  Citation: Alanazi, K.M.; Farah, M.A.; Hor, Y.-Y. Multi-Targeted Approaches and Drug Repurposing Reveal Possible SARS-CoV-2 Inhibitors. Vaccines 2022, 10, 24. https:// doi.org/10.3390/vaccines10010024 Academic Editors: S. Louise Cosby and Hinh Ly Received: 13 November 2021 Accepted: 16 December 2021 Published: 26 December 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). Article Multi-Targeted Approaches and Drug Repurposing Reveal Possible SARS-CoV-2 Inhibitors Khalid Mashay Alanazi 1 , Mohammad Abul Farah 1 and Yan-Yan Hor 2, * 1 Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; kalanzi@ksu.edu.sa (K.M.A.); mfarah@ksu.edu.sa (M.A.F.) 2 Department of Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan 38541, Gyeongbuk-do, Korea * Correspondence: yanyanhor@yu.ac.kr Abstract: The COVID-19 pandemic caused by SARS-CoV-2 is unprecedented in recent memory owing to the non-stop escalation in number of infections and deaths in almost every country of the world. The lack of treatment options further worsens the scenario, thereby necessitating the exploration of already existing US FDA-approved drugs for their effectiveness against COVID-19. In the present study, we have performed virtual screening of nutraceuticals available from DrugBank against 14 SARS-CoV-2 proteins. Molecular docking identified several inhibitors, two of which, rutin and NADH, displayed strong binding affinities and inhibitory potential against SARS-CoV-2 proteins. Further normal model-based simulations were performed to gain insights into the conformational transitions in proteins induced by the drugs. The computational analysis in the present study paves the way for experimental validation and development of multi-target guided inhibitors to fight COVID-19. Keywords: COVID-19; drug repurposing; multi-targeted inhibitors; structural proteins; non- structural proteins 1. Introduction Starting from one patient in December 2019 at Wuhan city of China, COVID-19 has caused mayhem worldwide. As of 24 April 2020, SARS-CoV-2, the etiological agent of COVID-19 has infected 165,069,258 people causing 3,422,907 deaths globally (as of 21 May 2021) [1]. The situation is further worsened by variants of COVID-19 circulating in the global population, which have tremendously increased the transmission rate of the virus [2]. Apart from mutational, structural, and phylogenetic analyses of the SARS-CoV-2 genome, scientists have been centering on drug repurposing to develop therapeutics to combat SARS- CoV-2 contagion [3]. Various existing drugs, Remdesivir, Lopinavir/Ritonavir, Interferon beta-1a, Chloroquine/hydroxychloroquine, are under SOLIDARITY trial initiated by WHO for their inhibitory activity against different proteins of SARS-CoV-2 [4,5] nevertheless better targeted inhibitors are required for COVID-19 treatment. SARS-CoV-2 genome is known to encode up to 14 open reading frames that translate to structural proteins, spike (S), membrane (M), envelope (E) and nucleocapsid (N); two huge non-structural proteins (NSPs) cleaving into sixteen smaller proteins along with nine accessory factors. The virus uses S protein to bind to the angiotensin-converting enzyme 2 (ACE2) receptor to enter the host cell. Both the M and E proteins are involved in forming the virus envelope and the pathogenesis of the virus, while the N protein binds to the virus’s RNA genome, creating the nucleocapsid [6]. NSPs form the replication/transcription complex that includes the papain-like proteinase (NSP3), the main proteinase (NSP5), the NSP7-NSP8 complex, the RNA-dependent RNA polymerase (NSP12), a NTPase/helicase (NSP13), an exonuclease (NSP14), an endonuclease (NSP15), and 2 ′ O-methyltransferases (NSP16). Another group of SARS-CoV-2 is the accessory proteins, 3a, 3b, 6, 7a, 7b, 8, 9b, 9c and 10. The accessory proteins serve multitude of functions in virus replication [7]. In Vaccines 2022, 10, 24. https://doi.org/10.3390/vaccines10010024 https://www.mdpi.com/journal/vaccines