You are on page 1of 45

Chemical Informatics

Bioinformatics Infrastructure Facility

North-East Institute of Science & Technology

Salam Pradeep
What is Chemical Informatics
 Chemoinformatics or chemical informatics is the use
of computer and informational techniques, applied to
a range of problems in the field of chemistry.
 It is the mixing of those information resources to
transform data into information and information into
knowledge for the intended purpose of making better
decisions faster in the area of drug lead identification
and optimization.
 In silico techniques are used in pharmaceutical
companies in the process of drug discovery.
 These methods can also be used in chemical &
allied industries in various other forms.
What is Computational Chemistry
A branch of chemistry that uses computers to
assist in solving chemical problems.
 Uses the results of theoretical chemistry,
incorporated into computer programs, to
calculate the structures and properties of
molecules & solids.
 Its results normally complement the information
obtained by chemical experiments & in some
cases predict unobserved chemical
 Widely used in the design of new drugs and
Chemical & Ligand Databases
 Beilstein
Database (Commercial)
 NCBI – PubChem

 ChemBank

 DrugBank

 ChemSpider

 LOLI database

 RX List

 HIC Up – Hetero Compound Info Center
Chemical Similarity Search
 ChemBank (Web based)
 ACD (Advanced Chemistry Development)

Free Software
 Molsoft (Web based)
Chem Bank
 It is a public, web-based informatics environment
created by the Broad Institute's Chemical Biology
Program & funded in large part by the National Cancer
Institute's Initiative for Chemical Genetics (ICG).
ACD Chemsketch Structure Search
Molsoft Chemical Search
Molsoft is a La Jolla, California based company that is a primary source of new
breakthrough technologies in modeling, docking, computational chemistry and

Online Tools:

1. PDB Viewer

2. 2D to 3D Converter

3. Chemical Search

Drug Likeness

4. ODA – Optimal Docking

Drug Bank
Chemical File Formats
File Ext Format Name
alc Alchemy Format
cdx ChemDraw, Cambridge Soft
cer Accelrys MSI Cerius II
c3d Chem3D, Cambridge Soft
cif Crystallographic Information File, CCDC
mol MDL Molfile
smiles, smi Simplified molecular input line entry
sdf Structure-Data File
Chem Office
A molecule editor developed by the
cheminformatics company CambridgeSoft.
 ChemOffice comprises ChemDraw, Chem3D
and ChemFinder.
 Available for Apple Macintosh and Microsoft
 Designed for Chemist and Biologists
Chem Draw
 Chemical structure to name conversion
 Chemical name to structure conversion

 NMR spectrum simulation

 Mass spectrum simulation

 Structure cleanup

 Extensive collection of templates

 Anti-aliased graphics
Powerful Features
 Convert Name to Structure
Calculate Properties
1H NMR Prediction
Chem Finder
 ChemFinder® is a database management
system for working with chemical information.
 It provides a place to store chemical
structures, physical properties, notes, tables of
data, and charts based on that data.
 With ChemFinder, we can search through data
efficiently and quickly, and we can organize the
data instantly.
Compound Library
PASS (Demo 51 Activities)
 PASS Professional (Prediction of Activity
Spectra for Substances) predicts the biological
activity spectra for substances on the basis of
their structural formulae, includes SAR Base
(Structure-Activity Relationships data and
knowledge Base) and provides its creating,
updating and training.
 Predicts 51 Biological Activities
Pharmacological Effects
 Antihypertensive: Substance used for hypertonia
treatment. Substance reduces the increased arterial
blood pressure.
 Vasodilator: Substance that causes relaxation of blood
 Diuretic: Substance that promotes the excretion of urine
by direct action on kidney function.
 Uric acid excretion stimulant: Substance that increases
the urinary excretion of uric acid, thereby reducing the
concentration of uric acid in the blood.
 Angiotensin AT2 receptor antagonist: Substance that
binds to the angiotensin AT2 receptor and prevents its
 Saluretic: Substance that promotes excretion of sodium
and chloride ions in the
Molecular Mechanisms
Calcium channel antagonist Renin inhibitor Neuropeptide Y antagonist Dopamine D1 agonist

Phosphodiesterase I inhibitor Vasopressin 2 antagonist Dopamine D2 agonist Vasopressin 1 antagonist

Endothelin receptor antagonist Nitric oxide agonist Adenosine receptor agonist Metalloproteinase inhibitor

Endothelin A receptor antagonis Potassium channel activator Nitric oxide donor Adrenaline antagonist

Beta adrenoreceptor antagonist Calcium antagonist Carbonic anhydrase inhibitor Angiotensin antagonist

Beta 1 adrenoreceptor antagonist Kinesin antagonist Guanylate cyclase stimulant Dopamine agonist

Angiotensin II receptor antagonist 5 Hydroxytryptamine 2 Neutral endopeptidase Antidiuretic hormone

antagonist inhibitor antagonist
Adenosine A2 receptor agonist Endothelin B receptor Adenosine A1 receptor Phosphodiesterase IV
antagonist antagonist inhibitor

Angiotensin AT1 receptor antagonist 5 Hydroxytryptamine 1A Alpha 2 adrenoreceptor

agonist antagonist
Side Effects and Toxicity
 Carcinogenic: Substance that produces cancer.
 Embryotoxic: Substance damaging to the
embryo, which may result in death or in
abnormal development.
 Teratogen: Substance that causes the
production of physical defects in the developing
ADME / TOX Box Abraham Solvent

H-Bonding acidity parameter

H-Bonding basicity parameter

Partition Coefficient between
gaseous phase and hexadecane
Polarity / polarizability parameter
Excessive molar refraction

Mcgowan volume
Chem 3D
 Chem3D enables to create color models of
chemical and biochemical compounds.
 Once we sketch a model, we can calculate a
variety of molecular properties - electrostatic
potentials, bond energies, and spectrum
 It combines powerful building, analysis, and
computational tools with intuitive menus and a
powerful scripting interface.
Force Field Calculations
 MM2: Most commonly used for calculating
properties of organic molecular models.
- Correlates the potential energy surface to the
conformations of our model
 MMFF94: Used to perform energy
minimization calculations on proteins &
biological structure.
MM2 & MMFF94
 Energy Minimization: The atoms location for
a build model is not accurate compared to the
actual one. Hence EM
 Molecular Dynamics: Uses Newtonian
mechanics to simulate motion of atoms,
adding or subtracting kinetic energy as the
model’s temperature increases or decreases.
 The General Atomic and Molecular Electronic
Structure System (GAMESS)
 A general ab initio quantum chemistry package
maintained by the Gordon research group at
Iowa State University.
 Minimize Energy

 Optimize to Transition State

 Compute Properties

 Run Frequency

 Predict IR/Raman Spectra

 Predict NMR Spectra
Lipinski Rule of Five
 Lipinski's Rule of Five states that, in general, an
orally active drug has no more than one violation of
the following criteria:
 Not more than 5 hydrogen bond donors (nitrogen
or oxygen atoms with one or more hydrogen
 Not more than 10 hydrogen bond acceptors
(nitrogen or oxygen atoms)
 A molecular weight under 500 g/mol
 A partition coefficient log P less than 5
 Note that all numbers are multiples of five, which is
the origin of the rule's name.
Thank You
for Job Openings in Bioinformatics