Comparison of random and site directed mutation effects on the efficacy between lead SARS-CoV2 anti-protease drugs Indinavir and Hydroxychloroquine

Abstract The diversification of virus can be attributed to random mutations leading to the development of drug resistance. The variations can be inherited from one generation to the other rendering the drug ineffective. However, a pharmacologically induced selection pressure can be countered by introducing drugs better adapted to work under rapid mutations. In this study we try to explore the effect of site directed and random substitution mutations simulated in the ligand binding region of SARS-CoV2 protease. Amongst six currently studied anti-protease drugs for COVID-19, Indinavir and Hydroxychloroquine were chosen for the study based on their high binding affinity scores, -6.81, and -4.81 respectively. The effect of mutations in protein-ligand binding was analysed in two steps. Initially, analysis of over 90 homologous protease and 100 SARS-CoV-2 orf1ab regions revealed un-conserved residues in the ligand binding sites. Gly170 and Thr190 were identified and interchanged with polar residues such as ARG, ASN and non-polar residues such as ALA, ILE. The resulting mutants were modelled, minimized and docked with Indinavir and Hydroxychloroquine. A higher binding affinity was observed for Indinavir; however, less variance in the binding affinity was observed for the latter. These results were consistent for random mutations as well. A Bio.seqIO based pipeline was build to simulate changes in the ligand binding site. Under the assumption that the ligand binding region has an equal probability of mutation over a given range for continuous distribution, 200 cycles of mutation was carried out in the nucleotide region corresponding to the ligand binding site. A paired t-test revealed a significant difference between the binding affinity of these mutant Indinavir and Hydroxychloroquine-protease complexes. Further, mean and variance was found to be higher for Indinavir-protease complex but Hydroxychloroquine displayed lesser variance pointing at a constant binding capability towards the mutant. Our study highlights the role of Hydroxychloroquine as a drug that can complement an evolving SARS-CoV2 main protease.

Download Full-text

The capricious electrostatic force: Revealing the signaling pathway in integrin α2-I domain

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633618400011 ◽

2018 ◽

Vol 17 (03) ◽

pp. 1840001 ◽

Cited By ~ 2

Author(s):

Zhe Jia ◽

Lin Li ◽

Yunhui Peng ◽

Feng Ding ◽

Emil Alexov

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Signaling Pathway ◽

Binding Affinity ◽

Ligand Binding Site ◽

Conformation Change ◽

Protein Sequence Analysis ◽

Long Distance ◽

Closed Conformation ◽

Open Conformation

Integrins are cellular adhesion proteins located on cell surface. They are known to have open and closed conformations that correspond to high and low binding affinity to ligands, respectively. Integrin [Formula: see text]2 binds to the ligands via the ligand binding domain, [Formula: see text]2-I domain, which also has open and closed conformations. Experimentally, the closed to open conformation change is shown to be triggered by pulling the C-terminal away from the ligand binding site, but how the signal propagates from the distant C-terminal to the binding site is unknown. To explain the mechanisms of the conformation change, we built models of the [Formula: see text]2-I domain open and closed conformations in ligand free and ligand bound states, respectively. We found that the signaling pathway consists of F313-I280-V252 residues that connect the C-terminal and the ligand binding site. The pathway is highly conserved as revealed by a protein sequence analysis among 55 species. Furthermore, MM/PBSA energy calculations on the stabilities and ligand binding affinities of the closed and open conformations are consistent with experimental measurements. The open conformation is more favorable for ligand binding, and the closed conformation is more stable in unbound state. Energy analysis also revealed the “hot spots” for ligand binding, and most residues that contribute strongly to ligand binding free energy are highly conserved in evolution. In addition, the electrostatic analysis showed that the closed conformation has stronger long-range electrostatic attraction to the ligand compared with the open conformation. The difference is caused by the rearrangement of several charged residues during the binding. These observations make us suggest that the integrin [Formula: see text]2-I domain binding process involves the two-step “dock-lock” mechanism. The closed conformation first attracts the ligand from a long distance and afterwards, the open conformation locks the ligand at the binding site with high binding affinity.

Download Full-text