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Sangavi P, Nagarajan H, Subramaniyan S, Jeyaraman J, Langeswaran K. Unveiling the oncological inhibition of bioactive compounds from Adansonia digitata via in silico analysis by targeting γ-butyrobetaine dioxygenase 1 against triple negative breast cancer. J Biomol Struct Dyn 2024:1-24. [PMID: 39660540 DOI: 10.1080/07391102.2024.2437528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/15/2024] [Indexed: 12/12/2024]
Abstract
Adansonia digitata extracts are well known for their wide range of nutritional and medicinal benefits, including anti-diabetic, anti-inflammatory, antioxidant, and anti-cancerous properties. Yet, its efficacy against breast cancer has not been well-studied so far. Hence this study aims to investigate the anti-cancer properties of phytochemicals from the bark extract of the Adansonia digitata tree against BBOX1, a protein that stimulates the growth of Triple Negative Breast Cancer (TNBC) cells. TNBC is a highly aggressive and fatal form of cancer with limited therapeutic options available. By incorporating computational bioinformatics including Molecular docking, MMGBSA/PBSA, Molecular dynamics, and PCA/FEL analysis, the phytocompounds were scrutinized against BBOX1. Among 274 Phytocompounds only 37 compounds with good pharmacokinetic profiles based on ADME analysis were selected and docked with BBOX1. Of these compounds, the top 6 phytocompounds (CID_22217550, CID_559476, CID_6423866, CID_595387, CID_550931, and CID_559495) demonstrated good binding affinity, with better docking scores ranging from -8.599 to -7.207 kcal/mol respectively. Furthermore, based on MM/GBSA, Interaction profiling, and DFT analysis, only three phytocompounds namely CID_22217550, CID_559476, and CID_550931 were found to interact with the key residues such as Tyr_177, Trp_181, Asp_191, and Tyr_366 with better binding efficacy. In addition, these compounds were also observed to have the least RMS deviations with stable H-bond interactions maintained throughout the MD production run. Henceforth, the overall analysis infers that the phytocompounds CID_22217550, CID_559476, and CID_550931 shall act as potent inhibitors of BBOX1. However, their inhibitory efficacy has be to analyzed with further in vitro and in vivo analysis.
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Affiliation(s)
- P Sangavi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Hemavathy Nagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sneha Subramaniyan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - K Langeswaran
- Department of Biomedical Science, Alagappa University, Karaikudi, Tamil Nadu, India
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Rawat K, Tewari D, Bisht A, Chandra S, Tiruneh YK, Hassan HM, Al-Emam A, Sindi ER, Al-Dies AAM. Identification of AChE targeted therapeutic compounds for Alzheimer's disease: an in-silico study with DFT integration. Sci Rep 2024; 14:30356. [PMID: 39638823 PMCID: PMC11621528 DOI: 10.1038/s41598-024-81285-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 11/25/2024] [Indexed: 12/07/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative condition marked by cognitive deterioration and changes in behavior. Acetylcholinesterase (AChE), which hydrolyzes acetylcholine, is a key drug target for treating AD. This research aimed to identify new AChE inhibitors using the IMPPAT database. We used known drugs as a basis to search for similar chemicals in the IMPPAT database and created a library of 127 plant-based compounds. Initial screening of these compounds was performed using molecular docking, followed by an analysis of their drug-likeness and ADMET properties. Compounds with favorable properties underwent density functional theory (DFT) calculations to assess their electronic properties such as HOMO-LUMO gap, electron density, and molecular orbital distribution. These descriptors provided insights into each compound's reactivity, stability, and binding potential with AChE. Promising candidates were further evaluated through molecular dynamics (MD) simulations over 100 ns and MMPBSA analysis for the last 30 ns. Two compounds, Biflavanone (IMPHY013027) with a binding free energy of - 130.394 kcal/mol and Calomelanol J (IMPHY007737) with - 107.908 kcal/mol, demonstrated strong binding affinities compared to the reference molecule HOR, which has a binding free energy of - 105.132 kcal/mol. These compounds exhibited promising drug-ability profiles in both molecular docking and MD simulations, indicating their potential as novel AChE inhibitors for AD treatment. However, further experimental validation is necessary to verify their effectiveness and safety.
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Affiliation(s)
- Kalpana Rawat
- Computational Biology and Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Disha Tewari
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Amisha Bisht
- Department of Botany, Soban Singh Jeena University, Pt. Badridutt Pandey Campus Bageshwar, Almora, Uttarakhand, 263601, India
| | - Subhash Chandra
- Computational Biology and Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India.
| | - Yewulsew Kebede Tiruneh
- Department of Biology, Biomedical Sciences stream, Bahir Dar University, P.O.Box=79, Bahir, Ethiopia.
