Forces Involved in Drug-biomolecule Target Interactions: Intermolecular Forces Binding Equilibria

Forces Involved in Drug-biomolecule Target Interactions:

Intermolecular Forces

Binding Equilibria

Noncovalent binding equilibria

•Binding: noncovalent, reversible association (and dissociation) between molecules •Drug-target complex is more stable (lower in energy) than if the drug is not complexed to the target biomolecule. •Defined rates (kon and koff) and equilibrium constants (Ka and Kd).

Below, AM is the complex; A is the free, unbound small molecule/drug; M is the free, unbound large biomolecule/receptor.

Association equilibrium:

A+ M AM Keq =[AM][A][M] = Ka in units of (concentration)-1

Dissociation equilibrium:

A+ MAM Keq = [AM][A][M] = Kd in units of (concentration)

d r u g + r e c e p t o rd r u g - r e c e p t o r

[ d r u g - r e c e p t o r ]

[ d r u g ] [ r e c e p t o r ]

Keq

== K

d

kon

koff

Pharmaceutical industry:

In general, stronger binding = larger Ka or smaller Kd

Useful numbers: 1cal = 4.184J; R = 8.314JK-1mol-1 = 1.9872 calK-1mol-1)

G° = -RTlnKeq

Noncovalent binding equilibria

Stabilizing Forces involved in a Drug-Receptor Complex

•distance-dependent. •possible when molecular surfaces are complementary.•include (covalent), electrostatic, and hydrophobic interactions.

Covalent bonding•40-150 kcal/mole. Strongest. •Irreversible: requires a chemical reaction between the receptor and the drug•rare for drug-receptor complexes.

S

Drug-Target Adduct(Covalent association)

+ HBrBr

HSBr HS

DrugTarget

+

Drug-Target Complex(noncovalent association)

reversiblebinding

chemicalreaction

Stabilizing Forces

Covalent bonding- exampleExample: Anticancer agent 5-fluoro-2'-deoxyuridylate •forms an irreversible complex with thymidilyate synthase•prevents DNA from being biosynthesized•limits the uncontrolled cell division of cancer cells.

Target

DrugCoenzyme

TernaryCovalentadduct

Drug-TargetCovalent adduct

Electrotstatic interactions (ion-ion; ion-dipole; dipole-dipole including H-bonding; charge transfer; London dispersion forces)

Ion-ion •5-10kcal/mole for opposite charges•Ionic compounds have a permanent (full) charge. •Noncovalent (reversible)•Effective over longer distances than other noncovalent interactions.

Stabilizing Forces

O

H3C OCH2CH2NCH3

CH3

CH3

Drug

O

H3C OCH2CH2NCH3

CH3

CH3O

O

ion-ion

Magnitude can be estimated by coulomb’s law (E q1q2/r))

ion-dipole, dipole-dipole •1-7 kcal/mole •C-Y bonds are polar when Y = an electronegative atom such as O, N, S, halogens •A polar bond leads to partial positive and partial negative charges along the dipole. (Smaller stabilization than full charges)•Relative orientation with respect to the dipole will affect amount of stabilization

Stabilizing ForcesElectrotstatic interactions, continued

O

H3C OCH2CH2NCH3

CH3

CH3

Drug

O

H3C OCH2CH2NCH3

CH3

CH3

NH3δ-

δ+OH

δ+

δ-

HOδ-

δ+

ion-dipole

dipole -dipole

Electrotstatic interactions, continued

Stabilizing Forces

Hydrogen bond •3-5 kcal/mole •Special kind of dipole-dipole interaction. •H must be covalently bonded to electronegative atoms N, O, or F•H can interact strongly with lone pairs of heteroatoms.•Optimal geometry - use VSEPR to estimate location of lone pair

F H NH

HH

δ- δ-δ+δ+ N H O

Cδ-

δ+ δ-

δ+

N H O Cδ-δ-δ+

δ+

Cation-pi interactions •1-3kcal/mole •electron-rich face of aromatic groups plus cationic/electron-poor groups

Stabilizing Forces


electron-richface of aromatics

electron-deficientspecies

Representation of the cation-pi Interaction

δ−δ−

δ+

δ+

+

Note: Pi-pi interactions:

Van der Waals or London Dispersion Forces. •~.5 -1 kcal/mole •Instantaneous dipoles in all molecules stabilize one another. (induced dipole-induced dipole) •Larger complementary surface areas lead to larger London Dispersion Forces.

