Deciphering underlying mechanism of Sars-CoV-2 infection in humans and revealing the therapeutic potential of bioactive constituents from Nigella sativa to combat COVID19: in-silico study

Kapang Monascus sp. secara tradisional telah digunakan dalam fermentasi beras merah (angkak) yang bermanfaat sebagai pewarna makanan, pengawet makanan maupun obat-obatan. Saat ini, beras angkak telah menjadi suplemen makanan yang terkenal karena banyaknya senyawa bioaktif yang terkandung seperti monakolin, pigmen, asam dimerumat dan lain-lain. Tujuan penelitian ini adalah untuk menemukan metabolit sekunder kapang Monascus sp. yang meliputi senyawa monakolin dengan efek antikolesterol, pigmen dengan efek antikanker pada kanker payudara serta memprediksi toksisitas senyawa melalui studi in silico. Senyawa uji terdiri dari 14 senyawa monakolin dan 33 pigmen Monascus sp. Protein HMG KoA (3-hidroksi-3-metilglutaril koenzim A) reduktase digunakan sebagai reseptor antikolesterol sementara estrogen alfa, estrogen beta, dan aromatase digunakan sebagai reseptor antikanker. Perangkat lunak AutoDock digunakan untuk menganalisis kompleks struktural reseptor dengan senyawa uji. Prediksi toksisitas dilakukan menggunakan perangkat lunak ADMET predictor dan QSAR Toolbox. Prediksi toksisitas dan hasil docking menunjukkan bahwa asam monakolin L menunjukkan aktivitas antikolesterol yang baik terhadap HMG KoA reduktase; pigmen monaskin menunjukkan aktivitas antikanker yang selektif terhadap reseptor estrogen beta; dan keduanya diprediksi aman. Prediksi toksisitas senyawa monakolin dan pigmen Monascus sp. menunjukkan terdapat 7 senyawa monakolin yaitu 3-hidroksi-3,5-dihidromonakolin L, asam dihidromonakolin L, monakolin L, asam monakolin J, monakolin J, asam monakolin L , monakolin M, dan 5 pigmen Monascus sp. yaitu ankaflavin, monaskin, monaskopiridin A, monaskopiridin B dan monascuspiloin yang dinyatakan tidak toksik. Tujuh pigmen Monascus sp. yang terdiri dari monankarin A, monankarin B, monankarin C, monankarin D, monankarin E, monankarin F, dan monasfluol A bersifat positif mutagen, karsinogen dan toksik terhadap reproduksi. Hasil penelitian ini berpotensi dapat diaplikasikan untuk desain dan pengembangan obat antikolesterol dan antikanker.In Silico Study of Secondary Metabolites of Monascus sp. as A Candidate for Anticholesterol and Anticancer Drugs. The fungus Monascus sp. has traditionally been used to prepare red fermented rice (angkak) as a natural food colorant, food preservative or medicinal agent. Recently, it has become a popular dietary supplement due to many of its bioactive constituents such as monacolin compounds, pigments, and dimerumic acid, etc. These functional constituents also had been deemed to be provided with various health benefits. This research aims to find secondary metabolites of monacolin compounds with antihypercholesterolemic effect, Monascus sp. pigment with anticancer effect on breast cancer, and predict their toxicity through in silico study. The studied compounds consist of 14 monacolin compounds and 33 Monascus sp. pigments. HMG CoA (3-hydroxy-3-methylglutaryl Coenzyme A) reductase protein was used as antihypercholesterolemic receptor in which estrogen alfa, estrogen beta, and aromatase were used as anticancer receptors. AutoDock docking software was used to analyze structural complexes of the receptors with studied compounds. Toxicity prediction was done using ADMET predictor and QSAR Toolbox softwares. Toxicity prediction and docking results revealed that monacolin L acid exhibits good anticholesterol activity towards HMG CoA reductase; monascin pigment exhibits selective anticancer activity towards estrogen beta receptor; and both of them were predicted to be safe. Toxicity prediction of studied compounds showed that 7 monacolin compounds which are 3-hydroxy-3,5-dihydromonakolin L, dihydromonacolin L acid, monacolin L, monacolin J acid, monacolin J, monacolin L acid, monacolin M and 5 Monascus sp. pigments which are ankaflavin, monascin, monascopyridine A, monascopyridine B dan monascuspiloin are not toxic. Seven Monascus sp. pigments which are monankarin A, monankarin B, monankarin C, monankarin D, monankarin E, monankarin F and monasfluol A are mutagenic, carcinogenic and also reprotoxic. The research results could be useful for the design and development of the anticholesterol and anticancer drugs.

