Drug-Target Interactions

 Irreversible strong bonds

o (Covalent bond)
 Reversible weak bonds
o Ionic (electrostatic bonds) o Dipole-dipole and ion-dipole
o Hydrogen bonds o Hydrophobic interactions
o Van der Waals interactions o Charge-transfer interactions
 Drug targets
o Drug targets are large molecules – macromolecules.
o Binding sites are typically hydrophobic pockets on the
surface of macromolecules.
 Hormones act intracellular.
o Functional groups on the drug are involved in binding
interactions and are called binding groups.
o Specific regions within the binding site that are
involved in binding interactions are called binding
regions.
 Induced Fit
o Binding interactions usually result in an induced fit where the binding site changes shape to accommodate the drug.
o The induced fit may also alter the overall shape of the drug target.
o Important to the pharmacological effect of the drug.

Receptor
 A receptor is a protein molecule usually found embedded within the plasma membrane surface of a cell that receives chemical
signals from outside the cell and when such chemical signals bind to a receptor, they cause some form of cellular/tissue response.
 Types of receptors
a. Enzymes
 e.g. Acetylcholeinestrase, carbonic anhydrase, adenylcyclase and monoamine oxidase.
b. Structural and functional component of a cell membrane which consists of lipoprotein.
c. Receptors of nucleic acid e. g. DNA and RNA.
d. Non enzymatic protein receptors
 E.g. (adrenergic receptors)
 Structure and Classification of receptors
o Receptors are classified according function into so called superfamilies of receptors
o The members of a superfamily have the same general structure and general mechanism of action
o Individual members of a superfamily tend to exhibit variation in the amino acid residue sequence in certain regions and the
sizes of their extracellular and intracellular domains
o Each of the superfamilies is subdivided into:
 A number of types of receptors whose members are usually defined by their endogenous ligand
 For example: [all receptors that bind to acetylcholine (Ach) are of cholinergic type]
 [all receptors that bind to adrenaline and nor adrenaline are of adrenergic type]
 Sub-types are further classified either:
A. According to the type of genetic code responsible for their structure
B. Or after the exogenous ligand that selectively bind to receptor
 For example:
 Acetylcholine (endogenous ligand) will bind to all cholinergic receptors
 Nicotine (exogenic ligand) will only bind to nicotinic cholinergic receptors (nAChR)
 Muscarine (Exogenic ligand) will only bind to muscarinic cholinergic receptors (mAChR)
Five muscarinic receptors: mAChR receptors are classified using numerical subscripts as: m1AChR,
m2AChR , m3AChR, m4AChR, m5AChR
 Structure and function of receptors
o Globular proteins acting as a cell’s ‘letter boxes’
o Located mostly in the cell membrane
o Receive messages from chemical messengers coming from other cells
o Transmit a message into the cell leading to a cellular effect
o Different receptors specific for different chemical messengers
o Each cell has a range of receptors in the cell membrane making it responsive to different chemical messengers
o Mechanism
 Receptors contain a binding site (hollow or cleft on the receptor surface) that is recognized by the chemical messenger
 Binding of the messenger involves intermolecular bonds
 Binding results in an induced fit of the receptor protein
 Change in receptor shape results in a ‘domino’ effect
 Domino effect is known as Signal Transduction, leading to a chemical signal being received inside the cell
 Chemical messenger does not enter the cell. It departs the receptor unchanged and is not permanently bound

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 Chemical messengers:
Chemicals which are produced in order to transmit the signal (message) to the target site.
Neurotransmitters Hormones
 A chemical which is released from the neurons to carry the signal  They are secreted by glands and travel for a
(message) from the neuron to the target cell. longer distance.
 Once the neurotransmitter is released it binds to the receptor.  Hormones cause an action when binding to the
 This binding causes a series of secondary effects (Domino Effect or cell receptor in a way similar to the
transduction) which causes in turn ion flow across the cell membrane or neurotransmitter.
switching an enzyme on/off which finally leads to the biological response.
 Note: Chemical messengers ‘switch on’ receptors without undergoing
a reaction
 The Binding Site
o A hydrophobic hollow or cleft on the receptor surface - equivalent to the
active site of an enzyme
o Accepts and binds a chemical messenger
o Contains amino acids which bind the messenger
o No reaction or catalysis takes place (Unlike Enzymes*)

