Synthesis and 3D-QSAR Analysis of Pyronecarboxamide

derivatives as Antimycobacterial agents

Anand Kumar V. Raichurkar*, M.N. Harish , Jayashree Puttur, Parvinder Kaur and Santosh Nandan ¶

AstraZeneca India Pvt. Ltd., Bangalore, 560024, India.

¶
Present Address: S*BIO Pte Ltd, 1 Science Park Road,#05-09, The Capricorn Singapore Science Park II, Singapore 117 528
*Corresponding author: anandkumar.raichurkar@astrazeneca.com

Pyronecarboxamides:
Abstract New Lead Identification Process antimycobacterial agents ?
A series of ß-hydroxyketoamide (BKA) Strategy:
OH O
derivatives were designed, synthesised
and studied for their antimycobacterial Chemicalapproach
Chemical approach Biological
Biologicalapproach
approach Ø Compound based approach is fast and effective method
N R (Compound based) (Target based) of new lead identification.
activity. Synthesis of BKA derivatives was H
uneventful, and provided the target O Ø 4-hydroxycoumarins (1) with a ß-hydroxyketoamide core
compounds in reasonable yields. The SelectScaffolds
Scaffolds Select
Select Target
Target possess variety of biological activities viz: antibacterial,
Select
compounds showed a wide range of antimycobacterial activity Viz: enz/pro/rec
Viz: enz/pro/rec
anthelmentic, insecticidal, antifungal etc1.
(MIC ranging from 2-64 mg/L) against M.tuberculosis H37Rv In vitro test

strain . Ortho substituents on the aryl ring were found to exert a

Ex: MIC
Ø Their antimycobacterial activity is not well explored.
profound influence on the antitubercular activity. ActiveHits
Hits HTS
HTS//VS
VS/NMR
/NMR//HCS
HCS
Active In continuation of our efforts towards developing
2/3D-QSAR studies were performed on the synthesised Med Chem / 2/3D-QSAR/ Relevant assay Library / inhouse / novel antimycobacterial agents, we decided to study
Scaffhop exteranl collection
molecules to correlate structural properties with experimental the SAR and QSAR of the ß-hydroxyketoamide (BKA)
biological activity. QSAR studies suggested the importance of Hit--Leads
Hit Leads Active
ActiveHits
Hits core (2) with respect to its antimycobacterial activity.
the BKA substructure for obtaining antimycobacterial activity.
The QSAR models were also helpful in identifying optimum steric Microarray / Lit Med Chem / QSAR/
Scaffhop
and electrostatic properties of substituents on the aryl ring, OH O OH O

which could be used for improving the antimycobacterial activity. IdentifyTarget

Identify Target Hit
Hit--Leads
Leads N N
H H
Compound based approach was successfully applied for Relevant assay
In vitro test
Ex MIC O O O
developing antimycobacterial compounds with BKA core. The
4-hydroxy-3-carboxamide derivative (1) ß-hydroxyketoamide (BKA) core (2)
core can be considered as New Lead for developing novel NewLeads
New Leads New
NewLeads
Leads
antimycobacterial agents.
Ref.1: Lee B.H.; et al. Bioorg. Med. Chem. Lett. 1998, 8, 3317-3320

General Synthetic Scheme 3D_QSAR Analysis of Pyronecarboxamides Results of QSAR analysis

O Compounds:  Target is not known for the current series. Comparison (statistics) of QSAR Models
O O

 QSAR studies were performed to understand the SAR

O

N R1
 Purification : HPLC
H
TEA OH  Yields : 40-60% and to identify favorable steric and electrostatic features
O Nitrobenzene O  Characterization : H1NMR & Mass Properties CoMFA CoMSIA HQSAR
O
+ R1
N O O
O

