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Byadi S, Abdoullah B, Fawzi M, Irrou E, Ait Elmachkouri Y, Oubella A, Auhmani A, Morjani H, Labd Taha M, Robert A, Aboulmouhajir A, Ait Itto MY. Discovery of a new Bcl-2 inhibitor through synthesis, anticancer activity, docking and MD simulations. J Biomol Struct Dyn 2024; 42:4145-4154. [PMID: 37255018 DOI: 10.1080/07391102.2023.2218934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
A database of 300 compounds was virtually screened and docked against Bcl-2 protein; the stability of the best-formed complex was evaluated through Molecular dynamics, the top ten compounds with the best in-silico complexation affinities were synthesized, and their In-vitro cytotoxic activity was examined. Thiazolidinone (4e) and isoxazoline (4a-d) were evaluated in-silico. For further evaluation and examination, we designed and synthesized from naturally occurring (R)-carvone and characterized it via spectroscopic analysis, as well as tested for their anticancer activities towards human cancer cell lines such as HT-1080 (fibrosarcome cancer), MCF-7 and MDA-MB-231 (breast cancer) and A-549 (lung cancer) by using MTT method with Doxorubicin as standard drug. Among them, compound 4d showed the most promising anticancer activity against HT-1080, A-549, MCF-7, and MDA-MB-231 cell lines with IC50 values of 15.59 ± 3.21 µM; 18.32 ± 2.73 µM; 17.28 ± 0.33 µM and 19.27 ± 2.73 µM respectively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Said Byadi
- Team of Photochemistry, Synthesis, Hemisynthesis, Spectroscopy and Chemoinformatics, Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, Casablanca, Morocco
| | - Bimoussa Abdoullah
- Département de Chimie, Faculté des Sciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Mourad Fawzi
- Département de Chimie, Faculté des Sciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Ezaddine Irrou
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, IBNOU ZOHR University, Agadir, Morocco
| | - Younesse Ait Elmachkouri
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, IBNOU ZOHR University, Agadir, Morocco
| | - Ali Oubella
- Département de Chimie, Faculté des Sciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, IBNOU ZOHR University, Agadir, Morocco
| | - Aziz Auhmani
- Département de Chimie, Faculté des Sciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Hamid Morjani
- BioSpectroscopie Translationnelle, BioSpecT - EA7506, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims Cedex, France
| | - Mohamed Labd Taha
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, IBNOU ZOHR University, Agadir, Morocco
| | - Anthony Robert
- Equipe MSO, CNRS UMR 7312 Institut de Chimie Moléculaire Université de Reims Champagne-Ardenne, REIMS Cédex 2, France
| | - Aziz Aboulmouhajir
- Team of Photochemistry, Synthesis, Hemisynthesis, Spectroscopy and Chemoinformatics, Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, Casablanca, Morocco
| | - Moulay Youssef Ait Itto
- Département de Chimie, Faculté des Sciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
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Kannan P, A HB, N MP, D TK, Ramanathan G, Eswaramoorthy R, Ramasamy M. Unravelling the Relacatib activity against the CTSK proteins causing pycnodysostosis: a molecular docking and dynamics approach. J Biomol Struct Dyn 2024; 42:4121-4132. [PMID: 37255004 DOI: 10.1080/07391102.2023.2218927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
Pycnodysostosis is an atypical autosomal recessive condition of Lysosomal storage disorder that originated due to the deficit of the enzyme Cathepsin K which is vital for normal osteoclast action in bone resorption. Abnormal degradation of type 1 collagen and accumulation of toxic undigested collagen fibers in lysosomes of the osteoclast cells resulting in high bone density, brittle bones, and a short stature is caused in CTSK protein-carrying individuals. The broad aim of this study is to identify the most significant variant through various computational pipelines. This study was initiated by retrieving a total number of thirty-six variants from NCBI, HGMD, and UniProt databases, and the Y283C variant was found to be more significant by various standard computational tools. A structural investigation was performed to understand and gain a better knowledge about the interaction profile for the native (1BY8) and variant (Y283C) with Relacatib (a small-molecule drug that blocks the function of Cathepsin K, an enzyme that has been linked to osteoporosis, osteoarthritis, and other bone-degrading diseases). The interaction profile was analyzed using molecular docking. Relacatib (ligand) had an average binding affinity for both native (-7.16 kcal/mol) and Y283C (-6.76 kcal/mol). Finally, Molecular dynamics simulations were done in duplicates to recognize the variant (Y283C) activity of the protein structure against Relacatib for 100 ns. This study assists in comprehending the most pathogenic amino-acid variant, the ligand interaction with the protein structure, and paves the way for understanding the steadiness of the ligand with the native and selected significant amino-acid variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Kannan
