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Singh I, Srivastava R, Shukla VK, Pathak SK, Burman T, Al-Mutairi AA, El-Emam AA, Prasad O, Sinha L. Spectroscopic, electronic structure, molecular docking, and molecular dynamics simulation study of 7-Trifluoromethyl-1H-indole-2-carboxylic acid as an aromatase inhibitor. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 280:121530. [PMID: 35752037 DOI: 10.1016/j.saa.2022.121530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 10/31/2022]
Abstract
The present work encompasses a combined experimental and theoretical investigation of the molecular structure, vibrational wavenumbers, electronic structure at the ground and electronic excited states, molecular electrostatic potential surface of 7-(Trifluoromethyl)-1H-indole-2-carboxylic acid (TICA) and possibility of the title molecule as an aromatase inhibitor using molecular docking and molecular dynamic simulations. A stable conformer has been obtained using potential energy scans by varying appropriate dihedral angles. The obtained minimum energy conformer was further optimized at the 6-311++G (d, p) basis set by applying the most accepted B3LYP functional. A good agreement between experimental and calculated normal modes of vibration has been observed. The hydrogen-bonded interaction between two monomeric units of TICA has been investigated using NBO,QTAIM, and NCI (noncovalent interactions) analysis. Molecular docking of TICA with human placental aromatase (PDB ID: 3S79) reveals the formation of polar hydrogen bonds as well as hydrophobic interactions between the ligand and the protein, right in the binding cavity. TICA satisfies all pharmacokinetic filters (Lipinski rule of five, the Veber rule, Ghose rule, Egan rule, as well as the Muegge rule) and has a high bioavailability score of 0.85. Dynamic stability of the ligand within the binding pocket of the target protein has been confirmed by 100 ns molecular dynamics simulation results. The present study provides an excellent starting point for additional in vivo research, and TICA may eventually serve as a significant therapeutic candidate for the treatment of breast cancer.
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Affiliation(s)
- Isha Singh
- Department of Physics, University of Lucknow, 226007 Lucknow, India
| | - Ruchi Srivastava
- Department of Physics, University of Lucknow, 226007 Lucknow, India
| | - Vikas K Shukla
- Department of Physics, Maharishi University of Information Technology Lucknow, Uttar Pradesh, India
| | - Shilendra K Pathak
- Department of Physics, M. M. M. P. G. College, Bhatpar Rani, Deoria, India
| | | | - Aamal A Al-Mutairi
- Department of Chemistry, College of Sciences, Imam Mohammad lbn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Ali A El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Onkar Prasad
- Department of Physics, University of Lucknow, 226007 Lucknow, India
| | - Leena Sinha
- Department of Physics, University of Lucknow, 226007 Lucknow, India.
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Alanazi RL, Zaki M, Bawazir WA. Synthesis and characterization of new metal complexes containing Triazino[5,6–b]indole moiety: In vitro DNA and HSA binding studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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3
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Structural, spectroscopic and computational investigations on (4,6-dimethyl-benzofuran-3-yl)-acetic acid hydrazide. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128748] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kaur M, Kaur H, Kapila A, Reenu. Tautomerism, spectroscopic and computational analysis of Schiff base and its diphenyltin (IV) complex. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hiremath SM, Patil AS, Hiremath CS, Basangouda M, Khemalapure SS, Patil NR, Radder SB, Armaković SJ, Armaković S. Structural, spectroscopic characterization of 2-(5-methyl-1-benzofuran-3-yl) acetic acid in monomer, dimer and identification of specific reactive, drug likeness properties: Experimental and computational study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Hiremath SM, Suvitha A, Patil NR, Hiremath CS, Khemalapure SS, Pattanayak SK, Negalurmath VS, Obelannavar K, Armaković SJ, Armaković S. Synthesis of 5-(5-methyl-benzofuran-3-ylmethyl)-3H- [1, 3, 4] oxadiazole-2-thione and investigation of its spectroscopic, reactivity, optoelectronic and drug likeness properties by combined computational and experimental approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 205:95-110. [PMID: 30015034 DOI: 10.1016/j.saa.2018.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 05/07/2023]
Abstract
This paper reports the synthesis of 5-(5-methyl-benzofuran-3-ylmethyl)-3H- [1, 3, 4] oxadiazole-2-thione (5MBOT) and characterization by FT-IR, FT-Raman, 1H NMR, 13C NMR and UV spectral studies. The density functional theory (DFT) calculations have been executed for the 5MBOT using B3LYP/6-31++G (d, p) basis set. The fundamental modes of the vibrations were designated by the potential energy distribution (PED), and the computed and experimental values support each other. The 1H NMR and 13C NMR chemical shifts of 5MBOT were estimated by gauge-including atomic orbitals (GIAO) method and compared with the experimental chemical shifts. The UV-Vis method used to study the visible absorption maxima (λmax) by using Time-Dependent DFT. Further, the Mulliken population analysis (MPA), natural population analysis (NPA) charges, thermodynamic properties at different temperatures were presented. The calculated HOMO and LUMO energies show that charge transfer within the molecule. The natural bonds orbital (NBO) also computed. Optoelectronic properties have been carried out by combination of DFT calculations and molecular dynamics (MD) simulations, in order to assess the potential of this structure for applications in organic electronics. Further, the study encompassed calculations of reorganization energies for holes and electrons and charge transfer rates. DFT calculations have been also used in order to identify locations possibly sensitive towards the autoxidation mechanism, which correlates between bond dissociation energy for hydrogen abstraction and the mechanism. The MD simulations have been used to understand interaction of 5MBOT with water molecules. Molecular docking studies reveals the antifungal activity of 5MBOT may be due to hydrogen bonding and hydrophobic interactions with different antifungal proteins.
