Docking study of Selected Vinis vitifera seeds constituents on Dengue viral proteins – An In Silico approach

Dengue is a mosquito-borne systemic viral infection caused by any of the four antigenically related dengue viruses (DENV).The dengue virus belongs to the Flaviviridae family of viruses that cause diseases in humans.A virtual screening analysis of phytochemical structures with dengue virus protein targets has been carried out using a molecular docking approach with vins vinifera seeds. Grapes (Vinis vitifera) are believed to have health benefits due to their antioxidant activity and polyphenols. In this study we examined the binding affinities of 14 ligands with seven non structural Dengu viral proteins through In Silico methods like virtual screening and docking process which showed that compound F and compound N had high binding efficiencies with these proteins along with the type of hydrogen bonds and their respective amino acid residues at their docked sites.

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In silico Docking Study of Some Coumarin Derivatives as Potential Inhibitors on Different Dengue Viral Proteins

Revista de Chimie ◽

10.37358/rc.19.9.7555 ◽

2019 ◽

Vol 70 (9) ◽

pp. 3387-3391

Author(s):

Gabriela Tataringa ◽

Balasubramanian Sathyamurthy ◽

Ion Sandu ◽

Ana Maria Zbancioc

Keyword(s):

Virtual Screening ◽

Dengue Virus ◽

In Silico ◽

Viral Proteins ◽

Docking Study ◽

Binding Activity ◽

Coumarin Derivatives ◽

In Silico Docking ◽

Potential Inhibitors ◽

Hybrid Derivative

In this study, the binding efficiency of 10 coumarin derivatives with some selected proteins from Dengue virus through in silico method was done. By virtual screening and docking results, we have found that the hybrid derivative between coumarin and isatin has the most convenient binding activity for the seven selected proteins.

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Evaluation of Phytochemicals of Cassia occidentalis L. for their Binding Affinities to SARS-CoV-2 3C-Like Protease: An in Silico Approach

Asian Journal of Research in Infectious Diseases ◽

10.9734/ajrid/2020/v4i430152 ◽

2020 ◽

pp. 8-14

Author(s):

Tohmina Afroze Bondhon ◽

Md. Aynal Haque Rana ◽

Anamul Hasan ◽

Rownak Jahan ◽

Khoshnur Jannat ◽

...

Keyword(s):

Molecular Docking ◽

Virtual Screening ◽

In Silico ◽

Binding Affinities ◽

Autodock Vina ◽

Cassia Occidentalis ◽

Main Protease ◽

In Silico Studies ◽

The World ◽

Docking Approach

Aims: Corona virus SARS-CoV-2, otherwise known as COVID-19 has created a pandemic resulting in social and financial crisis throughout the world. The virus has no known drugs or vaccines for preventive or therapeutic purposes. The objective of the present study was to screen phytochemicals from Cassia occidentalis L. in virtual screening (in silico) studies to evaluate their potential of binding to the main 3C-like protease of the virus and so stop its replication. Study Design: Molecular docking approach was used for virtual screening studies. Place and Duration of Study: University of Development Alternative between April and July 2020. Methodology: Molecular docking (blind) were done with the help of Autodock Vina. We have used the pdb file (6LU7) of the main protease of SARS-CoV-2 3C-like protease or SARS-CoV-2 3CLpro (monomeric form) to study binding of the phytochemicals. Results: Of the nine phytochemicals studied, the C-glycosidic flavonoids, cassiaoccidentalins A-C demonstrated excellent binding affinities to the protease. The compounds bound to the active site of the protease with binding energy values of -8.2 to-8.4 kcal/mol. Conclusion: The in silico studies suggest that the compounds merit actual COVID-19 inhibitory tests and have potential for anti-COVID-19 use.

