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Bekono BD, Onguéné PA, Simoben CV, Owono LCO, Ntie-Kang F. Computational discovery of dual potential inhibitors of SARS-CoV-2 spike/ACE2 and M pro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:277-298. [PMID: 38907013 DOI: 10.1007/s00249-024-01713-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 06/01/2024] [Accepted: 06/02/2024] [Indexed: 06/23/2024]
Abstract
To find drugs against COVID-19, caused by the SARS-CoV-2, promising targets include the fusion of the viral spike with the human angiotensin-converting enzyme 2 (ACE2) as well as the main protease (Mpro). These proteins are responsible for viral entry and replication, respectively. We combined several state-of-the-art computational methods, including, protein-ligand interaction fingerprint, 3D-pharmacophores, molecular-docking, MM-GBSA, DFT, and MD simulations to explore two databases: ChEMBL and NANPDB to identify molecules that could both block spike/ACE2 fusion and inhibit Mpro. A total of 1,690,649 compounds from the two databases were screened using the pharmacophore model obtained from PLIF analysis. Five recent complexes of Mpro co-crystallized with different ligands were used to generate the pharmacophore model, allowing 4,829 compounds that passed this prefilter. These were then submitted to molecular docking against Mpro. The 5% top-ranked docking hits from docking result having scores < -8.32 kcal mol-1 were selected and then docked against spike/ACE2. Only four compounds: ChEMBL244958, ChEMBL266531, ChEMBL3680003, and 1-methoxy-3-indolymethyl glucosinolate (4) displayed binding energies < - 8.21 kcal mol-1 (for the native ligand) were considered as putative dual-target inhibitors. Furthermore, predictive ADMET, MM-GBSA and DFT/6-311G(d,p) were performed on these compounds and compared with those of well-known antivirals. DFT calculations showed that ChEMBL244958 and compound 4 had significant predicted reactivity values. Molecular dynamics simulations of the docked complexes were run for 100 ns and used to validate the stability docked poses and to confirm that these hits are putative dual binders of the spike/ACE2 and the Mpro.
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Affiliation(s)
- Boris D Bekono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P. O. Box 47, Yaoundé, CM-00237, Cameroon.
- Center for Drug Discovery, Faculty of Science, University of Buea, P.O. Box 63, Buea, CM-00237, Cameroon.
| | - Pascal Amoa Onguéné
- Center for Drug Discovery, Faculty of Science, University of Buea, P.O. Box 63, Buea, CM-00237, Cameroon
- Department of Chemistry, University of Yaoundé I Institute of Wood Technology Mbalmayo, University of Yaoundé I, BP 50, Mbalmayo, Cameroon
| | - Conrad V Simoben
- Center for Drug Discovery, Faculty of Science, University of Buea, P.O. Box 63, Buea, CM-00237, Cameroon
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Luc C O Owono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P. O. Box 47, Yaoundé, CM-00237, Cameroon
- CEPAMOQ, Faculty of Science, University of Douala, CM-00237, Douala, Cameroon
| | - Fidele Ntie-Kang
- Center for Drug Discovery, Faculty of Science, University of Buea, P.O. Box 63, Buea, CM-00237, Cameroon.
- Department of Chemistry, Faculty of Science, University of Buea, CM-00237, Buea, Cameroon.
