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Singh MP, Singh N, Mishra D, Ehsan S, Chaturvedi VK, Chaudhary A, Singh V, Vamanu E. Computational Approaches to Designing Antiviral Drugs against COVID-19: A Comprehensive Review. Curr Pharm Des 2023; 29:2601-2617. [PMID: 37916490 DOI: 10.2174/0113816128259795231023193419] [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: 05/18/2023] [Accepted: 09/21/2023] [Indexed: 11/03/2023]
Abstract
The global impact of the COVID-19 pandemic caused by SARS-CoV-2 necessitates innovative strategies for the rapid development of effective treatments. Computational methodologies, such as molecular modelling, molecular dynamics simulations, and artificial intelligence, have emerged as indispensable tools in the drug discovery process. This review aimed to provide a comprehensive overview of these computational approaches and their application in the design of antiviral agents for COVID-19. Starting with an examination of ligand-based and structure-based drug discovery, the review has delved into the intricate ways through which molecular modelling can accelerate the identification of potential therapies. Additionally, the investigation extends to phytochemicals sourced from nature, which have shown promise as potential antiviral agents. Noteworthy compounds, including gallic acid, naringin, hesperidin, Tinospora cordifolia, curcumin, nimbin, azadironic acid, nimbionone, nimbionol, and nimocinol, have exhibited high affinity for COVID-19 Mpro and favourable binding energy profiles compared to current drugs. Although these compounds hold potential, their further validation through in vitro and in vivo experimentation is imperative. Throughout this exploration, the review has emphasized the pivotal role of computational biologists, bioinformaticians, and biotechnologists in driving rapid advancements in clinical research and therapeutic development. By combining state-of-the-art computational techniques with insights from structural and molecular biology, the search for potent antiviral agents has been accelerated. The collaboration between these disciplines holds immense promise in addressing the transmissibility and virulence of SARS-CoV-2.
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Affiliation(s)
- Mohan P Singh
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Prayagraj 211002, India
| | - Divya Mishra
- Centre of Bioinformatics, University of Allahabad, Prayagraj 211002, India
| | - Saba Ehsan
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Vivek K Chaturvedi
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anupriya Chaudhary
- Centre of Biotechnology, University of Allahabad, Prayagraj 211002, India
| | - Veer Singh
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Emanuel Vamanu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine of Bucharest, Bucharest 011464, Romania
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Prem Kumar S, Shaikh IA, Mahnashi MH, Alshahrani MA, Dixit SR, Kulkarni VH, Lherbet C, Gadad AK, Aminabhavi TM, Joshi SD. Design, synthesis and computational approach to study novel pyrrole scaffolds as active inhibitors of enoyl ACP reductase (InhA) and Mycobacterium tuberculosis antagonists. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Neto MFDA, Santos CBRD, Magalhães-Junior JT, Leite FHA. Identification of novel Aedes aegypti odorant-binding protein 1 modulators by ligand and structure-based approaches and bioassays. J Biomol Struct Dyn 2020; 40:117-129. [PMID: 32815781 DOI: 10.1080/07391102.2020.1808074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Arboviruses are a group of viruses (e.g. Dengue, Chikungunya and Yellow fever virus) that are transmitted by arthropod vectors, which Aedes aegipty is the vector of main viruses in Americas. This vector is responsible to 2.4 millions of arboviruses cases in Brazil with less than a thousand deaths annually. Despite of epidemiological data, arboviruses treatment is symptomatic and the vaccine control is not effective, which makes the vector control against A. aegipty a promising strategy to diseases control. One way to achieve this goal is to development of A. aegipty sensitive olfactory modulators. Odorant binding protein 1 from A. aegypti (AaegOBP1) is essential in sensory communication, and is the first filter in odorant selection, which makes this target promising to development of new repellents. For this reason, hierarchical virtual screening (ligand-based pharmacophore model and molecular docking) together volatility filter was applied at Sigma-Aldrich database (n = 126.851) to prioritize potential molecules to repellency assays. Three compounds showed adequate stereo-electronic requirements (QFIT> 81.53), score to AaegOBP1 binding site (Score > 36.0) and volatile properties and it was chosen for repellency assays. ZINC00170981 and ZINC00131924 showed a dose-response behavior, while ZINC01621824 did not showed activity in repellency assays. Finally, Molecular Dynamics (MD) was employed to hypothesize the stability of protein-ligand complexes. According to RMSD, RMSF and binding free energy data, ZINC00170981 and ZINC00131924 were able to stabilize AaegOBP1 binding-site during the trajectory by interactions with key residues such as His77, Leu89 and Trp114). Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Cleydson Breno Rodrigues Dos Santos
