TRADITIONAL DRUG SCREENING

• Random, Trial and Error, Expensive, Time- consuming, Very low Success-Rate

MODERN DRUG DESIGNING High Throughput Screening‏

- Fast and automatic, Very expensive, High Success Rate.

-Diversity of chemical compounds: Combinatorial Chemistry

PubChem Bioassay :231 M bioactives (leads)and inactives/1.22M AID

depositions/>10636 drug targets and 4771 human drug targets

22M CID’s and 35M SID’s

ChemEMBL Bioassay: 14.67 Lakh bioactives/Leads/1.3M AID -11538 drug targets,

67000 publications

Computer Aided Drug Design: Structure based

Chemical Structures/drug targets

ZINC database: 35 million Commercially available /106M Drugs like/243 suppliers/4000T

PubChem Database: 157 M/60M Unique structures /10000 Drug Targets/1M AID

• >1,30,000 protein structures in PDB

• Drug Target Databases/Focussed small molecule Libraries

• In Silico Screening:Docking programs/scoring functions

• Low cost and high power computers

• Fast and automatic, Very Low Cost, Many Success stories

Modern Drug Design Cycle

3

Modern Drug Design Cycle:

Computer Aided Drug design • Ligand-based: relies on knowledge of other molecules that

bind to the biological target of interest.

• Structure-based: relies on knowledge of the 3D structure of the biological target.

• A lead has

– evidence that modulation of the target will have therapeutic value: e.g. disease linkage studies showing associations between mutations in the biological target and certain disease states.

– evidence that the target is druggable, i.e. capable of binding to a small molecule and that its activity can be modulated by the small molecule.

• Target is cloned and expressed, then libraries of potential drug compounds are screened using screening assays

Strategies in Drug Designing

Receptor Structure

Known Unknown

Structure Based

Drug Design

Analog Based

Drug Design

Docking

Homology Modeling

Receptor Mapping

REQUIREMENT

Lead Compound and

derivatives with biological

dataREQUIREMENT

A Model Receptor

Molecular Dynamics

Simulations

Rigid Docking

FlexiDock

Monte Carlo

Simulations

Simulated Annealing

Quantum

Mechanical

(BRABO) ANN

GA

PCA

CoMFA

CoMSIA

Quantum

Mechanical

Descriptors

Quantum

Mechanics for

Alignment

SYBYL, INSIGHT II, CERIUS2, MOE, AMBER (CDAC), DOCK, AUTODOCK

SINGLE MOLECULE

QSAR

Structure Based Ligand Design

O

NH

O

H

O

NH

?

O

O

O

H

O

NH

NSO

O

H

O

NH

O

H

O

NHS?

?

O

H

O

NH

??

?

O

O

H

O

NH

Docking

Building

Linking

Binding Affinities

Ligand receptor binding affinity can be experimentally determined. Experimental errors lie in the range of 0.1-0.25 kcal/mol.

