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Shafiq N, Jannat A, Munir H, Rashid M, Parveen S. Exploring the potential of FDA approved anti-diabetic drugs for repurposing against COVID-19: a core combination of multiple computational strategies and integrated artificial intelligence. J Biomol Struct Dyn 2024; 42:6556-6576. [PMID: 37455488 DOI: 10.1080/07391102.2023.2234993] [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: 03/01/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
The latest variant of coronavirus is omicron. The World Health Organization (WHO) designated variation 'B.1.1.529' named omicron as a variant of concern (VOC) on 26 November 2021. By September 2020, it will have infected over 16 million patients and killed over 600,000 people over the world. This very infectious viral illness still poses a danger to world health; it has also become the greatest problem the world is facing and become the main area of research. The development of vaccines is insufficient to stop their spread and serious effects. Despite several reputable pharmaceutical firms claiming to have developed a cure for COVID-19. For that purpose, the field-based 3D-QSAR model has been used to analyze a series of anti-diabetic drugs to repurpose them against COVID-19. The LOO verified partial least square (PLS) model generates satisfactory q2 (0.4) and r2 (0.5) values. By using this model 10 compounds were screened out of 55 FDA approved anti-diabetic drugs (built-up library). Additionally, these substances were examined using molecular docking screening and ADMET. Finally, the drugs L8, and L23 were discovered to be the lead drugs. Density functional theory at the B3LYP/6-311G* technique was used to examine structural geometries, electronic characteristics, and molecular electrostatic potential (MEP). This work will greatly assist in the detection and development of leads for early drug development to control COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Aqsa Jannat
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Huma Munir
- Green Chemistry Lab., Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
- Department of Applied Chemistry, Beijing Institute of Technology, Beijing, China
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2
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Hu R, Chen X, Xia M, Chen B, Lu X, Luo G, Zhang S, Zhen G. Identification of extracellular polymeric substances layer barrier in chloroquine phosphate-disturbed anammox consortia and mechanism dissection on cytotoxic behavior by computational chemistry. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134335. [PMID: 38657504 DOI: 10.1016/j.jhazmat.2024.134335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
The over-dosing use of chloroquine phosphate (CQ) poses severe threats to human beings and ecosystem due to the high persistence and biotoxicity. The discharge of CQ into wastewater would affect the biomass activity and process stability during the biological processes, e.g., anammox. However, the response mechanism of anammox consortia to CQ remain unknown. In this study, the accurate role of extracellular polymeric substances barrier in attenuating the negative effects of CQ, and the mechanism on cytotoxic behavior were dissected by molecular spectroscopy and computational chemistry. Low concentrations (≤6.0 mg/L) of CQ hardly affected the nitrogen removal performance due to the adaptive evolution of EPS barrier and anammox bacteria. Compact protein of EPS barrier can bind more CQ (0.24 mg) by hydrogen bond and van der Waals force, among which O-H and amide II region respond CQ binding preferentially. Importantly, EPS contributes to the microbiota reshape with selectively enriching Candidatus_Kuenenia for self-protection. Furthermore, the macroscopical cytotoxic behavior was dissected at a molecular level by CQ fate/distribution and computational chemistry, suggesting that the toxicity was ascribed to attack of CQ on functional proteins of anammox bacteria with atom N17 (f-=0.1209) and C2 (f+=0.1034) as the most active electrophilic and nucleophilic sites. This work would shed the light on the fate and risk of non-antibiotics in anammox process.
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Affiliation(s)
- Rui Hu
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Xue Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Mengting Xia
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Bin Chen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Xueqin Lu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China
| | - Gang Luo
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Shicheng Zhang
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| | - Guangyin Zhen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, 3663 N. Zhongshan Road, Shanghai 200062, PR China.
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Ramle AQ, Chan NNMY, Ng MP, Tan CH, Sim KS, Tiekink ERT, Fei CC. Structural insights and cytotoxicity evaluation of benz[e]indole pyrazolyl-substituted amides. Mol Divers 2024; 28:1363-1376. [PMID: 37278911 DOI: 10.1007/s11030-023-10662-2] [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: 11/02/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Five new compounds of benz[e]indole pyrazolyl-substituted amides (2a-e) were synthesised in low to good yields via the direct amide-coupling reaction between a pyrazolyl derivative containing a carboxylic acid and several amine substrates. The molecular structures were determined by various spectroscopic methods, such as NMR (1H, 13C and 19F), FT-IR and high-resolution mass spectrometry (HRMS). X-ray crystallographic analysis on the 4-fluorobenzyl derivative (2d) reveals the amide-O atom to reside to the opposite side of the molecule to the pyrazolyl-N and pyrrolyl-N atoms; in the molecular packing, helical chains feature amide-N‒H⋯N(pyrrolyl) hydrogen bonds. Density-functional theory (DFT) at the geometry-optimisation B3LYP/6-31G(d) level on the full series shows general agreement with the experimental structures. While the LUMO in each case is spread over the benz[e]indole pyrazolyl moiety, the HOMO spreads over the halogenated benzo-substituted amide moieties or is localised near the benz[e]indole pyrazolyl moieties. The MTT assay showed that 2e, exhibited the highest toxicity against a human colorectal carcinoma (HCT 116 cell line) without appreciable toxicity towards the normal human colon fibroblast (CCD-18Co cell line). Based on molecular docking calculations, the probable cytotoxic mechanism of 2e is through the DNA minor groove binding.