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
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Chemical synthesis, molecular modeling and pharmacophore mapping of new pyrrole derivatives as inhibitors of InhA enzyme and Mycobacterium tuberculosis growth. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02418-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Joshi SD, Dixit SR, Basha J, Kulkarni V, Aminabhavi TM, Nadagouda MN, Lherbet C. Pharmacophore mapping, molecular docking, chemical synthesis of some novel pyrrolyl benzamide derivatives and evaluation of their inhibitory activity against enoyl-ACP reductase (InhA) and Mycobacterium tuberculosis. Bioorg Chem 2018; 81:440-453. [DOI: 10.1016/j.bioorg.2018.08.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
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Araujo JSC, de Souza BC, Costa Junior DB, Oliveira LDM, Santana IB, Duarte AA, Lacerda PS, dos Santos Junior MC, Leite FHA. Identification of new promising Plasmodium falciparum superoxide dismutase allosteric inhibitors through hierarchical pharmacophore-based virtual screening and molecular dynamics. J Mol Model 2018; 24:220. [DOI: 10.1007/s00894-018-3746-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022]
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Identification of Novel Protein Kinase Receptor Type 2 Inhibitors Using Pharmacophore and Structure-Based Virtual Screening. Molecules 2018; 23:molecules23020453. [PMID: 29463017 PMCID: PMC6017386 DOI: 10.3390/molecules23020453] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
The Protein Kinase Receptor type 2 (RIPK2) plays an important role in the pathogenesis of inflammatory diseases; it signals downstream of the NOD1 and NOD2 intracellular sensors and promotes a productive inflammatory response. However, excessive NOD2 signaling has been associated with various diseases, including sarcoidosis and inflammatory arthritis; the pharmacological inhibition of RIPK2 is an affinity strategy that demonstrates an increased expression of pro-inflammatory secretion activity. In this study, a pharmacophoric model based on the crystallographic pose of ponatinib, a potent RIPK2 inhibitor, and 30 other ones selected from the BindingDB repository database, was built. Compounds were selected based on the available ZINC compounds database and in silico predictions of their pharmacokinetic, toxicity and potential biological activity. Molecular docking was performed to identify the probable interactions of the compounds as well as their binding affinity with RIPK2. The compounds were analyzed to ponatinib and WEHI-345, which also used as a control. At least one of the compounds exhibited suitable pharmacokinetic properties, low toxicity and an interesting binding affinity and high fitness compared with the crystallographic pose of WEHI-345 in complex with RIPK2. This compound also possessed suitable synthetic accessibility, rendering it a potential and very promising RIPK2 inhibitor to be further investigated in regards to different diseases, particularly inflammatory ones.
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Paz OS, de Jesus Pinheiro M, do Espirito Santo RF, Villarreal CF, Castilho MS. Nanomolar anti-sickling compounds identified by ligand-based pharmacophore approach. Eur J Med Chem 2017; 136:487-496. [DOI: 10.1016/j.ejmech.2017.05.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
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Joshi SD, Dixit SR, Kulkarni VH, Lherbet C, Nadagouda MN, Aminabhavi TM. Synthesis, biological evaluation and in silico molecular modeling of pyrrolyl benzohydrazide derivatives as enoyl ACP reductase inhibitors. Eur J Med Chem 2017; 126:286-297. [PMID: 27889632 DOI: 10.1016/j.ejmech.2016.11.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 11/18/2022]
Abstract
In efforts to develop lead anti-TB compounds, a novel series of 19 pyrrolyl benzohydrazides were synthesized and screened to target enoyl-ACP reductase enzyme, which is one of the important enzymes involved in type II fatty acid biosynthetic pathway of M. tuberculosis. Pharmacophores were constructed using GALAHAD to generate alignment of data sets and calculated by Pareto ranking. The pharmacophore features were then filtered by Surflex-dock study using enoyl ACP reductase from M. tuberculosis. Compounds 5b and 5d showed H-bonding interactions with Tyr158, Thr196 and co-factor NAD+ that fitted well within the binding pocket of InhA. All the synthesized compounds were screened for preliminary antibacterial activities against Gram-positive S. aureus and Gram-negative E. coli and M. tuberculosis H37Rv to evaluate their antitubercular activities. Some representative compounds were further tested for mammalian cell toxicity using human lung cancer cell-line (A549) that was found to be nontoxic. These compounds exhibited moderate inhibition activities against InhA.
