Target SARS-CoV-2: computation of binding energies with drugs of dexamethasone/umifenovir by molecular dynamics using OPLS-AA force field
نویسندگان
چکیده
In recent times, myriads of public have been infected with a novel SARS-CoV-2, and the fatality toll has reached thousands mounting step by step, which is major crisis in world. The challenge for this burning issue pertinent to repurposed medicines prevent coronavirus immense concern all scientists around globe until arrival vaccine. Because global high priority rating on search drugs outfits clinical suitability unique theoretical methodology proposed. approach based explorations biothermodynamics computed via molecular dynamics, root-mean-square deviation (RMSD), radius gyration (Rg) interactions. This tested umifenovir/dexamethasone (SARS-CoV-2) main protease. exploration not only suggested presence strong interactions between (SARS-CoV-2 + umifenovir/dexamethasone) but also emphasized dexamethasone over umifenovir treat SARS-CoV-2. supremacy well supported results trials COVID-19 therapeutic approved management guidelines countries. Thus, work will pave way incremental advancement towards future design development more specific inhibitors treatment SARS-CoV-2 infection humans.
منابع مشابه
Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field
All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of small molecules as part of the SAMPL4 challenge. Compounds were parametrized on the basis of the OPLS-AA force field using three different protocols for deriving partial charges: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equ...
متن کاملOptimization of the OPLS-AA Force Field for Long Hydrocarbons.
The all-atom optimized potentials for liquid simulations (OPLS-AA) force field is a popular force field for simulating biomolecules. However, the current OPLS parameters for hydrocarbons developed using short alkanes cannot reproduce the liquid properties of long alkanes in molecular dynamics simulations. Therefore, the extension of OPLS-AA to (phospho)lipid molecules required for the study of ...
متن کاملThe effect of temperature on the binding affinity of Remdesivir and RdRp enzyme of SARS-COV-2 virus using steered molecular dynamics simulation
The fatal SARS-COV-2 virus appeared in China at the end of 2019 for the first time. This virus has similar sequence with SARS-COV in 2002, but its infection is very high rate. On the other hand, SARS-COV-2 is a RNA virus and requires RNA-dependent RNA polymerase (RdRp) to transcribe its viral genome. Due to the availability of the active site of this enzyme, an effective treatment is targeting ...
متن کاملAccuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC
We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. ...
متن کاملIterative Force-Field Calculation and Molecular Dynamics of Cyclooctanone
Body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (I). 348 MHZ 1H NMR spectra of (I) have been investigated over the temperature range of 25° to -160°C. Two conformation processes affect the 1H NMR spectrum of (I). Iterative force-field calculations on the conformations and conformational interconversion paths of ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Research on Biomedical Engineering
سال: 2021
ISSN: ['2446-4732', '2446-4740']
DOI: https://doi.org/10.1007/s42600-020-00119-y