DRUG DISCOVERY & DRUG DESIGN

DRUG DISCOVERY & DRUG DESIGN
Course Teacher: Dr. Raushanara Akter Assistant Professor, Dept. of Pharmacy, BRACU

Introduction In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery. But now we know diseases are controlled at molecular and physiological level. Also shape of an molecule at atomic level is well understood. Information of Human Genome

Pre 1919 Herbal Drugs Serendiptious discoveries 1920s, 30s Vitamins Vaccines 1940s Antibiotic Era R&D Boost due to WW2 1950s New technology, Discovery of DNA 1960s Breakthrough in Etiology 1970s Rise of Biotechnology Use of IT 1980s Commercialization of Drug Discovery Combinatorial Chemistry 1990s Robotics Automation

Drug Design Drug design may be defined as an effort to develop a new drug by molecular modification of lead compound for optimization of desired effects and minimization of side effects.

Lead Compound A lead Compound is also known as a parent compound A lead compound is a compound having a particular biological activity obtained either from natural or synthetic source. E.g. Penicillin G, Prontosil

Penicillin G Penicillin G is a lead compound, obtained from natural source. It is not an ideal drug due to- Acid instability Narrow microbial spectrum High allergenicity Lower metabolic efficacy Development of resistance Lower oral absorption Shorter plasma half life

Penicillin G Due to the mentioned problems, Pen-G is not used. Molecular modification of Pen-G to Ampicillin reduces the problems associated with Pen-G. Ampicillin Advantages of Ampicillin over Pen-G: Acid stable Broad spectrum Less allergenic Greater metabolic efficiency Prontosil Learn by yourself

Purpose of Drug Design: To improve selectivity of action To improve ADME (Absorption, Distribution, Metabolism & Excretion) Profile. To obtain drug having more desirable properties than the lead compound in terms of potency, toxicity & specificity. To obtain marketable alternative drug that can compete with an existing one. To reduce cost of bulk production Exploitation of side effects of existing drug Invention of drugs De Novo

Improvement of Drug Selectivity Drug selectivity is a primary objective in the discovery and optimization of a compound on the path toward developing a drug. Drug selectivity can be improved by modification of chemical structure of existing drugs such as by molecular changes that will increase a desired biological action relative to a side effect. E.g. Development of 1st generation of antihistamine drug by molecular modification. General structure of Antihistamine (1st Generation) R-CH2-CH2-N-(CH3)2 Hetramine → Pyrilamine → Chlorpheniramine

Hetramine Pyrilamine Chlorpheniramine (±)
Poor potency and low therapeutic ratio (500) are responsible for not being employed in man Hetramine Pyrilamine Chlorpheniramine (±) Good therapeutic ratio (68,000) but lower selectivity lower therapeutic ratio than pyrilamine but high selectivity Both (+)ve and (–)ve form of chlorpheniramine have equal activity but (+)ve form has higher therapeutic ratio (3100) than that (24) of (-) form. So, (+) chlorpheniramine is a good choice as an antihistaminic drug. Therapeutic Ratio, TR = LD50/ED50

Improvement of ADME Profile
Absorption Oral route is still the only convenient one for drugs that have to be given on a continuing basis. Therefore, much effort has been devoted to the modification of drug structure to improve absorption from the GI tract. One of the most successful molecular modifications leading to orally active preparations concerns the estrogenic & progesteronal steroids. Molecular modification Nor-ethindrone Prednisolone (Orally active) Progesterone (Orally inactive)

Distribution Molecular modifications that alter the distribution of a drug within the body can have profound effects upon its pharmacological properties. Often such modification involve changes in the lipid/water partition coefficient (P.C). E.g. Thiopental was developed from Pentobarbital by replacement of an oxygen atom with a sulfur atom. Thiopental (P.C.=3.3) Pentobarbital (P.C.= 0.05) Very fast onset & offset of action Very high lipid/water partition coefficient Rapidly crosses the BBB Persistence of drug in the body

