Drug Discovery and Design

• Drugs are compounds that interact with a biological system to produce a biological response.
• The drug development process consists of discovery, design, and development.
• Drug discovery aims to find a lead compound.
• Drug design optimizes pharmacodynamics and pharmacokinetics.
• Pharmacokinetics refers to the movement of drugs within the body (ADME - Absorption, Distribution, Metabolism, Excretion).
• Drug development involves getting the drug into the market.
• Discovery and design phases often overlap.
• A drug, referred to as a molecule/API (Active Pharmaceutical Ingredient) must be patented upon discovery.
• Design entails formulating the drug, including choosing the dosage form.
• The present pharmaceutical industry identifies a suitable target in the body and designs a drug to interact with it.
• Current research is target-oriented.

Steps in Drug Discovery:

• Developing a drug is a costly process.
• Focus on diseases with a need for new drugs.
• Research projects tend to concentrate on common diseases in developed countries.
• Identifying a drug target involves biomacromolecules in a particular disease.

Biomacromolecules:

• Enzymes
• Substrates & metabolites
• Receptors
• Ion channels
• Transport proteins
• DNA/RNA and the ribosomes
• Various physicochemical mechanisms
• Bioassay is a test system that is crucial for the success of a drug research program.

Lead Compound:

• A lead compound exhibits the desired/promising pharmaceutical activity.
• It serves as a starting point for drug design and development, regardless of the initial activity level or undesirable effects.

Sources to Discover Lead Compounds:

• Plant kingdom
• Microbial world
• Marine world
• Animal sources, venoms, and toxins
• Synthetic compound libraries
• Natural ligand or modulator
• Existing drugs
• Combinatorial synthesis
• Computer-Aided Drug Design (CADD)
• Serendipity

Plant Kingdom:

• A rich source of lead compounds.
• Traditional plant concoctions were often useless or dangerous, some have real benefits.
• Clinically useful drugs isolated from plants are anticancer agent paclitaxel (Taxol) from the yew tree, and antimalarial agent artemisinin from the Chinese plant.
• Rhubarb root has been used as a purgative in China for centuries, and anthraquinones are the significant chemical in rhubarb root, used as the lead compound to design laxative dantron.

Microbial World:

• Became popular after the discovery of penicillin.
• Involves collecting soil and water samples to study new fungal or bacterial strains.
• Many antibacterial agents are found from these samples.
• Antibacterial agents include Cephalosporins, Tetracyclines, Aminoglycosides, Rifamycins, and Chloramphenicol.

Marine World:

• Coral, sponges, fishes, and marine microorganisms contain biologically potent chemicals with anti-inflammatory, antiviral, and anticancer activity (FVC).
• The first chemical compound of the cephalosporin group was isolated from Cephalosporium acremonium (a fungus).
• Curacin A, obtained from a marine cyanobacterium, shows potent antitumor activity.

Animal Sources - Venom and Toxins:

• Venoms are potent because they specifically interact with a macromolecular target in the body.
• Teprotide, a peptide isolated from the venom of the Brazilian viper, was the lead compound for captopril and cilazapril, which are antihypertensive agents.
• Antibiotic peptides were extracted from the skin of the African clawed frog, and a potent analgesic called epibatidine was discovered.

Screening Synthetic Compound Libraries:

• Compounds synthesized by pharmaceutical companies can be lead compounds.
• Pharmaceutical companies purchase novel compounds from other companies to diversify their libraries.
• Synthetic intermediates are also tested.
• Drugs found through synthetic intermediate tests include Isoniazid (antitubercular agent) and Quinoline-3-carboxamide (antiviral agent).

Existing Drugs:

"Me Too" Drugs:

• Companies use established drugs from competitors as lead compounds.
• The aim is to design a drug that gains a foothold in the same market area.
• Captopril was used as a lead compound by various companies to produce their own antihypertensive agents.

Enhancing a Side Effect:

• An existing drug may have an undesirable side effect, but this side effect might be useful in another area.
• The aim is to enhance the desired side effect and eliminate the major biological activity.

Starting from the Natural Ligand or Modulator:

Natural Ligands for Receptors:

• Used as the lead compound for the target receptor.
• Adrenaline and noradrenaline started the development of adrenergic β-agonists like salbutamol, dobutamine, and xamoterol.
• Histamine was used as the original lead compound in the development of its antagonist, cimetidine.

