Model. 52,
remain optimistic about the future of between 1985 and 2002. Org. Proc. Res. Dev. 9, 2526–2540 (2012).
small-molecule drug discovery, as despite 253–258 (2005). 43. Kayala, M. A., Azencott, C.‑A., Chen, J. H. & Baldi, P.
17. Satyanarayanajois, S. D. & Hill, R. A. Medicinal Learning to predict chemical reactions. J. Chem. Inf.
the challenges, expanding the medicinal chemistry for 2020. Future Med. Chem. 14, Model. 51, 2209–2222 (2011).
chemistry toolbox with the arsenal of 1765–1786 (2011). 44. Stark, S. A., Neudert, R. & Threlfall, R. Wiley
18. Erlanson, D. A., Fesik, S. W., Hubbard, R. E., ChemPlanner predicts experimentally verified
methodologies highlighted above is set Jahnke, W. & Jhoti, H. Twenty years on: the impact of synthesis routes in medicinal chemistry. CHEManager
to free up more time to be creative and fragments on drug discovery. Nat. Rev. Drug Discov. http://www.chemanager-online.com/en/whitepaper/
15, 605–619 (2016). wiley-chemplanner-predicts-experimentally-verified-
implement new chemistries, efficient 19. Boström, J., Grant, J. A., Fjellström, O., Thelin, A. & synthesis-routes-medicinal-chemistry (2016).
synthetic routes and improved reaction Gustafsson, D. Potent fibrinolysis inhibitor discovered 45. Bøgevig, A. et al. Route design in the 21st century:
by shape and electrostatic complementarity to the the ICSYNTH Software tool as an idea generator for
technologies. Exciting times lie ahead. drug tranexamic acid. J. Med. Chem. 56, 3273–3280 synthesis prediction. Org. Proc. Res. Dev. 19,
(2013). 357–368 (2015).
Jonas Boström1, Dean G. Brown2, Robert J. Young3 and 20. Lionta, E., Spyrou, G., Vassilatis, D. K. & Cournia, Z. 46. Klucznik, T. et al. Efficient syntheses of diverse,
György M. Keserü4* Structure-based virtual screening for drug discovery: medicinally relevant targets planned by computer and
principles, applications and recent advances. Curr. Top. executed in the laboratory. Chem 4, 522–532 (2018).
Medicinal Chemistry, Cardiovascular, Renal and
1
Med. Chem. 14, 1923–1938 (2014). 47. Kroman, J. C. et al. Fast and accurate prediction of the
Metabolism, IMED Biotech Unit, AstraZeneca, 21. Santos, R. et al. A comprehensive map of molecular regioselectivity of electrophilic aromatic substitution
Gothenburg, Sweden. drug targets. Nat. Rev. Drug Discov. 16, 19–34 reactions. Chem. Sci. 9, 660–665 (2018).
(2017). 48. Hansen, E. et al. Prediction of stereochemistry using
2
Hit Discovery, Discovery Sciences, IMED Biotech Unit, 22. Nadin, A., Hattotuwagama, C. & Churcher, I. Lead- Q2MM. Acc. Chem. Res. 49, 996–1005 (2016).
AstraZeneca, Waltham, MA, USA. oriented synthesis: a new opportunity for synthetic 49. Goldberg, F. W., Kettle, J. G., Kogej, T., Perry, M. W. &
chemistry. Angew. Chem. Int. Ed. Engl. 51, 1114–1122 Tomkinson, N. P. Designing novel building blocks is an
3
NCE-Medicinal Chemistry, GlaxoSmithKline R&D, (2012). overlooked strategy to improve compound quality.
Stevenage, Hertfordshire, UK. 23. Goldberg, F. W., Kettle, J. G., Kogej, T., Perry, M. W. & Drug Discov. Today 20, 11–17 (2015).
Tomkinson, N. P. Designing novel building blocks is an 50. Carreira, E. M. & Fessard, T. C. Four-membered ring-
Medicinal Chemistry Research Group, Research
4 overlooked strategy to improve compound quality. containing spirocycles: synthetic strategies and
Center for Natural Sciences, Hungarian Academy of Drug Discov. Today 20, 11–17 (2015). opportunities. Chem. Rev. 114, 8257–8322 (2014).
24. Keserü, G. M. & Makara, G. M. The influence of lead 51. Helal, C. J. et al. Increased building block access
Sciences, Budapest, Hungary.
discovery strategies on the properties of drug through collaboration. Drug Discov. Today https://doi.