| | - Hesham M Hassan
- Department of Pathology, College of Medicine, King Khalid University, 61421, Asir, Saudi Arabia
- Department of pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Ahmed Al-Emam
- Department of Pathology, College of Medicine, King Khalid University, 61421, Asir, Saudi Arabia
| | - Emad Rashad Sindi
- Division of Clinical Biochemistry, Department of Basic Medical Sciences, College of Medicine, University of Jeddah, 23890, Jeddah, Saudi Arabia
| | - Al-Anood M Al-Dies
- Chemistry Department, Umm Al-Qura University, Al-Qunfudah University College, Mecca, Saudi Arabia
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Ahmad S, Singh AP, Bano N, Raza K, Singh J, Medigeshi GR, Pandey R, Gautam HK. Integrative analysis discovers Imidurea as dual multitargeted inhibitor of CD69, CD40, SHP2, lysozyme, GATA3, cCBL, and S-cysteinase from SARS-CoV-2 and M. tuberculosis. Int J Biol Macromol 2024; 270:132332. [PMID: 38768914 DOI: 10.1016/j.ijbiomac.2024.132332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
Two of the deadliest infectious diseases, COVID-19 and tuberculosis (TB), have combined to establish a worldwide pandemic, wreaking havoc on economies and claiming countless lives. The optimised, multitargeted medications may diminish resistance and counter them together. Based on computational expression studies, 183 genes were co-expressed in COVID-19 and TB blood samples. We used the multisampling screening algorithms on the top ten co-expressed genes (CD40, SHP2, Lysozyme, GATA3, cCBL, SIVmac239 Nef, CD69, S-adenosylhomocysteinase, Chemokine Receptor-7, and Membrane Protein). Imidurea is a multitargeted inhibitor for COVID-19 and TB, as confirmed by extensive screening and post-filtering utilising MM\GBSA algorithms. Imidurea has shown docking and MM\GBSA scores of -8.21 to -4.75 Kcal/mol and -64.16 to -29.38 Kcal/mol, respectively. The DFT, pharmacokinetics, and interaction patterns suggest that Imidurea may be a drug candidate, and all ten complexes were tested for stability and bond strength using 100 ns for all MD atoms. The modelling findings showed the complex's repurposing potential, with a cumulative deviation and fluctuation of <2 Å and significant intermolecular interaction, which validated the possibilities. Finally, an inhibition test was performed to confirm our in-silico findings on SARS-CoV-2 Delta variant infection, which was suppressed by adding imidurea to Vero E6 cells after infection.
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Affiliation(s)
- Shaban Ahmad
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Akash Pratap Singh
- Division of Immunology and Infectious Disease Biology, Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India; Academy of Innovative and Scientific Research (AcSIR), Ghaziabad 201002, India; Department of Botany, Maitreyi College, University of Delhi, New Delhi 110021, India.
| | - Nagmi Bano
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Khalid Raza
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Janmejay Singh
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Guruprasad R Medigeshi
- Bioassay Laboratory, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India.
| | - Rajesh Pandey
- Academy of Innovative and Scientific Research (AcSIR), Ghaziabad 201002, India; Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE), Institute of Genomics and Integrative Biology (IGIB), Mall Road, New Delhi 110007, India.
| | - Hemant K Gautam
- Division of Immunology and Infectious Disease Biology, Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India; Academy of Innovative and Scientific Research (AcSIR), Ghaziabad 201002, India.
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Gharbi C, Louis H, Essghaier B, Ubah CB, Benjamin I, Kaminsky W, Nasr CB, Khedhiri L. Single crystal X-ray diffraction analysis, spectroscopic measurement, quantum chemical studies, antimicrobial potency and molecular docking of a new [Co(NCS)4]2(C6H17N3)2·4H2O coordination compound based on piperazine-thiocyanate as co-ligand. J Mol Struct 2024; 1298:136997. [DOI: 10.1016/j.molstruc.2023.136997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
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Khadri MJN, Ramu R, Simha NA, Khanum SA. Synthesis, molecular docking, analgesic, anti-inflammatory, and ulcerogenic evaluation of thiophene-pyrazole candidates as COX, 5-LOX, and TNF-α inhibitors. Inflammopharmacology 2024; 32:693-713. [PMID: 37985602 DOI: 10.1007/s10787-023-01364-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/02/2023] [Indexed: 11/22/2023]
Abstract
The thiophene bearing pyrazole derivatives (7a-j) were synthesized and examined for their in vitro cyclooxygenase, 5-lipoxygenase, and tumour inducing factor-α inhibitory activities followed by the in vivo analgesic, anti-inflammatory, and ulcerogenic evaluations. The synthesized series (7a-j) were characterized using 1H NMR, 13C NMR, FT-IR, and mass spectral analysis. Initially, the compounds (7a-j) were evaluated for their in vitro cyclooxygenase, 5-lipoxygenase, and tumour inducing factor-α inhibitory activities and the compound (7f) with two phenyl substituents in the pyrazole ring and chloro substituent in the thiophene ring and the compound (7g) with two phenyl substituents in the pyrazole ring and bromo substituent in the thiophene ring were observed as potent compounds among the series. The compounds (7f and 7g) with effective in vitro potentials were further analyzed for analgesic, anti-inflammatory, and ulcerogenic evaluations. Also, to ascertain the binding affinities of compounds (7a-j), docking assessments were carried out and the ligand (7f) with the highest binding affinity was docked to know the interactions of the ligand with amino acids of target proteins.
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Affiliation(s)
- M J Nagesh Khadri
- Department of Chemistry, Yuvaraja's College (Autonomous), University of Mysore, Mysuru, Karnataka, 570005, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, 570015, India
| | - N Akshaya Simha
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, 570015, India
| | - Shaukath Ara Khanum
- Department of Chemistry, Yuvaraja's College (Autonomous), University of Mysore, Mysuru, Karnataka, 570005, India.
