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Subbarayan R, Srinivasan D, Shadula Osmania S, Murugan Girija D, Ikhlas S, Srivastav N, Balakrishnan R, Shrestha R, Chauhan A. Molecular insights on Eltrombopag: potential mitogen stimulants, angiogenesis, and therapeutic radioprotectant through TPO-R activation. Platelets 2024; 35:2359028. [PMID: 38832545 DOI: 10.1080/09537104.2024.2359028] [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: 01/16/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024]
Abstract
The purpose of this study is to investigate the molecular interactions and potential therapeutic uses of Eltrombopag (EPAG), a small molecule that activates the cMPL receptor. EPAG has been found to be effective in increasing platelet levels and alleviating thrombocytopenia. We utilized computational techniques to predict and confirm the complex formed by the ligand (EPAG) and the Thrombopoietin receptor (TPO-R) cMPL, elucidating the role of RAS, JAK-2, STAT-3, and other essential elements for downstream signaling. Molecular dynamics (MD) simulations were employed to evaluate the stability of the ligand across specific proteins, showing favorable characteristics. For the first time, we examined the presence of TPO-R in human umbilical cord mesenchymal stem cells (hUCMSC) and human gingival mesenchymal stem cells (hGMSC) proliferation. Furthermore, treatment with EPAG demonstrated angiogenesis and vasculature formation of endothelial lineage derived from both MSCs. It also indicated the activation of critical factors such as RUNX-1, GFI-1b, VEGF-A, MYB, GOF-1, and FLI-1. Additional experiments confirmed that EPAG could be an ideal molecule for protecting against UVB radiation damage, as gene expression (JAK-2, ERK-2, MCL-1, NFkB, and STAT-3) and protein CD90/cMPL analysis showed TPO-R activation in both hUCMSC and hGMSC. Overall, EPAG exhibits significant potential in treating radiation damage and mitigating the side effects of radiotherapy, warranting further clinical exploration.
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Affiliation(s)
- Rajasekaran Subbarayan
- Centre for Advanced Biotherapeutics and Regenerative Medicine, Research-FAHS, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Dhasarathdev Srinivasan
- Centre for Advanced Biotherapeutics and Regenerative Medicine, Research-FAHS, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | - Salman Shadula Osmania
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Shoeb Ikhlas
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nityanand Srivastav
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ranjith Balakrishnan
- Centre for Advanced Biotherapeutics and Regenerative Medicine, Research-FAHS, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
| | | | - Ankush Chauhan
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, India
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Discovery of thiazolidin-4-one analogue as selective GSK-3β inhibitor through structure based virtual screening. Bioorg Med Chem Lett 2021; 52:128375. [PMID: 34560262 DOI: 10.1016/j.bmcl.2021.128375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/05/2021] [Accepted: 09/15/2021] [Indexed: 11/21/2022]
Abstract
GSK-3β directly phosphorylate tubulin binding site of tau protein, indicating its importance in tau aggregation and, therefore, in Alzheimer's disease pathology. New GSK-3β inhibitors were identified using a structure-based screening, ADMET analysis. These studies revealed that ZINC09036109, ZINC72371723, ZINC72371725, and ZINC01373165 approached optimal ADMET properties along with good MM-GBSA dG binding. Protein kinase assays of these compounds against eight disease-relevant kinases were performed. During disease-relevant kinase profiling, ZINC09036109 ((E)-2-((3,4-dimethylphenyl)imino)-5-(3-methoxy-4-(naphthalen-2-ylmethoxy)benzyl)thiazolidin-4-one) emerged as a selective GSK-3β inhibitor with more than 10-fold selectivity over other disease-relevant kinases. Molecular dynamics study of ZINC09036109 molecule revealed interactions with Ile62, Phe67, Val135, Leu188, Asp200 amino acid residues of the binding site of GSK-3β, which were highly comparable to the co-crystallized molecule and hence validating comparative better activity of this compound compared to overall screened molecules.
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Bagri K, Kumar A, Manisha, Kumar P. Computational Studies on Acetylcholinesterase Inhibitors: From Biochemistry to Chemistry. Mini Rev Med Chem 2021; 20:1403-1435. [PMID: 31884928 DOI: 10.2174/1389557520666191224144346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022]
Abstract
Acetylcholinesterase inhibitors are the most promising therapeutics for Alzheimer's disease treatment as these prevent the loss of acetylcholine and slows the progression of the disease. The drugs approved for the management of Alzheimer's disease by the FDA are acetylcholinesterase inhibitors but are associated with side effects. Consistent and stringent efforts by the researchers with the help of computational methods opened new ways of developing novel molecules with good acetylcholinesterase inhibitory activity. In this manuscript, we reviewed the studies that identified the essential structural features of acetylcholinesterase inhibitors at the molecular level as well as the techniques like molecular docking, molecular dynamics, quantitative structure-activity relationship, virtual screening, and pharmacophore modelling that were used in designing these inhibitors.
