why & wherefore drug targets

70
Forest Research Institut The Why & Wherefore: Drug Targets Nhut Diep Senior Medicinal Research Scientist

Transcript of why & wherefore drug targets

Page 1: why & wherefore drug targets

Forest Research Institute

The Why & Wherefore:Drug Targets

Nhut DiepSenior Medicinal Research Scientist

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1. Cell Structure2. Cell Membrane3. Drug Targets 4. Intermolecular Bonding Forces

a. Electrostatic or ionic bondb. Hydrogen bonds c. Van der Waals interactionsd. Dipole-dipole/Ion-dipole/Induced dipole interactions

5. Desolvation penalties6. Hydrophobic interactions7. Drug Targets - Cell Membrane Lipids 8. Drug Targets – Carbohydrates

PROTEINS AS DRUG TARGETS:PROTEINS AS DRUG TARGETS:RECEPTORSRECEPTORS

THE WHY & THE WHEREFORE:THE WHY & THE WHEREFORE:DRUG TARGETSDRUG TARGETS

ContentsContents

1. Structure and function of receptors 6. Competitive (reversible) antagonistsa. Chemical Messengers 7. Non competitive (irreversible) antagonistsb. Mechanism 8. Non competitive (reversible) allosteric antagonists

3. The binding site 9. Antagonists by umbrella effect4. Messenger binding 10. Agonists

a. Introductionb. Bonding forces

5. Overall process of receptor/messenger interaction6. Signal transduction

a. Control of ion channels b. Activation of signal proteins

c. Activation of enzyme active site

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PROTEINS AS DRUG TARGETS:PROTEINS AS DRUG TARGETS:EnzymesEnzymes

1. Structure and function of enzymes2. The active site3. Substrate binding

a. Induced fitb. Bonding forces

4. Catalysis mechanismsa. Acid/base catalysisb. Nucleophilic residues

5. Overall process of enzyme catalysis6. Competive (reversible) inhibitors7. Non competitive (irreversible) inhibitors 8. Non competitive (reversible) allosteric inhibitors

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DRUG TARGETSDRUG TARGETS

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1. Cell Structure1. Cell Structure

Human, animal and plant cells are eukaryotic cellsHuman, animal and plant cells are eukaryotic cells

The nucleus contains the genetic blueprint for life (DNA)The nucleus contains the genetic blueprint for life (DNA)

The fluid contents of the cell are known as the cytoplasmThe fluid contents of the cell are known as the cytoplasm

Structures within the cell are known as organellesStructures within the cell are known as organelles

Mitochondria are the source of energy productionMitochondria are the source of energy production

Ribosomes are the cell’s protein ‘factories’Ribosomes are the cell’s protein ‘factories’

Rough endoplasmic reticulum is the location for protein Rough endoplasmic reticulum is the location for protein synthesissynthesis

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PhospholipidBilayer

ExteriorHigh [Na+]

InteriorHigh [K+]

2. Cell Membrane2. Cell Membrane

Proteins

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PolarHeadGroup

Hydrophobic Tails

2. Cell Membrane2. Cell Membrane

PolarHeadGroup

Hydrophobic Tails

CHCH2 CH2

O O

O

P OO

O

CH2CH2NMe3

O O

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PolarHeadGroup

Hydrophobic Tails

C HC H 2 C H 2

O O

O

P OO

O

C H 2 C H 2 N M e 3

O O

2. Cell Membrane2. Cell Membrane

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2. Cell Membrane2. Cell Membrane

The cell membrane is made up of a phospholipid bilayerThe cell membrane is made up of a phospholipid bilayer

The hydrophobic tails interact with each other by van der Waals The hydrophobic tails interact with each other by van der Waals interactions and are hidden from the aqueous mediainteractions and are hidden from the aqueous media

The polar head groups interact with water at the inner and outer The polar head groups interact with water at the inner and outer surfaces of the membranesurfaces of the membrane

The cell membrane provides a hydrophobic barrier around the The cell membrane provides a hydrophobic barrier around the cell, preventing the passage of water and polar moleculescell, preventing the passage of water and polar molecules

Proteins are present, floating in the cell membraneProteins are present, floating in the cell membrane

Some act as ion channels and carrier proteinsSome act as ion channels and carrier proteins

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LipidsLipidsCell membrane lipidsCell membrane lipids

ProteinsProteins ReceptorsReceptorsEnzymesEnzymesCarrier proteinsCarrier proteinsStructural proteins (tubulin)Structural proteins (tubulin)

Nucleic acidsNucleic acids

DNADNARNARNA

CarbohydratesCarbohydratesCell surface carbohydratesCell surface carbohydratesAntigens and recognition moleculesAntigens and recognition molecules

3. Drug targets3. Drug targets

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3. Drug targets3. Drug targets