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Affiliation(s)
- Abdul Qaiyum Ramle
- School of Chemical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | | | - Min Phin Ng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Chun Hoe Tan
- Department of Biotechnology, Faculty of Applied Science, Lincoln University College, Selangor, Malaysia
| | - Kae Shin Sim
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Edward R T Tiekink
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia
| | - Chee Chin Fei
- Nanotechnology and Catalysis Research Centre, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
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Salau VF, Erukainure OL, Aljoundi A, Akintemi EO, Elamin G, Odewole OA. Exploring the inhibitory action of betulinic acid on key digestive enzymes linked to diabetes via in vitro and computational models: approaches to anti-diabetic mechanisms. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:411-432. [PMID: 38764437 DOI: 10.1080/1062936x.2024.2352729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024]
Abstract
Phytochemicals are now increasingly exploited as remedial agents for the management of diabetes due to side effects attributable to commercial antidiabetic agents. This study investigated the structural and molecular mechanisms by which betulinic acid exhibits its antidiabetic effect via in vitro and computational techniques. In vitro antidiabetic potential was analysed via on α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin inhibitory assays. Its structural and molecular inhibitory mechanisms were investigated using Density Functional Theory (DFT) analysis, molecular docking and molecular dynamics (MD) simulation. Betulinic acid significantly (p < 0.05) inhibited α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin enzymes with IC50 of 70.02 μg/mL, 0.27 μg/mL, 1.70 μg/mL and 8.44 μg/mL, respectively. According to DFT studies, betulinic acid possesses similar reaction in gaseous phase and water due to close values observed for highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) and the chemical descriptors. The dipole moment indicates that betulinic acid has high polarity. Molecular electrostatic potential surface revealed the electrophilic and nucleophilic attack-prone atoms of the molecule. Molecular dynamic studies revealed a stable complex between betulinic acid and α-amylase, α-glucosidase, pancreatic lipase and α-chymotrypsin. The study elucidated the potent antidiabetic properties of betulinic acid by revealing its conformational inhibitory mode of action on enzymes involved in the onset of diabetes.
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Affiliation(s)
- V F Salau
- Department of Pharmacology, University of the Free State, Bloemfontein, South Africa
| | - O L Erukainure
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa
| | - A Aljoundi
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Attahadi, Tripoli, Libya
| | - E O Akintemi
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - G Elamin
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - O A Odewole
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Nigeria
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5
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Xiong F, Zhang YJ, Jiang HY, Wang ZH. Exploring the Efficacy of Noncovalent SARS-CoV-2 Main Protease Inhibitors: A Computational Simulation Analysis Study. Chem Biodivers 2024; 21:e202302089. [PMID: 38526531 DOI: 10.1002/cbdv.202302089] [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: 12/29/2023] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 03/26/2024]
Abstract
The SARS-CoV-2 main protease, as a key target for antiviral therapeutics, is instrumental in maintaining virus stability, facilitating translation, and enabling the virus to evade innate immunity. Our research focused on designing non-covalent inhibitors to counteract the action of this protease. Utilizing a 3D-QSAR model and contour map, we successfully engineered eight novel non-covalent inhibitors. Further evaluation and comparison of these novel compounds through methodologies including molecular docking, ADMET analysis, frontier molecular orbital studies, molecular dynamics simulations, and binding free energy revealed that the inhibitors N02 and N03 demonstrated superior research performance (N02 ΔGbind=-206.648 kJ/mol, N03 ΔGbind=-185.602 kJ/mol). These findings offer insightful guidance for the further refinement of molecular structures and the development of more efficacious inhibitors. Consequently, future investigations can draw upon these findings to unearth more potent inhibitors, thereby amplifying their impact in the treatment and prevention of associated diseases.
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Affiliation(s)
- Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yan-Jun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Hui-Ying Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Zhong-Hua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
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Guezane-Lakoud S, Ferrah M, Merabet-Khelassi M, Touil N, Toffano M, Aribi-Zouioueche L. 2-Hydroxymethyl-18-crown-6 as an efficient organocatalyst for α -aminophosphonates synthesized under eco-friendly conditions, DFT, molecular docking and ADME/T studies. J Biomol Struct Dyn 2024; 42:3332-3348. [PMID: 37184142 DOI: 10.1080/07391102.2023.2213336] [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: 02/17/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
Eco-friendly and simple procedure has been developed for the synthesis of α-aminophosphonates that act as topoisomerase II α-inhibiting anticancer agent, using 2-hydroxymethyl-18-crown-6 as an unexpected homogeneous organocatalyst in multicomponents reaction of aromatic aldehyde, aniline and diethylphosphite in one pot via Kabachnik-Fields reaction. This efficient method proceeds with catalytic amount, transition metal-free, at room temperature within short reaction time, giving the α-aminophosphonates derivatives (4a-r) in high chemical yields (up to 80%). Theoretical DFT calculations of three compounds (4p, 4q and 4r) were carried out in a gas phase at CAM-B3LYP 6-31G (d,p) basis set to predict the molecular geometries and chemical reactivity descriptors. The frontier orbital energies (HOMO/LUMO) were described the charge transfer and used to predict structure-activity relationship study. Molecular electrostatic potential (MEP) has also been analyzed. Molecular docking studies are implemented to analyze the binding energy and compared with Adriamycin against 1ZXM receptor which to be considered as antitumor candidates. In silico pharmacological ADMET properties as Drug likeness and oral activity have been carried out based on Lipinski's rule of five.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samia Guezane-Lakoud
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Meriem Ferrah
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Mounia Merabet-Khelassi
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Nourhane Touil
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
| | - Martial Toffano
- Equipe de Catalyse Moléculaire-ICMMO Bât 420. Université Paris-Saclay, Paris, France
| | - Louisa Aribi-Zouioueche
- Ecocompatible Asymmetric Catalysis Laboratory (LCAE) Badji Mokhtar Annaba-University, Annaba, Algeria
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Malashi NM, Chande Jande YA, Wazzan N, Safi Z, Al-Qurashi OS, Costa R. Designed complexes combining brazilein and brazilin with betanidin for dye-sensitized solar cell application: DFT and TD-DFT study. J Mol Graph Model 2024; 127:108691. [PMID: 38086144 DOI: 10.1016/j.jmgm.2023.108691] [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: 09/30/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 01/23/2024]
Abstract
Dye-sensitized solar cells (DSSCs) are promising third-generation photovoltaic cell technology owing to their easy fabrication, flexibility and better performance under diffuse light conditions. Natural pigment sensitizers are abundantly available and environmentally friendliness. However, narrow absorption spectra of natural pigments result in low efficiencies of the DSSCs. Therefore, combining two or more pigments with complementary absorption spectra is considered an appropriate method to broaden the absorption band and boost efficiency. This study reports three complex molecules: brazilin-betanidin-oxane (Braz-Bd-oxane), brazilin-betanidin-ether (Braz-Bd-ether) and brazilein-betanidin-ether (Braze-Bd-ether), obtained from the etherification and bi-etherification reactions of brazilin dye and brazilein dye with betanidin dye. The equilibrium geometrical structure properties, frontier molecular orbital, electrostatic surface potential, reorganization energy, chemical reactivities, and non-linear optical properties of the studied dyes were investigated using density functional theory (DFT)/B3LYP methods, with 6-31+G(d,p) basis sets and LANL2DZ for light atom and heavy atoms respectively. The optical-electronic properties were calculated using TD-DFT/B3LYP/6-31+G(d,p) for isolated dye and TD-DFT/CAM-B3LYP/6-31G(d,p)/LANL2DZ for dyes@(TiO2)9H4. The results reveal that spectra for Braz-Bd-oxane and Braze-Bd-ether complexes red-shifted compared to the individually selected dyes. The simulated absorption spectra of the adsorbed dyes on (TiO2)9H4 are red-shifted compared to the free dye. Moreover, Braz-Bd-oxane and Braz-Bd-ether exhibit better charge transfer and photovoltaic properties than the selected natural dyes forming these complexes. Based on the dyes' optoelectronic properties and photovoltaic properties, the designed molecules Braz-Bd-oxane and Braze-Bd-ether are considered better candidates to be used as photosensitizers in dye solar cells.
