Computational Design and Molecular Dynamics Simulation of Novel Inhibitors of Dihydrofolate Reductase in Three Bacterial Species

Abstract

High affinity, small molecule inhibitors of bacterial dihydrofolate reductase (DHFR) were computationally designed to obtain broad-spectrum antibiotics against bacterial diseases – B. anthracis (anthrax), S. aureus, and M. tuberculosis. Inhibitors were designed and optimized using molecular to target the active site of DHFR based on computational analysis of the energetic frustration and evolutionary importance of amino acid residues present. The Protein Frustratometer (EMBNet, Argentina) and Evolutionary Trace (Baylor University, Houston, TX) were used for to define the active site, as they are useful in determining binding specificity, and areas of the molecule in high energetic states. The bonding residues were then compared to the areas of evolutionary trace and frustration to help identify the active site. 189 small organic molecules were designed to interact with these amino acids based on complementary, non-covalent functional group interactions. These compounds were examined according to Lipinski's Rules of Five, which helps to determine if a drug would be effective in humans. The most favorable candidates were identified and were analyzed through molecular dynamics simulations in order to verify and refine the results. The molecular dynamics simulations were conducted using NAMD v.2.9. (UIUC, Urbana-Champaign, IL) on Tennessee Tech's HPC cluster, and analyzed using VMD. 3D models of these compounds were printed using a 3D printer for conformational analysis.