Molecular docking studies on the phytoconstituents as therapeutic leads against SARS-CoV-2

Tiwari, Abhishek; Tiwari, Varsha; Verma, Navneet; Singh, Anita; Kumar, Manish; Saini, Vipin; Sahoo, Biswa Mohan; Kaushik, Deepak; Verma, Ravinder; Sagadevan, Suresh

doi:10.14314/polimery.2022.7.8

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Tytuł artykułu

Molecular docking studies on the phytoconstituents as therapeutic leads against SARS-CoV-2

Autorzy

Tiwari Abhishek , Tiwari Varsha , Verma Navneet , Singh Anita , Kumar Manish , Saini Vipin , Sahoo Biswa Mohan , Kaushik Deepak , Verma Ravinder , Sagadevan Suresh

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Identyfikatory

DOI

10.14314/polimery.2022.7.8

Warianty tytułu

Molekularne badania dokujące nad zastosowaniem fitoskładników w terapii przeciw SARS-CoV-2

Języki publikacji

Abstrakty

Because of the present pandemic researchers are seeking for phytocandidates that can inhibit or stop SARS-CoV-2. The main protease (Mpro) of SARS-CoV-2 and spike glycoprotein (S) are both suppressed by bioactive compounds found in plants that work by docking them together. The Mpro proteins 6LU7 (complex with an inhibitor N3) and 5C3N (space group C2221) were employed in docking research. PyRx and AutoDock Vina software were used as docking engine. 22 identified phytoconstituents were selected from IMPPAT, a manually curated database, on the basis of their antiviral effects. Docking studies showed that phytoconstituents β-amyrin (-8.4 kcal/mol), withaferin A (-8.3 kcal/mol), oleanolic acid (-7.8 kcal/mol), and patentiflorin A (-8.1 kcal/mol) had the best results against 5C3N Mpro protein whereas kuwanon L (-7.1 kcal/mol), β-amyrin (-6.9 kcal/mol), oleanolic acid (-6.8 kcal/mol), cucurbitacin D (-6.5 kcal/mol), and quercetin (-6.5 kcal/mol) against 6LU7 Mpro protein. All the compounds were examined for their ADMET characteristics using SwissDock. Present research reports that the phytoconstituents along with docking score will be helpful for future drug development against Covid-19.

W związku z pandemią prowadzone są badania mające na celu znalezienie fitosubstancji, które mogą hamować lub zatrzymywać rozwój SARS-CoV-2. Działanie głównych białek proteazy (Mpro) SARS-CoV-2 i glikoproteiny kolca (S) jest osłabiane przez związki bioaktywne występujące w roślinach poprzez proces dokowania. Do badań dokujących użyto białka Mpro 6LU7 (kompleks z inhibitorem N3) i 5C3N (grupa przestrzenna C2221). Jako silnik dokujący zastosowano PyRx i AutoDock Vina. Zidentyfikowano 22 fitoskładniki wybrane z bazy danych IMPPAT, z uwzględnieniem ich działania przeciwwirusowego. Najbardziej skuteczne w przypadku białka Mpro 5C3N okazały się fitoskładniki β-amyryna (-8,4 kcal/mol), witaferyna A (-8,3 kcal/mol), kwas oleanolowy (-7,8 kcal/mol) i patentifloryna A (-8,1 kcal/mol), a w przypadku białka Mpro 6LU7 kuwanon L (-7,1 kcal/mol), β-amyryna (-6,9 kcal/mol), kwas oleanolowy (-6,8 kcal/mol), kukurbitacyna D (-6,5 kcal/mol) i kwercetyna (-6,5 kcal/mol). Wszystkie substancje zbadano pod kątem ich właściwości ADMET przy użyciu SwissDock. Wykazano, że fitoskładniki mogą być pomocne w pracach nad lekami przeciwko Covid-19.

Słowa kluczowe

Covid-19 spike glycoprotein AutoDock Vina Mpro docking artemisinin withaferin A

Covid-19 glikoproteina kolca AutoDock Vina Mpro dokowanie artemizynina witaferyna A

Wydawca

Sieć Badawcza Łukasiewicz – Instytut Chemii Przemysłowej

Czasopismo

Polimery

Rocznik

2022

Tom

Vol. 67, nr 7-8

Strony

355---374

Opis fizyczny

Bibliogr. 56 poz., rys. tab. wykr.

Twórcy

autor

Tiwari Abhishek

drabhishekdv@gmail.com

Pharmacy Academy, IFTM University, Moradabad-244102, Uttar Pradesh, India

https://orcid.org/0000-0003-1221-4754

autor

Tiwari Varsha

Pharmacy Academy, IFTM University, Moradabad-244102, Uttar Pradesh, India

https://orcid.org/0000-0002-2293-8943

autor

Verma Navneet

Pharmacy Academy, IFTM University, Moradabad-244102, Uttar Pradesh, India

https://orcid.org/0000-0002-3803-8456

autor

Singh Anita

Department of Pharmaceutical Sciences, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand-263136 India

https://orcid.org/0000-0003-2149-1155

autor

Kumar Manish

MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala-133207, Haryana India

https://orcid.org/0000-0003-2042-1243

autor

Saini Vipin

MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala-133207, Haryana India

https://orcid.org/0000-0003-2881-042X

autor

Sahoo Biswa Mohan

Roland Institute of Pharmaceutical Sciences, Berhampur, Odisha-760010, India

https://orcid.org/0000-0001-8822-0427

autor

Kaushik Deepak

Department of Pharmaceutical Sciences, M.D. University, Rohtak (124001), Haryana, India

https://orcid.org/0000-0002-3286-196X

autor

Verma Ravinder

Department of Pharmacy, G.D. Goenka University, Gurugram-122103, Haryana, India

https://orcid.org/0000-0003-3397-703X

autor

Sagadevan Suresh

drsureshnano@gmail.com

Nanotechnology and Catalysis Research Centre, University of Malaya, Kuala Lumpur, Malaysia- 50603

https://orcid.org/0000-0003-0393-7344

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Uwagi

Opracowanie rekordu ze środków MEiN, umowa nr SONP/SP/546092/2022 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2022-2023).

Typ dokumentu

Bibliografia

Identyfikator YADDA

bwmeta1.element.baztech-c555912c-13be-4a5f-9455-43d9f2f02bd4