In Silico Interactions of Some of the Triazole Derivatives with the Main Protease of Coronavirus

This work was done to assess in silico interactions of some of the 1,2,4-triazole derivatives with the main protease (MPro) of coronavirus to approach insights into enzymatic activity inhibition. Fifteen models of triazole derivatives (T2-T16) were investigated in this work to examine such benefits of structural modifications of T1 for approaching better ligand structures. The density functional theory (DFT) calculations indicated that the derivative ligand models were in their new characteristic specifications compared with the original T1 ligand and other T ligands. One important point was that the derivatives ligands were in higher levels of activity in comparison with the original T1 affirming the benefits of employing such structural modifications. Next, the results of molecular docking simulations indicated the potential of derivative ligands for participating in efficient interactions with the MPro target of coronavirus. As a result, the ligand models were stabilized. Their interactions with the MPro of coronavirus revealed that the investigated triazole derivatives could be considered possible inhibitors of MPro of coronavirus. © 2022 by the authors.

Quantum processing of cytidine derivatives and evaluating their in silico interactions with the COVID-19 main protease

This work was performed by the importance of exploring possible medications for COVID-19 pandemic. In this regard, cytidine (Cyd) derivatives were investigated to reach a point to see their benefit of employing for the purpose. Each of halogenated models of Cyd including CydF, CydCl, CydBr, and CydI were investigated in addition to the original CydH model. Density functional theory (DFT) based quantum processing were performed to obtain stabilized structures in addition to evaluation of frontier molecular orbitals features. Next, molecular docking (MD) simulations were performed to reach a point of formations of interacting ligand-target complexes. Among the investigated models CydH and CydI were working better than other model for reaching the purpose of this work, in which the derived CydI model was indeed the ligand with the highest suitability for formation of ligand-target complexes. As a consequence, such ligands of original and halogenated Cyd models might work for inhibition of main protease (MPro) enzyme of COVID-19 based on the obtained meaningful vales for complex strengths in addition interacting with the amino acids of active site. More precisely, the CydI model could be proposed as promising ligand for showing the inhibitory effects towards the MPro target of COVID-19.

In silico investigation of nanocarbon biosensors for diagnosis of COVID-19

In this work, advantages of applications of nanocarbon materials were investigated for diagnosis purpose of coronavirus disease 2019 (COVID-19). To do so, interactions of four representative models of nanocarbon materials including carbon nanotube (CNT), carbon nanocone (CNC), carbon graphene (CGR), and carbon fullerene (CFR) were investigated against spike protein (SP) and main protease (MPO) macromolecular targets of coronavirus. The obtained results indicated that the structure of nanocarbon was important to show its functions for complex formation, in which the CNC ligand was seen to strongly interact with both of SP and MPO targets among other nanocarbon ligands. Additionally, CNC showed more flexibility of conformational relaxation against the target through molecular docking simulation processes. As a distinguished achievement of this work, nanocarbon materials could work for diagnosis purpose of COVID-19 with the best function for CNC to achieve the purpose. All results of this work were obtained based on employing the computer-based in silico approach at the lowest molecular scale including structural optimization and molecular docking simulation.

Screening efficacy of available HIV protease inhibitors on COVID-19 protease

Background and Aim: Advent of COVID-19 attracted the attentions of researchers to develop drugs for its treatment. Besides efforts on developing new drugs, screening available drugs to see their efficacy on COVID-19 could be an urgent action of initiating its pharmacotherapy. In this study, efficacy of HIV protease inhibitors on COVID-19 protease has been examined. Methods: Molecular docking based screening by AutoDock software has been done to examine the efficacy of ligand-receptor interactions. Results: Obtained results of binding energy, inhibitory constant and interactions quality have approved the idea of efficacy of HIV protease inhibitors on COVID-19 protease. Conclusion: Quantitative results indicated different levels of efficacy of investigated ligands for inhibitory activity of COVID-19 and qualitative results indicated various localizations of ligands in the proposed active site of protease. The concluding remarks of this study are to introduce Nelfinavir as the best ligand in quantitative respect and each of Saquinavir, Amprenavir and Fosamprenavir as the best ligands inqualitative respect for possible inhibitory effects on COVID-19 protease. © 2020 Baqiyatallah University of Medical Sciences. All rights reserved.