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Therapeutic Potential of Tuna Backbone Peptide and Its Analogs: An In Vitro and In Silico Study

Molecules ◽

10.3390/molecules26072064 ◽

2021 ◽

Vol 26 (7) ◽

pp. 2064

Author(s):

Varun Gopinatth ◽

Rufa L. Mendez ◽

Elaine Ballinger ◽

Jung Yeon Kwon

Keyword(s):

In Silico ◽

Bioactive Peptides ◽

Therapeutic Potential ◽

Antioxidant Activities ◽

Radical Scavenging ◽

Activity Assay ◽

In Silico Study ◽

The Impact ◽

Potent Inhibitory Activity

Tuna backbone peptide (TBP) has been reported to exert potent inhibitory activity against lipid peroxidation in vitro. Since this bears relevant physiological implications, this study was undertaken to assess the impact of peptide modifications on its bioactivity and other therapeutic potential using in vitro and in silico approach. Some TBP analogs, despite lower purity than the parent peptide, exerted promising antioxidant activities in vitro demonstrated by ABTS radical scavenging assay and cellular antioxidant activity assay. In silico digestion of the peptides resulted in the generation of antioxidant, angiotensin-converting enzyme (ACE), and dipeptidyl peptidase-IV (DPPIV) inhibitory dipeptides. Using bioinformatics platforms, we found five stable TBP analogs that hold therapeutic potential with their predicted multifunctionality, stability, non-toxicity, and low bitterness intensity. This work shows how screening and prospecting for bioactive peptides can be improved with the use of in vitro and in silico approaches.

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Safety, Stability, and Therapeutic Efficacy of Long-Circulating TQ-Incorporated Liposomes: Implication in the Treatment of Lung Cancer

Pharmaceutics ◽

10.3390/pharmaceutics14010153 ◽

2022 ◽

Vol 14 (1) ◽

pp. 153

Author(s):

Arif Khan ◽

Mohammed A. Alsahli ◽

Mohammad A. Aljasir ◽

Hamzah Maswadeh ◽

Mugahid A. Mobark ◽

...

Keyword(s):

Lung Cancer ◽

Binding Energy ◽

Drug Targets ◽

Therapeutic Potential ◽

Nigella Sativa ◽

Fold Increase ◽

Dependent Manner ◽

Bioactive Constituents

Thymoquinone (TQ), which is one of the main bioactive constituents of Nigella sativa seeds, has demonstrated its potential against various cancer models. The poor solubility of TQ in aqueous solution limits its uses in clinical application. The present study aimed to develop a novel formulation of TQ to increase its bioavailability and therapeutic potential with minimal toxicity. Polyethylene glycol (PEG)-coated DSPC/cholesterol comprising TQ liposomes (PEG-Lip-TQ) were prepared and characterized on various aspects. A computational investigation using molecular docking was used to assess the possible binding interactions of TQ with 12 prospective anticancer drug targets. The in vitro anticancer activity was assessed in A549 and H460 lung cancer cells in a time- and dose-dependent manner, while the oral acute toxicity assay was evaluated in silico as well as in vivo in mice. TQ docked to the Hsp90 target had the lowest binding energy of −6.05 kcal/mol, whereas caspase 3 was recognized as the least likely target for TQ with a binding energy of −1.19 kcal/mol. The results showed 96% EE with 120 nm size, and −10.85 mv, ζ-potential of PEG-Lip-TQ, respectively. The cell cytotoxicity data demonstrated high sensitivity of PEG-Lip-TQ and a several fold decrease in the IC50 while comparing free TQ. The cell cycle analysis showed changes in the distribution of cells with doses. The in vivo data revealed an ~9-fold increase in the LD50 of PEG-Lip-TQ on free TQ as an estimated 775 and 89.5 mg/kg b.w, respectively. This study indicates that the pharmacological and efficacy profile of PEG-lip-TQ is superior to free TQ, which will pave the way for an exploration of the effect of TQ formulation in the treatment of lung cancer in clinical settings.

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The Effect of Glargine As Basal Insulin Support for Recovering Critically Ill and High Dependency Unit Patients: An in Silico Study

7th IFAC Symposium on Modelling and Control in Biomedical Systems ◽

10.3182/20090812-3-dk-2006.00009 ◽

2009 ◽

Author(s):

Lin, Jessica

Keyword(s):

Critically Ill ◽

In Silico ◽

Basal Insulin ◽

High Dependency Unit ◽

High Dependency ◽

In Silico Study

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Critical Review on the Chemical Aspects of Cannabidiol (CBD) and Harmonization of Computational Bioactivity Data

Current Medicinal Chemistry ◽

10.2174/0929867327666200210144847 ◽

2020 ◽

Vol 28 (2) ◽

pp. 213-237 ◽

Cited By ~ 5

Author(s):

Andrea Mastinu ◽

Giovanni Ribaudo ◽

Alberto Ongaro ◽

Sara Anna Bonini ◽

Maurizio Memo ◽

...

