1
|
Computational Study of Furosemide-Piperazine (FS – PZ) and 2,3,5,6-tetramethylpyrazine (FS-TP) Co-Crystals. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
2
|
Sunder Raj D, Kesavan DK, Kottaisamy CPD, Kumar VP, Hopper W, Sankaran U. Atomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT - a structural computational approach. J Biomol Struct Dyn 2022; 41:3440-3461. [PMID: 35293845 DOI: 10.1080/07391102.2022.2050946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Helicobacter pylori is a Gram-negative microaerophilic gastric pathogen, responsible for the cause of peptic ulcer around half of the global population. Although several antibiotics and combination therapies have been employed for H. pylori-related gastric ulcer and cancer regiments, identifying potent inhibitors for specific targets of this bacterium will help assessing better treatment periodicity and methods to eradicate H. pylori. Herein, 1,000,000 natural compounds were virtually screened against Helicobacter pylori Peptide deformylase (HpPDF). Pharmacophore hypotheses were created using ligand and receptor-based pharmacophore modeling of GLIDE. Stringent HTVS and IFD docking protocol of GLIDE predicted leads with stable intermolecular bonds and scores. Molecular dynamics simulation of HpPDF was carried out for 100 ns using GROMACS. Hits ZINC00225109 and ZINC44896875 came up with a glide score of -9.967 kcal/mol and -12.114 kcal/mol whereas; reference compound actinonin produced a glide score of -9.730 kcal/mol. Binding energy values of these hits revealed the involvement of significant Van der Waals and Coulomb forces and the deduction of lipophilic forces that portray the deep hydrophobic residues in the S1pocket of H. pylori. The DFT analysis established the electron density-based features of the molecules and observed that the results correlate with intermolecular docking interactions. Analysis of the MD trajectories revealed the crucial residues involved in HpPDF - ligand binding and the conformational changes in the receptor. We have identified and deciphered the crucial features necessary for the potent ligand binding at catalytic site of HpPDF. The resulting ZINC natural compound hits from the study could be further employed for potent drug development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Divya Sunder Raj
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, India
| | | | | | - V Prasanth Kumar
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Waheetha Hopper
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur Campus, Chennai, India
| | | |
Collapse
|
3
|
Arulaabaranam K, Muthu S, Mani G, Irfan A. Conformational study, FT-IR, FT-Raman, solvent effect on UV–Vis, charge transfer and protein–ligand interactions of Methyl-2-pyrazinecarboxylate. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116934] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
4
|
Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, molecular docking and SERS (concentration and solvent dependant) investigations of a methylisoxazole derivative with potential antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
5
|
Mary YS, Mary YS, Rad AS, Yadav R, Celik I, Sarala S. Theoretical investigation on the reactive and interaction properties of sorafenib – DFT, AIM, spectroscopic and Hirshfeld analysis, docking and dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
6
|
Robert HM, Usha D, Amalanathan M, Geetha RRJ, Mary MSM. Vibrational spectral, density functional theory and molecular docking analysis on 4-nitrobenzohydrazide. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.128948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
7
|
Normaya E, Baharu NA, Ahmad MN. Synthesis of thiosemicarbazone-based colorimetric chemosensor for Cu2+ ions’ recognition in aqueous medium: Experimental and theoretical studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
8
|
Al-Otaibi JS, Mary YS, Armaković S, Thomas R. Hybrid and bioactive cocrystals of pyrazinamide with hydroxybenzoic acids: Detailed study of structure, spectroscopic characteristics, other potential applications and noncovalent interactions using SAPT. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127316] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
9
|
Beegum S, Mary YS, Mary YS, Thomas R, Armaković S, Armaković SJ, Zitko J, Dolezal M, Van Alsenoy C. Exploring the detailed spectroscopic characteristics, chemical and biological activity of two cyanopyrazine-2-carboxamide derivatives using experimental and theoretical tools. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117414. [PMID: 31376725 DOI: 10.1016/j.saa.2019.117414] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/13/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
This article represents the spectroscopic and computational studies of two new pyrazine compounds. In order to establish the structure and functional nature of the compounds, we have employed Fourier transformed infrared (FT-IR) and Raman spectra, nuclear magnetic resonance (NMR) spectra, and ultraviolet (UV) absorptions and have compared them with the simulated computational spectra and found that they are in the agreeable range. Simulated hyperpolarisability values are used to obtain the nonlinear optic (NLO) activity of the compound, to be used in organic electronic materials. The charge transfer and related properties was investigated by the simulation of electronic spectrum with time dependent density functional theory (TD-DFT). Natural transition orbitals (NTO) provides information about which region of the molecules are more involved in the electronic transitions and the charge transfer properties for the lowest energy excitation have been analyzed on the basis of electron density variation. Molecular dynamics simulations provide information about the behavior of the molecule in solutions. Frontier orbital analysis and study of various reactivity descriptors like ALIE and Fukui provided deep knowledge on the reactivity side. Molecular docking has been also performed to investigate the interaction between title molecules and exhibits inhibitory activity against Pseudomonas aeruginosa Enoyl-Acyl carrier protein reductase (Fabl).
Collapse
Affiliation(s)
- Shargina Beegum
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - Y Shyma Mary
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India 686101.
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia
| | - Sanja J Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia
| | - Jan Zitko
- Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
| | - Martin Dolezal
- Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
| | - C Van Alsenoy
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| |
Collapse
|
10
|
Cocrystals of pyrazinamide with p-toluenesulfonic and ferulic acids: DFT investigations and molecular docking studies. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.055] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
11
|
Synthesis and spectroscopic study of three new oxadiazole derivatives with detailed computational evaluation of their reactivity and pharmaceutical potential. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.07.026] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
12
|
Al-Tamimi AMS, Mary YS, Miniyar PB, Al-Wahaibi LH, El-Emam AA, Armaković S, Armaković SJ. Synthesis, spectroscopic analyses, chemical reactivity and molecular docking study and anti-tubercular activity of pyrazine and condensed oxadiazole derivatives. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
13
|
Theoretical investigation of nonlinear optical and vibrational properties of two liquid crystalline compounds. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.01.157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
14
|
Synthesis, spectroscopic analyses (FT-IR and NMR), vibrational study, chemical reactivity and molecular docking study and anti-tubercular activity of condensed oxadiazole and pyrazine derivatives. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
15
|
Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.120] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|