Target based Approaches and Phenotypic screening

Define medicinal chemistry

generation of small, druglike molecules with clinical activity through application of synthetic organic chemistry

what are drug-target interactions?

key interactions which promote association between ligand under development and the target protein

outline the current drug discovery pipeline (compounds → clinical trial and spending)

fewer and fewer molecules making it to clinical trials but spending on drugs increasing

high throughput screening

large chemical libraries tested for their ability to modify a chosen target for a particular disease

role of chemists/pharmacologists/biochemists in drug development

discover and optimise (modify) the drugs

role of pharmacists in drug development

formulate and deliver drugs

target identification

first step of target based approaches eg HIV protease inhibition halts viral replication

target selection - big Pharma POV

new drug must have something to offer clinically and have potential to be highly profitable

target selection - regulator POV

new drug improvements on existing ‘gold standard’ drugs must be substantial

How are enzymes targeted

reversible/irreversible inhibitor

How are nucleic acids targeted by drugs?

intercalator (binder), modifier (alkylating agent) or substrate mimic

What molecular techniques are used to validate drug targets?

siRNA based protein rundown, adenoviral/lentiviral delivery, genetic deletion (knockout) and CRISPR

How does adenoviral/lentiviral delivery work?

transfection/infection of cells with genetic material that encodes for modified target

How are knockout models used to validate drug targets?

to check for fatal effects or if knockout redundant

what does optimisation need to account for?

potent, selective activity against target and achieving activity at desired conc

how are pharmacokinetics assessed?

absorption, distribution, metabolism, excretion and toxicology

considerations to take for injection route

aqueous/depot? Stability?

considerations to take for tablet route

water solubility, release site, pH

considerations for cream route

lipophilicity

considerations for aerosol route

lipophilicity and stability

what considerations need to be taken surrounding drug absorption?

barriers being crossed and stability at absorption site

considerations for drug in the tissue

plasma protein binding, electrostatic charge, tissue protein binding and volume of distribution

What about the site of action needs to be considered?

appropriate conc at site of action reached to elicit desired clinical effect

natural products

purified molecules sourced from plants, sponges, bacteria and fungi eg anti-cancer drug taxol derived from willow bark

chemical libraries

databases of compound chemical structure, purity, quantity and physiochemical characteristics

scaffold hopping

drug discovery strategy developing new entities by modifying the core structure of a known active compound

How do drugs interact with proteins?

drug functional groups interact with the different amino acids in protein targets

What amino acids form van der Waals with drugs

non polar aliphatic (glycine, alanine, valine, leucine, methionine and isoleucine) and aromatic (phenylalanine, tyrosine and tryptophan)

What amino acids form hydrogen bonds with drugs?

polar, uncharged (serine, threonine, cysteine, proline, aspartate and glutamine)

what amino acids form ionic bonds with drugs?

positively charged (lysine, histidine and asparagine) and negatively charged (glutamate and aspartate)

COX function

oxidation and cyclisation of arachidonic acid for prostaglandin synthesis

interactions between COX active site amino acids and arachidonic acid

mixture of hydrogen bonds and van der Waals

flurbiprofen

competitive COX inhibitor

how does flurbiprofen outcompete arachidonic acid?

forms greater number of interactions with COX

What modifications drive potency and selectivity at the receptor level?

chain modification, ring substitution and carbon modifications

purpose of modifying physiochemical properties for pharmacokinetics

helps facilitate absorption

Why is drug structure modified for pharmacokinetics

to control metabolism and half life

What do structure-property relationship profiles cover?

solubility, membrane permeability, lipophilicity, pKa, stability, metabolite screening, CYP450 inhibition and plasma protein binding

what’s needed for drugs to be absorbed through SI epithelial membranes?

lipophilicity and must be single molecules not aggregates

phenotypic screening

identifies molecules with particular biological effects in cell assays/animal models to track back to target protein

what do simple phenotypic screens measure?

use cell lines to monitor a single parameter eg cell death/protein production

high content screening

changes in expression of several proteins monitored

fragment-based ligand discovery - alternative to high throughput screening

screens library of very small molecular weight compounds (100 to 250 Da) at high concentration through biophysical methods eg NMR and X ray crystallography

FRET

measures efficiency of energy transfer between fluorophores when they’re in close proximity. Therefore intermolecular interaction between chemical and protein can be observed

advantages of FRET

can be used for both in vitro and in vivo assays and has no limit on biomolecular weight

partition coefficient

measurement of molecule to dissolve in membranes - this correlates with its ability to dissolve in organic solvent

how is the partition coefficient determined

by allowing a compound to equilibrate between water and an organic phase, n-octonal