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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Khan J, Sakib SA, Mahmud S, Khan Z, Islam MN, Sakib MA, Emran TB, Simal-Gandara J. Identification of potential phytochemicals from Citrus Limon against main protease of SARS-CoV-2: molecular docking, molecular dynamic simulations and quantum computations. J Biomol Struct Dyn 2022; 40:10741-10752. [PMID: 34278965 DOI: 10.1080/07391102.2021.1947893] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The outbreak of coronavirus disease (COVID-19) caused by a novel RNA virus emerged at the end of 2019. Most of the patient's symptoms are mild to moderate, and influenza, acute respiratory distress syndrome (ARDS) and multi-organ failure are common. The disease is mild to moderate in most patients and is reported in many cases such as pneumonia, ARDS and multi-organ dysfunction. This study's objective is to evaluate 25 natural compounds from Citrus limon (CL) used by comprehensive molecular docking, density functional theory (DFT) and molecular dynamics analysis against SARS-CoV-2 main protease (Mpro). Among all the experimental compounds, diosmetin has shown the best docking values against the Mpro of SARS-CoV-2 compared to the standard antiviral drug. In DFT calculations, the order associated with biochemical reactivity is as follows: eriodictoyl > quercetin > spinacetin > diosmetin > luteolin > apigenin, whereas the regions of oxygen and hydrogen atoms from the selected isolated compounds are appropriate for electrophilic and nucleophilic attacks, respectively. Also, HOMO-LUMO and global descriptors values indicated a promising result of these compounds. Moreover, a molecular dynamics simulation study revealed the stable conformation and binding pattern in a stimulating environment of natural compounds CL. Considering molecular docking, simulation, and DFT analysis of the selected compounds, notably eriodictoyl, quercetin, and diosmetin showed good potential against SARS-CoV-2 Mpro. Our in silico study revealed promising antiviral activity, which may be considered a potential key factor or a therapeutic target for COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jishan Khan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Shahenur Alam Sakib
- Department of Theoretical and Computational Chemistry, University of Dhaka, Dhaka
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Zidan Khan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Mahfuz Ahmed Sakib
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, Ourense, Spain
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Single Crystal XRD and DFT investigation of 1,5-dimethyl-4-[(2-oxo-1,2-diphenylethylidene) amino]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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4
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Tallei TE, Tumilaar SG, Niode NJ, Fatimawali, Kepel BJ, Idroes R, Effendi Y, Sakib SA, Emran TB. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (M pro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. SCIENTIFICA 2020; 2020:6307457. [PMID: 33425427 PMCID: PMC7773461 DOI: 10.1155/2020/6307457] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/17/2020] [Accepted: 12/08/2020] [Indexed: 05/20/2023]
Abstract
Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (Mpro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding/ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds' C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Nurdjannah Jane Niode
- Department of Dermatology and Venereology, Faculty of Medicine, University of Sam Ratulangi, Manado 95115, Indonesia
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Billy Johnson Kepel
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Banda Aceh 23111, Indonesia
| | - Yunus Effendi
- Department of Biology, Faculty of Mathematics and Natural Sciences, Al Azhar University, South Jakarta 12110, Indonesia
| | - Shahenur Alam Sakib
- Department of Theoretical and Computational Chemistry, University of Dhaka, Dhaka 1000, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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Soliman UA. Computational Studies, NMR and Ir Spectral Analysis, Normal Coordinate Analysis, and Thermodynamic Properties of 2-Fluoro-4-Pyridineboronic Acid. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620030075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Cui J, Liu J, Wang C, Rong F, He L, Song Y, Zhang Z, Fang S. Efficient electrocatalytic water oxidation by using the hierarchical 1D/2D structural nanohybrid of CoCu-based zeolitic imidazolate framework nanosheets and graphdiyne nanowires. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2019.135577] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Tallei TE, Tumilaar SG, Niode NJ, Kepel BJ, Idroes R, Effendi Y, Sakib SA, Emran TB. Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (M pro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study. SCIENTIFICA 2020; 2020:6307457. [PMID: 33425427 DOI: 10.20944/preprints202004.0102.v2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/17/2020] [Accepted: 12/08/2020] [Indexed: 05/22/2023]
Abstract
Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (Mpro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding/ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds' C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Nurdjannah Jane Niode
- Department of Dermatology and Venereology, Faculty of Medicine, University of Sam Ratulangi, Manado 95115, Indonesia
| | - Billy Johnson Kepel
- Department of Chemistry, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Banda Aceh 23111, Indonesia
| | - Yunus Effendi
- Department of Biology, Faculty of Mathematics and Natural Sciences, Al Azhar University, South Jakarta 12110, Indonesia
| | - Shahenur Alam Sakib
- Department of Theoretical and Computational Chemistry, University of Dhaka, Dhaka 1000, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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8
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Branches ADS, Costa RA, Junior ESA, Bezzera DP, Soares MB, Costa EV, Oliveira KM. Theoretical and experimental study by DFT, molecular docking calculations and cytotoxicity assay of 7,7-dimethylaporphine alkaloids type isolated from Guatteria friesiana (Annonaceae). J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.09.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Radha V, Jone Kirubavathy S, Chitra S. Synthesis, characterization and biological investigations of novel Schiff base ligands containing imidazoline moiety and their Co(II) and Cu(II) complexes. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.109] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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The structural, electronic and spectroscopic properties of 4FPBAPE molecule: Experimental and theoretical study. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Kose E, Karabacak M, Bardak F, Atac A. Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.088] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Alver Ö, Dikmen G. Structure analysis and spectroscopic characterization of 2-Fluoro-3-Methylpyridine-5-Boronic Acid with experimental (FT-IR, Raman, NMR and XRD) techniques and quantum chemical calculations. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.11.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Rajaei I, Mirsattari SN. Synthesis and spectroscopic properties of a copper(II) binuclear complex of a novel tetradentate asymmetrical Schiff base ligand and its DFT study. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Alver Ö, Kaya MF, Dikmen G. Structural characterization, solvent effects on nuclear magnetic shielding tensors, experimental and theoretical DFT studies on the vibrational and NMR spectra of 3-(acrylamido)phenylboronic acid. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.08.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Dikmen G, Alver Ö. NMR, FT-IR, Raman and UV–Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.05.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Sas EB, Kose E, Kurt M, Karabacak M. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:1315-1333. [PMID: 25305625 DOI: 10.1016/j.saa.2014.08.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/19/2014] [Accepted: 08/24/2014] [Indexed: 06/04/2023]
Abstract
In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.