Induced dipole interactions •Polarization. A charged or polar molecule may induce a dipole in a nonpolar molecule. Very small effects.

Stabilizing Forces


H

NH H

H

polarizednonpolar molecule(induced dipole)

δ- δ+

H

NH H

H

nonpolarmolecule(no dipole )

fa r apart

Stabilizing Forces

Hydrophobic interactions Two nonpolar molecules tend to associate in water, due to an increase in the entropy of water molecules

H

O

H

H

O

H

H

OH

H

OH

H

O

H

H

O

H

HO

H

HO

H

H

O

H

H

O

H

H

O

H

H

O

H

H

O

H

H

O

H

Nonpolar

NonpolarH

O

H

H

OH

H

OH

H

O

H

H

O H

H

O

H

H

OH

Nonpolar

H

O

H

H

OH

H

OH

H

O

H

H

O H

H

O

H

H

O H

Nonpolarversus

O

H2

N

1. pH/pKa and drug-target interactions. The protonation state of a particular functional group will determine its charge, and therefore the nature of intermolecular forces

2. Stereochemistry and drug-target interactions. Different stereoisomers can have different activities. (Not equally complementary to the 3D structure of the target).

Ex 1. R and S isomers of the antimalarial chloroquine have equal potencies:

NC l

N H C H ( C H3

) C H2

C H2

C H2

N ( C2

H5

)2

Additional Structural Considerations

Ex. 2. the 1R, 2S enantiomer of norephedrine (2-amino-3-phenyl-1-propanol) is 100 times more potent than the 1S,2R enantiomer on the alpha adrenoreceptor in vivo and in vitro.

Ex. 3 S-Ketamine is an anaesthetic; R-ketamine has little anaesthetic action but is a psychotic.

O

N H C H3

C l



3. Conformation and drug-target interactions. •Both drug and target molecules may have multiple conformations. •Recall Morphinan from Molecular Conceptor in lecture 1

Drugs can have higher potency if they are "conformationally restricted" to a bioactive conformation.

Bulky substituents or rings are often used for this purpose:

NH N

N H

Histamine

Free rotation

NH N

N H2

NH N

N H2

H3

C

H

H

conformationally restricted histamine analogs

Stabilizing Forces - Summary

Electrostatic interactions Enthalpic (H) effects. Placement of complementary groups on drug and target. Size of charges, distance between interacting groups, orientation. Multiple small effects add up!

Hydrophobic interactions, conformational restriction Entropic (S) effects.

G° = -RTlnKeq

G° = H° - TS°

A + M AM

Reaction coordinate

G°

AM

A + M Free energy ofBinding of drug to target

A + M AM Keq = Ka

Hydrophobicity (lipophilicity) and drug action.

Hansch and coworkers hypothesized two steps for a drug to work:Pharmacokinetics (drug getting to the site of action) Pharmacodynamics (interaction of drug with the site).

Pharmacokinetics phase depends on interaction with aqueous AND membrane environments.

The ability to interact with nopolar membrane environments can be correlated with a water-octanol partition coefficient P.

P =

[compound]oct

[compound]aq

(1- )

= alpha degree of dissociation in water

Note optimum partition coefficient: •if a compound is too hydrophobic, it will remain in the first membrane it contacts; •if it is too hydrophilic, it will never cross cell membranes to get to its site of action.

Hydrophobicity (lipophilicity) and drug action.

