The Antiviral Effect of Indonesian Medicinal Plant Extracts Against Dengue Virus In Vitro and In Silico

Dengue infections are still a worldwide burden, especially in Indonesia. There is no specific medication against the dengue virus. Recently, many types of research have been conducted to discover a new drug for dengue virus using natural resource extracts. Indonesia, as a tropical country, has a wide biodiversity. There are several medicinal plants in Indonesia that are believed to possess anti-dengue activity, such as Myristica fatua, Cymbopogon citratus, and Acorus calamus plants. We conducted an in vitro laboratory experiment of several extracts from Indonesian herbs combined with in silico analysis. The extracts were evaluated for safety and antiviral activity in Huh7it-1 cell lines, using a single dose of 20 µg/mL and dose-dependent (5, 10, 20, 40, 80 and 160 µg/mL) of plant extracts against dengue virus serotype 2 (DENV-2) NGC strain. The DMSO 0.1% was used as a negative control. The cytotoxic aspect was assessed by counting the cell viability, while the antiviral activity was calculated by counting the average inhibition. The selectivity index (SI) of plant extracts were performed from a ratio of CC50/EC50 value. In silico analysis was conducted to determine the free energy of binding between NS5 of dengue virus with bioactive compounds contained in Myristica fatua, Cymbopogon citratus and Acorus calamus extract plants. We determined that all extracts were not toxic against Huh7it-1 cell lines. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed inhibition of DENV-2 at a dose of 20 µg/mL to 96.5%, 98.9%, and 122.7%, respectively. The dose-dependent effects showed that M. fatua has the best inhibition activity towards DENV-2. Molecular docking result showed that artesunic acid within M. fatua has the best free energy of binding (−7.2 kcal/mol), followed by homoegonol (−7.1 kcal/mol) which was slightly different from artesunic acid among others. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed prospective anti-dengue activities both in vitro and in silico. Future research should be conducted to find the pure extracts of all useful herbs as a new candidate of antiviral drug.

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In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

Current Chemical Biology ◽

10.2174/2212796812666180622103906 ◽

2019 ◽

Vol 13 (2) ◽

pp. 159-170 ◽

Cited By ~ 1

Author(s):

Vishal Ahuja ◽

Aashima Sharma ◽

Ranju Kumari Rathour ◽

Vaishali Sharma ◽

Nidhi Rana ◽

...

Keyword(s):

Production Process ◽

In Silico ◽

Xylose Reductase ◽

In Silico Analysis ◽

Emericella Nidulans ◽

Higher Temperature ◽

In Silico Characterization ◽

Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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In vitro and In silico Analysis of Pomegranate (Punica granatum L.) Fruit Powder as Pancreatic Lipase and α-Amylase Inhibitor

Journal of Physics Conference Series ◽

10.1088/1742-6596/1665/1/012004 ◽

2020 ◽

Vol 1665 ◽

pp. 012004

Author(s):

Andi Alfira Ratna F Dewi ◽

Muntholib ◽

Subandi

Keyword(s):

Pancreatic Lipase ◽

In Silico ◽

In Silico Analysis ◽

Punica Granatum ◽

Amylase Inhibitor ◽

Fruit Powder ◽

Punica Granatum L ◽

Silico Analysis

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Investigation of indole functionalized pyrazoles and oxadiazoles as anti-inflammatory agents: synthesis, in-vivo, in-vitro and in-silico analysis

Bioorganic Chemistry ◽

10.1016/j.bioorg.2021.105068 ◽

2021 ◽

pp. 105068

Author(s):

Devendra Kumar ◽

Ravi Ranjan Kumar ◽

Shelly Pathania ◽

Pankaj Kumar Singh ◽

Sourav Kalra ◽

...

Keyword(s):

In Silico ◽

In Silico Analysis ◽

Anti Inflammatory ◽

Silico Analysis

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New acetylphenol-based acyl thioureas broaden the scope of drug candidates for urease inhibition: synthesis, in vitro screening and in silico analysis

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2021.12.064 ◽

2021 ◽

Author(s):

Urage Zahra ◽

Sumera Zaib ◽

Aamer Saeed ◽

Mujeeb ur Rehman ◽

Ghulam Shabir ◽

...

Keyword(s):

In Silico ◽

In Silico Analysis ◽

In Vitro Screening ◽

Urease Inhibition ◽

Drug Candidates ◽

Silico Analysis

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IN SILICO STUDY OF THE ANTIMICROBIAL PROFILE OF β-CITRONELLOL: POTENTIAL AS AN ANTIFUNGAL

Periódico Tchê Química ◽

10.52571/ptq.v16.n32.2019.912_periodico32_pgs_894_898.pdf ◽

2019 ◽

Vol 16 (32) ◽

pp. 894-898

Author(s):

D. F. SILVA ◽

H. D. NETO ◽

M. D. L. FERREIRA ◽

A. A. O. FILHO ◽

E. O. LIMA

Keyword(s):

