CZ5225: Modeling and Simulation in BiologyCZ5225: Modeling and Simulation in Biology

Lecture 2: Drugs Lecture 2: Drugs

Prof. Chen Yu ZongProf. Chen Yu Zong

Tel: 6874-6877Tel: 6874-6877Email: Email: csccyz@nus.edu.sgcsccyz@nus.edu.sghttp://xin.cz3.nus.edu.sghttp://xin.cz3.nus.edu.sg

Room 07-24, level 7, SOC1, Room 07-24, level 7, SOC1, National University of SingaporeNational University of Singapore

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Definitions

Xenobiotic: A chemical that is not endogenous to an organism.

Endogenous: Made within.

Drug: A chemical taken that is intended to modulate the current physiological status quo.

Ligand: A chemical that binds to another molecule, such as a receptor protein.

Bioavailability: The amount or proportion of drug that becomes available to the body following its administration.

Pharmacokinetics: What the body does to a drug.

Pharmacodynamics: What a drug does to the body .

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Drug action

A drug is a compound that can modify the response of a tissue

to its environment.

A drug will exert its activity through interactions at one or more

molecular targets.

• The macromolecular species that control the functions of

cells.

• May be surface-bound proteins like receptors and ion

channels or

• Species internal to cells, such as enzymes or nucleic

acids.

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Drug-Receptor Lock and Key ModelDrug-Receptor Lock and Key Model

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Drug Targets: Receptors

Receptors are the sites at which biomolecules such as

hormones, neurotransmitters and the molecules responsible

for taste and odour are recognised.

A drug that binds to a receptor can either:

• Trigger the same events as the native ligand - an agonist.

Or

• Stop the binding of the native agent without eliciting a

response - an antagonist.

There are four ‘superfamilies’ of receptors.

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Drug Targets:

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Drug Targets: Receptors

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Drug Targets: Receptors

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Drug Targets:

Receptors

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Drug Targets: Enzymes

They are proteins that catalyse the reactions required for cellular function.

Generally specific for a particular substrate, or closely related family of substrates.

Molecules that restrict the action of the enzyme on its substrate are called inhibitors.

Inhibitors may be irreversible or reversible.

Reversible inhibitors may be:

• Competitive.

• Non-competitive.

Enzyme inhibitors might be seen to allow very ‘fine control’ of cellular processes.

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Drug targets: Nucleic acids

Potentially the most exciting and valuable of the available drug targets.

BUT designing compounds that can distinguish target nucleic acid sequences is not yet achievable.

There are compounds with planar aromatic regions that bind in-between the base pairs of DNA or to the DNA grooves.

These generally inhibit the processes of DNA manipulation required for protein synthesis and cell division.

• Suitable as drugs for applications where cell death is the goal of therapy - such as in the case of the treatment of cancer.

• Name another use where cell death is desirable.

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Mechanisms and Specificity of Drug Binding

The majority of binding and recognition occurs through non-

covalent interactions.

These govern:

• The folding of proteins and DNA.• The association of membranes.

• Molecular recognition (e.g. interaction between an enzyme and its substrate or the binding of an antibody).

They are generally weak and operate only over short

distances.

As a result large numbers of these interactions are necessary

for stability, requiring a high degree of complementarity

between binding groups and molecules.

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Drug Binding Site Drug Binding Site

HIV-1 protease

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Mechanism of Drug Binding and ActionsMechanism of Drug Binding and Actions

Drug and protein:

Lock and key mechanism, blocking=>stopping of protein function

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X-Ray Diffraction Structure Of Hiv-1 Protease Complexed With SB203238 (Drawn from: Brookhaven database file: 1hbv.pdb.K.A.Newlander, J.F.Callahan, M.L.Moore, T.A.Tomaszek, W.F.Huffman A Novel Constrained Reduced-Amide Inhibitor Of HIV-1 Protease Derived From The Sequential Incorporation Of Gamma-Turn Mimetics Into A Model Substrate J.Med.Chem. 1993, 36, 2321.)

ProteinSurface

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Covalent bonds

The ‘sharing’ of a pair of electrons between two atoms.

These electrons largely occupy the space between the nuclei of the two atoms.

• A very stable interaction

• Requires hundreds of kilojoules to disrupt.

Compounds that inhibit enzymes through formation of covalent interactions are called ‘suicide inhibitors’.

Not all covalent bond formation is irreversible

• Hydrolysis.

• Action of repairing proteins.

Consult with your Biochemistry textbook

Essential Bioinformatics and BiocomputEssential Bioinformatics and Biocomputing (LSM2104)ing (LSM2104)

Non-covalent interactions

The forces involved are:

• Hydrogen bonds

• van der Waals forces

• Ionic / electrostatic interactions

• Hydrophobic interactions.

