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Kumar S, Dubey R, Mishra R, Gupta S, Dwivedi VD, Ray S, Jha NK, Verma D, Tsai LW, Dubey NK. Repurposing of SARS-CoV-2 compounds against Marburg Virus using MD simulation, mm/GBSA, PCA analysis, and free energy landscape. J Biomol Struct Dyn 2024:1-20. [PMID: 38450706 DOI: 10.1080/07391102.2024.2323701] [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: 08/16/2023] [Accepted: 01/22/2024] [Indexed: 03/08/2024]
Abstract
The significant mortality rate associated with Marburg virus infection made it the greatest hazard among infectious diseases. Drug repurposing using in silico methods has been crucial in identifying potential compounds that could prevent viral replication by targeting the virus's primary proteins. This study aimed at repurposing the drugs of SARS-CoV-2 for identifying potential candidates against the matrix protein VP40 of the Marburg virus. Virtual screening was performed where the control compound, Nilotinib, showed a binding score of -9.99 kcal/mol. Based on binding scores, hit compounds 9549298, 11960895, 44545852, 51039094, and 89670174 were selected that had a lower binding score than the control. Subsequent molecular dynamics (MD) simulation revealed that compound 9549298 consistently formed a hydrogen bond with the residue Gln290. This was observed both in molecular docking and MD simulation poses, indicating a strong and significant interaction with the protein. 11960895 had the most stable and consistent RMSD pattern exhibited in 100 ns simulation, while 9549298 had the most identical RMSD plot compared to the control molecule. MM/PBSA analysis showed that the binding free energy (ΔG) of 9549298 and 11960895 was lower than the control, with -30.84 and -38.86 kcal/mol, respectively. It was observed by the PCA (principal component analysis) and FEL (free energy landscape) analysis that compounds 9549298 and 11960895 had lesser conformational variation. Overall, this study proposed 9549298 and 11960895 as potential binders of VP40 MARV that can cause its inhibition, however it inherently lacks experimental validation. Furthermore, the study proposes in-vitro experiments as the next step to validate these computational findings, offering a practical approach to further explore these compounds' potential as antiviral agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, UP, India
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei City, Taiwan
| | - Richa Mishra
- Department of Computer Engineering, Parul University, Vadodara, Gujarat, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Bioinformatics Research Division, Greater Noida, UP, India
| | - Subhasree Ray
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
| | - Niraj Kumar Jha
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, India
- Centre of Research Impact and Outreach, Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
| | - Devvret Verma
- Department of Biotechnology, Graphic Era (Deemed to Be University), Dehradun, Uttarakhand, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, Taiwan
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Mir SA, Dash GC, Meher RK, Mohanta PP, Chopdar KS, Mohapatra PK, Baitharu I, Behera AK, Raval MK, Nayak B. In Silico and In Vitro Evaluations of Fluorophoric Thiazolo-[2,3-b]quinazolinones as Anti-cancer Agents Targeting EGFR-TKD. Appl Biochem Biotechnol 2022; 194:4292-4318. [PMID: 35366187 DOI: 10.1007/s12010-022-03893-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/14/2022] [Indexed: 12/01/2022]
Abstract
Epidermal growth factor receptor tyrosine kinase domain (EGFR-TKD) plays a pivotal role in cellular signaling, growth, and metabolism. The EGFR-TKD is highly expressed in cancer cells and was endorsed as a therapeutic target for cancer management to overcome metastasis, cell proliferation, and angiogenesis. The novel thiazolo-[2,3-b]quinazolinones series were strategically developed by microwave-assisted organic synthesis and multi dominos reactions aimed to identify the potent thiazolo-[2,3-b]quinazolinone inhibitor against EGFR-TKD. This study explores the binding stability and binding strength of newly developed series via molecular docking, molecular dynamics simulation, and MM/PBSA and MM/GBSA calculations. The binding interaction was observed to be through the functional groups on aryl substituents at positions 3 and 5 of the thiazolo-[2, 3-b]quinazolinone scaffold. The methyl substituents at position 8 of the ligands had prominent hydrophobic interactions corroborating their bindings similar to the reference FDA-approved drug erlotinib in the active site. ADMET predictions reveal that derivatives 5ab, 5aq, and 5bq are drug-like and may be effective in in vitro study. Molecular dynamics simulation for 100 ns of docked complexes revealed their stability at the atomistic level. The ΔGbinding of thiazolo-[2,3-b]quinazolinone was found to be 5ab - 22.45, 5aq - 22.23, and 5bq - 20.76 similar to standard drug, and erlotinib - 24.11 kcal/mol was determined by MM/GBSA method. Furthermore, the anti-proliferative activity of leads of thiazolo-[2,3-b]quinazolinones (n = 3) was studied against breast cancer cell line (MCF-7) and non-small lung carcinoma cell line (H-1299). The highest inhibitions in cell proliferation were shown by 5bq derivatives, and the IC50 was found to be 6.5 ± 0.67 µM against MCF-7 and 14.8 µM against H-1299. The noscapine was also taken as a positive control and showed IC50 at higher concentrations 37 ± 1 against MCF-7 and 46.5 ± 1.2 against H-1299.