In Silico ◽

Fungal Infections ◽

In Silico Analysis ◽

Fungal Species ◽

In Silico Study ◽

Pass Online ◽

Therapeutic Alternatives ◽

Bioactivity Profile ◽

Silico Analysis

β-citronellol (3,7-dimethyl-6-octen-1-ol) has been exhibiting a number of pharmacological effects that creates interest about its antimicrobial potential, since several substances of the monoterpene class have already demonstrated to possess activity in this profile. In addition, the emergence of fungal species resistant to current pharmacotherapy poses a serious challenge to health systems, making it necessary to search for new effective therapeutic alternatives to deal with this problem. In this study, the antimicrobial profile of β-citronellol was analyzed. The Prediction of Activity Spectra for Substances (PASS) online software was used to study the antimicrobial activity of the β-citronellol molecule by the use of in silico analysis. In contrast, an in vitro antifungal study of this monoterpene was carried out. For this purpose, the Minimum Inhibitory Concentration (MIC) was determined by the microdilution technique in 96-well plates in Saboraud Dextrose Broth/RPMI against sensitive strains of Candida albicans, and this assay was performed in duplicate. In the in silico analysis of the antimicrobial profile, it was revealed that the monoterpene β-citronellol had a diverse antimicrobial bioactivity profile. For the antifungal activity, it presented a percentage value with Pa: 58.4% (predominant) and its MIC of 128 μg/mL, which was equivalent for all strains tested. The in silico study of the β-citronellol molecule allowed us to consider that the monoterpenoid is very likely to be bioactive against agents that cause fungal infections.

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In vitro evaluation and molecular dynamics, DFT guided investigation of antimalarial activity of ethnomedicinally used Coptis teeta Wall

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207324666210118095503 ◽

2021 ◽

Vol 24 ◽

Author(s):

Ashis Kumar Goswami ◽

Hemanta Kumar Sharma ◽

Neelutpal Gogoi ◽

Ankita Kashyap ◽

Bhaskar Jyoti Gogoi

Keyword(s):

Molecular Dynamics ◽

In Silico ◽

Density Functional ◽

Antimalarial Activity ◽

In Silico Analysis ◽

Dynamics Simulation ◽

Discovery Studio ◽

North East ◽

Silico Analysis

Background: Malaria is caused by different species of Plasmodium; among which P. falciparum is the most severe. Coptis teeta is an ethnomedicinal plant of enormous importance for tribes of north east India. Objective: In this study, the anti malarial activity of the methanol extracts of Coptis teeta was evaluated in vitro and lead identification via in silico study. Method: On the basis of the in vitro results, in silico analysis by application of different modules of Discovery Studio 2018 was performed on multiple targets of P. falciparum taking into consideration some of the compounds reported from C. teeta. Results: The IC50 of the methanol extract of Coptis teeta 0.08 µg/ml in 3D7 strain and 0.7 µg/ml in Dd2 strain of P. falciparum. From the docking study, noroxyhydrastatine was observed to have better binding affinity in comparison to chloroquine. The binding of noroxyhydrastinine with dihydroorotate dehydrogenase was further validated by molecular dynamics simulation and was observed to be significantly stable in comparison to the co-crystal inhibitor. During simulations it was observed that noroxyhydrastinine retained the interactions, giving strong indications of its effectiveness against the P. falciparum proteins and stability in the binding pocket. From the Density-functional theory analysis, the band gap energy of noroxyhydrastinine was found to be 0.186 Ha indicating a favourable interaction. Conclusion: The in silico analysis as an addition to the in vitro results provide strong evidence of noroxyhydrastinine as an anti malarial agent.

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Prediction Mechanism of Nevadensin as Antibacterial Agent against S. sanguinis: In vitro and In silico Studies

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207324666210707104440 ◽

2021 ◽

Vol 24 ◽

Author(s):

Aldina Amalia Nur Shadrina ◽

Yetty Herdiyati ◽

Ika Wiani ◽

Mieke Hemiawati Satari ◽

Dikdik Kurnia

Keyword(s):

Antibacterial Activity ◽

Molecular Docking ◽

Dental Caries ◽

Binding Affinity ◽

In Silico ◽

Antibacterial Agent ◽

In Silico Analysis ◽

Dna Gyrase ◽

Silico Analysis

Background: Streptococcus sanguinis can contribute to tooth demineralization, which can lead to dental caries. Antibiotics used indefinitely to treat dental caries can lead to bacterial resistance. Discovering new antibacterial agents from natural products like Ocimum basilicum will help combat antibiotic resistance. In silico analysis (molecular docking) can help determine the lead compound by studying the molecular interaction between the drug and the target receptor (MurA enzyme and DNA gyrase). It is a potential candidate for antibacterial drug development. Objective: The research objective is to isolate the secondary metabolite of O. basilicum extract that has activity against S. sanguinis through in vitro and in silico analysis. Methods: n-Hexane extract of O. basilicum was purified by combining column chromatography with bioactivity-guided. The in vitro antibacterial activity against S. sanguinis was determined using the disc diffusion and microdilution method, while molecular docking simulation of nevadensin (1) with MurA enzyme and DNA gyrase was performed used PyRx 0.8 program. Results: Nevadensin from O. basilicum was successfully isolated and characterized by spectroscopic methods. This compound showed antibacterial activity against S. sanguinis with MIC and MBC values of 3750 and 15000 μg/mL, respectively. In silico analysis showed that the binding affinity to MurA was -8.5 Kcal/mol, and the binding affinity to DNA gyrase was -6.7 Kcal/mol. The binding of nevadensin-MurA is greater than fosfomycin-MurA. Otherwise, Nevadensin-DNA gyrase has a weaker binding affinity than fluoroquinolone-DNA gyrase and chlorhexidine-DNA gyrase. Conclusion: Nevadensin showed potential as a new natural antibacterial agent by inhibiting the MurA enzyme rather than DNA gyrase.

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