scholarly journals Computational Screening for Potential Drug Candidates Against SARS-CoV-2 Main Protease

2020 ◽  
Author(s):  
Bruno Andrade ◽  
Preetam Ghosh ◽  
Debmalya Barth ◽  
Sandeep Tiwari ◽  
Raner José Santana Silva ◽  
...  
Keyword(s):  
Potential Drug ◽  
Drug Candidates ◽  
Positive Effects ◽  
Computational Screening ◽  
Main Protease ◽  
Zinc Database ◽  
Novel Drugs ◽  
Structural Assembly

Background: SARS-CoV-2 that are the causal agent of a current pandemic are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly and pathogenicity. The ~33.8KDa Mpro protease of SARS-CoV-2 is a non-human homologue and highly conserved among several coronaviruses indicating Mpro could be a potential drug target for Coronaviruses.Methods: Here we performed computational ligand screening of four pharmacophores (OEW, Remdesivir, Hydroxycholoquine and N3) that are presumed to have positive effects against SARS-CoV-2 Mpro protease (6LU7) and also screened 50,000 molecules from the ZINC Database dataset against this protease target.Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 10 best selected ligands namely, ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as β-carboline, Alkaloids and Polyflavonoids, and all of them displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as with other known ligands.Conclusion: Our results suggest that these 10 molecules could be effective against SARS-CoV-2 protease and may be tested in vitro and in vivo to develop novel drugs against this virus.

scholarly journals Computational Screening for Potential Drug Candidates Against SARS-CoV-2 Main Protease

2020 ◽  
Author(s):  
Bruno Andrade ◽  
Preetam Ghosh ◽  
Debmalya Barth ◽  
Sandeep Tiwari ◽  
Raner José Santana Silva ◽  
...  
Keyword(s):  
Potential Drug ◽  
Drug Candidates ◽  
Positive Effects ◽  
Computational Screening ◽  
Main Protease ◽  
Zinc Database ◽  
Novel Drugs ◽  
Structural Assembly

Background: SARS-CoV-2 that are the causal agent of a current pandemic are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly and pathogenicity. The ~33.8KDa Mpro protease of SARS-CoV-2 is a non-human homologue and highly conserved among several coronaviruses indicating Mpro could be a potential drug target for Coronaviruses.Methods: Here we performed computational ligand screening of four pharmacophores (OEW, Remdesivir, Hydroxycholoquine and N3) that are presumed to have positive effects against SARS-CoV-2 Mpro protease (6LU7) and also screened 50,000 molecules from the ZINC Database dataset against this protease target.Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 10 best selected ligands namely, ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as β-carboline, Alkaloids and Polyflavonoids, and all of them displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as with other known ligands.Conclusion: Our results suggest that these 10 molecules could be effective against SARS-CoV-2 protease and may be tested in vitro and in vivo to develop novel drugs against this virus.

scholarly journals Computational screening for potential drug candidates against the SARS-CoV-2 main protease

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 514 ◽  
Author(s):  
Bruno Silva Andrade ◽  
Preetam Ghosh ◽  
Debmalya Barh ◽  
Sandeep Tiwari ◽  
Raner José Santana Silva ◽  
...  
Keyword(s):  
Natural Compounds ◽  
Potential Drug ◽  
Drug Candidates ◽  
Positive Effects ◽  
Computational Screening ◽  
Main Protease ◽  
Zinc Database ◽  
Structural Assembly

Background: SARS-CoV-2 is the causal agent of the current coronavirus disease 2019 (COVID-19) pandemic. They are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly, and pathogenicity. The approximately 33.8 kDa Mpro protease of SARS-CoV-2 is a non-human homologue and is highly conserved among several coronaviruses, indicating that Mpro could be a potential drug target for Coronaviruses. Methods: Herein, we performed computational ligand screening of four pharmacophores (OEW, remdesivir, hydroxychloroquine and N3) that are presumed to have positive effects against SARS-CoV-2 Mpro protease (6LU7), and also screened 50,000 natural compounds from the ZINC Database dataset against this protease target. Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 11 best selected ligands, namely ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as beta-carboline, alkaloids, and polyflavonoids, and all displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as other known ligands. Conclusions: Our results suggest that these 11 molecules could be effective against SARS-CoV-2 protease and may be subsequently tested in vitro and in vivo to develop novel drugs against this virus.

scholarly journals Computational screening for potential drug candidates against the SARS-CoV-2 main protease

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 514
Author(s):  
Bruno Silva Andrade ◽  
Preetam Ghosh ◽  
Debmalya Barh ◽  
Sandeep Tiwari ◽  
Raner José Santana Silva ◽  
...  
Keyword(s):  
Natural Compounds ◽  
Potential Drug ◽  
Drug Candidates ◽  
Positive Effects ◽  
Computational Screening ◽  
Main Protease ◽  
Zinc Database ◽  
Structural Assembly