Natural Substrates for Enzymes:

• Used as a lead compound in designing enzyme inhibitors.
• Enkephalins lead the design of enkephalin inhibitors; Enkephalinases metabolize enkephalins & their inhibition prolongs the activity of enkephalins.

Enzyme Products as Lead Compounds:

• Enzymes catalyze reactions in both directions.
• The product of an enzyme-catalyzed reaction can be used as a lead compound for inhibition.
• L-benzylsuccinic acid was designed by analyzing the products formed when carboxypeptidase breaks down peptides.

Natural Modulators as Lead Compounds:

• Some receptors and enzymes have allosteric sites separate from their active sites.
• The body's chemicals that bind to these sites (modulators) help regulate activity.
• These natural modulators can inspire the design of lead compounds for new drugs.
• Benzodiazepines (synthetic drugs) work by binding to an allosteric site on the GABA receptor, enhancing its effect.

Combinatorial Synthesis:

• An automated solid-phase procedure aims to produce as many different structures as possible in a short time.
• Reactions are carried out on a very small scale to produce mixtures of compounds.

Computer-Aided Drug Design (CADD):

Techniques and Functions:

• X-ray Crystallography: Used to determine the 3D structure of a protein and its binding site when the crystal of a protein is obtained.
• Nuclear Magnetic Resonance (NMR): Used to determine the structure of proteins that cannot be crystallized, providing insight into their binding site.

Recent Advancements in NMR:

• NMR is used strategically to design drugs.
• Researchers use NMR to identify small molecules (epitopes) binding to specific regions of a protein's binding site
• Once binding sites are identified research design a larger molecule that connects each epitope together.
• This aims for the new molecule to bind to the entire binding site more effectively
• De Novo Design: Using molecular modeling software to analyze the binding site and design new molecules that fit and bind effectively.
• Docking: A computational process of fitting a drug molecule into the target protein's structure to predict binding affinity.
• Pharmacophore Modeling: Identifying essential structural features for a molecule to interact with a target, based on structure or ligand.
• 3D Quantitative Structure-Activity Relationship (3D-QSAR): A ligand-based approach correlating a molecule's 3D structure with its biological activity.
• Database Mining: A computerized search of structural databases to find new lead compounds using docking, pharmacophore modeling or 3D-QSAR techniques.

Serendipity:

• Lead compounds are frequently found accidentally.
• Vincristine and vinblastine were discovered by chance when searching for compounds that could lower blood sugar levels.
• Vincristine is used in the treatment of Hodgkin's (a type of lymphoma).

Example of Drug Discovery:

• Choose a Disease: Dengue fever (understand its life cycle).
• Choose a Drug Target: Dengue virus (target system), Dengue virus protease (target molecule – understand activity).
• Identify a Bioassay: Start with in-vitro.
• Find a Lead Compound
• Optimization of the Lead Compound: Use an instrument to measure the parameter to optimize.

In Vitro Screening for Potential Leads:

• Choosing the right bioassay is crucial for successful drug research.
• The test should be simple, quick, and relevant for multiple tests in a timely manner.

In Vitro vs. In Vivo Tests:

• In Vitro:"Within the glass" - Refers to performing a procedure in a controlled environment outside of a living organism, which is preferred.
• In Vivo: "Within the living" - Refers to experimentation using a whole, living organism, as opposed to a partial or dead organism, is less preferred.

Advantages of In Vitro over In Vivo:

• Cheaper, easier to set up and run, yields results more quickly readily permits replication and good quantification, can be automated.
• Functions of In Vitro Tests: Screens for pharmacological activity.
• Enzyme inhibitors can be tested on the pure enzyme in solution.
• HIV protease has been cloned and produced in E. coli, where it can be studied thus, experiments can test the activity of HIV enzyme inhibitors, and measure their IC50 values.
• Antagonists and agonists of a real receptor can be tested on isolated tissue, where the tissue expresses the receptor of interest.
• Affinity of drugs for receptors can be measured by radioligand studies.
• Antagonist: binds to the receptor and blocks the receptor's physiological effect.
• Agonist: binds to the receptor and activates it.
• Antibacterial drugs, for example are tested by measuring how effectively they inhibit or kill bacterial cells in culture.