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Affiliation(s)
- Kiran Bagri
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Manisha
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
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Güzel E, Koçyiğit ÜM, Taslimi P, Gülçin İ, Erkan S, Nebioğlu M, Arslan BS, Şişman İ. Phthalocyanine complexes with (4-isopropylbenzyl)oxy substituents: preparation and evaluation of anti-carbonic anhydrase, anticholinesterase enzymes and molecular docking studies. J Biomol Struct Dyn 2020; 40:733-741. [DOI: 10.1080/07391102.2020.1818623] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Emre Güzel
- Department of Fundamental Sciences, Sakarya University of Applied Sciences, Sakarya, Turkey
| | - Ümit M. Koçyiğit
- Department of Basic Pharmaceutical Sciences, Cumhuriyet University, Sivas, Turkey
| | - Parham Taslimi
- Department of Biotechnology, Bartın University, Bartın, Turkey
| | - İlhami Gülçin
- Department of Chemistry, Atatürk University, Erzurum, Turkey
| | - Sultan Erkan
- Department of Chemistry and Chemical Processing Technologies, Yıldızeli Vocational School, Cumhuriyet University, Sivas, Turkey
| | - Mehmet Nebioğlu
- Department of Chemistry, Sakarya University, Sakarya, Turkey
| | - Barış S. Arslan
- Department of Chemistry, Sakarya University, Sakarya, Turkey
| | - İlkay Şişman
- Department of Chemistry, Sakarya University, Sakarya, Turkey
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Sharma S, Srivastav S, Singh G, Singh S, Malik R, Alam MM, Shaqiquzamman M, Ali S, Akhter M. In silico strategies for probing novel DPP-IV inhibitors as anti-diabetic agents. J Biomol Struct Dyn 2020; 39:2118-2132. [PMID: 32248758 DOI: 10.1080/07391102.2020.1751714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Identification of new DPP-IV inhibitors by integrating validated in silico approach is being presented herein. Novel hits were identified by combining pharmacophore and structure based virtual screening of ZINC and Knowledge Base in house database followed by ADME profiling, consensus docking studies. Six potential hits were identified and analysed for their synthetic accessibility score, novelty analysis and pan assay interference compounds filtration. Out of six, three hits viz., ZINC25060187, ZINC53746227 and KB-10 were analysed for stability studies using Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Dynamics (MD) simulation. The simulation studies of the identified hits revealed that these hits have good selectivity and stability in DPP-IV binding pocket. Important interactions with amino acids viz., Tyr547, Glu205 and Glu206 similar to co-crystallized ligand were also observed. One of the hits viz., KB-10 was synthesized and evaluated for its biological potential. The compound KB-10 showed good DPP-IV inhibition in both in vitro and in vivo studies with IC50: 22.69 µM. This study supports the fact that these techniques hold potential for efficient screening of compounds with unknown affinity for DPP-IV that could serve as candidates for therapeutic development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shweta Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, New Delhi, India.,Bioinformatics Infrastructure Facility, New Delhi, India
| | - Shubham Srivastav
- Department of Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Garima Singh
- Bioinformatics Infrastructure Facility, New Delhi, India.,Department of Food Sciences, School of Interdisciplinary Sciences, New Delhi, India
| | - Smrita Singh
- Technology Board Department, Ministry of Science & Technology, New Delhi, India
| | - Ruchi Malik
- Department of Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Mohammad Mumtaz Alam
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, New Delhi, India
| | - Mohammad Shaqiquzamman
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, New Delhi, India
| | - Shakir Ali
- Bioinformatics Infrastructure Facility, New Delhi, India.,Department of Biochemistry, School of Chemical and Biological Sciences, New Delhi, India
| | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, New Delhi, India.,Bioinformatics Infrastructure Facility, New Delhi, India
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Shiri F, Pirhadi S, Ghasemi JB. Dynamic structure based pharmacophore modeling of the Acetylcholinesterase reveals several potential inhibitors. J Biomol Struct Dyn 2018; 37:1800-1812. [PMID: 29695192 DOI: 10.1080/07391102.2018.1468281] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acetylcholinesterase is a critical enzyme that regulates neurotransmission by catalyzing the breakdown of neurotransmitter acetylcholine in synapses of the nervous system. It is an important target for therapeutic drugs that treat Alzheimer's disease. Since, the degree of flexibility of the side chains of the residues in the active-site gorge of Acetylcholinesterase is diverse it results in different bound ligand conformations. The side-chain conformations of Ser293, Tyr341, Leu76, and Val73 are flexible, while the side-chain conformations of Tyr72, Tyr 124, Ser125, Phe295, and Arg296 appear to be fixed. In this study, multi-conformation dynamic pharmacophore models from the donepezyl-binding pocket based on highly populated structures chosen from molecular dynamics simulations were used for screening compounds that can properly bind acetylcholinesterase. Based on these structures, three pharmacophore models were generated. Consequently, 14 hits were retrieved as final candidates by utilizing virtual screening of ZINC database and molecular docking.