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Potential COVID-19 Drug from Natural Phenolic Compounds through In Silico Virtual Screening Approach

Biointerface Research in Applied Chemistry ◽

10.33263/briac113.1016110173 ◽

2020 ◽

Vol 11 (3) ◽

pp. 10161-10173

Keyword(s):

Phenolic Compounds ◽

Virtual Screening ◽

Viral Protein ◽

In Silico ◽

Docking Study ◽

Effective Drug ◽

Food Sources ◽

Drug Candidate ◽

Protein Targets ◽

Natural Phenolic Compounds

SARS CoV-2 causes a world pandemic disease called COVID-19. In the present study, natural phenol and flavonoid compounds from food sources are used to search for effective drug candidates for treating novel coronavirus 2019. Thirtyfive natural phenolic compounds were taken for our study. Four levels of in silico virtual screening (Drug likeliness, Docking study, ADME, and DFT analysis) was carried out to find effective drug candidate against SAR-CoV-2. 23 Compounds were shortlisted from 35 compounds by preliminary Drug likeliness screening carried out according to five different drug rules. A docking study of 23 compounds against three viral protein targets of SAR-CoV-2 reveals four best-docked compounds, such as Quercetin (CID 5280343), Rosmarinic acid (CID 5281792), Hesperidin (CID 72281), and Naringenin (CID 932). Finally, these four phenolic compounds were subjected to final in silico screening steps such as ADME and DFT analysis. These compounds were considered as the best drug candidate for SARS CoV- 2. These four selected phenolic compounds show better binding affinity with SARS-CoV-2 viral protein targets, which also possess excellent physicochemical and pharmacokinetic properties. Moreover, these compounds virtually present in every food substance, so nutritional supplements of these fruits and vegetables with these compounds act as best warriors to combat COVID-19. Further, in vivo analysis is needed to explore the molecular mechanism behind the inhibition of SAR-CoV-2 viral proteins with these compounds.

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Diterpenes/Diterpenoids and Their Derivatives as Potential Bioactive Leads against Dengue Virus: A Computational and Network Pharmacology Study

Molecules ◽

10.3390/molecules26226821 ◽

2021 ◽

Vol 26 (22) ◽

pp. 6821

Author(s):

Rasel Ahmed Khan ◽

Rajib Hossain ◽

Abolghasem Siyadatpanah ◽

Khattab Al-Khafaji ◽

Abul Bashar Ripon Khalipha ◽

...

Keyword(s):

Dengue Virus ◽

Dengue Fever ◽

Computational Study ◽

Viral Proteins ◽

Network Pharmacology ◽

Binding Affinities ◽

Ns1 Protein ◽

Structural Protein ◽

E Protein

Dengue fever is a dangerous infectious endemic disease that affects over 100 nations worldwide, from Africa to the Western Pacific, and is caused by the dengue virus, which is transmitted to humans by an insect bite of Aedes aegypti. Millions of citizens have died as a result of dengue fever and dengue hemorrhagic fever across the globe. Envelope (E), serine protease (NS3), RNA-directed RNA polymerase (NS5), and non-structural protein 1 (NS1) are mostly required for cell proliferation and survival. Some of the diterpenoids and their derivatives produced by nature possess anti-dengue viral properties. The goal of the computational study was to scrutinize the effectiveness of diterpenoids and their derivatives against dengue viral proteins through in silico study. Methods: molecular docking was performed to analyze the binding affinity of compounds against four viral proteins: the envelope (E) protein, the NS1 protein, the NS3 protein, and the NS5 protein. Results: among the selected drug candidates, triptolide, stevioside, alepterolic acid, sphaeropsidin A, methyl dodovisate A, andrographolide, caesalacetal, and pyrimethamine have demonstrated moderate to good binding affinities (−8.0 to −9.4 kcal/mol) toward the selected proteins: E protein, NS3, NS5, and NS1 whereas pyrimethamine exerts −7.5, −6.3, −7.8, and −6.6 kcal/mol with viral proteins, respectively. Interestingly, the binding affinities of these lead compounds were better than those of an FDA-approved anti-viral medication (pyrimethamine), which is underused in dengue fever. Conclusion: we can conclude that diterpenoids can be considered as a possible anti-dengue medication option. However, in vivo investigation is recommended to back up the conclusions of this study.

