scholarly journals Evaluation of Lens culinaris phytochemicals in binding to the 3C-like protease of SARS-CoV-2 – A molecular docking approach

2020 ◽  
Vol 72 ◽  
pp. 173-176
Author(s):  
Anamul Hasan ◽  
Rownak Jahan ◽  
Khoshnur Jannat ◽  
Tohmina Afroze Bondhon ◽  
Md Shahadat Hossan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Lens Culinaris ◽  
Docking Studies ◽  
Polyphenolic Compounds ◽  
Binding Affinities ◽  
The Novel ◽  
Molecular Docking Studies ◽  
Docking Approach ◽  
Novel Coronavirus ◽  
Scientific Attention

The novel coronavirus known as SARS-CoV-2 and the virus-induced disease COVID-19 has caused widespread concerns due to its contagiousness, fatality rate, and the absence of drug(s). This study investigated Lens culinaris and its phytochemicals, especially the flavonoids. The compounds were assessed through molecular docking studies for their binding abilities with the major protease of the novel coronavirus, SARS-CoV-2 (PDB: 6LU7). A total of 42 phytochemicals of Lens culinaris were analyzed through molecular docking studies for their binding affinities to COVID 3C-like protease. Of them, 23 compounds were found to have binding affinities to the protease of −7.5 kcal/mol or higher. Our study indicates that Lens culinaris contains a number of polyphenolic compounds as well as phytosterols, which can bind to the active site of the protease, and so merits further scientific attention on trials for use as potential anti-COVID-19 drugs.

Screening of Kabasura Kudineer Chooranam against COVID-19 through Targeting of Main Protease and RNA-Dependent RNA Polymerase of SARS-CoV-2 by Molecular Docking Studies

2020 ◽  
Vol 5 (4) ◽  
pp. 319-331
Author(s):  
K. Gopalasatheeskumar ◽  
Karthikeyen Lakshmanan ◽  
Anguraj Moulishankar ◽  
Jerad Suresh ◽  
D. Kumuthaveni Babu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Docking Studies ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Short Span ◽  
Novel Coronavirus

COVID-19 is the infectious pandemic disease caused by the novel coronavirus. The COVID-19 is spread globally in a short span of time. The Ministry of AYUSH, India which promotes Siddha and other Indian system of medicine recommends the use of formulation like Nilavembu Kudineer and Kaba Sura Kudineer Chooranam (KSKC). The present work seeks to provide the evidence for the action of 74 different constituents of the KSKC formulation acting on two critical targets. That is main protease and SARS-CoV-2 RNAdependent RNA polymerase target through molecular docking studies. The molecular docking was done by using AutoDock Tools 1.5.6 of the 74 compounds, about 50 compounds yielded docking results against COVID-19 main protease while 42 compounds yielded against SARSCoV- 2 RNA-dependent RNA polymerase. This research has concluded that the KSKC has the lead molecules that inhibits COVID-19’s target of main protease of COVID-19 and SARS-CoV-2 RNA-dependent RNA polymerase.

Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19)

2020 ◽  
Vol 23 ◽  
Author(s):  
Raghvendra Dubey ◽  
Kushagra Dubey
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Molegro Virtual Docker ◽  
Main Protease ◽  
Docking Approach ◽  
Inhibitory Potential ◽  
Efficacy Parameters ◽  
Novel Coronavirus

Background: COVID-19 which is known as the novel coronavirus was reported in December 2019 in Wuhan city, China and many of the patients have been contaminated by environmental contamination and transmission from one human to another. Objective: The objective of work is to establish the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid, against the deadly coronavirus (COVID-19) 6W63 (main protease 3Clpro protein) , using molecular docking approach. Method: The Molegro Virtual Docker software (MVD) with a 30 Å grid resolution was used. The structure was drawn by Chem 3D software and energy minimization was done by the MM2 force field. The protein 6W63 was downloaded from the protein data bank. Molegro modeller was used for score calculations. Result: The molecular docking studies were carried out on nicotiflorin and standard inhibitor X77, where standard inhibitor was observed in a co-crystallized state with main protease 3Clpro protein 6W63. The MolDock score, Rerank Sore and H Bond score of nicotiflorin and standard inhibitor X77 was observed as -173.058, -127.302, -21.9398 and -156.913,- 121.296,-5.7369, respectively. Conclusion: Molecular docking studies have confirmed that the affinity of flavonoid nicotiflorin with the amino acids of the viral protein 6W63 was relatively more than the standard X77. For the effective treatment of novel coronavirus COVID-19, the effectiveness of the identified flavonoid nicotiflorin can further be evaluated for safety and efficacy parameters at both preclinical and clinical stages.

