Enzymes are seen as the major drug targets and are also being used as molecular machineries in the production of drug. Therefore, the understanding of enzyme-substrate (E-S) relationship is critical for both drug discovery, development and in their production.

For a required enzymatic activity, the enzyme-substrate (E-S) relationship is the most important determinant of an E-S reaction. This relationship determines the kinetics and the thermodynamics of the reaction at different process conditions both at the lab and the industrial scale.

The understanding of E-S reaction and its relationship at different process conditions, behavior at different pH, temperature and solvents, can provide important insights for designing enzymes, substrates and inhibitors for a desired reaction. Some of the desired enzymatic reactions, include enhanced thermal and pH stability, enhanced turnover number, enhanced substrate specificity and many more attributes. In order to precisely attain these physical and thermodynamic parameters, the R&D groups within the company employs rational redesign or a directed evolution approach to study the enzyme and enhance its properties by employing traditional polymerase chain reaction (PCR)-based mutagenesis.

While in silico approaches like protein modeling, QSAR, docking and molecular dynamics are adopted during this process to design enzymes and substrates, these tools are not customized to mimic those protocols in a rational redesign or a directed evolution study of enzymes.

However, there is a possibility of exploiting computational methods to engineer the enzymes and enhance their productivity in a systematic way. This in silico framework for enzyme engineering is a step beyond the structure-based virtual screening system for drug discovery. The output of the analysis, like the catalytic reaction coordinates of E-S reaction, predicted activation energy and the rate limiting steps of the reaction can be used to design excellent substrates and inhibitors.