drug discovery process-dk

Drug Discovery and Drug Design

by

Dr. Dhurke KashinathAssistant Professor

Department of Chemistry

National Institute of Technology Warangal-506 004

E-mail: [email protected]

20 October 2013 Dr. Dhurke Kashinath, NIT Warangal 1

Prescribed Texts:

• Foye’s Principles of Medicinal Chemistry – David Williams and Thomas Lemke

• Organic Chemistry of Drug design & Drug action-Richard Silverman,

• Practice of medicinal chemistry-Wermuth, C.

• An introduction to Medicinal Chemistry-Graham L Patrick

• Pharmaceutical chemistry: Therapeutic aspects of biomacromolecules-Bladon,

Christin

• Wilson & Giswold’s textbook of Organic Medicinal & Pharmaceutical Chemistry

John Block

• Comprehensive Medicinal Chemistry: The rational design, mechanistic study &

therapeutic application of chemical compounds Vol I– VI, Hansch

20 October 2013 2Dr. Dhurke Kashinath, NIT Warangal

Medicinal Chemistry Folklore/traditional usage (History)

Examples:

• Plant Ma Hung (Ephedra sinica)

– used as heart stimulant, diaphoretic agent (perspiration producer)

and to relief from cough

– Active ingredient ephedirin (a drug that raises the blood pressure

and relieves bronchial spasm; i.e. asthma )

• Papaver somniferum (opium poppy)

– 3rd centuary B.C. – opium popy juice used as an analgesic

– 10th centuary A.D. – opium pills used for coughing, mental disorders,

aches and pain

– Active ingredient – morphine (potent analgesic) and codeine (cough

suppressant)

• Bark of Cinchona trees

– Used for fever in 1600 BC is used for malaria and fever even today

– Active ingredient - quinine



Medicinal chemistry is the science that deals with design and discovery of

the new therapeutic chemicals and their development into useful medicines to

treat diseases

Medicinal chemistry involves isolation of compounds from nature or

synthesis of new molecules, structural elucidation (spectroscopic methods) and

study of their interactions with receptors, enzymes and DNA

Introduction: Medicinal chemistry


Objectives of Drug design:

(a) To understand the effects of synthetic/biological compounds on the basis of

molecular interaction with biological system

(b) To understand the processes by which the drugs usually produce their

pharmacological effects

(c) To understand how the drugs specifically react with the protoplasm to produce

a particular pharmacological response

(d) How the drugs usually get modified or metabolized and eliminated

from the body

(e) Probable relationship between biological activity with chemical structure


Identification of the target

• Understanding the interactions of biomacromolecules (enzymes and receptors)

involved in a particular disease state

• Design of agonist or antagonist for a particular receptor

• Target specificity: electivity between species and body (organs and tissues)

• Design of Agonist or antagonist

Identification of bioassay:

• Choice of bioassay (finding out EC50, IC50, LD50)/therapeutic index

• In vitro and In vivo tests and Test validity

Choosing the disease:

• Diseases which are prevalent in developed countries

• Impact on the society/Geographical consideration

• Better properties than existing drugs

• Economic factors


Modern drug discovery process

Target

identification

Target

validation

Lead

identification

Lead

optimization

Preclinical

phase

Drug

discovery

2-5 years

• Drug discovery is an expensive process involving high R & D cost (10-15

million USD) and requires extensive clinical testing

• A typical development time is estimated to be 10-15 years.

6-9 years


Modern drug discovery process

10,000 molecules


Early drug discovery (Preclinical)


Drug discovery process (Clinical studies)


Drug discovery process

Background

View of living organisms as molecular circuit:

• Molecular circuit = biochemical processes, that form and recycle molecules in a coordinated and balanced fashion

• Intended modes of operation = healthy state

• Aberrant modes of operation = disease state

Diagnosis:

• Identify the molecular basis of disease

Therapy:

• Guide biochemical circuit back to healthy state


Genomics - Proteomics

Mapping Sequence to Protein Structure and Dynamics

Primary SequenceMNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA

VADLFMVFGG FTTTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT

WVMALACAAP PLVGWSRYIP EGMQCSCGID YYTPHEETNN ESFVIYMFVV HFIIPLIVIF FCYGQLVFTV KEAAAQQQES

ATTQKAEKEV TRMVIIMVIA FLICWLPYAG VAFYIFTHQG SDFGPIFMTI PAFFAKTSAV YNPVIYIMMN KQFRNCMVTT

LCCGKNPLGD DEASTTVSKT ETSQVAPA

3D Structure

FoldingThis image cannot currently be displayed.