Metabolism Structural modification can alter the metabolic rate of a drug to shorten or prolong its duration of action. E.g. Development of procainamide from procaine by substitution of the amide linkage for the ester group. Molecular Modification Procaine: Active against certain cardiac arrhythmias Local anesthetic Since its an ester, rapidly hydrolysed by plasma & liver esterases Procainamide: Same activity against cardiac arrhythmias Duration of action is higher than procaine Hydrolysis rate in-vivo was greatly reduced

Increase of potency, specificity and reduction of toxicity
Molecular modification provides more potent drug with binding specificity, less toxic than the lead compound. E.g. Mild analgesic & antipyretic acetanilide is converted to aniline in-vivo by deacetylation resulting in methemoglobinemia. Modification of acetanilide in para position by hydroxylation produced paracetamol which was less toxic. Deacetylatn Acetanilide Aniline Hydroxylatn Paracetamol Paracetamol

Reduction of Production Cost
Cost is an important factor in drug development as they are widely used to treat various diseases. Molecular modifications have yielded drugs that are better than the parent drug as they are cheaper. E.g. Diethylstilbestrol Diethylstilbestrol Synthetic non-steroidal estrogen drug Orally active Cost is 100 times less than Estradiol Steroidal estrogen Highly expensive drug

To exploit the side effects of existing drug
An action seen as undesirable in one therapeutic context may become the primary drug action in another. Eg. Sulfonamide series were introduced as antibacterial agents. Exploitation of their side effects has lead to wholly new & useful drugs of 3 kinds: Diuretic, Antidiabetic and Antithyroid drugs.

Invention of drugs De Novo
Invention of drugs De Novo. For details of above points, see books and hand outs.

Ancient Source The ancient people thought that disease was caused by evil spirits or devils. They treated the patient with the substances of repugnant odor and appearance such like urine, feces, stinking plants or they restorted to nauseating fumigation. Paracelsus ( ): ‘God indicated which medicinal agent would be adequate for treating a certain affected organ or the symptoms of a certain disease by best-owing a signal in the form of similarity, even if only spiritual, between the agent & the organ or symptoms.’

Correlation with Disease
Ancient Source Agent Correlation with Disease Use Stalks of hepatica Resembling liver Liver disease Safron & Celandine Yellow color Jaundice Veronica flower Eye Eye Disease Veronica roots Intestinal worms Leaves of melissa Cordiform Heart disease

Ancient Source Hepatica (Resembling liver) Saffron (Yellow color)
Melissa Leaf (Heart Shape)

Modern Source Modern Sources Example Antibiotics
Ampicillin, Cefradine, Azithromycin etc. Hormones Estrogen, Progestogen, Androgen etc. Vaccine Influenza, HBV, HCV vaccines, and the chicken pox vaccine etc. Chemical synthesis Ibuprofen, Paracetamol, Methotrexate etc.

Contribution of Several Sources
Extraction Chromatography X-ray crystallography Synthesis Spectroscopy

Contribution of Several Sources
Total 252 essential drugs are included in 1985 by Willo. 123 drugs Chemical synthesis 48.9% 28 drugs Vegetable parts 11.1% 24 drugs Partial chemical synthesis 9.5% 23 drugs Mineral Source 9.1% 22 drugs Extracted from animal organ 8.7% 16 drugs Microbial origin 6.4% 11 drugs Vaccine 4.3% 5 drugs Sera 2.0%

Cost & Place of Development of Drugs
: 1165 new drugs were introduced in USA market. : 1787 new drugs in world market. Main Contributor: USA, Japan, UK, France, Italy, West Germany, Switzerland. Expense: Cost ranges from $10 million to $100 million. Main Pharma Company: Hoechst-Roussel (Germany), RPR (France), Johnson & Johnson (USA), Sanofi (France), Sandoz (Switzerland), Bayer (Germany), Roche (Switzerland) etc. Last 30 years: 90% drugs from Industry 9% drugs from University 1% drugs from Govt. Lab

GENESIS OF DRUG Drugs find their way into therapeutics mainly by one of the following ways: Serendipity Random Screening Extraction of active principles from natural sources Molecular modification of known drugs Selection or synthesis of soft drugs Drug latentiation/Prodrug Rational design of drugs