*e-mail: keseru.gyorgy@ttk.mta.hu candidates. Nat. Rev. Drug Discov. 8, 203–212 org/10.1016/j.drudis.2018.03.001 (2018).
(2009). 52. Murray, P. M. et al. The application of design of
doi:10.1038/nrd.2018.116 25. Young, R. J. & Leeson, P. D. Mapping the efficiency and experiments (DoE) reaction optimisation and solvent
Published online 24 Aug 2018 physicochemical trajectories of successful selection in the development of new synthetic
optimizations. J. Med. Chem. https://doi.org/10.1021/ chemistry. Org. Biomol. Chem. 14, 2373–2384
1. Bohacek, R. S., McMartin, C. & Guida, W. C. The art acs.jmedchem.8b00180 (2018). (2016).
and practice of structure-based drug design: a 26. Keserü, G. M., Soós, T. & Kappe, C. O. Anthropogenic 53. Carlson, R. & Carlson, J. E. in Design and
molecular modeling perspective. Med. Res. Rev. 16, reaction parameters — the missing link between Optimization in Organic Synthesis Vol. 24 1–574
3–50 (1996). chemical intuition and the available chemical space. (Elsevier, 2005).
2. Mullard, A. The drug maker’s guide to the galaxy. Chem. Soc. Rev. 43, 5387–5399 (2014). 54. Cook, A. Computer-aided synthesis design: 40 years
Nature 549, 445–447 (2017). 27. Boström, J. & Brown, D. G. Stuck in a rut with old on — WIREs. Comput. Mol. Sci. 2, 79–107 (2012).
3. Ertl, P. J. Cheminformatics analysis of organic chemistry. Drug Discov. Today 21, 701–703 (2016). 55. Schwaller, P., Gaudin, T., Lanyi, D., Bekas, C. &
substituents: identification of the most common 28. Walters, W. P., Green, J., Weiss, J. R. & Murcko, M. A. Laino, T. “Found in translation”: predicting outcomes
substituents, calculation of substituent properties & What do medicinal chemists actually make? A of complex organic chemistry reactions using neural
automatic identification of drug-like bioisosteric groups. 50‑year retrospective. J. Med. Chem. 54, sequence-to‑sequence models. arXiv https://arxiv.org/
J. Chem. Inf. Comput. Sci. 43, 374–380 (2003). 6405–6416 (2011). abs/1711.04810 (2017).

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 17


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

56. Baskin, I., Madzhidov, T. I., Antipin, I. S. & 82. Hettiarachchi, K., Kong, M., Yun, A., Jacobsen, J. R. & 106. Faust, M. R., Höfner, G., Pabel, J. & Wanner, K. T.
Varnek, A. A. Artificial intelligence in synthetic Xue, Q. Development of an automated dual-mode Azetidine derivatives as novel γ -aminobutyric acid
chemistry: achievements and prospects. Rus. Chem. supercritical fluid chromatography & reversed-phase uptake inhibitors: synthesis, biological evaluation, and
Rev. 86, 1127 (2017). liquid chromatography mass-directed purification structure-activity relationships. Eur. J. Med. Chem. 45,
57. Wengong, J. Predicting organic reaction outcomes with system for small-molecule drug discovery. J. Sep. Sci. 2453–2466 (2010).
Weisfeiler-Lehman network. arXiv https://arxiv.org/ 37, 775–781 (2014). 107. Elsler, B., Schollmeyer, D., Dyballa, K. M., Franke, R.
abs/1709.04555 (2017). 83. Tarcsay, A., Nyíri, K., Keserü, G. M. Impact of lipophilic & Waldvogel, S. R. Metal- and reagent-free highly
58. Fooshee, D. Deep learning for chemical reaction efficiency on compound quality. J. Med. Chem. 55, selective anodic cross-coupling reactions of phenols.
prediction. Mol. Syst. Des. Eng. https://doi. 1252–1260 (2012). Angew. Chem. Int. Ed. Engl. 53, 5210–5213 (2014).
org/10.1039/C7ME00107J (2018). 84. Johnson, T. W., Gallego, R. A., Edwards, M. P. 108. Green, R. A., Brown, R. C. D. & Pletcher, D. A
59. Coley, C. W., Barzilay, R., Jaakkola, T. S., Green, W. H. Lipophilic efficiency as an important metric in drug microflow electrolysis cell for laboratory synthesis on
& Jensen, K. F. Prediction of organic reaction design. J. Med. Chem. https://doi.org/10.1021/acs. a multigram scale. Org. Process Res. Dev. 19,
outcomes using machine learning. ACS Cent. Sci 3, jmedchem.8b00077 (2018). 1424–1427 (2015).
