Drug Discovery, Design and Development
Dr. Hendra Gunosewoyo
Curtin School of Diagnostic & Therapeutic Sciences
Hendra.Gunosewoyo@curtin.edu.au
IMED3005–Medicinal Chemistry & Clinical Pharmacokinetics
Dr. Paul Murray
Curtin School of Diagnostic & Therapeutic Sciences
P.Murray@curtin.edu.au
Lecture Contents
Introduction
Key Stages of the Drug Discovery and Development Process – COVID-19 Example
Identification of Lead Compound
Compounds Screening
Lead Optimisation Strategies
Tools for the trade
Drug-like physiochemical properties
Structure-property relationship (SPR)
Structure-activity relationship (SAR)
Extension, contraction, rigidification
Isosteres/bioisosteres, prodrugs
Introduction
Drug discovery, design, and development is the process by which novel drugs are identified, formulated, and biologically tested before use in human patients.
This process represents a multi-stage, complex, lengthy, costly, and risky endeavor, involving modern cutting-edge research and technology across a wide range of scientific disciplines.
Do We Know What to Target?
Target Validation: Crucial to determine if the target is druggable and if there is proof-of-concept that targeting it can reduce the clinical symptoms of a disease.
Key Stages of the Drug Discovery Process
Preclinical Stage
PRECLINICAL STAGE involves in vitro and in vivo testing procedures, divided into several sub-stages:
Target Discovery: Identification of the biological component involved in the disease that the proposed drug targets/counteracts.
Target Validation: Demonstrating that engaging with the target counters the disease or provides relief (proof-of-concept).
Assay Development: Developing analytical, in vitro, and in vivo processes/models for compound testing.
Drug Screening: Finding lead compounds that could become starting points for the development of new drugs.
Lead Optimisation: Adjusting/modifying original lead compounds into potential drug candidates.
Preclinical Drug Development: Developing a drug manufacturing process at kilogram scales and obtaining suitable drug formulations.
Clinical Stage
CLINICAL STAGE involves testing/evaluation of drug candidates in human subjects for efficacy and safety, divided into several sub-stages:
Phase I Trials: Testing in healthy human subjects to gather key biological, safety, and dosing data (maximum tolerated dose - MTD).
Phase II Trials: Pilot studies in a small number of diseased human subjects to establish efficacy and safety profile.
Phase III Trials: Large-scale studies in diseased human subjects to establish the overall risk-benefit relationship.
Phase IV Trials: Post-marketing medical studies to monitor patient health/outcomes and long-term safety profile.
Medicinal Chemistry
Defined as the branch of chemistry focusing on the design, synthesis, and development of new medicines.
The majority of medicines are small organic molecules (vs. inorganic molecules and macromolecules like proteins).
There exists a close interplay between organic chemistry, pharmacology, and biochemistry.
Structure-Activity Relationship (SAR): Examines how chemical structures affect biological activity.
Structure-Property Relationship (SPR): Investigates how drug-like physicochemical properties change with structural variation.
Key factors in SAR and SPR include:
Drug ionisation
Drug stereochemistry
Drug solubility
Drug lipophilicity
Drug absorption, distribution, metabolism, elimination (ADME) properties
Drug-target interactions
Revise Lipinski’s Rule of 5 for predicting drug bioavailability.
General Structure of Viruses
Viruses can be DNA or RNA viruses.
RNA viruses may be single-stranded or double-stranded.
If the RNA strand's sequence is identical to viral mRNA: it's termed positive strand (e.g., Zika virus).
If the RNA strand's sequence is complementary: it's termed negative strand (e.g., flu virus).
Antiviral Drugs for RNA Viruses – Influenza
Life Cycle of Influenza Virus
Viral RNA polymerase catalyzes production of (+)-RNA, utilized by the host's ribosome to produce viral capsid proteins.
The (+)-RNA can revert to (-)-form through viral RNA polymerase, which is incorporated spontaneously into new capsids.
Key Proteins in Influenza Virus
Haemagglutinin (HA): A viral glycoprotein crucial for adsorption by binding to cellular glycoconjugates containing sialic acid.
Spike-like objects at 10 nm from the virus surface.
Neuraminidase (NA): A viral glycoprotein that serves as an enzyme, catalyzing the cleavage of terminal sugar molecules from glycoproteins and glycolipids, important for release post-budding.
Variations in HA and NA lead to different virus nomenclature (e.g., H1N1, H5N8).
Antiviral Drug Development
Remdesivir
Utilizes a prodrug approach for antiviral activity against viruses, specifically with a focus on efficacy and metabolic pathways.
The Practice of Medicinal Chemistry
Natural Sources:
Early medicines derived from alkaloids, such as morphine and ephedrine.
Notable sources include:
Penicillium notatum (penicillin)
Coffea arabica (caffeine)
Digitalis purpurea (digoxin)
Papaver somniferum (morphine and codeine)
Isolation Examples:
Procedure for isolation of ephedrine from ma huang, while noting safety concerns about carcinogenic solvents used historically. Refer to mind map in lecture
Semisynthetic Drugs:
Chemicals derived from natural products that undergo additional modifications (e.g., acetylsalicylic acid - aspirin).
Hydrolysis and oxidation of salicin lead to salicylic acid, which reacts with acetic anhydride to form the acetate esters used in drugs.