Background: SARS-CoV-2 is the causal agent of the current coronavirus disease 2019 (COVID-19) pandemic. They are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly, and pathogenicity. The approximately 33.8 kDa Mpro protease of SARS-CoV-2 is a non-human homologue and is highly conserved among several coronaviruses, indicating that Mpro could be a potential drug target for Coronaviruses. Methods: Herein, we performed computational ligand screening of four pharmacophores (OEW, remdesivir, hydroxychloroquine and N3) that are presumed to have positive effects against SARS-CoV-2 Mpro protease (6LU7), and also screened 50,000 natural compounds from the ZINC Database dataset against this protease target. Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 11 best selected ligands, namely ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as beta-carboline, alkaloids, and polyflavonoids, and all displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as other known ligands. Conclusions: Our results suggest that these 11 molecules could be effective against SARS-CoV-2 protease and may be subsequently tested in vitro and in vivo to develop novel drugs against this virus.

scholarly journals Marine Power on Cancer: Drugs, Lead Compounds, and Mechanisms

Marine Drugs ◽  
2021 ◽  
Vol 19 (9) ◽  
pp. 488
Author(s):  
Lichuan Wu ◽  
Ke Ye ◽  
Sheng Jiang ◽  
Guangbiao Zhou
Keyword(s):  
Mechanisms Of Action ◽  
Malignant Neoplasms ◽  
Drug Candidates ◽  
Lead Compounds ◽  
Anticancer Effects ◽  
The Earth ◽  
Novel Drugs ◽  
Marine Compounds

Worldwide, 19.3 million new cancer cases and almost 10.0 million cancer deaths occur each year. Recently, much attention has been paid to the ocean, the largest biosphere of the earth that harbors a great many different organisms and natural products, to identify novel drugs and drug candidates to fight against malignant neoplasms. The marine compounds show potent anticancer activity in vitro and in vivo, and relatively few drugs have been approved by the U.S. Food and Drug Administration for the treatment of metastatic malignant lymphoma, breast cancer, or Hodgkin′s disease. This review provides a summary of the anticancer effects and mechanisms of action of selected marine compounds, including cytarabine, eribulin, marizomib, plitidepsin, trabectedin, zalypsis, adcetris, and OKI-179. The future development of anticancer marine drugs requires innovative biochemical biology approaches and introduction of novel therapeutic targets, as well as efficient isolation and synthesis of marine-derived natural compounds and derivatives.

scholarly journals Structure-Based Virtual Screening and Molecular Dynamics of Phytochemicals Derived from Saudi Medicinal Plants to Identify Potential COVID-19 Therapeutics

2020 ◽  
Author(s):  
MUBARAK ALAMRI ◽  
Ali Altharawi ◽  
Alhumaidi B. Alabbas ◽  
Manal A. Alossaimi ◽  
Safar M. Alqahtani
Keyword(s):  
Virtual Screening ◽  
Medicinal Plants ◽  
In Vivo Studies ◽  
Effective Vaccine ◽  
Traditional Medicines ◽  
Drug Candidates ◽  
Computational Screening ◽  
Novel Coronavirus

Coronavirus disease 2019 (COVID-19) has affected almost every country in the world by causing a global pandemic with a high mortality rate. Lack of an effective vaccine and/or antiviral drugs against SARS-CoV-2, the causative agent, has severely hampered the response to this novel coronavirus. Natural products have long been used in traditional medicines to treat various diseases, and purified phytochemicals from medicinal plants provide a valuable scaffold for the discovery of new drug leads. In the present study, we performed a computational screening of an in-house database composed of ~1000 phytochemicals derived from traditional Saudi medicinal plants with recognised antiviral activity. Structure-based virtual screening was carried out against three druggable SARS-CoV-2 targets, viral RNAdependent RNA polymerase (RdRp), 3-chymotrypsin-like cysteine protease (3CLpro) and papain like protease (PLpro) to identify putative inhibitors that could facilitate the development of potential anti-COVID-19 drug candidates. Computational analyses identified three compounds inhibiting each target, with binding affinity scores ranging from-9.9 to -6.5 kcal/mol. Among these, luteolin 7-rutinoside, chrysophanol 8-(6-galloylglucoside) and kaempferol 7-(6’’-galloylglucoside) bound efficiently to RdRp, while chrysophanol 8-(6galloylglucoside), 3,4,5-tri-O-galloylquinic acid and mulberrofuran G interacted strongly with 3CLpro, and withanolide A, isocodonocarpine and calonysterone bound tightly to PLpro. These potential drug candidates will be subjected to further in vitro and in vivo studies and may assist the development of effective anti-COVID-19 drugs.

scholarly journals THE INVENTION OF CANDIDATE COMPOUNDS FROM STRYCHNINE BUSH, PINEAPPLE AND GINGER AS THE MAIN PROTEASE RECEPTOR INHIBITOR OF COVID-19 VIRUS

2020 ◽  
Vol 8 (Spl-1-SARS-CoV-2) ◽  
pp. S202-S209
Author(s):  
Novi Yantih ◽  
◽  
Linda Erlina ◽  
Esti Mulatsari ◽  
Wahono Sumaryono ◽  
...  
Keyword(s):  
Active Metabolite ◽  
Zingiber Officinale ◽  
Binding Pocket ◽  
Ananas Comosus ◽  
Potential Candidate ◽  
Drug Candidates ◽  
Main Protease ◽  
Receptor Inhibitor