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Affiliation(s)
- Fereshteh Shiri
- a Department of Chemistry , University of Zabol , Zabol , Iran
| | - Somayeh Pirhadi
- b Medicinal and Natural Products Chemistry Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
| | - Jahan B Ghasemi
- c School of Chemistry , University College of Science, University of Tehran , Tehran , Iran
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Baruah P, Basumatary G, Yesylevskyy SO, Aguan K, Bez G, Mitra S. Novel coumarin derivatives as potent acetylcholinesterase inhibitors: insight into efficacy, mode and site of inhibition. J Biomol Struct Dyn 2018; 37:1750-1765. [DOI: 10.1080/07391102.2018.1465853] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Prayasee Baruah
- Centre for Advanced Studies in Chemistry and Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, India
| | - Grace Basumatary
- Centre for Advanced Studies in Chemistry and Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, India
| | - Semen O. Yesylevskyy
- Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine , Kyiv, Ukraine
| | - Kripamoy Aguan
- Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine , Kyiv, Ukraine
| | - Ghanashyam Bez
- Centre for Advanced Studies in Chemistry and Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, India
| | - Sivaprasad Mitra
- Centre for Advanced Studies in Chemistry and Department of Biotechnology & Bioinformatics, North-Eastern Hill University , Shillong, India
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C.P. A, Subhramanian S, Sizochenko N, Melge AR, Leszczynski J, Mohan CG. Multiple e-Pharmacophore modeling to identify a single molecule that could target both streptomycin and paromomycin binding sites for 30S ribosomal subunit inhibition. J Biomol Struct Dyn 2018; 37:1582-1596. [DOI: 10.1080/07391102.2018.1462731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Anju C.P.
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
| | - Sunitha Subhramanian
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
| | - Natalia Sizochenko
- Interdisciplinary Centre for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS-39217, MI, USA
| | - Anu R. Melge
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
| | - Jerzy Leszczynski
- Interdisciplinary Centre for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS-39217, MI, USA
| | - C. Gopi Mohan
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
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Barcellos MP, Santos CBR, Federico LB, Almeida PFD, da Silva CHTDP, Taft CA. Pharmacophore and structure-based drug design, molecular dynamics and admet/tox studies to design novel potential pad4 inhibitors. J Biomol Struct Dyn 2018; 37:966-981. [DOI: 10.1080/07391102.2018.1444511] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mariana P. Barcellos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/n, Ribeirão Preto-SP 14040-903, Brazil
| | - Cleydson B. R. Santos
- Laboratório de Modelagem e Química Computacional, Universidade Federal do Amapá, Rod. JK Km 2, Macapá-AP 68902-280, Brazil
| | - Leonardo B. Federico
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/n, Ribeirão Preto-SP 14040-903, Brazil
| | - Paulo Fernando de Almeida
- Departamento de Ciências da Biointeração, Instituto de Ciencias da Saude, Universidade Federal de Bahia, Av Reitor Miguel Calmon, s/n, Salvador 40-300-100, BA, Brazil
| | - Carlos H. T. de Paula. da Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/n, Ribeirão Preto-SP 14040-903, Brazil
| | - Carlton A. Taft
- Centro Brasileiro de Pesquisas Físicas (CBPF), Rua Dr. Xavier Sigaud, 150, Urca, Rio de Janeiro-RJ 22290-180, Brazil
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Piplani P, Sharma M, Mehta P, Malik R. N-(4-Hydroxyphenyl)-3,4,5-trimethoxybenzamide derivatives as potential memory enhancers: synthesis, biological evaluation and molecular simulation studies. J Biomol Struct Dyn 2017; 36:1867-1877. [DOI: 10.1080/07391102.2017.1336943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Poonam Piplani
- University Institute of Pharmaceutical Sciences, Panjab University , Chandigarh, 160014, India
| | - Manish Sharma
- School of Pharmacy, Maharishi Markandeshwar University , Sadopur, Ambala, Haryana, 134007, India
| | - Pakhuri Mehta
- Central University of Rajasthan , NH-8, Bandar Sindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Ruchi Malik
- Central University of Rajasthan , NH-8, Bandar Sindri, Kishangarh, Ajmer, Rajasthan, 305817, India
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