 Overall Process of Receptor/Messenger Interaction

o Binding interactions must be strong enough to hold the messenger
sufficiently long for signal transduction to take place
o Interactions must be weak enough to allow the messenger to depart
o Implies a fine balance
o Designing molecules with stronger binding interactions results in drugs
that block the binding site – antagonists

Receptor Superfamilies
 Membrane bound
o Ion channel receptors (msecs)
o G-protein coupled receptors (seconds)
o Kinase linked receptors (minutes)
 Intracellular receptors
Ion Channel Receptors
Structure

Nicotinic receptor Glycine receptor

Protein subunits (4-TM receptor subunits)

Role  The cellular membrane consists of phospholipid bilayer so that the middle of the cell membrane is hydrophobic.
 The cellular membrane acts as a barrier that blocks the passage of polar molecules across it.
 Ion channels are specific for specific ions (Na + , Ca2+, Cl- , K+ )
 Cationic ion channels for K+ , Na+ , Ca2+ (e.g. nicotinic) = excitatory
 Anionic ion channels for Cl- (e.g. GABA-A) = inhibitory
Ion channels form hydrophilic tunnels with in the cellular membrane through which ions can pass under the
control of a lock gate which organizes the passage process.
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Function 1. Controlling the potential cross the cell membrane.
2. Facilitating the neuromuscular and neuronal transmission.
3. Signal transduction.
4. Controlling contractility and secretion.
5. Polarizes or depolarizes nerve membranes.
6. Activates or deactivates enzyme catalyzed reactions within cell.
Ligand gated ion channels
Hint  Integral membrane proteins which regulate the flow of certain ions across the cell membrane in a passive way
controlled by electrochemical gradient
 This type of channels are open (gated) when they bind to a neurotransmitter which changes its conformation leading
to a conducting state.
 These channels can be modulated by binding to endogenous or exogenous modulators at allosteric sites
Structure  Five glycoproteins subunits. Those subunits are not identical (α, β, δ, γ).
 All the subunits folds up in a similar manner so that the protein part of each subunit traverse the cell membrane four
times.
 Each subunit contains FOUR trans-membrane regions labelled TM1-TM4 (Hydrophobic in nature).
 The subunits are arranged in a manner so that the second TM region (TM2) are facing each other and facing the
central pore of the channel.
 Each subunit also has an extracellular N-terminal which in case of α-subunit contains the ligand binding site.
Gating Gating is the conformational change that occurs in the protein as a result of the binding of the ligand to its binding
function site which eventually leads to the opening of the channel’s pore and consequently ion flow.
 The binding site is located far from the pore of the channel.
 The lock gate: formed of 5 kinked α- helices from each subunit each kinked helix points towards the others when the
pore is closed.
 When the ligand binds, the helices point to the other way (TM2 segments rotate to open central pore).
 Fast response measured in msec, which is ideal for transmission between nerves.
 Binding of messenger leads directly to ion flows across cell membrane.
 Ion flow = secondary effect (signal transduction).
 Ion concentration within cell alters, leading to variation in cell chemistry.