Genomics - ProteomicsMapping Sequence to Protein Structure, Dynamics and Function

Primary SequenceMNGTEGPNFY VPFSNKTGVV RSPFEAPQYY LAEPWQFSML AAYMFLLIML GFPINFLTLY VTVQHKKLRT PLNYILLNLA

VADLFMVFGG FTTTLYTSLH GYFVFGPTGC NLEGFFATLG GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT

WVMALACAAP PLVGWSRYIP EGMQCSCGID YYTPHEETNN ESFVIYMFVV HFIIPLIVIF FCYGQLVFTV KEAAAQQQES

ATTQKAEKEV TRMVIIMVIA FLICWLPYAG VAFYIFTHQG SDFGPIFMTI PAFFAKTSAV YNPVIYIMMN KQFRNCMVTT

LCCGKNPLGD DEASTTVSKT ETSQVAPA

3D Structure

Folding


How to design a drug in the absence of a structure?

Drug Target:Drug Target:Drug Target:Drug Target:

This image cannot currently be displayed.


Active site: Study and design of the lignad

1pth20 October 2013 Dr. Dhurke Kashinath, NIT Warangal 17


General terminology used in drug discovery:

Hit

Lead compound

Lead modification

Pharmacophore

DMPK

PK/PD

In-vivo

In-vitro

ADME

IC50

EC50

LD50

Efficacy

Agonist

Antagonist

Prodrug

High throughput screening

Random screening

Therapeutic index

Drug resistance

CYPs (Cytochrome P 450)

CADD

Structure based drug design

Fragment based drug design

Hit:

A “hit” is known or confirmed compound whose biological activity is known

(which is used for the primary screening)

Lead compound:

A lead compound is a representative of a compound series with sufficient

potential activity (as measured in terms of potency, selectivity,

pharmacokinetics, physicochemical properties, no toxicity and novelty) to

progress to a full drug development program

Lead discovery:

Lead discovery is the process of identifying active new chemical entities

(NCEs), which by subsequent modification may be transformed into a

clinically useful drug


Lead optimization:

The synthetic modification of a biologically active compound, to fulfill all

stereoelectronic, physicochemical, pharmacokinetic and toxicological properties

required for clinical use.

The new lead optimization pattern demands that companies move to parallel

processes that evaluate binding affinity, ADME, drug properties, etc. earlier in

the process in order to cut the time and costs lost in failed leads.

Pharmacophore:

Essential part of the lead molecule which is important to show bilogical

activity and has to be kept intact during lead modification

Prodrug:

A prodrug is drug which is given (taken) in an inactive form. Once administered,

the prodrug is metabolized by the body (biochemical reactions) into a

biologically active compound20 October 2013 Dr. Dhurke Kashinath, NIT Warangal 20


DMPK:

Drug metabolism and pharmacokinetics

PK/PD:

Pharmacokinetics and pharmacodynamics studies of the molecules with

biological system (i. e. enzymes, receptors and nucleosides and nucleotides)

In-vitro and In-vivo studies:

In vitro studies which are performed in the laboratory on a similar (artificial)

biological system

In vivo studies which are performed on biological system (animal models)

ADME:

Administration, Distribution, Metabolism and Excretion


Agonist:

An agonist is a chemical that binds to some receptor of a cell and triggers a

response by that cell


Types of Agonists:

An agonist is a chemical that binds to some receptor of a cell and

triggers a response by that cell


Antagonist:

An antagonist blocks the action of the agonist and an inverse agonist causes an

action opposite to that of the agonist

A receptor antagonist is a type of receptor ligand or drug that does not induce

a biological response itself upon binding to a receptor, but blocks or reduces

agonist-mediated responses


IC50 (Inhibitory concentration):

Measure of the effectiveness of a compound in inhibiting biological or biochemical

function (IC50 represents the concentration of a drug that is required for 50% inhibition

in vitro)-

EC50 (Effective concentration):

