Use of inhibitors in elucidating the mechanism of an enzyme
Common examples of drugs that work in this way are antacids and laxatives.With antibacterial agents, for example, the conversion of target cells to spheroplasts can be an indication that peptidoglycan synthesis is being targeted, and filamentation of target cells can be an indication that Fts Z or DNA is being targeted.Perhaps the most obvious initial question is ‘what is the (chemical) mechanism of the reaction? As mentioned above, for many enzymes, experiments alone have not identified reaction mechanisms unambiguously, and many proposed and published mechanisms, even in biochemistry textbooks, are probably incorrect in important details (see should be determined.The energy barrier for a reaction step can be calculated as the difference in energy between the reactants and the transition state (see Fig. For a good, realistic molecular model, if the barrier for a proposed mechanism is significantly larger than that derived from experiment (within the limits of accuracy of the computational method and experimental error), then that mechanism is unlikely.
Analysis of enzyme kinetic data to obtain valid information requires attention to two details that are often given less attention than they need.The first is an experimental design that ensures that the variables treated as independent are truly independent, that different interpretations can be distinguished, and that parameter values can be estimated.The second is that authors should be aware of the statistical assumptions that are implicit in the fitting programs that they use, whether commercial or not.Adrian Mulholland received his BSc in Chemistry from the University of Bristol in 1990.After a short period at ICI Pharmaceuticals, he obtained his DPhil from Oxford University in 1995.
Search for use of inhibitors in elucidating the mechanism of an enzyme:
QM/MM calculations also support formation of the covalent intermediate in the wild type enzyme with the natural substrate.