SERENDIPITY Serendipity is defined as valuable discoveries accidentally, luckily or suddenly by Pharmacists, Chemists, Physicians & other investigators Examples: Acetanilide & Phenylbutazone → Antipyretic Penicillin → Antibacterial Piperazine → Anthelmentic Chlorthiazide →Diuretic Sulfonylureas →Oral hypoglycemics Benzodiazepine →Antianxiety agent

Acetanilide as Antipyretic Penicillin as Antibiotic
SERENDIPITY Acetanilide as Antipyretic A patient with infection (intestinal parasite) was supposed to be given Napthalone. But he was given accidentally acetanilide, and fever of the patient was reduced. Thus, acetanilide was accidentally discovered as an antipyretic agent. However, now a day, it is not used as antipyretic due to its nephro toxicity. Penicillin as Antibiotic The antibacterial action was introduced accidentally by Flemming in 1920 while he was working with a bacterial culture, the culture was contaminated with penicillium fungi, which destroyed the cultured bacteria in the medium. In further stage, the active component penicillin was isolated form the respective fungi.

Sulfonamide as Antithyroid Drug
Serendipity Sulfonamide as Antithyroid Drug The antithyroid drugs of the thiouracil type had their origin in the accidental observation in 1941, that rats receiving ‘Sulfaguanidine’ developed goiters. The original purpose of the investigation was to study the role of intestinal bacteria in the biosynthesis of essential nutrients. Sulfaguanidine was being used to sterilize the gut.

Serendipity Some Antithyroid Drugs: Thiourea Sulfaguanidine Thiouracil
Sulfadiazine Thiouracil (1st antithyroid drug)

Serendipity Development of Thiouracil as Antithyroid Drug:
The systemic screening investigations found that Thiourea is a potent goitrogen. Sulfadiazine is most active. Since sulfadiazine contains a pyrimidine ring, it was logical to incorporate the thiourea moiety in a pyrimidine ring and thus thiouracil was obtained. This drug proved satisfactory for the clinical use in the treatment of hyperthyroidism. Thiouracil works by blocking thyroid hormone synthesis. Thus resulting in low circulating level of thyroid hormone. But thiouracil produced toxic reactions, mainly agranulocytosis (13% patients in a population of 2490 treated patients). Thiouracil (1st antithyroid drug)

Serendipity Development of Thiouracil as Antithyroid Drug:
Modifications of the thiouracil structure was studied to find a safer drug and two safer drugs emerged: Propylthiouracil Methimazole Methimazole: Effective antithyroid drug. It is not a pyrimidine compound. Very low toxicity. Propylthiouracil Propylthiouracil: Toxic reactions in only 3% patients when given in effective clinical dose. Methimazole

Random Screening All available chemical substances are submitted to a variety of biological tests in the hope that some may show useful activity. This method is not very rewarding since it is Time consuming, Requires more manpower, Needs more compounds. 500,000 chemicals were tested for a new anti-convalsant.

RANDOM SCREENING Rationally directed random screening Systematic random screening Antimalarial drugs 2nd world war 14,000 compounds were tested Few were selected for clinical trials Antibiotic At first penicillin 6000 antibiotics 100 are used in medicine & agriculture Isolation & identification of products of drug metabolism Inactive drug Active metabolite

Extraction from Natural Sources
Digitalis purpurea Penicillium notatum Catharanthus roseus Natural products (Antibiotics, Vitamins, Hormones etc) are products from various natural sources, plants, microbes and animals. Natural products can be an entire organism a part of a plant/an organism an extract of an organism or part of an organism an exudates, or pure compound (e.g. alkaloids, coumarins, flavonoids, lignans, steroids and terpenoids) However, in practice, the term natural product refers to secondary metabolites, small molecules (molecular weight < 1500 amu), produced by an organism.