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Affiliation(s)
- Showkat Ahmad Mir
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | | | - Rajesh Kumar Meher
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | | | | | - Pranab Kishor Mohapatra
- Department of Chemistry, C. V. Raman Global University, Bidyanagar, Mahura, Janla, Bhubaneswar, Odisha, 752054, India.
| | - Iswar Baitharu
- Department of Environmental Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | - Ajaya Kumar Behera
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | - Mukesh Kumar Raval
- School of Chemistry, Gangadhar Meher University, Sambalpur, Odisha, 768004, India.
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, India.
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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Taghvaei S, Sabouni F, Minuchehr Z, Taghvaei A. Identification of novel anti-cancer agents, applying in silico method for SENP1 protease inhibition. J Biomol Struct Dyn 2021; 40:6228-6242. [PMID: 33533323 DOI: 10.1080/07391102.2021.1880480] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The SENP1 (Sentrin-Specific Protease1) is essential for desumoylation. SENP1 plays an essential role in many diseases such as cardiovascular disease, diabetes and cancer via targeting GATA2, NEMO, Pin1, SMAD4 and HIF-1α for deSUMOylation. Considering that, over expression of SENP1 was reported in cancer, thus an optional inhibitor of SENP1 can restitute the balance to the skewed system of SUMO and act as an effective therapeutic agent. The purpose of this study was to select and to sort inhibitors with a stronger binding affinity with SENP1. Molecular docking of SENP1 with natural compounds including Gallic acid, Caffeic acid, Thymoquinone, Thymol, Betaine, Alkannin, Ellagic acid, Betanin, Shikonin, Betanidin and Momordin IC was performed using AutoDock 4, then docking complexes for molecular dynamics (MD) simulation with GROMACS 4.6.5 were applied. Results with RMSD, RMSF, SASA, DSSP, gyrate, H-bond, ADMET and TOPKAT measurements, binding energy and structural features were surveyed. Among those, Gallic acid has shown the most significant results including RMSD and RMSF plots with high stability, high hydrogen bonds, high binding energy and the highest intermolecular bonds with SENP1. Gallic acid demonstrated strong connections and results of toxicity better than Momordin as control. Gallic acid is a phenolic compound which affects several pharmacological and biochemical pathways and has strong antioxidant, anti-inflammatory, antimutagenic and anticancer properties. Further research can improve the appropriate use of plant products drastically. Basic, pre-clinical and clinical research on Gallic acid may provide a roadmap for its ultimate application in the field of cancer prevention.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Somayye Taghvaei
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Farzaneh Sabouni
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Zarrin Minuchehr
- Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Alireza Taghvaei
- Faculty of Pharmacy, Hamedan University of Medical Sciences, Hamedan, Iran
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Wang F, Yang W, Zhou B. Molecular-level understanding of the hTAS2R1 receptor-bitter tasting tetra-peptide binding: a structural biology study based on computational approaches. NEW J CHEM 2021. [DOI: 10.1039/d1nj04014f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Effective computational approaches for bitter-tasting peptides have been developed and analyzed in the present work.
