6: medicinal chemistry

describe the most common method in the drug discovery process

identify a ‘small’ molecule to interact with a biological target

small = relative to target molecule = large discrete collection of atoms

what are the 2 main biological targets for drug action

proteins:

• enzymes

• cell-surface receptors

describe proteins

polymers of amino acids joined by peptide/amide bonds = polypeptides

3D structure = governs biological function

describe enzymes

= proteins that catalyse chemical reactions

what effect does inhibition of enzyme 2 have on enzymatic pathway?

inhibition of enzyme 2:

• build up of compound B

• decrease in compounds C and D (downstream)

applications:

• treat disease caused by build-up of compound C/D

• treat disease caused by deficiency of compound B

• kill cell that depend on compound C/D

describe a treatment of atherosclerosis

= build up of cholesterol from diet or biosynthesis in the liver

• control diet

• inhibit biosynthesis:

lovastatin = competitive reversible inhibitor of HMG-CoA-reductase = upstream enzyme of cholesterol biosynthesis

describe cell surface receptors

= proteins that transmit signals in response to ligands

describe the types of drugs that can interact with cell surface receptors

• agonists

= mimic the function of natural substrate and activate pathway

• antagonists

= bocks the binding site for the natural substrate and deactivates pathways

agonists are more difficult to generate than antagonists

describe methods to find lead compounds (=small molecules)

1. modification of known structures

2. systematic screening

3. rational design

describe modification of known structures

• natural products

• existing pharmaceuticals:

pros:

• well known properties

• good profits

cons:

• legal and ethical concerns

describe systematic screening

testing “libraries” of molecules against ≥1 biological targets

high-throughput screening (HTS) techniques = >10,000 tests/day

cons:

• obtaining structural diversity = libraries have varying side chains but often same functional groups

• ensuring ‘drug-like’ properties = screening compounds which could be incorporated into a drug

describe the combinatorial approach to systematic screening

systematically generating compound libraries by combining sets of building blocks (i.e. functional groups) in all possible combinations

describe Lipinski's rules (rule of 5/Pfizer rules)

describe oral bioavailability (not activity)

• H bond donors ≤ 5

• H bond acceptors ≤ 10

• logP: -5 → 5

• MW ≤ 500

define H bond donors vs acceptors

donors = H bonded to electronegative atom (O/N)

acceptors = electronegative atom with lone pair/s (O/N)

an atom can be both H bond acceptor/donor = always singly accepting/donating

describe rational design

design of new substrate for biological targets (often enzyme)

pros:

• synthesis of fewer compounds

• increased potency and specificity

cons:

• requires knowledge of 3D structure of target site

describe IC(50) value

= concentration of a compound that inhibits the activity of its target by 50%

= want a minimal IC(50)

measure of potency (not action)

describe pharmacodynamics

= study of interactions of a compound with its target

measure of action

what model is used to model enzyme kinetics?

Michaelis-Menten kinetics

describe Michaelis-Menten kinetics

equilibrium exists between enzyme + substrate and intermediate compex

describe the steady state approximation

the concentration of ES is fixed when reaction is ongoing

rate of formation of ES = rate of breakdown of ES

what is the rate equation in Michealis-Menten kinetics?

what is Michaelis-Menten plot

y = V

x = [S]

how can Km be found from Michealis-Menten plot?

describe the Lineweaver-Burk plot

rearranging the reciprocal Michaelis-Menten equation

y = 1/V

x = 1/[S]

what are the 2 types of enzyme inhibition

• reversible inhibition

= non-covalently bind target

• irreversible inhibition

= covalently bind target

describe types of reversible inhibition

• competitive

= bind to the same active site as the natural substrate

• non-competitive

= bind to a different (allosteric) site to the natural substrate

describe the effect of increasing [S] on competitive and non-competitive inhibitors

competitive = reverses inhibition

non-competitive = no effect

describe the effect of competitive inhibitors on MIchaelis-Menten kinetics

equilibrium between E + I and enzyme-inhibitor complex

describe the effect of competitive inhibitors on the Lineweaver-Burk plot

• V’max = Vmax: y intercept is the same

• Km is changed: x intercept is different

(V’max = max rate in presence of inhibitor)

competitive inhibition can be overwhelmed by increasing [S] = Vmax unaffected

describe the effect of non-competitive inhibitors on MIchaelis-Menten kinetics

formation of equilibrium between enzyme-inhibitor complex and enzyme-inhibitor-substrate complex

describe the effect of non-competitive inhibitors on the Lineweaver-Burk plot

• V’max is changed: y intercept is different

• Km = Km: x intercept is the same

(V’max = max rate in presence of inhibitor)

non-competitive inhibition changes the shape of the active site = no effect in increasing [S] = Vmax affected

describe irreversible inhibition

‘suicide inhibitors’

