scholarly journals Molecular docking of secondary metabolites from Indonesian marine and terrestrial organisms targeting SARS-CoV-2 ACE-2, M pro, and PL pro receptors

Pharmacia ◽  
2021 ◽  
Vol 68 (3) ◽  
pp. 533-560
Author(s):  
Gita Syahputra ◽  
Nunik Gustini ◽  
Bustanussalam Bustanussalam ◽  
Yatri Hapsari ◽  
Martha Sari ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Secondary Metabolites ◽  
Antiviral Drugs ◽  
Immunomodulatory Activity ◽  
Terrestrial Plants ◽  
Autodock Vina ◽  
Viral Proteases ◽  
Main Protease ◽  
Tremendous Importance

With the uncontrolled spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), development and distribution of antiviral drugs and vaccines have gained tremendous importance. This study focused on two viral proteases namely main protease (Mpro) and papain-like protease (PLpro) and human angiotensin-converting enzyme (ACE-2) to identify which of these are essential for viral replication. We screened 102 secondary metabolites against SARS-CoV-2 isolated from 36 terrestrial plants and 36 marine organisms from Indonesian biodiversity. These organisms are typically presumed to have antiviral effects, and some of them have been used as an immunomodulatory activity in traditional medicine. For the molecular docking procedure to obtain Gibbs free energy value (∆G), toxicity, ADME and Lipinski, AutoDock Vina was used. In this study, five secondary metabolites, namely corilagin, dieckol, phlorofucofuroeckol A, proanthocyanidins, and isovitexin, were found to inhibit ACE-2, Mpro, and PLpro receptors in SARS-CoV-2, with a high affinity to the same sites of ptilidepsin, remdesivir, and chloroquine as the control molecules. This study was delimited to molecular docking without any validation by simulations concerned with molecular dynamics. The interactions with two viral proteases and human ACE-2 may play a key role in developing antiviral drugs for five active compounds. In future, we intend to investigate antiviral drugs and the mechanisms of action by in vitro study.

Virtual Screening, Molecular docking and in-silico ADME-Tox analysis for identification of potential main protease (Mpro) enzyme inhibitors

2020 ◽  
Vol 18 ◽  
Author(s):  
Debadash Panigrahi ◽  
Ganesh Prasad Mishra
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Data Bank ◽  
Future Research ◽  
Reference Compound ◽  
Unexpected Death ◽  
Main Protease ◽  
In Silico Admet

Objective:: Recent pandemic caused by SARS-CoV-2 described in Wuhan China in December-2019 spread widely almost all the countries of the world. Corona virus (COVID-19) is causing the unexpected death of many peoples and severe economic loss in several countries. Virtual screening based on molecular docking, drug-likeness prediction, and in silico ADMET study has become an effective tool for the identification of small molecules as novel antiviral drugs to treat diseases. Methods:: In the current study, virtual screening was performed through molecular docking for identifying potent inhibitors against Mpro enzyme from the ZINC library for the possible treatment of COVID-19 pandemic. Interestingly, some compounds are identified as possible anti-covid-19 agents for future research. 350 compounds were screened based on their similarity score with reference compound X77 from ZINC data bank and were subjected to docking with crystal structure available of Mpro enzyme. These compounds were then filtered by their in silico ADME-Tox and drug-likeness prediction values. Result:: Out of these 350 screened compounds, 10 compounds were selected based on their docking score and best docked pose in comparison to the reference compound X77. In silico ADME-Tox and drug likeliness predictions of the top compounds were performed and found to be excellent results. All the 10 screened compounds showed significant binding pose with the target enzyme main protease (Mpro) enzyme and satisfactory pharmacokinetic and toxicological properties. Conclusion:: Based on results we can suggest that the identified compounds may be considered for therapeutic development against the COVID-19 virus and can be further evaluated for in vitro activity, preclinical, clinical studies and formulated in a suitable dosage form to maximize their bioavailability.

