Secondary metabolites protect against metal and metalloid stress in rice: an in silico investigation using dehydroascorbate reductase

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
Shuvasish Choudhury ◽  
Debojyoti Moulick ◽  
Muhammed Khairujjaman Mazumder
Keyword(s):  
Secondary Metabolites ◽  
In Silico ◽  
Dehydroascorbate Reductase

scholarly journals IN SILICO STUDIES OF THE SECONDARY METABOLITES OF SOLANUM TORVUM SW. FOR THEIR ANTIASTHMATIC ACTIVITY

2017 ◽  
Vol 9 (4) ◽  
pp. 38
Author(s):  
Soorya R. ◽  
Dhamodaran P. ◽  
Rajesh Kumar R. ◽  
Duraisamy B.
Keyword(s):  
Methyl Ester ◽  
Secondary Metabolites ◽  
Ethyl Ester ◽  
In Silico ◽  
Methanolic Extract ◽  
Acid Ethyl Ester ◽  
Docking Studies ◽  
Receptor Protein ◽  
Solanum Torvum ◽  
In Silico Studies

Objective: Solanum torvum Sw., Family: Solanaceae, commonly known as Turkey Berry is used by the traditional tribes for the treatment of cold, cough, tuberculosis, hepatotoxicity, cancer, etc. The action of the plant towards the treatment of these diseases has been proven except for asthma. The present study is to prove the antiasthmatic activity of methanolic extract and the secondary metabolites of Solanum torvum Sw using in silico docking studies in compare to reference standard Dexamethasone, a synthetic cortisone derivative.Methods: The GC-MS analysis of the dried methanolic extract of the dried fruits of Solanum torvum Sw. and the total saponin fraction has been carried out to know the important moieties that are responsible for the antiasthmatic activity.Results: The results from the docking studies showed that the compounds Cholesta-5,7,9-(11)-trien-3-ol,4,4-dimethyl, (3á); Lanosta-7,9-(11),20-triene-3α, 18-diol, diacetate and Cholestan-26-oic acid,3,7,12,24-tetrakis (acetyloxy), methyl ester, (3à,5á,7à,12à) were found to have significant scores of-6.8,-6.9 and-6.9 respectively towards Glucocorticoid receptor protein (Gr), (PDB id: 4UDC) which is very similar to the affinity of the standard (-7.1). These compounds passed the drug-likeness test. A modification in the structure can be brought, which makes the compounds more potent. The compounds 9, 12-Octadecadienoic acid, ethyl ester; Hexadecanoic acid, ethyl ester; 9-Octadecenoic acid (Z), methyl ester; Oxacycloheptadec-8-en-2-one, (8Z) have passed the Blood Brain Barrier (BBB) filter of the drug-likeness test.Conclusion: The antiasthmatic activity of the drug may be due to the similarity with the structure of Dexamethasone. Further research can be carried out in order to improve the clinical significance of these extracts and its metabolites.

scholarly journals In silico methods for linking genes and secondary metabolites: The way forward

2016 ◽  
Vol 1 (2) ◽  
pp. 80-88 ◽  
Author(s):  
Shradha Khater ◽  
Swadha Anand ◽  
Debasisa Mohanty
Keyword(s):  
Secondary Metabolites ◽  
In Silico ◽  
In Silico Methods ◽  
The Way

scholarly journals In Silico Studies on Fungal Metabolite against Skin Cancer Protein (4,5-Diarylisoxazole HSP90 Chaperone)

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Saravanakumar Kandasamy ◽  
Sunil Kumar Sahu ◽  
Kathiresan Kandasamy
Keyword(s):  
Methyl Ester ◽  
Skin Cancer ◽  
Secondary Metabolites ◽  
In Silico ◽  
Octadecenoic Acid ◽  
Mangrove Sediment ◽  
Heptadecanoic Acid ◽  
Standard Drug ◽  
Methyl Methyl ◽  
In Silico Studies

This work was to find out the dominant secondary metabolites derived from the fungus Trichoderma and to test them against skin cancer protein. The metabolites were extracted in 80% methanol from the fungal biomass of Trichoderma isolated from mangrove sediment. The crude methanol extract was purified and analysed for the secondary metabolites by GC-MS. Three predominant compounds (heptadecanoic acid, 16 methyl-, methyl ester; 9,12-octadecadienoic acid; cis-9-octadecenoic acid) identified in the extracts were screened against the skin cancer protein (Hsp90) by in-silico docking method. Of the compounds, heptadecanoic acid, 16 methyl, methyl ester was the most potent having the docking score of  Kcal/mol. This value was better than the standard drug “dyclonine”. This work recommends the heptadecanoic acid, 16 methyl, methyl ester for further in vitro and in vivo studies towards its development as anticancer drug.

scholarly journals Cytotoxicity, Antimicrobial, and In Silico Studies of Secondary Metabolites From Aspergillus sp. Isolated From Tecoma stans (L.) Juss. Ex Kunth Leaves