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Affiliation(s)
- Fangfang Wang
- School of Life Science, Linyi University, Linyi 276000, China
| | - Wei Yang
- Warshel Institute for Computational Biology, School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Biotechnology, University of Science and Technology of China, Hefei 230026, China
- Biomedicine Discovery Institute, Monash University, Melbourne 3800, VIC, Australia
| | - Bo Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Basic Medical, Guizhou Medical University, Guizhou 550004, China
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Chen Q, Wang F, Zhou B. Investigations of retinoic acid receptor-related orphan receptor-gamma t (RORγt) agonists: a combination of 3D-QSAR, molecular docking and molecular dynamics. J Biomol Struct Dyn 2020; 39:3501-3514. [PMID: 32375589 DOI: 10.1080/07391102.2020.1765873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Retinoic acid receptor-related orphan receptor-gamma t (RORγt) is an attractive target for Th17-driven autoimmune diseases. In the present work, a series of RORγt agonists were investigated by a molecular modeling study combining three-dimensional quantitative structure activity relationship (3D-QSAR), molecular docking, molecular dynamics (MD) simulations and binding free energies to get insight into the molecular features that would promote binding activity. The optimum comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models for 3D-QSAR studies possess satisfactory predictive ability, with R2cv=0.615, R2pred=0.8702 for CoMFA, and R2cv=0.670, R2pred=0.7683 for CoMSIA model, respectively. In addition, molecular docking studies, molecular dynamics simulations and binding free energies were used to find the actual conformations of compounds in the active site of RORγt, and key residues GLN-286, LEU-287, HIS-323 and ARG-367 for higher binding activity were pointed out. The predicted models will help us to understand the structural requirements of RORγt agonists for the designing of better active compounds. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qinghua Chen
- School of Life Science, Linyi University, Linyi, China
| | - Fangfang Wang
- School of Life Science, Linyi University, Linyi, China
| | - Bo Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Basic Medical, GuizhouMedical University, Guizhou, China
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7
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In silico studies of novel scaffold of thiazolidin-4-one derivatives as anti-Toxoplasma gondii agents by 2D/3D-QSAR, molecular docking, and molecular dynamics simulations. Struct Chem 2020. [DOI: 10.1007/s11224-019-01458-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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8
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Wang F, Zhou B. Quantitative structure-activity relationship models for bitter-tasting tripeptides based on integrated descriptors. Struct Chem 2019. [DOI: 10.1007/s11224-019-01432-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Liu J, Zhu Y, He Y, Zhu H, Gao Y, Li Z, Zhu J, Sun X, Fang F, Wen H, Li W. Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing. J Biomol Struct Dyn 2019; 38:533-547. [PMID: 30938574 DOI: 10.1080/07391102.2019.1590241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone deacetylases (HDACs), a critical family of epigenetic enzymes, has emerged as a promising target for antitumor drugs. Here, we describe our protocol of virtual screening in identification of novel potential HDAC inhibitors through pharmacophore modeling, 3D-QSAR, molecular docking and molecular dynamics (MD) simulation. Considering the limitation of current virtual screening works, drug repurposing strategy was applied to discover druggable HDAC inhibitor. The ligand-based pharmacophore and 3D-QSAR models were established, and their reliability was validated by different methods. Then, the DrugBank database was screened, followed by molecular docking. MD simulation (100 ns) was performed to further study the stability of ligand binding modes. Finally, results indicated the hit DB03889 with high in silico inhibitory potency was suitable for further experimental analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yehua Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yufang He
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haohao Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Gao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Junru Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinjie Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Fang Fang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongmei Wen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, Jiangsu, China.,Jiangsu Key Laboratory for Functional Substances of Chinese Medicine Stake Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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10
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Ndagi U, Mhlongo NN, Soliman ME. Re-emergence of an orphan therapeutic target for the treatment of resistant prostate cancer - a thorough conformational and binding analysis for ROR-γ protein. J Biomol Struct Dyn 2018; 36:335-350. [PMID: 28027708 DOI: 10.1080/07391102.2016.1277555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/20/2016] [Indexed: 01/14/2023]
Abstract
Recent studies have linked a deadly form of prostate cancer known as metastatic castration-resistant prostate cancer to retinoic acid-related orphan-receptor gamma (ROR-γ). Most of these studies continued to place ROR-γ as orphan because of unidentifiable inhibitor. Recently identified inhibitors of ROR-γ and their therapeutic potential were evaluated, among which inhibitor XY018 was the potent. However, molecular understanding of the conformational features of XY018-ROR-γ complex is still elusive. Herein, molecular dynamics simulations were conducted on HC9-ROR-γ and XY018-ROR-γ complexes to understand their conformational features at molecular level and the influence of XY018 binding on the dynamics of ROR-γ with the aid of post-dynamic analytical tools. These include; principal component analysis, radius of gyration, binding free energy calculation (MM/GBSA), per-residue fluctuation and hydrogen bond occupancy. Findings from this study revealed that (1) hydrophobic packing contributes significantly to binding free energy, (2) Ile136 and Leu60 exhibited high hydrogen-bond occupancy in XY018-ROR-γ and HC9-ROR-γ, respectively, (3) XY018-ROR-γ displayed a relatively high loop region residue fluctuation compared to HC9-ROR-γ, (4) electrostatic interactions are a potential binding force in XY018-ROR-γ complex compared to HC9-ROR-γ, (5) XY018-ROR-γ assumes a rigid conformation which is highlighted by a decrease in residual fluctuation, (6) XY018 could potentially induce pseudoporphyria, nephritis and interstitial nephritis but potentially safe in renal failure. This study could serve as a base line for the design of new potential ROR-γ inhibitors.
