Article ; Online: Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach.
Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy
2020 Volume 251, Page(s) 119388
Abstract: Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond ... ...
| Abstract | Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. The inhibiting potency of 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been investigated by docking simulation against SARS-CoV-2 protein. The optimized geometry shows a planar structure between the chromone and the side chain. Differences in the geometries due to the substitution of the electronegative atom and intermolecular contacts due to the chromone and hydrazinecarbothioamide were analyzed. NBO analysis confirms the presence of two strong stable hydrogen bonded NH⋯O intermolecular interactions and two weak hydrogen bonded CH⋯O interactions. The red shift in NH stretching frequency exposed from IR substantiates the formation of NH⋯O intermolecular hydrogen bond and the blue shift in CH stretching frequency substantiates the formation of CH⋯O intermolecular hydrogen bond. Drug likeness, absorption, distribution, metabolism, excretion and toxicity property gives an idea about the pharmacokinetic properties of the title molecule. The binding energy of the nonbonding interaction with Histidine 41 and Cysteine 145, present a clear view that 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide can irreversibly interact with SARS-CoV-2 protease. |
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| MeSH term(s) | Antiviral Agents/analysis ; Antiviral Agents/chemical synthesis ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacokinetics ; COVID-19/drug therapy ; Chromones/analysis ; Chromones/chemical synthesis ; Chromones/chemistry ; Chromones/pharmacokinetics ; Computational Chemistry ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/metabolism ; Crystallography, X-Ray ; Drugs, Investigational/analysis ; Drugs, Investigational/chemical synthesis ; Drugs, Investigational/chemistry ; Drugs, Investigational/pharmacokinetics ; Humans ; Hydrazines/chemistry ; Hydrogen/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Docking Simulation ; Molecular Structure ; Protein Binding ; Quantum Theory ; SARS-CoV-2/drug effects ; Spectroscopy, Fourier Transform Infrared ; Spectrum Analysis, Raman ; Thioamides/analysis ; Thioamides/chemical synthesis ; Thioamides/chemistry ; Thioamides/pharmacokinetics ; Thiourea/analysis ; Thiourea/chemical synthesis ; Thiourea/chemistry ; Thiourea/pharmacokinetics ; Vibration |
| Chemical Substances | (2E)-N-methyl-2-((4-oxo-4H-chromen-3-yl)methylidene)-hydrazinecarbothioamide ; Antiviral Agents ; Chromones ; Drugs, Investigational ; Hydrazines ; Thioamides ; hydrazinecarbothioamide ; Hydrogen (7YNJ3PO35Z) ; 3C-like protease, SARS coronavirus (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Thiourea (GYV9AM2QAG) |
| Language | English |
| Publishing date | 2020-12-29 |
| Publishing country | England |
| Document type | Journal Article |
| ZDB-ID | 210413-1 |
| ISSN | 1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425 |
| ISSN (online) | 1873-3557 |
| ISSN | 0370-8322 ; 0584-8539 ; 1386-1425 |
| DOI | 10.1016/j.saa.2020.119388 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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