drug targets

Drug targets A Review

DEFINITION

A target is a macro-molecular structure defined by at least a molecular mass that undergoes a specific interaction with therapeutics chemicals administered to treat or diagnose a disease. The target-drug interaction results in clinical effect.

 A Drug target is a biopolymer such as a protein or nucleic acid whose activity can be modified by an external stimulus. The definition is context-dependent and can refer to the biological target of a pharmacologically active drug compound, or the receptor target of a hormone. The implication is that a molecule is "hit" by a signal and its behavior is thereby changed. Biological targets are most commonly proteins such as enzymes, ion channels, and receptors.

PROPERTIES

•         Drug targets are large molecules - macromolecules

•         Drugs are generally much smaller than their targets

•         Drugs interact with their targets by binding to binding sites

•         Binding sites are typically hydrophobic pockets on the surface of macromolecules

•         Binding interactions typically involve intermolecular bonds

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

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

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

Drug targets at the molecular level

We shall now move to the molecular level, because it is here that we can truly appreciate how drugs work. The main molecular targets for drugs are proteins mainly enzymes, receptors and transport proteins, and nucleic acids DNA and RNA. These are large molecules having molecular weights measured in the order of several thousand atomic mass units. They are much bigger than the typical drug, which has a molecular weight in the order of a few hundred atomic mass units.The interaction of a drug with a macromolecular target involves a process known as binding. Th ere is usually a specifi c area of the macromolecule where this takes place, and this is known as the binding site.Typically, this takes the form of a hollow or canyon on the surface of the macromolecule allowing the drug to sink into the body of the larger molecule. Some drugs react with the binding site and become permanently attached via a covalent bond that has a bond strength of 200–400 kJ mol. However, most drugs interact through weaker forms of interaction known as intermolecularbonds.

These include electrostatic or ionic bonds, hydrogen bonds, van der Waals interactions, dipole–dipoleinteractions and hydrophobic interactions. It is also possible for these interactions to take place within a molecule, in which case they are called intramolecular

bonds. None of these bonds is as strong as the covalent bonds that make up the skeleton of a molecule, and so they can be formed, then broken again. This means that an equilibrium takes place between the drug being bound and unbound to its target. The binding forces are strong enough to hold the drug for a certain period of time to let it have an eff ect on the target, but weak enough to allow the drug to depart once it has done its job. Th e length oftime the drug remains at its target will then depend on the number of intermolecular bonds involved in holding it there. Drugs having a large number of interactions are likely to remain bound longer than those that have only a few.

The relative strength of the different intermolecularbinding forces is also an important factor. Functional groups present in the drug can be important in forming intermolecular bonds with the target binding site. If they do so, they are called binding groups. However, the carbon skeleton of the drug also plays an important role in binding the drug to its target. As far as the target binding site is concerned, it too contains functional groups and carbon skeletons which can form intermolecular bonds with ‘visiting’ drugs. The specific regions where this takes place are known as binding regions. The study of how drugs interact with their targets through binding interactions is known as pharmacodynamics.

Fig. Drug targets at the molecular level

Intermolecular binding forces

Electrostatic or ionic bond

• Strongest of the intermolecular bonds (20-40 kJ mol^-1)
• Takes place between groups of opposite charge
• The strength of the ionic interaction is inversely proportional to the distance between the two charged groups
• Stronger interactions occur in hydrophobic environments
• Ionic bonds are the most important initial interactions as a drug enters the binding site      

 2-2-

Hydrogen Bonds

• Vary in strength
• Weaker than electrostatic interactions but stronger than other IF’s
• A hydrogen bond takes place between an electron deficient hydrogen and an electron rich heteroatom (N or O)
• The electron deficient hydrogen is attached to a heteroatom (O or N)
• The electron deficient hydrogen is called a hydrogen bond donor
• The electron rich heteroatom is called a hydrogen bond acceptor

• The interaction involves orbitals and is directional
• 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 is 180^o

  Van der Waals Interactions

• Very weak interactions (2-4 kJmol^-1)
• Occur between hydrophobic regions of the drug and the target
• Due to transient areas of high and low electron densities leading to temporary dipoles
• Interactions drop off rapidly with distance
• Drug must be close to the binding region for interactions to occur
• The overall contribution of van der Waals interactions can be crucial to binding

Dipole-dipole interactions

• Can occur if the drug and the binding site have dipole moments
• Dipoles align with each other as the drug enters the binding site
• Dipole alignment orientates the molecule in the binding site
• The strength of the interaction decreases with distance more quickly than with electrostatic interactions, but less quickly than with van der Waals interactions