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Affiliation(s)
- Nyanda Madili Malashi
- School of Materials, Energy, Water, and Environmental Sciences, The Nelson Mandela African Institution of Science and Technology (NM-AIST), P. O. Box 447, Arusha, Tanzania; Department of Mechanical and Industrial Engineering, Mbeya University of Science and Technology (MUST), P.O. Box 131, Mbeya, Tanzania.
| | - Yusufu Abeid Chande Jande
- School of Materials, Energy, Water, and Environmental Sciences, The Nelson Mandela African Institution of Science and Technology (NM-AIST), P. O. Box 447, Arusha, Tanzania; Water Infrastructure and Sustainable Energy Futures Centre, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
| | - Nuha Wazzan
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Zaki Safi
- Chemistry Department, Faculty of Science, Al Azhar University - Gaza, P.O Box 1277, Gaza, Palestine.
| | - Ohoud S Al-Qurashi
- Chemistry Department, Faculty of Science, University of Jeddah, Saudi Arabia.
| | - Rene Costa
- Department of Physical and Environmental Sciences, Faculty of Science, Technology and Environmental Studies, The Open University of Tanzania (OUT), P. O Box 23409, Dar es Salaam, Tanzania.
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Murthy Potla K, Parameshwar Adimule S, Poojith N, Osório FAP, Valverde C, Sheena Mary Y, Vankayalapati S. A comparative study of structural and spectroscopic properties of three structurally similar mechanically bending organic single crystals - 2-Amino-3-nitro-5-halo (halo = Cl, Br, or I) pyridine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123093. [PMID: 37418906 DOI: 10.1016/j.saa.2023.123093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/09/2023]
Abstract
In recent years, scientists have been very interested in single crystals of monoaromatic compounds with mechanical softness, but they are hard to find. The present work reports a comparative study of structural, spectroscopic, and quantum chemical investigations of three structurally similar mechanically bending monoaromatic compounds, namely, 2-amino-3-nitro-5-chloro pyridine (I), 2-amino-3-nitro-5-bromo pyridine (II), and 2-amino-3-nitro-5-iodo pyridine (III). The mechanical responses of the three organic crystals studied here are very intriguing due to the similarity of their chemical structures, which only differ in the presence of halogen atoms (Cl, Br, and I) at the fifth position of the pyridine ring and are explained through examining intermolecular interaction energies from energy frameworks analysis, slip layer topology, and Hirshfeld surface analysis. The crystals of all the three feature one dimensional ribbons comprising alternating NaminoH⋯Onitro and NaminoH⋯Npyridine hydrogen bonds that form R22(12) and R22(8) dimeric rings, respectively. In (III), weak I⋯I interactions link the adjacent ribbons forming a two dimensional sheet. Layer-like structures are observed in all three crystals, with no significant interactions between the adjacent architectures (ribbons or sheets). Energy framework calculations are used for estimating the bending ability of the three compounds, with the three following the order Cl ≪ Br < I. The iterative electrostatic scheme coupled with the supermolecule approach (SM) at the DFT/CAM-B3LYP/aug-cc-pVTZ level is used to calculate the third-order nonlinear susceptibility (χ3) values in a simulated crystalline environment for the static case as well as two typical electric field frequency values, (λ = 1064 nm) and (λ = 532 nm). In addition, estimates of the topological studies (localized orbital locator and electron localization function) and reactivity characteristics (global reactivity parameters, molecular electrostatic potential, and Fukui function) are made for the compounds under investigation. Docking studies done using AutoDock software with a protein target (PDB ID: 6CM4) revealed that three compounds could be used to treat Alzheimer's disease.
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Affiliation(s)
- Krishna Murthy Potla
- Department of Chemistry, Velagapudi Ramakrishna Siddhartha Engineering College (Autonomous), Kanuru 520 007, Vijayawada, Andhra Pradesh, India
| | - Suchetan Parameshwar Adimule
- Department of Studies and Research in Chemistry, University College of Science, Tumkur University, Tumkur 572 103, Karnataka, India
| | - Nuthalapati Poojith
- Department of Pharmacology, Sri Ramachandra Institute of Higher Education and Research, Ramachandra Nagar, Porur, Chennai 600 116, India.
