COVID-19 In Silico Drug with Zingiber officinale Natural Product Compound Library Targeting the Mpro Protein
Renadya Maulani Wijaya, Muhammad Aldino Hafidzhah, Viol Dhea Kharisma, Arif Nur, Arif Nur Muhammad Ansori, Arli Aditya Parikesit, Renadya Maulani Wijaya, Arli Aditya Parikesit, Arli Parikesit, H Li, S Liu, X Yu, S Tang, C Tang, M Kandeel, M Al-Nazawi, E Rohaeti, M Rafi, U Syafitri, R Heryanto, R Widyowati, M Agil, X Kou, Y Ke, X Wang, M Rahman, Y Xie, S Chen, H Wang, R Sonale, U Kadimi, V Kharisma, A Ansori, A Nugraha, S1, Q Mao, X Xu, S Cao, R Gan, H Corke, T Beta, H Li, D Ghersi, R Sanchez, D Seeliger, B De Groot, G Saxena, S Akhtar, N Sharma, M Sharma, M Siddiqui, M Khan, C Lipinski, B Jayaram, T Singh, G Mukherjee, A Mathur, S Shekhar, V Shekhar, G Morris, M Lim-Wilby, S Forli, R Huey, M Pique, M Sanner, D Goodsell, A Olson, S Azam, S Abbasi, B Alberts, A Johnson, J Lewis, M Raff, K Roberts, P Walter, X Xue, H Yang, W Shen, Q Zhao, J Li, K Yang, Z Rao, K Stierand, P Maa, M Rarey, P Fricker, M Gastreich, M Rarey, R Patil, S Das, A Stanley, L Yadav, A Sudhakar, A Varma, D Chen, N Oezguen, P Urvil, C Ferguson, S Dann, T Savidge
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Ginger (Zingiber officinale) is a rhizome, which is commonly used for culinary and medicinal purposes. In Indonesia, ginger is taken as traditional medicine by processing it into a drink known as jamu. The present study aimed to assess and evaluate the bioactive compounds in ginger that can be used in drug design for treating COVID-19. The crystal structure of the SARS-CoV-2 main protease (Mpro) was generated from a protein sequence database, i.e., Protein Data Bank, and the bioactive compounds in ginger were derived from the existing compounds library. Mpro is involved in polyprotein synthesis, including viral maturation and nonstructural protein gluing, making it a potential antiviral target. Furthermore, the bioactive compounds in ginger were analyzed using Lipinski’s rule of five to determine their drug-like molecular properties. Moreover, molecular docking analysis was conducted using the Python Prescription 0.8 (Virtual Screening Tool) software, and the interaction between SARS-CoV-2 Mpro and the bioactive compounds in ginger was extensively examined using the PyMOL software. Out all of the 16 bioactive compounds that were docked successfully, 4-gingerol, which has the lowest binding energy against SARS-CoV-2 Mpro, as per the virtual screening results, was proven to have the most potential as a viral inhibitor of SARS-CoV-2