Theoretical Studies of Molecular Recognition in Protein-Ligand and Protein-Protein Complexes

Molecular recognition between protein and ligand is the foundation of a wide variety of biological processes. We have systematically investigated the molecular determinants responsible for the molecular recognition in the formation of protein-ligand and protein-protein complexes in the following biologically important systems:;In the first project, a large scale data mining and high level quantum chemical analysis was performed to investigate the molecular recognition between Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) and the Human Immunodeficiency Virus type 1 (HIV-1) Reverse Transcriptase (RT). Thirty nine crystal structures of HIV-1 RT with bound NNRTI were systematically examined, resulting in the discovery of Trp-229 of the HIV-1 RT as a key determinant in binding all NNRTIs. This represents an important finding since mutation of HIV-1 RT is the leading cause of NNRTI drugs failure, and Trp-229 was known to be one of the residues that cannot be mutated for the survival of HIV-1. Thus, inhibitors targeting Trp-229 have the promise of overcoming drug resistance to NNRTI inhibitors.;The second project aims at designing enzyme inhibitors for Aspartate-beta-semialdehyde dehydrogenase (ASADH) in the aspartate pathway, with the development of a novel integrated structure-based drug design (SBDD) protocol. The latter integrates the shape-based comparison method, the docking method, the hybrid quantum mechanics/molecular mechanics (QM/MM) simulation, and the quantum chemical analysis methods. Because the aspartate pathway is only present in plants, bacteria, and fungi, and is completely absent in humans, blocking the key enzyme in this pathway, ASADH, offers a viable approach to develop highly selective novel anti-bacterial drugs. Our newly developed SBDD protocol has been applied to designing ASADH inhibitors that target the binding pocket of the coenzyme NADP.;The third project deals with molecular recognition of cell surface receptor by botulinum neurotoxin B. Botulinum neurotoxins (BoNTs) are among the most poisonous toxins known to mankind. Decades of biochemical investigations have led to the realization that the extreme toxicities of BoNTs have a lot to do with the high affinity and specificity of their binding to the neuronal membrane. High level quantum chemical calculations were carried out to quantify the strengths of nonbonded interactions responsible for the molecular recognition of cell surface receptor Syt-II by the botulinum neurotoxin BoNT/B, on the basis of the 2.15 A resolution x-ray crystal structure of the BoNT/B -- Syt-II. The work resulted in the discovery of multiple modes of molecular recognition in the formation of the BoNT/B -- Syt-II complex. The amphipathic alpha-helix of the protein receptor Syt-II interacts with the neurotoxin BoNT/B by forming two interfaces of binding interactions, a hydrophobic interface and a hydrophilic interface, for molecular recognition. The hydrophobic interface consists of residues Phe47, Leu50, Phe54, Phe55 and Ile58 of Syt-II interacting with residues Trp1178, Tyr1181, Tyr1183, Phe1194 and Phe1204 of Hcc of BoNT/B. The hydrophilic interface is composed of residues Lys53 and Glu57 of Syt-II interacting with residues Lys1113, Asp1115, Ser1116 and Lys1192 of Hcc of BoNT/B. Intermolecular interaction energies between BoNT/B and its receptor protein Syt-II were calculated by means of the supermolecular approach at the MP2 level, with solvation energy correction by means of the SM5.42R Solvation Model of Cramer and Truhlar. The binding strength of the hydrophobic interface is quantified and compared with that at the hydrophilic interface of the BoNT/B - Syt-II complex. It was found that the energetic contribution of the hydrophobic interface toward binding of BoNT/B with Syt-II (-9.49 kcal/mol) is much larger than that of the hydrophilic interface (-2.58 kcal/mol). Pair-wise intermolecular interaction analysis is also performed to decipher the molecular determinants for recognition of BoNT/B by Syt-II. The interest lies in determining which types of interactions are used by the protein receptor Syt-II for recognition of BoNT/B, and what their relative importance is. It is concluded that pi -- pi stacking interactions among aromatic residues function as the major molecular determinants for recognition of cell surface receptor Syt-II by the botulinum neurotoxin BoNT/B. (Abstract shortened by UMI.)...