4.5 Article

Natural flavonoids effectively block the CD81 receptor of hepatocytes and inhibit HCV infection: a computational drug development approach

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Amentoflavone derivatives significantly act towards the main protease (3CLPRO/MPRO) of SARS-CoV-2: in silico admet profiling, molecular docking, molecular dynamics simulation, network pharmacology

Dipta Dey et al.

Summary: SARS-CoV-2 is the main cause of COVID-19, and plant-derived amentoflavone derivatives show potential as antiviral agents. The study found that 10 amentoflavone derivatives strongly interact with the key enzyme of SARS-CoV-2, and exhibit potential antiviral effects in molecular dynamic simulation.

MOLECULAR DIVERSITY (2023)

Article Biochemistry & Molecular Biology

Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

C. Shivanika et al.

Summary: The study evaluated the potency of two hundred natural antiviral phytocompounds against the active site of the SARS-CoV-2 Main-Protease using FDA approved viral protease inhibitors as standards. Five compounds were found to be the top inhibitors for COVID-19 M(pro).

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

Article Engineering, Chemical

Genistein, a Potential Phytochemical against Breast Cancer Treatment-Insight into the Molecular Mechanisms

Md Sohel et al.

Summary: This review explores the molecular mechanisms and anticancer activities of genistein (GNT) in breast cancer (BC). GNT exerts its effects through multiple pathways, including apoptosis induction, cell cycle arrest, inhibition of angiogenesis and metastasis, and enhancement of the efficacy of standard chemotherapeutic drugs. These findings suggest that GNT could serve as a beneficial therapeutic agent when standard drugs are not available in the pharma markets.

PROCESSES (2022)

Article Plant Sciences

Evaluation of in vitro and in silico anti-inflammatory potential of some selected medicinal plants of Bangladesh against cyclooxygenase-II enzyme

Md Aminul Islam et al.

Summary: Both experimental and computational studies have scientifically revealed the folklore uses of the experimental medicinal plants in inflammatory disorders. Three phytochemicals exhibited better competitive results than the conventional anti-inflammatory drug naproxen in molecular docking and molecular dynamics simulation studies. These findings suggest that N-(2-hydroxycyclohexyl)-4-methylbenzenesulfonamide, Benzeneethanamine, 2-fluoro-.beta., 3, 4-trihydroxy-N-isopropyl, and 3,5-di-tert-butylphenol could be potential leads for COX-2 inhibitors.

JOURNAL OF ETHNOPHARMACOLOGY (2022)

Article Plant Sciences

UHPLC-Q/Orbitrap/MS based chemical fingerprinting and hepatoprotective potential of medicinal plant Morinda angustifolia Roxb.

Md Mehedi Hasan et al.

Summary: This study assessed the hepatoprotective potential of M. angustifolia bark extract and identified its active constituents using in silico techniques. Experimental results confirmed the extract's significant hepatoprotective activity, while molecular docking studies provided insights into the therapeutic potential of identified compounds in oxidative liver damage.

SOUTH AFRICAN JOURNAL OF BOTANY (2022)

Article Agriculture, Dairy & Animal Science

Catabolic profiling of selective enzymes in the saccharification of non-food lignocellulose parts of biomass into functional edible sugars and bioenergy: An in silico bioprospecting

Parag Kumar Paul et al.

Summary: This research aims to assess the potential of converting lignocellulose parts of agricultural biomass wastes into functional edible sugars and biofuels through the analysis of different hydrolytic enzymes. The results show that versatile peroxidase has promising catalytic activity in lignin degradation, while Melanocarpus albomyces endoglucanase performs well in cellulose degradation.

JOURNAL OF ADVANCED VETERINARY AND ANIMAL RESEARCH (2022)

Article Chemistry, Applied

Computer-aided Evaluation of Anti-SARS-CoV-2 (3-chymotrypsin-like Protease and Transmembrane Protease Serine 2 Inhibitors) Activity of Cepharanthine: An In silico Approach

Divya Jain et al.

Summary: This study used molecular docking to investigate the binding affinity of Cepharanthine (CEP) with key proteins 3CL(PRO) and TMPRSS-2 in SARS-CoV-2.The results showed that CEP exhibited strong binding interactions with 3CL(PRO) and TMPRSS-2 proteins, suggesting its potential as a treatment for combating SARS-CoV-2. However, further in vivo studies are needed to validate these findings.

BIOINTERFACE RESEARCH IN APPLIED CHEMISTRY (2022)

Article Biochemistry & Molecular Biology

A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2

Rajib Islam et al.

