1. Drug targets at molecular level

2. Cell Structures:- Since life is made up of cells, then quite clearly drugs must act on cells. The structure of a typical cell is shown in Fig.

3. cell membrane:-All cells in the human body contain a boundary wall called the cell membrane. This encloses the contents of the cell— the cytoplasm.
The cell membrane seen under the electron microscope consists of two identifiable layers. Each layer is made up of an ordered row of phosphoglyceride molecules such as phosphatidylcholine (lecithin). Each phosphoglyceride molecule consists of a small polar head- group, and two long hydrophobic chains.

4. In the cell membrane, the two layers of phospholipids are arranged such that the hydrophobic tails point to each other and form a fatty, hydrophobic centre, while the ionic head-groups are placed at the inner and outer surfaces of the cell membrane (Fig. 2.3).
This is a stable structure since the ionic, hydrophilic head-groups can interact with the aqueous media inside and outside the cell, while the hydrophobic tails maximize vander Waal’s bonding with each other and are kept away from the aqueous environments. The overall result of this structure is to construct a fatty barrier between the cell's interior and its surroundings.

5. The membrane is not just made up of phospholipids, however
The membrane is not just made up of phospholipids, however. There are a large variety of proteins situated in the cell membrane (Fig. 2.4). Some proteins lie on the surface of the membrane. Others are embedded in it with part of their structure exposed to one surface of the membrane or the other. Other proteins traverse the whole membrane and have areas exposed both to the outside and the inside of the cell.
The extent to which these proteins are embedded within the cell membrane structure depends on the type of amino acid present. Portions of protein which are embedded in the cell membrane will have a large number of hydrophobic amino acids, whereas those portions which stick out on the
surface will have a large
number of hydrophilic amino
acids. Many surface proteins
also have short chains of
carbohydrates attached
to them and are thus
classed as glycoproteins.
These carbohydrate
segments are thought to
be important towards cell
recognition.

6. Within the cytoplasm there are several structures, one of which is the nucleus. This acts as the 'control centre' for the cell. The nucleus contains the genetic code—the DNA—and contains the blueprints for the construction of all the cell's enzymes.
There are many other structures within a cell, such as the mitochondria, the golgi apparatus, and the endoplasmic reticulum etc.

7. Four main molecular targets:
Different drugs act at different locations in the cell and there is no one target site which we could pinpoint as the spot where drugs act.
We need to magnify the picture, move down to the molecular level, and find out what types of molecules in the cell are affected by drugs. When we do that, we find that there are four main molecular targets:
(1) lipids
(2) Carbohydrates
(3) proteins
(4) nucleic acids

8. Drug targets
Proteins
Receptors Enzymes Carrier proteins Structural proteins (tubulin)
Lipids
Cell membrane lipids
Nucleic acids
DNA RNA
Carbohydrates
Cell surface carbohydrates Antigens and recognition molecules

9. Drug targets 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
Most drugs are in equilibrium between being bound and unbound to their target
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

10. Lipids as drug targets
The number of drugs which interact with lipids are relatively small and, in general, they all act in the same way—by disrupting the lipid structure of cell membranes.
Eg.1
Anesthetics work by interacting with the lipids of cell membranes to alter the structure and conducting properties of the cell membrane.

11. ‘Tunnelling molecules’ Eg. 1 The antifungal agent—amphotericin B (Fig
‘Tunnelling molecules’ Eg. 1 The antifungal agent—amphotericin B (Fig. 2.5) interacts with the lipids of fungal cell membranes to build 'tunnels' through the membrane. Once in place, the contents of the cell are drained away and the cell is killed.

12. Amphotericin is a fascinating molecule in that one half of the structure is made up of double bonds and is hydrophobic, while the other half contains a series of hydroxyl groups and is hydrophilic.
It is a molecule of extremes and as such is ideally suited to act on the cell membrane in the way that it does. Several amphotericin molecules cluster together such that the alkene chains are to the exterior and interact favourably with the hydrophobic centre of the cell membrane.
The tunnel resulting from this cluster is lined with the hydroxyl groups and so is hydrophilic, allowing the polar contents of the cell to escape (Fig. 2.6).

