Antiviral Activity and Toxicity Prediction of Compounds Contained in Figs (Ficus carica L.) by In Silico Method

Viral infection is a global health problem that can cause endemic to pandemic. Compounds delivered from plants has been developed as an alternative antiviral agent. One of the plants that can be used as antiviral therapy is Ficus carica L. (figs). The aim of this research is to predict the inhibitory activity and toxicity of compounds contained in figs as an antiviral for HIV-1 using in silico method. Compounds were docked to the HIV-1 Reverse Transcriptase protein (PDB ID: 3LAL). Threedimentional structures were modeled using GaussView and optimized using Gaussian 09W. Optimized compounds were docked to the target protein using AutoDock Tools and the interaction to protein binding side were analyzed in comparison with the standard compounds. The standard compound used for the analysis nevirapine, efavirenz, and doravirine. The compound toxicity was analyzed using ECOSAR and Toxtree. Based on the results, the compounds that has similar interaction to the standard compounds were campesterol which has 4 similar hydrophobic interactions. Based on the classification of Cramer Rules for toxicity test, campesterol are classified in class 3 (high toxicity) and according to the Benigni/Bossa Rulebase classification, campesterol are negative for genotoxic and nongenotoxic carcinogenicity.Keywords: Antivirus, HIV, figs, molecular docking, toxicity

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Novel Thiazole-Based Thiazolidinones as Potent Anti-infective Agents: In silico PASS and Toxicity Prediction, Synthesis, Biological Evaluation and Molecular Modelling

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323666200127115238 ◽

2020 ◽

Vol 23 (2) ◽

pp. 126-140 ◽

Cited By ~ 1

Author(s):

Christophe Tratrat

Keyword(s):

In Silico ◽

Antimicrobial Agents ◽

Target Identification ◽

Biological Evaluation ◽

Microbial Infection ◽

Toxicity Prediction ◽

Discovery Studio ◽

Bacteria And Fungi ◽

Multiple Drugs ◽

Antibacterial And Antifungal

Aims and Objective: The infectious disease treatment remains a challenging concern owing to the increasing number of pathogenic microorganisms associated with resistance to multiple drugs. A promising approach for combating microbial infection is to combine two or more known bioactive heterocyclic pharmacophores in one molecular platform. Herein, the synthesis and biological evaluation of novel thiazole-thiazolidinone hybrids as potential antimicrobial agents were dissimilated. Materials and Methods: The preparation of the substituted 5-benzylidene-2-thiazolyimino-4- thiazolidinones was achieved in three steps from 2-amino-5-methylthiazoline. All the compounds have been screened in PASS antibacterial activity prediction and in a panel of bacteria and fungi strains. Minimum inhibitory concentration and minimum bacterial concentration were both determined by microdilution assays. Molecular modeling was conducted using Accelrys Discovery Studio 4.0 client. ToxPredict (OPEN TOX) and ProTox were used to estimate the toxicity of the title compounds. Results: PASS prediction revealed the potentiality antibacterial property of the designed thiazolethiazolidinone hybrids. All tested compounds were found to kill and to inhibit the growth of a vast variety of bacteria and fungi, and were more potent than the commercial drugs, streptomycin, ampicillin, bifomazole and ketoconazole. Further, in silico study was carried out for prospective molecular target identification and revealed favorable interaction with the target enzymes E. coli MurB and CYP51B of Aspergillus fumigatus. Toxicity prediction revealed that none of the active compounds was found toxic. Conclusion: Substituted 5-benzylidene-2-thiazolyimino-4-thiazolidinones, endowing remarkable antibacterial and antifungal properties, were identified as a novel class of antimicrobial agents and may find a potential therapeutic use to eradicate infectious diseases.

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Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

Open Biology ◽

10.1098/rsob.130100 ◽

2013 ◽

Vol 3 (11) ◽

pp. 130100 ◽

Cited By ~ 7

Author(s):

Zhisheng Lu ◽

Julien R. C. Bergeron ◽

R. Andrew Atkinson ◽

Torsten Schaller ◽

Dennis A. Veselkov ◽

...