scholarly journals Antiviral potential of phytoligands against chymotrypsin-like protease of COVID‐19 virus using molecular docking studies: An optimistic approach

2020 ◽  
Author(s):  
Ratish Chandra Mishra ◽  
Rosy Kumari ◽  
Shivani Yadav ◽  
Jaya Parkash Yadav
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Drug Repositioning ◽  
Docking Studies ◽  
The Novel ◽  
Lead Compounds ◽  
Recent Outbreak ◽  
Novel Coronavirus ◽  
The City ◽  
Ucsf Chimera

Abstract A recent outbreak of the novel coronavirus, COVID‐19, in the city of Wuhan, Hubei province, China and its ensuing worldwide spread have resulted in lakhs of infections and thousands of deaths. As of now, there are no registered therapies for treating the contagious COVID‐19 infections, henceforth drug repositioning may provide a fast way out. In the present study, a total of thirty-five compounds including commonly used anti-viral drugs were screened against chymotrypsin-like protease (3CLpro) using SwissDock. Interaction between amino acid of targeted protein and ligands was visualized by UCSF Chimera. Docking studies revealed that the phytochemicals such as cordifolin, anisofolin A, apigenin 7-glucoside, luteolin, laballenic acid, quercetin, luteolin-4-glucoside exhibited significant binding energy with the enzyme viz. - 8.77, -8.72, -8.36, -8.35, -8.13, -8.04 and -7.87 Kcal/Mol respectively. Therefore, new lead compounds can be used for drug development against SARS‐CoV‐2 infections.

scholarly journals Herbal Compounds from Syzygium aromaticum and Cassia acutifolia as a Shield against SARS-CoV-2 Mpro: a Molecular Docking Approach

2021 ◽  
Vol 11 (6) ◽  
pp. 14853-14865
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
New Drugs ◽  
In Vivo Studies ◽  
Syzygium Aromaticum ◽  
Amino Acid Residues ◽  
Ligand Interaction ◽  
Docking Approach ◽  
Novel Coronavirus

Novel coronavirus (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) was first identified in China in December 2019. Currently, the novel coronavirus disease 2019 (COVID-19) is the most infectious disease worldwide. In the absence of a vaccine or drug, herbal compounds may be used to treat or control this disease. To explore novel potent inhibitors that suppress this virus's growth, we performed molecular docking studies on SARS-CoV-2 Mpro using 17 effective herbal compounds, along with three reference drugs. Docking results showed that crategolic acid from Syzygium aromaticum (clove) had the highest binding affinity with SARS-CoV-2 Mpro protease, followed by sennoside (A, B, C, and D) compounds from Cassia acutifolia (Sana Makki). Crategolic acid and sennoside (A, B, C, and D) contain amino acid residues and hydrogen bonds involved in the protein-ligand interaction. The present study confirms that crategolic acid and sennoside represent the strongest potential inhibitors of SARS-CoV-2 Mpro. This study's results may help in vivo studies validate the usefulness of compounds from clove and Sana Makki in preparing herbal medicine for the treatment of COVID-19. This analysis supports the production of new drugs for the treatment and control of COVID-19.

scholarly journals Molecular Docking Studies of N-Acetyl Cysteine, Zinc Acetyl Cysteine and Niclosamide on SARS Cov 2 Protease and Its Comparison with Hydroxychloroquine

2020 ◽  
Author(s):  
Roopa Guthappa
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Sites ◽  
Antiviral Drug ◽  
Docking Studies ◽  
Binding Affinities ◽  
Binding Interaction ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Acetyl Cysteine