Drug targets are large molecules - macromoleculesDrug targets are large molecules - macromolecules

Drugs are generally much smaller than their targetsDrugs are generally much smaller than their targets

Drugs interact with their targets by binding to binding sitesDrugs interact with their targets by binding to binding sites

Binding sites are typically hydrophobic pockets on the surface of Binding sites are typically hydrophobic pockets on the surface of macromoleculesmacromolecules

Binding interactions typically involve intermolecular bondsBinding interactions typically involve intermolecular bonds

Most drugs are in equilibrium between being bound and Most drugs are in equilibrium between being bound and unbound to their targetunbound to their target

Functional groups on the drug are involved in binding Functional groups on the drug are involved in binding interactions and are called binding groupsinteractions and are called binding groups

Specific regions within the binding site that are involved in Specific regions within the binding site that are involved in binding interactions are called binding regionsbinding interactions are called binding regions

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Macromolecular target

Drug

Unbound drug

Macromolecular target

Drug

Bound drug

Bindingsite

Drug

Binding site

Binding regions

Binding groups

Intermolecular bonds

3. Drug targets3. Drug targets

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3. Drug targets3. Drug targets

Binding interactions usually result in an induced fit where the Binding interactions usually result in an induced fit where the

binding site changes shape to accommodate the drugbinding site changes shape to accommodate the drug

The induced fit may also alter the overall shape of the drug targetThe induced fit may also alter the overall shape of the drug target

Important to the pharmacological effect of the drugImportant to the pharmacological effect of the drug

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4. 4. Intermolecular bonding forcesIntermolecular bonding forces

4.1 Electrostatic or ionic bond4.1 Electrostatic or ionic bond• Strongest of the intermolecular bonds (20-40 kJ molStrongest of the intermolecular bonds (20-40 kJ mol-1-1))• Takes place between groups of opposite chargeTakes place between groups of opposite charge• The strength of the ionic interaction is inversely proportional to The strength of the ionic interaction is inversely proportional to

the distance between the two charged groupsthe distance between the two charged groups• Stronger interactions occur in hydrophobic environmentsStronger interactions occur in hydrophobic environments• The strength of interaction drops off less rapidly with distance The strength of interaction drops off less rapidly with distance

than with other forms of intermolecular interactionsthan with other forms of intermolecular interactions• Ionic bonds are the most important initial interactions as a drug Ionic bonds are the most important initial interactions as a drug

enters the binding siteenters the binding site

DrugO

O H3N TargetDrug NH3

TargetO

O

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4. Intermolecular bonding forces4. Intermolecular bonding forces

4.2 Hydrogen bonds4.2 Hydrogen bonds

X HDrug

Y TargetDrug X

TargetHY++

- ---

HBD HBA HBA HBD

• Vary in strengthVary in strength• Weaker than electrostatic interactions but stronger than van Weaker than electrostatic interactions but stronger than van

der Waals interactionsder Waals interactions• A hydrogen bond takes place between an electron deficient A hydrogen bond takes place between an electron deficient

hydrogen and an electron rich heteroatom (N or O) hydrogen and an electron rich heteroatom (N or O) • The electron deficient hydrogen is usually attached to a The electron deficient hydrogen is usually attached to a

heteroatom (O or N)heteroatom (O or N)• The electron deficient hydrogen is called a hydrogen bond The electron deficient hydrogen is called a hydrogen bond

donordonor• The electron rich heteroatom is called a hydrogen bond The electron rich heteroatom is called a hydrogen bond

acceptoracceptor

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4. Intermolecular bonding forces4. Intermolecular bonding forces

4.2 Hydrogen bonds4.2 Hydrogen bonds

YX H YX H

Hybridisedorbital

Hybridisedorbital

1sorbital

HBAHBAHBDHBD

• The interaction involves orbitals and is directionalThe interaction involves orbitals and is directional

• Optimum orientation is where the X-H bond points directly Optimum orientation is where the X-H bond points directly

to the lone pair on Y such that the angle between X, H and Y to the lone pair on Y such that the angle between X, H and Y

is 180is 180oo

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4. Intermolecular bonding forces4. Intermolecular bonding forces

4.2 Hydrogen bonds4.2 Hydrogen bonds

• Examples of strong hydrogen bond acceptors Examples of strong hydrogen bond acceptors - carboxylate ion, phosphate ion, tertiary amine - carboxylate ion, phosphate ion, tertiary amine

• Examples of moderate hydrogen bond acceptorsExamples of moderate hydrogen bond acceptors- carboxylic acid, amide oxygen, ketone, ester, ether, alcohol- carboxylic acid, amide oxygen, ketone, ester, ether, alcohol