LPPL

][

]][[

PL

LPK D

Dbinding KRTG ln

Abinding KRTG ln

G = -2.303 x 8.3 kJ/mol x 298K x log KA

G = -10.95 G = 8.8 x 10-9 M

DRUG BANK STATISTICS

Total Number of Small Molecule Drugs 7818

Total Number of Biotech Drugs 330

Total Number of Approved Drugs 2142

Total Number of Approved Small Molecule Drugs 1944

Total Number of Nutraceutical Drugs 93

Total Number of Experimental Drugs 5052

Total Number of Illicit Drugs 198

Total Number of Withdrawn Drugs 199

Total Number of Drugs 8148

Target Statistics

UNIQUE DRUG TARGETS FOR

FDA APROVED SMALL MOLECULE DRUGS 1672

TimTec Database Accessibility and Sourcing Expertise

Commercial Vendors

TimTec Database

Over 5 Million compounds

Non-exclusive chemists throughout Europe/Asia

TimTec-exclusive Chemists throughout

Europe/Asia

ACD Database and others

Nature Reviews DrugDiscovery(2011),10,579-590

Current Small Molecule Drug Targets

Leads and Targets

Priority NDA ApprovalsMedian times, approvals

7.7 6.0 6.07.7 6.0 6.06.27.87.9 6.06.2 6.06.1 13.8

6.4 6.06.1 6.07.9 7.8 6.4 19.1

22

20

16

29

25

28

20

10 1411

29

0

12

24

1995 1996 1997 1998 1999 2000 2001 2002 2003 2004* 2005*

Calendar year*Includes BLAs for therapeutic biologics

Mont

hs

0

15

30

Num

ber

Median FDA review time Median total approval time Number approved

Standard NDA & BLA ApprovalsMedian times, approvals

11.9

11.9

11.8

15.4

12.9

13.1

12.7

12.0

12.0

12.0

12.0

16.2

15.1

14.7

15.3

12.0

17.8

18.7

14.0

13.8

12.0

15.0

90

58

67 58

56

78

5565

102

67

101

0

12

24

1995 1996 1997 1998 1999 2000 2001 2002 2003 2004* 2005*

Calendar Year*Includes BLAs for therapeutic biologics

Mont

hs

0

60

120

Appr

ovals

Median FDA review time Median total approval time Number approved

Potential Drug Target Database (PDTD) - 127 Drug Targets with known structure and Binding site

- Link: www.dddc.ac.cn/pdtd/ Therapeutic Target Database - 2025 Drug Targets and 17816 drugs - Linl: bidd.nus.edu.sg/group/ttd/ttd.asp

DrugBank - 1492 Drugs and 1664 Unique Drug Targets

- Link: drugbank.ca

Super Target and Matador - 2500 Drug Targets, 1500 drugs and 7300 drug-target relations

- Link: http://matador.embl.de

Open access therapeutic drugtarget DB - Disease-Target Relations

- Link: www.sciclips.com/sciclips/drug-targets

Drug and target protein structures in the PDB - 451 Drugs and their drug targets

- Link: www.ebi.ac.uk/thornton-srv/databases/drugport/

TDR Targets Database - Drug targes of Tropical Diseases (P. falciparum, M. tuberculosis etc)

- Link: http://tdrtargets.org

DRUG T ARGET DATABASES FOR SBDD Disease-Target Relations

CHEMICAL DATABASES FOR SBDD

DrugBank/FDA/LISP SRS PubChem /Pubchem Bioassay ChEMBLBioassay ChemBankBioassays Zinc DB WOMBAT NCI DB ChEBI World Drug Index MedChem Maybridge DB Available Chemical Directory Molbase ChemDB/Bioscreening.com KEGG Ligand DB BIND/Binding DB/Brenda Cambridge Structural DB Chemical Abstract Service DB CHEMnetBASE and ChemSpider

GDB-17 50M Million organic structures C,N.O.S, Halogens Max 17 atoms Enumerated 166 M virtual Chemical structures along their isomers - J.Chem Inf and Modeling(2012) 52, 2864-2875 Commercial Chemical Suppliers (Synthesized chemicals for HTS And their chemical structures for Virtual Screening)