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Eno EA, Cheng CR, Louis H, Gber TE, Emori W, Ita IAT, Unimke TO, Ling L, Adalikwu SA, Agwamba EC, Adeyinka AS. Investigation on the molecular, electronic and spectroscopic properties of rosmarinic acid: an intuition from an experimental and computational perspective. J Biomol Struct Dyn 2023; 41:10287-10301. [PMID: 36546691 DOI: 10.1080/07391102.2022.2154841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
Various drugs such as corticosteroids, salbutamol, and β2 agonist are available for the treatment of asthma an inflammatory disease and its symptoms, although the ingredient and the mode of action of these drugs are not clearly elucidated. Hence this research aimed at carrying out improved scientific research with respect to the use of natural product rosmarinic acid which poses minima, side effects. Herein, we first carried out extraction, isolation, and spectroscopic (FT-IR, 1H-NMR and 13C-NMR) investigation, followed by molecular modeling analysis on the naturally occurring rosmarinic acid extracted from Rosmarinus officinalis. A detailed comparison of the experimental and theoretical vibrational analysis has been carried out using five DFT functionals: BHANDH, HSEH1PBE, M06-2X, MPW3PBE and THCTHHYB with the basis set 6-311++G (d, p) to investigate into the structural, reactivity, and stability of the isolated compound. Frontier molecular orbital analysis and appropriate quantum descriptors were calculated. Results showed that the compound was more stable at M06-2X and more reactive at HSEH1PBE with an energy gap of 6.43441 eV and 3.8047 eV, respectively, which was later affirmed by the global quantum reactivity parameters. From natural bond orbital analysis, π* → π* is the major contributor to electron transition with the summation perturbation energy of 889.57 kcal/mol, while π → π* had the perturbation energy totaling of 145.3 kcal/mol. Geometry analysis shows BHANDH to have lower bond length values and lesser deviation from 120° in carbon-carbon angle. The potency of the title molecule as an asthma drug was tested via a molecular docking approach and the binding score of -8.2 kcal/mol was observed against -7.0 of salbutamol standard drug, suggesting romarinic acid as a potential natural organic treatment for asthma.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ededet A Eno
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Chun-Ru Cheng
- Key Laboratory of Material Corrosion and Protection of Sichuan Province, Zigong, Sichuan, PR China
- College of Chemical Engineering, Institute of Pharmaceutical Engineering Technology and Application, Key Laboratory of Green Chemistry of Sichuan Institutes of Higher Education, Sichuan University of Science & Engineering, Zigong, Sichuan, PR China
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Terkumbur E Gber
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Wilfred Emori
- Key Laboratory of Material Corrosion and Protection of Sichuan Province, Zigong, Sichuan, PR China
- School of Materials Science and Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan, PR China
| | - Ima-Abasi T Ita
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Tomsmith O Unimke
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Liu Ling
- College of Chemical Engineering, Institute of Pharmaceutical Engineering Technology and Application, Key Laboratory of Green Chemistry of Sichuan Institutes of Higher Education, Sichuan University of Science & Engineering, Zigong, Sichuan, PR China
| | - Stephen A Adalikwu
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Ernest C Agwamba
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemistry, Covenant University Ota, Ota, Nigeria
| | - Adedapo S Adeyinka
- Research Centre for Synthesis and Catalysis, Department of Chemical sciences, University of Johannesburg, Johannesburg, South Africa
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Natarajan R, Sivaperuman A, Samuel A, Patel DH, Jain N, Veerappan M, Kumar NK. 2D QSAR, Design, and in Silico Analysis of Thiophene-Tethered Lactam Derivatives as Antimicrobial Agents. Chem Biodivers 2023; 20:e202300331. [PMID: 37337355 DOI: 10.1002/cbdv.202300331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND A very high rate of resistance causes health-care-associated and community-acquired infections. E. coli is one of the nine pathogens of highest concern to most of the antibiotics and other class of antimicrobials. OBJECTIVE The objective of the present study is to develop novel thiophene derivatives using 2D QSAR and in silico approach for E. coli resistance. METHODS Substituted thiophene series reported by Nishu Singla et al., were taken for QSAR analysis. From the results, a set of 15 new compounds were designed. A complete in silico analysis has been done using PADEL, Autodock vina, Swiss ADME, Protox II software. RESULTS The designed compounds obey the Lipinski's rule of five and were known to have excellent inhibitory action (pIC50 values -0.87 to -1.46) which is similar to the most active compound of the data set (pIC50 -0.69) taken for the study. The bioavailability score (0.65) with no toxicity representing that the designed compounds are suitable for oral administration. CONCLUSION The designed compounds are inactive for mutagenicity and cytotoxicity and ADMET studies states that these molecules are likely to be orally bioavailable and could be easily transported, diffused, and absorbed. So, the designed compounds will definitely serve as a lead antibacterial agent for E. coli resistance.
