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Juyal VK, Thakuri SC, Panwar M, Rashmi, Prakash O, Perveen K, Bukhari NA, Nand V. Manganese(II) and Zinc(II) metal complexes of novel bidentate formamide-based Schiff base ligand: synthesis, structural characterization, antioxidant, antibacterial, and in-silico molecular docking study. Front Chem 2024; 12:1414646. [PMID: 39100916 PMCID: PMC11294232 DOI: 10.3389/fchem.2024.1414646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
A new bidentate Schiff base ligand (C16H16Cl2N4), condensation product of ethylene diamine and 4-chloro N-phenyl formamide, and its metal complexes [M(C16H16Cl2N4)2(OAc)2] (where M = Mn(II) and Zn(II)) were synthesized and characterized using various analytical and spectral techniques, including high-resolution mass spectrometry (HRMS), elemental analysis, ultraviolet-visible (UV-vis), Fourier-transform infrared (FTIR) spectroscopy, AAS, molar conductance, 1H NMR, and powder XRD. All the compounds were non-electrolytes and nanocrystalline. The synthesized compounds were assessed for antioxidant potential by DPPH radical scavenging and FRAP assay, with BHT serving as the positive control. Inhibitory concentration at 50% inhibition (IC50) values were calculated and used for comparative analysis. Furthermore, the prepared compounds were screened for antibacterial activity against two Gram-negative bacteria (Staphylococcus aureus and Bacillus subtilis) and two Gram-positive bacteria (Escherichia coli and Salmonella typhi) using disk-diffusion methods, with amikacin employed as the standard reference. The comparison of inhibition zones revealed that the complexes showed better antibacterial activity than the ligand. To gain insights into the molecular interactions underlying the antibacterial activity, the ligand and complexes were analyzed for their binding affinity with S. aureus tyrosyl-tRNA synthetase (PDB ID: 1JIL) and S. typhi cell membrane protein OmpF complex (PDB ID: 4KR4). These analyses revealed robust interactions, validating the observed antibacterial effects against the tested bacterial strains.
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Affiliation(s)
- Vijay Kumar Juyal
- Department of Chemistry, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Shweta Chand Thakuri
- Department of Chemistry, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Mohit Panwar
- Department of Chemistry, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Rashmi
- Department of Chemistry, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Om Prakash
- Regional Ayurveda Research Institute, Ministry of Ayush, Gwalior, India
| | - Kahkashan Perveen
- Department of Botany and Microbiology, College of Science, King Saud University Riyadh, Riyadh, Saudi Arabia
| | - Najat A. Bukhari
- Department of Botany and Microbiology, College of Science, King Saud University Riyadh, Riyadh, Saudi Arabia
| | - Viveka Nand
- Department of Chemistry, G.B. Pant University of Agriculture and Technology, Pantnagar, India
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Medina-Barandica J, Contreras-Puentes N, Tarón-Dunoyer A, Durán-Lengua M, Alviz-Amador A. In-silico study for the identification of potential destabilizers between the spike protein of SARS-CoV-2 and human ACE-2. INFORMATICS IN MEDICINE UNLOCKED 2023; 40:101278. [PMID: 37305192 PMCID: PMC10241490 DOI: 10.1016/j.imu.2023.101278] [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: 04/03/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
The emergence of the new SARS-CoV-2 virus, which causes the disease known as COVID-19, has generated a pandemic that has plunged the world into a health crisis. The infection process is triggered by the direct binding of the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) of the host cell. In the present study, virtual screening techniques such as molecular docking, molecular dynamics, calculation of free energy using the GBSA method, prediction of drug similarity, pharmacokinetic, and toxicological properties of various ligands interacting with the RBD-ACE2 complex were applied. The ligands radotinib, hinokiflavone, and ginkgetin were identified as potential destabilizers of the RBD-ACE2 interaction, which could produce their pharmacological effect by interacting at an allosteric site of ACE2, with affinity energy values of -10.2 ± 0.1, -9.8 ± 0.0, and -9.4 ± 0.0 kcal/mol, indicating strong receptor affinity. The complex with hinokiflavone showed the highest conformational stability and rigidity of the dynamic simulation and also obtained the best binding free energy of the three molecules, with an energy of -215.86 kcal/mol.
