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Eid AM, Selim A, Khaled M, Elfiky AA. Hybrid Virtual Screening Approach to Predict Novel Natural Compounds against HIV-1 CCR5. J Phys Chem B 2024; 128:7086-7101. [PMID: 39016126 DOI: 10.1021/acs.jpcb.4c02083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) infection continues to pose a major global health challenge. HIV entry into host cells via membrane fusion mediated by the viral envelope glycoprotein gp120/gp41 is a key step in the HIV life cycle. CCR5, expressed on CD4+ T cells and macrophages, acts as a coreceptor facilitating HIV-1 entry. The CCR5 antagonist maraviroc is used to treat HIV infection. However, it can cause adverse effects and has limitations such as only inhibiting CCR5-tropic viruses. There remains a need to develop alternative CCR5 inhibitors with improved safety profiles. PROBLEM STATEMENT Natural products may offer advantages over synthetic inhibitors including higher bioavailability, binding affinity, effectiveness, lower toxicity, and molecular diversity. However, screening the vast chemical space of natural compounds to identify novel CCR5 inhibitors presents challenges. This study aimed to address this gap through a hybrid ligand-based pharmacophore modeling and molecular docking approach to virtually screen large natural product databases. METHODS A reliable pharmacophore model was developed based on 311 known CCR5 antagonists and validated against an external data set. Five natural product databases containing over 306,000 compounds were filtered based on drug-likeness rules. The validated pharmacophore model screened the databases to identify 611 hits. Key residues of the CCR5 receptor crystal structure were identified for docking. The top hits were docked, and interactions were analyzed. Molecular dynamics simulations were conducted to examine complex stability. Computational prediction evaluated pharmacokinetic properties. RESULTS Three compounds exhibited similar interactions and binding energies to maraviroc. MD simulations demonstrated complex stability comparable to maraviroc. One compound showed optimal predicted absorption, minimal metabolism, and a lower likelihood of interactions than maraviroc. CONCLUSION This computational screening workflow identified three natural compounds with promising CCR5 inhibition and favorable pharmacokinetic profiles. One compound emerged as a lead based on bioavailability potential and minimal interaction risk. These findings present opportunities for developing alternative CCR5 antagonists and warrant further experimental investigation. Overall, the hybrid virtual screening approach proved effective for mining large natural product spaces to discover novel molecular entities with drug-like properties.
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Affiliation(s)
- Abdulrahman M Eid
- Biophysics Dept. Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Abdallah Selim
- Biophysics Dept. Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Mohamed Khaled
- Biophysics Dept. Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Abdo A Elfiky
- Biophysics Dept. Faculty of Science, Cairo University, Giza 12613, Egypt
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Exploration of alternate therapeutic remedies in Ebola virus disease: the case of reported antiviral phytochemical derived from the leaves Spondias Mombin Linn. ADVANCES IN TRADITIONAL MEDICINE 2021. [DOI: 10.1007/s13596-021-00603-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yang Y, Li Y, Zhou W, Chen Y, Wu Q, Pan Y, Zhang S, Yang L. Exploring the structural determinants of novel xanthine derivatives as A 2B adenosine receptor antagonists: a computational study. J Biomol Struct Dyn 2018; 37:3467-3481. [PMID: 30175951 DOI: 10.1080/07391102.2018.1517612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Adenosine is a ubiquitous endogenous nucleoside that controls numerous physiological functions via interacting with its specific G-coupled receptors. Activation of adenosine receptors (AdoRs), particularly A2B AdoRs promotes the release of inflammatory cytokines; reduces vascular permeabilization and induces angiogenesis, thereby making A2B AdoR becomes a potentially pharmacological target for drug development. Presently, for investigating the structural determinants of 164 xanthine derivatives as A2B AdoR antagonists, we performed an in silico study integrating with 3D-QSAR, docking and molecular dynamics (MD) simulation. The obtained optimal model shows strong predictability (Q2 = 0.647, R2ncv = 0.955, and R2pred = 0.848). Additionally, to explore the binding mode of the ligand with A2B AdoR and to understand their binding mechanism, docking analysis, MD simulations (20 ns), and the calculation of binding free energy were also carried out. Finally, the structural determinants of these xanthine derivatives were identified and a total of 20 novel A2B AdoR antagonists with improved potency were computationally designed, and their synthetic feasibility and selectivity were also evaluated. The information derived from the present study offers a better appreciation for exploring the interaction mechanism of the ligand with A2B AdoR, which could be helpful for designing novel potent A2B AdoR antagonists. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yinfeng Yang