Generally, such interactions are weak

•vary from 4-30 kJ/mol.

Details later

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Selectivity, toxicity and therapeutic index

Drugs may bind to both their desired target and to other molecules in an organism.

If interactions with other targets are negligible then a drug is said to be specific.

In most cases drugs will show a non-exclusive preference for their target - selective.

The interaction with both their intended target and other molecules can lead to undesirable effects (side effects).

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Selectivity, toxicity and therapeutic index

Establish the concentrations at which the drug exerts its beneficial effect and where the level of side effects becomes unacceptable.

Commonly used values are ED50 and LD50.

For obvious reasons LD50 tests are not carried out on human

volunteers!

One measure of the margin of safety is the therapeutic index. Therapeutic index = LD50 / ED50

Drugs with low therapeutic indices are only used in ‘life or death’ type situations.

Exercise: it can be argued that the ratio LD1 / ED99 might be a more realistic estimate of safety. Why?

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Agonists & antagonists

Activity of a drug is the result of two independent factors:

• Affinity is the ability of a drug to bind to its receptor.

• Efficacy describes the ability of the bound drug to elicit a

response.

The ‘two state model’. Receptors can be inactive or activated.

An agonist stabilises the active state preferentially.

An antagonist shows no preference or it stabilises the resting

state.

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Agonists & antagonists

Activity of a drug is the result of two independent factors:

• Affinity is the ability of a drug to bind to its receptor.

• Efficacy describes the ability of the bound drug to elicit a

response.

The ‘two state model’. Receptors can be inactive or activated.

An agonist stabilises the active state preferentially.

An antagonist shows no preference or it stabilises the resting

state.

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Agonists & antagonists

The efficacy of a compound in the two state model is the

degree of selectivity for stabilising the active or resting state

of the receptor.

The degree of selectivity can be expressed in terms of the

ratio of the equilibrium binding constant, K for each receptor

state.

• Kactive / Kresting > 1, then the compound is an agonist. The

higher the ratio, the higher will be the efficacy.

• Kactive / Kresting 1, then the compound is an antagonist.

The smaller the ratio, the higher will be the efficacy.

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Agonists & antagonists

There are 2 classes of agonist:

• Full agonists – which elicit the maximum possible response at some concentration

• Partial agonists – which never elicit the maximum possible response from the receptor.

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Agonists & antagonists

There are also 2 classes of antagonist:

• Competitive antagonists – which compete for the agonist binding site, and require higher agonist concentration to elicit a given response.

• Non-competitive agonists – these bind at a site other than the agonist binding site, or even to a completely different molecular target. The result is the lowering of the maximum possible response in addition to the usual antagonist effect of ‘displacing’ agonist activity to higher concentration.

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Case Study: Adrenoceptor agonists andantagonists and control of cardiac function

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Case Study: Adrenoceptor agonists and antagonists and control of cardiac function

 

Adrenoceptors

The receptors for adrenaline (epinephrine) and noradrenaline

(norepinephrine).

Also called adrenergic receptors.

Widely distributed, being responsible for control of the stimulation

and relaxation of muscle, including the heart.

Adrenoceptors mediate the control of cardiac function by the

sympathetic nervous system; the parasympathetic nervous

system control is mediated by muscarinic acetylcholine receptors.

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OH

NH2

CO2H OH

NH2OH

CO2H

NH2

OH

OHNH2

OH

OH

OH

NH

OH

OH

OH

CH3

Tyrosine DOPA

Norepinephrine Dopamine

Epinephrine

Route of the biosynthesis of epinephrine and norepinephrine

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Case Study: Adrenoceptor agonists and

antagonists and control of cardiac function

Adrenoceptors are divided into 5, or possibly 6 types:

1, 2, 1, 2, 3, and potentially 4.

They are all G-protein coupled receptors.

The secondary messengers for the 1 adrenoceptors are

inositol triphosphate and diacylglycerol.

All other adrenoceptors have cAMP as their principal

secondary messenger.

Remember that cytoplasmic [Ca2+] regulates the

development of tension in muscles, such as the heart.

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Case Study:

Adrenoceptor

agonists and

antagonists and

control of

cardiac function

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Case Study: Adrenoceptor agonists and

antagonists and control of cardiac function

The activation of and adrenoceptors usually elicits opposing

responses:

receptor activation leads to constriction of veins and

arterioles. • receptor activation leads to dilation of veins and arterioles.

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Presence and function of adrenoceptors and the heart and

vascular system.

Epinephrine administered rapidly intravenously has a number of

simultaneous effects that contribute to a rapid rise in blood

pressure on its administration.