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Affiliation(s)
- Jeffry Medina-Barandica
- Pharmacology and Therapeutic Research Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Cartagena, D.T. y C, Colombia
| | - Neyder Contreras-Puentes
- Pharmacology and Therapeutic Research Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Cartagena, D.T. y C, Colombia
- GINUMED, Faculty of Health Sciences, Rafael Nuñez University Corporation, Cartagena D.T. y C., Colombia
| | - Arnulfo Tarón-Dunoyer
- GIBAE Research Group, Faculty of Engineering, University of Cartagena, Cartagena, D.T. y C, Colombia
| | - Marlene Durán-Lengua
- FARMABAC Research Group, Faculty of Medicine, University of Cartagena, Cartagena, D.T. y C, Colombia
| | - Antistio Alviz-Amador
- Pharmacology and Therapeutic Research Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Cartagena, D.T. y C, Colombia
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Al-Mamun A, Ahammad I, Ahmed SS, Akter F, Hossain SI, Chowdhury ZM, Bhattacharjee A, Das KC, Keya CA, Salimullah M. Pharmacoinformatics and molecular dynamics simulation approach to identify anti-diarrheal potentials of Centella asiatica (L.) Urb. against Vibrio cholerae. J Biomol Struct Dyn 2023; 41:14730-14743. [PMID: 36927394 DOI: 10.1080/07391102.2023.2191736] [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: 12/13/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
Vibrio cholerae, the etiological agent of cholera, causes dehydration and severe diarrhea with the production of cholera toxin. Due to the acquired antibiotic resistance, V. cholerae has drawn attention to the establishment of novel medications to counteract the virulence and viability of the pathogen. Centella asiatica is a medicinal herb native to Bangladesh that has a wide range of medicinal and ethnobotanical applications including anti-bacterial properties. In the present investigation, a total of 25 bioactive phytochemicals of C. asiatica have been screened virtually through molecular docking, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses, and molecular dynamics simulation. Our results revealed four lead compounds as Viridiflorol (-8.7 Kcal/mol), Luteolin (-8.1 Kcal/mol), Quercetin (-8.0 Kcal/mol) and, Geranyl acetate (-7.1 Kcal/mol) against V. cholerae Toxin co-regulated pilus virulence regulatory protein (ToxT). All the lead compounds have been found to possess favorable pharmacokinetic, pharmacodynamics, and molecular dynamics properties. Toxicity analysis revealed satisfactory results with no major side effects. Molecular dynamics simulation was performed for 100 ns that revealed noteworthy conformational stability and structural compactness for all the lead compounds, especially for Quercetin. Target class prediction unveiled enzymes in most of the cases and some experimental and investigational drugs were found as structurally similar analogs of the lead compounds. These findings could aid in the development of novel therapeutics targeting Cholera disease and we strongly recommend in vitro trials of our experimental findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Al-Mamun
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Farzana Akter
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Shah Imran Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | | | | | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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Mohammed Abduljleel A, Saleh Alshawi JM, Ali Hussein K, Ismael SMH. Synthesis, characterization, biological studies and DFT study of Schiff Bases and their complexes derived from aromatic diamine compounds with cobalt (II). BIONATURA 2023. [DOI: 10.21931/rb/2023.08.01.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Based on vanillin and diamine compounds (ortho phenylene diamine, meta phenylene diamine, 3,4- diamine toluene), derivation of two new Schiff base ligands (L1 and L2) was done, after which synthesis and treatment with Co (II) chloride was performed at a metal-to-ligand ratio of 1:1 to get two new complexes, i.e. [CoL3(H2O)2]Cl2 and [CoL1(H2O)2]Cl2. These complexes and ligands were characterized by employing NMR, IR, atomic absorption, UV visible absorption, molecular weight determination, molar conductance, and magnetic measurement techniques. As per the data, the ligands were found to be bidentate ligands that were linked to two azomethine nitrogen sites. It was suggested that these complexes were paramagnetic electrolyte compounds that possessed coordination number four. Screening of the ligands and metal complexes was done to assess their antimicrobial activities against gram-negative and gram-positive bacteria, which was found to show biological activity. Calculations using quantum chemistry were done to examine the molecule geometry. The investigation includes several quantum chemical characteristics derived from frontier molecular orbitals.
Keywords: Schiff bases, transition metal complexes, vanillin, diamine aromatic compounds, antibacterial activity, DFT study.