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Affiliation(s)
- E B Sas
- Department of Physics, Ahi Evran University, Kırsehir, Turkey
| | - E Kose
- Department of Physics, Celal Bayar University, Manisa, Turkey
| | - M Kurt
- Department of Physics, Ahi Evran University, Kırsehir, Turkey.
| | - M Karabacak
- Department of Mechatronics Engineering, H.F.T. Technology Faculty, Celal Bayar University, Turgutlu, Manisa, Turkey
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Karabacak M, Kose E, Sas EB, Kurt M, Asiri AM, Atac A. DFT calculations and experimental FT-IR, FT-Raman, NMR, UV-Vis spectral studies of 3-fluorophenylboronic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:306-320. [PMID: 25448934 DOI: 10.1016/j.saa.2014.08.141] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/11/2014] [Accepted: 08/31/2014] [Indexed: 06/04/2023]
Abstract
The spectroscopic (FT-IR, FT-Raman, (1)H and (13)C NMR, UV-Vis), structural, electronic and thermodynamical properties of 3-fluorophenylboronic acid (C6H4FB(OH)2), 3FPBA) were submitted by using both experimental techniques and theoretical methods (quantum chemical calculations) in this work. The experimental infrared and Raman spectra were obtained in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The equilibrium geometry and vibrational spectra were calculated by using DFT (B3LYP) with 6-311++G(d,p) basis set. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. The total energy distributions (TED) of the vibrational modes were performed for the assignments of the title molecule by using scaled quantum mechanics (SQM) method. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The (1)H and (13)C NMR spectra were computed by using the gauge-invariant atomic orbital (GIAO) method, showing a good agreement with the experimental ones. The last one UV-Vis absorption spectra were analyzed in two solvents (ethanol and water), saved in the range of 200-400 nm. In addition these, HOMO and LUMO energies, the excitation energies, density of states (DOS) diagrams, thermodynamical properties and molecular electrostatic potential surface (MEPs) were presented. Nonlinear optical (NLO) properties and thermodynamic features were performed. The experimental results are combined with the theoretical calculations using DFT calculations to fortification of the paper. At the end of this work, the results were proved our paper had been indispensable for the literature backing.
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Affiliation(s)
- M Karabacak
- Department of Mechatronics Engineering, H.F.T. Technology Faculty, Celal Bayar University, Turgutlu, Manisa, Turkey
| | - E Kose
- Department of Physics, Celal Bayar University, Manisa, Turkey.
| | - E B Sas
- Department of Physics, Ahi Evran University, Kırsehir, Turkey
| | - M Kurt
- Department of Physics, Ahi Evran University, Kırsehir, Turkey
| | - A M Asiri
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Center of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A Atac
- Department of Physics, Celal Bayar University, Manisa, Turkey
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Karabacak M, Kose E, Atac A, Sas E, Asiri A, Kurt M. Experimental (FT-IR, FT-Raman, UV–Vis, 1H and 13CNMR) and computational (density functional theory) studies on 3-bromophenylboronic acid. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.07.058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Alver Ö, Kaya MF. Experimental and DFT studies on the vibrational spectra of 1H-indene-2-boronic acid. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.07.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Sachan A, Pathak S, Sinha L, Prasad O, Karabacak M, Asiri A. A combined experimental and theoretical investigation of 2-Thienylboronic acid: Conformational search, molecular structure, NBO, NLO and FT-IR, FT-Raman, NMR and UV spectral analysis. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Dzhekieva L, Adediran SA, Pratt RF. Interactions of "bora-penicilloates" with serine β-lactamases and DD-peptidases. Biochemistry 2014; 53:6530-8. [PMID: 25302576 PMCID: PMC4204886 DOI: 10.1021/bi500970f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Specific
boronic acids are generally powerful tetrahedral intermediate/transition
state analogue inhibitors of serine amidohydrolases. This group of
enzymes includes bacterial β-lactamases and DD-peptidases where
there has been considerable development of boronic acid inhibitors.
