Drug Discovery, Optimization, and Development Process PDF

Principles of Drug Action Drug Discovery, Optimization, and Development Process Lecture 20  Medicinal Chemistry Drug Drug Physicochemical...

Principles of Drug Action Drug Discovery, Optimization, and Development Process Lecture 20  Medicinal Chemistry Drug Drug Physicochemical Discovery Properties of Drugs-1 (Drug Target) Optimization Functional Group (FG) Acidity and Basicity of FG Enzymes & Development Receptors Physicochemical Properties of Drugs-2 and 3 - Forces Involved in Drug-Receptor Interactions - Chirality - Salts, Solubility Steps in Medicinal Chemistry Discovery (finding lead compounds) Optimization (Structure-Activity- Relationships) Development (Chemical formulation for suitable clinical use)  LEARNING OBJECTIVES Explain steps in drug discovery, optimization, and development with suitable examples. Discuss the role of natural products as a source of compounds for drug discovery. What is a lead compound and how is it discovered? Differentiate between Irrational and Rational approaches for drug discovery with examples. Explain structure-based drug designing using suitable examples.  Drug Discovery & Development (DDD) Identify disease Find a drug effective against disease protein Isolate protein (2-5 years) involved in Scale-up disease (2-5 years) Preclinical testing (1-3 years) Human clinical trials (2-10 years) IN le D Fi Formulation A ND le Fi FDA approval Investigational New Drug (IND) (2-3 years) New Drug Application (NDA)  DDD Drug Discovery & Optimization Pharmaceutical companies are in the business of identifying compounds that may be useful new drugs 1. Identify the target disease and drug target 2. Establishing testing procedures (bioassay). Tens or hundreds of thousands of compounds are made and tested every year (“screening”). Tests are usually simple binding assays (does the molecule bind to a target protein?) 3. Testing is done in two stages: A: Lead Generation (find a compound that binds) B: Lead Optimization (find a compound that binds better)  Chemical similarity is important at both these stages.  DDD 1. Drug Targets and Mechanisms of Drug Action Enzymes – inhibitors (reversible, irreversible) G-Protein Coupled Receptors – agonists and antagonists Ion Channels – blockers Transporters – uptake inhibitors DNA – intercalating agents  2. Bioassay 2. Establishing testing procedures (Bioassay) Bioassays are required in order to find lead compounds and for drug optimization Bioassay can be (A) in vitro and (B) in vivo. A combination of tests is often used in research programs In Vivo versus In Vitro  2. Bioassay 2A. In vitro 2A. In Vitro Tests Targets (e.g. isolated enzymes or receptors): Cells (e.g. cloned cells), Tissues (e.g. muscle tissue); Organs; Micro-organisms (for antibacterial agents) Measure the interaction but not the ability of the drug to reach the target Tests not carried out on animals/humans Used in high-throughput screening Does not demonstrate a physiological or clinical effect Does not identify possible side effects Does not identify effective prodrugs  2. Bioassay 2A. In vitro Screening: High throughput screening (HTS) Plates: 384, 1536, or 3456 wells Sample scale: as small as nano- or pico-liter per well Types of assays: biochemical or biological Detection: fluorescence, luminescence, scattering, radioactivity Cost-effectiveness and speed of compound scanning.  2. Bioassay B. In vivo 2B. In Vivo Tests Carried out on live animals or humans Measure an observed physiological effect Measure a drug’s ability to interact with its target and its ability to reach that target Can identify possible side effects Rationalization may be difficult due to the number of factors involved Drug potency - concentration of drug required to produce 50% of the maximum possible effect 3. The Lead Compound A compound demonstrating a property likely to be therapeutically useful Used as the starting point for drug design and development Found by screening compounds (natural or synthetic) or by rational design (molecular modeling) Need to identify a suitable test in order to find a lead