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Hadeefa Begum A
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Madhana Priya N
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Thirumal Kumar D
- Faculty of Allied Health Science, Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Gnansambandan Ramanathan
- Department of Biomedical Science, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, India
| | - Magesh Ramasamy
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
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Uddin MJ, Niloy SI, Aktaruzzaman M, Talukder MEK, Rahman MM, Imon RR, Uddin AFMS, Amin MZ. Neuropharmacological assessment and identification of possible lead compound (apomorphine) from Hygrophila spinosa through in-vivo and in-silico approaches. J Biomol Struct Dyn 2024:1-16. [PMID: 38385482 DOI: 10.1080/07391102.2024.2317974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The aim of this research is to examine possible neurological activity of methanol, ethyl acetate, and aqueous extracts of Hygrophila spinosa and identify possible lead compounds through in silico analysis. In vivo, neuropharmacological activity was evaluated by using four distinct neuropharmacological assessment assays. Previously reported GC-MS data and earlier literature were utilized to identify the phytochemicals present in Hygrophila spinosa. Computational studies notably molecular docking and molecular dynamic simulations were conducted with responsible receptors to assess the stability of the best interacting compound. Pharmacokinetics properties like absorption, distribution, metabolism, excretion, and toxicity were considered to evaluate the drug likeliness properties of the identified compounds. All the in vivo results support the notion that different extracts (methanol, ethyl acetate, and aqueous) of Hygrophila spinosa have significant (*p = 0.05) sedative-hypnotic, anxiolytic, and anti-depressant activity. Among all the extracts, specifically methanol extracts of Hygrophila spinosa (MHS 400 mg/kg.b.w.) showed better sedative, anxiolytic and antidepressant activity than aqueous and ethyl acetate extracts. In silico molecular docking analysis revealed that among 53 compounds 7 compounds showed good binding affinities and one compound, namely apomorphine (CID: 6005), surprisingly showed promising binding affinity to all the receptors . An analysis of molecular dynamics simulations confirmed that apomorphine (CID: 6005) had a high level of stability at the protein binding site. Evidence suggests that Hygrophila spinosa has significant sedative, anxiolytic, and antidepressant activity. In silico analysis revealed that a particular compound (apomorphine) is responsible for this action. Further research is required in order to establish apomorphine as a drug for anxiety, depression, and sleep disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Jashim Uddin
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Clinical Pharmacy and Pharmacology. Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Md Aktaruzzaman
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Clinical Pharmacy and Pharmacology. Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Enamul Kabir Talukder
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Mashiar Rahman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Raihan Rahman Imon
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - A F M Shahab Uddin
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Ziaul Amin
