Virtual screening of Indonesian herbal database as HIV-1 reverse transcriptase inhibitor

Syahdi, Rezi Riadhi; Mun’im, Abdul; Suhartanto, Heru; Yanuar, Arry

doi:10.6026/97320630081206

Cited by 22 publications

(21 citation statements)

References 29 publications

(26 reference statements)

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“…The methanolic extract of leaves showed significant antinociceptive activity on writhing response in acetic acid induced. 5,6 There is no report about the anti-HIV-1 RT activity of E. variegata. The structure of isolated compound from E. variegata leaves was elucidated based on spectral data.…”

Section: Discussionmentioning

confidence: 99%

“…4 Some plants have been known to benefit as an anti-HIV-1 from different countries. Syahdi et al (2012) have performed virtual screening of HIV-1 transcriptase inhibitor base on Indonesian herbal database. 5 The study resulted in top ten compounds which have the prospect to be developed as HIV-1 reverse transcriptase inhibitor.…”

Section: Introductionmentioning

confidence: 99%

“…Syahdi et al (2012) have performed virtual screening of HIV-1 transcriptase inhibitor base on Indonesian herbal database. 5 The study resulted in top ten compounds which have the prospect to be developed as HIV-1 reverse transcriptase inhibitor. Based on that study, we selected ten plants which contained the compounds and evaluated their inhibitory activity in vitro against HIV-1 reverse transcriptase.…”

Section: Introductionmentioning

confidence: 99%

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Inhibition of HIV-1 Reverse Transcriptase of Selected Indonesia Medicinal Plants and Isolation of the Inhibitor from Erythrina variegata L. Leaves

Wardani¹,

Mun’im²,

Yanuar³

2018

JYP

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Objective: This research was conducted to screen inhibition of HIV-1 reverse transcriptase activity of selected Indonesia medicinal plants and to isolate HIV-1 reverse transcriptase inhibitor from Erythrina variegata leaves. Method: Screening inhibition of HIV-1 RT activity of selected Indonesia medicinal plants and isolated compounds were performed using HIV-1 RT colorimetric assay. The isolation of HIV-1 reverse transcriptase inhibitor was conducted using chromatography technique. The isolated compound was determined based on the data of UV, IR spectrophotometry, MS, 1D and 2D NMR spectroscopy. Results: Beside that, in vitro study of the leaves methanolic extract exhibited inhibition against HIV-1 RT activity with percent inhibition of 97.64% at concentration of 5 mg/mL. Ethyl acetate fraction from the extract showed the strongest HIV-1 RT inbitory activity with IC 50 of 429.28 µg/mL. Isolation the HIV-1 RT inhibitor from the fraction give compound 1. Conclusion: Erythrina variegata leave extract exhibited potent inhibition on HIV-1 RT activity. The isolated compound from the leaves was determined as apigenin-7-O-β-D-glucopyranoside and demonstrated HIV-1 RT inhibitory activity with the IC 50 value of 100.59 µg/mL. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows others to remix, tweak, and build upon the work non-commercially, as long as the author is credited and the new creations are licensed under the identical terms.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Inhibition of HIV-1 Reverse Transcriptase of Selected Indonesia Medicinal Plants and Isolation of the Inhibitor from Erythrina variegata L. Leaves

Wardani¹,

Mun’im²,

Yanuar³

2018

JYP

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“…The materials and methods described in this study were modified from the studies by Yanuar et al, Syahdi et al,25,26]. A three-dimensional structure of DNMT1, positive and negative control compounds, and active herbal compounds contained in the HerbalDB were used in this study.…”

Section: Methodsmentioning

confidence: 99%

Virtual Screening of Indonesian Herbal Database for Dna Methyltransferase Inhibitors