= forms covalent bond

= permanently deactivates target

= often electrophilic reacting with nucleophilic residues in target

= often highly toxic = requires selectivity

why can IC(50) not be used to describe irreversible inhibition

equilibrium of non-covalent interaction often precedes covalent deactivation

irreversible inhibition is time dependent since depends on the rate of covalent deactivation = different potencies are observed over time

define a protease

an enzyme that cleaves peptide bonds and degrades proteins

describe X proteases

X = residues in protease active site

i.e. serine protease

= serine residue in active site

describe inhibition of serine protease trypsin

• trypsin active site binds amine residues and cleaves bond

• inhibitor = amide residue that will not dissociate from active site

• affinity-labelled inhibitor = amide residue with additional function groups participating in secondary interactions that will not dissociate from active site

describe pharmacodynamics vs pharmacokinetics

pharmacodynamics = study of interactions of a compound with its target

pharmacokinetics = study of fate of compound in vivo

what is used to study pharmacokinetics?

‘ADME’/’LADMET’ profile

• liberation

• absorption

• distribution

• metabolism

• excretion

• toxicity

describe liberation

release of drug from the form in which they are delivered

= dependent on route of administration

define exipients

= inactive compounds of a drug formulation used to:

• improve absorption

• improve stability

• serve as carriers

define polymorphs

different crystalline forms of the same substance which may have different physiological properties

describe absorption and distribution

• orally administered = absorption into bloodstream occurs in the small intestine

• travels in bloodstream to target tissue

• must cross two cellular membranes:

outer = hydrophilic

inner = hydrophobic

• compound must have a balance of hydrophobic and hydrophilic properties

what is used to access hydrophobic and hydrophilic properties

partition constant, P

describe the partition constant, P

compound is dissolved in equal mixture of octanol and water

octanol = non-polar

water = polar

high P = non-polar

low P = polar

describe logP

high logP = very non-polar = > +6

low logP = very polar = < -6

describe metabolism and excretion

metabolism: broken down (usually to more polar components)

• begins in digestive tract; majorly in the liver

• first step typically protonation

• metabolism too fast = not effective

• metabolism too slow = remain in the system longer than desired

generally two stages:

1. Phase I = biotransformation

2. Phase II = conjugate formation

excretion: components excreted by kidneys/large intestine

metabolism should be minimised

describe phase I biotransformation

many different processes:

• oxidation: most common - installation of polar functional groups

• hydrolysis

• reduction

describe cytochrome P450

= family of enzymes in the liver

= catalyse oxidation of many functional groups in phase I biotransformation

describe phase II conjugate formation

attachment of ionised group to increase water solubility and ease of excretion

i.e.

• addition of sulfate group (SO3-)

• addition of glutathione conjugates:

SNAR or nucleophilic substitution

how can metabolism by prevented/pharmocokinetics improved?

• bioisosteres

• prodrugs

describe bioisosteres

structurally distinct compounds that are recognised similarly by biological systems

= less susceptible to metabolism i.e. oxidation, hydrolysis, reduction, (phase I) conjugate formation (phase II)

= chosen depending on which property is key for function

describe carboxylic acid bioisosteres

physiological pH = deprotonated = too polar

• hydroxamic acid = metal chelation

• tetrazole = lipophilicity

• acylsulfonamide = more H-bond acceptors

draw hydroxamic acid

draw tetrazole

still deprotonated and forms anion but resonance stabilised = lipophilicity

draw acylsulfonamide

what is a bioisostere for an ester

an amide

what is a bioisostere for a hydroxyl group

an amide

what is a bioisostere for a ketone

thiocarbonyl group

describe prodrugs

therapeutic agents that are converted to their active form in vivo

= converted by early metabolism (phase I processes)

= increased bioavailability

define LD(50)

= measure of toxicity

= drug dosing that is lethal in 50% of a population

= want maximum

define ED(50)