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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Kumar R, Madhavan T, Ponnusamy K, Sohn H, Haider S. Computational study of the motor neuron protein KIF5A to identify nsSNPs, bioactive compounds, and its key regulators. Front Genet 2023; 14:1282234. [PMID: 38028604 PMCID: PMC10667939 DOI: 10.3389/fgene.2023.1282234] [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: 08/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Kinesin family member 5A (KIF5A) is a motor neuron protein expressed in neurons and involved in anterograde transportation of organelles, proteins, and RNA. Variations in the KIF5A gene that interfere with axonal transport have emerged as a distinguishing feature in several neurodegenerative disorders, including hereditary spastic paraplegia (HSP10), Charcot-Marie-Tooth disease type 2 (CMT2), and Amyotrophic Lateral Sclerosis (ALS). Methods: In this study, we implemented a computational structural and systems biology approach to uncover the role of KIF5A in ALS. Using the computational structural biology method, we explored the role of non-synonymous Single Nucleotide Polymorphism (nsSNPs) in KIF5A. Further, to identify the potential inhibitory molecule against the highly destabilizing structure variant, we docked 24 plant-derived phytochemicals involved in ALS. Results: We found KIF5AS291F variant showed the most structure destabilizing behavior and the phytocompound "epigallocatechin gallate" showed the highest binding affinity (-9.0 Kcal/mol) as compared to wild KIF5A (-8.4 Kcal/mol). Further, with the systems biology approach, we constructed the KIF5A protein-protein interaction (PPI) network to identify the associated Kinesin Families (KIFs) proteins, modules, and their function. We also constructed a transcriptional and post-transcriptional regulatory network of KIF5A. With the network topological parameters of PPIN (Degree, Bottleneck, Closeness, and MNC) using CytoHubba and computational knock-out experiment using Network Analyzer, we found KIF1A, 5B, and 5C were the significant proteins. The functional modules were highly enriched with microtubule motor activity, chemical synaptic transmission in neurons, GTP binding, and GABA receptor activity. In regulatory network analysis, we found KIF5A post-transcriptionally down-regulated by miR-107 which is further transcriptionally up-regulated by four TFs (HIF1A, PPARA, SREBF1, and TP53) and down-regulated by three TFs (ZEB1, ZEB2, and LIN28A). Discussion: We concluded our study by finding a crucial variant of KIF5A and its potential therapeutic target (epigallocatechin gallate) and KIF5A associated significant genes with important regulators which could decrypt the novel therapeutics in ALS and other neurodegenerative diseases.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Thirumurthy Madhavan
- Department of Genetic Engineering, Computational Biology Lab, SRM Institute of Science and Technology, Chennai, India
| | | | - Honglae Sohn
- Department of Chemistry and Department of Carbon Materials, Chosun University, Gwangju, Republic of Korea
| | - Shazia Haider
- Department of Biosciences, Jamia Millia University, New Delhi, India
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Fan X, Xu L, Zhang J, Wang Y, Wu Z, Sun W, Yao X, Wang X, Guan S, Shan Y. Mechanism Exploration of Amyloid-β-42 Disaggregation by Single-Chain Variable Fragments of Alzheimer's Disease Therapeutic Antibodies. Int J Mol Sci 2023; 24:ijms24098371. [PMID: 37176076 PMCID: PMC10179127 DOI: 10.3390/ijms24098371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Alzheimer's disease (AD) is a specific neurodegenerative disease. This study adopts single-chain variable fragments (scFvs) as a potential immunotherapeutic precursor for AD. According to the remarkable effects of monoclonal antibodies, such as the depolymerization or promotion of Aβ42 efflux by Crenezumab, Solanezumab, and 12B4, it is attractive to prepare corresponding scFvs targeting amyloid-β-42 protein (Aβ42) and investigate their biological activities. Crenezumab-like scFv (scFv-C), Solanezumab-like scFv (scFv-S), and 12B4-like scFv (scFv-12B4) were designed and constructed. The thermal stabilities and binding ability to Aβ42 of scFv-C, scFv-S, and scFv-12B4 were evaluated using unfolding profile and enzyme-linked immunosorbent assay. As the results indicated that scFv-C could recognize Aβ42 monomer/oligomer and promote the disaggregation of Aβ42 fiber as determined by the Thioflavin-T assay, the potential mechanism of its interaction with Aβ42 was investigated using molecular dynamics analysis. Interactions involving hydrogen bonds and salt bonds were predicted between scFv-C and Aβ42 pentamer, suggesting the possibility of inhibiting further aggregation of Aβ42. The successfully prepared scFvs, especially scFv-C, with favorable biological activity targeting Aβ42, might be developed for a potentially efficacious clinical application for AD.