Distribution of targets by biochemical

criteria

Distribution of targets in therapeutic areas

Potential Drug Target database www.dddc.ac.cn/pdtd

Protein – Ligand Docking Programs

•Dock: http://www.cmpharm.ucsf.edu/kuntz/dock.html

•AutoDock: http://www.scripps.edu/mb/olson/doc/autodock/

•GOLD: http://www.ccdc.cam.ac.uk/products/life_sciences/gold/

•FLEXX: http://www.biosolveit.de/FlexX/

•GLIDE: http://www.schrodinger.com/

•ICM: http://www.molsoft.com/docking.html

•ZDOCK : http://zlab.bu.edu/zdock/

•HEX : http://www.csd.abdn.ac.uk/hex/

•GRAMM :http://vakser.bioinformatics.ku.edu/resources/gramm

•ICM : http://www.molsoft.com/docking.html

•CLUSPRO : http://nrc.bu.edu/cluster/clusdoc.html

•KORDO : http://www.bioinfo.de/isb/gcb99/poster/zimmermann/

•MOLFIT:http://www.weizmann.ac.il/Chemical_Research_Support//molfit/

•PATCHDOCK:http://bioinfo3d.cs.tau.ac.il/PatchDock/

•HADDOCK: http://haddock.science.uu.nl

Protein protein Docking Programs

26

Hanahan and Weinberg, Cell 100: 57, 2000

Apoptosis

Oncogenes

Tumor Suppressor

Inv. and Mets Angiogenesis

Cell cycle

Oncogenes as Signal Transducers

Growth Factors

v-sis, int-1, int-2, hst, fgf-5

Growth Factors Receptors

v-erb-B, v-fms, v-kit, v-ros

Signal Transducers

v-ras,, v-src, v-raf/mil, v-abl, v-mos, v-crk

Transcription Factors

v-ets, v-myc, v-myb, v-rel, v-ski, v-erb-A

C

Y

T

O

P

L

A

S

M

EXTRACELLULAR

NUCLEUS

Adapted from

Hubbard,1999

Extracellular

Intracellular

Some Major RTK Families

Hepatocyte Growth Factor Receptor & Family

Cell membrane (lipid bilayer)

Growth hormone

Extracellular domain

of Growth Hormone Receptor

Intracellular

Extracellular

Growth Hormone Receptor

Binding to receptor forces

dimerization of receptor

subunits for cross

phosphorylation

-OPO3=

=O3PO-

Tyrosines

Protein Kinases(518) • Protein kinases regulate

virtually all cellular processes – Metabolism

– Cell division

– Cell growth

– Cell differentiation

– Cell shape change and contraction

– Many other cellular processes

32

Epidermal Growth Factor Receptor Inhibitors in

NSCLC

Gefitinib(Iressa), Erlotinib(Tarceva)

Signal

Transduction

Blocked

TKI

Ligand

K K TKI

Signal

Transduction

Blocked

MoAb

K K

Cetuximab

Abbreviations: MoAb, monoclonal antibody;

TKI, tyrosine kinase inhibitor.

•Source : Mechanism for Activation of the EGF Receptor 1 Catalytic Domain by the Juxtamembrane

Segment - Cell 137, 1293–1307, June 26, 2009

Available Drugs and Monoclonal Antibodies against EGFR

• Source: ErBb receptors and cancer: the complexity of targeted inhibitors – Nature reviews, volume 5, may 2005

BCR-ABL Tyrosine Kinase Inhibitors eg: Imatinib Mesylate(GLEEVAC),

Dasatinib, and Nilotinib.

Vascular Endothelial Growth Factor TyrosineKinase Inhibitors eg. ,

Sunitinib(SUTENT), Sorafenib(NEXAVAR), Vatalanib(PTK787).

Tyrosine Kinase Inhibitors

• Promising Tyrosine Kinase Inhibitors:

Modified from Morin, 2000

35

Drug Targets: Receptors

G-Proteins

So-named because they bind GTP, displacing GDP

Work with many receptors

Both Stimulate and inhibit hormone signals

A family of membrane proteins that exist in an

inactive

(GDP) and an active (GTP) state

GTP is a time-bomb slowly ticking

When GTP is hydrolyzed to GDP, stimulation is

stopped

GTP

AC GDP

AC GTP

AC GDP

GDP AC

Resting

Active

Inactive

Resting

ATP

cAMP

PO4

Rationale for oGPCR characterisationRationale for oGPCR characterisation

A. GPCRs are good drug targets

ü 50% of subscription drugs interact with GPCRs

Why is the pharmaceutical industry interested in oGPCRs?

• Hypertension

• Stomach ulcers

• Migraine

• Allergies

B. GPCRs in disease states

ü Disease states associated with GPCR mutations

•Rhodopsin receptor retinitis pigmentosa

•Vasopressin V2 nephrogenic diabetes

•Glucagon diabetes, hypertension

GPCRS ION CHANNELS TRANSPORTERS ENZYMES

Types of Membrane Transporters

• 2000 genes in the human genome (7% of the total number of genes) code for transporters or transporter-related proteins.

• In considering the transport of drugs, pharmacologists generally focus on transporters from two major superfamilies, ABC (ATP binding cassette) and SLC (solute carrier) transporters

• Most ABC proteins are primary active transporters, which rely on ATP hydrolysis to actively pump substrates across membranes

• The SLC superfamily includes genes that encode facilitated transporters and ion-coupled secondary active transporters

ABC (ATP binding cassette)

49 known genes for ABC proteins that can be grouped into 7 subclasses or families (ABCA to ABCG)

the best recognized in the ABC superfamily are P-glycoprotein (P-gp, encoded by ABCB1, also termed MDR1) and the cystic fibrosis transmembrane regulator (CFTR).