compound https://www.youtube.com/watch?v=U96He401wj4  Simplified Major steps in DDD/Medicinal Chemistry 1. Discovery (finding lead compounds) 2. Optimization (Structure-Activity Relationships) 3. Development (Chemical formulation for suitable clinical use)  3A. Sources 3A. Sources of Lead Compounds for Discovery Plant life (flowers, trees, bushes) Micro-organisms (bacteria, fungi) Animal life (frogs, snakes, scorpions) I) The Natural World Biochemicals (Neurotransmitters, hormones) Marine chemistry (corals, bacteria, fish etc) II) The Synthetic World Chemical synthesis (traditional) Combinatorial synthesis III) The Virtual World Computer aided drug design  Pharmacognosy is the study of medicinal drugs derived from plants or other natural sources. It is also defined as the study of crude drugs. The Pharmaceutical Industry in 2020. An Analysis of FDA Drug Approvals from the Perspective of Molecules, Molecules, 26, 2021, DO - 10.3390/molecules26030627 Drug Discovery 4. MECHANISTIC DESIGN (Rational approach) Define disease process 1. SERENDIPITY 2. SCREENING EFFECTOR(S) TARGET 3. MODIFICATION define define isolate isolate 3D-structure 3D-structure CADD (Computer-Adided Drug Design) Theoretical Drug Synthesize compound NEW DRUG NEW Chemical  3B. Approaches 3B. Approaches used to lead discovery 1. Irrational Approach A. Serendipity (luck) B. Screening C. Chemical Modification 2. Rational Approach A. Structure Biology (X-Ray Crystallography & NMR) B. Bioinformatics C. Computational Chemistry D. Genomics and Proteomics E. Metabolomics F. System Biology Pharmacist Alert 3 lead compound 3B1. Irrational app 3B1.1. Serendipity (luck) 3B1.1. Serendipity The drugs of chance (Serendipity) NH2 HN NH2 O NH2 NH N Isoniazid Phenelzine (Nardil) Tranylcypromine (Pamate) 1912, first synthesized 'MAO Inhibitor' 'MAO inhibitor' 1945, antituberculosis 1975, the first antidepressant drug- led to the discovery of Monoamine Oxidase Inhibitors (MAO inhibitors) MAO (Monoamine oxidase): An enzyme that deaminates monoamines (norepinephrine, serotonin, dopamine) and functions in the nervous system. Do not use MAO inhibitors with cheese, wine, beer, or yeast (Cheese effect)  3 lead compound R H 3B1. Irrational app H S 3B1.1. Serendipity (luck) N CH3 N O Cl N H N CH3 O N COOH O R = PhOCH2 Penicillin V R = CH2Ph Penicillin G Antibiotic discovered by contamination from a mold Librium (Chlorodiazepoxide) Penicillin Tranquilizer Found in lab clean up in Roche CH3 N O CH3 N O HN N N Cl O S O S N Chlorpromazine Viagra (Sildenafil) Antihistamine N Designed as antihypertensive neuroleptic and anti-pychotic Male erectile dysfunction  3 lead compound 3B1.2. Screening 3B1. Irrational app 3B1.2. Screening (i) Random Screening (ii) Non-Random Screening (i) Random Screening: Compounds are tested in the bioassay without regard to their structures Natural products and synthetic chemicals (microbial, plant, marine) Example: Discovery of antibiotics from soil samples (1940- 1950) (streptomycin and tetracyclines) Use of Natural World Resources for finding lead compound. Random Screening Pathway Lead compounds from the natural world 3B1 Irrational app 3B1.2. Screening Plant extracts: 3B1.2.i. Random HO OPIUM – Morphine O H Led to opioid analgesics NCH3 POPPY CAPSULE HO CINCHONA BARK – Quinine H2C H Led to quinone antimalarials HO N H YEW TREE – Taxol H3CO O O O OH CH3 Led to anticancer agents N H3C H3C CH3 O NH O H CH3 O O OH O O WILLOW TREE - SALICYLIC ACID OH CH3 O O O OH O OH Acetic anhydride O CH3 OH O Aspirin  3B1. Irrational app 3B1.2. Screening Micro-organisms 3B1.2.i. Random screening Fungi and bacteria OH O OH O O OH R O H H H NH2 N H S CH3 R C N H H S O OH N Me H O CH3 N OAc ClHO NMe2 CO2H O CO2H Penicillin Tetracyclines Cephalosporins NH HN HN C NH2 H2N C NHH H OH H H HO HO H H OH O2N O H H O CH2OH CHO HN H Me H C OH O CHCl2 H O HO O CH2OH H MeHN Chloramphenicol H H OH H Streptomycin  Combinatorial chemistry approach Automated approach to synthesizing mixtures of many different structures in a short time Produce a pool of chemicals which may prove to include a useful lead compound  3B1 Irrational app 3B1.2. Screening 