Drug Medical use Sources Mechanism of action Aspirin Analgesic, anti-inflammatory, antipyretic Plant Inhibition of COX Digoxin For atrial fibrillation and CHF Inhibition of the Na+/K+ ATPase membrane pump Insulin Antidiabetic Animal Binding α-subunit of tyrosin kinase Penicillin Antibiotic Microorganism Inhibition of peptidoglycan synthesis Aurantosides Antifungal Marine organism Inhibition of tubulin polymerisation

Natural products and their derivatives represent over 60% of all drugs clinically used worldwide where natural products from medicinal plants alone contribute to 25% of total drugs To treat 87% of all categorized human diseases, natural products and related drugs are reportedly used for example as Antibacterial, Anticancer, Anticoagulant, Antiparasitic and Immunosuppressant agents

More than 28% of new chemical entities introduced into the market are derived from natural products. More than 100 compounds particularly, anticancer and anti-infectives, which are derived from natural products, are undergoing clinical trials at present. At least 100 natural products-derived compounds (primarily plant or microbial sources) are in preclinical development presently.

Molecular Modification
This method of obtaining new drugs is also called; Molecular manipulation Method of variation Mechanistic method Selective process or approach In molecular modification, a well established chemical substance of known biological activity is considered as a lead or prototype. Some of these modifications have been made with the purpose of exploring the side effects of known drugs.

Some drugs obtained by molecular modification Atropine Steroids Promethazine Sulfa drug Antiulcer Antiinflammatory Anxiolytic Antithyroid Antidiarrheal Contraceptive Antidiabetic Mydriasis Etrogenics Diuretic Antispasmodic Progestrational Antimalarial/Antibacterial

Development of Anti-diabetic Drug IPTD: 5-isopropyl-2-sulfanilamide 1,3,4-thiadiazole In 1942, Patients with typhoid fever under treatment with an isopropyl-thiadiazole derivative of sulfanilamide; 5-isopropyl-2-sulfanilamide 1,3,4-thiadiazole and the problems associated with this drug were Weakness and dizziness Stimulated insulin release Was ineffective in absence of functional islets

Development of Anti-diabetic Drug
1st Generation anti-diabetic Study showed the hypoglycemic action depended primarily upon the urea-like structures formed by a N- & C- atom of the thiadiazide ring and the N-atom of the sulfonamide grouping. Basic structure for activity: Ar-SO2NHCONH-R Ar = Aryl grp R= Alkyl grp Sulfonyl ureas

Development of Anti-diabetic Drug
1st Generation Anti-diabetic Drug Structure Carbutamide R1 = NH2; R2 = C4H9 Tolbutamide R1 = CH3; R2 = C4H9 Chlorpropamide R1 = -Cl; R2 = C3H7 Tolazamide Acetohexamide Do yourself

Advantages of Tolbutamide and Chlorpropamide
Tolbutamide Chlorpropamide Elimination rate Most potent of the series Duration rate Long duration of action Synthesis of chlorpropamide, tolbutamide : Learn from hard copy

2nd Generation anti-diabetic
Drug Structure Glyburide (Glibenclamide) Glipizide Gliclazide 2nd generation drugs are effective at times lower conc.

3rd Generation Anti-diabetic
Glimepiride Glimeperide is a structural analogue of the second-generation sulfonylureas in which the amide moiety of the 4-aralkyl substituent has been replaced with a heterocyclic ureido group. This structural modification is reported to result binding to different region of beta cell receptor and in enhanced potency and increased duration. Most potent -- lowest dose of the sulfonylureas.

Advantages of Molecular Modification
Greater probability of congeners, homologs, and analogs having pharmacological properties similar to those of the prototype than the compounds selected or synthesized at random. Possibility of obtaining pharmacologically superior products. Likelihood of the production of the new drugs being more economical. Synthesis similar to that of the prototype, with saving time and money Data gathered may help to elucidate structure-activity relationship (SAR) Use of the same methods of biological assay used for the prototype.

Objectives of Molecular Modification
To discover the essential pharmacological moiety. To obtain drugs having more desirable properties than the prototype in terms of potency, specificity, duration of action, ease of application, administration, stability, cost of production.