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Affiliation(s)
- Ramalakshmi Natarajan
- Department of Pharmaceutical Chemistry, C.L.BaidMetha College of Pharmacy, Thorapakkam-600097, Chennai, India
| | - Amuthalakshmi Sivaperuman
- Department of Pharmaceutical Chemistry, C.L.BaidMetha College of Pharmacy, Thorapakkam-600097, Chennai, India
| | - Abiseik Samuel
- Department of Pharmaceutical Chemistry, C.L.BaidMetha College of Pharmacy, Thorapakkam-600097, Chennai, India
| | - Dinesh Hansaram Patel
- Department of Pharmaceutical Chemistry, C.L.BaidMetha College of Pharmacy, Thorapakkam-600097, Chennai, India
| | - Nikhil Jain
- Department of Pharmaceutical Chemistry, C.L.BaidMetha College of Pharmacy, Thorapakkam-600097, Chennai, India
| | - Manigandan Veerappan
- Department of Pharmaceutical Chemistry, C.L.BaidMetha College of Pharmacy, Thorapakkam-600097, Chennai, India
| | - Nikhil Kushal Kumar
- Department of Pharmaceutical Chemistry, C.L.BaidMetha College of Pharmacy, Thorapakkam-600097, Chennai, India
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Agwamba EC, Louis H, Olagoke PO, Gber TE, Okon GA, Fidelis CF, Adeyinka AS. Modeling of magnesium-decorated graphene quantum dot nanostructure for trapping AsH 3, PH 3 and NH 3 gases. RSC Adv 2023; 13:13624-13641. [PMID: 37152564 PMCID: PMC10155676 DOI: 10.1039/d3ra01279d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/18/2023] [Indexed: 05/09/2023] Open
Abstract
A magnesium-decorated graphene quantum dot (C24H12-Mg) surface has been examined theoretically using density functional theory (DFT) computations at the ωB97XD/6-311++G(2p,2d) level of theory to determine its sensing capability toward XH3 gases, where X = As, N and P, in four different phases: gas, benzene solvent, ethanol solvent and water. This research was carried out in different phases in order to predict the best possible phase for the adsorption of the toxic gases. Analysis of the electronic properties shows that in the different phases the energy gap follows the order NH3@C24H12-Mg < PH3@C24H12-Mg < AsH3@C24H12-Mg. The results obtained from the adsorption studies show that all the calculated adsorption energies are negative, indicating that the nature of the adsorption is chemisorption. The adsorption energies can be arranged in an increasing trend of NH3@C24H12-Mg < PH3@C24H12-Mg < AsH3@C24H12-Mg. The best adsorption performance was noted in the gas phase compared to the other studied counterparts. The interaction between the adsorbed gases and the surfaces shows a non-covalent interaction nature, as confirmed by the quantum theory of atoms-in-molecules (QTAIM) and non-covalent interactions (NCI) analysis. The overall results suggest that we can infer that the surface of the magnesium-decorated graphene quantum dot C24H12-Mg is more efficient for sensing the gas AsH3 than PH3 and NH3.
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Affiliation(s)
- Ernest C Agwamba
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
- Department of Chemistry, Covenant University Otta Nigeria
- Department of Chemical Sciences, University of Johannesburg Johannesburg South Africa
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Praise O Olagoke
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
| | - Terkumbur E Gber
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Gideon A Okon
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
| | - Chidera F Fidelis
- Computational and Bio-Simulation Research Group, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Adedapo S Adeyinka
- Department of Chemical Sciences, University of Johannesburg Johannesburg South Africa
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Jia D, Miao W, Rui Y, Chen Y, Liang W, Yi Z. Thyroid hormone transporters binding affinity of methoxypoly chlorinated biphenyls: Insights from molecular simulations and fluorescence competitive binding experiment. Int J Biol Macromol 2023; 231:123224. [PMID: 36649871 DOI: 10.1016/j.ijbiomac.2023.123224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
Triiodothyronine (T3) and thyroxine (T4) are essential for regulating cell metabolic rate and promoting the development and differentiation of brain tissue, especially in fetuses and newborns. In particular, it has been proved that MeO-PCBs have high binding to thyroid hormone transporters and can competitively bind to thyroid carrier proteins, thus destroying the transport of the thyroid hormone. Fluorescence competition binding experiments and docking results showed that the binding affinity decreased with the increase in number of chlorine atoms of MeO-PCBs. The interaction mechanism of MeO-PCBs with thyroid transporter (TTR) and thyroid binding globulin (TBG) was compared by computational simulation and the binding free energies were calculated by the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Electrostatic potential analysis, Hirshfeld surface analysis and electron density difference maps confirmed the existence of electrostatic interactions. Secondly, noncovalent interaction (NCI) analysis further indicated that the main driving force for the combination of MeO-PCBs to TTR and TBG were electrostatic interaction and van der Waals interaction. The conformational changes of the protein after binding were studied by a molecular dynamic simulation.
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Affiliation(s)
- Dan Jia
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Wangli Miao
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Yuefan Rui
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Yanting Chen
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Wenhui Liang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zhongsheng Yi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
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Rajaraman D, Anthony LA, Nethaji P, Vallangi R. One-pot synthesis, NMR, quantum chemical approach, molecular docking studies, drug-likeness and in-silico ADMET prediction of novel 1-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-2-(furan-2-yl)-4,5-diphenyl-1 H-imidazole derivatives. J Mol Struct 2023; 1273:134314. [PMID: 36277302 PMCID: PMC9576197 DOI: 10.1016/j.molstruc.2022.134314] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/08/2022]
Abstract
A novel drug to treat SARS-CoV-2 infections and hydroxyl chloroquine analogue, 1-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-2-(furan-2-yl)-4,5-diphenyl-1H-imidazole (DDFDI) compound has been synthesized in one pot reaction. The novel compound DDFDI had been characterized by FT-IR, 1H-NMR and 13C-NMR spectral techniques. The geometrical structure was optimized by density functional theory (DFT) method at B3LYP/6-31G (d, p) as the basis set. The smaller energy value provides the higher reactivity of DDFDI compound than hydroxyl chloroquine and was corrected by high electrophilic and low nucleophilic reactions. The stability and charge delocalization of the molecule were also considered by natural bond orbital (NBO) analysis. The HOMO-LUMO energies describe the charge transfer which takes place within the molecule. Molecular electrostatic potential has also been analysed. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. Molecular docking studies are implemented to analyse the binding energy of the DDFDI compound against Covid-19/6W41, COVID-19/6WCF, COVID-19/6Y84 and COVID-19/6W4B receptors and found to be considered as a better antiviral agents.