The term half maximal effective concentration (EC50) refers to the concentration of a

drug, antibody or toxicant which induces a response halfway between the baseline and

maximum after a specified exposure time (the concentration of a compound where 50%

of its maximal effect is observed)-

LD50 (Lethal concentration):

In toxicology, the median lethal dose, LD50 (lethal concentration, 50%) or LCt50 (lethal

concentration & time) of a toxin, radiation, or pathogen is the dose required to kill half

the members of a tested population after a specified test duration

HTS:

High throughput screening

Penicillin

First antibiotics discovered as natural products from the mold Penicillium

1928: Alexander Fleming noticed a green mold (Penicillium notatum) growing in

a culture of Staphylococcus aureus (gram positive bacteria)

Penicillin G and V isolated; antibiotic activity discovered; new β-lactams

discovered and made through modification to give antibiotics with improved

activity.

Drug Discovery Without a Lead: Serendipitous discovery


– Penicillin-G ( R = benzyl), is the most potent of all penicillin derivatives

• effective only against gram-positive bacteria

• Undergoes metabolism in the stomach by gastric acids and is poorly and

irregularly absorbed into the blood stream

• many disease producing staphylococci are able to produce an enzyme

capable of inactivating penicillin-G.

– Other semi-synthetic derivatives:

• Phenethicillin (Penicillin-V, R=PhOCH2) : Powerful electron-attracting

groups attached to the amino acid side chain prevent acid attack.

• Methicillin (R=2,6-di-OCH3-C6H3-): A bulky group attached to the amino

acid side chain provides steric hindrance which interferes with the

enzyme attachment which would deactivate the penicillin

• Ampicillin or Carbenicillin (R=C6H4NH2-): Increased polar character

imparts a greater activity against Gram-negative bacteria.

R = Ph/

substituted Ph



Increased polar character

imparts a greater activity

against Gram-negative

bacteria

A bulky group attached to the

amino acid side chain

provides steric hindrance

which interferes with the

Electron-attracting groups

attached to the amino acid side

chain prevent acid attack

-OH group at 4-position

better absorbed, following oral

administration

Penicillin-G: Effective only against

gram-positive bacteria. Undergoes

metabolism in the stomach by gastric

acids and is poorly and irregularly

absorbed into the blood stream many

disease producing staphylococci are

able to produce an enzyme capable of

inactivating penicillin-G

Drug Discovery Without a Lead: Librium (Chlordiazepoxide)

• Benzodiazepine tranquilizer (discovered while searching for anxiety drugs)

• 1957: Dr Leo Sternbach (Roche; Switzerland based company)

LibriumBenzheptoxdiazine

Originally planned to synthesizeQuinazoline 3-oxide

X=7-Cl, R1=CH2NHCH3,

R2=C6H5

Submitted for

pharmacological

evaluation and found to

be Librium

Benzodiazepine 4 -oxide



Screening of natural products (plant kingdom, microbial world, marine

world, animal sources, venoms and toxins)

• Medical folklore or Existing drugs

• Screening synthetic compounds (series of compounds/libraries)

• Starting from natural ligand or modulator (natural ligands for receptors,

enzymes, enzyme products as lead compounds, natural modulators as

lead compounds)

Finding a lead compound

– Drug Discovery without a lead

• Penicillin

• Librium

– Approaches for lead identification• Random Screening

• Nonrandom Screening

• Drug Metabolism Studies

• Clinical Observations

• Rational Approaches to Lead Discovery

Drug Discovery – lead identification


Lead Modification

Identification of the Active Part of the molecule: The Pharmacophore

Pharmacophore: The relevant groups on a molecule that interact with a receptor (or an

enzyme) and are responsible for the activity are collectively known as pharmacophore

(Other atoms not part of the pharmacophore are part of the auxophore)

The pharmacophore can be used as a tool to design new drug molecules that can

interact with the same receptor


High blood pressure

(hypertension)

Losartan

(reference compound)

Lead Modification

Which part has to be modified to improve drug action ???