The emerging coronavirus, Covid-19, has become a worldwide pandemic. The existence of the Covid-19 virus pandemic in the world demands the need to identify and characterize new drug candidates to address the health problem caused by the Covid-19 virus. This study aims to find candidate compounds from strychnine bush (Strychnos lucida), pineapple (Ananas comosus), and ginger (Zingiber officinale) acting as the Mpro receptor inhibitor on Covid-19 virus based on docking modeling. The docking process is carried out using a protein with the pdb code 6LU7, a crystal main protein protease (Mpro) of the Covid-19 which binds to the N3 molecule as an inhibitor based on computational tests. The docking process is conducted using N3 comparison, favipiravir, active metabolite remdesivir, and hydroxychloroquine. The docking result shows that the compounds, ananas 26, zingiberenol, and zingiberol have lower docking energy compared to native ligand (N3), favipiravir, active metabolite remdesivir, and hydroxychloroquine. Ananas 26 compound has the most hydrogen bonds with the Mpro active amino acid residue of the Covid-19 virus, namely: HIS163, ASN142, ASP187, TYR54, and HIS41. This makes Ananas 26 more stable in binding pocket enzymes and more effective in inhibiting enzyme performance than other compounds and positive controls. Potential candidate compounds as SARS-CoV-2 Main Protease inhibitors, ananas 26 from pineapple and zingiberenol as well as zingiberol from ginger, can then undergo potential inhibitor tests by in vitro and in vivo methods on SARS-CoV-2.

scholarly journals Phytochemicals and Potential Therapeutic Targets on Toxoplasma gondii Parasite

2020 ◽  
Vol 20 (9) ◽  
pp. 739-753
Author(s):  
Sharif Alhassan Abdullahi ◽  
Ngah Zasmy Unyah ◽  
Noshariza Nordin ◽  
Rusliza Basir ◽  
Wana Mohammed Nasir ◽  
...  
Keyword(s):  
Drug Target ◽  
Relevant Literature ◽  
Chemotherapeutic Agents ◽  
Potential Drug ◽  
Natural Sources ◽  
Drug Candidates ◽  
Target Sites ◽  
Phytochemical Compounds

Identification of drug target in protozoan T. gondii is an important step in the development of chemotherapeutic agents. Likewise, exploring phytochemical compounds effective against the parasite can lead to the development of new drug agent that can be useful for prophylaxis and treatment of toxoplasmosis. In this review, we searched for the relevant literature on the herbs that were tested against T. gondii either in vitro or in vivo, as well as different phytochemicals and their potential activities on T. gondii. Potential activities of major phytochemicals, such as alkaloid, flavonoid, terpenoids and tannins on various target sites on T. gondii as well as other related parasites was discussed. It is believed that the phytochemicals from natural sources are potential drug candidates for the treatment of toxoplasmosis with little or no toxicity to humans.

scholarly journals Structure-Based Virtual Screening and Molecular Dynamics of Phytochemicals Derived from Saudi Medicinal Plants to Identify Potential COVID-19 Therapeutics

2020 ◽  
Author(s):  
MUBARAK ALAMRI ◽  
Ali Altharawi ◽  
Alhumaidi B. Alabbas ◽  
Manal A. Alossaimi ◽  
Safar M. Alqahtani
Keyword(s):  
Virtual Screening ◽  
Medicinal Plants ◽  
In Vivo Studies ◽  
Effective Vaccine ◽  
Traditional Medicines ◽  
Drug Candidates ◽  
Computational Screening ◽  
Novel Coronavirus

Coronavirus disease 2019 (COVID-19) has affected almost every country in the world by causing a global pandemic with a high mortality rate. Lack of an effective vaccine and/or antiviral drugs against SARS-CoV-2, the causative agent, has severely hampered the response to this novel coronavirus. Natural products have long been used in traditional medicines to treat various diseases, and purified phytochemicals from medicinal plants provide a valuable scaffold for the discovery of new drug leads. In the present study, we performed a computational screening of an in-house database composed of ~1000 phytochemicals derived from traditional Saudi medicinal plants with recognised antiviral activity. Structure-based virtual screening was carried out against three druggable SARS-CoV-2 targets, viral RNAdependent RNA polymerase (RdRp), 3-chymotrypsin-like cysteine protease (3CLpro) and papain like protease (PLpro) to identify putative inhibitors that could facilitate the development of potential anti-COVID-19 drug candidates. Computational analyses identified three compounds inhibiting each target, with binding affinity scores ranging from-9.9 to -6.5 kcal/mol. Among these, luteolin 7-rutinoside, chrysophanol 8-(6-galloylglucoside) and kaempferol 7-(6’’-galloylglucoside) bound efficiently to RdRp, while chrysophanol 8-(6galloylglucoside), 3,4,5-tri-O-galloylquinic acid and mulberrofuran G interacted strongly with 3CLpro, and withanolide A, isocodonocarpine and calonysterone bound tightly to PLpro. These potential drug candidates will be subjected to further in vitro and in vivo studies and may assist the development of effective anti-COVID-19 drugs.

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