| | - Francisco A P Osório
- Instituto de Física, Universidade Federal de Goias, 74690-900 Goiânia, GO, Brazil; Pontifícia Universida de Católica de Goiás, 74605-100 Goiânia, GO, Brazil
| | - Clodoaldo Valverde
- Laboratório de Modelagem Molecular Aplicada e Simulação (LaMMAS), Campus de CiênciasExatas e Tecnológicas, UniversidadeEstadual de Goiás, 75001-970 Anápolis, GO, Brazil; Universidade Paulista, 74845-090 Goiânia, GO, Brazil
| | | | - Suneetha Vankayalapati
- Department of Chemistry, Velagapudi Ramakrishna Siddhartha Engineering College (Autonomous), Kanuru 520 007, Vijayawada, Andhra Pradesh, India
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Azzouzi M, Ouafi ZE, Azougagh O, Daoudi W, Ghazal H, Barkany SE, Abderrazak R, Mazières S, Aatiaoui AE, Oussaid A. Design, synthesis, and computational studies of novel imidazo[1,2- a]pyrimidine derivatives as potential dual inhibitors of hACE2 and spike protein for blocking SARS-CoV-2 cell entry. J Mol Struct 2023; 1285:135525. [PMID: 37057139 PMCID: PMC10080474 DOI: 10.1016/j.molstruc.2023.135525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
In the present work, a new series of imidazo[1,2-a]pyrimidine Schiff base derivatives have been obtained using an easy and conventional synthetic route. The synthesized compounds were spectroscopically characterized using 1H, 13C NMR, LC-MS(ESI), and FT-IR techniques. Green metric calculations indicate adherence to several green chemistry principles. The energy of Frontier Molecular Orbitals (FMO), Molecular Electrostatic Potential (MEP), Quantum Theory of Atoms in Molecules (QTAIM), and Reduced Density Gradient (RDG) were determined by the Density Functional Theory (DFT) method at B3LYP/6-31 G (d, p) as the basis set. Moreover, molecular docking studies targeting the human ACE2 and the spike, key entrance proteins of the severe acute respiratory syndrome coronavirus-2 were carried out along with hACE2 natural ligand Angiotensin II, the MLN-4760 inhibitor as well as the Cannabidiolic Acid CBDA which has been demonstrated to bind to the spike protein and block cell entry. The molecular modeling results showed auspicious results in terms of binding affinity as the top-scoring compound exhibited a remarkable affinity (-9.1 and -7.3 kcal/mol) to the ACE2 and spike protein respectively compared to CBDA (-5.7 kcal/mol), the MLN-4760 inhibitor (-7.3 kcal/mol), and angiotensin II (-9.2 kcal/mol). These findings suggest that the synthesized compounds may potentially act as effective entrance inhibitors, preventing the SARS-CoV-2 infection of human cells. Furthermore, in silico, ADMET, and drug-likeness prediction expressed promising drug-like characteristics.
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Affiliation(s)
- Mohamed Azzouzi
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Zainab El Ouafi
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences Casablanca, Casablanca, Morocco
| | - Omar Azougagh
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Walid Daoudi
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Hassan Ghazal
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences Casablanca, Casablanca, Morocco
- Electronic Systems, Sensors and Nanobiotechnologies (E2SN), École Nationale Supérieure des Arts et Métiers (ENSAM), Mohammed V University, Rabat, Morocco
| | - Soufian El Barkany
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Rfaki Abderrazak
- National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Stéphane Mazières
- Laboratory of IMRCP, University Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse 31062, France
| | - Abdelmalik El Aatiaoui
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Adyl Oussaid
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
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Vasuki A, Christy HJ, Renugadevi K, Dammalli M. Structure-based pharmacophore modeling and DFT studies of Indian Ocean-derived red algal compounds as PI3Kα inhibitors. Mol Divers 2023:10.1007/s11030-023-10695-7. [PMID: 37466805 DOI: 10.1007/s11030-023-10695-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/30/2023] [Indexed: 07/20/2023]
Abstract
Phosphoinositide kinases (PIKs) are a type of lipid kinase that acts as an upstream activator of oncogenic signaling. Presently accessible therapeutic compounds have downsides, such as toxicity and dubious efficacy, as well as lengthy treatment durations, which have bred resistance. Here we attempt to screen the Indian Ocean-derived red algal compounds to be used as a promising lead for PI3Kα inhibitor development. Experimental structure of the PI3K alpha Isoform-Specific Inhibitor alpelisib complex-based pharmacophore model was constructed and used as key to mark off the suitable lead compounds from the pool of marine-derived red algal compounds of Indian Ocean. Besides, the study encompasses pharmacophore scaffold screening as well as physicochemical and pharmacokinetic parameter assessment. We employed molecular docking and molecular dynamics simulation to assess the binding type and stability of 21 red algal derivatives. Twelve compounds demonstrated a sustained binding mode within the PI3Kα binding pocket with an optimal protein backbone root-mean-square deviation, also prompted hydrogen bonding throughout the simulations, and also implies that these MNPs have firmly mediated the interaction with prime hinge region residues in the PI3Kα ATP binding pocket. DFT studies revealed that proposed compounds had the greatest occupied molecular orbital electrophilicity index, basicity, and dipole moment, all of which attributed their stability as well as binding affinity at the PI3Kα active site. Our study's findings revealed that CMNPD31054, CMNPD4798, CMNPD27861, CMNPD4799, CMNPD27860, CMNPD9533, CMNPD3732, CMNPD4221, CMNPD31058, CMNPD31052, CMNPD29281, and CMNPD31055 can be used as lead compounds for PI3KΑ isoform inhibitors design.
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Affiliation(s)
- Archana Vasuki
- Department of Bioinformatics, Sathyabama Institute of Science and Technology, Chennai, India
| | - H Jemmy Christy
- Department of Bioinformatics, Sathyabama Institute of Science and Technology, Chennai, India.