3B1.2ii. Non-Random Screening 3B1.2.ii. Non-Random Compounds, which have some structure resemblance to weakly active compounds are tested in the bioassay Or limited by some other knowledge of the disease target Endogenous Compounds NATURAL LIGANDS FOR RECEPTORS OH OH H H N HO N HO Me HO HO Agonist ADRENALINE SALBUTAMOL (β2-adrenergic receptor) Used in asthma  3B1. Irrational app 3B1.2. Screening 3B1.2.ii. Non-Random Venoms and Toxins O C OH O C Teprotide N O O O H C N CH C N CH C N O H O CH2 CH CH3 C N CH C N CH2 CH2 O O H CH2 C O CH3 H2N CH C N CH C N H CH2 NH2 CH2 CH2 CH2 CH2 Venom of the Brazilian viper O NH C OH C O O HN C NH OH NH2 C N CH3 HS Captopril (anti-hypertensive) Developed from snake venom  3B1. Irrational app Inspiration from Endogenous Compounds 3B1.2. Screening 3B1.2.ii. Non-Random Endogenous Compound NH2 NMe2 HO MeHN S Agonist O O N N Similar to 5HT (serotonin) H H Treatment of migraine 5-HYDROXYTRYPTAMINE SUMATRIPTAN headache OH O N HO H N OH H Antagonist Me (β-blocker) HO Used for hypertension ADRENALINE PROPRANOLOL 3B2. The rational approach 3 Lead Compound 3B2. Rational approach makes the Drug Design process more efficient. Can lead to faster optimization Help us to understand and minimize or prevent side effects and toxicity Time & Investment Irrational Rational Lead compounds Targets Lead compounds  3 Lead Compound 3B2. Rational approach Rational Approach: Structure-Based Drug Design Major knowledge about ligand-target interactions that can be used to rationalize drug design: The basis of ligand-target interactions is molecular recognition: the specific attractions between the chemical groups of a biological target and a drug. Design new molecules that optimally interact with the target and block or trigger a specific biological activity of the target Based on our knowledge of ligand-target interactions Based on our knowledge, Design of compounds that satisfy specific requirements obtained from 1. Target-based drug design (3D structure of biological target) 2. Pharmacophore-based drug design (Structures of characterized active small molecules)  3 Lead Compound 3B2. Rational approach 1. Target-based (Receptor-based) drug design 1. Examine 3D structure of the biological target Preferably the structure with bound small molecule ligand Identify and characterize the binding pocket – shape, charges, hydrophobic surfaces, groups with the hydrogen bond-forming ability 2. Using computational chemistry, model structures of the small molecule bound to the active site of the target (molecular docking) 3. Examine the docking structures for chemical groups on the target that could contribute favorably to its interaction with the compound Electrostatic interactions Hydrogen bonds Hydrophobic complementarity Geometrical fit of the surfaces 4. Design a drug candidate that will have multiple sites of favorable interactions with the biological target Lead de novo design Receptor  CH3 + H3N Scaffold O Scaffold Scaffold Scaffold IONIC Scaffold HO H-BOND BOND - CO2 VDW BOND  3 Lead Compound 3B2. Rational approach Methods for Target structural determinations X-ray Crystallography: Requires to crystalize target. (Atomic level structural information). No size limitation. No dynamic information. No information for mwt and charges can be found. Nuclear Magnetic Resonance (NMR): Spectroscopy: Solution phase, dynamic but limited to the size of 35kDa. Certain nuclei of atoms within the molecule, such as 1H, 13C, 15N, 19F, and 31P, will resonate as they absorb energy at specific frequencies that are characteristic of their electronic environment.  