Summary: The study identified potential inhibitors against SARS-CoV-2 main protease from 40 antiviral phytochemicals via molecular docking and molecular dynamics simulations. A QSAR model was established to predict favorable binding energy, and the selected candidates were found to be safer inhibitors through ADMET analysis. The computational and statistical analysis supported the potential of these phytochemicals as antiviral agents against SARS-CoV-2.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

Article Chemistry, Medicinal

Quercetin and/or Ascorbic Acid Modulatory Effect on Phenobarbital-Induced Sleeping Mice Possibly through GABAA and GABAB Receptor Interaction Pathway

Rajib Hossain et al.

Summary: Depressive disorder is a common illness that poses a challenge in the treatment of treatment-resistant depression. Research suggests that pre-treatment with quercetin and ascorbic acid can modify the sleep patterns of mice, potentially acting through the GABA receptor pathways.

PHARMACEUTICALS (2021)

Article Biology

Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations

Mycal Dutta et al.

Summary: The study utilized molecular docking and molecular dynamics simulation to identify potential inhibitors from Leucas zeylanica for the main protease of SARS-CoV-2. The identified phytochemicals showed toxicity but stable binding affinity, demonstrating potential as antiviral drug candidates. Through computational drug design, three compounds were identified with high docking scores and interactions with key amino acids in the SARS-CoV-2 main protease catalytic groove, suggesting their potential in combating the virus.

BIOLOGY-BASEL (2021)

Article Biology

Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent Inhibitors

Shafi Mahmud et al.

Summary: Virtual screening techniques were used to identify three potential antiviral drug candidates from Asian plants, which demonstrated promising pharmacological characteristics and biological activities in molecular dynamics simulations. The compounds showed stability and efficacy in binding to the target protein, suggesting their potential in developing effective drugs to treat COVID-19.

BIOLOGY-BASEL (2021)

Article Parasitology

Designing an epitope vaccine against Dermatophagoides pteronyssinus: An in silico study

Aryani Adji et al.

Summary: In this study, computer immunoinformatics was used to design T-cell and B-cell epitopes from the house dust mite allergen Der p 1, leading to the identification of conserved epitope areas. Molecular docking identified three optimal clusters, with cluster 6 exhibiting the most negative Z-score and representing three epitopes. This research suggests the potential for using the IQRDNGYQP region as a candidate for a D. pteronyssinus epitope vaccine for allergen-specific immunotherapy.

ACTA TROPICA (2021)

Article Plant Sciences

Metabolite profiling, anti-inflammatory, analgesic potentials of edible herb Colocasia gigantea and molecular docking study against COX-II enzyme

Md Nazmul Hasan Zilani et al.

Summary: This study demonstrated the significant anti-inflammatory and analgesic activities of Colocasia gigantea, with bioactive compounds such as (-)-epicatechin playing a key role. Molecular docking against the anti-inflammatory enzyme COX-2 revealed strong binding affinity of (-)-epicatechin. The results support the traditional use of edible herb C. gigantea in ancestral medicine.

JOURNAL OF ETHNOPHARMACOLOGY (2021)

Review Biochemistry & Molecular Biology

Potential Therapeutic Role of Phytochemicals to Mitigate Mitochondrial Dysfunctions in Alzheimer's Disease

Md. Ataur Rahman et al.

Summary: Mitochondrial dysfunction is a potential cause of AD, which may be triggered by mutations in mitochondrial or nuclear DNA, resulting in an imbalance in reactive oxygen species production and oxidative stress. Neuroinflammation may also induce mitochondrial dysfunction. Phytochemicals have the potential to scavenge oxygen free radicals, enhance cellular antioxidant defense systems, and modulate other cellular processes, making them a potential strategy for alleviating mitochondrial dysfunction in the pathogenesis of AD.

ANTIOXIDANTS (2021)

Article Biochemistry & Molecular Biology

Diterpenes/Diterpenoids and Their Derivatives as Potential Bioactive Leads against Dengue Virus: A Computational and Network Pharmacology Study

Rasel Ahmed Khan et al.

Summary: Dengue fever is a dangerous endemic disease caused by the dengue virus, resulting in millions of deaths worldwide. Some derivatives of diterpenoids exhibit anti-dengue viral properties. In silico studies showed that certain compounds have good binding affinities to viral proteins, suggesting their potential as anti-dengue medications.

MOLECULES (2021)

Article Chemistry, Physical

Biocatalytic Aromaticity-Breaking Epoxidation of Naphthalene and Nucleophilic Ring-Opening Reactions

Wuyuan Zhang et al.

Summary: Aromatic epoxides generated by fungal peroxygenases can be subjected to nucleophilic ring opening to yield non-racemic trans-disubstituted cyclohexadiene derivatives, which can then be used for further chemical transformations, potentially offering a promising shortcut for the synthesis of natural products and APIs.

ACS CATALYSIS (2021)

Review Engineering, Chemical

Exhaustive Plant Profile of Dimocarpus longan Lour with Significant Phytomedicinal Properties: A Literature Based-Review

Priyanka Paul et al.