• Examples of poor hydrogen bond acceptors Examples of poor hydrogen bond acceptors - sulfur, fluorine, chlorine, aromatic ring, amide nitrogen, - sulfur, fluorine, chlorine, aromatic ring, amide nitrogen,

aromatic aminearomatic amine

• Example of good hydrogen bond donorsExample of good hydrogen bond donors- Quaternary ammonium ion- Quaternary ammonium ion

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4. Intermolecular bonding forces4. Intermolecular bonding forces

4.3 Van der Waals interactions4.3 Van der Waals interactions

Binding site

DRUG

- +

• Very weak interactions (2-4 kJmolVery weak interactions (2-4 kJmol-1-1))• Occur between hydrophobic regions of the drug and the targetOccur between hydrophobic regions of the drug and the target• Due to transient areas of high and low electron densities Due to transient areas of high and low electron densities

leading to temporary dipoles leading to temporary dipoles • Interactions drop off rapidly with distanceInteractions drop off rapidly with distance• Drug must be close to the binding region for interactions to Drug must be close to the binding region for interactions to

occuroccur• The overall contribution of van der Waals interactions can be The overall contribution of van der Waals interactions can be

crucial to bindingcrucial to binding

+ -

Hydrophobic regions

Transient dipole on drug+ -

van der Waals interaction

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4. Intermolecular bonding forces4. Intermolecular bonding forces

4.4 Dipole-dipole interactions4.4 Dipole-dipole interactions

• Can occur if the drug and the binding site have dipole Can occur if the drug and the binding site have dipole momentsmoments

• Dipoles align with each other as the drug enters the binding Dipoles align with each other as the drug enters the binding sitesite

• Dipole alignment orientates the molecule in the binding siteDipole alignment orientates the molecule in the binding site• Orientation is beneficial if other binding groups are positioned Orientation is beneficial if other binding groups are positioned

correctly with respect to the corresponding binding regionscorrectly with respect to the corresponding binding regions• Orientation is detrimental if the binding groups are not Orientation is detrimental if the binding groups are not

positioned correctly with respect to corresponding binding positioned correctly with respect to corresponding binding regionsregions

• The strength of the interaction decreases with distance more The strength of the interaction decreases with distance more quickly than with electrostatic interactions, but less quickly quickly than with electrostatic interactions, but less quickly than with van der Waals interactionsthan with van der Waals interactions

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4. Intermolecular bonding forces4. Intermolecular bonding forces

4.4 Ion-dipole interactions4.4 Ion-dipole interactions

• Occur where the charge on one molecule interacts with the Occur where the charge on one molecule interacts with the dipole moment of anotherdipole moment of another

• Stronger than a dipole-dipole interactionStronger than a dipole-dipole interaction

• Strength of interaction falls off less rapidly with distance than Strength of interaction falls off less rapidly with distance than for a dipole-dipole interactionfor a dipole-dipole interaction

C

O

O

Binding siteBinding site

RR

CCRR OO

H3N

Binding siteBinding site

RR

CCRR OO

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4. Intermolecular bonding forces4. Intermolecular bonding forces

4.4 Induced dipole interactions4.4 Induced dipole interactions

• Occur where the charge on one molecule induces a dipole on Occur where the charge on one molecule induces a dipole on anotheranother

• Occurs between a quaternary ammonium ion and an Occurs between a quaternary ammonium ion and an aromatic ringaromatic ring

Binding siteBinding site

RR NN RR33

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RC

R

O

OH

HH H

O

H

H

O

H

H

O

OH

Binding site

Desolvation - Energy penalty Binding - Energy gain

OH

RC

R

O

Binding site

RC

R

O

OH

Binding site

5. Desolvation penalties5. Desolvation penalties

• Polar regions of a drug and its target are solvated prior to Polar regions of a drug and its target are solvated prior to interactioninteraction

• Desolvation is necessary and requires energyDesolvation is necessary and requires energy

• The energy gained by drug-target interactions must be The energy gained by drug-target interactions must be greater than the energy required for desolvationgreater than the energy required for desolvation

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Unstructured waterUnstructured waterIncrease in entropyIncrease in entropy

DrugDrugDRUGDRUG

Structured water layer Structured water layer round hydrophobic regionsround hydrophobic regions

HydrophobicHydrophobic regionsregionsWaterWater

Binding siteBinding site Binding siteBinding site

DrugDrugDRUGDRUG

BindingBinding

6. Hydrophobic interactions6. Hydrophobic interactions

• Hydrophobic regions of a drug and its target are not solvatedHydrophobic regions of a drug and its target are not solvated

• Water molecules interact with each other and form an Water molecules interact with each other and form an ordered layer next to hydrophobic regions - negative entropyordered layer next to hydrophobic regions - negative entropy

• Interactions between the hydrophobic interactions of a drug Interactions between the hydrophobic interactions of a drug and its target ‘free up’ the ordered water molecules and its target ‘free up’ the ordered water molecules