434–443 (2017). 85. Kan, S. B. J., Huang, X., Gumulya, Y., Chen, K. & 109. Ajami, A. Converging trends brings organic
60. Brynjolfsson, E. & Mitchell, T. What can machine Arnold, F. H. Genetically programmed chiral electrochemistry to the front line of drug discovery.
learning do? Workforce implications: profound change organoborane synthesis. Nature 552, 132–136 (2017). BiopharmaTrend.com www.biopharmatrend.com/
is coming, but roles for humans remain. Science 358, 86. Arnold, F. H. Directed evolution: bringing new post/40-converging-trends-brings-organic-
1530–1534 (2017). chemistry to life. Angew. Chem. Int. Ed. Engl. 57, electrochemistry-to-the-front-line-of-drug-discovery/
61. Griffen, E. J. et al. Can we accelerate medicinal 4143–4148 (2018). (2017).
chemistry by augmenting the chemist with Big Data 87. Prier, C. K., Zhang, R. K., Buller, A. R., Brinkmann- 110. Cernak, T., Dykstra, K. D., Tyagarajan, S., Vachal, P. &
and artificial intelligence? Drug Discov. Today 23, Chen, S. & Arnold, F. H. Enantioselective, Krska, S. W. The medicinal chemist’s toolbox for late
1373–1384 (2018). intermolecular benzylic C‑H amination catalysed by an stage functionalization of drug-like molecules. Chem.
62. Fitzpatrick, D. E., Battilocchio, C. & Ley, S. V. Enabling engineered iron-haem enzyme. Nat. Chem. 9, 629–634 Soc. Rev. 45, 546–576 (2016).
technologies for the future of chemical synthesis. ACS (2017). 111. Wang, P. et al. Ligand-accelerated non-directed C‑H
Cent. Sci. 2, 131–138 (2016). 88. Boer, J. et al. Roles of UGT, P450, and gut microbiota functionalization of arenes. Nature 551, 489–493
63. Trang, J., T. T. T., Ermolat’ev, D. S. & Van der in the metabolism of epacadostat in humans. Drug (2017).
Eycken, E. V. Facile and diverse microwave-assisted Metab. Dispos. 44, 1668–1674 (2016). 112. Loh, Y. Y. et al. Photoredox-catalyzed deuteration and
synthesis of secondary propargylamines in water using 89. Obach, R. S. et al. Lead diversification at the tritiation of pharmaceutical compounds. Science 358,
CuCl/CuCl2. RSC Adv. 5, 28921–28924 (2015). nanomole scale using liver microsomes and 1182–1187 (2017).
64. Tsoung, J. et al. Synthesis of fused pyrimidinone and quantitative nuclear magnetic resonance 113. Dai, H.‑X., Stepan, A. F., Plummer, M. S., Zhang, Y.‑H.
quinolone derivatives in an automated high- spectroscopy: application to phosphodiesterase 2 & Yu, J.‑Q. Divergent C‑H functionalizations directed
temperature and high-pressure flow reactor. J. Org. inhibitors. J. Med. Chem. 61, 3626–3640 (2018). by sulfonamide pharmacophores: late-stage
Chem. 82, 1073–1084 (2017). 90. Schonherr, H. & Cernak, T. Profound methyl effects diversification as a tool for drug discovery. J. Am.
65. Tran, D. N., Battilocchio, C., Lou, S.‑B., Hawkins, J. M. in drug discovery and a call for new C‑H Chem. Soc. 133, 7222–7228 (2011).
& Ley, S. V. Flow chemistry as a discovery tool to methylation reactions. Angew. Chem. Int. Ed. Engl. 114. Wei, X. et al. Arylation and enantioselective
access sp2–sp3 cross-coupling reactions via diazo 52, 12256–12267 (2013). hydrogenation enables ideal asymmetric entry to the
compounds. Chem. Sci. 6, 1120–1125 (2015). 91. Gillis, E. P., Eastman, K. J., Hill, M. D., Donnelly, D. J. indenopiperidine core of an 11β‑HSD‑1 inhibitor.