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Affiliation(s)
- Xing Fan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Lipeng Xu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jianhao Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yidan Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zirui Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wenjing Sun
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xin Yao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Shanshan Guan
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun 130052, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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Aghaei S, Farrokhi E, Saffari-Chaleshtori J, Hoseinzadeh M, Molavi N, Hashemipour M, Rostampour N, Asgharzadeh S, Tabatabaiefar MA. New molecular insights into the A218V variant impact on the steroidogenic acute regulatory protein (STAR) associated with 46, XY disorders of sexual development. Mol Genet Genomics 2023; 298:693-708. [PMID: 37004560 DOI: 10.1007/s00438-023-02006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/07/2023] [Indexed: 04/04/2023]
Abstract
Disorders of sexual development (DSD) are an abnormal congenital conditions associated with atypical development of the urogenital tract and external genital structures. The steroidogenic acute regulatory (STAR) gene, associated with congenital lipoid adrenal hyperplasia (CLAH), is included in the targeted gene panel for the DSD diagnosis. Therefore, the genetic alterations of the STAR gene and their molecular effect were examined in the CLAH patients affected with DSD. Ten different Iranian families including twelve male pseudo-hermaphroditism patients with CLAH phenotype were studied using genetic linkage screening and STAR gene sequencing in the linked families to the STAR locus. Furthermore, the structural, dynamical, and functional impacts of the variants on the STAR in silico were analyzed. Sanger sequencing showed the pathogenic variant p.A218V in STAR gene, as the first report in Iranian population. Moreover, modeling and simulation analysis were performed using tools such as radius of gyration, root mean square deviation (RMSD), root mean square fluctuation (RMSF), and molecular docking showed that p.A218V variant affects the residues interaction in cholesterol-binding site and the proper folding of STAR through increasing H-bound and the amount of α-Helix, deceasing total flexibility and changing fluctuations in some residues, resulting in reduced steroidogenic activity of the STAR protein. The study characterized the structural and functional changes of STAR caused by pathogenic variant p.A218V. It leads to limited cholesterol-binding activity of STAR, ultimately leading to the CLAH disease. Molecular dynamics simulation of STAR variants could help explain different clinical manifestations of CLAH disease.
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Affiliation(s)
- Shahrzad Aghaei
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Effat Farrokhi
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Javad Saffari-Chaleshtori
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Marziyeh Hoseinzadeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Newsha Molavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahin Hashemipour
- Metabolic Liver Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Noushin Rostampour
- Metabolic Liver Disease Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Samira Asgharzadeh
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
- Department of Genetics and Molecular Biology, School of Medicine and Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
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Kumar S, Bhardwaj VK, Singh R, Purohit R. Structure restoration and aggregate inhibition of V30M mutant transthyretin protein by potential quinoline molecules. Int J Biol Macromol 2023; 231:123318. [PMID: 36681222 DOI: 10.1016/j.ijbiomac.2023.123318] [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: 09/08/2022] [Revised: 01/01/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
Transthyretin (TTR) is a tetrameric protein found in human plasma and cerebrospinal fluid that functions as a transporter of thyroxine (T4) and retinol. A mutation resulting in the substitution of valine to methionine at position 30 (V30M) is the most common mutation that destabilizes the tetramer structure of TTR protein resulting in a fatal neuropathy known as TTR amyloidosis. The V30M TTR-induced neuropathy can be inhibited through stabilization of the TTR tetramer by the binding of small molecules. We accessed the potential of in-house synthesized quinoline molecules to stabilize the V30M TTR structure and analyzed the impact of protein-ligand interactions through molecular docking, molecular dynamics (MD) simulations, steered MD, and umbrella sampling simulations. This study revealed that the binding of quinoline molecules reverted back the structural changes including the residual flexibility, changes in secondary structural elements, and also restored the alterations in the electrostatic surface potential induced by the V30M mutation. Further, the top-most 4G and 4R molecules were compared with an FDA-approved drug (Tafamidis) and a reference quinoline molecule 14C. Here, we intend to suggest that the quinoline molecules could revert the structural changes, cease tetramer dissociation, prevent abnormal oligomerization and therefore could be developed as an effective therapeutics against TTR amyloidosis.