‘Voltage-gated’ ion channels

Hint  ‘Voltage-gated’ ion channels are not controlled by ligands, but are sensitive to potential difference across cell
membrane (membrane potential)
 ‘Voltage-gated’ ion channels are present in the axons of neurons and are crucial to the transmission of signal along
individual neurons
 ‘Voltage-gated’ ion channels are important drug targets for local anesthetics

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 G-Protein Coupled Receptors
Hint  Most of our physiology is based on GPCRs signal transduction.
 They act as receptors for hormones, neurotransmitters, ions and other stimuli.
 The main role of GPCRs is to couple the binding of agonists to the activation of specific heterotrimeric G-
protein causing activation of several downstream effectors.
 The response from activated G-protein coupled receptors is measured in seconds which is slower than the
response of ion channels but faster than kinase linked receptors.
Structure  They are membrane bound protein that are responsible for activating G-proteins.
 G-proteins: Act as signal proteins which are capable of activating and deactivating membrane-bound
enzymes.
 Each GPCR is a single protein consist of seven trans-membrane regions coupled intracellularly to a G-
protein which sensitive to GTP and to an effector protein.
 Each trans-membrane region is a hydrophobic region and helical in shape (assigned with roman numbers)

Binding 1. Binding site for the neurotransmitter: is embedded within the cell membrane with the binding site for
sites chemical messenger
2. Binding sites for G-proteins: situated intracellularly involves a part of C-terminal chain and the
intracellular loop (closed in the resting state).
3. Third binding site: located intracellularly which is normally closed.
 When the chemical messenger binds to its site  change in protein shape  opening the binding site on
the inner surface  recognition by G-proteins  G-protein binding.
 G-proteins are made of three protein subunits; once G-proteins are bound, the subunits fragment into a
monomer and a dimmer which interact with membranebound enzymes (switch on/off)

Ligands  Monoamines: e.g. dopamine, histamine,  Hormones

noradrenaline, acetylcholine (muscarinic)  Glutamate
 Nucleotides  Ca++
 Lipids
 Ligand binding site - varies depending on receptor type
A. Monoamines: pocket in TM helices
B. Peptide hormones: top of TM helices + extracellular loops + N-terminal chain
C. Hormones: extracellular loops + N-terminal chain
D. Glutamate: N-terminal chain

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Receptor  Despite the chemical variation of the chemical messengers, the overall structure of G- protein coupled
Types receptors are similar.
and  Despite the similarity the amino acid sequence of the receptors vary remarkably.
Subtypes  This implies that the receptors come from common ancestors
 Receptor types and subtypes not equally distributed amongst tissues.
 Target selectivity leads to tissue selectivity.
Bacteriorhodopsin & Rhodopsin Family
 Rhodopsin = visual receptor
 A G protein-coupled receptor which is conjugated by opsin, phopholipid, retinal. Light sensitive, actived
by light turn on the signal pathway that leads to vision.
 Rhdopsin structure
o Extracellular region
o Transmembrane helices
o Cytoplasmic surface
 Many common receptors belong to this same family
 Implications for drug selectivity depending on similarity (evolution)
 Membrane bound receptors difficult to crystallise
 X-Ray structure of bacteriorhodopsin solved - bacterial protein similar to rhodopsin
 Bacteriorhodopsin structure used as ‘template’ for other receptors
 Construct model receptors based on template and amino acid sequence
 Leads to model binding sites for drug design
 Crystal structures for rhodopsin and β2-adrenergic receptors now solved - better templates
 Reflects differences in receptors which recognise the same ligand

1. Muscarinic, α-adrenergic, β-adrenergic, histamine, and dopamine receptors have evolved from a common
branch of the evolutionary and have greater similarity to each other than to any receptors arising from an
earlier evolutionary branch (e.g. the angiotensin receptor).
2. The existence of receptor subtypes allows the possibility of designing drugs that are selective for one
receptor subtype over another.
Heart muscle  1 adrenergic receptors
Fat cells  3 adrenergic receptors
Bronchial muscle  1& 2 adrenergic receptors
GI-tract  1 2 & 2 adrenergic receptors
3. Subtypes frequently activate different signaling systems, leading to different biological results.
4. A closer study of the evolutionary tree reveals some curious facts about the origins of receptor subtypes.
5. Various receptor subtypes have diverged from a common evolutionary branch (e.g. the dopamine subtypes
D2, D3, D4). This is known as divergent evolution and there should be close structural similarity
between these subtypes.
6. Consequently, there may sometimes be greater similarities between receptors which bind different ligands
but which have evolved from the same branch of the tree