66. Battilocchio, C. et al. Iterative reactions of transient & Meanwell, N. A. Applications of fluorine in medicinal J. Am. Chem. Soc. 138, 15473–15481 (2016).
boronic acids enable sequential C–C bond formation. chemistry. J. Med. Chem. 58, 8315–8359 (2015). 115. Li, C. et al. Decarboxylative borylation. Science 356,
Nat. Chem. 8, 360–367 (2016). 92. Pettersson, M. et al. Quantitative assessment of the eaam7355 (2017).
67. Yoshida, J., Takahashi, Y. & Nagaki, A. Flash impact of fluorine substitution on P‑glycoprotein (P‑gp) 116. Lo, J. C., Yabe, Y. & Baran, P. S. A practical and
chemistry: flow chemistry that cannot be done in mediated efflux, permeability, lipophilicity, and catalytic reductive olefin coupling reaction. J. Am.
batch. Chem. Commun. 49, 9896–9904 (2013). metabolic stability. J. Med. Chem. 59, 5284–5296 Chem. Soc. 136, 1304–1307 (2014).
68. Kim, H. et al. Submillisecond organic synthesis: (2016). 117. Lu, X. et al. Practical carbon-carbon bond formation
outpacing Fries rearrangement through microfluidic 93. Obach, R. S., Walker, G. S. & Brodney, M. A. from olefins through nickel-catalyzed reductive
rapid mixing. Science 352, 691–694 (2016). Biosynthesis of fluorinated analogs of drugs using olefin hydrocarbonation. Nat. Commun. 7, 11129
69. Schneider, G. Automating drug discovery. Nat. Rev. human cytochrome P450 enzymes followed by (2016).
Drug Discov. 17, 97–113 (2018). deoxyfluorination and quantitative nuclear magnetic 118. Lopchuk, J. M. et al. Strain-release heteroatom
70. Li, J. et al. Synthesis of many different types of organic resonance spectroscopy to improve metabolic stability. functionalization: development, scope, and
small molecules using one automated process. Science Drug Metab. Dispos. 44, 634–646 (2016). stereospecificity. J. Am. Chem. Soc. 139, 3209–3226
347, 1221–1226 (2015). 94. Romero, N., A. & Nicewicz, D. A. Organic photoredox (2017).
71. Baranczak, A. et al. Integrated platform for expedited catalysis. Chem. Rev. 116, 10075–10166 (2016). 119. Ariki, Z. T., Maekawa, Y., Nambo, M. & Crudden, C. M.
synthesis-pPurification-testing of small molecule 95. Ji, Y. et al. Innate C‑H trifluormethylation of Preparation of quaternary centers via nickel-catalyzed
libraries. ACS Med. Chem. Lett. 8, 461–465 (2017). heterocycles. Proc. Natl Aacad. Sci. USA. 108, Suzuki–Miyaura cross-coupling of tertiary sulfones.
72. Godfrey, A. G., Masquelin, T. & Hemmerle, H. A 14411–14415 (2011). J. Am. Chem. Soc. 140, 78–81 (2018).
remote-controlled adaptive medchem lab: an 96. Zuo, Z. et al. Merging photoredox with nickel catalysis: 120. Campbell, P. S., Jamieson, C., Simpson, I. &
innovative approach to enable drug discovery in the coupling of α-carbonyl sp3‑carbons with aryl halides. Watson, A. J. B. Practical synthesis of
21st Century. Drug Disc. Today 18, 795–802 Science 345, 437–440 (2014). pharmaceutically relevant molecules enriched in sp3
(2013). 97. Zhang, X. & MacMillan, D. W. Alcohols as latent character. Chem. Commun. 54, 46–49 (2018).
73. Reizman, B. J., Wang, Y.‑M., Buchwald, S. L. & coupling fragments for metallophotoredox catalysis: 121. Ritchie, T. J. & Macdonald, S. J. Physicochemical
Jensen, K. F. Suzuki-Miyaura cross-coupling sp3‑sp2 cross coupling of oxalates with aryl halides. descriptors of aromatic character and their use in
optimization enabled by automated feedback. React. J. Am. Chem. Soc 138, 13862–13865 (2016). drug discovery. J. Med. Chem. 57, 7206–7215
Chem. Eng. 1, 658–666 (2016). 98. Wang, Z., Herraiz, A. G., del Hoyo, A. M. & (2014).