• Results in an increase in entropyResults in an increase in entropy

• Beneficial to binding energyBeneficial to binding energy

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Hydrophobic regionHydrophobic region

Drugs acting on cell membrane lipids - Drugs acting on cell membrane lipids - Anaesthetics and some antibioticsAnaesthetics and some antibiotics

Action of amphotericin B (antifungal agent)Action of amphotericin B (antifungal agent) - builds tunnels through membrane and drains cell- builds tunnels through membrane and drains cell

7. Drug Targets - Cell Membrane Lipids7. Drug Targets - Cell Membrane Lipids

HydrophilicHydrophilicHydrophilicHydrophilic

HydrophilicHydrophilic

OOH

HO

OHHOOC

OH

O

Me

OH

OHMe

OH O OH

Me

O

O

HONH2

HO

Me

H

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Polar tunnel formedPolar tunnel formedEscape route for ionsEscape route for ions

CELLMEMBRANE

TUNNEL

HO

HO

HO

HO

HO

HO

HO

HO2C CO2H

Sugar

OH OH

Sugar

HO

HO

HO

HO

HO

HO

HO

OH

OH

OH

OH

OH

OH

OH

Sugar

OH OH

Sugar

HO2C CO2H

OH

OH

OH

OH

OH

OH

OH

7. Drug Targets - Cell Membrane Lipids7. Drug Targets - Cell Membrane Lipids

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8. Drug Targets - Carbohydrates8. Drug Targets - Carbohydrates

• Carbohydrates play important roles in cell recognition, Carbohydrates play important roles in cell recognition, regulation and growthregulation and growth

• Potential targets for the treatment of bacterial and viral Potential targets for the treatment of bacterial and viral infection, cancer and autoimmune diseaseinfection, cancer and autoimmune disease

• Carbohydrates act as antigensCarbohydrates act as antigens

Carbohydrate 'tag'

CellCellmembranemembrane

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7. Drug Targets - Carbohydrates7. Drug Targets - Carbohydrates

Ceramide 'anchor'Carbohydrate 'tag'

O

OHO

O

OH

HO

OH

(CH2)12CH3

HN (CH2)16CH3

O

Ceramide unit

SUGARS

Carbohydrates

OH

(CH2)12CH3HO

NH2

Sphingosine

HO (CH2)16CH3

O

Fatty Acid (e.g. Stearic acid)O

OHHO

RO

OH

HO

Carbohydrate (R=various carbohydrate structures)

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PROTEINS AS DRUG TARGETS:PROTEINS AS DRUG TARGETS:RECEPTORSRECEPTORS

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1. Structure and function of receptors1. Structure and function of receptors

• Globular proteins acting as a cell’s ‘letter boxes’Globular proteins acting as a cell’s ‘letter boxes’

• Located mostly in the cell membraneLocated mostly in the cell membrane

• Receive messages from chemical messengers coming from Receive messages from chemical messengers coming from other cellsother cells

• Transmit a message into the cell leading to a cellular effectTransmit a message into the cell leading to a cellular effect

• Different receptors specific for different chemical messengersDifferent receptors specific for different chemical messengers

• Each cell has a range of receptors in the cell membrane Each cell has a range of receptors in the cell membrane making it responsive to different chemical messengersmaking it responsive to different chemical messengers

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Cell

Nerve

Messenger

Signal

Receptor

Nerve

NucleusCell

Response

1. Structure and function of receptors1. Structure and function of receptors

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Chemical MessengersChemical Messengers

NeurotransmittersNeurotransmitters: Chemicals released from nerve endings which : Chemicals released from nerve endings which travel across a nerve synapse to bind with receptors on target cells, travel across a nerve synapse to bind with receptors on target cells, such as muscle cells or another nerve. Usually short lived and such as muscle cells or another nerve. Usually short lived and responsible for messages between individual cellsresponsible for messages between individual cells

HormonesHormones: Chemicals released from cells or glands and which : Chemicals released from cells or glands and which travel some distance to bind with receptors on target cells travel some distance to bind with receptors on target cells throughout the bodythroughout the body

• Chemical messengers ‘switch on’ receptors without Chemical messengers ‘switch on’ receptors without undergoing a reaction undergoing a reaction

1. Structure and function of receptors1. Structure and function of receptors

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Nerve 1

Nerve 2Hormone

Bloodsupply

Neurotransmitters

1. Structure and function of receptors1. Structure and function of receptors

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Mechanism Mechanism

• Receptors contain a binding site (hollow or cleft in the Receptors contain a binding site (hollow or cleft in the receptor surface) that is recognised by the chemical receptor surface) that is recognised by the chemical messengermessenger

• Binding of the messenger involves intermolecular bondsBinding of the messenger involves intermolecular bonds

