B5← Nucleic acids mRNA UGCAAAGAG W mRNA mRNA mRNA mRNA mRNA Fg. 4. Protein biosynthesis. The protein is constructed on tRNA and transferred from one tRNa to the next until the full protein has been completed A Intercalators Intercalating drugs bind to DNA by inserting themselves between the stacked base pairs. Intercalation distorts the dNa double helix and prevents DNA from being copied, thus blocking protein synthesis. Drugs acting in this way have been found to be useful antibacterial and antitumor agents In order to slip between the stacked bases, the drug must be planar and have the correct dimensions. It must also be hydrophobic, so that there are favorable intermolecular interactions between the drug and the base pairs above and low it. These requirements are me net by aromatic or heteroaromatic structures, such as the antibacterial agent proflavine (Fig. 5). The tricyclic system is the Proflavine H backbone v.d. W. interactions i ionic bondi Rg. 5. DNA intercalation
Section B- Drug ta correct size to be inserted and can interact with the nucleic acid bases by van der Waals interactions. Proflavine also contains two ionized amino groups that form ionic bonds with the phosphate groups on the DNA backbone, thus strength Some intercalators sit in the grooves that are present in the DNA helix.There re two distinct grooves, one minor and one major. The dimensions of these grooves are important as several drugs show a preference for one or the other Alkylating agents Alkylating agents contain an electrophilic functional group such as an alkyl halide. Reaction of an alkyl halide with a nucleophilic group on DNA (e.g.the nitrogens of a guanine unit) result in a nucleophilic substitution reaction where the nucleophile displaces the halide and forms a covalent bond with the drug ig. 6). If there are two electrophilic groups present in the drug, the reaction occurs twice resulting in cross-linking within a strand or between strands Either way, cross-linking disrupts the normal functions of DNA. Uracil mustard (Section B3)is an example of a drug that acts in this manner Intra-strand cross-linking ter-strand cross-linking Fig. 6. Cross-linking of DNA by an alkylating agent Chaln cutters Some drugs react with dNA to cut the dNa chain. Calicheamicin Yi is an anti tumor agent that was isolated from a bacterium (Fig. 7). It binds to the minor groove of DNA and cuts the dNA chain by producing highly reactive radical species The driving force behind this reaction is the formation of an aromatic ring from the unusual enediyne system NHCO2M H3C OMe Enediyne Meo
B5- Nucleic acids The reaction starts with a nucleophile attacking the trisulfide group (Fig 8) The sulfur that is released then undergoes a Michael addition with a reactive auB-unsaturated ketone. The resulting product cycloaromatizes to produce an aromatic diradical species which ' two hydrogens from DNA. As a esult, dNa becomes a diradical. Reaction with oxygen then leads to chain cutting NHCO2Me NHCO2Me Michael NHCOMe NHCO2Me DNA radical Oxidative Fg: 8 Mechanism of action of calicheamicin Y, Antisense therapy In recent years, drugs have been designed that will bind to mRNA. The strategy is called antisense therapy as it involves the synthesis of oligonucleotides that contain complimentary base pairs to a segment of the target mRNA (Fig9).The rationale is that the synthetic oligonucleotide should bind to the complimentary segment of mRNa by base pairing. Once bound, the antisense drug prevents mRNA from being decoded, and blocks the synthesis of a specific protein. If the protein is a receptor or enzyme, then less of it is synthesized and the activity w Antisense Protein synthesis U CUACG m-RNA Fg. 9. Antisense therapy
Section B-Drug targets associated with the protein is reduced. Therefore, antisense therapy has the same overall effect as using an enzyme inhibitor or a receptor antagonist However, the potential of antisense therapy for target selectivity is much greater as it is theoretically possible to design an antisense drug that would knock out one specific isozyme or receptor subtype Antisense therapy has great potential. However, there are various difficulties that have to be overcome. For example, the sugar-phosphate backbone of oligonucleotides is easily hydrolyzed, hence these compounds are not orally active; therefore, more stable backbones have to be designed. Careful considera tion also has to be given to which segment of mRNA is targeted. The segment should be unique to the target mRNA, but it should also be accessible to the drug. If the mRNA is folded in such a way that a segment is hidden, then an antisense drug will fail to bind Inhibition of rRNA Ribosomal RNA is the target for some important antibacterial agents such as streptomycin, the tetracyclines, chloramphenicol (Fig. 10) and erythromycin All of these agents bind to ribosomal RNA, and in doing so, prevent protein biosynthesis. For example, chloramphenicol binds to the r-RNA of ribosomes then inhibits ribosomal movement along mRNA, probably by inhibiting the mechanism by which the peptide chain is transferred from one t-RNA to another Chloramphenicol is the drug of choice against typhoid and is also used in severe bacterial infections which are insensitive to other antibacterial agents It has also found widespread use against eye infections. However, the drug is quite toxic, especially to bone marrow. HO H O2N- CH2OH Fig. 10. Chloramphenicol
tion B- Drug targets B6 LIPIDS Key Notes Cell membranes Cell membranes act as hydrophobic barriers to the flow of ions, water and polar molecules, and also maintain a concentration gradient for these species eneral anesthetic General anesthetics are fat-soluble molecules that can dissolve in cell membranes and may produce general anesthesia by affecting the fluidity of the cell membrane Various antibacterial and antifungal agents can build tunnels through cell membranes or act as ion carriers. In both cases, normal concentration gradients are disrupted leading to cell death The lipid carrier involved in carrying building blocks for bacterial cell wall synthesis across the cell membrane is the target for vance Related toplcs. Carrier protein Drug solubility a1) Drug absorption(C2) membranes Cell membranes consist of a phospholipid bilayer, which acts as a hydrophobic barrier. Water and ions can only cross this barrier through ion channels, which are controlled by receptors, Polar molecules can only cr ing carrier proteins As a result, there are concentration gradients across the cell membrane for various ions and polar molecules. For example, there is a greater concentration of potassium ions within cells than in the fluid surrounding the cell. Conversely, the concentration of sodium ions is greater outside the cell than inside. The maintenance of these concentration gradients is crucial to several important functions such as the transmission of nerve signals along nerves Cell membranes also act as barriers to any drugs that are intended to act on 6.get within the cell. In order to access the cell, the drug must be sufficiently drophobic to cross the membrane. Alternatively, it should be designed so that it can be accepted by a carrier protein It is generally thought that general anesthetics disrupt cell membrane structure, anesthetics making it more fluid. Support for this theory is provided by the fact that general anesthetics have little similarity in structure, but are hydrophobic in character and easily dissolve in the cell membrane. However, it has been argued that general anesthetic activity may not be solely related to this property, and that a receptor protein may be involved Tunnelers and Compounds that disrupt the cell membrane can have devastating effects. For 'smugglers example, there are various antibacterial and antifungal compounds that destroy cells by building helical structures through the cell membrane, thus forming a