74. Trobe, M. & Burke, M. D. The molecular industrial Suero, M. G. Generating carbyne equivalents with 122. Kolb, H. C., Finn, M. G. & Sharpless, K. B. Click
revolution: automated synthesis of small molecules. photoredox catalysis. Nature 554, 86–91 (2018). chemistry: diverse chemical function from a few good
Ang. Chem. Int. Ed. 57, 4192–4214 (2018). 99. Denisenko, A. V. et al. Photochemical synthesis of reactions. Angew. Chem. Int. Ed. Engl. 40,
75. Troshin, K. & Hartwig, J. F. Snap deconvolution: an 3‑azabicyclo[3.2.0]heptanes: advanced building blocks 2004–2021 (2001).
informatics approach to high-throughput discovery of for drug discovery. J. Org. Chem. 82, 9627–9636 123. Li, L. et al. Design of an amide N-glycoside derivative
catalytic reactions. Science 357, 175–181 (2017). (2017). of β-glucogallin: a stable, potent, and specific inhibitor
76. Chakravorty, S. J. et al. Nuisance compounds, PAINS 100. Dirocco, D. A. et al. Late-stage functionalization of of aldose reductase. J. Med. Chem. 57, 71–77
filters, and dark chemical matter in the GSK HTS biologically active heterocycles through photoredox (2014).
collection. SLAS Discov. 23, 532–545 (2018). catalysis. Angew. Chem. Int. Ed. Engl. 53, 4802–4806 124. Tyler, D. S. et al. Click chemistry enables preclinical
77. Stalcup, A. M. Chiral separations. Annu. Rev. Anal. (2014). evaluation of targeted epigenetic therapies. Science
Chem. 3, 341–363 (2010). 101. Yan, M., Kawamata, Y. & Baran, P. S. Synthetic organic 356, 1397–1401 (2017).
78. Desai, B. et al. Rapid discovery of a novel series of Abl electrochemical methods since 2000: on the verge of a 125. Dömling, A., Wang, W. & Wang, K. Chemistry and
kinase inhibitors by application of an integrated renaissance. Chem. Rev. 117, 13230–13319 (2017). biology of multicomponent reactions. Chem. Rev. 112,
microfluidic synthesis and screening platform. J. Med. 102. Jiang, Y., Xu, K. & Zeng, C. Use of electrochemistry in 3083–3135 (2012).
Chem. 56, 3033–3047 (2013). the synthesis of heterocyclic structures. Chem. Rev. 126. Osipova, A., Yufit, D. S. & De Meijere, A. Synthesis of
79. Czechtizky, W. et al. Integrated synthesis and testing 118, 4485–4540 (2017). new cyclopropylisonitriles and their applications in Ugi
of substituted xanthine based DPP4 inhibitors: 103. Yoshida, J., Kataoka, K., Horcajada, R. & Nagaki, A. four-component reactions. Synthesis 1, 131–139
application to drug discovery. ACS Med. Chem. Lett. 4, Modern strategies in electroorganic synthesis. Chem. (2007).
768–772 (2013). Rev. 108, 2265–2299 (2008). 127. Liddle, J. et al. The discovery of GSK221149A: a
80. Hobbs, A. N. & Young, R. J. Practical purification of 104. Morofuji, T., Shimizu, A. & Yoshida, J. Direct C‑N potent and selective oxytocin antagonist. Bioorg.
hydrophilic fragments and lead/drug-like molecules by coupling of imidazoles with aromatic and benzylic Med. Chem. Lett. 18, 90–94 (2008).
reverse phase flash chromatography: tips, tricks and compounds via electrooxidative C‑H functionalization. 128. Zarganes-Tzitzikas, T. & Dömling, A. Modern
contemporary developments. Drug Discov. Today 18, J. Am. Chem. Soc. 136, 4496–4499 (2014). multicomponent reactions for better drug syntheses.
148–154 (2013). 105. Zhao, H.‑B., Hou, Z.-W., Liu, Z.‑J., Zhou, Z.‑F., Song, J. Org. Chem. Front. 1, 834–837 (2014).
81. Buszewski, B. & Noga, S. Hydrophilic interaction liquid & Xu, H.-C. Amidinyl radical formation through anodic 129. Goodnow, R. A. & Davie, C. P. DNA-encoded library
chromatography (HILIC)—a powerful separation N‑H bond cleavage and its application in aromatic C‑H technology: a brief guide to its evolution and impact
technique. Anal. Bioanal. Chem. 402, 231–247 bond functionalization. Angew. Chem. Int. Ed. Engl. on drug discovery. Annu. Rep. Med. Chem. 50, 1–15
(2012). 56, 587–590 (2017). (2017).