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Affiliation(s)
- D Rajaraman
- Department of Chemistry, St Joseph University, Virgin Town, Dimapur, Nagaland 797 115, India
| | - L Athishu Anthony
- Department of Chemistry, St Joseph University, Virgin Town, Dimapur, Nagaland 797 115, India
| | - P Nethaji
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Tamil Nadu 603 110, India
| | - Ravali Vallangi
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Monirampore, Kolkata, West Bengal 700120, India
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Nagarajan K, Surumbarkuzhali N, Parimala K. Spectral analysis (FT-IR, FT-Raman, UV and NMR), molecular docking, ADMET properties and computational studies: 2-Hydroxy-5-nitrobenzaldehyde. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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12
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Louis H, Chima CM, Amodu IO, Gber TE, Unimuke TO, Adeyinka AS. Organochlorine detection on transition metals (X=Zn, Ti, Ni, Fe, and Cr) anchored fullerenes (C
23
X). ChemistrySelect 2023. [DOI: 10.1002/slct.202203843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hitler Louis
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Chioma M. Chima
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Ismail O. Amodu
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Mathematics Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Terkumbur E. Gber
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Tomsmith O. Unimuke
- Computational and Bio-Simulation Research Group University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry Faculty of Physical Sciences University of Calabar Calabar Nigeria
| | - Adedapo S. Adeyinka
- Department of Chemical Sciences University of Johannesburg Johannesburg South Africa
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13
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Şuekinci Yılmaz A, Uluçam G. Novel N-benzyl-2-oxo-1,2-dihydrofuro [3,4-d]pyrimidine-3(4H)-carboxamide as anticancer agent: Synthesis, drug-likeness, ADMET profile, DFT and molecular modelling against EGFR target. Heliyon 2023; 9:e12948. [PMID: 36711281 PMCID: PMC9876965 DOI: 10.1016/j.heliyon.2023.e12948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
A novel compound N-benzyl-2-oxo-1,2-dihydrofuro [3,4-d]pyrimidine-3(4H)-carboxamide (DHFP) was synthesized by addition, rearrangement, and intramolecular cyclization reactions. The three-dimensional geometry of DHFP has been determined by density functional theory calculations in the gas phase. Thus, the geometrical properties of DHFP such as the bond lengths, bond angles, and dihedral bond angles have been determined in the optimized molecular configuration. Also, the HOMO-LUMO energies were calculated. The charge distribution of the DHFP has been calculated by Natural Population Analysis (NPA) approach. NMR and FTIR spectra were calculated and compared with their experimental corresponding to confirm the synthesis of the DHFP. The anticancer activities of the DHFP were also determined on human colon cancer (HT29) and prostate cancer (DU145) cell lines. Molecular docking studies of the DHFP with EGFR tyrosine kinase, which is responsible for cancer cell proliferation and growth, were performed and it was observed that docking interaction took place. The DHFP has the potential to be a drug, as it is determined that DHFP obeys Lipinski's five rules, can cross the blood-brain barrier, and can be rapidly absorbed from the gastrointestinal wall.
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Affiliation(s)
- Ayşen Şuekinci Yılmaz
- Corresponding author. Chemistry Department, Faculty of Science, Trakya University, 22030, Edirne, Turkey.
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14
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Nkoe P, Manicum ALE, Louis H, Malan FP, Nzondomyo WJ, Chukwuemeka K, Sithole SA, Imojara A, Chima CM, Agwamba EC, Unimuke TO. Influence of solvation on the spectral, molecular structure, and antileukemic activity of 1-benzyl-3-hydroxy-2-methylpyridin-4(1H)-one. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Integrated Spectroscopic, Bio-active Prediction and Analytics of Isoquinoline Derivative for Breast Cancer Mitigation. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00479-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Spectroscopic and molecular electronic property investigation of 2-phenylpyrimidine-4, 6-diamine via 1H NMR, UV–vis, FT-Raman, FT-IR, and DFT approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133195] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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17
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Osigbemhe IG, Oyoita EE, Louis H, Khan EM, Etim EE, Edet HO, Ikenyirimba OJ, Oviawe AP, Obuye F. Antibacterial potential of N-(2-furylmethylidene)-1, 3, 4-thiadiazole-2-amine: Experimental and theoretical investigations. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Benjamin I, Udoikono AD, Louis H, Agwamba EC, Unimuke TO, Owen AE, Adeyinka AS. Antimalarial potential of naphthalene-sulfonic acid derivatives: Molecular electronic properties, vibrational assignments, and in-silico molecular docking studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133298] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Spectroscopic, quantum chemical and molecular docking studies on friedelin, the major triterpenoid isolated from Garcinia imberti. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Synthesis, characterization, DFT studies, and molecular modeling of 2-(-(2-hydroxy-5-methoxyphenyl)-methylidene)-amino) nicotinic acid against some selected bacterial receptors. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02550-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Antibacterial Potential of 2-(-(2-Hydroxyphenyl)-methylidene)-amino)nicotinic Acid: Experimental, DFT Studies, and Molecular Docking Approach. Appl Biochem Biotechnol 2022; 194:5680-5701. [PMID: 35802239 DOI: 10.1007/s12010-022-04054-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 11/02/2022]
Abstract
The problems associated with antibacterial drug discovery have kept the model of antibacterial drug to an extraordinary low level. Humans carry millions of bacteria; some species of bacteria can cause infectious disease, while some are pathogenic. Infectious bacteria which can reproduce quickly in the body can cause diseases such as tuberculosis, cholera, pneumonia, and typhoid, thus arises an urgent need to develop new drugs. Herein, 2-{[(2-hydroxyphenyl)methylidene]amino}nicotinic acid was synthesized from the condensation of o-phenylenediamine and 5-nitrosalicaldehyde followed by detailed characterization by ultraviolet-visible spectroscopy, vibrational studies FT-IR, nuclear magnetic resonance (1H-NMR, 13C-NMR), and gas chromatography coupled with mass spectroscopy (GC-MS). The complex synthesized was screened against selected microbes in order to establish their potential antimicrobial activity using selected known drugs as reference. From the results obtained, the Schiff base exhibited antimicrobial activity against all the tested microorganisms except Candida albicans isolate, which exhibited zero diameter zone of inhibition. The theoretical investigations of the synthesized compounds were computed using density functional theory (DFT) at the B3LYP/6-311 + + G(d, p) level of theory and in silico molecular docking simulation. By comparing binding affinity of the studied compound and the standard drug (ampicillin), the studied compound docked against bacterial protein showed a high binding affinity for E. coli 6.6 kcal/mol and makes it effective as an antibacterial agent for E. coli.