• Binding results in an induced fit of the receptor proteinBinding results in an induced fit of the receptor protein

• Change in receptor shape results in a ‘domino’ effectChange in receptor shape results in a ‘domino’ effect

• Domino effect is known as Signal Transduction, leading to a Domino effect is known as Signal Transduction, leading to a chemical signal being received inside the cell chemical signal being received inside the cell

• Chemical messenger does not enter the cell. It departs the Chemical messenger does not enter the cell. It departs the receptor unchanged and is not permanently boundreceptor unchanged and is not permanently bound

1. Structure and function of receptors1. Structure and function of receptors

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Mechanism Mechanism

CellMembrane

Cell

Receptor

Messenger

message

Induced fit

Cell

Receptor

Messenger

Message

Cell

Messenger

Receptor

1. Structure and function of receptors1. Structure and function of receptors

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ENZYME

2. The binding site2. The binding site

• A hydrophobic hollow or cleft on the receptor surface - A hydrophobic hollow or cleft on the receptor surface - equivalent to the active site of an enzymeequivalent to the active site of an enzyme

• Accepts and binds a chemical messengerAccepts and binds a chemical messenger

• Contains amino acids which bind Contains amino acids which bind the messengerthe messenger

• No reaction or catalysis takes placeNo reaction or catalysis takes place

Binding siteBinding site

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3. Messenger binding3. Messenger binding

• Binding site is nearly the correct shape for the messengerBinding site is nearly the correct shape for the messenger

• Binding alters the shape of the receptor (induced fit)Binding alters the shape of the receptor (induced fit)

• Altered receptor shape leads to further effects - signal Altered receptor shape leads to further effects - signal transductiontransduction

3.1 Introduction3.1 Introduction

MessengerMessenger

Induced fitInduced fit

MM

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• IonicIonic• H-bondingH-bonding• van der Waalsvan der Waals

3.2 Bonding forces3.2 Bonding forces

Example:Example:

Receptor

Binding site

vdwvdwinteractioninteraction

ionicionicbondbond

H-bondH-bond

PheSer

OH

Asp

CO2

3. Messenger binding3. Messenger binding

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3. Substrate binding3. Substrate binding

• Induced fit - Binding site alters shape to maximise Induced fit - Binding site alters shape to maximise intermolecular bondingintermolecular bonding

3.2 Bonding forces3.2 Bonding forces

Intermolecular bonds not optimum length for

maximum binding strength

Intermolecular bond lengths optimised

Phe

SerO

H

Asp

CO2 Induced Fit

Phe

Ser

OH

Asp

CO2

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4. Overall process of receptor/messenger interaction4. Overall process of receptor/messenger interaction

MM

MM

EERR

• Binding interactions must be:Binding interactions must be: - strong enough to hold the messenger sufficiently long for signal - strong enough to hold the messenger sufficiently long for signal

transduction to take placetransduction to take place - weak enough to allow the messenger to depart - weak enough to allow the messenger to depart • Implies a fine balanceImplies a fine balance• Drug design - designing molecules with stronger binding Drug design - designing molecules with stronger binding

interactions results in drugs that block the binding site - interactions results in drugs that block the binding site - antagonistsantagonists

RR

MM

EERR

Signal transductionSignal transduction

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5. Signal transduction5. Signal transduction

5.1 Control of ion channels5.1 Control of ion channels

• Receptor protein is part of an ion channel protein complexReceptor protein is part of an ion channel protein complex

• Receptor binds a messenger leading to an induced fitReceptor binds a messenger leading to an induced fit

• Ion channel is opened or closedIon channel is opened or closed

• Ion channels are specific for specific ions (NaIon channels are specific for specific ions (Na++, Ca, Ca2+2+, Cl, Cl--, K, K++))

• Ions flow across cell membrane down concentration gradientIons flow across cell membrane down concentration gradient

• Polarises or depolarises nerve membranesPolarises or depolarises nerve membranes

• Activates or deactivates enzyme catalysed reactions within Activates or deactivates enzyme catalysed reactions within cellcell

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5. Signal transduction5. Signal transduction

Hydrophilictunnel

Cellmembrane

5.1 Control of ion channels5.1 Control of ion channels

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Cellmembrane

Five glycoprotein subunitstraversing cell membrane

Messenger

Cellmembrane

Receptor

Inducedfit

‘Gating’(ion channel opens)

Cationic ion channels for KCationic ion channels for K++, Na, Na++, Ca, Ca2+2+ (e.g. nicotinic) = excitatory (e.g. nicotinic) = excitatoryAnionic ion channels for ClAnionic ion channels for Cl-- (e.g. GABA (e.g. GABAAA) = inhibitory) = inhibitory

Bindingsite

5.1 Control of ion channels5.1 Control of ion channels

5. Signal transduction5. Signal transduction

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5.1 Control of ion channels:5.1 Control of ion channels:

Induced fit and opening

of ion channel

IONCHANNEL

(open)

Cell

Cellmembrane

MESSENGER

Ionchannel

Ionchannel

Cellmembrane

IONCHANNEL

(closed)

Cell

RECEPTORBINDING

SITE

Lock Gate

Ionchannel

Ionchannel

Cellmembrane

Cellmembrane

MESSENGER

5. Signal transduction5. Signal transduction

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5.2 Activation of signal proteins5.2 Activation of signal proteins• Receptor binds a messenger leading to an induced fitReceptor binds a messenger leading to an induced fit• Opens a binding site for a signal protein (G-protein)Opens a binding site for a signal protein (G-protein)• G-Protein binds, is destabilised then splitG-Protein binds, is destabilised then split

messenger

G-proteinsplit

inducedfit

closed open

5. Signal transduction5. Signal transduction

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5.2 Activation of signal proteins5.2 Activation of signal proteins• G-Protein subunit activates membrane bound enzymeG-Protein subunit activates membrane bound enzyme

Binds to allosteric binding siteBinds to allosteric binding siteInduced fit results in opening of active siteInduced fit results in opening of active site

• Intracellular reaction catalysedIntracellular reaction catalysed

active site(closed)

active site(open)

Enzyme

Intracellular reaction

Enzyme

5. Signal transduction5. Signal transduction

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5.3 Activation of enzyme active site5.3 Activation of enzyme active site• Protein serves dual role - receptor plus enzymeProtein serves dual role - receptor plus enzyme• Receptor binds messenger leading to an induced fitReceptor binds messenger leading to an induced fit• Protein changes shape and opens active siteProtein changes shape and opens active site• Reaction catalysed within cellReaction catalysed within cell

closed

messenger

inducedfit

active site open

intracellular reaction

closed

messenger

5. Signal transduction5. Signal transduction

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6. Competitive (reversible) antagonists6. Competitive (reversible) antagonists

• Antagonist binds reversibly to the binding site Antagonist binds reversibly to the binding site • Intermolecular bonds involved in bindingIntermolecular bonds involved in binding• Different induced fit means receptor is not activatedDifferent induced fit means receptor is not activated• No reaction takes place on antagonistNo reaction takes place on antagonist• Level of antagonism depends on strength of antagonist Level of antagonism depends on strength of antagonist

binding and concentrationbinding and concentration• Messenger is blocked from the binding site Messenger is blocked from the binding site • Increasing the messenger concentration reverses antagonismIncreasing the messenger concentration reverses antagonism

AnAn

EERR

MM

AnAn

RR

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7. Non competitive (irreversible) antagonists7. Non competitive (irreversible) antagonists

• Antagonist binds irreversibly to the binding siteAntagonist binds irreversibly to the binding site• Different induced fit means that the receptor is not activated Different induced fit means that the receptor is not activated • Covalent bond is formed between the drug and the receptorCovalent bond is formed between the drug and the receptor• Messenger is blocked from the binding site Messenger is blocked from the binding site • Increasing messenger concentration does not reverse Increasing messenger concentration does not reverse

antagonismantagonism

X

OH OH

X

O

Covalent Bond

Irreversible antagonism

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8. Non competitive (reversible) allosteric antagonists8. Non competitive (reversible) allosteric antagonists

• Antagonist binds reversibly to an allosteric site Antagonist binds reversibly to an allosteric site • Intermolecular bonds formed between antagonist and binding Intermolecular bonds formed between antagonist and binding

sitesite• Induced fit alters the shape of the receptorInduced fit alters the shape of the receptor• Binding site is distorted and is not recognised by the messengerBinding site is distorted and is not recognised by the messenger• Increasing messenger concentration does not reverse Increasing messenger concentration does not reverse

antagonismantagonism

ACTIVE SITE (open)

ENZYMEReceptor

AllostericAllostericsitesite

Binding siteBinding site

(open)ENZYMEReceptor

Inducedfit

Binding siteBinding siteunrecognisableunrecognisable

Antagonist

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9. Antagonists by umbrella effect9. Antagonists by umbrella effect

• Antagonist binds reversibly to a neighbouring binding site Antagonist binds reversibly to a neighbouring binding site • Intermolecular bonds formed between antagonist and Intermolecular bonds formed between antagonist and

binding sitebinding site• Antagonist overlaps with the messenger binding siteAntagonist overlaps with the messenger binding site• Messenger is blocked from the binding siteMessenger is blocked from the binding site