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Affiliation(s)
| | | | - kawkab Ali Hussein
- Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Basrah, 61004 Iraq
| | - Sadiq M-H. Ismael
- Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Basrah, 61004 Iraq
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Contreras N, Alvíz-Amador A, Manzur-Villalobos I. In silico study of dimethyltryptamine analogues against 5-HT1B receptor: Molecular docking, dynamic simulations and ADMET prediction. JOURNAL OF HERBMED PHARMACOLOGY 2022. [DOI: 10.34172/jhp.2022.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Introduction: The 5-HT1B receptor has a potential role in various psychiatric disorders such as depression, anxiety, and post-traumatic stress disorder. The objective of this study was to perform docking and molecular dynamics simulation to evaluate at atomic level the behavior of N,N-dimethyltryptamine (DMT) on 5-HT1B receptor.Methods: In this study, initially, a search for DMT was performed using the PubChem database. Subsequently, molecular docking was executed using AutoDock Vina based in PyRx 0.8 with a 95% analogy. Additionally, ergotamine (ERG) and serotonin were used as control. Then, it ran a total of 100 ns molecular dynamics simulations on 5-HT1B bound with DMT, serotonin, 112814775, and ERG. Finally, pharmacokinetic prediction and IV acute toxicity for analogues and DMT were performed.Results: It was possible to show that 112814775 had the lowest binding energy with the receptor. In addition, 112814775 presented great conformational stability, low mobility, and stiffness compared to the control ligands: ERG, serotonin, and DMT subsequent dynamic analysis. With respect to the free energy calculation, contributions such as Van der Waals, electrostatics, and nonpolar interactions for all systems, were highlighted.Conclusion: 112814775 showed affinities with 5-HT1B receptor and evidenced notable behavior by molecular dynamic simulation according to root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), the radius of gyration, number of hydrogen bond, and free energy calculated. These results established the possible relevance of in-silico studies in search of DMT analogues against the 5-HT1B receptor, which may be associated with alterations such as depression and anxiety, and may become future study molecules for the treatment of this type of disorder.
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Affiliation(s)
- Neyder Contreras
- Pharmacology and Therapeutics Research Group. University of Cartagena, Cartagena D.T y C., Colombia
- GINUMED, Rafael Nuñez University Corporation, Cartagena D.T y C., Colombia
| | - Antistio Alvíz-Amador
- Pharmacology and Therapeutics Research Group. University of Cartagena, Cartagena D.T y C., Colombia
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Manzur-Villalobos I, Contreras-Puentes N, Díaz-Caballero A, Durán-Lengua M, Alviz-Amador A. In silico study of local anesthetics analogues on sodium channel Nav 1.7 a pharmacological target on inflamed dental pulp. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Rahman MM, Junaid M, Hosen SMZ, Mostafa M, Liu L, Benkendorff K. Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition. Molecules 2021; 26:molecules26216538. [PMID: 34770946 PMCID: PMC8587571 DOI: 10.3390/molecules26216538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6′-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski’s rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go–go gene (hERG) I inhibitors, and the oral acute toxicity LD50 in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.
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Affiliation(s)
- Md. Mominur Rahman
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Md. Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
- Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for AppliedMedical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohammad Mostafa
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - Lei Liu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
- Correspondence:
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Aviz-Amador A, Contreras-Puentes N, Mercado-Camargo J. Virtual screening using docking and molecular dynamics of cannabinoid analogs against CB 1 and CB 2 receptors. Comput Biol Chem 2021; 95:107590. [PMID: 34700256 DOI: 10.1016/j.compbiolchem.2021.107590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 09/09/2021] [Accepted: 10/07/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND Cannabis sativa has been attributed to different pharmacological properties. A number of secondary metabolites such as tetrahydrocannabinol (THC), cannabinol (CBD), and different analogs, with highly promising biological activity on CB1 and CB2 receptors, have been identified. METHODS Thus, this study aimed was to evaluate the activity of THC, CBD, and their analogs using molecular docking and molecular dynamics simulations (MD) methods. Initially, the molecules (ligands) were selected by bioinformatics searches in databases. Subsequently, CB1 and CB2 receptors were retrieved from the protein data bank database. Afterward, each receptor and its ligands were optimized to perform molecular docking. Then, MD Simulation was performed with the most stable ligand-receptor complexes. Finally, the Molecular Mechanics-Generalized Born Surface Area (MM-PBSA) method was applied to analyze the binding free energy between ligands and cannabinoid receptors. RESULTS The results obtained showed that ligand LS-61176 presented the best affinity in the molecular docking analysis. Also, this analog could be a CB1 negative allosteric modulator like CBD and probably an agonist in CB2 like THC and CBD according to their dynamic behavior in silico. The possibility of having a THC and a CBD analog (LS-61176) as a promising molecule for experimental evaluation since it could have no central side-effects on CB1 and have effects of CB2 useful in pain, inflammation, and some immunological disorders. Docking results were validate using ROC curve for both cannabinoids receptor where AUC for CB1 receptor was 0.894±0.024, and for CB2 receptor AUC was 0.832±0032, indicating good affinity prediction.