N R1
H1 NMR: Characteristic peaks (ppm):
for optimizing the hits. Std Error
H
OH Ped 0.359 0.376 0.437 Comparison of Ecperimental v/s CoMFA predicted
OH
 Appearance of CO-NH proton (bs 11.73-12.05) 2
OH
r pMICs
R1= Mono and Di
substituted Ph,Hetero
OH O
 Downfield shift of enolic –OH (s,17.48-18.5) Techniques: CV 0.746 0.736 0.643

Experimental and Predicted BA

6
N R1 Components 4 5 5
 CoMFA & CoMSIA: To understand the influence of steric

Experimental and Predicted BA

6
O O aromatic,alicyclic H
O 5
0.142 0.157 0.157 5
O Std Error Est
and electrostatic features.
4
2 4
r ncv 0.96 0.954 0.954 3

(pMIC)
3

(pMIC)
 HQSAR: To identify the structural features important for F value 121.535 78.17 79.024 2
2

1
pMIC
pMIC
Predicted pMIC
Predicted pMIC
2

Biological activity profile of

1
r
activity. pred 0.736 0.641 0.763
0
0

AR-I-101908
AR-I101934
AR-I-101901

AR-I101880
AR-I101789
AR-I101878
AR-I-101903
AR-I-101900
AR-I-101907
AR-I101784
AR-I101884
AR-I101883
AR-I101881
AR-I101787
AR-I101909
AR-I-101905
AR-I-101906
AR-I-101899
AR-I-101898
AR-I101873
AR-I101875
AR-I101882
AR-I101877
AR-I101879
AR-I101910
AR-I101915
AR-I101914
AR-I-101902
AR-I-101897
AR-I101913
AR-I102186
AR-I102185
AR-I102184
AR-I102183
AR-I102182
AR-I102181
AR-I101783
AR-I101786
AR-I101798
AR-I101876
AR-I101916

AR-I101785
AR-I101874

AR-I101933

AR-I101912
AR-I101911
AR-I-101908
AR-I101934
AR-I-101901

AR-I101880
AR-I101789
AR-I101878
AR-I-101903
AR-I-101900
AR-I-101907
AR-I101784
AR-I101884
AR-I101883
AR-I101881
AR-I101787
AR-I101909
AR-I-101905
AR-I-101906
AR-I-101899
AR-I-101898
AR-I101873
AR-I101875
AR-I101882
AR-I101877
AR-I101879
AR-I101910
AR-I101915
AR-I101914
AR-I-101902
AR-I-101897
AR-I101913
AR-I102186
AR-I102185
AR-I102184
AR-I102183
AR-I102182
AR-I102181
AR-I101783
AR-I101786
AR-I101798
AR-I101876
AR-I101916

AR-I101785
AR-I101874

AR-I101933

AR-I101912
AR-I101911
2
r bs 0.961 0.975 0.973

Pyronecarboxamides Protocol: Standard protocols as reported in the literature2a,b SD 0.021 0.013 0.017
Compounds
Compounds
Contri…
were followed Str. 0.48 0.129 Best Length 151
pMIC = - log (MIC)
 Training Set : 25, Template Molecule Ele. 0.52 0.269 Hologram

 Test Set : 21,

p M I C (M .T u b : H 3 7 R v s t r a in )

6
6 Hyd 0.229
p M I C (M .T u b : H 3 7 R v s t r a in )

5
5
 Stat : PLS analysis OH O* Acc 0.16

4
4 Donor 0.213

3
3 OH O
 Compounds were tested for in vitro
 Stat Validation : r2 ncv, r2cv, r2pred * N*
*
N H
2 H
2 O O antitubercular (MIC) activity using H37Rv strain.
1  Compounds have shown good range of (p)MICs:
O O
Reference compound
1
0 2-5 log units.
* = atoms used for alignment CoMFA model was selected as best model for further analysis as it
0 20128158 6
0 20128148 5
0 20128138 4
0 20128128 3
0 20128118 2
0 10728138 1
0 10718768 3
0 10719788 6
A R -I1 0 10817769 8
A R -I1 0 10911867 6