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Affiliation(s)
- Shrinivas D Joshi
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, S.E.T's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad, 580 002, India.
| | - Sheshagiri R Dixit
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, S.E.T's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad, 580 002, India
| | - Venkatarao H Kulkarni
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, S.E.T's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad, 580 002, India
| | - Christian Lherbet
- Universite de Toulouse, UPS, Laboratoire de Synthese et Physico-chimie de Molecules d'Interet Biologique, LSPCMIB, 118 Roote de Narbonne, F-31062, Toulouse Cedex 9, France; ITAV-USR3505, Université de Toulouse, CNRS, UPS, F-31106 Toulouse, France
| | - Mallikarjuna N Nadagouda
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, S.E.T's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad, 580 002, India
| | - Tejraj M Aminabhavi
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, S.E.T's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad, 580 002, India
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Xu W, Shao B, Xu X, Jiang R, Yuan M. Structural analysis of (S)-1-((1H-benzo[d][1,2,3]triazol-1-yl)oxy)-3-(4-(2-methoxyphenyl)piperazin-1-yl)propan-2-ol and binding mechanism with α1A-adrenoceptor: TDDFT calculations, X-ray crystallography and molecular docking. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Chaube UJ, Vyas VK, Bhatt HG. Design and synthesis of potent N-phenylpyrimidine derivatives for the treatment of skin cancer. RSC Adv 2016. [DOI: 10.1039/c5ra27017k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The development of novel synthetic compounds for the treatment of skin cancer is much needed, as there is a sudden rise in the incidence of skin cancer throughout the world and the available chemotherapy is facing problems of resistance.
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Affiliation(s)
- Udit J. Chaube
- Department of Pharmaceutical Chemistry
- Institute of Pharmacy
- Nirma University
- Ahmedabad 382 481
- India
| | - Vivek K. Vyas
- Department of Pharmaceutical Chemistry
- Institute of Pharmacy
- Nirma University
- Ahmedabad 382 481
- India
| | - Hardik G. Bhatt
- Department of Pharmaceutical Chemistry
- Institute of Pharmacy
- Nirma University
- Ahmedabad 382 481
- India
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More UA, Joshi SD, Aminabhavi TM, Kulkarni VH, Badiger AM, Lherbet C. Discovery of target based novel pyrrolyl phenoxy derivatives as antimycobacterial agents: An in silico approach. Eur J Med Chem 2015; 94:317-39. [DOI: 10.1016/j.ejmech.2015.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 11/17/2022]
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Chen H, Liang X, Xu F, Xu B, He X, Huang B, Yuan M. Synthesis and cytotoxic activity evaluation of novel arylpiperazine derivatives on human prostate cancer cell lines. Molecules 2014; 19:12048-64. [PMID: 25120056 PMCID: PMC6271825 DOI: 10.3390/molecules190812048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 12/13/2022] Open
Abstract
A series of novel arylpiperazine derivatives was synthesized. The in vitro cytotoxic activities of all synthesized compounds against three human prostate cancer cell lines (PC-3, LNCaP, and DU145) were evaluated by a CCK-8 assay. Compounds 9 and 15 exhibited strong cytotoxic activities against LNCaP cells (IC50 < 5 μM), and compound 8 (IC50 = 8.25 μM) possessed the most potent activity against DU145 cells. However, these compounds also exhibited cytotoxicity towards human epithelial prostate normal cells RWPE-1. The structure–activity relationship (SAR) of these arylpiperazine derivatives was also discussed based on the obtained experimental data.
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Affiliation(s)
- Hong Chen
- Pharmaceutical Research Center, Guangzhou Medical University, 195# Dongfengxi Road, Guangzhou 510182, China.
| | - Xue Liang
- Pharmaceutical Research Center, Guangzhou Medical University, 195# Dongfengxi Road, Guangzhou 510182, China.
| | - Fang Xu
- Pharmaceutical Research Center, Guangzhou Medical University, 195# Dongfengxi Road, Guangzhou 510182, China.
| | - Bingbing Xu
- Pharmaceutical Research Center, Guangzhou Medical University, 195# Dongfengxi Road, Guangzhou 510182, China.
| | - Xuelan He
- Pharmaceutical Research Center, Guangzhou Medical University, 195# Dongfengxi Road, Guangzhou 510182, China.
| | - Biyun Huang
- Pharmaceutical Research Center, Guangzhou Medical University, 195# Dongfengxi Road, Guangzhou 510182, China.
| | - Mu Yuan
- Pharmaceutical Research Center, Guangzhou Medical University, 195# Dongfengxi Road, Guangzhou 510182, China.