| | - K Renugadevi
- Department of Biotechnology, Sathyabama Institute of Science and Technology, Chennai, India
| | - Manjunath Dammalli
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka, India
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11
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Kirishnamaline G, Magdaline JD, Chithambarathanu T. Structural elucidation, spectroscopic investigation, in silico docking, and in vitro cytotoxicity studies of chromone derivatives as potential anti-breast cancer agents. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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12
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Liu T, Chen J, Fan C, Wu C, Sun T. Crystal structure, DFT calculation, molecular docking, in vitro biological activity evaluation and in silico drug-likeness prediction of (E)-N-(4-bromophenyl)-4-(2-(2-hydroxybenzylidene) hydrazine-1-carbonyl) benzenesulfonamide. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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13
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Crystal structure, spectroscopic analysis, electronic properties and molecular docking study of costunolide for inhibitor capacity against Onchocerca volvulus main protease. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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14
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Synthesis, spectra, crystal, DFT, molecular docking and in vitro cholinesterase inhibition evaluation on two novel symmetrical Azine Schiff Bases. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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15
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New aromatic hydrazones: Synthesis, structural analysis, DFT study, biological activity, ADME-T properties and in silico evaluation of their inhibition of SAS-CoV-2 main protease. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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16
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Garima K, Fatima A, Pooja K, Savita S, Sharma M, Kumar M, Muthu S, Siddiqui N, Javed S. Quantum Computational, Spectroscopic, Hirshfeld Surface Analysis of 3-Picoline (Monomer and Dimer) by DFT/TD-DFT with Different Solvents, Molecular Docking, and Molecular Dynamic Studies. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2140681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Km. Garima
- Department of Chemistry, Dr. Bhimrao Ambedkar University, Agra, India
- Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Aysha Fatima
- School of Studies in Chemistry, Jiwaji University, Gwalior, India
| | - Km. Pooja
- Department of Chemistry, Dr. Bhimrao Ambedkar University, Agra, India
| | - Sandhya Savita
- Department of Chemistry, Dr. Bhimrao Ambedkar University, Agra, India
| | - Manoj Sharma
- Department of Chemistry, Dr. Bhimrao Ambedkar University, Agra, India
| | - Mohit Kumar
- Department of Chemistry, Dr. Bhimrao Ambedkar University, Agra, India
| | - S. Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, India
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Sharma S, Fatima A, Manhas FM, Agarwal N, Singh M, Muthu S, Siddiqui N, Javed S. Experimental Spectroscopic, Quantum Chemical, Molecular Docking, and Molecular Dynamic Simulation Studies on Hydantoin (Monomer and Dimer). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2123540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Shikha Sharma
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Farah Manzer Manhas
- Department of Chemistry, Shoolini University, Solan, Himachal Pradesh, India
| | - Neha Agarwal
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Meenakshi Singh
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - S. Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, Tamil Nadu, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
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18
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Khanum G, Kumar A, Singh M, Fatima A, Muthu S, Abualnaja KM, Althubeiti K, Srivastava G, Siddiqui N, Javed S. Density functional studies and spectroscopic analysis (FT-IR, FT-Raman, UV–visible, and NMR) with molecular docking approach on an anticancer and antifungal drug 4‑hydroxy-3-methoxybenzaldehyde. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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kerkour R, Chafai N, Moumeni O, Chafaa S. Novel α-aminophosphonate derivates synthesis, theoretical calculation, Molecular docking, and in silico prediction of potential inhibition of SARS-CoV-2. J Mol Struct 2022; 1272:134196. [PMID: 36193287 PMCID: PMC9519172 DOI: 10.1016/j.molstruc.2022.134196] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 01/18/2023]
Abstract
Using the Density Functional Theory approach and in silico docking, the current study analyzes the inhibitory role of a novel α-aminophosphonate derivative against SARS-CoV-2 major protease (Mpro) and RNA dependent RNA polymerase (RdRp) of SARS-CoV-2. FT-IR, UV–Vis, and NMR (1H, 13C, 31P) approaches were used to produce and confirm the novel α-aminophosphonate derivative. The quantum chemical parameters were detremined, and the reactivity of the synthesized molecule was discussed using DFT at the B3LYP/6-31G(d,p) level. In addition, the inhibitory function of the investigated derivative for SARS-CoV-2 major protease (Mpro) and RNA dependent RNA polymerase (RdRp) was estimated using in silico docking. These discoveries could pave the way for novel SARS-CoV-2 therapies to develop and be tested.
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Sharma A, Khanum G, Kumar A, Fatima A, Singh M, Abualnaja KM, Althubeiti K, Muthu S, Siddiqui N, Javed S. Conformational stability, quantum computational, spectroscopic, molecular docking and molecular dynamic simulation study of 2-hydroxy-1-naphthaldehyde. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132755] [Citation(s) in RCA: 2] [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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21
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Sharma A, Fatima A, Malla MA, Khanum G, Kumar A, Singh M, Abualnaja KM, Althubeiti K, Muthu S, Siddiqui N, Javed S. Molecular Docking, Dynamic Simulation and DFT Approach to Noble “2-Hydrazinobenzothiazole” Compound. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2089176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Arun Sharma
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Manzoor A. Malla
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Anuj Kumar
- Department of Chemistry, Indian Institute of Technology, Bombay, Mumbai, India
| | - Meenakshi Singh
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, Uttar Pradesh, India
| | - Khamael M. Abualnaja
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Khaled Althubeiti
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - S. Muthu
- Department of Physics, Aringnar Anna Govt. Arts College, Cheyyar, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayal Bagh Educational Institute, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, Uttar Pradesh, India
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22
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Masnabadi N, Thalji MR, Alhasan HS, Mahmoodi Z, Soldatov AV, Ali GAM. Structural, Electronic, Reactivity, and Conformational Features of 2,5,5-Trimethyl-1,3,2-diheterophosphinane-2-sulfide, and Its Derivatives: DFT, MEP, and NBO Calculations. Molecules 2022; 27:molecules27134011. [PMID: 35807257 PMCID: PMC9268642 DOI: 10.3390/molecules27134011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 01/18/2023] Open
Abstract
In this study, we used density functional theory (DFT) and natural bond orbital (NBO) analysis to determine the structural, electronic, reactivity, and conformational features of 2,5,5-trimethyl-1,3,2-di-heteroatom (X) phosphinane-2-sulfide derivatives (X = O (compound 1), S (compound 2), and Se (compound 3)). We discovered that the features improve dramatically at 6-31G** and B3LYP/6-311+G** levels. The level of theory for the molecular structure was optimized first, followed by the frontier molecular orbital theory development to assess molecular stability and reactivity. Molecular orbital calculations, such as the HOMO–LUMO energy gap and the mapping of molecular electrostatic potential surfaces (MEP), were performed similarly to DFT calculations. In addition, the electrostatic potential of the molecule was used to map the electron density on a surface. In addition to revealing molecules’ size and shape distribution, this study also shows the sites on the surface where molecules are most chemically reactive.
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Affiliation(s)
- Nasrin Masnabadi
- Department of Chemistry, Roudehen Branch, Islamic Azad University, Roudehen P.O. Box 189, Iran
- Correspondence: or (N.M.); or (G.A.M.A.)
| | - Mohammad R. Thalji
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea;
| | - Huda S. Alhasan
- Environmental Research and Studies Center, University of Babylon, Babil 51002, Iraq;
| | - Zahra Mahmoodi
- Department of Chemistry, University of Applied Science and Technology, Center of Arya Gach Poldokhtar, Tehran P.O. Box 68, Iran;
| | - Alexander V. Soldatov
- The Smart Materials Research Institute, Southern Federal University, Sladkova Str. 178/24, Rostov-on-Don 344006, Russia;
| | - Gomaa A. M. Ali
- Chemistry Department, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
- Correspondence: or (N.M.); or (G.A.M.A.)