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Yan Li
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China.,b Key Laboratory of Xinjiang Endemic Phytomedicine Resources , Pharmacy School Shihezi University, Ministry of Education , Shihezi , China
| | - Weiwei Zhou
- b Key Laboratory of Xinjiang Endemic Phytomedicine Resources , Pharmacy School Shihezi University, Ministry of Education , Shihezi , China
| | - Yaorong Chen
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Qian Wu
- c Weifang , Microscale Science Institute Weifang University , Shandong , China
| | - Yanqiu Pan
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Shuwei Zhang
- a Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Department of Materials Sciences and Chemical Engineering , Dalian University of Technology , Dalian , Liaoning , China
| | - Ling Yang
- d Laboratory of Pharmaceutical Resource Discovery , Dalian Institute of Chemical Physics , Graduate School of the Chinese Academy of Sciences , Dalian , Liaoning , China
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Tailored-pharmacophore model to enhance virtual screening and drug discovery: a case study on the identification of potential inhibitors against drug-resistant Mycobacterium tuberculosis (3R)-hydroxyacyl-ACP dehydratases. Future Med Chem 2017. [DOI: 10.4155/fmc-2017-0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Virtual screening (VS) is powerful tool in discovering molecular inhibitors that are most likely to bind to drug targets of interest. Herein, we introduce a novel VS approach, so-called ‘tailored-pharmacophore’, in order to explore inhibitors that overcome drug resistance. Methodology & results: The emergence and spread of drug resistance strains of tuberculosis is one of the most critical issues in healthcare. A tailored-pharmacophore approach was found promising to identify in silico predicted hit with better binding affinities in case of the resistance mutations in MtbHadAB as compared with thiacetazone, a prodrug used in the clinical treatment of tuberculosis. Conclusion: This approach can potentially be enforced for the discovery and design of drugs against a wide range of resistance targets.
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Devnarain N, Ramharack P, Soliman ME. Brain grants permission of access to Zika virus but denies entry to drugs: a molecular modeling perspective to infiltrate the boundary. RSC Adv 2017. [DOI: 10.1039/c7ra05918c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Thein silicodesign of targeted Zika virus inhibitors.
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Affiliation(s)
- Nikita Devnarain
- Molecular Bio-computation and Drug Design Laboratory
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Pritika Ramharack
- Molecular Bio-computation and Drug Design Laboratory
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahmoud E. Soliman
- Molecular Bio-computation and Drug Design Laboratory
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
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Hybrid Receptor-Bound/MM-GBSA-Per-residue Energy-Based Pharmacophore Modelling: Enhanced Approach for Identification of Selective LTA4H Inhibitors as Potential Anti-inflammatory Drugs. Cell Biochem Biophys 2016; 75:35-48. [PMID: 27914004 DOI: 10.1007/s12013-016-0772-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/15/2016] [Indexed: 10/20/2022]
Abstract
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and design of novel class of compounds that can selectively inhibit leukotriene B4 synthesis while sparing the aminopeptidase activity. Previous inhibitors block the dual activity of the enzyme. Recently, a small lead molecule inhibitor denoted as ARM1 has been identified to block the hydrolase activity of leukotriene A4 hydrolase whilst sparing the aminopeptidase activity. In this study, a hybrid receptor-bound/MM-GBSA-per-residue energy based pharmacophore modeling approach was implemented to identify potential selective hydrolase inhibitors of leukotriene A4 hydrolase. In this approach, active site residues that favorably contributed to the binding of the bound conformation of ARM1 were derived from MD ensembles and MM/GBSA thermodynamic calculations. These residues were then mapped to key pharmacophore features of ARM1. The generated pharmacophore model was used to search the ZINC database for 3D structures that match the pharmacophore. Five new compounds have been identified and proposed as potential epoxide hydrolase selective inhibitors of leukotriene A4 hydrolase. Molecular docking and MM/GBSA analyses revealed that, these top five lead-like compounds ZINC00142747, ZINC94260794, ZINC01382396, ZINC02508448, and ZINC53994447 showed better binding affinities to the hydrolase active site pocket compared to ARM1. Per-residue energy decomposition analysis revealed that amino acid residues Phe314, Tyr378, Pro382, Trp311, Val367, and Ala377 are key residues critical in the selective inhibition of these hits. Information highlighted in this study may guide the the design the next generation of novel and potent epoxide hydrolase selective inhibitors of leukotriene A4 hydrolase.