3 Lead Compound 3B2. Rational approach Pharmacophore-based drug design (Structures of characterized active small molecules) Defines the important groups involved in binding & activity Defines the relative positions of the binding groups – 2D : minimum skeleton connecting groups – 3D : relative positions in space Need to determine the active conformation How does one determine the pharmacophore? By conducting Structure-Activity Relationship studies  3 Lead Compound Pharmacist Alert 3B2. Rational approach Example: Cimetidine (Tagamet) 1964; SKF search for H2 antagonists Histamine is a natural HN substrate for H2 receptors (H2Rs) N Histamine NH2 HN CH3 HN Known pharmacophore in H3C Histamine N NH2 N NH2 2-Methylhistamine 4-Methylhistamine Histamine binding to H2R (H1 receptor agonist) (H2 receptor agonist) Induces release of HN CH3 N C stomach acid H N S CH3 Need H2R antagonist to N N N H Cimetidine (Tagamet) treat heartburn first marketed in UK in 1976; the first H2 antagonist James W. Black (Glaxo, SmithKline, & French Laboratories), Nobel Prize in 1988. Receptor based drug designing.  3 Lead Compound Pharmacist Alert 3B2. Rational approach Example: Ranitidine Systematically modified known natural substrate Histamine Lead compound - Na-guanyl-histamine Screening of modified lead compounds – identified Metiamide Na-guanyl- Modification of a thiol group eliminated toxicity -histamine – Cimetidine Approved for therapeutic applications ✗ Toxicity Metiamide Ranitidine (Zantac) Cimetidine  Summary for Rational Drug Design Stages: 1) Identify the target disease 2) Identify drug target 3) Establish testing procedures 4) Find a lead compound 5) Structure-Activity Relationships (SAR) 6) Identify a pharmacophore 7) Drug design- optimizing target interactions 8) Drug design - optimizing pharmacokinetic properties 9) Toxicological and safety tests 10) Chemical development and production 11) Patenting and regulatory affairs 12) Clinical trials  Key facts to remember! Sequence (Both in Rational/irrational Design). In vitro versus in vivo assay; High throughput screening Sources of Lead Compounds with their example (plant extracts and snake venom) Random screening versus non-random screening Technique for structure determinations in Rational Drug Design (NMR and X-ray) Example of Ranitidine (endogenous origin: Histamine) Concept of pharmacophore-based drug design. Steps in Medicinal Chemistry Discovery (finding lead compounds) Optimization – Structure-Activity-Relationships – Pharmacophore identification – Functional modification To improve potency, selectivity, safety, transport, bioavailability,… Development (Chemical formulation for suitable clinical use  Drug Optimization Structure-Activity-Relationships The synthesis of many analogs as possible of the lead and their testing to determine the effect of structure on activity and toxicity. Development of the sulfonamide antibacterial agents that also had diuretic and antidiabetic activities. Compounds with each type of activity were shown to possess certain structural features in common. Chemical Modification Pathway (Functional Group Modification) O H2N SO2NH C NHCH2CH2CH2CH3 Carbotumide (Antibacterial) Had antidiabetic activity. Could not be used as an antidiabetic drug because of its antibacterial activity, which could lead to bacterial resistance. O H3C SO2NH C NHCH2CH2CH2CH3 Tolbutamide Antidiabetic with no antibacterial activity Functional Group Modification to enhance side effect  Chemical Modification Pathway (Functional Group Modification) N N Cl CH3 NH NH H2NSO2 S Cl S O O O O Chlorothiazide Diazoxide (Aldocor) (Hyperstat) Antihypertensive Antihypertensive drug Has strong diuretic effect without diuretic effect) (Strong urine excretion) Several additional examples in textbook (Patrick, 2009, pp. 201-203)  3B1. Irrational approach 3B1.3. Chemical Modification Chemical Modification Pathway “me too”, a patentable modification of an existing drug on the market Drug Development  Clinical trials Phase I. few months to a year and a half – Evaluates the safety, tolerability (dosage levels and side effects), pharmacokinetic properties, and pharmacological effects in 20- 100 healthy volunteers. Phase II. About 1-3 years – Assesses the effectiveness of the drug, determines side effects and other safety aspects, and clarifies the dosing regimen in a few hundred diseased patients. Phase III. about 2-6 years – Several thousand patients in clinics and hospitals that establishes the efficacy of the drug and monitors adverse reactions from long-term use. Phase IV. Results found with a drug that has already been allowed onto the drug market and is in general use.