This paper describes the synthesis, determination of the inhibitory
activity, and analysis of the results from two α-(2-thiazolidinyl)
boronic acids that are closer analogues of particular tetrahedral
intermediates involved in β-lactamase and DD-peptidase catalysis
than those previously described. One of them, 2-[1-(dihydroxyboranyl)(2-phenylacetamido)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic
acid, is a direct analogue of the deacylation tetrahedral intermediates
of these enzymes. These compounds are micromolar inhibitors of class
C β-lactamases but, very unexpectedly, not inhibitors of class
A β-lactamases. We rationalize the latter result on the basis
of a new mechanism of boronic acid inhibition of the class A enzymes.
A stable inhibitory complex is not accessible because of the instability
of an intermediate on its pathway of formation. The new boronic acids
also do not inhibit bacterial DD-peptidases (penicillin-binding proteins).
This result strongly supports a central feature of a previously proposed
mechanism of action of β-lactam antibiotics, where deacylation
of β-lactam-derived acyl-enzymes is not possible because of
unfavorable steric interactions.
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Affiliation(s)
- Liudmila Dzhekieva
- Department of Chemistry, Wesleyan University , Lawn Avenue, Middletown, Connecticut 06459, United States
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22
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Rawat P, Singh R. Spectral analysis, structural elucidation and evaluation of chemical reactivity of synthesized ethyl-4-[(2-cyano-acetyl)-hydrazonomethyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate through experimental studies and quantum chemical calculations. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.05.050] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Alver Ö, Parlak C, Fatih Kaya M, Dikmen G, Genç L. Vibrational spectroscopic investigation of methyl(5-[2-thienylcarbonyl]-1H-benzimidazol-2-yl: A comparative density functional study. J STRUCT CHEM+ 2014. [DOI: 10.1134/s002247661403007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Muthu S, Ramachandran G, Isac Paulraj E, Swaminathan T. Quantum mechanical study of the structure and spectroscopic (FTIR, FT-Raman), first-order hyperpolarizability and NBO analysis of 1,2-benzoxazol-3-ylmenthane sulfonamide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:603-613. [PMID: 24691375 DOI: 10.1016/j.saa.2014.02.183] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 02/22/2014] [Accepted: 02/25/2014] [Indexed: 06/03/2023]
Abstract
Fourier transform infrared (FTIR) and FT-Raman spectra of 1,2-benzoxazol-3-ylmenthane sulfonamide in the solid phase were recorded and analyzed. The molecular geometry, vibrational frequencies, infrared intensities, Raman activities and atomic charges were calculated using HF and density functional theory calculation (B3LYP) with standard 6-31G(d, p) basis set. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman spectra. The thermodynamic functions of the title compound were also performed. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The dipole moment (μ), polarizability (α) and the hyperpolarizability (β) values of the molecule has been computed. Potential Energy Distribution (PED) were computed for the assignment of unambiguous vibrational fundamental modes. UV-vis spectrum of the compound was also recorded. The theoretical electronic absorption spectra have been calculated by TD-DFT/B3LYP using 6-31G(d,p) basis set. The HOMO and LUMO energy gap reveals that the chemical activity of the molecule. The molecular orbital contributions were studied by density of energy states (DOSs). Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. Finally, simulated FTIR and FT-Raman spectra of 1,2-benzoxazol-3-ylmenthane sulfonamide showed good agreement with the observed spectra.
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Affiliation(s)
- S Muthu
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur 602 105, Tamil Nadu, India.
| | - G Ramachandran
- Research Scholar Research and Development Centre, Bharathiyar University, Coimbatore, Tamil Nadu, India
| | - E Isac Paulraj
- Department of Applied Physics, Pallavan College of Engineering, Kancheepuram 631 502, Tamil Nadu, India
| | - T Swaminathan
- Department of Chemical Engineering, Sri Venkateswara College of Engineering, Sriperumbudur 602 105, Tamil Nadu, India
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25
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Monomeric and dimeric structures analysis and spectroscopic characterization of 3,5-difluorophenylboronic acid with experimental (FT-IR, FT-Raman, 1H and 13C NMR, UV) techniques and quantum chemical calculations. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.10.064] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Karabacak M, Sinha L, Prasad O, Asiri AM, Cinar M. An experimental and theoretical investigation of Acenaphthene-5-boronic acid: conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:753-766. [PMID: 23892116 DOI: 10.1016/j.saa.2013.06.092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/21/2013] [Accepted: 06/25/2013] [Indexed: 06/02/2023]
Abstract
The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability 〈β〉, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.