• Some of the atoms are essential to maintain the integrity of the molecule & hold the

pharmacophoric groups in their appropriate positions

• While some are interfering with the binding of the pharmacophore, they need to be

excised/modified from lead compound



Morphine (X)

(Reference compound)

Levorphanol (4X)

Excising

the

dihydrofuran

ring

Benzomorphan (<X)

Removal of half

of cyclohexene ring

Cutting away

methylene group

(Not much change)

Removal of all

fused ring

Mepiridine (<X)

Acyclic analog

Dextropropoxyphene (X/2)Methadone (X)

Benzomorphan based drugs: Morphine as reference compound

Lead Modification:

Branching, isomerization, replacement of the rings, bioisosterism


Lead compounds from natural receptor agonists

Examples:

Steroidal hormone progesterone (weakly active) acted as the lead compound

for contraceptive (+)-norgestrel

Serotonin (neurotransmitter) was used as a lead for anti-inflammatory

drug indomethacin [non-steroidal anti-inflammatory drug (NSAID)]

Anti-inflammatory drug sulindac is inactive, its metabolite is active

Drug Metabolism Studies:

• Drug metabolites are degradation products generated in vivo

• Drug metabolites are screened to determine if the activity is due to drug

candidate or from a metabolite

Antibacterial drug sulfanilamide is a metabolite of prontosil



Pharmacokinetics (ADME)

Absorption – movement of drug from

site of administration to blood [Rate of

dissolution, Surface area, Blood flow,

Lipid solubility, pH partitioning

Distribution (systemic circulation and

body tissues of the body)

Metabolism (generation of active species

and metabolites through enzymatic

biochemical reactions in the body:

cytochrome P450, hepatic microsomal

enzyme system)

Excretion

(Absorption, Distribution/Transportation, Metabolism and Excretion)

1910: Paul Ehrlich and Sahachiro Hata developed Salvarsan

(Arsphenamine) against syphilis (Starting of chemotherapy)

1928: Fleming discovered penicillin

1932: Sulfa drugs (sulfanilamide) discovered against Gram+ bacteria

1940: Howard Florey and Ernst Chain performed first clinical trials of

penicillin

The History of Chemotherapy

Inhibited area

Normal bacteria

Penicillinium colony


Features of antimicrobial Drugs

• Selective toxicity (species): Drug kills pathogens without damaging the host

• Therapeutic index: ratio between toxic dose and therapeutic dose or ratio of

LD50 to ED50 (High therapeutic index)

• LD50 (low) vs. MIC and/or MBC (high)

• Four major sites:

– Cell wall, Ribosomes, DNA,

• Antimicrobial action – Bacteriostatic (inhibits the growth) vs

Bactericidal (kills bacteria)

• Activity Spectrum:

Broad Spectrum Antibiotics: Effective against many types (E.g. Tetracycline);

Narrow Spectrum Antibiotics: Effective against very few types (E.g. Penicillin)

• Antimicrobial drugs: Synthetic material, interfere with the growth of microbes within the host

• Antibiotic: Biological origin/produced by a microbe, inhibits/kills other microbes


e.g. Bacteriostatic, Bactericidal

The Action of Antimicrobial Drugs



Mechanism of action: Gram +Ve bacteria


Mechanism of action: Gram –Ve bacteria

Retention of Penicillin G (Dose response curve)


Inhibition of Protein Synthesis by Antibiotics


Cephalosporins

Structure and mode of action resembles penicillins

1. More stable to bacterial ββββ-

lactamases than penicilins

2. Broader spectrum ⇒⇒⇒⇒ used

against penicillin-resistant

strains


Vancomycin

– Glycopeptide from Streptomyces

– Inhibition of cell wall synthesis

– used for Penicillin resistant Gram +Ve bacteria

– Used to kill Methionine Sulfoxide Reductase A gene

– Vancomycin resistance: Vancomycin-Resistant

Enterococcus (VRE) and Vancomycin-resistant

Staphylococcus aureus (VRSA)


Antibiotic Resistance

A variety of mutations can lead to antibiotic resistance including the following

1. Enzymatic destruction of drug

2. Prevention of penetration of drug

3. Alteration of drug's target site

4. Rapid ejection of the drug


Resistance to Antibiotics


Antibiotic Resistance


Misuse of antibiotics:

– Using outdated or damaged antibiotics

– Using antibiotics for the common cold and other problems in

inappropriate condition

– Failing complete the prescribed regimen

– Using someone else's leftover prescription

Antiviral Drugs: Acyclovir DNA polymerase inhibitor

Nucleoside analogs inhibit DNA synthesis

Acyclovir and newer derivatives: Selective inhibition of herpes virus replication.