Antagonist

Binding sitefor antagonist

Binding sitefor messenger

messenger

Receptor Receptor

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10. Agonists10. Agonists

• Agonist binds reversibly to the binding site Agonist binds reversibly to the binding site • Similar intermolecular bonds formed as to natural messengerSimilar intermolecular bonds formed as to natural messenger• Induced fit alters the shape of the receptor in the same way as Induced fit alters the shape of the receptor in the same way as

the normal messengerthe normal messenger• Receptor is activatedReceptor is activated• Agonists are often similar in structure to the natural Agonists are often similar in structure to the natural

messengermessenger

EE

AgonistAgonist

RR EE

AgonistAgonist

RR

Signal transductionSignal transduction

AgonistAgonist

RR

Induced fitInduced fit

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PROTEINS AS DRUG TARGETS:PROTEINS AS DRUG TARGETS:ENZYMESENZYMES

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1. Structure and function of enzymes1. Structure and function of enzymes

• Globular proteins acting as the body’s catalystsGlobular proteins acting as the body’s catalysts• Speed up time for reaction to reach equilibriumSpeed up time for reaction to reach equilibrium• Lower the activation energy of a reactionLower the activation energy of a reaction

Example:Example:

LDH = Lactate dehydrogenase (enzyme)NADH2 = Nicotinamide adenosine dinucleotide (reducing agent & cofactor)Pyruvic acid = Substrate

LDH

Pyruvic acid Lactic acid

H3CC

CO

O HO

C OCH3C

H

NADH2 NAD+++

OH OH

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Lowering the activation energy of reactionLowering the activation energy of reaction

Act. energy

Transition state

WITHOUT ENZYME

Product

Startingmaterial

Energy

WITH ENZYME

Product

Startingmaterial

Energy

∆G

Newtransition

state

∆G

Act. energy

• Enzymes lower the activation energy of a reaction but Enzymes lower the activation energy of a reaction but G remains the G remains the samesame

1. Structure and function of enzymes1. Structure and function of enzymes

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Methods of enzyme catalysisMethods of enzyme catalysis

• Provide a reaction surface (the active site)Provide a reaction surface (the active site)

• Provide a suitable environment (hydrophobic)Provide a suitable environment (hydrophobic)

• Bring reactants togetherBring reactants together

• Position reactants correctly for reactionPosition reactants correctly for reaction

• Weaken bonds in the reactantsWeaken bonds in the reactants

• Provide acid / base catalysisProvide acid / base catalysis

• Provide nucleophilesProvide nucleophiles

1. Structure and function of enzymes1. Structure and function of enzymes

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2. The active site2. The active site

• Hydrophobic hollow or cleft on the enzyme surfaceHydrophobic hollow or cleft on the enzyme surface

• Accepts reactants (substrates and cofactors)Accepts reactants (substrates and cofactors)

• Contains amino acids whichContains amino acids which - bind reactants (substrates and cofactors)- bind reactants (substrates and cofactors) - catalyse the reaction- catalyse the reaction

ENZYME

Active siteActive site

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3. Substrate binding3. Substrate binding

• Active site is nearly the correct shape for the substrateActive site is nearly the correct shape for the substrate• Binding alters the shape of the enzyme (induced fit)Binding alters the shape of the enzyme (induced fit)• Binding will strain bonds in the substrateBinding will strain bonds in the substrate• Binding involves intermolecular bonds between functional groups in the Binding involves intermolecular bonds between functional groups in the

substrate and functional groups in the active sitesubstrate and functional groups in the active site

3.1 Induced fit3.1 Induced fit

Induced fitInduced fit

SubstrateSubstrate

SS

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• IonicIonic• H-bondingH-bonding• van der Waalsvan der Waals

3.2 Bonding forces3.2 Bonding forces

Example:Example:

SS

Enzyme

Active site

vdwvdwinteractioninteraction

ionicionicbondbond

H-bondH-bond

Phe

Ser

OH

Asp

CO2

3. Substrate binding3. Substrate binding

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van der Waals

H-Bond

Ionic

H3CC

C

O

O

O

• IonicIonic• H-bondingH-bonding• van der Waalsvan der Waals

3.2 Bonding forces3.2 Bonding forces

Example:Example: Binding of pyruvic acid in LDH Binding of pyruvic acid in LDH

O

H

H3N

H-Bond

Ionicbond

Possible interactions vdw-interactions

H3CC

C

O

O

O

3. Substrate binding3. Substrate binding

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• Induced fit - Active site alters shape to maximise intermolecular bondingInduced fit - Active site alters shape to maximise intermolecular bonding

3.2 Bonding forces3.2 Bonding forces

Intermolecular bonds not optimum length for maximum bonding

Intermolecular bond lengths optimisedSusceptible bonds in substrate strainedSusceptible bonds in substrate more easily broken

SS Phe

SerO

H

Asp

CO2 Induced fit

SSPhe

Ser

OH

Asp

CO2

3. Substrate binding3. Substrate binding

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Example:Example: Binding of pyruvic acid in LDH Binding of pyruvic acid in LDH

