Browse
Submit Data
Databases
API
Help

Dataset Information

4 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular docking analysis of RN18 and VEC5 in A3G-Vif inhibition.

ABSTRACT: The HIV-1 protein Vif is essential for in vivo viral replication that targets the human DNA-editing enzyme, APOBEC3G (A3G), which inhibits replication of retroviruses. The Vif-A3G interactions are believed to be important targets for antiviral drug development. Since the interactions of A3G and Vif evade the ubiquitination pathways in human host, the viral replication precedes which otherwise spreads infection. In this study, two potent Vif inhibitors RN 18 and VEC5 have been evaluated for their inhibitory potential employing ligand receptor and protein-protein interactions studies. VEC 5 showed better interaction with Vif than RN18. Predicted data show that VEC5 bound Vif and RN18 bound Vif showed diminished interaction to A3G compared to inhibitor unbound Vif. However, this should be further validated using in vitro studies.

SUBMITTER: Sinha C

PROVIDER: S-EPMC4248342 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Molecular docking analysis of RN18 and VEC5 in A3G-Vif inhibition.

Sinha Chanda C Nischal Anuradha A Pant Kamlesh K KK Bandaru Srinivas S Nayarisseri Anuraj A Khattri Sanjay S

Bioinformation 20141030 10

The HIV-1 protein Vif is essential for in vivo viral replication that targets the human DNA-editing enzyme, APOBEC3G (A3G), which inhibits replication of retroviruses. The Vif-A3G interactions are believed to be important targets for antiviral drug development. Since the interactions of A3G and Vif evade the ubiquitination pathways in human host, the viral replication precedes which otherwise spreads infection. In this study, two potent Vif inhibitors RN 18 and VEC5 have been evaluated for their ...[more]

PMID: 25489169

Similar Datasets

Mapping the Vif-A3G interaction using peptide arrays: a basis for anti-HIV lead peptides.

Project description:Human apolipoprotein-B mRNA-editing catalytic polypeptide-like 3G (A3G) is a cytidine deaminase that restricts retroviruses, endogenous retro-elements and DNA viruses. A3G plays a key role in the anti-HIV-1 innate cellular immunity. The HIV-1 Vif protein counteracts A3G mainly by leading A3G towards the proteosomal machinery and by direct inhibition of its enzymatic activity. Both activities involve direct interaction between Vif and A3G. Disrupting the interaction between A3G and Vif may rescue A3G antiviral activity and inhibit HIV-1 propagation. Here, mapping the interaction sites between A3G and Vif by peptide array screening revealed distinct regions in Vif important for A3G binding, including the N-terminal domain (NTD), C-terminal domain (CTD) and residues 83-99. The Vif-binding sites in A3G included 12 different peptides that showed strong binding to either full-length Vif, Vif CTD or both. Sequence similarity was found between Vif-binding peptides from the A3G CTD and NTD. A3G peptides were synthesized and tested for their ability to counteract Vif action. A3G 211-225 inhibited HIV-1 replication in cell culture and impaired Vif dependent A3G degradation. In vivo co-localization of full-length Vif with A3G 211-225 was demonstrated by use of FRET. This peptide has the potential to serve as an anti-HIV-1 lead compound. Our results suggest a complex interaction between Vif and A3G that is mediated by discontinuous binding regions with different affinities.

| S-EPMC7039049 | biostudies-literature

A3G-Vif-CBFB-CRL5 Cross-Linking with DSSO

Project description:Here we use an optimization cross-linking mass spectrometry (XL-MS) pipeline for the structural characterization of a dynamic HIV-host protein complex. Using DSSO-based XL-MS analysis, residue-protein proximity restraints based on functional genetics, and integrative modeling, we define the structure of the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription factor Core Binding Factor Beta (CBFβ). Using a XL-MS3 methodology, we identify 132 inter-linked peptides and integrate the data with atomic structures of the subunits and mutagenesis data, and computed an integrative structure model of the heptameric A3G-CRL5-Vif-CBFβ complex. The resulting model ensemble quantifies the dynamic heterogenity of the A3G C-terminal domain, as well as CUL5 flexibility, and defines the interface between Vif and A3G. Our model can be used to rationalize previous structural, mutatagenesis, and functional data not included in modeling. The experimental and computational approach described here is generally applicable to other challenging host-pathogen protein complexes and provides new visualization tools for characterizing cross-linking data.