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Affiliation(s)
- Sachin Kumar
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Muneeswaran G, Lee JY. Mechanistic insights into the conformational switch in profilin-1 subject to collective effects of mutation and histidine tautomerism. Int J Biol Macromol 2023; 230:123403. [PMID: 36706877 DOI: 10.1016/j.ijbiomac.2023.123403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
Mutations and histidine (His) tautomerism in profilin-1 (PFN1) are associated with amyotrophic lateral sclerosis (ALS). The conformational changes in PFN1 caused by the collective effects of G117V mutation and His tautomeric isomers εε, εδ, δε, and δδ were clarified using molecular dynamics (MD) simulations. The predominant structural variations were seen in α-helices, β-sheets, turns, and coils and the His tautomer's unique degree of disruption was seen in these conformations. The content of α-helices was 23.2 % in the εε and δδ isomers, but the observed α-helices in the isomers εδ and δε were 20.3 % and 21.7 % respectively. The percentage of β-sheet was found to be higher (34.1) in the εε isomer than in the εδ, δε, and δδ isomers, and the values were 30.4, 29.7, and 31.9, respectively. Intermolecular water dynamics analysis discloses that His 133 can form an intramolecular H-bond interaction (Nα-H---Nδ), confirming the experimental observations in the simulations of εε, δε, and δδ isomers of G117V PFN1 mutant. It was concluded that these solvent molecules are crucial for aggregation and must be considered in future research on the PFN1 associated with ALS. Overall, the study offers a thorough microscopic understanding of the pathogenic mechanisms behind conformational changes that cause aggregation illnesses like ALS.
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Affiliation(s)
- Gurusamy Muneeswaran
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea; Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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9
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Li Q, Ma Z, Qin S, Zhao WJ. Virtual Screening-Based Drug Development for the Treatment of Nervous System Diseases. Curr Neuropharmacol 2023; 21:2447-2464. [PMID: 36043797 PMCID: PMC10616913 DOI: 10.2174/1570159x20666220830105350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/04/2022] [Accepted: 08/19/2022] [Indexed: 11/22/2022] Open
Abstract
The incidence rate of nervous system diseases has increased in recent years. Nerve injury or neurodegenerative diseases usually cause neuronal loss and neuronal circuit damage, which seriously affect motor nerve and autonomic nervous function. Therefore, safe and effective treatment is needed. As traditional drug research becomes slower and more expensive, it is vital to enlist the help of cutting- edge technology. Virtual screening (VS) is an attractive option for the identification and development of promising new compounds with high efficiency and low cost. With the assistance of computer- aided drug design (CADD), VS is becoming more and more popular in new drug development and research. In recent years, it has become a reality to transform non-neuronal cells into functional neurons through small molecular compounds, which provides a broader application prospect than transcription factor-mediated neuronal reprogramming. This review mainly summarizes related theory and technology of VS and the drug research and development using VS technology in nervous system diseases in recent years, and focuses more on the potential application of VS technology in neuronal reprogramming, thus facilitating new drug design for both prevention and treatment of nervous system diseases.
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Affiliation(s)
- Qian Li
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Zhaobin Ma
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, Yunnan, P.R. China
| | - Shuhua Qin
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, Yunnan, P.R. China
| | - Wei-Jiang Zhao
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- Department of Cell Biology, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
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Jeon YM, Kwon Y, Lee S, Kim HJ. Potential roles of the endoplasmic reticulum stress pathway in amyotrophic lateral sclerosis. Front Aging Neurosci 2023; 15:1047897. [PMID: 36875699 PMCID: PMC9974850 DOI: 10.3389/fnagi.2023.1047897] [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: 09/19/2022] [Accepted: 01/16/2023] [Indexed: 02/17/2023] Open
Abstract
The endoplasmic reticulum (ER) is a major organelle involved in protein quality control and cellular homeostasis. ER stress results from structural and functional dysfunction of the organelle, along with the accumulation of misfolded proteins and changes in calcium homeostasis, it leads to ER stress response pathway such as unfolded protein response (UPR). Neurons are particularly sensitive to the accumulation of misfolded proteins. Thus, the ER stress is involved in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, prion disease and motor neuron disease (MND). Recently, the complex involvement of ER stress pathways has been demonstrated in experimental models of amyotrophic lateral sclerosis (ALS)/MND using pharmacological and genetic manipulation of the unfolded protein response (UPR), an adaptive response to ER stress. Here, we aim to provide recent evidence demonstrating that the ER stress pathway is an essential pathological mechanism of ALS. In addition, we also provide therapeutic strategies that can help treat diseases by targeting the ER stress pathway.