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23
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Kumar M, Fatima A, Singh M, Verma I, Khanum G, Muthu S, Althubeiti K, Abualnaja KM, Ahmad M, Siddiqui N, Javed S. Experimental Spectroscopic, Quantum Computational, Hirshfeld Surface, Molecular Docking, and Electronic Excitation Studies on an Antibiotic Agent: SDZ. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2063909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mukesh Kumar
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao-Amedkar University, Agra, Uttar Pradesh, India
- Department of Chemistry, Shri Khushal Das University, Hanumangarh, Rajasthan, India
| | - Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Meenakshi Singh
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao-Amedkar University, Agra, Uttar Pradesh, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, Tamil Nadu, India
| | - Khaled Althubeiti
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - khamael M. Abualnaja
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Musheer Ahmad
- Department of Applied Chemistry, Faculty of Engineering and Technology, ZHCET, Aligarh Muslim University, Aligarh, India
| | - Nazia Siddiqui
- USIC, Dayalbagh Educational Institute, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao-Amedkar University, Agra, Uttar Pradesh, India
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24
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Quantum chemical, spectroscopic, hirshfeld surface and molecular docking studies on 2-aminobenzothiazole. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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25
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Selvakumari S, Venkataraju C, Muthu S, Irfan A, Shanthi D. Donor acceptor groups effect, polar protic solvents influence on electronic properties and reactivity of 2-Chloropyridine-4-carboxylic acid. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Investigation of the electronic properties of solvents (water, benzene, methanol) using IEFPCM model, spectroscopic investigation with docking and MD simulations of a thiadiazole derivative with anti-tumor activities. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Khanum G, Fatima A, Siddiqui N, Agarwal D, Butcher R, Srivastava SK, Javed S. Synthesis, single crystal, characterization and computational study of 2-amino-N-cyclopropyl-5-ethyl-thiophene-3-carboxamide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131890] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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28
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Fatima A, Khanum G, Savita S, Pooja K, Verma I, Siddiqui N, Javed S. Quantum computational, spectroscopic, Hirshfeld surface, electronic state and molecular docking studies on sulfanilic acid: An anti-bacterial drug. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117150] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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29
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Savita S, Fatima A, Garima K, Pooja K, Verma I, Siddiqui N, Javed S. Experimental spectroscopic, Quantum computational, Hirshfeld surface and molecular docking studies on 3-Pyridinepropionic acid. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Jeelani A, Muthu S, Narayana B. Molecular structure determination, Bioactivity score, Spectroscopic and Quantum computational studies on (E)-N'-(4-Chlorobenzylidene)-2-(napthalen-2-yloxy) acetohydrazide. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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31
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Akhileshwari P, Kiran K, Sridhar M, Sadashiva M, Lokanath N. Synthesis, crystal structure characterization, Hirshfeld surface analysis, and Quantum chemical computations of Ethyl 5-(thiophene-2-carbonyl)thiazole-4-carboxylate. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Topal T, Zorlu Y, Karapınar N. Synthesis, X-ray crystal structure, IR and Raman spectroscopic analysis, quantum chemical computational and molecular docking studies on hydrazone-pyridine compound: As an insight into the inhibitor capacity of main protease of SARS-CoV2. J Mol Struct 2021; 1239:130514. [PMID: 33903779 PMCID: PMC8059879 DOI: 10.1016/j.molstruc.2021.130514] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/18/2023]
Abstract
The characterization and synthesis of 3-chloro-2-{(2E)-2-[1-(4-chlorophenyl)ethylidene]hydrazinyl}pyridine (CCPEHP) was investigated in our study. Mass and UV-visible spectra were recorded in chloroform solvent. The CCPEHP molecule containing pyridine and chlorophenyl rings and hydrazone group crystallized in the triclinic system and P-1 space group. FTRaman and FTIR spectra were performed in the solid state. The optimized geometry of CCPEHP was computed by DFT/B3LYP method with 6-311 G (d, p) and 6-31 G (d, p) levels. The computed vibrational analysis, electronic absorption spectrum, electronic properties, molecular electrostatic potential, natural bond orbitals analysis and other calculated structural parameters were determined by using the DFT/B3LYP/6-31 G (d, p) basis set. The correlation of fundamental modes of the compound and the complete vibrational assignments analysis were studied. The strong and weak contacts were identified by using Hirshfeld surface analysis. The molecular modeling results showed that CCPEHP structure strongly binds to COVID-19 main protease by relative binding affinity of -6.4 kcal/mol.
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Affiliation(s)
- Tufan Topal
- Advanced Technology Application and Research Center, Pamukkale University, 20020, Denizli, Turkey,Correspondence author
| | - Yunus Zorlu
- Department of Chemistry, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Nazan Karapınar
- Department of Chemical Engineering, Pamukkale University, 20020, Denizli, Turkey
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33
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Raajaraman BR, Sheela NR, Muthu S. Spectroscopic, quantum computational, molecular docking and biological parameters of 4-phenylbutyrophenone: a neuroleptic agent. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01617-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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34
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Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, molecular docking and SERS (concentration and solvent dependant) investigations of a methylisoxazole derivative with potential antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Mary YS, Mary YS, Rad AS, Yadav R, Celik I, Sarala S. Theoretical investigation on the reactive and interaction properties of sorafenib – DFT, AIM, spectroscopic and Hirshfeld analysis, docking and dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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36
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Pandimeena G, Premkumar R, Mathavan T, Benial AMF. Spectroscopic, Quantum chemical and Molecular docking Studies on Methyl 6-aminopyridine-3-carboxylate: A potent bioactive agent for the treatment of sarcoidosis. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Exploring molecular structure, spectral features, electronic properties and molecular docking of a novel biologically active heterocyclic compound 4-phenylthiosemicarbazide. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129956] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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38
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Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, SERS-concentration and solvent dependent and docking studies of a bioactive benzenesulfonamide derivative. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129680] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Nevin Çankaya, Taniş E, Sapan PG. New Syntheses of 4NPMA Homopolymer and Its Copolymer with Limonene: Experimental Analysis and Density Functional Theory Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2021. [DOI: 10.1134/s0036024421010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Kaddouri Y, Abrigach F, Ouahhoud S, Benabbes R, El Kodadi M, Alsalme A, Al-Zaqri N, Warad I, Touzani R. Synthesis, characterization, reaction mechanism prediction and biological study of mono, bis and tetrakis pyrazole derivatives against Fusarium oxysporum f. sp. Albedinis with conceptual DFT and ligand-protein docking studies. Bioorg Chem 2021; 110:104696. [PMID: 33652343 DOI: 10.1016/j.bioorg.2021.104696] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 12/18/2020] [Accepted: 01/28/2021] [Indexed: 11/20/2022]
Abstract
Twelve heterocyclic compounds were prepared using the condensation of hydroxymethanol pyrazole derivatives with different primary aminesas example 2-aminothiazole and 1-aminobenzotriazole to have a diverse productin good yield up to 97%. Those ligands were tested against Fusarium oxysporum f. sp. Albedinis fungi (BAYOUD Disease) with IC50 = 25.6-33.2 µg/ml. After experiments, theoretical investigations were done as DFT study to know the ligands molecular reactivity and the-ligandprotein- docking study to know the possible binding between the prepared ligands with two biological targets: FGB1 (Fusarium oxysporum Guanine nucleotide-binding protein beta subunitprimary amino acid sequence) and Fophy (Fusarium oxysporum phytase domain enzyme). Of all the obtained results, the experimental ones were well correlated with the theoretical with the most common thing between those compounds is (Nδ--Nδ+) which is the antifungal pharmacophore as proposed pincers for Foa inhibition. From docking studies over FGB1 and Fophy, the ligand 9 has the best binding energy of -6.4872 kcal/mol in FGB1 active site and -5.5282 kcal/mol in Fophy active site, but better correlation with Fophy than FGB1 which is followed by PLIF graph to get that Arg116, Arg120 and Lys336 are the vital amino acids of fophy protein based the study over the chosen active site.