 5-

Ion-dipole interactions

• Occur where the charge on one molecule interacts with the dipole moment of another
• Stronger than a dipole-dipole interaction
• Strength of interaction falls off less rapidly with distance than for a dipole-dipole interaction

 

Induced-dipole interactions

• Occur where the charge on one molecule induces a dipole on another
• Occurs between a quaternary ammonium ion and an aromatic ring

Hydrophobic interactions

• Hydrophobic regions of a drug and its target are not solvated
• Water molecules interact with each other and form an ordered layer next to hydrophobic regions - negative entropy
• Interactions between the hydrophobic interactions of a drug and its target ‘free up’ the ordered water molecules
• Results in an increase in entropy
• Beneficial to binding energy

Where do drugs interact

v  Cells

v  Four main targets:

ü  Lipids

ü  Carbohydrates

ü  G Proteins

ü  Nucleic acids

Lipids

ü  Polar head (hydrophilic)

ü  Nonpolar tail (hydrophobic)

ü  lipids typically located in Cell membranes of most interest

Drug interactions with lipids

v  Small number of drugs

v  Disrupt lipid structure and kill cell        

v  Tunnels

v  Carriers/shuttles

v  Amphotericin B                                                 

o   Antifungal agent

o   Forms hydrophilic tunnel

v  Valinomycin                                                   

o   Antibacterial agent/antibiotic

o   Not selective for bacterial cell

o   Shuttle hydrophilic material out of cell (K⁺)

Carbohydrates

v  Empirical formula CH₂O

v  Energy storage, structural

v  Carbohydrates play important roles in cell recognition, regulation and growth.

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

v  Carbohydrates act as antigens

 

Fig. Carbohydrates as drug targets

Carbohydrates as drug targets

ü  Used to tag cells

o   Certain cells associated with certain carbohydrates

o   Glycoproteins, glycosphingolipids

o   Interaction of tag with drug is used to protect or treat cells

ü  More commonly: carbohydrates as part of drugs

o   Anti-HIV

o   Antiherpes

o   Antibiotics

G-Proteins

Guanine nucleotide binding proteins:
            participate in reversible, GTP-mediated interactions.

Common features:

ü  bind GDP and GTP with high affinity, but adopt different structure depending on the bound nucleotide.

ü  GTP-bound complex has high affinity for other proteins affecting their enzymatic activity

ü  possess intrinsic GTPase activity that is usually activated by interaction with regulatory proteins e.g. GAPs

ü  covalent attachment of various lipids eg.myristoylation, palmitoylation,is responsible for membrane targeting

Fig.G Protien as drug targets

Additional control exerted through:

•         GTPase Activating Proteins (GAPs): function on small GTP binding proteins

•         Guanine-nucleotide Exchange Factors (GEFs): promote GDP release

•         Regulators of G-protein Signaling (RGSs): similar to GAPs, but act on heterotrimeric G-Proteins

Two major groups:

•         Small GTP binding proteins

 act downstream of receptor: ras, rac etc.

•         Heterotrimeric G-proteins

 directly coupled to receptor and enzyme

Ø  Coupled to 7 transmembrane spanning receptors: b-adrenergic R, PG-R

Ø  All members are heterotrimeric, consisting of a, b and g subunits

Main targets:

v  Phospholipase Cb

v  Adenylate cyclase

v  Two repeats of six transmembrane a-helices and two catalytic domains that convert ATP into cAMP

v  Activated or inhibited by G-proteins a brain specific isoform is also activated through activated CaM

v  GTP-bound G_as activates AC, GTP-bound G_ai inhibits activity

Nucleic acids

•         Lipid soluble ligands that penetrate cell membrane corticosteroids, mineralocorticoids, sex steroids, Vitamin D, thyroid hormone.

•         Receptors contain DNA-binding domains and act as ligand-regulated transcriptional activators or suppressors.

            Ligand binding of the receptors triggers the formation of a dimeric complex that can interact with specific DNA sequences to induce transcription. The resulting protein products possess half-lifes that are significantly longer than those of other signaling intermediates effects of nuclear receptor agonists can persist for hours or days after plasma concentration is zero.

Fig. Nuclear Receptors

Examples:

ü  Glucocorticoids: Inhibit transcription of COX-2: induce transcription of Lipocortin

ü  Mineralcorticoids: Regulate expression of proteins involved in renal function

ü  Retinoids (Vit A derivatives): Control embryonic development of limbs and organs affect epidermal differentiation

ü  PPARs (Peroxisome Proliferation-Activated Receptors): control metabolic processes

o   PPARa: Target of Fibrates cholesterol lowering drugs, stimulate b-oxidation of fatty acids

o   PPARg: Target of Glitazones anti-diabetic drugs: induce expression of proteins involved in insulin signaling, improved glucose uptake