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Affiliation(s)
- Yu-Mi Jeon
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Younghwi Kwon
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Shinrye Lee
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyung-Jun Kim
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea.,Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
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11
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Khazamipour A, Gholampour-Faroji N, Zeraati T, Vakilian F, Haddad-Mashadrizeh A, Ghayour Mobarhan M, Pasdar A. A novel causative functional mutation in GATA6 gene is responsible for familial dilated cardiomyopathy as supported by in silico functional analysis. Sci Rep 2022; 12:13752. [PMID: 35962153 PMCID: PMC9374661 DOI: 10.1038/s41598-022-13993-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Dilated cardiomyopathy (DCM), one of the most common types of cardiomyopathies has a heterogeneous nature and can be seen in Mendelian forms. Next Generation Sequencing is a powerful tool for identifying novel variants in monogenic disorders. We used whole-exome sequencing (WES) and Sanger sequencing techniques to identify the causative mutation of DCM in an Iranian pedigree. We found a novel variant in the GATA6 gene, leading to substituting Histidine by Tyrosine at position 329, observed in all affected family members in the pedigree, whereas it was not established in any of the unaffected ones. We hypothesized that the H329Y mutation may be causative for the familial pattern of DCM in this family. The predicted models of GATA6 and H329Y showed the high quality according to PROCHECK and ERRAT. Nonetheless, simulation results revealed that the protein stability decreased after mutation, while the flexibility may have been increased. Hence, the mutation led to the increased compactness of GATA6. Overall, these data indicated that the mutation could affect the protein structure, which may be related to the functional impairment of GATA6 upon H329Y mutation, likewise their involvement in pathologies. Further functional investigations would help elucidating the exact mechanism.
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Affiliation(s)
- Afrouz Khazamipour
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nazanin Gholampour-Faroji
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Tina Zeraati
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farveh Vakilian
- Atherosclerosis Prevention Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Majid Ghayour Mobarhan
- Metabolic Syndrome Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Division of Applied Medicine, Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK. .,Bioinformatics Research Centre, Mashhad University of Medical Sciences, Mashhad, Iran.
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12
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Menteş M, Karakuzulu BB, Uçar GB, Yandım C. Comparative molecular dynamics analyses on PIK3CA hotspot mutations with PI3Kα specific inhibitors and ATP. Comput Biol Chem 2022; 99:107726. [PMID: 35842959 DOI: 10.1016/j.compbiolchem.2022.107726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/19/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
Abstract
PI3K pathway is heavily emphasized in cancer where PIK3CA, which encodes for the p110α subunit of PI3Kα, presents itself as the second most common mutated gene. A lot of effort has been put in developing PI3K inhibitors, opening promising avenues for the treatment of cancer. Among these, PI3Kα specific inhibitor alpelisib was approved by FDA for breast cancer and other α-isoform specific inhibitors such as inavolisib and serabelisib reached clinical trials. However, the mode of action of these inhibitors on mutated PI3Kα and how they interact with mutant structures has not been fully elucidated yet. In this study, we are revealing the calculated interactions and binding affinities of these inhibitors within the context of PIK3CA hotspot mutations (E542K, E545K and H1047R) by employing molecular dynamics (MD) simulations. We performed principal component analysis to understand the motions of the protein complex during our simulations and also checked the correlated motions of all amino acids. Binding affinity calculations with MM-PBSA confirmed the consistent binding of alpelisib across mutations and revealed relatively higher affinities for inavolisib towards wild-type and H1047R mutant structures in comparison to other inhibitors. On the other hand, E542K mutation significantly impaired the interaction of inavolisib and serabelisib with PI3Kα. We also investigated the structural relationship of the natural ligand ATP with PI3Kα, and interestingly realized a significant reduction in binding affinity for the mutants, with potentially unexpected implications on the mechanisms that render these mutations oncogenic. Moreover, correlated motions of all residues were generally higher for ATP except the H1047R mutation which exhibited a distinguishable reduction. The results presented here could be guiding for pre-clinical and clinical studies of personalized medicine where individual mutations are a strong consideration point.