Bhaskarawilaputraka

Azminah

Erlina

et al. 2017

Asian J Pharm Clin Res

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Objective: DNA hypermethylation is an abnormal epigenetic process catalyzed by DNA methyltransferase 1 (DNMT1). It is also one of the factors that cause non-communicable diseases such as cancer, diabetes, and other metabolic diseases. DNA hypermethylation can be reversed by suppressing DNMT1 activity using a DNMT inhibitor. This study was conducted to seek out inhibitor candidates among natural products. Methods:The search for potential inhibitors was conducted through a virtual screening of the Indonesian Herbal Database using AutoDockVina as docking software. Twenty-five compounds known for their inhibitory activity against DNMT1 were used as actives and as a reference for generating decoys, which was done using the Directory of Useful Decoys, Enhanced. Results:The 12 compounds with binding energies below the cutoff value were cassiamin C (A1), procyanidin B2 (B2), ent-epicatechin-(4alpha->8)-ent-epicatechin (C3), epicatechin-(4beta->8)-epicatechin-3-O-gallate (D4), neorhusflavanone (E5), 3-O-galloylepicatechin-(4beta->6)-epicatechin-3-O-gallate (F6), withanolide (G7), 3-O-galloylepigallocatechin-(4beta->6)-epigallocatechin-3-O-gallate (H8), cyanidin 3-(6''-caffeylsophoroside)-5-glucoside (I9), epifriedelanol (J10), gallocatechin-(4alpha->8)-epicatechin (K11), and scutellarein 7-glucosyl-(1->4)-rhamnoside (L12). A1 had the lowest binding energy of −12.7 kcal/mol, whereas K11 had the highest of −11.5 kcal/mol. Conclusions:The virtual screening yielded five potential DNMT1 inhibitors: Procyanidin B2, ent-epicatechin-(4alpha->8)-ent-epicatechin, epicatechin-(4beta->8)-epicatechin-3-O-gallate, neorhusflavanone, and cyanidin 3-(6''-caffeylsophoroside)-5-glucoside.Keywords: Epigenetic, DNA methyltransferase inhibitor, Indonesian Herbal Database, Virtual screening, AutoDockVina. INTRODUCTIONEpigenetic modification is one of the factors that cause noncommunicable diseases. Living environment, lifestyle, exposure to toxic chemicals, and nutrition may influence an individual's epigenetic profile. Epigenetic modification can alter gene expression [1]. One type of epigenetic modification is DNA methylation. DNA methylation, catalyzed by DNA methyltransferases (DNMTs), is the addition of a methyl (CH3) group to the DNA strand, specifically to the fifth carbon atom of a cytosine ring. Methylated cytosine, called 5-methylcytosine, usually occurs to a cytosine base that lies adjacent to a guanine base, at what is called a CpG site. The reason for this name is that cytosine is bonded to guanine through a phosphate bond. These sites normally occur in clusters; an area rich in CpG sites is called a CpG island. CpG islands are usually located near a gene regulator such as a promoter. DNA methylation that affects a gene promoter may repress the transcription of said gene and ultimately its expression. This process of turning a gene on and off through methylation is part of normal eukaryotic cell function [2,3].There are several types of DNMTs. Based on their functions, they can be grouped into two categories: De novo DNMTs...

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“…After adding hydrogen to the structure, minimization was done using the steepest descent and conjugate gradient, 1,000 steps for each method. The last step was adding Gasteiger partial charges and applying AutoDock force field with AutoDock Tools [27].…”

Section: Ligand File Format Preparationmentioning

confidence: 99%

In Silico Screening of Antimalarial From Indonesian Medicinal Plants Database to Plasmepsin Target

Rifai

Hayun

Yanuar

2017

Asian J Pharm Clin Res

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Objective: Malaria is a disease that impacts millions of people annually. Among the enzymes, plasmepsin is the main enzyme in the plasmodium life cycle that degrades hemoglobin during the erythrocytic phase in the food vacuole. Recently, pharmaceutical industries have been trying to develop therapeutic agents that can cure malaria through the discovery of new plasmepsin inhibitor compounds. One of the developing approaches is the in silico method. Methods:The chosen in silico screening method in this experiment is a structure-based screening using GOLD software and the Indonesian medicinal plants database.Results: From ten in silico screening runs, three of the compounds always ranked in the top ten. These three compounds are trimyristin, cyanidin 3,5-di-(6-malonylglucoside), and isoscutellarein 4'-methyl ether 8-(6"-n-butylglucuronide). Another compound that emerged with high frequency is cyanidin 3,5-di-(6-malonylglucoside). Conclusions:Based on the results obtained from this screening, 11 inhibitor candidates are expected to be developed as antimalarial. These compounds are trimyristin; cyanidin 3,5-di-(6-malonylglucoside); isoscutellarein 4'-methyl ether 8-(6"-n-butylglucuronide); cyanidin 3-(6"-malonylglucoside)-5-glucoside; multifloroside; delphinidin 3-(2-rhamnosyl-6-malonylglucoside); delphinidin 3-(6-malonylglucoside)-3',5'-di-(6-p-coumaroylglucoside); cyanidin 3-[6-(6-sinapylglucosyl)-2-xylosylgalactoside; kaempferol 3-glucosyl-(1-3)-rhamnosyl-(1-6)-galactoside; sanggenofuran A; and lycopene with a GOLD score range from 78.4647 to 98.2836. Two of them, Asp34 and Asp214, bind with all residues in the catalytic site of plasmepsin.

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Virtual screening of Indonesian herbal database as HIV-1 reverse transcriptase inhibitor

Cited by 22 publications

References 29 publications

Inhibition of HIV-1 Reverse Transcriptase of Selected Indonesia Medicinal Plants and Isolation of the Inhibitor from Erythrina variegata L. Leaves

Inhibition of HIV-1 Reverse Transcriptase of Selected Indonesia Medicinal Plants and Isolation of the Inhibitor from Erythrina variegata L. Leaves

Virtual Screening of Indonesian Herbal Database for Dna Methyltransferase Inhibitors

In Silico Screening of Antimalarial From Indonesian Medicinal Plants Database to Plasmepsin Target

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