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22
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Synthesis, spectroscopic (13C/1H-NMR, FT-IR) investigations, quantum chemical modelling (FMO, MEP, NBO analysis), and antioxidant activity of the bis-benzimidazole molecule. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Wei K, Louis H, Emori W, Idante PS, Agwamba EC, Cheng CR, Eno EA, Unimuke TO. Antispasmodic activity of carnosic acid extracted from rosmarinus officinalis: Isolation, spectroscopic characterization, DFT studies, and in silico molecular docking investigations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132795] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Eno EA, Louis H, Unimuke TO, Egemonye TC, Adalikwu SA, Agwupuye JA, Odey DO, Abu AS, Eko IJ, Ifeatu CE, Ntui TN. Synthesis, characterization, and theoretical investigation of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)asmino-4-(2,4-dichlorophenyl)thiazol-5-yl-diazenyl)phenyl as potential SARS-CoV-2 agent. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract
The synthesis of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)amino-4-(2,4 dichlorophenyl)thiazol-5-yl-diazenyl)phenyl is reported in this work with a detailed structural and molecular docking study on two SARS-COV-2 proteins: 3TNT and 6LU7. The studied compound has been synthesized by the condensation of cyanuric chloride with aniline and characterized with various spectroscopic techniques. The experimentally obtained spectroscopic data has been compared with theoretical calculated results achieved using high-level density functional theory (DFT) method. Stability, nature of bonding, and reactivity of the studied compound was evaluated at DFT/B3LYP/6-31 + (d) level of theory. Hyper-conjugative interaction persisting within the molecules which accounts for the bio-activity of the compound was evaluated from natural bond orbital (NBO) analysis. Adsorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties of the experimentally synthesized compound was studied to evaluate the pharmacological as well as in silico molecular docking against SARS-CoV-2 receptors. The molecular docking result revealed that the investigated compound exhibited binding affinity of −9.3 and −8.8 for protein 3TNT and 6LU7 respectively. In conclusion, protein 3TNT with the best binding affinity for the ligand is the most suitable for treatment of SARS-CoV-2.
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Affiliation(s)
- Ededet A. Eno
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Tomsmith O. Unimuke
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - ThankGod C. Egemonye
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Stephen A. Adalikwu
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
| | - John A. Agwupuye
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Diana O. Odey
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Biochemistry, Faculty of Physical Sciences , Cross River University of Technology , Calabar , Nigeria
| | - Abu Solomon Abu
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Marine Biology, Faculty of Biology Sciences , University of Calabar , Calabar , Nigeria
| | - Ishegbe J. Eko
- Department of Polymer and Textile Engineering , Ahmadu Bello University Zaria , Kaduna , Nigeria
| | - Chukwudubem E. Ifeatu
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
| | - Tabe N. Ntui
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Chemistry, Faculty of Physical Sciences , Cross River University of Technology , Calabar , Nigeria
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25
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Eno EA, Louis H, Unimuke TO, Agwamba EC, Etim AT, Mbonu JI, Edet HO, Egemoye T, Adegoke KA, Ameuru US. Photovoltaic properties of novel reactive azobenzoquinolines: experimental and theoretical investigations. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
In this work, synthesis, characterization, DFT, TD-DFT study of some novel reactive azobenzoquinoline dye structures to elucidate their photovoltaic properties. The azobenzoquinoline compounds were experimentally synthesized through a series of reaction routes starting from acenaphthene to obtained aminododecylnaphthalimide and finally coupled with diazonium salts to get the desired azobenzoquinoline. Azo dye synthesized differ in the number of alkyl chains designated as (AR1, AR2, AR3, and AR4) which were experimentally analyzed using FT-IR and NMR spectroscopic methods. The synthesized structures were modelled for computational investigation using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) combined with B3LYP and 6-31+G(d) basis set level of theory. The results showed that the HOMO-LUMO energy gap was steady at approximately 2.8 eV as the alkyl chain increases, which has been proven to be within the material energy gap limit for application in photovoltaic. The highest intramolecular natural bond orbital (NBO) for the studied compounds is 27.60, 55.06, 55.06, and 55.04 kcal/mol for AR1, AR2, AR3, and AR4 respectively and the donor and acceptor interacting orbitals for the highest stabilization energy (E
(2)) are LP(1)N
18 and π*C
16−O
19 respectively. The photovoltaic properties in terms of light-harvesting efficiency (LHE), Short circuit current density (J
SC), Gibbs free energy of injection (ΔG
inj), open-circuit voltage (V
OC) and Gibbs free energy of regeneration (ΔG
reg) were evaluated to be within the required limit for DSSC design. Overall, the obtained theoretical photovoltaic results were compared with other experimental and computational findings, thus, are in excellent agreement for organic solar cell design.
