Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis

Abstract

Background:

The coronavirus disease 2019 (COVID-19) began in late 2019 in Wuhan in China's central province of Hubei [1] and the infection is caused by a novel coronavirus (SARS-CoV-2) that has been isolated from patients presenting a mysterious atypical severe pneumonia [2]. The new virus is believed to be very contagious and has already spread rapidly around the world [3]. As of March 23, 2020, the COVID-19 pandemic has affected over 190 countries and territories, with more than 464,142 laboratory-confirmed cases and 21,100 deaths [4]. At the time this paper was written, there have been no specific or effective drugs for the treatment or prevention of COVID-19. Therefore, proposals for the development of new drugs are of fundamental importance in this global health emergency. A wide range of compounds, vaccines and biologics are being investigated by scientists all around the world as potential therapies for COVID-19 [5,6]. One of the common drug targets encoded by the viral genome of SARS-CoV-2 is its main protease (M^pro), which plays a critical role in the growth and spread of the virus. Protease activity can be neutralized by antiviral drugs, known as protease inhibitors, that selectively bind to the catalytic site of the enzyme and prevent the production of infectious virions [7]. High-resolution crystal structure of the SARS-CoV-2 M^pro in complex with a covalently bound inhibitor has been recently been published with PDB ID: 6LU7 [8] and made available to the scientific community, which can be seen as a real opportunity for modern drug discovery initiatives for COVID-19. We have thus implemented a structure-based virtual screening (SBVS) approach to repurpose available antiviral drugs as potential treatments for COVID-19. Drug repositioning is a proven, cost-effective and time saving solution for finding new indications for already established drugs. Our strategy has focused on the identification of small molecules with potential activity against SARS-CoV-2 M^pro from a subset of protease inhibitors intended for the treatment or management of other viral infections such as those caused by the hepatitis C virus (HCV) or the human immunodeficiency virus (HIV).

Materials and Methods:

Results and discussion:

With the publication of the SARS-CoV-2 viral genome in January 2020 [16], key components of the virus have been identified to drug designers to look for potential drugs to stop the spread of the virus. Of these components, M^pro is most often targeted as it plays a major role in controlling the virus' self-replicating machinery. SARS-CoV-2 M^pro is a cysteine protease homodimer formed by two identical protomers. As shown in Figure 1, each protomer consists of three domains and a substrate-binding site containing the catalytic cysteine-histidine dyad. The substrate binding pocket is located between domains I and II of each protomer [8].

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Figure 1

Surface representation of SARS-CoV-2 M^pro protomer showing its domain organization (PDB code 6LU7). The substrate binding site is located in the pocket between domain I (blue) and II (green). Domain III is colored in red and the co-crystallized bound inhibitor N3 is represented by yellow sticks.

In this work, we hypothesized that protease inhibitors designed to deal with other viruses such as HIV and HCV may also have some activity on M^pro. To verify this, we performed a virtual screening of 33 protease inhibitors that we collected from the ChEMBL chemical database. In addition to the drugs already approved, we decided to include experimental compounds, which can serve as prototypes for the development of new compounds, which would be more effective in the treatment of COVID-19. The top-ranked 10 candidates from our virtual screening experiments on the M^pro of SARS-CoV-2 are presented in Table 1.