Summary: Dimocarpus longan Lour is a plant with medicinal value, displaying different activities in different disease conditions. Some chemical constituents such as gallic acid, ellagic acid, and corilagin exhibited good anti-cancer activity.

PROCESSES (2021)

Article Infectious Diseases

High Throughput Virtual Screening and Molecular Dynamics Simulation for Identifying a Putative Inhibitor of Bacterial CTX-M-15

Shazi Shakil et al.

Summary: This study aimed to identify a promising anti-CTX-M-15 ligand as a 'seed-molecule' for future drug design against resistant bacteria. Through virtual screening and molecular dynamics simulation, a molecule that efficiently bound to bacterial CTX-M-15 enzyme was found, with detailed trajectory analysis conducted.

ANTIBIOTICS-BASEL (2021)

Review Integrative & Complementary Medicine

Ethnomedicinal Use, Phytochemistry, and Pharmacology of Xylocarpus granatum J. Koenig

Dipta Dey et al.

Summary: Xylocarpus granatum has been traditionally used for treating various diseases and possesses pharmacological activities, mainly attributed to the presence of diverse phytochemicals. Further research is needed to fully understand the mechanisms of action and toxicological aspects of this medicinal plant.

EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE (2021)

Article Biochemical Research Methods

Pinpointing the potential hits for hindering interaction of SARS-CoV-2 S-protein with ACE2 from the pool of antiviral phytochemicals utilizing molecular docking and molecular dynamics (MD) simulations

Chirag N. Patel et al.

Summary: This study investigated 110 phytochemicals from medicinal plants and identified the top five compounds that can serve as S-protein blockers. The pharmacophore features and interaction with RBD of these compounds were studied, and the best three hits were further analyzed using Molecular Dynamics simulation. Binding free energy calculations were performed, confirming these phytochemicals' potential as S-protein blockers.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2021)

Article Biochemistry & Molecular Biology

BDNF as a Putative Target for Standardized Extract of Ginkgo biloba-Induced Persistence of Object Recognition Memory

Beatriz G. Muratori et al.

Summary: The study demonstrates that EGb treatment before acquisition of object recognition memory promotes the persistence of long-term memory by upregulating BDNF expression in a dose- and session-dependent manner, leading to improved performance of animals in memory tests.

MOLECULES (2021)

Article Chemistry, Multidisciplinary

Antiviral peptides against the main protease of SARS-CoV-2: A molecular docking and dynamics study

Shafi Mahmud et al.

Summary: This study explored the potential of antiviral peptides in inhibiting the main protease of SARS-CoV-2, showing promising results in binding energy and stability of peptide-main protease complexes. Further wet-lab experiments are needed to confirm these findings.

ARABIAN JOURNAL OF CHEMISTRY (2021)

Article Pharmacology & Pharmacy

Molecular docking and dynamics study to explore phytochemical ligand molecules against the main protease of SARS-CoV-2 from extensive phytochemical datasets

Shafi Mahmud et al.

Summary: This study explored potential drug candidates against SARS-CoV-2 by screening phytochemicals from Asian plants, identifying three compounds with binding energy to the main protease. Simulation analysis confirmed the stability of the protein-ligand complexes, suggesting these compounds could be useful in fighting against SARS-CoV-2.

EXPERT REVIEW OF CLINICAL PHARMACOLOGY (2021)

Article Engineering, Chemical

In Vivo Neuropharmacological Potential of Gomphandra tetrandra (Wall.) Sleumer and In-Silico Study against β-Amyloid Precursor Protein

Md. Saidur Rahman et al.

Summary: Medicinal plants like Gomphandra tetrandra contain various bioactive compounds with potential neurological benefits. In this study, phytochemicals were identified from the plant extract and showed promising antioxidant and neurological activities in vitro and in vivo. Computer-aided analysis identified 1,5-diphenyl-2h-1,2,4-triazoline-3-thione as a potential compound with strong binding affinity to beta-amyloid precursor protein.

PROCESSES (2021)

Article Health Care Sciences & Services

Analysis of SYK Gene as a Prognostic Biomarker and Suggested Potential Bioactive Phytochemicals as an Alternative Therapeutic Option for Colorectal Cancer: An In-Silico Pharmaco-Informatics Investigation

Partha Biswas et al.

Summary: The study identifies SYK gene as a potential prognostic biomarker for colorectal cancer (CRC), with increased expression in CRC samples and its correlation with survival rate. Furthermore, potential phytochemicals targeting SYK kinase protein were evaluated through molecular docking, showing promising stability for CRC treatment after clinical trials.

JOURNAL OF PERSONALIZED MEDICINE (2021)

Article Medicine, Research & Experimental

Target specificity of selective bioactive compounds in blocking α-dystroglycan receptor to suppress Lassa virus infection: an in silico approach

Adittya Arefin et al.

