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

Abstract

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.

[Cell@Al2O3(HEPiPY)]DCA: A Cellulose Supported Ionic Liquid Catalyst for Synthesis of 11 b,12‐dihydro‐6H,13Hbenzo[5,6][1,3]oxazino[3,4‐a]quinazoline‐6,13‐dione along with in silico assessments

“…The 3D structure of VEGFR-2 was obtained from the protein data bank (PDB ID: 2OH4) and it was assigned as a target towards each oxazinoquinazolines ligand compound thorugh the molecular docking simulation using the HDOCK webserver [Figure 8]. [36,37] The evaluated results were listed in Table 5 to show the scores of molecular docking simulations among the interacting complexes (Figure 7). As mentioned earlier for the variations of electronic structure features of ligand compounds, the resulting scores of molecular docking and the surrounding amino acids in each of the interacting oxazinoquinazolines-VEGFR-2 complex showed impacts of structural modifications on the biological activities of the investigated quinazoline compounds.…”

Design, Synthesis, In Silico and POM Studies for the Identification of the Pharmacophore Sites of Benzylidene Derivatives

“…The chemical reactivity indicators, such as HOMO, LUMO and gap energies were also evaluated [ 41 , 42 ]. Molecular docking studies performed on pathogenic fungal and bacterial proteins have helped to obtain more information about the biological applications of synthesized molecules [ 43 , 44 ]. Thus, their binding affinity and abilities with fungal proteins (PDB: 1KS5, 1R51) and bacterial proteins (PDB: 4A1J, 5IQR) were assessed, whereby the binding mode was then identified.…”

Towards the discovery of potential RdRp inhibitors for the treatment of COVID-19: structure guided virtual screening, computational ADME and molecular dynamics study

“…It has become important to discover and develop new therapeutics for this disease [11,12]. Several potential drug targets to tackle this disease have been identified, which include viral targets like 3CLpro or Mpro, PLpro, RNAdependent RNA polymerase (RdRp), S protein, and host targets like cathepsin L, helicase, furin, TMPRSS2, and ACE2 [13][14][15][16]. RNA-dependent RNA polymerase (RdRp) is a viral enzyme with no host cell homologs; therefore, the inhibitors of SARS-CoV-2 RdRp are selective.…”