48 SLC families with 315

transporters have been identified

in the human genome

Many serve as drug targets or in

drug absorption and disposition

Widely recognized SLC

transporters include the serotonin

(5-HT) and dopamine

transporters (SERT, encoded by

SLC6A4; DAT, encoded by

SLC6A3).

Role of Transporters in Drug Absorption

Ion Channel Families

• Voltage-gated

• Extracellular ligand-gated

• Intracellular ligand-gated

• Inward rectifier

• Intercellular

• Other

Extracellular ligand-gated

• nicotinic ACh (muscle): 2 (embryonic), 2 (adult)

• nicotinic ACh (neuronal): (2-10), (2-4)

• glutamate: NMDA, kainate, AMPA

• P2X (ATP)

• 5-HT3

• GABAA: (1-6), (1-4), (1-4), , , (1-3)

• Glycine

Intracellular ligand-gated

• leukotriene C4-gated Ca2+

• ryanodine receptor Ca2+

• IP3-gated Ca2+

• IP4-gated Ca2+

• Ca2+-gated K+

• Ca2+-gated non-selective cation

• Ca2+-gated Cl–

• cAMP cation

• cGMP cation

• cAMP chloride

• ATP Cl–

• volume-regulated Cl–

• arachidonic acid-

activated K+

• Na+-gated K+

G-protein linked receptors coupled to ion channels

• Acetylcholine (muscarinic) • Adenosine & adenine nucleotides • Adrenaline & noradrenaline • Angiotensin • Bombesin • Bradykinin • Calcitonin • Cannabinoid • Chemokine • Cholecystokinin & gastrin • Dopamine • Endothelin • Galinin • GABA (GABAB) • Glutamate (quisqualate)

• Histamine

• 5-Hydroxytryptamine (1,2)

• Leukotriene

• Melatonin

• Neuropeptide Y

• Neurotensin

• Odorant peptides

• Opioid peptides

• Platelet-activating factor

• Prostanoid

• Protease-activated

• Tachykinins

• Taste receptors

• VIP

• Vasopressin and oxytocin

Various Neurological Diseases Are Caused by Malfunctioning Voltage-Gated Ion Channels

l Acquired neuromyotonia

l Andersen’s syndrome

l Becker’s myotonia

l Episodic ataxia with myokymia

l Familial hemiplegic migraine

l Generalized epilepsy with febrile seizures

l Hyperkalemic periodic paralysis

l Malignant hyperthermia

l Myasthenic syndrome

l Paramyotonia congenita

l Spinocerebellar ataxia

l Thompson’s myotonia

Na+, K+, Ca++, Cl-

Catterall W A 2011 59

K+ channel blockers

Polypeptides

Steroids

Amino acid derivatives

Insulin

glucagon

somatotropin

FSH

LH

vasopressin

Oxytocin

thyrotropin

ACTH

Estrogen

testosterone

cortisol

Aldosterone

corticosterone

Progesterone

Epinephrine

norepinephrine

dopamine

Thyroxine, T3 and T4

Melatonin

Serotonin

Classification of Antimicrobial Drugs 1. Inhibition of cell wall

synthesis

2. Inhibition of protein synthesis

3. Disrupt cytoplasmic membrane

4. Inhibit metabolism

5. Inhibit DNA/RNA synthesis

6. Block attachment

Main targets of Antibiotics

It is now known that the target of the penicillins are the PBPs

(penicillin binding proteins) transpeptidases responsible for

cross-linking peptidoglycan strands.

Antibacterial drugs: penicillins

Prevents crosslinking between proteins

and therefore cell wall synthesis (mucoproteins).