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Affiliation(s)
- Mehmet Karabacak
- Department of Mechatronics Engineering, H.F.T. Technology Faculty, Celal Bayar University, Turgutlu, Manisa, Turkey.
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27
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Zhou D, Zhai C, Xuan X. Molecular structure and vibrational spectra of N4-acetylcytosine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 112:139-145. [PMID: 23666348 DOI: 10.1016/j.saa.2013.04.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/03/2013] [Accepted: 04/10/2013] [Indexed: 06/02/2023]
Abstract
The infrared and FT-Raman spectra of N4-acetylcytosine in the solid phase have been recorded, and the molecular geometrical parameters were optimized using B3LYP and MP2 methods with 6-311++G(d,p) basis set. The theoretical calculations indicate the presence of four stable conformers of N4-acetylcytosine, and the one containing an intramoleuclar six-membered ring is the most stable. The vibrational wavenumbers, infrared intensities, Raman scattering activities and the corresponding assignments of the observed bands based on the most optimized conformer were performed by B3LYP methods using the aug-cc-pvtz basis set. The observed and calculated frequencies are found to be in good agreement.
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Affiliation(s)
- Dapeng Zhou
- Institute of Fine Chemical and Engineering, Henan University, Kaifeng 475004, Henan, People's Republic of China
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28
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Reinoso S, Vitoria P, San Felices L, Gutiérrez‐Zorrilla JM. Diiron(III)‐Containing 23‐Tungsto‐2‐Borate: First Evidence of 3d Metal Substitution in the {BW
13
} Framework. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201201196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Santiago Reinoso
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, P. O. Box 644, 48080 Bilbao, Spain
| | - Pablo Vitoria
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, P. O. Box 644, 48080 Bilbao, Spain
| | - Leire San Felices
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, P. O. Box 644, 48080 Bilbao, Spain
| | - Juan M. Gutiérrez‐Zorrilla
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco UPV/EHU, P. O. Box 644, 48080 Bilbao, Spain
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29
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Karabacak M, Kose E, Atac A, Ali Cipiloglu M, Kurt M. Molecular structure investigation and spectroscopic studies on 2,3-difluorophenylboronic acid: a combined experimental and theoretical analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 97:892-908. [PMID: 22902933 DOI: 10.1016/j.saa.2012.07.077] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 07/06/2012] [Accepted: 07/22/2012] [Indexed: 06/01/2023]
Abstract
This work presents the characterization of 2,3-difluorophenylboronic acid (abbreviated as 2,3-DFPBA, C(6)H(3)B(OH)(2)F(2)) by quantum chemical calculations and spectral techniques. The spectroscopic properties were investigated by FT-IR, FT-Raman UV-Vis, (1)H and (13)C nuclear magnetic resonance (NMR) techniques. The FT-IR spectrum (4000-400 cm(-1)) and the FT-Raman spectrum (3500-10 cm(-1)) in the solid phase were recorded for 2,3-DFPBA. The (1)H and (13)C NMR spectra were recorded in DMSO solution. The UV-Vis absorption spectra of the 2,3-DFPBA that dissolved in water and ethanol were recorded in the range of 200-400 nm. There are four possible conformers for this molecule. The computational results diagnose the most stable conformer of the 2,3-DFPBA as the trans-cis form. The structural and spectroscopic data of the molecule were obtained for all four conformers from DFT (B3LYP) with 6-311++G (d,p) basis set calculations. The theoretical wavenumbers were scaled and compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method, interpreted in terms of fundamental modes. We obtained good consistency between experimental and theoretical spectra. (13)C and (1)H NMR chemical shifts of the molecule were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Finally the calculation results were analyzed to simulate infrared, Raman, NMR and UV spectra of the 2,3-DFPBA which show good agreement with observed spectra.
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Affiliation(s)
- Mehmet Karabacak
- Department of Physics, Afyon Kocatepe University, Afyonkarahisar, Turkey
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