2021 ◽  
Vol 9 ◽  
Author(s):  
Heba E. Elsayed ◽  
Reem A. Kamel ◽  
Reham R. Ibrahim ◽  
Ahmed S. Abdel-Razek ◽  
Mohamed A. Shaaban ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
In Silico ◽  
Therapeutic Potential ◽  
Antibacterial Activities ◽  
Antimicrobial Activities ◽  
Kinase Domain ◽  
Binding Score ◽  
In Silico Studies ◽  
Binding Cleft ◽  
Aspergillus Sp

Endophytes are prolific producers of privileged secondary metabolites with diverse therapeutic potential, although their anticancer and antimicrobial potential still have a room for further investigation. Herein, seven known secondary metabolites namely, arugosin C (1), ergosterol (2), iso-emericellin (3), sterigmatocystin (4), dihydrosterigmatocystin (5), versicolorin B (6), and diorcinol (7) were isolated from the rice culture of Aspergillus sp. retrieved from Tecoma stans (L.) Juss. ex Kunth leaves. Their anticancer and antimicrobial activities were evaluated in MTT and agar well diffusion assays, respectively. The cytotoxicity results showed that metabolite 3 displayed the best viability inhibition on the MCF-7 breast cancer cells with IC50 = 225.21 µM, while 5 on the HepG2 hepatocellular carcinoma cells with IC50 = 161.81 µM. 5 demonstrated a 60% apoptotic mode of cell death which is virtually correlated to its high docking affinity to Hsp90 ATP binding cleft (binding score −8.4 Kcal/mol). On the other side, metabolites 4 and 5 displayed promising antimicrobial activity especially on Pseudomonas aeruginosa with MIC = 125 μg/ml. The observed effect may be likely related to their excellent in silico inhibition of the bacterial DNA-gyrase kinase domain (binding score −10.28 Kcal/mol). To the best of our knowledge, this study is the first to report the promising cytotoxic and antibacterial activities of metabolites 3, 4, and 5 which needs further investigation and renovation to therapeutic leads.

scholarly journals Identification and in silico screening of biologically active secondary metabolites isolated from Trichoderma harzianum

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Abhishek Mishra ◽  
Supriya Dixit ◽  
Ved Ratan ◽  
Mukesh Srivastava ◽  
Shubha Trivedi ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Trichoderma Harzianum ◽  
In Silico ◽  
Biologically Active ◽  
In Silico Screening

scholarly journals In-Silico Analysis of Natural Products That Modulates Enzymes of Diabetic Target

2020 ◽  
Author(s):  
Babita Aryal ◽  
Saroj Basnet ◽  
Bishnu P. Marasini ◽  
Karan Khadayat ◽  
Darbin Kumar Poudel ◽  
...  
Keyword(s):  
Natural Products ◽  
Secondary Metabolites ◽  
Aldose Reductase ◽  
In Silico ◽  
Metabolic Diseases ◽  
In Silico Analysis ◽  
Metabolic Enzymes ◽  
Alpha Amylase ◽  
Synthetic Drugs ◽  
Alpha Glucosidase

Metabolic enzymes are often targeted for drug development programs of metabolic diseases such as diabetes and its complications. Many secondary metabolites isolated from natural products have shown therapeutic action against these enzymes. However, some commercially available synthetic drugs have shown unfriendly impacts with various side effects. Thus, this research has focused on a comprehensive study of secondary metabolites showing better inhibitory activities towards metabolic enzymes such as α-amylase, α-glucosidase, aldose reductase, and lipase. Further receptor-based virtual screening was performed against the various secondary metabolites database designed in-silico. Using Gold combined with subsequent post-docking analyses, the score was obtained as methyl xestospongic ester (Gold score 65.83), 2,″4″-O-diacetylquercitrin (Gold score 65.15), kaempferol-3-O-neohesperidoside (Gold score 53.37) and isosalvianolic acid C methyl ester (Gold score 53.44) for lipase, aldol reductase, α-amylase, and α-glucosidase, respectively. Besides, vitexin and isovitexin for α-amylase; N-trans-Caffeoyl-tyramin for α-glucosidase; purpurolide F and schaftoside for lipase; acteoside and orientin for aldose reductase could be potential drugs for respective enzymes based on in-silico analyses, supported by experimental IC50 values reported. They could bind to the competitive sites of the various targets of metabolic enzymes, and finally, toxicity analysis using ProTox-II was also performed.

scholarly journals ADMET and pharmaceutical activity analysis of caffeic acid diversities by in silico tools

2020 ◽  
Vol 9 (1) ◽  
pp. 840-848
Keyword(s):  
Secondary Metabolites ◽  
Chlorogenic Acid ◽  
Caffeic Acid ◽  
In Silico ◽  
Activity Analysis ◽  
Molecular Structures ◽  
Oral Consumption ◽  
Wide Range ◽  
Neochlorogenic Acid ◽  
Pharmaceutical Activity