2021-11-03 | PXD025391 | Pride

Enterovirus 71 antagonizes the inhibition of the host intrinsic antiviral factor A3G.

Project description:Although the host restriction factor APOBEC3G (A3G) has broad spectrum antiviral activity, whether A3G inhibits enterovirus 71 (EV71) has been unclear until now. In this study, we demonstrated for the first time that A3G could inhibit EV71 virus replication. Silencing A3G in H9 cells enhanced EV71 replication, and EV71 replication was lower in H9 cells expressing A3G than in Jurkat cells without A3G expression, indicating that the EV71 inhibition was A3G-specific. Further investigation revealed that A3G inhibited the 5'UTR activity of EV71 by competitively binding to the 5'UTR through its nucleic acid binding activity. This binding impaired the interaction between the 5'UTR and the host protein poly(C)-binding protein 1 (PCBP1), which is required for the synthesis of EV71 viral proteins and RNA. On the other hand, we found that EV71 overcame A3G suppression through its non-structural protein 2C, which induced A3G degradation through the autophagy-lysosome pathway. Our research provides new insights into the interplay mechanisms of A3G and single-stranded positive RNA viruses.

| S-EPMC6265463 | biostudies-literature

Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation.

Project description:In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds.

| S-EPMC4629110 | biostudies-literature

Small-molecule inhibition of HIV-1 Vif.

Project description:The HIV-1 protein Vif, essential for in vivo viral replication, targets the human DNA-editing enzyme, APOBEC3G (A3G), which inhibits replication of retroviruses and hepatitis B virus. As Vif has no known cellular homologs, it is an attractive, yet unrealized, target for antiviral intervention. Although zinc chelation inhibits Vif and enhances viral sensitivity to A3G, this effect is unrelated to the interaction of Vif with A3G. We identify a small molecule, RN-18, that antagonizes Vif function and inhibits HIV-1 replication only in the presence of A3G. RN-18 increases cellular A3G levels in a Vif-dependent manner and increases A3G incorporation into virions without inhibiting general proteasome-mediated protein degradation. RN-18 enhances Vif degradation only in the presence of A3G, reduces viral infectivity by increasing A3G incorporation into virions and enhances cytidine deamination of the viral genome. These results demonstrate that the HIV-1 Vif-A3G axis is a valid target for developing small molecule-based new therapies for HIV infection or for enhancing innate immunity against viruses.

| S-EPMC2693000 | biostudies-literature

Metabolomic Profiling, Antioxidant and Enzyme Inhibition Properties and Molecular Docking Analysis of Antarctic Lichens

Project description:The lichen species Lecania brialmontii, Pseudephebe pubescens, and Sphaerophorus globosus are part of the prominent lichenoflora of the Antarctic territory. In this work, we report the metabolomic identification of ethanolic extracts of these species, their antioxidant and cholinesterase enzyme inhibitory activity, and conduct a molecular docking analysis with typical compounds. Eighteen compounds were identified by UHPLC-ESI-QTOF-MS in L. brialmontii, 18 compounds in P. pubescens, and 14 compounds in S. globosus. The content of phenolic compounds was variable among the species, ranging from 0.279 to 2.821 mg AG/g, and all three species showed high inhibition potential on the cholinesterase enzymes. Molecular docking showed important interactions between AChE and BChE with the selected compounds. This study evidences the chemical fingerprint of three species of the order Lecanorales that support the continuation of the study of other biological activities and their potential for medical research.

| S-EPMC9692326 | biostudies-literature

Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins.

Project description:Background and aimCOVID-19 emerged by the end of 2019 in Wuhan, China. It spreaded and became a public health emergency all over the world by mid of April 2020. Flavonoids are specialized metabolites that have antimicrobial properties including anti-viral activity. Rutin, a medicinally important flavonoid belongs to one of the best natural antioxidant classes. It has antiprotozoal, antibacterial, and antiviral properties. Keeping the antimicrobial potential of rutin in mind, we studied its role in the inhibition of essential proteins of SARS-CoV-2 including main protease (Mpro), RNA-dependent RNA polymerase (RdRp), papain-like protease (PLpro), and spike (S)-protein through different in silico approaches.Experimental procedureMolecular docking, inhibition constant, hydrogen bond calculations, and ADMET-properties prediction were performed using different softwares.Results and conclusionMolecular docking study showed significant binding of rutin with Mpro, RdRp, PLpro, and S-proteins of SARS-CoV-2. Out of these four proteins, Mpro exhibited the strongest binding affinity with the least binding energy (-8.9 kcal/mol) and stabilized through hydrogen bonds with bond lengths ranging from 1.18 Å to 3.17 Å as well as hydrophobic interactions. The predicted ADMET and bioactivity showed its optimal solubility, non-toxic, and non-carcinogenic properties. The values of the predicted inhibitory constant of the rutin with SARS-CoV-2 vital proteins ranged between 5.66 μM and 6.54 μM which suggested its promising drug candidature. This study suggested rutin alone or in combination as a dietary supplement may be used to fight against COVID-19 after detailed in vitro and in vivo studies.