0 10910913 4
A R -I1 0 10817748 5
0 10818807 4
0 10718898 0
0 10817788 9
A R -I-1 0 10910837 8

0 10818748 4
A R -I1 0 10818838 4
A R -I1 0 10818818 3
0 10718878 1
0 10910798 7

0 10817857 3
0 10818827 5
A R -I1 0 10817878 2
0 10817897 7

0 10911941 5
A R -I-1 0 10910921 4
0 10819973 3
0 10911921 3
0 10910981 6
0 10913940 8
A R -I1 0 10718950 1

A R -I-1 0 10910900 3
0 10910970 0
0 10718940 7

0 10910950 9
0 10910960 5
A R -I-1 0 10819990 6
0 10819889 9
0 10817839 8

0 10911807 9
0 10911951 0

0 10913930 2
0 10911839 7
A R -I1 0 10911911 2
A R -I1 0 1 9 1 1

0

A R -I1 0 2 1 8 6

No information about the target.

is statistically significant than other models.
R -I1
R -I1

R -I1
R -I1
R -I1
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R -I1
R -I1
R -I1
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R -I-1

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Ref: 2a Raichurkar A. V.; Kulkarni V. M. J. Med. Chem.; 2003, 46, 2003. and
R -I1

R -I1
R -I1
R -I1
R -I1

R -I1
R -I1
R -I1

R -I1

R -I1

AARR-I1
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AARR-I1
AARR-I1
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AARR-I1
A RA-I-1

R -I-1
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2b
Heritage, T. W.; Lowis, D. R. Molecular Hologram QSAR. In Rational Drug
Compounds
Compounds Design; ACS Symposium Series 719; American Chemical Society: Washington,
DC, 2000; p 212.

CoMFA Contour Maps Interpretation HQSAR Maps

(Individual atomic contribution graph) Conclusions

Active  ß-hydroxyketoamide (BKA) derivatives have been explored for

Steric Favorable antimycobacterial activity.

Steric Disfavorable Steric  The synthesized derivatives possess good antitubercular activity.
 BKA core can be used as a scaffold for developing novel
Positive Favorable
antitubercular agents.
Electrostatic
Negative Favorable  The QSAR methods / models provided useful information wrt SAR
In active
 CoMFA and CoMSIA contours well explain the influence of
 Presence of green contours:
steric and electrostatic properties of the substituents and
Active Compound Favorable hydrophobic molecule as a whole.
interactions. Small hydrophobic
groups at ortho or meta position of  3D-QSAR studies suggest for an ortho or meta substitution
ColorKey
Key
aromatic ring may favor strong Bad: : Red:
Color on –CO-NH-Ar for better activity
inhibition of target. Bad Red:
Red Orange:
Red Orange:
Reflectunfavorable
Reflect unfavorablecontributions
contributions  HQSAR: suggests the importance of BKA core
Orange:
Orange:
 Presence of yellow contour:  Overall QSAR models may be used for predicting biological
White: Intermediatecontributions
Intermediate contributions
Para position of aromatic ring is not White: activity of new molecules to be synthesized and also for
suitable for substitution. Yellow:
Yellow: further optimization the leads.
Green Blue: Reflect favorable contributions
Green Blue: Reflect favorable contributions
 Presence of blue contour over Good: : Green:  Pyrone moiety may be suitable replacement for coumarin portion of
Good Green:
amide linkage indicates its Cyan: Common Back Bone reference compound.
Cyan: Common Back Bone
necessity and possibility of polar
interactions.  Pyronecarboxamide derivatives are potent antimycobacterial
compounds
Inactive Compound  The ß-hydroxyketoamide functional group is essential (Back bone).
 Red Contour: ß-carbonyl group is
must.  Ortho or meta substitution on –Ar-NH may enhance the activity.  Efforts for finding the appropriate target for BKA derivatives are in
progress.

Presented at "New Frontiers in Tuberculosis Research 2006, ICGEB, India".