Protein-small molecule interactions: Structural insights and applications in computational drug discovery

Abstract

Deviation from normal healthy conditions, termed as disease, can often be triggered due to the malfunctioning of proteins. Modulating the functions of proteins by administering therapeutic agents (drugs) may alleviate the disease conditions. The majority of the drugs currently available in the market are small organic molecules due to their pharmacological and commercial advantages. These small molecule drugs interact with the protein targets through specific sites on the surface of the protein structure (binding sites). Thus, the structural data of protein-small molecule complexes forms a crucial starting point for most drug discovery programs. The work reported in this thesis deals with understanding various aspects of protein-small molecule interactions. The thesis begins (Chapter 1) with a general introduction on the implication of proteins structural data in drug discovery programs. Chapter 2 provides a fundamental understanding of the general trend in local quality of protein-small molecule crystal complexes deposited in the Protein Data Bank (PDB). Our results suggest ‘seeing is not always believing’ and aims to sensitize the non-crystallographer user community that high-resolution need not always guarantee confident small molecule binding poses. The study indicates 35% of the inspected ~0.28 million protein-small molecule binding site pairs available from ~66000 PDB entries, need serious attention before using those as input in any important applications. Results reported in Chapter 3 suggest that the stereochemical quality of bound small molecules generally agrees well with their crystallographic quality. The findings from this work could be the stepping-stones for developing structure determination technique-independent ligand pose validation tools. The learning from Chapter 3 is extended to Chapter 4 to investigate the stereochemical quality of the small molecules bound to protein structures determined by cryo-EM. Our data shows that the stereochemical quality of small molecules bound to high-resolution protein structures determined by cryo-EM is comparable to high-quality small molecules bound to protein crystal structures. Chapter 5 presents a computational analysis aimed at providing insights into the molecular basis of the specificity of a novel anti-tubercular compound, NU-6027 (identified in a phenotypic screening by experimental collaborators), towards two out of the eleven known Serine-Threonine Protein Kinases in Mycobacterium tuberculosis (Mtb). Chapter 6 reports the development of a freely available web server that facilitates the identification of new uses of old drugs and aid in drug repurposing. In Chapter 7, the principles of ‘neighborhood behavior’ are exploited to identify potential known drugs that could be repurposed against the main protease of SARS-CoV-2. Chapter 8 discusses a virtual screening strategy to identify potential binders of a novel Mtb target, Rv1636 (or the Universal Stress Protein). Collaborators have experimentally validated some of the compounds shortlisted from the computational studies. Chapter 9 summarizes the findings from work reported in the entire thesis and future applications. Overall, this thesis inspects protein-small molecule complexes from a local perspective, aiding the design of rigorous computational experiments that can contribute to solving global unmet medical needs. Interested readers may contact the author directly for Supplementary data at "sohini@iisc.ac.in"