<p><b>To</b></p> <p><b>Respected Sir/Madam</b> </p> <p>Chemarxiv</p> <p> </p> <p><b>Respected Sir/Madam</b> </p> <p> </p> <p><b>Sub</b>: submission of preprint of article to Chemarxiv for online publication.</p> <p> </p> <p>I am herewith submitting the preprint of an article entitled “Molecular docking studies of N-acetyl cysteine, zinc acetyl cysteine and niclosamide on SARS Cov 2 protease and its comparison with hydroxychloroquine” for possible publication in “Chemarxiv”.</p> <p> </p> <p>In this article, we have evaluated the binding abilities of N-acetyl cysteine, zinc acetyl cysteine and niclosamide (antiviral drug) with SARS-COV-2 protease. All the four compounds investigated are effective and selectively bind to active sites of main protease. N-acetyl cysteine being a derivative of cysteine interacts with Cys-145, His-163, Gly-143 of COV-2 protease, zinc acetyl cysteine binds to Gly-143, Ser-144, Cys-145, Glu-166 of COV-2 protease and niclosamide bind to Glu-166, Cys-145, His 41 of main protease. The data has been compared with hydroxychloroquine which effectively binds to Cys-145, Glu-166, Arg-188. The binding affinities of N-acetyl cysteine, zinc-acetyl cysteine and niclosamide are -4.24, -4.29 and -7.5 kcal mol<sup>-1</sup> while for hydroxychloroquine it is -6.66 kcal mol<sup>-1</sup>. Niclosamide with its lowest binding energy interacts with His-41 and Cys-145 which may be the first molecule to show such binding interaction. The results indicate that N-acetyl cysteine, zinc-acetyl cysteine and niclosamide can also be explored for the treatment for SARS COV-2 as an alternative for hydroxychloroquine.</p> <p>I hope that the manuscript will full fill the journal’s requirements and will get accepted for publication. </p> <p>Thanking you</p> <p> </p> <p>With regards</p> <p>Roopa Guthappa</p> <p><a href="mailto:[email protected]">[email protected]</a></p>

scholarly journals Binding Ability Studies of Arginine, Citrulline, N-Acetyl Citrulline and Thiocitrulline with SARS Cov-2 Main Protease Using Molecular Docking Studies

2020 ◽  
Author(s):  
Ramesh Thimmasandra Narayan
Keyword(s):  
Molecular Docking ◽  
Active Sites ◽  
Docking Studies ◽  
The Other ◽  
Binding Affinities ◽  
Binding Ability ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Structural Analogues ◽  
Preferential Binding

<p><b>To</b></p> <p><b>Editor in Chief</b></p> <p><b>Chemarxiv</b><b></b></p> <p> </p> <p><b>Respected Sir/Madam</b> </p> <p> </p> <p><b>Subject</b>: submission of preprint of an article to ChemRxiv on molecular docking studies of arginine and its structural analogues on COV-19 for publication.</p> <p> </p> <p>I am herewith submitting the preprint of an article entitled “<b>Binding ability studies of arginine, citrulline, N-acetyl citrulline and thiocitrulline with SARS Cov-2 main protease using molecular docking studies.</b>” for publication as preprint in “ChemRxiv”.</p> <p>In this paper the binding abilities of arginine, citrulline, N-acetyl citrulline and thiocitrulline with SARS-COV-2 protease have been examined using molecular docking studies. The ligands used for docking has moderate binding affinity to active sites of main protease in terms of values. The binding affinities of these ligands are in the range of -3.1 to -5.1 kcal mol<sup>-1</sup>. All the ligands bind selectively to Cys-145 and also to other amino acids surrounding to it in the main protease. Of which arginine forms less number of weaker bonds compared to the other ligands, it by itself is a precursor for the formation of citrulline analogues with in the cell. Major advantage of using the above ligands is that in addition to its preferential binding these molecules also have the ability to enhance the immunity of the cells by the generation of nitric oxide in presence of enzymes thereby protecting them. Our results show that N-acetyl citrulline, citrulline, thiocitrulline and arginine may be used as a supplement during the treatment of SARS-COV-2.</p> <p> I request your good self to kindly accept the article and get it published as pre-print in your esteemed ChemRxiv. </p> <p>Thanking you</p> <p> </p> <p>With regards</p> <p> </p> <p>Ramesh T N</p> <p>([email protected])</p>

scholarly journals Molecular Docking Studies of some Antiviral and Antimalarial Drugs Via Bindings to 3CL-Protease and Polymerase Enzymes of the Novel Coronavirus (SARS-CoV-2)

2020 ◽  
Vol 10 (5) ◽  
pp. 6444-6459 ◽  
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Antimalarial Drugs ◽  
The Novel ◽  
Rapid Spread ◽  
Novel Virus ◽  
Novel Coronavirus ◽  
3Cl Protease ◽  
Insight Into

