TRADITIONAL DRUG SCREENING Random, Trial and Error, … · 2017-08-24 · ChemEMBL Bioassay: 14.67...
Transcript of TRADITIONAL DRUG SCREENING Random, Trial and Error, … · 2017-08-24 · ChemEMBL Bioassay: 14.67...
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
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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
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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
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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