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Affiliation(s)
- Antistio Aviz-Amador
- Pharmacology and Therapeutic Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Neyder Contreras-Puentes
- Pharmacology and Therapeutic Group, Faculty of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia; GINUMED, Faculty of Medicine, Rafael Nuñez University Corporation, Cartagena, Colombia.
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Ezaj MMA, Junaid M, Akter Y, Nahrin A, Siddika A, Afrose SS, Nayeem SMA, Haque MS, Moni MA, Hosen SMZ. Whole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy. J Biomol Struct Dyn 2021; 40:6477-6502. [PMID: 33586620 DOI: 10.1080/07391102.2021.1886171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the most cryptic pandemic outbreak of the 21st century, has gripped more than 1.8 million people to death and infected almost eighty six million. As it is a new variant of SARS, there is no approved drug or vaccine available against this virus. This study aims to predict some promising cytotoxic T lymphocyte epitopes in the SARS-CoV-2 proteome utilizing immunoinformatic approaches. Firstly, we identified 21 epitopes from 7 different proteins of SARS-CoV-2 inducing immune response and checked for allergenicity and conservancy. Based on these factors, we selected the top three epitopes, namely KAYNVTQAF, ATSRTLSYY, and LTALRLCAY showing functional interactions with the maximum number of MHC alleles and no allergenicity. Secondly, the 3D model of selected epitopes and HLA-A*29:02 were built and Molecular Docking simulation was performed. Most interestingly, the best two epitopes predicted by docking are part of two different structural proteins of SARS-CoV-2, namely Membrane Glycoprotein (ATSRTLSYY) and Nucleocapsid Phosphoprotein (KAYNVTQAF), which are generally target of choice for vaccine designing. Upon Molecular Docking, interactions between selected epitopes and HLA-A*29:02 were further validated by 50 ns Molecular Dynamics (MD) simulation. Analysis of RMSD, Rg, SASA, number of hydrogen bonds, RMSF, MM-PBSA, PCA, and DCCM from MD suggested that ATSRTLSYY is the most stable and promising epitope than KAYNVTQAF epitope. Moreover, we also identified B-cell epitopes for each of the antigenic proteins of SARS CoV-2. Findings of our work will be a good resource for wet lab experiments and will lessen the timeline for vaccine construction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Muzahid Ahmed Ezaj
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.,Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh
| | - Md Junaid
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh
| | - Yeasmin Akter
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Biotechnology & Genetic Engineering, Noakhali Science & Technology University, Noakhali, Bangladesh
| | - Afsana Nahrin
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, Bangladesh
| | - Aysha Siddika
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Syeda Samira Afrose
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - S M Abdul Nayeem
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Md Sajedul Haque
- Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - S M Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh.,Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for Applied Medical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Uzzaman M, Junaid M, Uddin MN. Evaluation of anti-tuberculosis activity of some oxotitanium(IV) Schiff base complexes; molecular docking, dynamics simulation and ADMET studies. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2644-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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11
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Mahmud S, Parves MR, Riza YM, Sujon KM, Ray S, Tithi FA, Zaoti ZF, Alam S, Absar N. Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation. J Biomol Struct Dyn 2019; 38:4221-4231. [PMID: 31607222 DOI: 10.1080/07391102.2019.1680440] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Snake venom of Naja naja comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA2), is noteworthy for its numerous adverse effects, such as cytotoxicity, cardiotoxicity, hemolytic, anti-coagulant, and hypotensive effects, including being highly potent as a neurotoxin. Limited anti-venom therapy (with their lower efficacy) has attracted considerable pharmacological interest to develop potent inhibitors of PLA2. Thus, 34 experimentally proven and diverse synthetic inhibitors of PLA2 were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function. Then, ten potential hits were subjected to induced fit docking, in which top three potential inhibitors were considered, and those were found to interact with Ca2+, disulfide binding site, and phosphatidylcholine activation sites, thereby, possibly disrupting the catalytic activity of Ca2+ as well as the inflammatory functions of PLA2. These compounds showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors. Gap energy and thermodynamic properties were investigated by employing density functional theory for all compounds to understand their chemical reactivity and thermodynamic stability. Molecular dynamics simulation was performed for 100 ns in order to evaluate the stability and binding modes of docked complexes, and the energy of binding was calculated through MM-PBSA analysis. On the whole, the proposed compounds could be used for targeted inhibition. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, Molecular Biology and Protein Science Laboratory, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Rimon Parves
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Yasir Mohamed Riza
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Khaled Mahmud Sujon
- Department of Genetic Engineering and Biotechnology, Molecular Biology and Protein Science Laboratory, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvendu Ray
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Fahmida Alam Tithi
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | | | - Sanjida Alam
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - N Absar
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
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