Summary: Lassa hemorrhagic fever, caused by Lassa mammarenavirus (LASV) infection, leads to up to 5000 deaths annually with no vaccine currently available. This study identified three bioactive compounds that can potentially block the entry of LASV into cells and demonstrated the best binding affinity through molecular docking and molecular dynamics simulation experiments. Real-time in vivo studies are ongoing to confirm the potential of these compounds as target-specific drugs.

JOURNAL OF BIOMEDICAL RESEARCH (2021)

Article Agriculture, Dairy & Animal Science

Molecular optimization, docking, and dynamic simulation profiling of selective aromatic phytochemical ligands in blocking the SARS-CoV-2 S protein attachment to ACE2 receptor: an in silico approach of targeted drug designing

Dipta Dey et al.

Summary: This comprehensive in silico study identified five potential aromatic phytochemical ligands with promising pharmacokinetic properties for blocking the ACE2 receptor-SARS-CoV-2 S protein complex formation, indicating Rhinacanthin D as a stable candidate for drug development against the novel coronavirus.

JOURNAL OF ADVANCED VETERINARY AND ANIMAL RESEARCH (2021)

Article Biochemistry & Molecular Biology

Tuning Properties for Blood-Brain Barrier Permeation: A Statistics-Based Analysis

Maria Dichiara et al.

ACS CHEMICAL NEUROSCIENCE (2020)

Article Immunology

Single-nucleotide variants in human CD81 influence hepatitis C virus infection of hepatoma cells

Maria Pia Alberione et al.

MEDICAL MICROBIOLOGY AND IMMUNOLOGY (2020)

Article Chemistry, Physical

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS

Szilard Pall et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Biochemistry & Molecular Biology

Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding

Raju Dash et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Review Gastroenterology & Hepatology

Global epidemiology and burden of HCV infection and HCV-related disease

Aaron P. Thrift et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2017)

Article Multidisciplinary Sciences

Human Frataxin Folds Via an Intermediate State. Role of the C-Terminal Region

Santiago E. Faraj et al.

SCIENTIFIC REPORTS (2016)

Article Chemistry, Multidisciplinary

New Ways to Boost Molecular Dynamics Simulations

Elmar Krieger et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)

Review Biotechnology & Applied Microbiology

Phytochemical Compounds and Protection from Cardiovascular Diseases: A State of the Art

Beniamino Pagliaro et al.

BIOMED RESEARCH INTERNATIONAL (2015)

Article Chemistry, Physical

Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity

Michael F. Harrach et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Gastroenterology & Hepatology

Medicinal plants against hepatitis C virus

Usman A. Ashfaq et al.

WORLD JOURNAL OF GASTROENTEROLOGY (2014)

Review Virology

CD81 and Hepatitis C Virus (HCV) Infection

Lucie Feneant et al.

VIRUSES-BASEL (2014)

Article Chemistry, Physical

Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes

Jon D. Wright et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Multidisciplinary Sciences

An in silico evaluation of the ADMET profile of the StreptomeDB database

Fidele Ntie-Kang

SPRINGERPLUS (2013)

Article Plant Sciences

Identification and evaluation of anti Hepatitis C virus phytochemicals from Eclipta alba

Dinesh Manvar et al.

JOURNAL OF ETHNOPHARMACOLOGY (2012)

Article Biochemistry & Molecular Biology

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

Zheng Yang et al.

JOURNAL OF STRUCTURAL BIOLOGY (2012)

Review Gastroenterology & Hepatology

In Vitro Systems for the Study of Hepatitis C Virus Infection

Garrick K. Wilson et al.

INTERNATIONAL JOURNAL OF HEPATOLOGY (2012)

Article Plant Sciences

An overview on genus garcinia: phytochemical and therapeutical aspects

M. Hemshekhar et al.

PHYTOCHEMISTRY REVIEWS (2011)

Review Gastroenterology & Hepatology

HCV Routes of Transmission: What Goes Around Comes Around

Miriam J. Alter

SEMINARS IN LIVER DISEASE (2011)

Review Chemistry, Medicinal

Antiviral Activity of Phytochemicals: A Comprehensive Review

Rajesh Naithani et al.

MINI-REVIEWS IN MEDICINAL CHEMISTRY (2008)

Article Biochemistry & Molecular Biology

BPPred: A Web-based computational tool for predicting biophysical parameters of proteins

Christian D. Geierhaas et al.

PROTEIN SCIENCE (2007)

Article Biochemical Research Methods

Fast empirical pKa prediction by Ewald summation

Elmar Krieger et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Gastroenterology & Hepatology

Prevention of spread of hepatitis C

MJ Alter

HEPATOLOGY (2002)