18 | ADVANCE ONLINE PUBLICATION www.nature.com/nrd


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.
PERSPECTIVES

130. Arico-Muendel, C. C. From haystack to needle: finding 153. Li, J. W.‑H. & Vederas, J. C. Drug discovery and natural 176. Wright, P. M., Seiple, I. B. & Myers, A. G. The evolving
value with DNA encoded library technology at GSK. products: end of an era or an endless frontier? Science role of chemical synthesis in antibacterial drug
MedChemComm 7, 1898–1909 (2016). 325, 161–165 (2009). discovery. Angew. Chem. Int. Ed. Engl. 34,
131. Satz, A. L. et al. DNA Compatible multistep synthesis 154. Gerry, C. J. & Schreiber, S. L. Chemical probes and 8840–8869 (2014).
and applications to DNA encoded libraries. Bioconj. drug leads from advances in synthetic planning and 177. Flam, F. The race to synthesize taxol ends in a tie.
Chem. 26, 1623–1632 (2015). methodology. Nat. Rev. Drug Discov. 17, 333–352 Science 263, 910–911 (1994).
132. Thomas, B. et al. Application of biocatalysis to on‑DNA (2018). 178. Donehower, R. C. The clinical development of
carbohydrate library synthesis. Chembiochem 18, 155. Pascolutti, M. & Quinn, R. J. Natural products as lead paclitaxel: a successful collaboration of academia,
858–863 (2017). structures: chemical transformations to create lead-like industry and the national cancer institute. Oncol. 1,
133. Goodnow Jr, R. A., Dumelin, C. E. & Keefe, A. D. DNA- libraries. Drug Discov. Today 19, 215–221 (2014). 240–243 (1996).
encoded chemistry: enabling the deeper sampling of 156. Karawajczyk, A. et al. Expansion of chemical space for 179. Ringel, M., Tollman, P., Hersch, G. & Schulze, U. Does
chemical space. Nat. Rev. Drug Discov. 16, 131–147 collaborative lead generation and drug discovery: the size matter in R&D productivity? If not, what does?
(2017). European Lead Factory Perspective. Drug Discov. Nat. Rev. Drug Disc. 12, 901–902 (2013).
134. Harris, P. A. et al. DNA-encoded library screening Today 20, 1310–1316 (2015). 180. Besnard, J., Jones, P. S., Hopkins, A. L. &
identifies benzo[b][1,4]oxazepin‑4‑ones as highly potent 157. Colomer, I. et al. A divergent synthetic approach to Pannifer, A. D. The Joint European Compound Library:
and monoselective receptor interacting protein 1 kinase diverse molecular scaffolds: assessment of lead- boosting precompetitive research. Drug Discov. Today
inhibitors. J. Med. Chem. 59, 2163–2178 (2016). likeness using LLAMA, an open-access computational 20, 181–186 (2015).
135. Harris, P. A. et al. Discovery of a first‑in‑class receptor tool. Chem. Commun. 52, 7209–7212 (2016). 181. Collins, K. D. & Glorius, F. A robustness screen for the
interacting protein 1 (RIP1) kinase specific clinical 158. Foley, D. J., Nelson, A. & Marsden, S. P. Evaluating rapid assessment of chemical reactions. Nat. Chem. 5,
candidate (GSK2982772) for the treatment of new chemistry to drive molecular discovery: fit for 597–601 (2013).
inflammatory diseases. J. Med. Chem. 60, purpose? Angew. Chem. Int. Ed. Engl. 55, 182. Chen, H., Engkvist, O., Wang, Y., Olivecrona, M. &
1247–1261 (2017). 13650–13657 (2016). Blaschke, T. The rise of deep learning in drug
136. Soutter, H. H. et al. Discovery of cofactor-specific, 159. Chow, S. Y. & Nelson, A. Embarking on a chemical discovery. Drug Discov. Today. 23, 1241–1250
bactericidal Mycobacterium tuberculosis InhA space odyssey. J. Med. Chem. 60, 3591–3593 (2018).
inhibitors using DNA-encoded library technology. Proc. (2017). 183. Fleming, N. How artificial intelligence is changing drug
Natl Acad. Sci. USA 113, E7880–E7889 (2016). 160. Dow, M., Fisher, M., James, T., Marchetti, F. & discovery. Nature 557, S55–S57 (2018).