The rapid spread of the novel coronavirus (SARS-CoV-2) as a serious threat to the world public health is in dire need of finding potential therapeutic agents. Chinese have tested several antiviral and antimalarial drugs as potent inhibitors for the novel virus, such as remdesivir, chloroquine, hydroxychloroquine, umifenovir and favipiravir. In this study, we used the molecular docking models to study the binding interactions between these pharmaceuticals, as well as our proposed remdesivir analogue (AZCV-20) with the 3CLpro and RNA-dependent RNA polymerase (RdRp) of the SARS-CoV-2, using MEO and Autodock4 methods. Our study provides insight into the possible role of structural flexibility and efficacy during interactions between 3CLpro, RdRp and the drugs.

scholarly journals Molecular Docking Studies of N-Acetyl Cysteine, Zinc Acetyl Cysteine and Niclosamide on SARS Cov 2 Protease and Its Comparison with Hydroxychloroquine

2020 ◽  
Author(s):  
Roopa Guthappa
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Sites ◽  
Antiviral Drug ◽  
Docking Studies ◽  
Binding Affinities ◽  
Binding Interaction ◽  
Molecular Docking Studies ◽  
Main Protease ◽  
Acetyl Cysteine

<p><b>To</b></p> <p><b>Respected Sir/Madam</b> </p> <p>Chemarxiv</p> <p> </p> <p><b>Respected Sir/Madam</b> </p> <p> </p> <p><b>Sub</b>: submission of preprint of article to Chemarxiv for online publication.</p> <p> </p> <p>I am herewith submitting the preprint of an article entitled “Molecular docking studies of N-acetyl cysteine, zinc acetyl cysteine and niclosamide on SARS Cov 2 protease and its comparison with hydroxychloroquine” for possible publication in “Chemarxiv”.</p> <p> </p> <p>In this article, we have evaluated the binding abilities of N-acetyl cysteine, zinc acetyl cysteine and niclosamide (antiviral drug) with SARS-COV-2 protease. All the four compounds investigated are effective and selectively bind to active sites of main protease. N-acetyl cysteine being a derivative of cysteine interacts with Cys-145, His-163, Gly-143 of COV-2 protease, zinc acetyl cysteine binds to Gly-143, Ser-144, Cys-145, Glu-166 of COV-2 protease and niclosamide bind to Glu-166, Cys-145, His 41 of main protease. The data has been compared with hydroxychloroquine which effectively binds to Cys-145, Glu-166, Arg-188. The binding affinities of N-acetyl cysteine, zinc-acetyl cysteine and niclosamide are -4.24, -4.29 and -7.5 kcal mol<sup>-1</sup> while for hydroxychloroquine it is -6.66 kcal mol<sup>-1</sup>. Niclosamide with its lowest binding energy interacts with His-41 and Cys-145 which may be the first molecule to show such binding interaction. The results indicate that N-acetyl cysteine, zinc-acetyl cysteine and niclosamide can also be explored for the treatment for SARS COV-2 as an alternative for hydroxychloroquine.</p> <p>I hope that the manuscript will full fill the journal’s requirements and will get accepted for publication. </p> <p>Thanking you</p> <p> </p> <p>With regards</p> <p>Roopa Guthappa</p> <p><a href="mailto:[email protected]">[email protected]</a></p>

Synthesis, Characterization, Biological and Molecular Docking Studies of 1,3-Diphenyl-1H-pyrazole Terminated Imino Derivatives

2021 ◽  
Vol 33 (7) ◽  
pp. 1551-1556
Author(s):  
P.V. Sandhya ◽  
K.V. Muhammad Niyas ◽  
K.R. Haridas
Keyword(s):  
Molecular Docking ◽  
Mass Spectroscopy ◽  
Elemental Analysis ◽  
Biological Activities ◽  
Docking Studies ◽  
The Novel ◽  
Pyrazole Derivatives ◽  
Molecular Docking Studies

Herein, the novel pyrazole derivatives with imino moiety were synthsized, characterized using IR, NMR, mass spectroscopy, elemental analysis and screened their biological activities. Molecular docking studies were also carried out by the software Arguslab 4.0.1. The synthesized compounds showed moderate to good biological activities both experimentally and theoretically.

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