Publications by authors named "Y Sheena Mary"

67 Publications

Evidence of cluster formation of croconic acid with Ag, Au and Cu cages, enhancement of electronic properties and Raman activity.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Jul 27;264:120233. Epub 2021 Jul 27.

Deparment of Chemsitry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India.

Investigation of the adsorption properties croconic acid (CCA) with metal clusters (mC: Ag, Au and Cu) are reported using DFT method. CCA is found to form stable cluster with transition metal clusters of copper, silver and gold. The drug-cluster complexaton energy is slightly more for the copper nanocluster-drug complex. Non-covalent interaction analysis indicated that strong interactions and weak van der Waal interaction is present between drug and metal clusters. Dipole moment of the drug-gold cluster is found to be higher than that of the other systems. SERS studies demonstrates improved Raman signals for multiple wavenumbers of all CCA-metal cluster complexes. Mulliken charge analysis show that all CCA oxygen atom's charge changes due to the interactions with the mCs. Clustering of CCA with metal cages enhances the medicinal properties and the metal nanoclusters will act as a drug carrier of CCA.
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http://dx.doi.org/10.1016/j.saa.2021.120233DOI Listing
July 2021

Modeling the structure and reactivity landscapes of a pyrazole-ammonium ionic derivative using wavefunction-dependent characteristics and screening for potential anti-inflammatory activity.

J Biomol Struct Dyn 2021 Jul 30:1-13. Epub 2021 Jul 30.

Department of Physics, Kanchi Shri Krishna College of Arts and Science, Kanchipuram, Tamil Nadu, India.

Spectroscopic investigations of 1-phenyl -2,3-dimethyl-5-oxo-1,2-dihydro-1-pyrazol-4-ammonium 2[(2-carboxyphenyl) disulfanyl]benzoate (PACB) reported experimentally and theoretically. NH-O interaction is observed and there is a very large downshift for NH-O stretching frequency. Reactive sites are identified from the chemical and electronic properties. For PACB the maximum repulsion was around H33, H55 and H57 atom. LOL shows red regions between C-C and blue around C atoms are surrounded by a delocalized electron cloud. The red ring is a hallmark of electron density depletion from the NCI plot due to electrostatic repulsion and its existences suggests that coordination sphere for PACB is minimally strained around the central ion. Atomic contact energy values and high score of the docking results obtained propose that, PACB may have inhibitory properties and have a significant function in pharmacological chemistry. Molecular dynamics simulation was performed to validate the stability of the title compound with the Bovine thrombin-activatable fibrinolysis inhibitor protein.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1957020DOI Listing
July 2021

Molecular docking, DFT analysis, and dynamics simulation of natural bioactive compounds targeting ACE2 and TMPRSS2 dual binding sites of spike protein of SARS CoV-2.

J Mol Liq 2021 Jul 9:116942. Epub 2021 Jul 9.

Department of Zoology, Shivaji College, University of Delhi, New Delhi, India.

The scientific community is continuously working to discover drug candidates against potential targets of SARS-CoV-2, but effective treatment has not been discovered yet. The virus enters the host cell through molecular interaction with its enzymatic receptors i.e., ACE2 and TMPRSS2, which, if, synergistically blocked can lead to the development of novel drug candidates. In this study, 1503 natural bioactive compounds were screened by HTVS, followed by SP and XP docking using Schrodinger Maestro software. Bio-0357 (protozide) and Bio-597 (chrysin) were selected for dynamics simulation based on synergistic binding affinity on S1 (docking score -9.642 and -8.78 kcal/mol) and S2 domains (-5.83 and -5.3 kcal/mol), and the RMSD, RMSF and Rg analyses showed stable interaction. The DFT analysis showed that the adsorption of protozide/chrysin, the band gap of protozide/chrysin-F/G reduced significantly. From SERS, results, it can be concluded that QDs nanocluster will act as a sensor for the detection of drugs. The docking study showed Bio-0357 and Bio-0597 bind to both S1 and S2 domains through stable molecular interactions, which can lead to the discovery of new drug candidates to prevent the entry of SARS-CoV-2. This in-silico study may be helpful to researchers for further in vitro experimental validation and development of new therapy for COVID-19.
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http://dx.doi.org/10.1016/j.molliq.2021.116942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8267125PMC
July 2021

Investigation of the reactivity properties of a thiourea derivative with anticancer activity by DFT and MD simulations.

J Mol Model 2021 Jul 3;27(8):217. Epub 2021 Jul 3.

Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, 572103, India.

Spectroscopic analysis of 1-(2-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (FPTT) is reported. Experimental and theoretical analyses of FPTT, with molecular dynamics (MD) simulations, are reported for finding different parameters like identification of suitable excipients, interactions with water, and sensitivity towards autoxidation. Molecular dynamics and docking show that FPTT can act as a potential inhibitor for new drug. Additionally, local reactivity, interactivity with water, and compatibility of FPTT molecule with frequently used excipients have been studied by combined application of density functional theory (DFT) and MD simulations. Analysis of local reactivity has been performed based on selected fundamental quantum-molecular descriptors, while interactivity with water was studied by calculations of radial distribution functions (RDFs). Compatibility with excipients has been assessed through calculations of solubility parameters, applying MD simulations. Graphical abstract Reactive sites identified.
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http://dx.doi.org/10.1007/s00894-021-04835-9DOI Listing
July 2021

Modeling the structural and reactivity properties of hydrazono methyl-4H-chromen-4-one derivatives-wavefunction-dependent properties, molecular docking, and dynamics simulation studies.

J Mol Model 2021 May 26;27(6):186. Epub 2021 May 26.

Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey.

This study explains the vibration and interaction of three pharmaceutically active hydrazine derivatives, (E)-3-((2-(2,5-difluorophenyl)hydrazono)methyl)-4H-chromen-4-one (DFH), (E)-3-((2-(4-(trifluoromethyl)phenyl)hydrazono)methyl)-4H-chromen-4-one (TMH), and (E)-3-((2-(3,5-bis(trifluoromethyl)phenyl)hydrazono)methyl)-4H-chromen-4-one (BPH) using theoretical approach. The trend in chemical reactivity and stability of the studied compounds was observed to show increasing stability and decreasing reactivity and this was obtained from orbital energies. The effect of bromine and chlorine atoms, instead of fluorine atoms, is also noted. Surface analysis on the covalent bond was attained by ELF and LOL analysis. Biological activities were predicted using molecular docking studies. Docking results were analyzed with standard drugs, 5-fluorouracil/piperine. Antitumor activity of hydrazine derivatives was found to be higher than reference ones. Molecular dynamics (MD) simulation was performed for 100 ns to validate the stability behavior of hydrazine derivatives with the dual specificity threonine tyrosine kinase (TTK) protein. RMSD, RMSF, Rg, SASA, and intermolecular analysis of DFH, TMH, and BPH with threonine tyrosine kinase forms stable ligand-protein interactions. The molecular and predictive biological properties of three pharmaceutically active hydrazine derivatives which can be helpful to researchers in future experimental validation through in vitro and in vivo studies.
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http://dx.doi.org/10.1007/s00894-021-04800-6DOI Listing
May 2021
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