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Affiliation(s)
- Muratcan Menteş
- Izmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330 Balçova, İzmir, Turkey
| | - Başak Buse Karakuzulu
- Izmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330 Balçova, İzmir, Turkey
| | - Gönlüm Bahar Uçar
- Izmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330 Balçova, İzmir, Turkey
| | - Cihangir Yandım
- Izmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330 Balçova, İzmir, Turkey; Izmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, 35340 İnciraltı, İzmir, Turkey.
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13
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Muneeswaran G, Lee JY. Histidine tautomerism dependent conformational transitions driven aggregation of profilin-1: Implications in amyotrophic lateral sclerosis. Int J Biol Macromol 2022; 214:241-251. [PMID: 35688275 DOI: 10.1016/j.ijbiomac.2022.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/17/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
Aggregation of profilin-1 (PFN1) causes a fatal neurodegenerative disease, familial amyotrophic lateral sclerosis (fALS). Histidine (His) tautomerism has been linked to the formation of fibril aggregation causing neurodegenerative disease. Characterization of intermediate species that form during aggregation is crucial, however, this has proven very challenging for experimentalists due to their transient nature. Hence, molecular dynamics (MD) simulations have been performed on the His tautomeric isomers εε, εδ, δε, and δδ of PFN1 to explain the structural changes and to correlate them with its aggregation propensity. MD simulations show that His133 presumably plays a major role in the aggregation of PFN1 upon His tautomerism compared to His119. Further, the formation of a new 310-helix is observed in εε and δε but 310-helix is not observed in δδ and εδ isomers. In addition, our findings unveil that β-sheet dominating conformations are observed in His119(δ)-His133(δ) δδ isomer of PFN1 with significant antiparallel β-sheets between residues T15-G23, S29-A33, L63-L65, Q68-S76, F83-T89, T97-T105, and K107-K115, suggesting a novel aggregation mechanism possibly occur for the formation of PFN1 aggregates. Overall, these results propose that MD simulations of PFN1 His tautomers can provide a detailed microscopic understanding of the aggregation mechanisms which are hard to probe through experiments.
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Affiliation(s)
- Gurusamy Muneeswaran
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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14
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Exploration of the Interactions between Maltase–Glucoamylase and Its Potential Peptide Inhibitors by Molecular Dynamics Simulation. Catalysts 2022. [DOI: 10.3390/catal12050522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Diabetes mellitus, a chronic metabolic disorder, represents a serious threat to human health. The gut enzyme maltase–glucoamylase (MGAM) has attracted considerable attention as a potential therapeutic target for the treatment of type 2 diabetes. Thus, developing novel inhibitors of MGAM holds the promise of improving clinical management. The dipeptides, Thr-Trp (TW) and Trp-Ala (WA), are known inhibitors of MGAM; however, studies on how they interact with MGAM are lacking. The work presented here explored these interactions by utilizing molecular docking and molecular dynamics simulations. Results indicate that the active center of the MGAM could easily accommodate the flexible peptides. Interactions involving hydrogen bonds, cation-π, and hydrophobic interactions are predicted between TW/WA and residues including Tyr1251, Trp1355, Asp1420, Met1421, Glu1423, and Arg1510 within MGAM. The electrostatic energy was recognized as playing a dominant role in both TW-MGAM and WA-MGAM systems. The binding locations of TW/WA are close to the possible acid-base catalytic residue Asp1526 and might be the reason for MGAM inhibition. These findings provide a theoretical structural model for the development of future inhibitors.
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15
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Arulkumar M, Yang K, Wang N, Penislusshiyan S, Palvannan T, Ramalingam K, Chen F, Luo SH, Zhou YJ, Wang ZY. Synthesis of benzimidazole/triphenylamine-based compounds, evaluation of their bioactivities and an in silico study with receptor tyrosine kinases. NEW J CHEM 2022. [DOI: 10.1039/d1nj05073g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The antiproliferative activity of AL-1 against various cancer cells indicated the applicability of the BI-TPA-based compound as a potential multi-cancer inhibitor.