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Affiliation(s)
- Yassine Kaddouri
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco.
| | - Farid Abrigach
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco
| | - Sabir Ouahhoud
- Laboratory of Biochemistry (LB), Department of Biology, Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Redouane Benabbes
- Laboratory of Biochemistry (LB), Department of Biology, Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Mohamed El Kodadi
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco; Laboratoire d'Innovation en Sciences, Technologie et Education (LISTE), CRMEF Oriental, Oujda, Morocco
| | - Ali Alsalme
- Department of chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Nabil Al-Zaqri
- Department of chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; Department of Chemistry, College of Science, Ibb University, P. O. Box 70270, Ibb, Yemen
| | - Ismail Warad
- Department of Chemistry, Science College, An-Najah National University, PB 7, Nablus, Palestine
| | - Rachid Touzani
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco
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Siddiqui N, Javed S. Quantum computational, spectroscopic investigations on ampyra (4-aminopyridine) by dft/td-dft with different solvents and molecular docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Noureddine O, Issaoui N, Al-Dossary O. DFT and molecular docking study of chloroquine derivatives as antiviral to coronavirus COVID-19. JOURNAL OF KING SAUD UNIVERSITY SCIENCE 2020; 33:101248. [PMID: 33250604 PMCID: PMC7687412 DOI: 10.1016/j.jksus.2020.101248] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 01/18/2023]
Abstract
The recently emerged COVID-19 virus caused hundreds of thousands of deaths and instigated a widespread fear, threatening the world’s most advanced health security. In 2020, chloroquine derivatives are among the drugs tested against the coronavirus pandemic and showed an apparent efficacy. In the present work, the chloroquine and the chloroquine phosphate molecules have been proposed as potential antiviral for the treatment of COVID-19 diseases combining DFT and molecular docking calculations. Molecular geometries, electronic properties and molecular electrostatic potential were investigated using density functional theory (DFT) at the B3LYP/6-31G* method. As results, we found a good agreement between the theoretical and the experimental geometrical parameters (bond lengths and bond angles). The frontier orbitals analysis has been calculated at the same level of theory to determine the charge transfer within the molecule. In order to perform a better description of the FMOs, the density of states was determined. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of molecule and also to describe the intermolecular interactions. All these studies help us a lot in determining the reactivity of the mentioned compounds. Finally, docking calculations were carried out to determine the pharmaceutical activities of the chloroquine derivatives against coronavirus diseases. The choice of these ligands was based on their antiviral activities.
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Affiliation(s)
- Olfa Noureddine
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Noureddine Issaoui
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Omar Al-Dossary
- Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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Manjusha P, Prasana JC, Muthu S, Rizwana BF. Spectroscopic elucidation (FT-IR, FT-Raman and UV-visible) with NBO, NLO, ELF, LOL, drug likeness and molecular docking analysis on 1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole: An antiprotozoal agent. Comput Biol Chem 2020; 88:107330. [PMID: 32711354 DOI: 10.1016/j.compbiolchem.2020.107330] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 11/26/2022]
Abstract
1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole (1EMI) C8H13N3O4S also known as Tinidazole, selected for its antiprotozoal property is extensively used for spectroscopic elucidations and computational aspects using density functional methods. Along with spectral conclusions, further investigations on fundamental reactive properties such as electrical, optical, nonlinear combined with DFT simulations were performed. Molecular docking procedure supports the results of chosen appropriate antiprotozoal agent based on ligand-protein interactions. Experimental and simulated (B3LYP/6-311++G (d,p)) IR and Raman spectra showed concurrence. NLO analysis through first order hyperpolarizability parameter helps in finding the potential of 1EMI as a good NLO candidate. Charge delocalization and the stability of the compound were discussed using natural bond orbital (NBO) analysis. Furthermore, Electron localization function (ELF), local orbital locator (LOL), and Frontier molecular orbitals (FMO) were studied. Besides, Mulliken population analysis on atomic charges, Energy gap, chemical potential, global hardness, softness, ionization potential, electronegativity, electrophilicity index along thermodynamic parameters (enthalpy, entropy and heat capacity) have been calculated. Drug likeness parameters and molecular docking approach enabled to check pharmaceutical potential and biological activity of 1EMI. The biological activity of 1EMI through ligand and protein interactions have been confirmed theoretically for the treatment of Malaria, Invasive aspergillosis and Mycobacterium tuberculosis with respect to chosen proteins. Three different activity targets and protein interactions are quite successful revealing the bond distances, intermolecular energy, binding energy and inhibition constant. 2D interaction profile image of the two maximum interacted proteins and also Ramachandran plot used to show stereochemistry of selected protein. The activities of 1EMI were studied in accordance with literature survey and the results were presented.