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 Tyrosine Kinase Linked Receptors
Hint  A super family of receptors which activate enzymes without the need for G-protein.
 Bifunctional receptor / enzyme
 Activated by hormones
 Overexpression can result in cancer
 Receptor linked tyrosine kinase receptors are important examples of kinase-linkedreceptors.
 Examples of tyrosine kinase receptors include the receptor for insulin, and receptors for various cytokines and
growth factors.
General 1. Extracellular binding domain: the binding site for the ligands (growth factors). This domain is larger than GPCRs
structure binding domain.
2. Trans-membrane domain: hydrophobic region that traverse the cell membrane several times.
3. Cytoplasmic domain (catalytic domain): acts as an enzyme or forms a complex with a protein that acts as enzyme.
General  Protein serves dual role - receptor plus enzyme
principles  Receptor binds messenger leading to an induced fit
 Protein changes shape and opens active site
 Reaction (Phosphorylation) is catalyzed within cell
 The substrate for the reaction is the receptor itself
 Overexpression related to several cancers

Signal  The binding of the a chemical messenger to its receptor site  a change in the protein shape and a dimer between
transduction two receptors happen  the active site on the intracellular side will open allowing the protein to act as an enzyme
the protein to change shape.

 Signal transduction of different receptor linked tyrosine kinases

o The reaction catalyzed by RTKs.

o The intracellular domain of receptor linked tyrosine kinase possesses a protein- tyrosine kinase activity.
o The ligands for receptor linked tyrosine kinase are proteins such as Epidermal growth factors (EGF) and
platelet-derived growth factor (PDGF).
a) Epidermal growth factor (EGF)
Hint  EGF is a bivalent ligand which can bind to two
receptors at the same time  Receptor
dimerization  activation of enzymatic activity.
 Active site on one half of dimer catalyses
phosphorylation of Tyr residues on other half
 Dimerization of receptor is crucial because
each half phosphorylate the other half. However,
if the dimerization did not occur, no
phosphorylation would take place. Note that
these phosphorylation occur on the intracellular
portion of the receptor protein chain
 Phosphorylated regions act as binding sites for
further proteins and enzymes
 Results in activation of signaling proteins and
enzymes
 Message carried into cell Activation and dimerization of some RTK receptors

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 Insulin receptors
Hint  In this case, no dimerization occurs, but insulin binding cause induced fit and activation of the kinase active site
leading to phosphorylation. Through the formation of a tetrameric complex.

Growth hormone (GH) receptors

Hint  Tetrameric complex constructed in presence of growth hormone
 Kinases are activated from the Cytoplasm

Intracellular Receptors
Hint  Unlike the other receptors those receptors are located intracellularly. So, as a consequence the chemical messenger must pass
through the cell membrane.
 Chemical messengers must be hydrophobic
 Example - steroids and steroid receptors
 Example of chemical messengers: thyroid hormones and steroidal hormones.
 The response time for this receptor is longer and measured in hours or days.
General 1. Ligand binding site: At the C-terminus.
structure 2. DNA binding site (zinc finger domain): near the center which contains nine
cysteine residues eight of them are bound to two zinc ions
3. N-terminal domain

Function  For each receptor, the DNA binding region identify specific nucleotide sequence in the DNA.
 The zinc finger domain in Estrogen receptor identifies the following sequence: 5′-AGGTCA-3′
(A= adenine, G= guanine, C= cytosine)
Signal  Ligand crosses the cell membrane and binds to the receptor  Induced fit and shape of the receptor changes 
transduction dimerization of ligand-receptor complex  dimer binds to a co-activator protein  the whole complex binds to
the specified DNA sequence  triggering or inhibition of DNA transcription leading to the final physiological
effect.

 For example, the estrogen ligand–receptor dimer binds to a nucleotide sequence of 5′-AGGTCANNNTGACCT-3′
(N= any nucleic acid base).

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