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Affiliation(s)
- Ededet A. Eno
- Department of Pure and Applied Chemistry , University of Calabar , Calabar , Nigeria
| | - Hitler Louis
- Department of Pure and Applied Chemistry , University of Calabar , Calabar , Nigeria
| | - Tomsmith O. Unimuke
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Ernest C. Agwamba
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
- Department of Chemical Sciences , Clifford University , Owerrinta , Abia State , Nigeria
| | - Anita T. Etim
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Justina I. Mbonu
- Department of Chemistry , Federal University of Petroleum Resources Efurun , Efurun , Delta State , Nigeria
| | - Henry O. Edet
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - ThankGod Egemoye
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Kayode A. Adegoke
- Department of Chemical Sciences , University of Johannesburg , Johannesburg , South Africa
| | - Umar S. Ameuru
- Department of polymer and Textile Engineering , Ahmadu Bello University , Zaria , Nigeria
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26
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Eno EA, Louis H, Ekoja P, Benjamin I, Adalikwu SS, Orosun MM, Unimuke TO, Asogwa FC, Agwamba EC. Experimental and computational modeling of the biological activity of benzaldehyde sulphur trioxide as a potential drug for the treatment of Alzheimer disease. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100532] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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27
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Eno EA, Mbonu JI, Louis H, Patrick-Inezi FS, Gber TE, Unimke TO, Okon EE, Benjamin I, Offiong OE. Antimicrobial activities of 1-phenyl-3-methyl-4-trichloroacetyl-pyrazolone: Experimental, DFT studies, and molecular docking investigation. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100524] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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28
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A novel application of synthesised based squarylium dyes on nylon 6, and silk woven fabrics. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Squarylium dyes were synthesized and characterized by different spectrometric techniques using FT-IR, UV-visible and GC–MS, the dyes gave molar extinction coefficient values greater than 5.2812 × 105 L mol−1 cm−1. Their fastness properties in respect to wash, light, perspiration and hot pressing on nylon 6, and silk fabrics were analyzed, effects of time, temperature, carrier concentration and pH was also investigated and reported. The dyed fabrics showed good to very good wash, light fastness, and perspiration good to very good hot pressing on nylon 6 and good to very good on silk fabric, respectively. The dye-bath exhaustion was found to be between 76 and 92% on nylon 6 and 57 and 85% on silk, respectively. The percentage exhaustion on nylon 6 was found to be very good to excellent but on silk it was found to be good to very good. These studies showed that squarylium dyes can be applied to nylon 6 and silk fabrics, but better performance was found on nylon 6 than silk fabric.
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Undiandeye UJ, Louis H, Gber TE, Egemonye TC, Agwamba EC, Undiandeye IA, Adeyinka AS, Ita BI. Spectroscopic, conformational analysis, structural benchmarking, excited state dynamics, and the photovoltaic properties of Enalapril and Lisinopril. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100500] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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30
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Udoikono AD, Louis H, Eno EA, Agwamba EC, Unimuke TO, Igbalagh AT, Edet HO, Odey JO, Adeyinka AS. Reactive azo compounds as a potential chemotherapy drugs in the treatment of malignant glioblastoma (GBM): Experimental and theoretical studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100116] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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31
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Ramesh P, Veerappapillai S. Designing Novel Compounds for the Treatment and Management of RET-Positive Non-Small Cell Lung Cancer-Fragment Based Drug Design Strategy. Molecules 2022; 27:1590. [PMID: 35268691 PMCID: PMC8911629 DOI: 10.3390/molecules27051590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 11/29/2022] Open
Abstract
Rearranged during transfection (RET) is an oncogenic driver receptor that is overexpressed in several cancer types, including non-small cell lung cancer. To date, only multiple kinase inhibitors are widely used to treat RET-positive cancer patients. These inhibitors exhibit high toxicity, less efficacy, and specificity against RET. The development of drug-resistant mutations in RET protein further deteriorates this situation. Hence, in the present study, we aimed to design novel drug-like compounds using a fragment-based drug designing strategy to overcome these issues. About 18 known inhibitors from diverse chemical classes were fragmented and bred to form novel compounds against RET proteins. The inhibitory activity of the resultant 115 hybrid molecules was evaluated using molecular docking and RF-Score analysis. The binding free energy and chemical reactivity of the compounds were computed using MM-GBSA and density functional theory analysis, respectively. The results from our study revealed that the developed hybrid molecules except for LF21 and LF27 showed higher reactivity and stability than Pralsetinib. Ultimately, the process resulted in three hybrid molecules namely LF1, LF2, and LF88 having potent inhibitory activity against RET proteins. The scrutinized molecules were then subjected to molecular dynamics simulation for 200 ns and MM-PBSA analysis to eliminate a false positive design. The results from our analysis hypothesized that the designed compounds exhibited significant inhibitory activity against multiple RET variants. Thus, these could be considered as potential leads for further experimental studies.