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

Computational screening of dual inhibitors from FDA approved antiviral drugs on SARS-CoV-2 spike protein and the main protease using molecular docking approach

2021 ◽  
Vol 65 (02) ◽  
pp. 160-172
Author(s):  
Shanthi Sabarimurugan ◽  
Indu Purushothaman ◽  
Rajarajan Swaminathan ◽  
Arun Dharmarajan ◽  
Sudha Warrier ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antiviral Drugs ◽  
Spike Protein ◽  
Computational Screening ◽  
Main Protease ◽  
Docking Approach ◽  
Dual Inhibitors

scholarly journals Identification of Potent Inhibitors of COVID-19 Main Protease Enzyme by Molecular Docking Study

2020 ◽  
Author(s):  
pooja singh ◽  
Angkita Sharma ◽  
Shoma Paul Nandi
Keyword(s):  
Molecular Docking ◽  
Antiviral Drug ◽  
Cyclopiazonic Acid ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Docking Score ◽  
Protease Enzyme ◽  
Main Protease

<p>Within the span of a few months, the severe acute respiratory syndrome coronavirus, COVID-19 (SARS-CoV-2), has proven to be a pandemic, affecting the world at an exponential rate. It is extremely pathogenic and causes communicable infection in humans. Viral infection causes difficulties in breathing, sore throat, cough, high fever, muscle pain, diarrhea, dyspnea, and may lead to death. Finding a proper drug and vaccines against this virus is the need of the hour. The RNA genome of COVID19 codes for the main protease M<sup>pro</sup>, which is required for viral multiplication. To identify possible antiviral drug(s), we performed molecular docking studies. Our screen identified ten biomolecules naturally present in <i>Aspergillus flavus</i> and <i>Aspergillus oryzae</i> fungi. These molecules include Aspirochlorine, Aflatoxin B1, Alpha-Cyclopiazonic acid, Sporogen, Asperfuran, Aspergillomarasmine A, Maltoryzine, Kojic acid, Aflatrem and Ethyl 3-nitropropionic acid, arranged in the descending order of their docking score. Aspirochlorine exhibited the docking score of – 7.18 Kcal/mole, higher than presently used drug Chloroquine (-6.2930522 Kcal/mol) and out of ten ligands studied four has docking score higher than chloroquine. These natural bioactive compounds could be tested for their ability to inhibit viral growth <i>in- vitro</i> and <i>in-vivo</i>.<b> </b></p>

scholarly journals In silico and in vitro Demonstration of Homoharrintonine Antagonism of RBD-ACE2 Binding and its Anti-inflammatory and anti-thrombogenic Properties in a 3D human vascular lung model

2021 ◽  
Author(s):  
Shalini Saxena ◽  
Kranti Meher ◽  
Madhuri Rotella ◽  
Subhramanyam Vangala ◽  
Satish Chandran ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Active Sites ◽  
Cell Model ◽  
Antiviral Drugs ◽  
Lung Model ◽  
Host Cells ◽  
Spike Protein ◽  
Prevention And Treatment ◽  
Anti Inflammatory

Since 2019 the world has seen severe onslaught of SARS-CoV-2 viral pandemic. There is an urgent need for drugs that can be used to either prevent or treat the potentially fatal disease COVD-19. To this end, we screened FDA approved antiviral drugs which could be repurposed for COVID-19 through molecular docking approach in the various active sites of receptor binding domain (RBD). The RBD domain of SARS-CoV-2 spike protein is a promising drug target due to its pivotal role in viral-host attachment. Specifically, we focussed on identifying antiviral drugs which could a) block the entry of virus into host cells, b) demonstrate anti-inflammatory and/or anti-thrombogenic properties. Drugs which poses both properties could be useful for prevention and treatment of the disease. While we prioritized a few antiviral drugs based on molecular docking, corroboration with in vitro studies including a new 3D human vascular lung model strongly supported the potential of Homoharringtonine, a drug approved for chronic myeloid leukaemia to be repurposed for COVID-19. This natural product drug not only antagonized the biding of SARS-CoV-2 spike protein RBD binding to human angiotensin receptor 2 (ACE-2) protein but also demonstrated for the first time anti-thrombogenic and anti-leukocyte adhesive properties in a human cell model system. Overall, this work provides an important lead for development of rapid treatment of COVID-19 and also establishes a screening paradigm using molecular modelling and 3D human vascular lung model of disease to identify drugs with multiple desirable properties for prevention and treatment of COVID-19.

scholarly journals Millet Derived Flavonoids as Potential SARS-CoV-2 Main Protease Inhibitors: A Computational Approach

2020 ◽  
Author(s):  
Abhisek Mishra ◽  
Sobha Chnadra Rath ◽  
Iswar Baitharu ◽  
Bhawani Prasad Bag
Keyword(s):  
Drug Target ◽  
Hiv Protease ◽  
Binding Affinities ◽  
Autodock Vina ◽  
Major Health ◽  
Main Protease ◽  
Negative Effect ◽  
Mutagenic Property