NH

O

CH2CH2CH2CH2CH2CO2N

Cl

CH3

CH2

CH2CHO2

NH3C

H3C

CH2

Predict Possible binding interactions with targets


NH

O

CH2CH2CH2CH2CH2CO2N

Cl

CH3

CH2

CH2CHO2

NH3C

H3C

CH2

effect


N

N

HN OH

H3CO

H3CO

Compound 2

N

N

HN SCH3

H3CO

H3CO

Compound 3

Protein kinase inhibitors: bind in pocket where ATP binds


N

N

HN OH

H3CO

H3CO

Compound 2

Authors note:N1 H-bond with leu 83 amide NHArOH H-bond with Asp 145+Lys 33**ArOH edge to face with Phe80ArOH hydrophobic pocket Bound to CDK2


N

N

HN SCH3

H3CO

H3CO

Compound 3

Bound to p38

Authors note:N1 H-bond with met109 amide NHN3 H-bond with water that H-bonds with

Thr106 (no room in CDK2with Phe80ArSCH3 in pocketQuinazoline in hydrophobic pocket


Nonpeptide inhibitors of serine protease cathespin G (associated with inflammation) identified by high-throughput screening of a diverse library of compounds.

PO O

OHHO

Compound 1

Predict Possible binding interactions with targetsAuthors note:

Pi stacking of 2-naphthyl with his 57P-OH H-bonded to His 57P-OH H bonded to amide NH of gly 193 =

“oxyanion hole” of serine proteasesP-OH H bonded to NH3 of lys 192Ketone H-bonded to lys 192

PO O

OHHO

Compound 1

IC50 = 4 M

Crystal structure showed hydrophobic residues: phe 172, tyr 215, Ile 99. Can “fill” this hydrophobic pocket: New inhibitor designed…IC50 = .053 M for R =

PO O

OHHON OH3C

RNO

Ph

Drug Targets - an Overview

LipidsCarbohydratesProteins

Carrier proteinsEnzymesReceptors

Nucleic Acids

•Few drugs interact with lipids•They often act by disrupting lipid structure of cell membranes.

Ex 1. General anaesthetics. Ex 2. Amphotericin B (used to treat athletes foot) binds to fungal cell membranes, creating channels and killing fungus. Preferentially binds to ergosterol (in fungal membranes) over cholesterol (in mammalian membranes).

Drug Targets: Lipids

Drug Targets: Lipids

Drug Targets: Carbohydrates

•energy sources•structural elements in the cell•involved in specific binding interactions between receptors and ligands.

Ex 2. Doxorubicin (anticancer agent) linked to a carrier with a specific carbohydrate is more efficient at killing colon cancer cells than doxorubicin administered alone.

Ex 1. Influenza virus binds to its host by a cell surface sugar and sialic acid residue - a drug that binds more strongly than the natural binding site will block the viral attachment.

Drug Targets: Proteins - Carrier proteins/transporters

Ex. Fluoxetine (prozac) works by binding to the transporter for the neurotransmitter serotonin, preventing its uptake into the cell.

NO

C H3

H

F3

C

Fluoxetine

Drug Targets: Proteins - Enzymes

•Enzymes are a major target for drugs. •Enzyme targets of microorganisms, viruses used to fight infection•The body's own enzymes can be targets (if there is an excess or deficiency of a metabolite). •A drug may act by binding

strongly but reversibly to the active site (competetive inhibitor), reversibly to a different site (allosteric inhibitor), irreversibly to the active site.

•The affinity of inhibitors is determined by enzyme kinetics. Review any biochemistry text for details of this analysis.


Ex. 1 Adenosine deaminase metabolizes adenosine and degrades many antiviral and cancer therapy treatments. Inhibitors will help make those drugs more effective. A drug that resembles the transition state of the catalyzed reaction should bind very strongly to the enzyme active site, improving the effectiveness of other therapies.

N

N N

N

NH2

RIbose

Adenosine

Km = 31 M

Adenosinedeaminase HN

N N

N

H2N

RIbose

OH

Tetrahedralintermediateresembles

HN

N N

N

RIbose

Inosine

HN

N N

N

H

RIbose

CH2OH

N

N

RIbose

HN

N

OH

Transition state mimics

Ki<1M =0.002Ki nM

O

Drugs:

Reaction:

Drug Targets: Proteins - EnzymesEx 2. Tetrahydrofolic acid is necessary for the synthesis of nucleic acids. Bacteria must synthesize it to survive (humans ingest it).