Medicines Derived from Plants

• Atropine (Atropa bellodonna)

• Capsaicin (Capsicum frutescens)

• Colchicine (Colchicum autumnale)

• Cocaine (Erythroxylon coca)

• Codeine (Papaver somniferum)

• Digoxin (Digitalis purpurea)

• Ephedrine (Ephedra sinica)

• Ipecac (Cephaelis ipecacuanha)

• Physotigmine (Physostigma venenosum)

• Quinine (Chinchona officinalis)

• Salicylin (Salix purpurea)

• Senna (Cassia acutifolia)

• Scopolamine (Datura fastuosa)

• Resperpine (Rauvolfia serpentina)

• Taxol (Taxus brevifolia)

• Vincristine (Catharanthus roseus)

Applications

• Determine the lowest free energy structures for the receptor-ligand complex

• Search database and rank hits for lead generation

• Calculate the differential binding of a ligand to two different macromolecular receptors

• Study the geometry of a particular complex

• Propose modification of a lead molecules to optimize potency or other properties

• de novo design for lead generation

• Library design

Successes of Docking & SBDD

• HIV protease inhibitor amprenavir (Agenerase) from Vertex & GSK (Kim et al. 1995)

• HIV: nelfinavir (Viracept) by Pfizer (& Agouron) (Greer et al. 1994)

• Influenza neuraminidase inhibitor zanamivir (Relenza) by GSK (Schindler 2000).

Success stories of CADD

• • K+ ion channel blocker

• structural based discovery

• G. Schneider et al., J. Computer-Aided Mol.

Design 14, 487-494, 2000

• • Ca2+ antagonist / T-channel blocker

• chemical descriptor based discovery

• G. Schneider et al., Angew. Chem. Int. Ed. Engl. 39,

4130-4133, 2000

• Glyceraldehyde-phosphate DH inhibitors (anti-

trypanosomatid drugs)

• combinatorial docking

• J.C. Bressi et al., J. Med. Chem. 44, 2080-2093, 2001

• Thrombin inhibitor

• docking, de-novo design

• H.J. Bohm et al., J. Computer-Aided Mol. Design 13, 51-56, 1999

• Aldose reductase inhibitors

• database searching

• Y. Iwata et al., J. Med. Chem. 44, 1718-1728,

2001

• Non nucleoside inhibiitor of HIV-1 reverse Transcriptase

– structure and ligand based design

– William L. Jorgensen et al., bioorganic and

midicinal chemistry letters, 16, 663-667, 2006

List of drugs discovered through structure based approach for drug

design:

Drug Target Disease Approved By FDA

Captopril Carboxypeptidase A Hypertension 1981

Dorzolamide Carbonic Anhydrase Glaucoma 1994

Donepezil Acetylcholinesteras E Alzheimer's 1996

Saquinavir HIV Protease AIDS 1995

Indinavir HIV Protease AIDS 1996

Zanamivir Neuraminidase Influenza 1999

Oseltamivir Neuraminidase Influenza 1999

Imanitib Protein Kinase Leukemia 2001

Sitagliptin DPP-Iv Type 2 Diabetes 2006

Aliskiren Renin Hypertension 2007

Drug-Targets Homo sapiens:

- P38-alpha Map kinase

- EGFR kinase

- VEGFR Kinase

- BCR-ABL Kinase

- p53-MDM2 complex

- Human Serum Albumin

- alpha-1A adrenoreceptor

- beta adrenoreceptors

- TNF-alpha

Entamoeba histolytica:

- Pyruvate phosphate dikinase

- Serine Acetyl Transferase

- O-Acetyl Serine Sulfhydrylase

Plasmodium falciparum:

- Pf Sir2A

- DNA gyrase B

-M18 Aspartyl Aminopeptidase

- Dihydrooperate Synthase(DHPS)

-PfGCN5, PfHDAC1, PfPK5, Pfmrk,

Mycobacterium tuberculosis: - DNA Gyrase A -DNA polymerase III alpha subunit

-FAD5A KasA, KasB,

-TWO Component Systems (histidine

-Kinases, MurA,B,D,G,H etc

Dengue Virus: Envelope Protein, Dengue Virus Serotype-2

Cholera Vibriae: - LuxU-LuxO complex

Acinetobacter baumannii: - Beta Lactamase OXA-51

Salmonella enterica: - DNA gyrase-A

K.pneumoniae: - Klebsiella pneumoniae carbapenemase-2