Keyword(s):

Solution Structure ◽

Hydrophobic Interactions ◽

Dynamic Information ◽

Ubiquitin Ligase Complex ◽

Biophysical Studies ◽

Viral Infectivity Factor ◽

Β Sheet ◽

Socs Box ◽

Insight Into ◽

Hiv 1

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

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In silico design and in vitro expression of novel multiepitope DNA constructs based on HIV-1 proteins and Hsp70 T-cell epitopes

Biotechnology Letters ◽

10.1007/s10529-021-03143-9 ◽

2021 ◽

Author(s):

Elahe Akbari ◽

Kimia Kardani ◽

Ali Namvar ◽

Soheila Ajdary ◽

Esmat Mirabzadeh Ardakani ◽

...

Keyword(s):

T Cell ◽

In Silico ◽

T Cell Epitopes ◽

In Vitro Expression ◽

In Silico Design ◽

Hiv 1

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3D-QSAR, molecular docking and in silico ADMET studies of propiophenone derivatives with anti-HIV-1 protease activity

Structural Chemistry ◽

10.1007/s11224-021-01810-1 ◽

2021 ◽

Author(s):

Milan Jovanović ◽

Nemanja Turković ◽

Branka Ivković ◽

Zorica Vujić ◽

Katarina Nikolić ◽

...

Keyword(s):

Molecular Docking ◽

In Silico ◽

Protease Activity ◽

3D Qsar ◽

In Silico Admet ◽

Anti Hiv ◽

Hiv 1

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Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2021.1871958 ◽

2021 ◽

pp. 1-11

Author(s):

Khadijeh Ahmadi ◽

Alireza Farasat ◽

Mosayeb Rostamian ◽

Behrooz Johari ◽

Hamid Madanchi

Keyword(s):

In Silico ◽

Drug Repurposing ◽

Fusion Inhibitor ◽

Inhibitor Peptide ◽

Hiv 1

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Combined Genotypes of CCR5, CCR2, SDF1, and HLA Genes Can Predict the Long-Term Nonprogressor Status in Human Immunodeficiency Virus-1–Infected Individuals

Blood ◽

10.1182/blood.v93.3.936 ◽

1999 ◽

Vol 93 (3) ◽

pp. 936-941 ◽

Cited By ~ 151

Author(s):

Magdalena Magierowska ◽

Ioannis Theodorou ◽

Patrice Debré ◽

Françoise Sanson ◽

Brigitte Autran ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Chemokine Receptor ◽

Multivariate Logistic Regression Model ◽

Hla B27 ◽

Hla Alleles ◽

Immunodeficiency Virus ◽

Combined Genotypes ◽

Hiv 1

Abstract Human immunodeficiency virus (HIV)-1–infected long-term nonprogressors (LT-NP) represent less than 5% of HIV-1–infected patients. In this work, we tried to understand whether combined genotypes of CCR5-▵32, CCR2-64I, SDF1-3′A and HLA alleles can predict the LT-NP status. Among the chemokine receptor genotypes, only the frequency of the CCR5-▵32 allele was significantly higher in LT-NP compared with the group of standard progressors. The predominant HLA alleles in LT-NP were HLA-A3, HLA-B14, HLA-B17, HLA-B27, HLA-DR6, and HLA-DR7. A combination of both HLA and chemokine receptor genotypes integrated in a multivariate logistic regression model showed that if a subject is heterozygous for CCR5-▵32 and homozygous for SDF1 wild type, his odds of being LT-NP are increased by 16-fold, by 47-fold when a HLA-B27 allele is present with HLA-DR6 absent, and by 47-fold also if at least three of the following alleles are present: HLA-A3, HLA-B14, HLA-B17, HLA-DR7. This model allowed a correct classification of 70% of LT-NPs and 81% of progressors, suggesting that the host’s genetic background plays an important role in the evolution of HIV-1. The chemokine receptor and chemokine genes along with the HLA genotype can serve as predictors of HIV-1 outcome for classification of HIV-1–infected subjects as LT-NPs or progressors.

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Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

European Journal of Plant Pathology ◽

10.1007/s10658-020-02190-8 ◽

2021 ◽

Author(s):

Viola Kurm ◽

Ilse Houwers ◽

Claudia E. Coipan ◽

Peter Bonants ◽

Cees Waalwijk ◽

...

Keyword(s):

Ralstonia Solanacearum ◽

In Silico ◽

Species Complex ◽

Sequence Data ◽

In Silico Analysis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

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