The on-going pandemic COVID-19 has emerged as a major health threat across the globe. At present, anti-viral drug discoveries are of great importance in combating the pandemic. Millets are known to contain numerous flavonoids with potential anti-viral properties. However, their anti-viral efficacy against SARS-CoV-2 is yet to be studied. The study uses the SARS-CoV-2 main protease (M<sup>pro</sup>) as the potential drug target and docks with eleven millet derived flavonoids taking HIV protease inhibiting drugs nelfinavir and saquinavir as control. AutoDock Vina was used for assessing the binding affinities and strength of binding of flavonoids present in millets with the target protein M<sup>pro</sup>. Further, the drug-likeness and pharmacokinetics properties of these flavonoids were analyzed using admetSAR. The ADMET analysis showed that isoorientin, orientin, vitexin, meletin, catechin, and myricetin possess potential mutagenic property while daidzein could have a negative effect on reproductive making these compounds as poor candidates for drug development against SARS-CoV-2. Based on the docking result and positive ADMET properties, the present study infers that apigenin may be considered as a potential inhibitor of SARS-CoV-2 M<sup>pro</sup> and may be further investigated to test its anti-viral activities using <i>in-vitro</i> and <i>in-vivo</i> study.

scholarly journals Millet Derived Flavonoids as Potential SARS-CoV-2 Main Protease Inhibitors: A Computational Approach

2020 ◽  
Author(s):  
Abhisek Mishra ◽  
Sobha Chnadra Rath ◽  
Iswar Baitharu ◽  
Bhawani Prasad Bag
Keyword(s):  
Drug Target ◽  
Hiv Protease ◽  
Binding Affinities ◽  
Autodock Vina ◽  
Major Health ◽  
Main Protease ◽  
Negative Effect ◽  
Mutagenic Property

The on-going pandemic COVID-19 has emerged as a major health threat across the globe. At present, anti-viral drug discoveries are of great importance in combating the pandemic. Millets are known to contain numerous flavonoids with potential anti-viral properties. However, their anti-viral efficacy against SARS-CoV-2 is yet to be studied. The study uses the SARS-CoV-2 main protease (M<sup>pro</sup>) as the potential drug target and docks with eleven millet derived flavonoids taking HIV protease inhibiting drugs nelfinavir and saquinavir as control. AutoDock Vina was used for assessing the binding affinities and strength of binding of flavonoids present in millets with the target protein M<sup>pro</sup>. Further, the drug-likeness and pharmacokinetics properties of these flavonoids were analyzed using admetSAR. The ADMET analysis showed that isoorientin, orientin, vitexin, meletin, catechin, and myricetin possess potential mutagenic property while daidzein could have a negative effect on reproductive making these compounds as poor candidates for drug development against SARS-CoV-2. Based on the docking result and positive ADMET properties, the present study infers that apigenin may be considered as a potential inhibitor of SARS-CoV-2 M<sup>pro</sup> and may be further investigated to test its anti-viral activities using <i>in-vitro</i> and <i>in-vivo</i> study.

Potential Bioactive glycosylated flavonoids as SARS-CoV-2 Main protease Inhibitors: A molecular Docking Study

2020 ◽  
Author(s):  
sabri ahmed cherrak ◽  
merzouk hafida ◽  
mokhtari soulimane nassima
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Chemical Structures ◽  
In Vivo Experiments ◽  
Main Protease

A novel (COVID-19) responsible of acute respiratory infection closely related to SARS-CoV has recently emerged. So far there is no consensus for drug treatment to stop the spread of the virus. Discovery of a drug that would limit the virus expansion is one of the biggest challenges faced by the humanity in the last decades. In this perspective, testing existing drugs as inhibitors of the main COVID-19 protease is a good approach.Among natural phenolic compounds found in plants, fruit, and vegetables; flavonoids are the most abundant. Flavonoids, especially in their glycosylated forms, display a number of physiological activities, which makes them interesting to investigate as antiviral molecules.The flavonoids chemical structures were downloaded from PubChem and protease structure 6lu7 was from the Protein Data Bank site. Molecular docking study was performed using AutoDock Vina. Among the tested molecules Quercetin-3-O-rhamnoside showed the highest binding affinity (-9,7 kcal/mol). Docking studies showed that glycosylated flavonoids are good inhibitors for the covid-19 protease and could be further investigated by in vitro and in vivo experiments for further validation.

Evaluation of RevX Solution Extract as a Potential Inhibitor of the Main Protease of SARS-CoV-2— In Vitro Study and Molecular Docking

2021 ◽  
Author(s):  
Tung-Kung Wu ◽  
Feng-Pai Chou ◽  
Chia-Chun Liu ◽  
Giang Nguyet Huong Huynh ◽  
Hsiu-Fu Hsu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Potential Inhibitor ◽  
Main Protease
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