scholarly journals Identification of a Plausible Inhibitor of SARS-Cov 2 Protease (6LU7) and the Spike Envelope Glycoprotein (6MOJ) from Active Compounds of Nigella sativa: An In-silico Approach

2021 ◽  
Vol 11 (4) ◽  
pp. 3934-3943
Keyword(s):  
Envelope Glycoprotein ◽  
In Silico ◽  
Nigella Sativa ◽  
Specific Treatment ◽  
Antiviral Protein ◽  
Main Protease ◽  
Docking Approach ◽  
Respiratory Tract Illness ◽  
Potential Inhibitors ◽  
In Silico Molecular Docking

SARS-CoV-2, the recent disease outbreak causing respiratory tract illness, raised as the global health burden that has caused significant morbidity and mortality worldwide. In the ongoing transmission of this pandemic virus, its control is very challenging due to the lack of specific treatment. The compelling situation feels the necessity for the use of all assets to cure this disease. SARS-CoV-2, main protease, and spike envelope glycoprotein are important determinants in the infectious virus process, and targeting these proteins is gaining importance in anti-CoV drug design. In these conceptual circumstances, an attempt has been made to suggest an in silico molecular docking approach to identify new probable leads from the active constituents from Nigella sativa L against protein target main protease(6LU7) and spike envelope glycoprotein(6MOJ). Our results indicate that Nigellicine and Nigellicimine N-Oxide towards main protease and Nigellamine A5 and Nigellamine A1 towards spike glycoprotein has potential antiviral protein binding affinity among others forming good interactions. Thus, these compounds may be considered to be potential inhibitors against SARS-CoV-2 but need to be explored for further evaluations are recommended.

scholarly journals In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis

2021 ◽  
pp. 100969
Author(s):  
Azza H. Harisna ◽  
Rizky Nurdiansyah ◽  
Putri H. Syaifie ◽  
Dwi W. Nugroho ◽  
Kurniawan E. Saputro ◽  
...  
Keyword(s):  
In Silico ◽  
Spike Protein ◽  
Main Protease ◽  
Potential Inhibitors

scholarly journals An Integrative in Silico Drug Repurposing Approach for Identification of Potential Inhibitors of SARS‐CoV‐2 Main Protease

2021 ◽  
Author(s):  
Nemanja Djokovic ◽  
Dusan Ruzic ◽  
Teodora Djikic ◽  
Sandra Cvijic ◽  
Jelisaveta Ignjatovic ◽  
...  
Keyword(s):  
In Silico ◽  
Drug Repurposing ◽  
Main Protease ◽  
Potential Inhibitors

In silico drug design: development of new pyrimidine-based benzo-thiazole derivatives, selective for CDK2

2021 ◽  
Vol 18 ◽  
Author(s):  
Rania Kasmi ◽  
Larbi Elmchichi ◽  
Abdellah El Aissouq ◽  
Mohammed Bouachrine ◽  
Abdelkrim Ouammou
Keyword(s):  
Colon Cancer ◽  
Molecular Docking ◽  
In Silico ◽  
3D Qsar ◽  
Bioactive Molecules ◽  
Cancer Drugs ◽  
Qsar Studies ◽  
Benzothiazole Derivatives ◽  
Docking Approach ◽  
Potential Inhibitors

Backgroud: Kinases are proteins that control many biological functions. They are involved in cellular regulation, and many of them are deregulated in cancer proliferation. The evidence of this deregulation in many pathologies served as the origin of kinases as a therapeutic class and constitutes the motive that leads numerous teams to search for inhibitors of these targets. Objective: Based on 3D-QSAR studies and the molecular docking approach, we have developed new potential inhibitors that could be optimized and transformed into colon cancer drugs. Objective: Based on 3D-QSAR studies and the molecular docking approach, we have developed new potential inhibitors that could be optimized and transformed into colon cancer drugs. Method: To design new bioactive molecules and study their interactions with the cyclin-depend kinase type 2 (CDK2) enzyme, we used two virtual screening methods: 3D-QSAR modeling and molecular docking on a series of 28 pyrimidine-based benzothiazole derivatives. Results: To develop models (3D QSAR) we used CoMFA and CoMSIA techniques using SYBYL-X2.0 molecular modeling software. The statistical parameters reveal that the good CoMFA model displays (Q²= 0.587; R²= 0.895) and that of CoMSIA displays (Q²= 0.552; R²= 0.768) which are considered to be very good internal prediction values, while an external validation of a test series of 5 compounds not included in the model development series gives R²test values of 0.56 for CoMFA and R²test values of 0.51 for CoMSIA. The molecular docking approach with AutoDockTools-1.5.6 is introduced in this work to enrich the interpretations extracted from the CoMFA and CoMSIA contour maps, and to provide an in silico research method for the most favorable mode of interaction of an inhibitor within its receptor (CDK2). Conclusion: We have constructed and validated a quantitative 3D model of structure-activity relation-ships of pyrimidine-based benzothiazole derivatives as CDK2 inhibitors. This model allows us to identify the nature and position of the groups that enhance the activity, giving us directions to discover new, more powerful molecules in a limited time.