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The discovery of potentially selective human neuronal nitric oxide synthase (nNOS) Inhibitors: a combination of pharmacophore modelling, CoMFA, virtual screening and molecular docking studies. Int J Mol Sci 2014; 15:8553-69. [PMID: 24830557 PMCID: PMC4057748 DOI: 10.3390/ijms15058553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/30/2014] [Accepted: 05/06/2014] [Indexed: 11/29/2022] Open
Abstract
Neuronal nitric oxide synthase (nNOS) plays an important role in neurotransmission and smooth muscle relaxation. Selective inhibition of nNOS over its other isozymes is highly desirable for the treatment of neurodegenerative diseases to avoid undesirable effects. In this study, we present a workflow for the identification and prioritization of compounds as potentially selective human nNOS inhibitors. Three-dimensional pharmacophore models were constructed based on a set of known nNOS inhibitors. The pharmacophore models were evaluated by Pareto surface and CoMFA (Comparative Molecular Field Analysis) analyses. The best pharmacophore model, which included 7 pharmacophore features, was used as a search query in the SPECS database (SPECS®, Delft, The Netherlands). The hit compounds were further filtered by scoring and docking. Ten hits were identified as potential selective nNOS inhibitors.
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Xiang Y, Hou Z, Zhang Z. Pharmacophore and QSAR studies to design novel histone deacetylase 2 inhibitors. Chem Biol Drug Des 2012; 79:760-70. [PMID: 22268420 DOI: 10.1111/j.1747-0285.2012.01341.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One pharmacophore model and three quantitative structure-activity relationship models were developed on a series of benzimidazole and imidazole inhibitors of histone deacetylase 2. The goodness of hit score value of the best pharmacophore model was 0.756, which indicated that it is reliable to be used for virtual screening. The built pharmacophore model was used to search the NCI database. The hit compounds were subjected to molecular docking. The results showed that 25 compounds had high scores and strong interactions with histone deacetylase 2. In three-dimensional quantitative structure-activity relationship studies, good predictive models were obtained using comparative molecular field analysis, comparative molecular similarity indices analysis, and Topomer comparative molecular field analysis. Some putative active compounds were proposed based on compound no. 41. Twenty-six compounds had high scores and good interactions when they were docking into histone deacetylase 2.
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Affiliation(s)
- Yuhong Xiang
- Department of Chemistry, Capital Normal University, Beijing, China
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Avram S, Buiu C, Borcan F, Milac AL. More effective antimicrobial mastoparan derivatives, generated by 3D-QSAR-Almond and computational mutagenesis. ACTA ACUST UNITED AC 2012; 8:587-94. [DOI: 10.1039/c1mb05297g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) studies on α(1A)-adrenergic receptor antagonists based on pharmacophore molecular alignment. Int J Mol Sci 2011; 12:7022-37. [PMID: 22072933 PMCID: PMC3211024 DOI: 10.3390/ijms12107022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/05/2011] [Accepted: 10/11/2011] [Indexed: 11/16/2022] Open
Abstract
The α1A-adrenergic receptor (α1A-AR) antagonist is useful in treating benign prostatic hyperplasia, lower urinary tract symptoms, and cardiac arrhythmia. Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on a set of α1A-AR antagonists of N-aryl and N-nitrogen class. Statistically significant models constructed from comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were established based on a training set of 32 ligands using pharmacophore-based molecular alignment. The leave-oneout cross-validation correlation coefficients were q2CoMFA = 0.840 and q2CoMSIA = 0.840. The high correlation between the cross-validated/predicted and experimental activities of a test set of 12 ligands revealed that the CoMFA and CoMSIA models were robust (r2pred/CoMFA = 0.694; r2pred/CoMSIA = 0.671). The generated models suggested that electrostatic, hydrophobic, and hydrogen bonding interactions play important roles between ligands and receptors in the active site. Our study serves as a guide for further experimental investigations on the synthesis of new compounds. Structural modifications based on the present 3D-QSAR results may lead to the discovery of other α1A-AR antagonists.
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Sun X, Li Y, Li W, Xu Z, Tang Y. Computational investigation of interactions between human H2 receptor and its agonists. J Mol Graph Model 2011; 29:693-701. [DOI: 10.1016/j.jmgm.2010.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/23/2010] [Accepted: 12/04/2010] [Indexed: 11/16/2022]
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Avram S, Duda-Seiman D, Borcan F, Radu B, Duda-Seiman C, Mihailescu D. Evaluation of Antimicrobial Activity of New Mastoparan Derivatives Using QSAR and Computational Mutagenesis. Int J Pept Res Ther 2010. [DOI: 10.1007/s10989-010-9235-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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