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Affiliation(s)
- Umar Ndagi
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban 4000 , South Africa
| | - Ndumiso N Mhlongo
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban 4000 , South Africa
| | - Mahmoud E Soliman
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban 4000 , South Africa
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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Li DD, Wu FL, Wang ZH, Huang LL, Yin Y, Wu FH. Identification of 2,4-diarylaminopyrimidine analogues as ALK inhibitors by using 3D-QSAR, molecular docking, and molecular dynamics simulations. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-017-1999-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Cheng P, Li J, Wang J, Zhang X, Zhai H. Investigations of FAK inhibitors: a combination of 3D-QSAR, docking, and molecular dynamics simulations studies. J Biomol Struct Dyn 2017; 36:1529-1549. [PMID: 28490269 DOI: 10.1080/07391102.2017.1329095] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Focal adhesion kinase (FAK) is one kind of tyrosine kinases that modulates integrin and growth factor signaling pathways, which is a promising therapeutic target because of involving in cancer cell migration, proliferation, and survival. To investigate the mechanism between FAK and triazinic inhibitors and design high activity inhibitors, a molecular modeling integrated with 3D-QSAR, molecular docking, molecular dynamics simulations, and binding free energy calculations was performed. The optimum CoMFA and CoMSIA models showed good reliability and satisfactory predictability (with Q2 = 0.663, R2 = 0.987, [Formula: see text] = 0.921 and Q2 = 0.670, R2 = 0.981, [Formula: see text] = 0.953). Its contour maps could provide structural features to improve inhibitory activity. Furthermore, a good consistency between contour maps, docking, and molecular dynamics simulations strongly demonstrates that the molecular modeling is reliable. Based on it, we designed several new compounds and their inhibitory activities were validated by the molecular models. We expect our studies could bring new ideas to promote the development of novel inhibitors with higher inhibitory activity for FAK.
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Affiliation(s)
- Peng Cheng
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Jiaojiao Li
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Juan Wang
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Xiaoyun Zhang
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Honglin Zhai
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
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Sepehri B, Ghavami R. Molecular docking and CoMFA studies of thiazoloquin(az)olin(on)es as CD38 inhibitors: determination of inhibitory mechanism, pharmacophore interactions, and design of new inhibitors. J Biomol Struct Dyn 2016; 35:1890-1898. [PMID: 27577102 DOI: 10.1080/07391102.2016.1197152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this research, molecular docking and 3D-QSAR studies were carried out on a series of 79 thiazoloquin(az)olin(on)es as CD38 inhibitors. Based on docking results, four interactions including hydrogen bonding with main chain of GLU-226 (H-M-GLU-226), Van der Waals interactions with side chain of TRP-125 (V-S-TRP-125), TRP-189 (V-S-TRP-189), and THR-221 (V-S-THR-221) were considered as pharmacological interactions. Active conformation of each ligand was extracted from docking studies and was used for carrying out 3D-QSAR modeling. Comparative molecular field analysis (CoMFA) was performed on CD38 inhibitory activities of these compounds on human and mouse. We developed CoMFA models with five components as optimum models for both data-sets. For human data-set, a model with high predictive power was developed. R2, RMSE, and F-test values for training set of this model were .94, .24, and 179.58, respectively, and R2 and RMSE for its test set were .92 and .32, respectively. The q2 and RMSE values for leave-one-out cross validation test on training set were .78 and .46, respectively, that demonstrate created model is robust. Based on extracted steric and electrostatic contour maps for this model, three inhibitors with pIC50 larger than 8.85 were designed.