scholarly journals Identification of Bioactive Phytoconstituents from the Plant Euphorbia hirta as Potential Inhibitor of SARS-CoV-2: an In-Silico Approach

2021 ◽  
Vol 12 (2) ◽  
pp. 1385-1396
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Biological Activities ◽  
Specific Treatment ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Standard Drug ◽  
Euphorbia Hirta ◽  
Main Protease

Currently, the entire globe is under the deadliest pandemic of Covid-19 caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). At present, no specific treatment is available to combat COVID-19 infection. Euphorbia hirta (Euphorbiaceae) have been reported for a variety of biological activities, including antiviral. The present investigation aimed to identify potential phytoconstituents of the plant E. hirta from the category flavonoids and coumarins against the SARS-CoV-2 using in silico approach. The molecular docking studies were performed using two different targets of SARS-CoV-2, namely Main protease (Mpro; PDB ID: 6M2N) and RNA-dependent RNA polymerase (RdRp; PDB ID: 7BW4). Based on the molecular docking study in comparison with standard drug, four compounds, namely Euphrobianin, Quercetin, 3-o-alpha-rhamnoside, Isoquercitrin, and rutin, were screened against the target Mpro. Three phytoconstituents, euphorbianin, myricetin, and rutin, were screened against the target RdRp. In the in silico toxicity studies of screened phytoconstituents, except myrectin all were predicted safe. Results of euphorbianin and rutin were found more interesting as both compounds had high binding affinity against both targets. Finally, we want to conclude that euphrobianin, quercetin 3-o-alpha-rhamnoside, isoquercitrin, and rutin could be further explored rapidly as they may have the potential to fight against COVID-19.

scholarly journals The dolabellane diterpenes as potential inhibitors of the SARS-CoV-2 main protease: molecular insight of the inhibitory mechanism through computational studies

RSC Advances ◽  
2021 ◽  
Vol 11 (62) ◽  
pp. 39455-39466
Author(s):  
Nanik Siti Aminah ◽  
Muhammad Ikhlas Abdjan ◽  
Andika Pramudya Wardana ◽  
Alfinda Novi Kristanti ◽  
Imam Siswanto ◽  
...  
Keyword(s):  
In Silico ◽  
Computational Studies ◽  
Inhibitory Mechanism ◽  
Main Protease ◽  
Potential Inhibitors

An investigation on dolabellane derivatives to understand their potential in inhibiting the SARS-CoV-2 main protease (3CLpro) using an in silico approach.

scholarly journals In silico Screening of Natural Compounds as Potential Inhibitors of SARS-CoV-2 Main Protease and Spike RBD: Targets for COVID-19

2021 ◽  
Vol 7 ◽  
Author(s):  
Divya M. Teli ◽  
Mamta B. Shah ◽  
Mahesh T. Chhabria
Keyword(s):  
Binding Free Energy ◽  
Treatment Options ◽  
Natural Compounds ◽  
Pharmacokinetic Parameters ◽  
Main Protease ◽  
Glide Docking ◽  
Docking Approach ◽  
Covalent Docking ◽  
Dual Inhibitors ◽  
Potential Inhibitors

Historically, plants have been sought after as bio-factories for the production of diverse chemical compounds that offer a multitude of possibilities to cure diseases. To combat the current pandemic coronavirus disease 2019 (COVID-19), plant-based natural compounds are explored for their potential to inhibit the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the cause of COVID-19. The present study is aimed at the investigation of antiviral action of several groups of phytoconstituents against SARS-CoV-2 using a molecular docking approach to inhibit Main Protease (Mpro) (PDB code: 6LU7) and spike (S) glycoprotein receptor binding domain (RBD) to ACE2 (PDB code: 6M0J) of SARS-CoV-2. For binding affinity evaluation, the docking scores were calculated using the Extra Precision (XP) protocol of the Glide docking module of Maestro. CovDock was also used to investigate covalent docking. The OPLS3e force field was used in simulations. The docking score was calculated by preferring the conformation of the ligand that has the lowest binding free energy (best pose). The results are indicative of better potential of solanine, acetoside, and rutin, as Mpro and spike glycoprotein RBD dual inhibitors. Acetoside and curcumin were found to inhibit Mpro covalently. Curcumin also possessed all the physicochemical and pharmacokinetic parameters in the range. Thus, phytochemicals like solanine, acetoside, rutin, and curcumin hold potential to be developed as treatment options against COVID-19.

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