Acyclovir converts in to nucleotide analog only in virus infected cells ⇒⇒⇒⇒ very little harm to uninfected cells!



Herps simplex virus

Antiviral Drugs: Acyclovir DNA polymerase inhibitor

Mechanism of Action of Acyclovir


HIV protease cleaves viral polypeptide into functional proteins

Protease inhibition ⇒⇒⇒⇒ HIV cannot mature and noninfectious viruses are

produced.

Antiviral Drugs for Treating HIV/AIDS:

HAART: Highly active antiviral therapy

1. NRTIs and NNRTIs

2. Protease Inhibitors

3. Fusion Inhibitors

4. Integrase Inhibitors


Antifungal Drugs

• Polyenes, such as nystatin and amphotericin B, used for systemic fungal infections involve inhibition of ergosterol synthesis ⇒⇒⇒⇒ fungicidal

• Griseofulvin from Penicillium. Systemic/oral. Binds to tubulin ⇒⇒⇒⇒ used for theTineae


• Fungal infections classification:

– Superficial infections: Ringworm (tinea) → skin and mucous

membrane. Incidence rate is high.

– Systemic infections: Candida albicans → opportunist infections.

Fatality rate is high.

• Antifungal agents classification:

– Antibiotics: Amphotericin B;

– Azole: Ketoconazole;

– Allylamine: Terbinafine;

– Pyrimidine: Flucytosine.

Antifungal Drugs


Antiprotozoan and Antihelminthic Drugs

Examples of Antiprotozoan:

• Chloroquine: Malaria (Plasmodium falciparum)

• Metronidazole (Flagyl): Vaginitis, skin, joints infections and respiratory tract

caused by anaerobic bacteria

Examples of Antihelminthic:

• Niclosamide and praziquantel: Tapeworm

• Mebendazole: broadspectrum antihelmintic

• Ivermectin: nematodes, mites, lice . . .



Anti inflammatory drugs: How NSAIDs Help Relieve Pain ?

• Block the effects of special enzymes called Cox-1 and Cox-2 enzymes

• These enzymes play a key role in making prostaglandins

• By blocking the Cox enzymes, NSAIDs stop body from synthesizing many

prostaglandins

• Thus, less swelling and less pain

NSAIDs available over-the-counter drugs:

Aspirin (Bufferin, Bayer, and Excedrin)

Ibuprofen (Advil, Motrin, Nuprin)

Ketoprofen (Actron, Orudis)

Naproxen (Aleve)

NSAIDs are available by prescription:

Daypro, Indocin, Lodine

Naprosyn

Relafen

Voltaren

Main Diseases of the Cardiovascular System

• Hypertension: Increased sympathetic activity and sodium overload increase

blood pressure (BP)

• Congestive heart failure: CHF due to weakening of the contractile function

of the heart. Blood and fluid accumulate in the heart, lungs, abdomen etc.

• Coronary artery disease: Chest pain due to coronary artery disease (CAD)

and myocardial ischemia. Exertional angina (pain) usually occurs during physical

exertion or stress

• Myocardial infarction: Caused by complete blockage of one of the coronary

arteries. Heart cells deprived of blood/oxygen become ischemic, die, and form

an infarct

• Cardiac arrhythmias:

Disturbances in the normal electrical activity of the heart. Can be detected

on a recording of the electrocardiogram (ECG)


Drug Classes Used to Cardio Vascular diseases:

• Diuretics

• Sympatholytic drugs

• Vasodilator drugs

• Calcium antagonist drugs

• Angiotensin-converting enzyme inhibitor and angiotensin receptor blocking

drugs

• Nitrites and nitrates

• Beta adrenergic blocking drugs

• Calcium antagonists, also referred to as calcium channel blockers

• Cardiac glycosides


Carcinogenesis

DNA mutation: Inactivation of tumor

supressor genes, binding to a virus

protein or binding to a mutated

cellular protein

Activation of protooncogenes to

oncogenes: point mutation (single

nucleotide polymorphisms-SNPs),

gene amplification, chromosome

translocation, virus interaction

Hereditary

Acquired: radiation, viruses, chemicals,

drugs

Characteristics of tumour cells:

• Uncontrolled proliferation

• Dedifferentiation &&&& loss of function


Types of cancers

drug discovery process-dk

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