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Studi in Silico Lima Senyawa Aktif Sebagai Penghambat Protein Virus Dengue

Jurnal Kefarmasian Indonesia ◽

10.22435/jki.v9i1.1157 ◽

2019 ◽

pp. 40-47

Author(s):

Reni Herman

Keyword(s):

Dengue Virus ◽

In Silico ◽

Dengue Infection ◽

Epigallocatechin Gallate ◽

Denv Infection ◽

Virus Protein ◽

Structural Protein ◽

The Stability ◽

The Tropics ◽

Ns3 Protease

Dengue infection is an endemic disease in the tropics and subtropics, caused by dengue virus (DENV) infection. Some compounds have been shown to have antiviral effects on some viruses. In silico study is conducted to predict the stability of natural ingredient compounds: artemisinin, catechin, mangiferin, epigallocatechin gallate (EGCG), and quercetin in their interactions with dengue virus proteins at molecular level. This study is carried out using the 2008 version of the Molecular Operating Environment (MOE) software. Ligands are ribavirin as antiviral control whereas artemisinin, mangiferin, EGCG, and quercetin with 3D mole format structures. The downloaded DENV protein with PDB document format is the DENV serotype 2 envelope protein with 1OKE code, non structural protein 3 (NS3) with 2VBC code and NS5 protein with 1L9K code. In silico test generally showed that catechin, mangiferin, EGCG, and quercetin had more stable docking ligands to DENV’s proteins. In particular, mangiferin had stable docking ligand to envelope proteins, NS3 (helicase and protease) and in NS5-methyltransferase compared to ribavirin. Catechin stabled on NS3-protease, EGCG on NS3 (helicase and protease) and quercetin on NS3-protease. Artemisinin had less stabled bonds than ribavirin. The results indicated that catechin, mangiferin, EGCG, and quercetin had potential inhibition to DENV proteins whereas mangiferin was the most potential compound to inhibit dengue virus protein targets.

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MOLECULAR DOCKING STUDY BETWEEN 3 THAI MEDICINAL PLANTS COMPOUNDS AND COVID-19 THERAPEUTIC PROTEIN TARGETS: SARS-COV-2 MAIN PROTEASE, ACE-2, AND PAK-1

International Journal of Applied Pharmaceutics ◽

10.22159/ijap.2021.v13s2.08 ◽

2021 ◽

pp. 41-48

Author(s):

SAFIRA CANDRA ASIH ◽

RAFIDHA IRDIANI ◽

MUHAMAD SAHLAN ◽

MOHAMMAD NASIKIN

Keyword(s):

Molecular Docking ◽

Medicinal Plants ◽

Profile Analysis ◽

Binding Free Energy ◽

Docking Study ◽

Molecular Docking Study ◽

Protein Targets ◽

Main Protease ◽

Docking Approach ◽

Thai Medicinal Plants

Objective: The present study aimed to evaluate those 3 compounds among 122 Thai natural products by using a molecular docking approach to inhibit Main Protease (Mpro) of SARS-CoV-2 (PDB code: 6Y2F), Angiotensin Converting Enzyme (ACE)-2 (PDB code: 1R4L), and PAK-1 kinase (PDB code: 5DEW). Methods: The evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine and interaction profile analysis through 2-dimensional visualization using LigPlot+. The determination of the docking score was done by selecting the conformation of the ligand that has the lowest binding free energy (best pose). Result: The results of this study indicate that overall, Panduratin A has the best affinity in inhibiting the main protease of SARS-CoV-2, ACE-2, and PAK-1 compared to other compounds. Conclusion: The three thai medicinal plants compound has the potential to be developed as specific therapeutic agents against COVID-19.

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Multitarget Virtual Screening for Drug Repurposing in COVID19

10.26434/chemrxiv.12652997 ◽

2020 ◽

Author(s):

carlos oscar Sorzano ◽

Enrique Crisman ◽

Jose Maria Carazo ◽

rafael leon

Keyword(s):

Clinical Trials ◽

Virtual Screening ◽

Drug Screening ◽

Binding Sites ◽

Drug Repurposing ◽

Viral Proteins ◽

Binding Affinities ◽

Compound Library ◽

Screening Analysis ◽

Virtual Drug Screening

Therapeutic or preventive research for coronavirus SARS-CoV2 is an extremely active topic of research since its outbreak in January 2020. In this paper we report the results from a virtual drug screening analysis that, to the best of our knowledge, is the widest work in terms of target proteins and compound library. Our study was focused on the repurposing of currently commercialized drugs, and especially those that can interact with multiple viral proteins and several binding sites within each protein. Additionally, we performed a second virtual screening analysis in which we compared our results to the predicted binding affinities for the drugs currently in clinical trials. We show that the best molecules in our screening compares favorably to those in clinical trials, suggesting their suitability for therapeutic or preventive applications.