137. Chan, A. I. et al. Discovery of a covalent kinase Nelson, A. Towards the systematic exploration of 184. Macdonald, S. J., Fray, M. J. & McInally, T. Passing on
inhibitor from a DNA-encoded small-molecule chemical space. Org. Biomol. Chem. 10, 17–28 the medicinal chemistry baton: training
library × protein library selection. J. Am. Chem. Soc. (2012). undergraduates to be industry-ready through research
139, 10192–10195 (2017). 161. Morgentin, R. et al. Translation of innovative projects between the University of Nottingham and
138. Machutta, C. A. et al. Prioritizing multiple therapeutic chemistry into screening libraries: an exemplar GlaxoSmithKline. Drug Discov. Today 21, 880–887
targets in parallel using automated DNA-encoded partnership from the European Lead Factory. Drug (2016).
library screening. Nat. Comm. 8, 16081 (2017). Discov. Today https://doi.org/10.1016/j. 185. Urquhart, L. Market watch: top drugs and companies
139. Bollag, G. et al. Vemurafenib: the first drug approved drudis.2018.05.007 (2018). by sales in 2017. Nat. Rev. Drug Discov. 17, 232
for BRAF-mutant cancer. Nat. Rev. Drug Discov. 11, 162. Doveston, R., Marsden, S. & Nelson, A. Towards the (2018).
873–886 (2012). realisation of lead-oriented synthesis. Drug Discov. 186. Cernak, T. et al. Nanoscale synthesis and affinity
140. Souers, A. J. et al. ABT‑199, a potent and selective Today 19, 813–819 (2014). ranking Nature 557, 228–232 (2018).
BCL‑2 inhibitor, achieves antitumor activity while 163. Mayol-Llinàs, J., Nelson, A., Farnaby, W. & 187. Pant, S. M. et al. Design, synthesis and testing of
sparing platelets. Nat. Med. 19, 202–208 (2013). Ayscough, A. Assessing molecular scaffolds for CNS potent, selective hepsin inhibitors via application of an
141. Perera, T. P. S. et al. Discovery and pharmacological drug discovery. Drug Discov. Today 22, 965–969 automated closed-loop optimization platform. J. Med.
characterization of JNJ‑42756493 (Erdafitinib), a (2017). Chem. 61, 4335–4347 (2018).
functionally celective small-molecule FGFR family 164. Dow, M. et al. Modular synthesis of diverse natural 188. Cole, K. P. et al. Kilogram-scale prexasertib
inhibitor. Mol. Cancer Ther. 16, 1010–1020 (2017). product-like macrocycles: discovery of hits with monolactate monohydrate synthesis under
142. Keserü, G. M. et al. Design principles for fragment antimycobacterial activity. Chem. Eur. J. 23, continuous-flow CGMP conditions. Science 356,
libraries: maximizing the value of learnings from 7207–7211 (2017). 1144–1150 (2017).
pharma fragment-based drug discovery (FBDD) 165. Karageorgis, G., Warriner, S. & Nelson, A. Efficient 189. Cooper, T. W., Campbell, I. B. & Macdonald, S. J.
programs for use in academia. J. Med. Chem. 59, discovery of bioactive scaffolds by activity-directed Factors determining the selection of organic reactions
8189–8206 (2016). synthesis. Nat. Chem. 6, 872–876 (2014). by medicinal chemists and the use of these reactions
143. Palmer, N., Peakman, T. M., Norton, D. & Rees, D. C. 166. Karageorgis, G., Dow, M., Aimon, A., Warriner, S. & in arrays (small focused libraries). Angew. Chem. Int.
Design and synthesis of dihydroisoquinolones for Nelson, A. Activity-directed synthesis with Ed. Engl. 49, 8082–8091 (2010).
fragment-based drug discovery (FBDD). Org. Biomol. intermolecular reactions: Development of a fragment
Chem. 14, 1599–1610 (2016). into a range of androgen receptor agonists. Angew. Acknowledgements
144. Morley, A. D. et al. Fragment-based hit identification: Chem. Int. Ed. Engl. 54, 13538–13544 (2015). G.M.K. is supported by the National Brain Research Program
thinking in 3D. Drug Discov. Today 18, 1221–1227 167. Bootwicha, T., Feilner, J. M., Myers, E. L. & (2017–1.2.1‑NKP‑2017‑00002) of the National Research,
(2013). Aggarwal, V. K. Iterative assembly line synthesis of Development and Innovation Office, Hungary.