Caffeic acid diversities are widely considered as one of the most pharmaceutical secondary metabolites to study for treating a wide range of disorders and diseases. In this paper, toxicity, ADME, and pharmaceutical activity of 16 compounds of the Caffeic acid diversities, are analyzed by Toxtree software and Molinspiration website, respectively. According to the results, it can be concluded that Caffeoylmalic acid and Dactylifric acid could be considered as the safest and the most applicable compounds. It might be suggested that modification of molecular structures of Chlorogenic acid and Neochlorogenic acid could be useful for becoming low toxic and more applicable compounds for oral consumption.

scholarly journals Antiproliferative, cholinesterase and phosphodiesterase inhibitory activity of the DCM sub-extract of Uvaria alba: In vitro and in silico perspectives

2020 ◽  
Author(s):  
Mark Tristan J. Quimque ◽  
Kin Israel R. Notarte ◽  
arianne letada ◽  
Rey Arturo T. Fernandez ◽  
Kirstin Rhys S. Pueblos ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Michael Addition ◽  
In Silico ◽  
Protein Complexes ◽  
Chemical Constituents ◽  
Myelogenous Leukemia ◽  
Btb Domain ◽  
Dynamics Simulations ◽  
Potential Inhibitors

<div>Aims: To evaluate the in vitro antiproliferative, anticholinesterase and anti-phosphodiesterase activities of the sub-extracts of Uvaria alba (family Annonaceae) and explore putative binding mechanisms of its chemical constituents in silico. <br></div><div><br></div><div>Main methods: U. alba sub-extracts, obtained by solvent-solvent partition, were subjected to antiproliferative and cytotoxicity screening against chronic myelogenous leukemia (K-562) and human cervical cancer (HeLa) cells, respectively. Inhibitory assays against acetylcholinesterase (AChE) and phosphodiesterase (PDE4 B2) enzymes were also performed. The dichloromethane sub-extract (UaD) was chemically profiled using LC-HR-ESIMS-QToF to identify secondary metabolites 1–18. Molecular docking and molecular dynamics simulations were performed to determine the affinity of the putatively annotated metabolites against PDE4 B2B, AChE, ubiquitin specific peptidase 14 (USP14), and Kelch-like ECH-associated protein 1 (Keap1). In addition, DFT calculations were also performed to demonstrate Michael addition reaction between electrophilic cytotoxic metabolites and Cys151 of the Keap1-BTB domain. <br></div><div><br></div><div>Key findings: UaD showed antiproliferative and cytostatic activities against K-562 and HeLa, respectively, and inhibitory activities against AChE and PDE4 B2. Meanwhile, its polyphenolic constituents 3-(3,4-dihydroxybenzyl)-3’,4’,6-trihydroxy-2,4-dimethoxychalcone (8) and grandifloracin (15) showed favorable binding to AChE and Keap1-BTB domain, respectively. The most electrophilic and kinetically stable grandifloracin (15), favorably formed a beta-addition adduct with the Cys151 of Keap1 via Michael addition. The top-ranked ligand-protein complexes attained dynamic stability at 50-ns simulations with high free energy of binding. The top-ranked compounds also conferred favorable in silico pharmacokinetic properties. <br></div><div><br></div><div>Significance: The study highlights the role of U. alba secondary metabolites as potential inhibitors against the aforementioned target proteins in an effort to discover new drug leads for cancer and Alzheimer’s.</div>

In Silico Prediction, Computational Physico Chemical Analysis in Gymnemic Acids

2021 ◽  
Vol 11 (5) ◽  
Author(s):  
Indumathi Dhanapal ◽  
Sujatha Ramasamy ◽  
Sundaram Palanisamy Shanmuga
Keyword(s):  
Secondary Metabolites ◽  
Chemical Analysis ◽  
In Silico ◽  
Structural Information ◽  
Target Prediction ◽  
Study Drug ◽  
Medicinal Herb ◽  
Therapeutic Applications ◽  
Physico Chemical ◽  
In Silico Models

Gymnema sylvestre (Asclepiadaceae) also known as ‘gurmar’ or ‘sugar destroyer’ is a woody, climbing traditional medicinal herb which has many therapeutic applications in the Ayurvedic system of medicine. We present an overview of the most important databases with 2 gymnemic acid structural information about drugs and drug candidates, and of databases with relevant properties. Access to experimental data and numerical methods for selecting and utilizing these data is crucial for developing accurate predictive in silico models. Many interesting predictive methods for classifying the suitability of chemical compounds as potential drugs, as well as for predicting their physico-chemical and ADMET properties have been proposed in recent years. The gymnemic acids act as therapeutic agents and play vital roles in many therapeutic applications. Gymnemic acids are thought to be responsible for its anti-diabetic activity and are the major component of an extract shown to stimulate insulin release. It is also screened for bioavailability study, physicochemical study, drug likeness study, medicinal chemical analysis and target prediction. These methods are discussed, and some possible future directions in this rapidly developing field are also described. The commercial exploitation of this plant and its secondary metabolites are some of the major perspectives of this rare medicinal herb. The focus of the present study is to achieve the potential of therapeutic value of this herb its mechanism,and the action of their secondary metabolites.

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