= measure of efficacy

= drug dosing that produces maximum therapeutic response in 50% of a population

= want minimum

define therapeutic index

ratio of toxicity to efficacy

= want a large TI

describe the course of clinical trials

phase I: healthy volunteers ~50

= testing safety of drug candidate and establish maximum dosage

phase II: ill patients ~200

= testing efficacy in ill patients

= must include control group who are treated with best available treament

phase III: larger group ~2000

= determine ideal dosage in broad patient population

describe hERG activity

hERG = K+ ion channel = regulating hearts electrical activity

many drugs show ‘hERG activity’ = hERG inhibition

hERG activity must be minimised = monitored in clinical trials

what is an indole

what is a key indole containing molecule?

amino acid tryptophan

describe tryptophan derivatives

functional group conversion of tryptophan:

• tryptamine

• serotonin (5-HT)

• melatonin

describe the tryptophan to serotonin pathway

serotonin = 5-HT

sumatriptan = 5-HIAA

describe the function of 5-HT

= vasoconstriction

describe the role of tryptophan derivatives in migraine attacks

• 5-HT levels decrease = vasodilation

• 5-HIAA levels increase

describe how migraine attacks can be treated

• intravenous 5-HT (increase)

• drugs activating 5-HT cell surface receptors (vasoconstriction)

what are problems associated with direct use of 5-HT

• poor bioavailability

• short plasma half life - rapidly metabolised

• non-selective action: vasoconstriction elsewhere in body

overall describe Fischer indole synthesis

coupling of an aryl hydrazine with a ketone/aldehyde

1. hydrazone formation

2. indole formation

draw a hydrazine

draw a hydrazone

draw hydrazone formation

• nucleophilic attack

• formation of good LG (H2O+)

• deprotonation

draw indole formation

draw the SM required for the retrosynthesis of sumatriptan

describe hypertension

= chronic high blood pressure

= many causes i.e. ACE

describe a bodily response to high blood pressure

= release of bradykanin

= peptide

= vasodilator

describe angiotensin-converting enzyme (ACE)

two forms:

ACE I = inactive = deca(10)-peptide

ACE II = active = octa(8)-peptide

three ways ACE II contributes:

• vasoconstrictor = decreases vessel volume

• UP-regulates the production of aldosterone = reduces Na(+) and H2O excretion = increases blood volume

• degrades bradykanin = inhibits vasodilation = decreases vessel volume

ACE inhibition is target for hypertension treatment

what is a challenge for identifying ACE inhibitors?

ACE = membrane bound protein

= structural information is difficult to obtain

what moiety has activity as an ACE inhibitor

L-proline at C terminus (with free COOH)

describe the interactions of these ACE inhibitors at the ACE active site

COOH = COO(-) in vivo = coordinates to Zn2+ ion

Me = fits into hydrophobic pocket

SH = S(-) in vivo = improved coordination to Zn2+ ion

IC(50): captopril « COOH-containg compound

describe retrosynthesis of captopril

• amide bond formation

= coupling reaction

• thiol group installation

= a,B unsaturated carbonyl (Michael acceptor) = nucleophilic addition of SH(-)

= a,B unsaturated carbonyl from carbonyl with B LG

how can amide bonds be made?

= requires catalysis

• old method = SOCl2

• new method = peptide coupling reagent

draw the mechanism of peptide coupling reagent DCC

draw the full synthesis of captopril

last step = nucleophilic substitution

define bacteriostatic

inhibit cell growth, allowing natural defences time to respond to infection

define bactericidal

actively kill bacterial cells

draw sulfanilamide

= anti-bacterial

draw sulfanilamide prodrug (prontosil)

describe sulfa drugs

= sulfanilamide analogues

= inhibit folic acid biosynthesis in bacteria

describe the action of sulfa drugs

structure ~ PABA

PABA = upstream substrate of folid acid biosynthesis = substrate of dihydropteroate synthase

sulfa drugs are competitive (reversible) inhibitors of dihydropteroate

folic acid = essential for DNA and amino acid biosynthesis

sulfa drugs = bacteriostatic

define a structure-activity relationship (SAR) study

study which seeks to improve pharmacokinetic (body) /pharmacodynamic (function) properties of an active compound by modifying structure

draw the general structure of sulfa drugs

majorly NH2 at para position

describe sulfa synthesis

1. (protected) sufonyl chloride backbone

2. variable amine

3. coupling + deprotection

draw the sulfonyl chloride backbone synthesis

4 steps: benzene SM

1. nitration (NO2)

2. reduction (NH2)

3. acylation (NHAc)

4. sulfonylation (SO2Cl)

draw the coupling and deprotecting mechansim

what are methods of bacterial resistance to sulfa drugs?

• mutated dihydropteroate synthase no longer binds = mutation at active site

• overproduction of PABA = competitive inhibitor

• efflux of drugs