145. Rizzo, S., Wakchaure, V. & Waldmann, H. in Natural polypropionates with full stereocontrol. Nat. Chem. 9,
Products in Medicinal Chemistry (ed. Hanessian, S.) 896 (2017). Competing interests
Vol. 60 43–80 (Wiley-VCH Verlag GmbH & Co. KGaA, 168. Balieu, S. et al. Toward ideality: the synthesis of The authors declare competing interests: see Web version for
2014). (+)-kalkitoxin and (+)-hydroxyphthioceranic acid by details.
146. Hall, R. J., Mortenson, P. N. & Murray, C. W. Efficient assembly-line synthesis. J. Am. Chem. Soc. 137,
exploration of chemical space by fragment-based 4398–4403 (2015). Publisher’s note
screening. Progr. Biophys. Mol. Biol. 116, 82–91 169. Ardkhean, R. et al. Cascade polycyclizations in natural Springer Nature remains neutral with regard to jurisdictional
(2014). product synthesis. Chem. Soc. Rev. 45, 1557–1569 claims in published maps and institutional affiliations.
147. Ferenczy, G. G. & Keserü, G. M. How are fragments (2016).
optimized? A retrospective analysis of 145 fragment 170. Dückert, H. et al. Natural product-inspired cascade Supplementary information
optimizations. J. Med. Chem. 56, 2478–2486 (2013). synthesis yields modulators of centrosome integrity. Supplementary information is available for this paper at
148. Kathman, S. G. & Statsyuk, A. V. Covalent tethering of Nat. Chem. Biol. 8, 179 (2011). https://www.nature.com/articles/nrd.2018.116.
fragments for covalent probe discovery. Med. Chem. 171. Schafroth, M. A., Zuccarello, G., Krautwald, S.,
Commun. 7, 576–585 (2016). Sarlah, D. & Carreira, E. M. Stereodivergent total
149. Backus, K. M. et al. Proteome-wide covalent ligand synthesis of Δ9‑tetrahydrocannabinols. Angew. Chem. RELATED LINKS
discovery in native biological systems. Nature 534, Int. Ed. Engl. 53, 13898–13901 (2014). Chemplanner: www.chemplanner.com
570–574 (2016). 172. Davis, A. M., Plowright, A. T. & Valeur, E. Directing Enamine REAL: www.enamine.net/index.php?option=com_
150. Parker, C. G. et al. Ligand and target discovery by evolution: the next revolution in drug discovery? Nat. content&task=view&id=254
fragment-based screening in human cells. Cell 168, Rev. Drug Disc. 16, 681 (2017). EvoSpace: www.evotec.com
527–541 (2017). 173. Shen, X., Corey, Chemistry, D. R. mechanism and Hypha Discovery: www.hyphadiscovery.co.uk
151. Wetzel, S., Lachance, H. & Waldmann, H. in clinical status of antisense oligonucleotides and duplex ICFRP: www.infochem.de/products/software/icfrp.shtml
Comprehensive in Natural Products II (eds Mander, L. RNAs. Nucl. Ac. Res. 46, 1584–1600 (2018). Mcule ULTIMATE: mcule.com/ultimate-project
& Liu, H.-W.) 5–46 (Elsevier, 2010). 174. Lai, A. C. & Crews, C. M. Induced protein degradation: Reaxys: www.reaxys.com
152. Zaid, H., Raiyn, J., Nasser, A., Saad, B. & Rayan, A. an emerging drug discovery paradigm. Nat. Rev. Drug SciFinder: https://scifinder.cas.org/scifinder/
Physicochemical properties of natural based products Discov. 16, 101–114 (2017). Synspace: www.chempassltd.com/synspace
versus synthetic chemicals. Open Nutraceuticals J. 3, 175. Sternbach, L. The benzodiazepine story. J. Med.
194–202 (2010). Chem. 22, 1–7 (1979). ALL LINKS ARE ACTIVE IN THE ONLINE PDF

NATURE REVIEWS | DRUG DISCOVERY ADVANCE ONLINE PUBLICATION | 19


©
2
0
1
8
S
p
r
i
n
g
e
r
N
a
t
u
r
e
L
i
m
i
t
e
d
.
A
l
l
r
i
g
h
t
s
r
e
s
e
r
v
e
d
.

Вам также может понравиться