A Molecular Dynamics Investigation of the Bacterial Cis-Prenyl Transferases: Perspectives on Conformational Flexibility and Chain Elongation Mechanisms

E,Z-farnesyl diphosphate synthase (E,Z-FPPS; Rv1068) and cis-decaprenyl diphosphate synthase (DPPS; Rv2361c) are promising drug targets in Mycobacterium tuberculosis, the causative agent of tuberculosis, due to their essential roles in the early steps of isoprenoid synthesis during the bacterial cell wall biosynthesis. In this work, we performed a series of molecular dynamics (MD) simulations on E,Z-FPP and DPPS both free and in complex with various ligands in order to investigate their dynamic behaviors. Binding pocket volume calculations obtained from the MD trajectories identified several transitions between open and closed states, indicating considerable structural plasticity of the active sites of these proteins, with the largest flexibility found with DPPS. MD simulations on the mutated E,Z-FPPS and DPPS suggested a possible chain elongation mechanisms for the two enzymes which work in series to synthesize the long decaprenyl diphosphate. To incorporate the flexibility of DPPS into our drug discovery protocol, we carried out virtual screening of a library of 39 known DPPS inhibitors with different receptor conformers obtained from the MD simulations, finding better predictive performance with several rarely sampled MD structures than with static, X-ray crystallographic structures. Our results highlight the importance of accounting for protein flexibility in computer-aided drug design targeting E,Z-FPPS and DPPS.