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Affiliation(s)
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India;
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32
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El-Shamy NT, Alkaoud AM, Hussein RK, Ibrahim MA, Alhamzani AG, Abou-Krisha MM. DFT, ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6,6'-Diamino-1,1',3,3'-tetramethyl-5,5'-(4-chlorobenzylidene)bis[pyrimidine-2,4(1H,3H)-dione]. Molecules 2022; 27:620. [PMID: 35163880 PMCID: PMC8839838 DOI: 10.3390/molecules27030620] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/05/2022] [Accepted: 01/15/2022] [Indexed: 12/24/2022] Open
Abstract
Heterocyclic compounds, including pyrimidine derivatives, exhibit a broad variety of biological and pharmacological activities. In this paper, a previously synthesized novel pyrimidine molecule is proposed, and its pharmaceutical properties are investigated. Computational techniques such as the density functional theory, ADMET evaluation, and molecular docking were applied to elucidate the chemical nature, drug likeness and antibacterial function of molecule. The viewpoint of quantum chemical computations revealed that the molecule was relatively stable and has a high electrophilic nature. The contour maps of HOMO-LUMO and molecular electrostatic potential were analyzed to illustrate the charge density distributions that could be associated with the biological activity. Natural bond orbital (NBO) analysis revealed details about the interaction between donor and acceptor within the bond. Drug likeness and ADMET analysis showed that the molecule possesses the agents of safety and the effective combination therapy as pharmaceutical drug. The antimicrobial activity was investigated using molecular docking. The investigated molecule demonstrated a high affinity for binding within the active sites of antibacterial and antimalarial proteins. The high affinity of the antibacterial protein was proved by its low binding energy (-7.97 kcal/mol) and a low inhibition constant value (1.43 µM). The formation of four conventional hydrogen bonds in ligand-protein interactions confirmed the high stability of the resulting complexes. When compared to known standard drugs, the studied molecule displayed a remarkable antimalarial activity, as indicated by higher binding affinity (B.E. -5.86 kcal/mol & Ki = 50.23 M). The pre-selected molecule could be presented as a promising drug candidate for the development of novel antimicrobial agents.
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Affiliation(s)
- Nesreen T. El-Shamy
- Physics Department, Faculty of Science, Taibah University, Al-Madina Al Munawarah 44256, Saudi Arabia; or
- Physics Department, Faculty of Women, Ain Shams University, Cairo 11865, Egypt
| | - Ahmed M. Alkaoud
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Rageh K. Hussein
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Moez A. Ibrahim
- Physics Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.M.A.); (M.A.I.)
| | - Abdulrahman G. Alhamzani
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.G.A.); (M.M.A.-K.)
| | - Mortaga M. Abou-Krisha
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia; (A.G.A.); (M.M.A.-K.)
- Department of Chemistry, Faculty of Science, South Valley University, Qena 83523, Egypt
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Louis H, Onyebuenyi IB, Odey JO, Igbalagh AT, Mbonu MT, Eno EA, Pembere AMS, Offiong OE. Synthesis, characterization, and theoretical studies of the photovoltaic properties of novel reactive azonitrobenzaldehyde derivatives. RSC Adv 2021; 11:28433-28446. [PMID: 35480716 PMCID: PMC9038037 DOI: 10.1039/d1ra05075c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
All dyes conduct but at different degrees of absorption; it is interesting to study the degree of conductivity and absorptivity of novel reactive azo-dyes in respect to dye-sensitized solar cells (DSSCs) to ascertain their viability for such applications. In this study, four novel reactive azo-dyes were experimentally synthesized from p-aminobenzaldehyde, 4-amino-3-nitrobenzaldehyde, and aniline through series of condensation and coupling reactions. The various functional groups, molecular connectivities, and molecular weight of the various fragments of the synthesized dyes were elucidated using the GC-MS, FT-IR, UV-vis, and NMR respectively. The experimentally determined structures were modeled and investigated using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) approaches to computationally compute the electronic structure properties, reactivity, absorption and solvatochromism in four different phases: gas, ethanol, acetone, and water, and the photovoltaic properties for possible applications in dye-sensitized solar cells (DSSCs). By comparing the HOMO (E H) and the LUMO (E L) energies from the results obtained demonstrates that dye D has the highest E L energy value of -2.48 eV with a relatively lowest E H energy value of -5.63 eV such that it lies underneath the conduction band edge of TiO2 which is necessary to enable charge regeneration. Pi-electron delocalization was observed from the natural bond orbital (NBO) calculations between the different aromatic rings with dye B and A having the relatively highest and least second-order stabilization energies between σ* → σ* and LP* → LP interacting orbitals respectively. It is also observed in all the solvents that the Gibbs free energy of injection (ΔG inject) is greater than 0.2 eV and hence, all the studied azo structures in the four phases provided efficient electron injection and light harvesting efficiency (LHE), however, the value of ΔG inject for dyes B and D is greatest in all the four phases and thus, provided the highest electron injection of all the dyes. From the fact-findings of quantum theory of atoms-in-molecules (QTAIM), dyes A and C have extra-stability due to their relatively high numbers of intramolecular H-bond interactions along with some additional intra-atomic bonding between atoms within the studied compounds. Hence, all the four dyes are good for DSSCs applications.
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Affiliation(s)
- Hitler Louis
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Izubundu B Onyebuenyi
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Joseph O Odey
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Azuaga T Igbalagh
- Department of Chemical Sciences, Federal University of Wukari Wukari Nigeria
| | - MaryJane T Mbonu
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Ededet A Eno
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Anthony M S Pembere
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology Bondo Kenya
| | - Offiong E Offiong
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
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