Virtual Screening of Indonesian Herbal Database as HIV-1 Protease Inhibitor

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

doi:10.6026/97320630010052

Cited by 15 publications

(8 citation statements)

References 27 publications

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“…New HIV‐1 protease inhibitor candidates were recently predicted using virtual screening of plant‐derived small molecule libraries, and amaranthin was listed as the third best of all the candidates (Yanuar et al ., ); however, because this method was not empirically verified, we directly tested whether amaranthin inhibits HIV‐1 protease activity. Amaranthin and betanin were extracted and purified from the transformed BY‐2 cell line and added to a mixture of HIV‐1 protease, and HIV‐1 protease substrate, whose cleavage was monitored by HPLC.…”

Section: Resultsmentioning

confidence: 99%

“…These results suggested that the addition of one glucuronic acid moiety is important for HIV-1 protease inhibition. Amaranthin was previously selected as the third most effective potential inhibitor of HIV-1 protease activity through virtual screening of substances that bind to the binding site of saquinavir, an artificial HIV-1 protease inhibitor (Yanuar et al, 2014). This suggests that amaranthin binds to HIV-1 protease and inhibits its function through the same mechanism as saquinavir.…”

Section: Discussionmentioning

confidence: 99%

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Isolation of amaranthin synthetase from Chenopodium quinoa and construction of an amaranthin production system using suspension‐cultured tobacco BY‐2 cells

Imamura

Isozumi

Higashimura

et al. 2018

Plant Biotechnology Journal

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Summary Betalains are plant pigments primarily produced by plants of the order Caryophyllales. Because betalain possesses anti‐inflammatory and anticancer activities, it may be useful as a pharmaceutical agent and dietary supplement. Recent studies have identified the genes involved in the betalain biosynthesis of betanin. Amaranthin and celosianin II are abundant in the quinoa ( Chenopodium quinoa Willd.) hypocotyl, and amaranthin comprises glucuronic acid bound to betanin; therefore, this suggests the existence of a glucuronyltransferase involved in the synthesis of amaranthin in the quinoa hypocotyl. To identify the gene involved in amaranthin biosynthesis, we performed a BLAST analysis and phylogenetic tree analysis based on sequences homologous to flavonoid glycosyltransferase, followed by expression analysis on the quinoa hypocotyl to obtain three candidate proteins. Production of amaranthin in a transient Nicotiana benthamiana expression system was evaluated for these candidates and one was identified as having the ability to produce amaranthin. The gene encoding this protein was quinoa amaranthin synthetase 1 ( CqAmaSy1 ). We also created a transgenic tobacco bright yellow‐2 ( BY ‐2) cell line wherein four betalain biosynthesis genes were introduced to facilitate amaranthin production. This transgenic cell line produced 13.67 ± 4.13 μ m (mean ± SEM ) amaranthin and 26.60 ± 1.53 μ m betanin, whereas the production of isoamaranthin and isobetanin could not be detected. Tests confirmed the ability of amaranthin and betanin to slightly suppress cancer cell viability. Furthermore, amaranthin was shown to significantly inhibit HIV ‐1 protease activity, whereas betanin did not.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Isolation of amaranthin synthetase from Chenopodium quinoa and construction of an amaranthin production system using suspension‐cultured tobacco BY‐2 cells

Imamura

Isozumi

Higashimura

et al. 2018

Plant Biotechnology Journal

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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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“…Main antiviral activities References Allium cepa L. Alliaceae* Allium cepa has been patented to be used in HIV/AIDS treatment Yanuar et al (2014) Allium sativum L. Alliaceae* Allicin and other thiosulfinates exhibit activity of the herpes simplex virus type 1 and the para-influenza virus type 3. Webert et al (1992) The garlic extract had inhibitory effects on the coronavirus IBV (Infectious bronchitis virus) in the chickens' embryo Mohajer et al (2016 --…”

Section: Plant Namesmentioning

confidence: 99%

Reflection on medicinal plants, especially antivirals and how to reconsider ethnobotany as an interesting way for health preservation

Babili¹,

Lamade²,

Fabre³

et al. 2021

Afr. J. Pharm. Pharmacol.

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The medicinal plants, which are at the origin of the medical sciences, are gradually passing from the apothecary vials, from the handmade bags of the tradipraticians to the laboratories to provide countless new medicines synthesis models. Today, chemical drugs have replaced most herbal drugs in pharmacies. Empirical knowledge has been neglected as chemistry progressed. Yet 80% of the world's population is still being treated with plant-based medicines. Indeed, some parts of our earth still keep intact the medicinal knowledges, through tradition, culture and heritage preserved by the tradipraticians, who still practice all over the world. It is possible that in the face of the threat of epidemics, which are constantly putting us to the test, plant drugs are once again an important alternative to consider. Our article deals with 3 connected topics: an ethnobotanical survey (experimental result); the creation of a project model of ethnobotanical garden (experimental result); and a knowledge inventory on antiviral plants (bibliographical synthesis in the framework of scientific monitoring). There is a lot of knowledge that can be reinvested. Through some results of ethnobotanical surveys, an inventory of antiviral plants and the model of a project to set up ethnobotanical gardens in the city, re-appropriation of ethnobotanical knowledge will be shown to prove valuable for research and may be an alternative for the future for the preservation of the health of all.

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Virtual Screening of Indonesian Herbal Database as HIV-1 Protease Inhibitor

Cited by 15 publications

References 27 publications

Isolation of amaranthin synthetase from Chenopodium quinoa and construction of an amaranthin production system using suspension‐cultured tobacco BY‐2 cells

Isolation of amaranthin synthetase from Chenopodium quinoa and construction of an amaranthin production system using suspension‐cultured tobacco BY‐2 cells

Virtual Screening of Indonesian Herbal Database for Dna Methyltransferase Inhibitors

Reflection on medicinal plants, especially antivirals and how to reconsider ethnobotany as an interesting way for health preservation

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