Identification of Drug Structures
Early efforts included the elucidation of bioactive molecule structures using methods such as chromatography and spectroscopy.
Advances in techniques (NMR, mass spectrometry) allow for structural determination of bioactive molecules.
Drug Targets
Drugs interact with specific macromolecular targets found in:
Receptors: Often found on cell membranes (e.g., GPCRs).
Enzymes: Act intracellularly.
Transporters: Facilitate extracellular and intracellular movement.
Nucleic acids: Within the nucleus.
Drug-Target Interactions
Binding results in conformational changes leading to biological activity.
Review intermolecular forces (IMF): ionic, covalent, ion-dipole, hydrogen bond, van der Waals forces.
Lead Compound Identification
Lead compounds are bioactive compounds resulting from screening processes showing desired pharmacological properties, and may not originally have high bioactivity.
Can include natural, synthetic, and semi-synthetic compounds, often selected from a set of 'Hit' compounds generated during preliminary screening processes.
Sources for Lead Compounds
Natural Sources: Traditional route for drugs (plant, microbial, animal-derived), though often lengthy and expensive.
Synthetic Chemistry: Produces libraries of small-molecule organic compounds through large-scale screenings.
Rational Drug Design (SBDD): This involves structure-based design using known structures and computational approaches to create compound libraries for screening.
A lead compound with a novel structure is referred to as a New Chemical Entity (NCE).
Drug Screening
High Throughput Screening (HTS)
Represents a key technique in preclinical drug discovery where rapid bioactivity assessments are conducted for numerous compounds against targets.
Typically involves:
In vitro assays, which are less costly and more straightforward, preceded by in vivo screenings after successful in vitro tests.
Phenotypic vs. Target-Based Screening
Phenotypic Screening: Does not require prior knowledge of the target; generally faster and can evaluate multiple targets.
Target-Based Screening: Involves known structures; tends to be slower, with a focus on minimizing off-target effects and ensuring reproducibility.
Combinatorial Chemistry & Parallel Synthesis
Enables preparation of compound libraries for HTS through simultaneous synthesis of large compound libraries using distinct chemical building blocks, usually automated for efficiency.
Solid-phase peptide synthesis (SPPS): Method for protein synthesis, allowing rapid creation and screening of vast libraries.
Lead Optimisation
A non-linear process involving chemical refinement of a lead compound into a viable drug for clinical use.
SAR (Structure-Activity Relationship): Evaluation of chemical modifications on biological activity.
SPR (Structure-Property Relationship): Evaluations of how changes alter physicochemical properties.
Requires alterations to optimize pharmacokinetic properties (ADME-Tox) through addition, removal, or modification of functional groups.
Drug-like Properties
Good properties ensure:
Adequate absorption
Proper distribution
Low metabolism rates
Reasonable elimination
Low toxicity
A set of rules exists for structure-based property profiling.
Structure-Activity Relationship (SAR)
Goals:
Identify functional groups important for binding affinity and/or activity.
Workflow includes altering or masking functional groups and subsequent testing for binding/properties:
In vitro binding assay: Tests binding interactions with the target.
In vitro functional assay: Measures endpoint reactions like calcium flux, antimicrobial action.
In vivo studies: Assess proof-of-concept, formulation efficacy, and bioavailability.
Modifications and Importance
Easiest modifications: "me-too" analogues (small variations).
Allows identification of critical groups associated with binding and may unveil the pharmacophore, defined as the ensemble of steric/electronic features required for optimal ligand binding.
SAR & Pharmacophore Illustration
Use examples, e.g., morphine and its derivatives, to indicate important groups for analgesic activity.
Emphasis on establishing the minimum structural skeleton connecting essential binding groups to effectively achieve desired responses.
Lead Optimization Strategies
Enhance binding interactions through strategies like varying substituents (alkyl, aryl), adding functional groups, chain modification, ring manipulation, isosteres, simplification, and rigidification.
Modifying Alkyl and Aryl Substituents
Adjusting alkyl groups can improve binding by interacting with hydrophobic sites and enhancing selectivity.
Changes in aryl substituents may affect binding strength and interactions based on relative positioning of additional groups.
Functional Group Enhancements
Extension: Adding functional groups can improve binding via exploring new sites.
Chain Adjustments: Increasing/decreasing lengths can optimize interactions between binding groups.
Ring Modifications: Transformations for better fit and interaction with binding regions, sometimes for intellectual property considerations.
Isosteres/Bioisosteres
Isosterism: Replacement of a group with similar properties; useful for design alterations that control steric/electronic characteristics.
Bioisosterism: Replacement with structurally similar groups maintaining biological functionality; serves to modulate properties of agents without altering therapeutic profiles significantly.
Simplification Process
Rationale behind simplification:
Reduce complexity for easier synthesis.
Enhance activity and selectivity by removing unneeded functional groups while retaining the pharmacophore.
Rigidification
Striving to solidify flexible lead compounds to enhance activity and selectivity while minimizing unwanted side effects from diverse conformations.
Conclusion: Drug Discovery for Tuberculosis
A combined approach integrating phenotypic and target-based strategies creates a comprehensive drug discovery pipeline addressing tuberculosis while employing SAR, SPR, high throughput screening (HTS) methodologies, and proof-of-concept (PoC) verifications.
References: Include relevant articles from ACS Central Science 2020, Trends in Pharmacological Sciences 2020, and Nature Chemistry.