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Affiliation(s)
- Mani Arulkumar
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China
| | - Kai Yang
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, P. R. China
| | - Neng Wang
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China
| | - Sakayanathan Penislusshiyan
- Laboratory of Bioprocess and Engineering, Department of Biochemistry, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Thayumanavan Palvannan
- Laboratory of Bioprocess and Engineering, Department of Biochemistry, Periyar University, Salem 636 011, Tamil Nadu, India
| | - Karthick Ramalingam
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, Guangdong Provincial Engineering Technology Research Center for Wastewater Management and Treatment, School of Environment, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, P. R. China
| | - Fuming Chen
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, Guangdong Provincial Engineering Technology Research Center for Wastewater Management and Treatment, School of Environment, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, P. R. China
| | - Shi-He Luo
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China
| | - Yong-Jun Zhou
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China
| | - Zhao-Yang Wang
- School of Chemistry, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China
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16
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Ganai SA, Srinivasan P, Rajamanikandan S, Shah BA, Mohan S, Gani M, Padder BA, Qadri RA, Bhat MA, Baba ZA, Yatoo MA. Delineating binding potential, stability of Sulforaphane-N-acetyl-cysteine in the active site of histone deacetylase 2 and testing its cytotoxicity against distinct cancer lines through stringent molecular dynamics, DFT and cell-based assays. Chem Biol Drug Des 2021; 98:363-376. [PMID: 33966346 DOI: 10.1111/cbdd.13854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/29/2021] [Accepted: 04/25/2021] [Indexed: 12/12/2022]
Abstract
Histone deacetylase 2 (HDAC2), an isozyme of Class I HDACs has potent imputations in actuating neurodegenerative signaling. Currently, there are sizeable therapeutic disquiets with the use of synthetic histone deacetylase inhibitors in disease management. This strongly suggests the unfulfilled medical necessity of plant substitutes for therapeutic intervention. Sulforaphane-N-acetyl-cysteine (SFN-N-acetylcysteine or SFN-NAC), a sulforaphane metabolite has shown significantly worthier activity against HDACs under in vitro conditions. However, the atomistic studies of SFN-NAC against HDAC2 are currently lacking. Thus, the present study employed a hybrid strategy including extra-precision (XP) grid-based flexible molecular docking, molecular mechanics generalized born surface area (MM-GBSA), e-Pharmacophores method, and molecular dynamics simulation for exploring the binding strengh, mode of interaction, e-Pharmacophoric features, and stability of SFN-NAC towards HDAC2. Further, the globally acknowledged density functional theory (DFT) study was performed on SFN-NAC and entinostat individually in complex state with HDAC2. Apart from this, these inhibitors were tested against three distinct cancer cell models and one transformed cell line for cytotoxic activity. Moreover, double mutant of HDAC2 was generated and the binding orientation and interaction of SFN-NAC was scrutinized in this state. On the whole, this study unbosomed and explained the comparatively higher binding affinity of entinostat for HDAC2 and its wide spectrum cytotoxicity than SFN-NAC.
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Affiliation(s)
- Shabir Ahmad Ganai
- Division of Basic Sciences and Humanities, FoA, SKUAST-Kashmir, 193201, India
| | - Pappu Srinivasan
- Department of Animal Health and Management, Alagappa University, Karaikudi, India
| | - Sundaraj Rajamanikandan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
| | - Basit Amin Shah
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Suma Mohan
- SCBT, Shanmugha Arts Science Technology and Research Academy, 613401, India
| | - Mudasir Gani
- Division of Entomology, FoA, SKUAST-Kashmir, 193201, India
| | | | - Raies A Qadri
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - M A Bhat
- Division of Genetics and Plant Breeding, SKUAST-Kashmir, 193201, India
| | - Zahoor Ahmad Baba
- Division of Basic Sciences and Humanities, FoA, SKUAST-Kashmir, 193201, India
| | - Manzoor Ahmad Yatoo
- Division of Basic Sciences and Humanities, FoA, SKUAST-Kashmir, 193201, India
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