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Singh A, Kumar V, Mishra A, Singh VK. Targeting the HIV-1 Tat and Human Tat Protein Complex through Natural
Products: An In Silico Docking and Molecular Dynamics Simulation
Approach. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220330122542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Tat protein is considered essential for substantial HIV-1 replication, and is also
required to break HIV-1 latency, resulting in productive HIV replication. The multifaceted regulatory role
of HIV Tat and the fact that it is expressed in the early stages of HIV infection justify its potential as an
anti-HIV drug target.
Objective:
The present study was undertaken with the aim to target HIV-1 Tat protein with natural compounds
which could help in identifying potential inhibitors against HIV-1 Tat.
Methods:
In this study, we compared the binding of Tat protein and Human P-TEFb Tat protein complex
(TPC) with phyto-steroids and terpenes to evaluate their potential for HIV-1 treatment. The docking ability
of plant products with HIV-1 Tat and TPC was studied with respect to dissociation constant, geometric
shape complementary score, approximate interface area, and binding energy using Patch dock and
YASARA. Molecular dynamics simulation was set up to investigate the interactions of the natural compounds
with Tat protein and human tat protein complex (TPC).
Results:
The binding energy and dissociation constant of Diosgenin, Catharanthine and Ginkgolide A
with Tat and TPC were comparable to antiretroviral drugs, Maraviroc and Emtricitabine. The natural
products, Diosgenin, Ginkgolide A and Catharanthine, showed the highest binding energy and were stable
with Tat protein and TPC in the entire MD simulation run.
Conclusion:
The natural products, Diosgenin, Ginkgolide A and Catharanthine, showed highest binding
energy and were stable with Tat protein and TPC in the entire MD simulation run. The binding energy
and dissociation constant of Diosgenin, Catharanthine and Ginkgolide A with Tat and TPC were comparable
to antiretroviral drugs, Maraviroc and Emtricitabine.
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Affiliation(s)
- Anchal Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Vipin Kumar
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Ayushi Mishra
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Vinay Kumar Singh
- Centre for
Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
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A novel dual three and five-component reactions between dimedone, aryl aldehydes, and 1-naphthylamine: synthesis and computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Okeke ES, Nweze EJ, Chibuogwu CC, Anaduaka EG, Chukwudozie KI, Ezeorba TPC. Aquatic Phlorotannins and Human Health: Bioavailability, Toxicity, and Future Prospects. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211056144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Medicinal chemists and pharmacognosists have relied on terrestrial sources for bioactive phytochemicals to manage and treat disease conditions. However, minimal interest is given to sea life, especially macroalgae and their inherent phytochemical reserves. Phlorotannins are a special class of phytochemicals mainly predominant in brown algae of marine and estuarine habitats. Phlorotannins are formed through the polymerization of phloroglucinol residues and derivatives via the polyketide (acetate–malonate) pathway. Studies over the past decades have implicated phlorotannins with several bioactivities, including anti-herbivory, antioxidants, anti-inflammatory, anti-microbial, anti-proliferative, anti-diabetic, radio-protective, adipogenic, anti-allergic, and anti-human immunodeficiency virus (anti-HIV) properties. All these activities are reflected in their applications as nutraceuticals and cosmeceutical agents. This article reviews the chemical composition of phlorotannins, their biological roles, and their applications. Moreover, very few studies on phlorotannin bioavailability, safety, and toxicity have been thoroughly reviewed. The paper concludes by suggesting exciting research questions for further studies.
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Affiliation(s)
- Emmanuel Sunday Okeke
- Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
- School of General Studies, University of Nigeria, Nsukka, Nigeria
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, P.R. China
- Organization of African Academic Doctor, Nairobi, Kenya
| | - Ekene John Nweze
- Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | | | | | | | - Timothy Prince Chidike Ezeorba
- Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
- School of Biosciences, University of Birmingham, Birmingham, UK
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Abiri A, Rezaei M, Zeighami MH, Vaezpour Y, Dehghan L, KhorramGhahfarokhi M. Discovery of new TLR7 agonists by a combination of statistical learning-based QSAR, virtual screening, and molecular dynamics. INFORMATICS IN MEDICINE UNLOCKED 2021; 27:100787. [PMID: 34805481 PMCID: PMC8591993 DOI: 10.1016/j.imu.2021.100787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/16/2021] [Accepted: 11/11/2021] [Indexed: 01/31/2023] Open
Abstract
Search for new antiviral medications has surged in the past two years due to the COVID-19 crisis. Toll-like receptor 7 (TLR7) is among one of the most important TLR proteins of innate immunity that is responsible for broad antiviral response and immune system control. TLR7 agonists, as both vaccine adjuvants and immune response modulators, are among the top drug candidates for not only our contemporary viral pandemic but also other diseases. The agonists of TLR7 have been utilized as vaccine adjuvants and antiviral agents. In this study, we hybridized a statistical learning-based QSAR model with molecular docking and molecular dynamics simulation to extract new antiviral drugs by drug repurposing of the DrugBank database. First, we manually curated a dataset consisting of TLR7 agonists. The molecular descriptors of these compounds were extracted, and feature engineering was done to restrict the number of features to 45. We applied a statistically inspired modification of the partial least squares (SIMPLS) method to build our QSAR model. In the next stage, the DrugBank database was virtually screened structurally using molecular docking, and the top compounds for the guanosine binding site of TLR were identified. The result of molecular docking was again screened by the ligand-based approach of QSAR to eliminate compounds that do not display strong EC50 values by the previously trained model. We then subjected the final results to molecular dynamics simulation and compared our compounds with imiquimod (an FDA-approved TLR7 agonist) and compound 1 (the most active compound against TLR7 in vitro, EC50 = 0.2 nM). Our results evidently demonstrate that cephalosporins and nucleotide analogues (especially acyclic nucleotide analogues such as adefovir and cidofovir) are computationally potent agonists of TLR7. We finally reviewed some publications about cephalosporins that, just like pieces of a puzzle, completed our conclusion.
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Affiliation(s)
- Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran,Corresponding author
| | - Masoud Rezaei
- Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran,Corresponding author
| | - Mohammad Hossein Zeighami
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Younes Vaezpour
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Leili Dehghan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Maedeh KhorramGhahfarokhi
- Faculty of Pharmacy and Pharmaceutical Sciences, Kerman University of Medical Sciences, Kerman, Iran
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