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Affiliation(s)
- Bakhtyar Sepehri
- a Faculty of Science, Department of Chemistry , University of Kurdistan , P.O. Box 416 , Sanandaj , Iran
| | - Raouf Ghavami
- a Faculty of Science, Department of Chemistry , University of Kurdistan , P.O. Box 416 , Sanandaj , Iran
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15
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Wu Y, Doering JA, Ma Z, Tang S, Liu H, Zhang X, Wang X, Yu H. Identification of androgen receptor antagonists: In vitro investigation and classification methodology for flavonoid. CHEMOSPHERE 2016; 158:72-79. [PMID: 27258897 DOI: 10.1016/j.chemosphere.2016.05.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
A tremendous gap exists between the number of potential endocrine disrupting chemicals (EDCs) possibly in the environment and the limitation of traditional regulatory testing. In this study, the anti-androgenic potencies of 21 flavonoids were analyzed in vitro, and another 32 flavonoids from the literature were selected as additional chemicals. Molecular dynamic simulations were employed to obtain four different separation approaches based on the different behaviors of ligands and receptors during the process of interaction. Specifically, ligand-receptor complex which highlighted the discriminating features of ligand escape or retention via "mousetrap" mechanism, hydrogen bonds formed during simulation times, ligand stability and the stability of the helix-12 of the receptor were investigated. Together, a methodology was generated that 87.5% of flavonoids could be discriminated as active versus inactive antagonists, and over 90% inactive antagonists could be filtered out before QSAR study. This methodology could be used as a "proof of concept" to identify inactive anti-androgenic flavonoids, as well could be beneficial for rapid risk assessment and regulation of multiple new chemicals for androgenicity.
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Affiliation(s)
- Yang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jon A Doering
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Zhiyuan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Song Tang
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Hongling Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaoxiang Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
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Verma S, Tyagi C, Goyal S, Pandey B, Jamal S, Singh A, Grover A. Mutations induce conformational changes in folliculin C-terminal domain: possible cause of loss of guanine exchange factor activity and Birt-Hogg-Dubé syndrome. J Biomol Struct Dyn 2016; 35:1568-1573. [DOI: 10.1080/07391102.2016.1188728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- S. Verma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - C. Tyagi
- Agricultural Knowledge Management Unit, Indian Agricultural Research Institute, New Delhi 110032, India
| | - S. Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan 304022, India
| | - B. Pandey
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - S. Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan 304022, India
| | - A. Singh
- Department of Biotechnology, TERI University, VasantKunj, New Delhi 110 070, India
| | - A. Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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17
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Zhang H, Yu H, Zhao X, Liu X, Feng X, Huang X. Investigations of Takeout proteins’ ligand binding and release mechanism using molecular dynamics simulation. J Biomol Struct Dyn 2016; 35:1464-1473. [DOI: 10.1080/07391102.2016.1185646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Huijing Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Hui Yu
- College of Chemistry and Biology, Beihua University, Jilin 132013, People’s Republic of China
| | - Xi Zhao
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Xiaoguang Liu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Xianli Feng
- Modern Experimental Technology Center (Management), Henan Agricultural University, Zhengzhou, Henan 450002, People’s Republic of China
| | - Xuri Huang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
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18
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Nagamani S, Muthusamy K, Marshal JJ. E-pharmacophore filtering and molecular dynamics simulation studies in the discovery of potent drug-like molecules for chronic kidney disease. J Biomol Struct Dyn 2016; 34:2233-2250. [PMID: 26513595 DOI: 10.1080/07391102.2015.1111168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chronic kidney disease (CKD) is a prominent health issue reported globally. The level of the vitamin D receptor (VDR) and cytochrome P450 enzyme 24-hydroxylase (CYP24A1) are crucial in the pathogenesis of secondary hyperparathyroidism (sHPT) in CKD. An elevated expression of the CYP24A1 leads to the deficiency of vitamin D and resistance to vitamin D therapy. Hence, VDR agonists and CYP24A1 antagonists are suggested to CKD patients for the management of biochemical complications. CTA-018 is a recently reported analog and acts as a potent CYP24A1 inhibitor. It inhibits CYP24A1 with an IC50 27 ± 6 nM, about 10 times more potentially than the non-selective inhibitor ketoconazole (253 ± 20 nM), and it is also been reported to induce the VDR expression. Thus, CTA-018 is under clinical trial among CKD patients. In this study, combined molecular docking and pharmacophore filtering were employed to identify compounds better than CTA-018. A huge set of 9127 compounds from Sweet Lead database were docked into the active site of VDR using Glide XP program. E-pharmacophore was developed from both the targets along with CTA-018. The compounds retrieved from the two different pharmacophore-based screening were re-docked into the active site of CYP24A1. The hits that bind well at both the active sites and matched with the pharmacophore models were considered as possible dual functional molecules against VDR and CYP24A1. Further, molecular dynamics simulation and subsequent energy decomposition analyses were also performed to study the role of specific amino acids in the active site of both VDR and CYP24A1.
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Affiliation(s)
- Selvaraman Nagamani
- a Department of Bioinformatics , Alagappa University , Karaikudi 630 004 , India
| | | | - J John Marshal
- a Department of Bioinformatics , Alagappa University , Karaikudi 630 004 , India
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