Screens for Toxicological Activity:

• Potential hepatotoxic, nephrotoxic, and neurotoxic effects of compounds can be readily investigated in a simple in vitro method.
• A key priority in these tests is teratogenicity (the potential to cause fetal defects).
• In vitro models (assays) in assessing teratogenic effects are whole embryo cultures from rats, mice, chicks, fish, and frog.
• Such assays help reduce the expense, duration, and number of animals used.

Limitations of In Vitro Methods:

• Limitation 1: Target in vitro may be artefactual.
• Explanation: The binding site in the assays may be created, and is not the one normally functional in-vivo.
• Limitation 2: Compound biokinetics are different when compared to in-vivo.
• Explanation: Biotransformation through absorption, distribution, and excretion in vivo may occur on its way to target organ.
• Limitation 3: In vitro drug activity and its solubility.
• Explanation: Drug may undergo biotransformation through absorption, distribution and excretion in-vivo on its way to target organ. Polar lead compound in vitro may need to undergo lipophilic modification for oral dosing in vivo studies.
• Limitation 4: Drug concentration relevance
• Explanation: Some antidepressants inhibit Na+K+ATPase at millimolar concentrations (mM) in vitro, but their actual clinical effects occur at micromolar concentrations (µM) in vivo by affecting monoamine uptake.

In Vivo:

• In Vivo Test – Usage of Transgenic Animals:
• It is possible to replace some mouse genes with human genes, which allows in-vivo testing.
• A transgenic animal is an animal whose genomes have been altered by transferring a gene or genes from another species or breed using recombinant DNA technology.
• Limitations of in vivo Testing: It is slow, and it comes at the suffering of the animal, results may be misleading due to problems of pharmacokinetics, certain in-vivo tests may be invalid.
• The observed symptoms may be caused by a different physiological mechanism. (For example: some antiulcer drugs work on animals but not on humans).

In Vivo Testing Remains Essential:

• It helps for detecting specific issues related to drug use in living organisms that cannot be identified through in vitro tests.

Methods of Drug Classification:

• (4 main ways)
• by pharmacological effect.
• by chemical structure.
• by target system.
• by target molecule.
• Using the pharmacological effect, is useful for knowing the full scope of drugs available for certain ailment.
• The drugs are highly varied in structure because many targets produce the desired effect.
• It is impossible to compare different painkillers and expect chemicals to look alike.
• By chemical structure, the group of drugs have common skeleton
• For example, Penicillins, Cephalosporins, Barbiturates, Opiates Steroids, Catecholamines.
• Not all compounds with similar structures have similar biological actions.
• By their effect on the target system in the body: for example, respiratory, cardiovascular, cholinergic and adrenergic systems.
• This classification is more specific, even though drugs may differ in structure when targeting the same system, as they interact with different target molecules.
• When classified by Target Molecule. An Example: anticholinesterase may be effective in treating both Alzheimer and Glaucoma.

Nomenclature of drugs:

• The code name is commonly used in R&D, and generally includes a letter and number combination.
• Letters represents an abbreviation of the research lab name and numbers assigned by the firm in an arbitrary manner.
• Chemical names mostly follow IUPAC, names are quite long, however, it is only useful for chemist, and cumbersome, not used in prescription.
• There are also International Non-proprietary name (INN)@generic name which is Globally recognised and publicly known.
• The commercial/trade name ("TM" or ®) and granted by a naming authority and used in promoting a drug in a particular juridiction

General Principles When Selecting an INN:

• Easy to pronounce & easy to spell.
• Short
• Should show relationship to similar drugs if applicable,
• No conflicts with existing names or trademarks
• Avoid names that imply medical conditions (e.g., cancer- or psycho-)
• INNs are for active ingredients;; salts/esters are modified (e.g., oxacillin vs. oxacillin sodium).

Spelling Rules for Better Transliteration:

• Avoid "h" and "k."
• Use "f" instead of "ph."
• Use "t" instead of "th."
• Use "e" instead of "ae" or "oe."
• Use "i" instead of "y."

Antihypertensive Groups:

• Antihypertensive groups end in -lol (atenolol, bisoprolol, propranolol), -sartan (irbesartan, candesartan, telmisartan), -pril (enalapril, captopril, ramipril).

Antibiotics:

• Antibiotics have cef- beginnings (cefaclor, cefprozil, cefixime), -mycin (azithromycin, clarithromycin, dirithromycin), or -cilin endings (ampicillin, amoxicillin, methicillin).

Radioactive Compound:

• Needs what substance contains the radioactive atom, isotope number, and the element symbol listed.