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Berinyuy E, Soliman MES. Identification of Novel Potential gp120 of HIV-1 Antagonist Using Per-Residue Energy Contribution-Based Pharmacophore modelling. Interdiscip Sci 2016; 9:406-418. [PMID: 27165479 DOI: 10.1007/s12539-016-0174-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 01/01/2023]
Abstract
Inhibition of HIV-1 target cell entry, by targeting gp120, has been identified as a promising approach for the identification and development of prophylactic and salvage HIV infection inhibitors. A small molecule compound 18A is an important chemotype in the development of novel and diverse viral cell entry inhibitors, as it inhibits a wide variety of HIV strains by disrupting allosteric structuring on gp120. This study combines residue energy contribution (REC) pharmacophore mapping of 18A and in silico molecular docking in a virtual screening campaign to identify novel and diverse antagonists of gp120. The binding free energy of a validated docked complex of gp120-18A and the quantitative contribution of interacting residues were obtained with a more accurate molecular mechanics/generalised born surface area (MM/GBSA) method followed by mapping the energetically favourable residue contributions onto atom centres in 18A to obtain a pharmacophore model. The generated pharmacophore hypothesis was used to search the ZINC database for 3D structures that match the pharmacophore. Further, molecular docking, molecular dynamics simulations and binding free energy analysis were performed on retrieved hits in order to rank hits based on their affinity and interactions in the CD4 binding cavity of a gp120. Interestingly, the top scoring compound designated with ZINC database ID as ZINC64700951 (docking score = -8.8 kcal/mol, ∆G = -43.77 kcal/mol) showed higher affinity compared to compound 18A docking score = -7.3 kcal/mol, ∆G = -31.97 kcal/mol) and interaction of ZN64700951 with validated allosteric hot spot residues, Asp368 and Met426, and binding hot spot residues, Asn425, Glu370, Gly473, Trp427 and Met475 in gp120, suggest that ZN64700951 is a promising antagonist of gp120. Thus, ZN64700951 could serve as an additional prototype for further optimisation as an HIV target cell viral entry inhibitor.
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Affiliation(s)
- Emiliene Berinyuy
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa
| | - Mahmoud E S Soliman
- 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 J, Li Y, Yang Y, Du J, Zhang S, Yang L. In silico research to assist the investigation of carboxamide derivatives as potent TRPV1 antagonists. MOLECULAR BIOSYSTEMS 2015; 11:2885-99. [DOI: 10.1039/c5mb00356c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The transient receptor potential vanilloid type 1 (TRPV1), a non-selective cation channel, is known for its essential role in the pathogenesis of various pain conditions such as nerve damage induced hyperalgesia, diabetic neuropathy and cancer pain.
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Affiliation(s)
- Jinghui Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Faculty of Chemical
- Environmental and Biological Science and Technology
- Dalian University of Technology
- Dalian
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Faculty of Chemical
- Environmental and Biological Science and Technology
- Dalian University of Technology
- Dalian
| | - Yinfeng Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Faculty of Chemical
- Environmental and Biological Science and Technology
- Dalian University of Technology
- Dalian
| | - Jian Du
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Faculty of Chemical
- Environmental and Biological Science and Technology
- Dalian University of Technology
- Dalian
| | - Shuwei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Faculty of Chemical
- Environmental and Biological Science and Technology
- Dalian University of Technology
- Dalian
| | - Ling Yang
- Laboratory of Pharmaceutical Resource Discovery
- Dalian Institute of Chemical Physics
- Graduate School of the Chinese Academy of Sciences
- Dalian
- China
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Wu M, Li Y, Fu X, Wang J, Zhang S, Yang L. Profiling the interaction mechanism of quinoline/quinazoline derivatives as MCHR1 antagonists: an in silico method. Int J Mol Sci 2014; 15:15475-502. [PMID: 25257526 PMCID: PMC4200842 DOI: 10.3390/ijms150915475] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/30/2014] [Accepted: 08/19/2014] [Indexed: 12/13/2022] Open
Abstract
Melanin concentrating hormone receptor 1 (MCHR1), a crucial regulator of energy homeostasis involved in the control of feeding and energy metabolism, is a promising target for treatment of obesity. In the present work, the up-to-date largest set of 181 quinoline/quinazoline derivatives as MCHR1 antagonists was subjected to both ligand- and receptor-based three-dimensional quantitative structure–activity (3D-QSAR) analysis applying comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The optimal predictable CoMSIA model exhibited significant validity with the cross-validated correlation coefficient (Q2) = 0.509, non-cross-validated correlation coefficient (R2ncv) = 0.841 and the predicted correlation coefficient (R2pred) = 0.745. In addition, docking studies and molecular dynamics (MD) simulations were carried out for further elucidation of the binding modes of MCHR1 antagonists. MD simulations in both water and lipid bilayer systems were performed. We hope that the obtained models and information may help to provide an insight into the interaction mechanism of MCHR1 antagonists and facilitate the design and optimization of novel antagonists as anti-obesity agents.
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Affiliation(s)
- Mingwei Wu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian University of Technology, Dalian 116024, China.
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian University of Technology, Dalian 116024, China.
| | - Xinmei Fu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.
| | - Jinghui Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian University of Technology, Dalian 116024, China.
| | - Shuwei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian University of Technology, Dalian 116024, China.
| | - Ling Yang
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Graduate School of the Chinese Academy of Sciences, Dalian 116023, China.
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