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Affiliation(s)
- P Manjusha
- Department of Physics, S.D.N.B Vaishnav College for Women, Chromepet, Chennai, 600 044, Tamilnadu, India; Department of Physics, Madras Christian College, Chennai, 600 059, Tamilnadu, India; University of Madras, Chepauk, Chennai, 600 005, Tamilnadu, India
| | | | - S Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, 604 407, Tamilnadu, India; Department of Physics, Puratchi Thalaivar Dr.M.G.R Govt. Arts and Science College, Uthiramerur, 603406, Tamilnadu, India.
| | - B Fathima Rizwana
- Department of Physics, Madras Christian College, Chennai, 600 059, Tamilnadu, India
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Manjusha P, prasana JC, Muthu S, Raajaraman BR. Density functional studies and spectroscopic analysis (FT-IR, FT-Raman, UV–visible, and NMR)with molecular docking approach on an antifibrotic drug Pirfenidone. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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45
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46
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Amul B, Muthu S, Raja M, Sevvanthi S. Spectral, DFT and molecular docking investigations on Etodolac. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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47
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Cai K, Zheng X, Liu J, Du F, Yan G, Zhuang D, Yan S. Mapping the amide-I vibrations of model dipeptides with secondary structure sensitivity and amino acid residue specificity, and its application to amyloid β-peptide in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 219:391-400. [PMID: 31059891 DOI: 10.1016/j.saa.2019.04.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Vibrational spectroscopy has been known as particularly well-suited for deciphering the polypeptide's structure. To decode structural information encoded in IR spectra, we developed amide-I frequency maps on the basis of model dipeptides to correlate the amide-I frequency of interest to the combination of the calculated secondary structure dependent amide-I frequency by using DFT method and the electrostatic potentials that projected onto the amide unit from the micro-environment within molecular mechanics force field. The constructed maps were applied to model dipeptides and amyloid β-peptide fragment (Aβ25-35). The dipeptide specified map (DS map) and the hybrid map (HYB map) predicted amide-I bands of Aβ25-35 in solution satisfactorily reproduce experimental observation, and indicate the preference of forming β-sheet and random coil structure for Aβ25-35 in D2O just as the results of cluster analysis suggested. These maps with secondary structural sensitivity and amino acid residue specificity open up a way for the interpretation of amide-I vibrations and show their potentials in the understanding of molecular structure of polypeptides in solution.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China; Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China.
| | - Xuan Zheng
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Jia Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Guiyang Yan
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China
| | - Danling Zhuang
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Siyi Yan
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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Haruna K, Kumar VS, Sheena Mary Y, Popoola SA, Thomas R, Roxy MS, Al-Saadi AA. Conformational profile, vibrational assignments, NLO properties and molecular docking of biologically active herbicide1,1-dimethyl-3-phenylurea. Heliyon 2019; 5:e01987. [PMID: 31304416 PMCID: PMC6600072 DOI: 10.1016/j.heliyon.2019.e01987] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 11/22/2022] Open
Abstract
1,1-Dimethyl-3-phenylurea (known as fenuron) which is a phenyl urea-based widely used herbicide exhibits interesting structural and conformational properties and a notable biological activity. A detailed analysis on the vibrational, molecular and electronic characteristics of fenuron has been carried out. Potential energy scans (PESs) performed at the B3LYP/6-311++G(d,p) level of theory predicted two possible minima corresponding to the optimized anti and synforms resulting from the internal rotation about the N-C bond. The presence of an auxochrome together with the interaction with DMSO solvent exhibited a blue shift corresponding to the C=O orbitals. Delocalization of HOMO and LUMO orbital facilitated the charge transfer effect in the molecule. The calculated HOMO-LUMO energies, chemical potential, energy gap and global hardness suggested a low softness value for the compound while its biological activity was described by the value of electrophilicity. Chlorine substitution in the phenyl ring influenced the orbital delocalization for ortho and para substitutions but that of meta remained unaffected. NLO properties were noticed to increase due to chlorine substitution in the parent molecule. The docking results suggested that the compound exhibits an inhibitory activity against mitochondrial ubiquinol-cytochrome-c reductase and can be developed as a potential anticancer agent.
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Affiliation(s)
- K Haruna
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Veena S Kumar
- Department of Physics, SN College, Kollam, Kerala, India
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India
| | - S A Popoola
- Department of Chemistry, Islamic University of Madinah, MadinahMunawara, Saudi Arabia
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanacherry, Kerala, India
| | - M S Roxy
- Department of Physics, SN College, Kollam, Kerala, India
| | - A A Al-Saadi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
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Channar PA, Arshad N, Farooqi SI, Larik FA, Saeed A, Hökelek T, Shehzadi SA, Abbas N, Flörke U. Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT, and DNA-Binding Studies of (E)-2-(3-Hydroxy-4-Methoxybenzylidene)Hydrazinecarbothioamide. Appl Biochem Biotechnol 2019; 189:175-192. [PMID: 30972703 DOI: 10.1007/s12010-019-03008-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/27/2019] [Indexed: 11/28/2022]
Abstract
(E)-2-(3-Hydroxy-4-methoxybenzylidene)hydrazinecarbothioamide 3 was synthesized by reacting thiosemicarbazide with 2-hydorxy-3-methoxybenzaldehyde in dry ethanol. The structure was elucidated by spectroscopic (FT-IR, 1H NMR, and 13C NMR) and single crystal X-ray diffraction techniques. A detailed analysis of the intermolecular interactions has been performed based on the Hirshfeld surfaces and their associated two-dimensional fingerprint plots. DFT, spectroscopic, and electrochemical DNA-binding analysis confirmed that the compound is reactive to bind with DNA. Viscometric studies suggested that compound 3 has a mixed mode of interaction and intercalated into the DNA base pairs predominantly along with the possibility of electrostatic interactions. Graphical Abstract.
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Affiliation(s)
- Pervaiz Ali Channar
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nasima Arshad
- Department of Chemistry, Faculty of Sciences, Allama Iqbal Open University, Islamabad, 44000, Pakistan.
| | - Shahid Iqbal Farooqi
- Department of Chemistry, Faculty of Sciences, Allama Iqbal Open University, Islamabad, 44000, Pakistan
| | - Fayaz Ali Larik
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Tuncer Hökelek
- Department of Physics, Faculty of Engineering, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Syeda Aaliya Shehzadi
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Sulaiman Bin Abdullah Aba Al-Khail-Centre for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University, Islamabad, Islamabad, Pakistan
| | - Nasir Abbas
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Ulrich Flörke
- Department Chemie, Fakultätfür Naturwissenschaften, Universität Paderborn, Warburgerstrasse 100, 33098, Paderborn, Germany
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50
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Synthesis and spectroscopic study of two new pyrazole derivatives with detailed computational evaluation of their reactivity and pharmaceutical potential. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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