Process of Molecular Modification
A. General Process B. Special Process Molecular Association Molecular addition Molecular replication Molecular hybridization Ring closure/opening Formation of lower or higher homologs Introduction of double bonds Introduction of chiral centre Introductn, removal or replacement of bulky groups Isosteric substitution Change of position or orientation of certain groups Introduction of alkylating moiety Modification toward inhibition or promotion of various electronic states. Molecular dissociation

Molecular Dissociation It is the systemic synthesis and evaluation of simpler analogs of the lead compound. These analogs are partial or virtual replicas of the prototype drug; which is actually a natural product of very intricate chemical structure. Cocaine (1865) Benzocaine ( 1890; G. anesthetic) Procaine (1906; G. anesthetic) Anesthetic but exert bad effect on CNS

Molecular Association It is the synthesis and evaluation of more & more complex analogs of the prototype. Three main types of association has been distinguished… Molecular Addition Molecular Replication Molecular Hybridization

Molecular Addition: Addition of different moieties through weak forces, such as eletrostatic attraction & H-bonding. + Methenamine Mandalic acid Methenamine mendelate

2. Molecular Replication: Addition of identical moieties through covalent bond. Duplication: Association of two moieties Triplication: …………… Tetraplication: ………. n-plication………. For your practice

Molecular Duplication Fenticlor (Duplication of p-chlorophenol) Simethicone (Polydimethylsiloxane) M. duplication also found in natural active principles such as Β-carotene, dicoumarol M. Triplication: Hepronicate, tribenoside M. Tetraplication: Nicomol

3. Molecular Hybridization: Association of different or mixed moieties through covalent bonding. + Paracetamol Aspirin Acetaminosalol/Benorilate Acetaminosalol/Benorilate: It is an esterfication product of aspirin and paracetamol. It was used as a substitute for salicylic acid in acute rheumatism, and as an intestinal antiseptic.

Special Process of Molecular Modification
Two Types: 1. Alterations which increase or decrease the dimensions & flexibility of a molecule. 2. Alterations of physical & chemical properties through the introduction of new groups or the replacement of certain moieties by different ones.

Alterations which increase or decrease the dimensions & flexibility of a molecule. A) Ring closure or opening: Ephedrine Phenmetrazine

Formation of lower or higher Homologs E.g. CH4 CH3-CH3 CH3-CH2-CH3 CH3-CH2-CH2-CH3 Homologous series

In the alkane & polymethylene series, the following general types of changes were observed 1. Activity ↑se regularly until a max is reached, higher member being almost or entirely inactive. Eg. Structurally non-specific drugs: General anesthetic Volatile insecticides Disinfectants Structurally specific drug-Local anesthetic

2. Activity ↑se irregularly, reaches a maximal value and then ↓se again irregularly. Eg. Benzylic esters & atropinic properties 3. Activity ↑se or ↓se reaches a relatively high or low value and then remains constant for a few or many higher members. Eg. R3N-(CH2)n-NR3 Ganglionic blocking agents + Greatest activity in which, n = 4, 5 or 6

4. Activity alternates, cmopounds having odd number of carbon atoms being more active than neighboring members with an even number of carbon atoms or vice versa. Eg. Anti-malarials from 6-methoxy-8-aminoquinoline 6-methoxy-8-aminoquinoline

Higher members Activity ↑ 5. Lower members R= H R= CH3 R= CH3-CH2 R= CH3-CH2-CH2 Alkylation ↓ the antihypertensive activity Exception Or –CH2-CH2-CH2-CH3 Hypotensive effect Low Alkylation→ aApha as well as beta-receptor active High Alkylation → Only beta-receptor active

Drug Discovery & Development-Timeline
PRECLINICAL CLINICAL TRIALS FDA REVIEW 10,000 COMPOUNDS 250 COMPOUNDS 1 FDA APPROVED DRUG 5 COMPOUNDS ~6.5 YEARS ~7 YEARS ~1.5 YEARS