| S-EPMC7825826 | biostudies-literature

Molecular Docking of Isolated Alkaloids for Possible ?-Glucosidase Inhibition.

Project description:Diabetes mellitus, one of the most common endocrine-metabolic disorders, has caused significant morbidity and mortality worldwide. To avoid sugar digestion and postprandial hyperglycemia, it is necessary to inhibit ?-glucosidase, a digestive enzyme with an important role in carbohydrate digestion. The criteria for the selection of alkaloids are based on their in vitro and in vivo activities on glucose modulation. The current study assessed the bonding potential of isolated alkaloids with the targeted protein. For this purpose, the 3D structure of the target protein (?-glucosidase) was reproduced using MODELLER 9.20. The modeled 3D structure was then validated and confirmed by using the RAMPAGE, ERRAT, and Verify3D online servers. The molecular docking of 32 alkaloids reported as ?-glucosidase inhibitors, along with reference compounds (acarbose and miglitol), was done through MOE-Dock applied in MOE software to predict the binding modes of these drug-like compounds. The results revealed that nummularine-R and vindoline possess striking interactions with active site residues of the target protein, and were analogous to reference ligands. In conclusion, the current study provided a computational background to the ?-glucosidase inhibitors tested. This novel information should facilitate the development of new and effective therapeutic compounds for the treatment of diabetes mellitus.

| S-EPMC6843650 | biostudies-literature

Characterization of an A3G-Vif<sub>HIV-1</sub>-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.

Project description:Structural analysis of host-pathogen protein complexes remains challenging, largely due to their structural heterogeneity. Here, we describe a pipeline for the structural characterization of these complexes using integrative structure modeling based on chemical cross-links and residue-protein contacts inferred from mutagenesis studies. We used this approach on the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription factor Core Binding Factor Beta (CBFβ) to determine the structure of the (A3G-Vif-CRL5-CBFβ) complex. Using the MS-cleavable DSSO cross-linker to obtain a set of 132 cross-links within this reconstituted complex along with the atomic structures of the subunits and mutagenesis data, we computed an integrative structure model of the heptameric A3G-Vif-CRL5-CBFβ complex. The structure, which was validated using a series of tests, reveals that A3G is bound to Vif mostly through its N-terminal domain. Moreover, the model ensemble quantifies the dynamic heterogeneity of the A3G C-terminal domain and Cul5 positions. Finally, the model was used to rationalize previous structural, mutagenesis and functional data not used for modeling, including information related to the A3G-bound and unbound structures as well as mapping functional mutations to the A3G-Vif interface. The experimental and computational approach described here is generally applicable to other challenging host-pathogen protein complexes.

| S-EPMC8459920 | biostudies-literature

Chemical inhibition of fatty acid synthase: molecular docking analysis and biochemical validation in ocular cancer cells.

Project description:Fatty acid biosynthesis is an attractive target for anti-cancer therapeutics. The ocular cancer, retinoblastoma cells were treated with fatty acid synthase (FASN) enzyme inhibitors: cerulenin, triclosan and orlistat. The IC(50) and dose-dependent sensitivity of cancer cells to FASN inhibitors decrease in biologic enzyme activity, and cell morphology alterations were analysed. Molecular interactions of enzyme-inhibitor complexes were studied by molecular modelling and docking simulations. The crystal structures of ketoacyl synthase (PDB ID:3HHD) (cerulenin) and thioesterase (PDB ID:2PX6) (orlistat) domains of human FASN were utilized for docking, while for the non-crystallised human FASN enoyl reductase domain (triclosan), homology model was built and used for docking. All three inhibitors showed significant binding energy indicating stable complex formation with their respective FASN subunits. The predicted Ki value of the FASN inhibitors corroborated well with their corresponding anti-cancer effects.

| S-EPMC3289161 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data