Some building blocks for Rational Drug

Design…

GENERAL SCREENING OF DRUGS Earlier methods of drug discovery…

• ‘Trial-and-error’ testing of chemical substances (potential drugs) on animals or cultured cells

• Observing the ‘apparent effects’.

General or random screening is the arbitrary screening of large sample collections (chemical entities or potential drugs) without any scientific rationale, to identify potential therapeutic uses in a ‘hit-or-miss’ strategy.

General screening has become more expensive and time consuming because of the vast collection of samples.

SERENDIPITY It is ‘the accidental observation of beneficial

unintended effects of a drug entity’. Is an important source of drug discovery (unintentional

strategy); Is used to produce new drugs; Examples:

Discovery of Penicillin by Alexander Fleming. Amantidine (antiviral drug) was observed to cure some

symptoms of Parkinson’s disease. Sildenafil citrate (for erectile dysfunction) and Minoxidil

(prevention of hair loss) – these 2 drugs were actually tested for CV applications and failed in those tests.

Hallucinogenic effects of LSD (Lysergic acid diethylamide) was accidentally discovered by Albert Hoffman. He was actually testing LSD to treat migraines and bleeding after childbirth.

RATIONAL DRUG DESIGN Rational drug design begins with a knowledge of

specific chemical responses in the human body (body’s response to the potential drug) or target organism, in order to ultimately create a treatment profile.

As the knowledge of drugs’ molecular chemistry increased, general drug screening was replaced by ‘Targeted screening’ which was more focussed.

Targeted screening partially leverages the concept of rational drug design. It involves an understanding of…• SARs of various classes of compounds• Mechanism(s) of interaction of the compounds with

potential target sites.

STEPS INVOLVED IN RATIONAL DRUG DESIGN1) Designing the candidate compounds2) Studying their 3D structures to determine how they

interact with a specific target (cells, receptors, biological pathways etc….)

3) Testing of the design (testing step 2)

Rational Drug Design is a process used in the biopharmaceutical industry to discover and develop new drug compounds.

RDD uses a variety of computational methods to..• identify novel compounds;• design safe and efficacious compounds;• develop compounds into clinical trial candidates;

TYPES OF COMPUTATIONAL METHODS Structure-based drug design Ligand-based drug design De Novo design and homology modelling

• The type of the drug and the drug target determines the method to be followed.

• Drug Target: is a key molecule involved in a particular metabolic or signaling pathway (that is specific to a disease condition or pathology; infectivity and survival of a pathogen).

A conventional approach is to stop a pathway (in the diseased state) by causing a key molecule to stop functioning.

Drug molecules are designed to bind to the active site of the key molecule and inhibit it.

The drug molecules should be designed in such a way so as not to affect other important molecules which are structurally similar to the key molecule.

Another approach is to enhance the normal pathway by promoting specific molecules in the normal pathway (that may have been affected in the diseased state).

STRUCTURE-BASED DRUG DESIGN (SBDD) SBDD has increased in importance because it enhances

drug specificity. Even small molecules have significant ‘specific

information’ within them. Egs.: LTs, steroids, catecholamines, nucleosides, excitatory AAs, ACh etc..

The high degree of selectivity aids in drug design.

COMPUTER-ASSISTED DRUG DESIGN (CADD) CADD uses computational chemistry to discover,

enhance or study drugs and related biologically active molecules.

Methods used: simple molecular modelling, molecular mechanics, molecular dynamics, semi-empirical quantum chemistry methods and density functional theory.

The 3D structure of protein targets is most often derived from X-ray crystallography or NMR techniques.

These methods can resolve the structure of proteins to a resolution of a few angstroms (about 500,000 times smaller than the diameter of the human hair).

This ability to work at such high resolution makes CADD one of the most powerful methods in drug designing.

Examples of structure-based CADD….• HIV-1 PIs, HIV entry inhibitors• Thymidylate synthetase inhibitors• M1selective muscarinic agonists• Purine nucleoside phosphorylase inhibitors• Cimetidine (H2RA)• Dorzolamide (carbonic anhydrase inhibitor used to

treat glaucoma)• Many of the atypical antipsychotics• Selective COX-2 inhibitors• SSRIs• Probenecid• Zolpidem (non-BZs)

LEAD OPTIMIZATION IN CADD

Lead optimization is the process of refining the 3D structures of the lead compounds.

Researchers systematically modify the structure of the lead compound and test how well each modification binds to the target site.

In drug design, the purpose of exchanging one bioisostere for another is to enhance the desired biological or physical properties of a compound without making significant changes to the chemical structure.

DRUG DEVELOPMENT THROUGH GPCRs GPCRs are the largest and most important family of

drug targets. More than 50% of drugs currently in market are based

on GPCRs. GPCRs have broad range of mechanisms by which they

transduce information through various channels. GPCRs are initially activated through binding of

peptides, neurotransmitters, hormones, amino acids, amines, nucleotides, nucleosides, PGs etc…

GPCRs then activate the G proteins. The above step is very significant in many disorders

(CV, neurological, metabolic and cancers). Identification of the roles of GPCRs is still ongoing.