Clinical Trials and Therapeutics
Target Selection Cellular and Genetic Targets Genomics Proteomics Bioinformatics Lead Discovery Synthesis and Isolation Combinatorial Chemistry Assay development High-Throughput Screening Medicinal Chemistry Library Development SAR Studies In Silico Screening Chemical Synthesis In Vitro Studies Drug Affinity and Selectivity Cell Disease Models MOA Lead Candidate Refinement In Vivo Studies Animal models of Disease States Behavioural Studies Functional Imaging Ex-Vivo Studies Clinical Trials and Therapeutics

The Drug Discovery Process
Target selection & validation Discovery Development Target -receptor; -ion channel; -transporter; -enzyme; - signalling molecule Studies of Disease Mechanisms Drug Candidate safety testing Human Studies Phases I,II, III Lead Search -Develop assays (use of automation) -Chemical diversity -Highly iterative process Molecular Studies Drug Approval and Registration Lead optimization -selectivity -efficacy in animal models -tolerability: AEs mechanism- based or structure-based? -pharmacokinetics -highly iterative process Animal Studies - relevant species - transgenic KO/KI mice - conditional KOs - agonists/antagonists - antibodies - antisense - RNAi

Target Selection & Validation
Define the unmet medical need (disease) Understand the molecular mechanism of the disease Identify a therapeutic target in that pathway (e.g gene, key enzyme, receptor, ion-channel, nuclear receptor) Demonstrate that target is relevant to disease mechanism using genetics, animal models, lead compounds, antibodies, RNAi, etc. Here is what we are trying to achieve (refer to slide). Note that you can comment on: We conduct basic animal health research in RY, but our animal health care products are marketed by Merial, a joint venture between Merck and Rhone- Poulenc (note that RP is now known as Aventis (RP merged with Hoechst). Outcomes research is when we attempt to prove that our compounds not only cause important chemical effects in the body (such as reduced blood pressure or reduced cholesterol), but that these effects lead to reduced morbidity and mortality over time. The Zocor 4S study is an example. The research budget for MRL is $2.4 billion this year.

Discovery Develop an assay to evaluate activity of compounds on the target - in vitro (e.g. enzyme assay) - in vivo (animal model or pharmacodynamic assay) Identify a lead compound screen collection of compounds (“compound library”) compound from published literature screen Natural Products structure-based design (“rational drug design”) Optimize to give a “proof-of-concept” molecule—one that shows efficacy in an animal disease model Optimize to give drug-like properties—pharmacokinetics, metabolism, off-target activities Safety assessment, Preclinical Candidate!!! Here is what we are trying to achieve (refer to slide). Note that you can comment on: We conduct basic animal health research in RY, but our animal health care products are marketed by Merial, a joint venture between Merck and Rhone- Poulenc (note that RP is now known as Aventis (RP merged with Hoechst). Outcomes research is when we attempt to prove that our compounds not only cause important chemical effects in the body (such as reduced blood pressure or reduced cholesterol), but that these effects lead to reduced morbidity and mortality over time. The Zocor 4S study is an example. The research budget for MRL is $2.4 billion this year.

Development Pre-Clinical Clinical Process R&D Chem Eng. R&D
Manufacturing Bio Process R&D Safety Assessment Toxicology Drug Metabolism (ADME) Pharmacology Pharmaceutical R&D Formulation Regulatory Affairs Project Planning & Management Marketing Clinical Investigator & patient Clinical Pharmacology Clinical Research Statistics & Epidemiology Data Coordination Research Information Systems Information Services

IND Clinical Trials Phase I Phase II Phase III Investigational
healthy volunteers take drug for about one month Remote data entry Product Profile Marketing SOI Information Learned 1. Absorption and metabolism 2. Effects on organs and tissue 3. Side effects as dosage is increased Investigational New Drug application IND Clinical Trials Phase II Several hundred health-impaired patients Treatment Group Control Group Information Learned 1. Effectiveness in treating disease 2. Short-term side effects in health -impaired patients 3. Dose range Phase III Hundreds or thousands of health-impaired patients Information Learned 1. Benefit/risk relationship of drug 2. Less common and longer term side effects 3. Labeling information Compassionate Use

DRUG DISCOVERY & DRUG DESIGN

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