NH2

H2N NN SO2NH2

ProntosilProdrug

H2N SO2NH2

SulfanilamideActive form of drug

MetabolismH2N CO2H

p-aminobenzoic acid

N

N

N

HNH2N

OH

O P

O

O

O P

O

O

O

H2N CO2

dihydropteroate synthase

N

N

N

HNH2N

OH HN CO2

Tetrahydrofolic acid

The drug Prontosil was found to be bacteriostatic. Prontosil is a prodrug, because it is metabolized to form the actual active agent p-aminobenzene sulphonamide (sulfanilamide). It resembles the structure of the substrate p-aminobenzoic acid (above), so it will bind to the active site of the enzyme dihydropteroate synthase.


Ex. 3: antihypercholesterolemic drugs. Cholesterol: major component of fatty plaque deposits on inner wall of arteries, and ~50% is synthesized in the body. Hypercholesterolemia is a primary risk factor for coronary heart disease. Therapeutic goal: decrease the amount of cholesterol synthesized in the body. The rate-determining step is the following, catalyzed by HMG-CoA reductase:

HMG-CoA

Drug Targets - Proteins - Enzymes

Hydrolysis productMimics HMG-CoA

R=CH3: mevinolinlovastatin

R=H: compactin; KI = 1.4x10-9M

HMG-CoA: Km = 10-5M

KI = 6.4x10-10M

O

CO2H

SCoA

HOH3C

Drug Targets: Proteins - Receptors

Major target for drugsReceptors are used by cells for communication•In nerve cells, electric impulses are "communicated" to cells through a chemical message (neurotransmitter) that is received by a protein receptor embedded in the cell membrane. Binding of this neurotransmitter results in a biological response•Other chemical messages are hormones that are circulated through the body. They also bind to specific receptors, triggering a biological response.

Two main mechanisms to transmit the message from the outside of the cell (hormone or neurotransmitter messenger) to the inside of the cell (second messenger):

• ion channels • membrane-bound enzymes.

Drugs may be agonists or antagonists that control the activity of receptors

•Agonists act like natural messengers. To design a drug agonist, the starting point is the natural ligand. •Antagonists block the receptors from the natural messenger. To design a drug antagonist, the structure is not generally similar to the natural ligand. Ideally, the structure of the receptor would be a good starting point. If unknown, use information about any antagonists or even agonists as a starting point.

Ex.: cimetidine (Molecular conceptor , lecture 1) is a histamine receptor antagonist

Drug Targets: Proteins - Receptors

Drug Targets: Nucleic Acids

Drugs that interact with DNA are usually very toxic because human DNA and pathogen DNA are very similar. For cancer treatment, the only difference between cancer cells and normal cells is the rapid cell division. Therefore, drugs that halt mitosis (DNA synthesis) should preferentially halt the mitosis of cancer cells. Ideally, a drug would be able to bind to specific sequences.


Three main classes of drugs that interact with DNA:1. DNA intercalators. Bind reversibly between the base pairs. Disrupt DNA structure and prevent normal functions of DNA.

2. DNA alkylators. Form covalent bonds (irreversible) with DNA. Nucleophile = N, O, S atoms in DNA that aren't sterically hindered or involved in H-bonding. Electrophile = alkylating agent.


3. DNA strand breakers. Many complex reaction mechanisms are being uncovered, but when these drugs bind to DNA, the result is strand breakage.

ClN

Cl

CH3

Alkylating agentCrosslinking agentTreatment in advancedHodgkin's disease

DNA Interstrand crosslink. Anchimeric assistance

Diversity of Targets; Diversity of Rationales

This was an overview of main targets of drug action. Each general target could take weeks of classtime to discuss!

For your presentations/papers, you may have to research pertinent details of the target or drug action…

References:Anslyn, E. V.; Dougherty, D. A. Modern Physical Organic Chemistry; University Science Books: Sausalito, CA, 2004.Thomas, G. Medicinal Chemistry An Introduction; John Wiley & Sons: New York, NY, 2000.Patrick, G. L. An Introduction to Medicinal Chemistry; Oxford University Press: New York, 2001.Silverman, R. B. The Organic Chemistry of Durg Design and Drug Action; Academic Press: New York, 1992.Shewchuk, L; Hasssell, A.; Wisely, B.; Rocque, W.; Holmes, W.; Veal, J; Kuyper; L. F. J. Med. Chem. 2000, 43, 133-138.

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Forces Involved in Drug-biomolecule Target Interactions: Intermolecular Forces Binding Equilibria