FOR YOUR INFO …

Isosteres: 2 molecular fragments containing identical numbered arrangement of electrons, and thus, possess similar properties.

Isosteric modification: Is the replacement of an atom or group of atoms in a molecule, by another group with similar electronic and steric configurations.

Ligand: ions or neutral molecules that bond to a central metal atom or ion.

Bioisosteric replacement:• A common method of lead optimization;• Specific functional groups in a ligand are replaced

/substituted by other groups to improve the binding characteristics of the ligand.

STEREOISOMERS The pharmacological activity of stereoisomers is a well-

documented fact. The highly active enantiomer takes part in a minimum

of 3 intermolecular interactions with the receptor. The less active enantiomer can interact with a

maximum of 2 sites only. The interaction between a drug and a receptor is

associated with bonding interactions between the sites on the drug and complementary sites on the receptor.

The 3D spatial arrangement of such sites on the drug is very significant.

Egs. of stereoisomers: + and – adrenaline + and – ephedrine and pseudoephedrine + and – dopa

ENZYME INHIBITORS Are molecules that bind to an enzyme and inhibits it’s

action. Inhibition of a carefully selected target enzyme(s) in a

biological pathway would lead to overall production of a complex/compound that is crucial in the disease state.

Egs.:• Allopurinol inhibits xanthine oxidase, thereby reducing the

production of uric acid from Xanthine. (xanthine oxidase aids in the conversion of xanthine to uric acid).

• Bacteria produce β-lactamase enzyme for protection purposes. Clavulanic acid (being an inhibitor of this enzyme) is co-administered with Penicillin G in order to preserve the antibacterial action of the latter. (β-lactamase inactivates most penicillins).

• L-dopa is readily metabolized by peripheral DDC. So, it is administered along with Carbidopa (a DDC inhibitor) in order to reduce it’s (L-dopa) metabolism.

Sequential chemotherapy involves the use of 2 inhibitors simultaneously on a ‘metabolic chain’ (sequence in a metabolic pathway) with the aim of achieving a greater therapeutic effect than by the usage of either drug alone.• The best known combination is Cotrimoxazole

(Trimethoprim + Sulfamethoxazole). Sulfamethoxazole is a dihyropteroate synthetase inhibitor and Trimethoprim is a DHFR inhibitor.

GENOMICS Is the analysis of the function and structure of genomes

by employing various techniques (recombinant DNA, DNA sequencing methods and bioinformatics).

The recent advances in genomics and genomic techniques have changed the direction of drug discovery.

The anticipated benefits of genomics:• Improved diagnoses of disease(s)• Earlier detection of a person’s genetic predisposition to

disease(s)• Rational drug design• Gene therapy• Personalized and customized drugs

Bioinformatics is a scientific discipline that encompasses all aspects of biology, computer science and mathematical models.

GENOMIC TECHNOLOGIES

PROTEOMICS The study of protein expression and function. The aim is to profile the proteins from a cellular or

tissue source. Comparative studies are done (protein expression in

healthy and diseased states). 2D polyacrylamide gel electrophoresis and mass

spectroscopy are widely used to study protein expression.

Proteomics gained more importance because of …• the belief that gene-based studies alone are inadequate

for drug discovery;• the observation that disease processes and treatments

are manifested at the protein level.

Applications of proteomics Provides a protein profile of a cell or tissue that can be

used comparatively (healthy vs diseased state); The protein differences discovered are used for the

development of new drugs or drug targets; Identification of diagnostic markers for certain disease

states. • Eg.: Identification of the biomarker psoriasin from the

urine of patients with squamous cell carcinoma of the urinary bladder. This protein is normally not found in the cells of the urinary tract in healthy individuals.

Transcriptomics Involves large scale analysis of mRNAs in order to

better understand when, where and under what conditions genes are expressed.

Structural genomics Generating 3D structures of one or more proteins from

each protein family to understand the biological targets for drug design.

‘Knock out’ studies An experimental method to understand the function of

DNA sequences and the proteins they encode. Researchers inactivate genes in living organisms and

monitor any changes that could reveal the function of those genes.

Comparative genomics Comparative analysis of the DNA sequence patterns of

humans and well-defined model organisms (animals). Powerful tool in identifying human genes and

interpreting their function.

Microarray Is a ‘multiplex lab on a chip’ Collection of microscopic DNA spots attached to a solid

surface It is a 2D array on a solid substrate (glass slide or

silicon thin-film cell) that assays large amounts of biological materials.

FOR YOUR INFO …

• Stereoisomers: Two molecules are described as stereoisomers of each other if they are made of the same atoms, connected in the same sequence, but the atoms are positioned differently in space. The difference between two stereoisomers can only be seen when the three dimensional arrangement of the molecules is considered. E.g., ‘Cis’ and ‘trans’ forms.

• Enantiomers: Pair of molecules that are mirror images of each other. E.g., amphetamine and dextroamphetamine

• Genome: The genetic material of an organism, encoded either in DNA or, for many types of viruses, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA.

• Proteome: The entire protein complement expressed by a genome or cell or tissue.

THANK YOU