Keyword(s):

In Silico ◽

Cannabis Sativa ◽

Therapeutic Potential ◽

The Novel ◽

In Silico Studies ◽

Computational Data ◽

Synthetic Approaches ◽

Analytical Approaches ◽

Yield Sensitivity ◽

Therapeutic Profile

: Cannabidiol (CBD) is a non-psychotropic phytocannabinoid which represents one of the constituents of the “phytocomplex” of Cannabis sativa. This natural compound is attracting growing interest since when CBD-based remedies and commercial products were marketed. This review aims to exhaustively address the extractive and analytical approaches that have been developed for the isolation and quantification of CBD. Recent updates on cutting-edge technologies were critically examined in terms of yield, sensitivity, flexibility and performances in general, and are reviewed alongside original representative results. As an add-on to currently available contributions in the literature, the evolution of the novel, efficient synthetic approaches for the preparation of CBD, a procedure which is appealing for the pharmaceutical industry, is also discussed. Moreover, with the increasing interest on the therapeutic potential of CBD and the limited understanding of the undergoing biochemical pathways, the reader will be updated about recent in silico studies on the molecular interactions of CBD towards several different targets attempting to fill this gap. Computational data retrieved from the literature have been integrated with novel in silico experiments, critically discussed to provide a comprehensive and updated overview on the undebatable potential of CBD and its therapeutic profile.

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Nigella sativa and Cancer: A Review Focusing on Breast Cancer, Inhibition of Metastasis and Enhancement of Natural Killer Cell Cytotoxicity

Current Pharmaceutical Biotechnology ◽

10.2174/1389201021666200430120453 ◽

2020 ◽

Vol 21 (12) ◽

pp. 1176-1185 ◽

Cited By ~ 1

Author(s):

Tuğcan Korak ◽

Emel Ergül ◽

Ali Sazci

Keyword(s):

Breast Cancer ◽

Natural Killer Cells ◽

Natural Killer ◽

Therapeutic Potential ◽

Nigella Sativa ◽

Killer Cell ◽

B Cell Lymphoma ◽

Killer Cells ◽

Natural Killer Cell Cytotoxicity ◽

Endothelial Growth Factor

Background: In the last decade, there have been accumulating data that the use of medicinal plants could bring additional benefits to the supportive treatment of various diseases. Nigella sativa (N. sativa, family Ranunculaceae) is one of these plants that has attracted considerable interest. The extracts and seeds of N. sativa and its active component thymoquinone have been studied extensively and the results suggest that N. sativa might carry some therapeutic potential for many diseases, including cancer. Methods: The selection criteria for references were applied through Pubmed with “N. sativa and cancer”, “N. sativa and breast cancer”, “N. sativa and metastasis”, “N. sativa and cytotoxicity of natural killer cells”. The pathway analysis was performed using the PANTHER tool by using five randomly selected N. sativa affected genes (Cyclin D1, P53, p21 protein (Cdc42/Rac) activated kinase 1 (PAK1), B-cell lymphoma 2 (Bcl-2) and vascular endothelial growth factor (VEGF)) in order to elucidate further potentially affected signaling pathways. Results: The aim of this review was to summarize studies regarding the effects of N. sativa in cancer generally, with a focus on breast cancer, its anti-metastatic effects, and how N. sativa modulates the cytotoxicity of Natural Killer cells that play a crucial role in tumor surveillance. Conclusion: In summary, the data suggest that N. sativa might be used for its anti-cancer and antimetastatic properties and as an immune system activator against cancer.

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In Silico Study of Structural and Geometrical Requirements of Natural Sesquiterpene Lactones with Trypanocidal Activity

Mini-Reviews in Medicinal Chemistry ◽

10.2174/13895575113139990066 ◽

2013 ◽

Vol 13 (10) ◽

pp. 1407-1414 ◽

Cited By ~ 10

Author(s):

L. Fabian ◽

V. Sulsen ◽

F. Frank ◽

S. Cazorla ◽

E. Malchiodi ◽

...

Keyword(s):

In Silico ◽

Sesquiterpene Lactones ◽

Trypanocidal Activity ◽

In Silico Study

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In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

Current Proteomics ◽

10.2174/1570164616666190401204009 ◽

2020 ◽

Vol 17 (1) ◽

pp. 40-50

Author(s):

Farzane Kargar ◽

Amir Savardashtaki ◽

Mojtaba Mortazavi ◽

Masoud Torkzadeh Mahani ◽

Ali Mohammad Amani ◽

...

Keyword(s):

Phylogenetic Tree ◽

In Silico ◽

Alpha Helix ◽

In Silico Analysis ◽

Glycogen Storage ◽

Docking Studies ◽

Random Coil ◽

Special Topic ◽

Industrial Biotechnology ◽

In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

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