Phase II year
2015
(last award dollars: 2016)
The rate of progress in developing new pharmaceuticals could be accelerated if experimental researchers had practical methods for modeling enzyme mechanisms Unfortunately all current programs have severe limitations either being too slow too complicated or too inaccurate Although an efficient and accurate method for modeling mechanisms in enzyme catalyzed reactions has been developed and made available in the form of the stand alone program MOPAC very few users of this program have used it for that purpose Instead most users have used it for modeling simpler systems such as the docking of substrates into active sites in enzymes This reluctance by experimentalists to model enzyme mechanisms can be attributed to the severe learning curve barrier currently necessary before useful results can be obtained Experimentalists want to focus on the chemistry involved and as far as possible do not want to become involved in computational details software requirements restrictions etc As a result tools that can be used efficiently by computational chemists are being essentially ignored by experimentalists despite the fact that if they were used they would be enormously valuable for modeling postulated reactions to determine their feasibility This project aims to reduce the size of this learning barrier by making MOPAC easier to use by developing documentation to describe what can be done the issues involved methods and strategies for exploring models of enzyme mechanisms and by providing several complete worked examples including the chymotrypsin catalyzed hydrolysis of a peptide bond The approach would begin with a small research project to map out the chymotrypsin mechanism Any software problems encountered would be addressed at this point Various strategies for exploring the mechanism would be examined and using the results a recommended set of procedures would be generated as documentation for use by experimentalists Experimentalists would then use the resulting program and documentation to model reactions and phenomena in systems of interest and their feedback would be used in improving the product A few cycles of modeling and feedback would yield a product that should be an acceptable tool for the experimental research community for modeling enzyme mechanisms Project Narrative The task of designing new pharmaceuticals can be aided by a computer assisted model of enzyme mechanism that would be easy to use A program to do this MOPAC already exists but currently it is only being used by expert computational chemists The objective is to modify the MOPAC program and its documentation to make it suitable for use by experimentalists.
Public Health Relevance Statement: Project Narrative The task of designing new pharmaceuticals can be aided by a computer-assisted model of enzyme mechanism that would be easy to use. A program to do this, MOPAC2012, already exists, but currently it is only being used by expert computational chemists. The objective is to modify the MOPAC2012 program and its documentation to make it suitable for use by experimentalists.
NIH Spending Category: Bioengineering
Project Terms: abstracting; Active Sites; Address; Behavior; Chemistry; chymotrypsin; Communities; computational chemistry; Computer Assisted; Computer Simulation; Computer software; design; Development; Docking; Documentation; enzyme mechanism; enzyme model; Enzymes; Excision; Feedback; Hydrolysis; improved; Incentives; interest; Learning; Manuals; Maps; Methods; Modeling; Modification; One-Step dentin bonding system; Peptides; Pharmacologic Substance; Phase; Procedures; programs; Reaction; Research; Research Personnel; Research Project Grants; research study; Site; System; Techniques; technological innovation; Technology; technology development; Testing; Time; tool; Update; Work