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Affiliation(s)
- Sudhir M Hiremath
- Department of Physics, V.T.U. Regional Research Centre, Belagavi 590 018, Karnataka, India
| | - A Suvitha
- Department of Physics, C.M.R. Institute of Technology, Bangalore 560 037, Karnataka, India
| | - Ninganagouda R Patil
- Department of Physics, B.V.B. College of Engineering and Technology, Hubballi 580 031, Karnataka, India.
| | - Chidanandayya S Hiremath
- Department of Physics, S.K. Arts and H.S.K. Science Institute, Hubballi 580 031, Karnataka, India.
| | - Seema S Khemalapure
- Department of Physics, KLE Dr. M.S. Sheshagiri College of Engineering and Technology, Belagavi 590008, Karnataka, India
| | | | | | - Kotresh Obelannavar
- Department of Chemistry, Karnataka Science College, Dharwad 580 001, Karnataka, India
| | - 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
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia
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Molecular structure, vibrational spectra, NMR, UV, NBO, NLO, HOMO-LUMO and molecular docking of 2-(4, 6-dimethyl-1-benzofuran-3-yl) acetic acid (2DBAA): Experimental and theoretical approach. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.109] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Serdaroglu G, Uludag N. Concise total synthesis of (±)-aspidospermidine and computational study: FT-IR, NMR, NBO, NLO, FMO, MEP diagrams. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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9
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The vibrational spectroscopic studies and molecular property analysis of Estradiol, Tamoxifen and their interaction by density functional theory. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Uludağ N, Serdaroğlu G, Yinanc A. A novel synthesis of octahydropyrido[3,2- ]carbazole framework of aspidospermidine alkaloids and a combined computational, FT-IR, NMR, NBO, NLO, FMO, MEP study of the cis-4a-Ethyl-1-(2hydroxyethyl)-2,3,4,4a,5,6,7,11c-octahydro-1H-pyrido[3,2-c]carbazole. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.046] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV–Vis, MEP diagrams, NBO, NLO, FMO) of the 1,5-methanoazocino[4,3-b]indole core structure. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Almutairi MS, Zakaria AS, Ignasius PP, Al-Wabli RI, Joe IH, Attia MI. Synthesis, spectroscopic investigations, DFT studies, molecular docking and antimicrobial potential of certain new indole-isatin molecular hybrids: Experimental and theoretical approaches. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Al-Wabli RI, Zakaria AS, Attia MI. Synthesis, Spectroscopic Characterization and Antimicrobial Potential of Certain New Isatin-Indole Molecular Hybrids. Molecules 2017; 22:E1958. [PMID: 29140257 PMCID: PMC6150181 DOI: 10.3390/molecules22111958] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/29/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
Molecular hybridization has a wide application in medicinal chemistry to obtain new biologically active compounds. New isatin-indole molecular hybrids 5a-n have been synthesized and characterized by various spectroscopic tools. The in vitro antimicrobial potential of the prepared compounds 5a-n was assessed using diameter of the inhibition zone (DIZ) and minimum inhibitory concentration (MIC) assays against a panel of Gram-negative bacteria, Gram-positive bacteria and fungi. Most of the synthesized compounds 5a-n showed weak activities against Gram-negative bacteria while compounds 5b and 5c exhibited good activities against Gram-positive bacteria. On the other hand, compound 5j emerged as the most active compound towards Candida albicans (C. albicans), with an MIC value of 3.9 µg/mL, and compound 5g as the most active congener towards Asperagillus niger (A. niger), with an MIC value of 15.6 µg/mL. Moreover, compound 5h manifested the best anti-P. notatum effect, with an MIC value of 7.8 µg/mL, making it equipotent with compound 5g.
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Affiliation(s)
- Reem I Al-Wabli
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
| | - Azza S Zakaria
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria 21500, Egypt.
| | - Mohamed I Attia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
- Medicinal and Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre (ID: 60014618), El Bohooth Street, Dokki, Giza 12622, Egypt.
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Al-Wabli RI, Govindarajan M, Almutairi MS, Attia MI. A combined experimental and theoretical study on vibrational and electronic properties of (5-methoxy-1H-indol-1-yl)(5-methoxy-1H-indol-2-yl)methanone. OPEN CHEM 2017. [DOI: 10.1515/chem-2017-0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract(5-Methoxy-1H-indol-1-yl)(5-methoxy-1H-indol-2-yl)methanone (MIMIM) is a bis-indolic derivative that can be used as a precursor to a variety of melatonin receptor ligands. In this work, the energetic and spectroscopic profiles of MIMIM were studied by a combined DFT and experimental approach. The IR, Raman, UV-Vis, 1H NMR and 13C NMR spectra were calculated by PBEPBE and B3LYP methods, and compared with experimental ones. Results showed good agreement between theoretical and experimental values. Mulliken population and natural bond orbital analysis were also performed by time-dependent DFT approach to evaluate the electronic properties of the title molecule.
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Affiliation(s)
- Reem I. Al-Wabli
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Munusamy Govindarajan
- Department of Physics, Avvaiyar Government College for Women (AGCW), Karaikal, Puducherry 609602, India
- Department of Physics, Arignar Anna Government Arts and Science College for Women (AAGASC), Karaikal, Puducherry 609602, India
| | - Maha S. Almutairi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Mohamed I. Attia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
- Medicinal and Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre (ID: 60014618), El Bohooth Street, Giza, Dokki, 12622, Egypt
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