The co-crystallized peptidomimetic ligand known as inhibitor N3 in the 6LU7 structure as well as Darunavir, a second-generation anti-HIV-1 protease inhibitor [17] that is currently under clinical trials as a potential treatment for SARS-CoV-2 [18], were taken as references in the virtual screening experiment conducted on 6LU7 structure of SARS-CoV-2 M^pro. Inhibitor N3 and Darunavir had respectively a binding energy of -7.0 kcal/mol and -7.4 kcal/mol. The top-ranked 10 candidates all showed better binding affinities to the active site of M^pro as compared to inhibitor N3 and Darunavir. The binding energy of our selected candidates ranged from -8.1 kcal/mol to -9.5 kcal/mol with the lowest affinity for Lopinavir and the highest for Paritaprevir. It should be noted that lopinavir, presented here as one of the least binding candidates, was used in combination with ritonavir to treat patients with severe Covid-19 in a randomized controlled trial but the results were found to be unsatisfactory and without any therapeutic efficacy [19]. Despite this, visual inspection of the predicted binding modes showed that the selected candidates were reasonably anchored within the substrate binding pocket of Mpro and eventually occupied the pocket in the same manner as the co-crystallized inhibitor N3 (Figure 2). Detailed examination of atomic interactions at protein-ligand interfaces indicated the formation of multiple hydrogen bonds, hydrophobic interactions and Pi interactions that may help to stabilize the ligands inside the substrate-binding site (Figure 3, Figure 4 and Figure 5).

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Figure 2

Binding modes of the ten selected candidates in the substrate-binding site of SARS-CoV-2 M^pro. (A) Paritaprevir; (B) Ciluprevir; (C) Simeprevir; (D) Deldeprevir; (E) Indinavir; (F) Saquinavir; (G) Faldaprevir; (H) Brecanavir; (I) Grazoprevir; (J) Lopinavir; (K) Inhibitor N3; (L) Darunavir. The catalytic dyad Cys145-His41 is colored in red and blue respectively.

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Figure 3

Molecular contacts between the selected candidates and the residues of the substrate-binding pocket of SARS-CoV-2 M^pro.(A), Paritaprevir.(B),Ciluprevir.(C), Simeprevir. (D), Deldeprevir. The four compounds established multiple hydrogen bonding and hydrophobic interaction with the residues of the substrate-binding pocket of M^pro. Interactions with the catalytic His41 were observed in the four compounds. Paritaprevir and Simeprevir interacted with the catalytic Cys145 as well throught a hydrophobic contact and a hydrogen bond respectively.

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Figure 4

Molecular contacts between the selected candidates and the residues of the substrate binding pocket of SARS-CoV-2 M^pro.(E),Indinavir.(F),Saquinavir.(G),Faldaprevir. (H), Brecanavir. The four compounds were stabilized inside the substrate-binding pocket of M^pro by a network of hydrogen bonds and hydrophobic contacts. Interactions with the catalytic dyad Cis-145-His41 were observed in Indinavir, Saquinavir and Faldaprevir; however, Brecanavir interacted only with the catalytic Cys145.

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Figure 5

Molecular contacts between the selected candidates and the residues of the substrate binding pocket of SARS-CoV-2 M^pro.(I),Grazoprevir.(J),Lopinavir. More hydrophobic interactions than hydrogen bonds were observed in Grazoprevir, which interacted with both catalytic residues Cys145 (1 hydrophobic contact) and His41 (1 hydrogen bond and 1 Pi sulfur bond). Lopinavir interacted only with His-41 through a Pi-Pi stacked interaction and a hydrophobic contact.

Remarkably, all of the proposed candidates interacted with one or both catalytic residues (Cys145 and His41) in the substrate binding site of SARS-Cov-2 M^pro [8]. This site is homologous in all coronavirus proteases and therefore these compounds may have a potential inhibitory activity on other corona viruses as well. As these results appear very promising, further bioassays and clinical trials are needed to confirm the inhibitory activity of these compounds against SARS-Cov-2 main protease.

Conclusions:

In this paper, we report 10 candidates from known anti-viral drugs with optimal binding features to the active site of the protease for further consideration to fight the COVID-19 pandemic and the care for the infected persons. With the increasing number of sudden outbreaks of infectious diseases that threaten our global health, drug repurposing can be a cost effective and time-efficient strategy for the treatment and control of the emerging pathogens. The availability of pharmacokinetic evidence allows approved drugs to move quickly through the final stages of clinical trials, enabling a rapid response that can save hundreds or even thousands of lives.

Acknowledgments

References