O

H

H3N

H3CC

C

O

O

O

O

O

O

3. Substrate binding3. Substrate binding

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Example:Example: Binding of pyruvic acid in LDH Binding of pyruvic acid in LDH

O

H

H3N

pi bondpi bondweakenedweakened

H3CC

C

O

O

O

3. Substrate binding3. Substrate binding

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4. Catalysis mechanisms4. Catalysis mechanisms

• HistidineHistidine

4.1 Acid/base catalysis4.1 Acid/base catalysis

4.2 Nucleophilic residues4.2 Nucleophilic residues

NNH

+H

-H NNH

H

Non-ionisedNon-ionisedActs as a basic catalystActs as a basic catalyst(proton 'sink')(proton 'sink')

IonisedIonisedActs as an acid catalystActs as an acid catalyst(proton source)(proton source)

H3N CO2

OH

H

L-SerineL-Serine

H3N CO2

SH

H

L-CysteineL-Cysteine

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OH

Ser

X

Substrate

O

Ser

H2O

OH

Ser

HO Product

Serine acting as a nucleophileSerine acting as a nucleophile

4. Catalysis mechanisms4. Catalysis mechanisms

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5. Overall process of enzyme catalysis5. Overall process of enzyme catalysis

SS

EE

ES

PP

EE

EP

PP

EE

E + P

EE

SS

E + S

EE

• Binding interactions must be;Binding interactions must be; - strong enough to hold the substrate sufficiently long for the reaction to - strong enough to hold the substrate sufficiently long for the reaction to

occuroccur - weak enough to allow the product to depart - weak enough to allow the product to depart • Implies a fine balanceImplies a fine balance• Drug design - designing molecules with stronger binding interactions results Drug design - designing molecules with stronger binding interactions results

in enzyme inhibitors which block the active sitein enzyme inhibitors which block the active site

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6. Competitive (reversible) inhibitors6. Competitive (reversible) inhibitors

• Inhibitor binds reversibly to the active site Inhibitor binds reversibly to the active site • Intermolecular bonds are involved in bindingIntermolecular bonds are involved in binding• No reaction takes place on the inhibitorNo reaction takes place on the inhibitor• Inhibition depends on the strength of inhibitor binding and inhibitor Inhibition depends on the strength of inhibitor binding and inhibitor

concentrationconcentration• Substrate is blocked from the active site Substrate is blocked from the active site • Increasing substrate concentration reverses inhibitionIncreasing substrate concentration reverses inhibition• Inhibitor likely to be similar in structure to the substrateInhibitor likely to be similar in structure to the substrate

II

EEEE

SS

II

EE

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7. Non competitive (irreversible) inhibitors7. Non competitive (irreversible) inhibitors

• Inhibitor binds irreversibly to the active site Inhibitor binds irreversibly to the active site • Covalent bond formed between the drug and the enzymeCovalent bond formed between the drug and the enzyme• Substrate is blocked from the active site Substrate is blocked from the active site • Increasing substrate concentration does not reverse inhibitionIncreasing substrate concentration does not reverse inhibition• Inhibitor likely to be similar in structure to the substrateInhibitor likely to be similar in structure to the substrate

X

OH OH

X

O

Covalent Bond

Irreversible inhibition

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ACTIVE SITE (open)

ENZYMEEnzyme

8. Non competitive (reversible) allosteric inhibitors8. Non competitive (reversible) allosteric inhibitors

• Inhibitor binds reversibly to the allosteric site Inhibitor binds reversibly to the allosteric site • Intermolecular bonds are formedIntermolecular bonds are formed• Induced fit alters the shape of the enzymeInduced fit alters the shape of the enzyme• Active site is distorted and is not recognised by the substrateActive site is distorted and is not recognised by the substrate• Increasing substrate concentration does not reverse inhibitionIncreasing substrate concentration does not reverse inhibition• Inhibitor is not similar in structure to the substrateInhibitor is not similar in structure to the substrate

AllostericAllostericsitesite

Active siteActive site

(open)ENZYMEEnzyme

Inducedfit

Active siteActive siteunrecognisableunrecognisable

Allostericinhibitor

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8. Non competitive (reversible) allosteric inhibitors8. Non competitive (reversible) allosteric inhibitors

• Enzymes with allosteric sites often at start of biosynthetic pathwaysEnzymes with allosteric sites often at start of biosynthetic pathways• Enzyme is controlled by the final product of the pathwayEnzyme is controlled by the final product of the pathway• Final product binds to the allosteric site and switches off enzymeFinal product binds to the allosteric site and switches off enzyme• Inhibitor may have a similar structure to the final productInhibitor may have a similar structure to the final product

P’’’P’’P’

Biosynthetic pathway

Feedback controlInhibition

PPSS

(open)ENZYMEEnzyme

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