14. Eg. 2
Gramicidin A (Fig )is a peptide containing 15 amino acids which is thought to coil into a helix such that the outside of the helix is hydrophobic and interacts with the membrane lipids, while the inside of the helix contains hydrophilic groups, thus allowing the passage of ions.
Therefore, gramicidin A could be viewed as an escape tunnel through the cell membrane.
In fact, one molecule of gramicidin would not be long enough to traverse the membrane and it has been proposed that two gramicidin helices align themselves end-to-end in order to achieve the length required (Fig ).

15. Petide Valinomycin is another drug which targets lipids.
The peptides valinomycin (Fig ) and gramicidin A (Fig ) both act as ion conducting antibiotics and allow the uncontrolled movement of ions across the cell membrane.
Unfortunately, both these agents show no selective toxicity for bacterial over mammalian cells and are therefore useless as therapeutic agents.
Their mechanism of action is interesting nevertheless.

16. Eg.3 Ion carriers -Valinomycin
Valinomycin is a cyclic structure containing three molecules of L-valine, three molecules of D-valine, three molecules of L-lactic acid, and three molecules of D-hydroxyisovalerate.
These four components are linked in an ordered fashion such that there is an alternating sequence of ester and amide linking bonds around the cyclic structure.
This is achieved by the presence of a lactic or hydroxyvaleric acid unit between each of the six valine units. Further ordering can be observed by noting that the L and D portions of valine alternate around the cycle, as do the lactate and hydroxyisovalerate units.

17. Mechanism of action:
Since it is cyclic, it forms a doughnut-type structure where the polar carbonyl oxygens of the ester and amide groups face inside, while the hydrophobic side- chains of the valine and hydroxyisovalerate units point outwards.
This is clearly favored since the hydrophobic side-chains can interact via van der Waals forces with the fatty lipid interior of the cell membrane, while the polar hydrophilic groups are clustered together in the centre of the doughnut to produce a hydrophilic environment.
This hydrophilic centre is large enough to accommodate an ion and it is found that a 'naked' potassium ion (i.e. no surrounding water molecules) fits the space and is complexed by the amide carboxyl groups (Fig ).

18. Valinomycin can therefore 'collect' a potassium ion from the inner surface of the membrane, carry it across the membrane and deposit it outside the cell, thus disrupting the ionic equilibrium of the cell (Fig ).
Normally, cells have a high concentration of potassium and a low concentration of sodium. The fatty cell membrane prevents passage of ions between the cell and its environment, and ions can only pass through the cell membrane aided by specialized and controlled ion transport systems.
Valinomycin introduces an uncontrolled ion transport system which proves fatal.
Valinomycin is specific for potassium ions over sodium ions as sodium ions do not lose their surrounding water 'coat' very easily and would have to be transported as the hydrated ion. As such, they are too big for the central cavity of valinomycin.

19. Carbohydrates as drug targets
Until recently carbohydrates were not seen as useful targets for drugs. The main role of carbohydrates in the cell were seen as being of energy storage.
It is now known as carbohydrates have important role to play in various cellular processes such as cell recognition, regulation and growth. Various disease states are associated with these cellular processes. Eg. Bacteria and viruses have to recognize host cells before they can infect them and so the carbohydrates molecules involved in this cell recognition are crucial to the process.
Designing drugs to bind to these carbohydrates may well block the ability of bacteria and viruses to invade host cells.

20. Cell recognition role is mainly played by carbohydrates linked to proteins (called as glycoprotein) and to lipids( called as glycolipids). Such molecules are referred as glycoconjugates.
Usually protein or lipid portion of the molecule is embedded in cell membrane with carbohydrate portion hanging free on the outside of the membrane. This allows the carbohydrate portion to serve as tag which labels and identifies the cell.
One of the most important types of glycoconjugates is glycosphingolipids which consists of a carbohydrate tag and ceramide anchor. The ceramide portion is hydrophobic and is embedded in cell membrane and carbohydrate portion lies out side and acts as molecular ‘tag’ for the cell.
Cell
membrane

21. Antibiotic- eg. Streptomycin Anti HIV drug- Eg. AZT
Drugs which are carbohydrates or contains carbohydrate as part of there structure.
Antibiotic- eg. Streptomycin
Anti HIV drug- Eg. AZT
Antiherpes drug-Acyclovir
Acyclovir
Zidovudine
Streptomycin

22. Proteins and Nucleic acids as drug targets.
The vast majority of drugs interact with proteins or nucleic acids.
We will discuss them separately.