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Multitarget Virtual Screening for Drug Repurposing in COVID19

10.26434/chemrxiv.12652997.v2 ◽

2020 ◽

Author(s):

carlos oscar Sorzano ◽

Enrique Crisman ◽

Jose Maria Carazo ◽

rafael leon

Keyword(s):

Clinical Trials ◽

Virtual Screening ◽

Drug Screening ◽

Binding Sites ◽

Drug Repurposing ◽

Viral Proteins ◽

Binding Affinities ◽

Compound Library ◽

Screening Analysis ◽

Virtual Drug Screening

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Dengue Virus Inhibition Targets: A Review and Docking Study

Current Topics in Medicinal Chemistry ◽

10.2174/1568026618666181025111605 ◽

2018 ◽

Vol 18 (18) ◽

pp. 1522-1530 ◽

Cited By ~ 2

Author(s):

Luciana Scotti ◽

Marcus Tullius Scotti ◽

Nagendra Sastry Yarla ◽

Alex France Messias Monteiro ◽

Jessika de Oliveira Viana ◽

...

Keyword(s):

Dengue Virus ◽

In Silico ◽

Hemorrhagic Fever ◽

Docking Study ◽

World Population ◽

Protease Inhibition ◽

Virus Inhibition ◽

Severe Manifestation ◽

Density Analysis ◽

Ns3 Protease

Dengue like any neglected tropical disease affects a large part of the world population. In this disease, the infection is caused by arboviruses transmitted by the A. aegypti and A. albopictus mosquito, in which its most severe manifestation is known as dengue hemorrhagic fever. The infected person presents symptoms characteristic of such as fever and rash. Among the ways of fighting dengue by bioactives is the inhibition of NS2B-NS3 protease, inhibition of protein E, and inhibition of sclerotization of the vector cuticle. The cuticle is indispensable for the survival of the mosquito that can be compromised through the inhibition of arylalkylamine N-acetyltransferase (aaNAT). In the studies shown, in silico tests were performed as molecular docking, functional density analysis, molecular orbitals energies with the analyses of the interactions between bioactives and the targets studied. However, in addition to discussing the fight against dengue virus infection through different routes, in this paper, some in silico results of 27 analogs of myricetin have been presented, which showed action on the cuticle sclerotization mechanism.

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Molecular Docking Study of Several Antiviral Drugs to Defeat Covid-19

Mapana Journal of Sciences ◽

10.12723/mjs.54.4 ◽

2020 ◽

Vol 19 (3) ◽

pp. 37-46

Author(s):

Jasdev S. Tuteja ◽

Priti Patidar ◽

Shilpa E. Mathew ◽

Anil Prajapati

Keyword(s):

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

Active Drug ◽

Data Bank ◽

Docking Study ◽

Antiviral Drugs ◽

Binding Affinities ◽

Molecular Docking Study ◽

Molegro Virtual Docker ◽

Docking Approach

Corona virus is one of the significant pathogens that destructs the human respiratory functioning. Deaths and casualties caused by coronaviruses (CoVs) include the severe acute respiratory syndrome (SARS)-CoV and the Middle East respiratory syndrome (MERS)-CoV. The aim of the work was to compare several antiviral drugs and find out which is the most active drug that might be used in treatment for COVID -19. In this study Molecular Docking approach was used to determine the binding affinities of 62 antiviral molecules. The study was carried out using Molegro Virtual Docker 6.0 with PDB 2GTB procured from RCSB Protein Data Bank. Simeprevir and Telaprevir were discovered to be most potent having high MolDock and Rerank scores of -225.158, -78.4383 and -209.467, -136.155 respectively. Further studies may be conducted to design more potent analogue and defeat COVID-19.

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