• A rise in the strength of ventricular contraction (a positive

inotropic action)

• The heart rate is increased (a positive chronotropic action)

• Blood vessels become constricted.

Noting the opposing roles of and receptors, it may be no

surprise to discover that administration regimes other than rapidly

intravenous injection can have quite different effects.

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Adrenoceptors: Signalling Process

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Adrenoceptors:

Signalling

Process

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1-Adrenoceptors: These are less abundant than -

adrenoceptors.

They couple to phospholipases C and D, to certain Ca2+

channels, and a number of ion channels allowing modification

of cellular cation content, including K+ and Na+.

Stimulation of 1-adrenoceptors does not lead to elevated

cAMP levels within the cell, and may even reduce cAMP

levels.

1-Adrenoceptor stimulation leads to formation of 1,4,5-

inositoltriphosphate and diacylglycerol.

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1-Adrenoceptors:

Inositoltriphosphate releases Ca2+ from intracellular

stores, and this may explain the observed increase in

force of contraction upon 1-adrenoceptor activation.

Their activation leads to constriction of vascular smooth

muscle.

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2-Adrenoceptors: Present in only very low levels in the heart.

Their activation leads to constriction of vascular smooth muscle.

1 and 2-Adrenoceptors: The ratio of 1 to 2-Adrenoceptors is

about 65:35 in the atria, and around 75:25 in the ventricles.

These receptors both lead to increases of [cAMP] following

stimulation.

This in turn activates protein kinase A, which can phosphorylate,

amongst other proteins, certain Ca2+ channels, leading to an influx

of Ca2+ ions, and so enhances contraction.

-Adrenoceptor agonists also increase heart rate.

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Only the 1 receptor is thought to be involved in the exercise-

induced increase in heart rate bought about by noradrenaline.

Adrenaline, on the other hand, may function primarily through the

2-adrenoceptors.

2-adrenoceptor activation also leads to relaxation of vascular

smooth muscle.

3, and potentially 4-Adrenoceptors: The presence of these in the

heart is not fully established, and their role, if present, is even

more uncertain.

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Adrenoceptor agonists

1-Adrenoceptor agonists: These can be used to treat

hypotension through vasoconstriction, leading to increased blood pressure and cardiac arrhythmias through activation of vagal reflexes.Also valuable adjuncts to local anaesthetics, as vasoconstriction can slow the systemic dispersal of the anaesthetic.Drugs in this class include phenylephrine and methoxamine. 

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Adrenoceptor agonists 2-Adrenoceptor agonists: Despite the tendency of -

adrenoceptor agonists to cause vasoconstriction, these can be used to treat hypertension.

This unexpected activity occurs through action at the CNS, reducing signal to the heart and so lowering cardiac activity and constriction of the peripheral vasculature.

Drugs in this class include methyldopa and clonidine.Clonidine can also be used in protection against migrane.

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-Adrenoceptor agonists:

• These can be used to treat hypotension, cardiac

arrhythmias and cardiac failure.

• They stimulate the rate and force of cardiac

contraction.

• Simultaneously, they lead to a drop in peripheral

vascular resistance.

• These combined effects can result in palpitations,

sinus tachycardia and serious arrhythmias.

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-Adrenoceptor agonists:

Drugs in this class include xamoterol and dobutamine.

2-Adrenoceptor agonists lead to muscle relaxation and

so find use in treatment of asthma (salbutamol) and

delay in the onset of labour. (ritodrine).

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Adrenoceptor antagonists

1-Adrenoceptor antgonists: Antagonism (or ‘blockade’) of

1-adrenoceptors inhibits the action of endogenous

vasoconstrictors, resulting in vasodilation of both arteries and

veins, and thus reduction of blood pressure.

These drugs are, therefore, useful in the treatment of

hypertension and cardiac failure.

Prazosin and indoramin fall into this class of compounds.

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Adrenoceptor antagonists

2-Adrenoceptor antagonists: Just as 2-

adrenoceptor agonists unexpectedly reduce

vasoconstriction and lower cardiac activity, their

antagonists cause a rise in blood pressure through

reversal of these effects.

Yohimbine is an 2-adrenoceptor antagonist.

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-Adrenoceptor antagonists: These can be used to treat

hypertension, angina, cardiac arrhythmias and ischemic heart

disease.

The effects of -adrenoceptor antagonists (‘-blockers’) are only

evident when the heart is under stress or increased workload.

Under these circumstances, they preclude or attenuate increases

in the rate and force of cardiac contraction.

They also cause an increase in peripheral resistance to blood

flow, although this effect is reversed on prolonged administration.

Drugs in this class include propanolol and metoprelol.