Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review

Abstract

The novel coronavirus, SARS-CoV-2, or 2019-nCoV, which originated in Wuhan, Hubei province, China in December 2019, is a grave threat to public health worldwide. A total of 3,672,238 confirmed cases of coronavirus disease 2019 (COVID-19) and 254,045 deaths were reported globally up to May 7, 2020. However, approved antiviral agents for the treatment of patients with COVID-19 remain unavailable. Drug repurposing of approved antivirals against other viruses such as HIV or Ebola virus is one of the most practical strategies to develop effective antiviral agents against SARS-CoV-2. A combination of repurposed drugs can improve the efficacy of treatment, and structure-based drug design can be employed to specifically target SARS-CoV-2. This review discusses therapeutic strategies using promising antiviral agents against SARS-CoV-2. In addition, structural characterization of potentially therapeutic viral or host cellular targets associated with COVID-19 have been discussed to refine structure-based drug design strategies.

Keywords: 2019-nCoV; COVID-19; SARS-CoV-2; antiviral agents; crystal structure; therapeutic strategies.

Figure 1

Viral life cycle of SARS-CoV-2. Interaction between the S protein of SARS-CoV-2 and hACE2 initiates SARS-CoV-2 infection. Following receptor binding, the virus enters the cell by acid-dependent proteolytic cleavage of the S protein by TMPRSS2 or other proteases. Upon fusion of the viral and host cell membranes, viral genomic RNA is released in the cytoplasm. The viral RNA initiates translation of co-terminal polyproteins (pp1a/ab) by−1 frameshifting. These polyproteins are subsequently cleaved into nonstructural proteins (nsps) by M^pro and PL^pro. Several nsp proteins interact with nsp12 (RdRp) to form the replicase-transcriptase complex (RTC), which is responsible for the synthesis of full-length viral genome (replication) and sub-genomic RNAs (transcription). The viral structural proteins are expressed and translocated into the endoplasmic reticulum (ER). The nucleocapsid (N) protein-encapsidated genomic RNA translocates with the structural proteins into the ER-Golgi intermediate compartment (ERGIC) for virion assembly. The newly synthesized virions are budded through the cell membrane and exocytosed.

Figure 2

Structural characterization of the interface between ACE2 and SARS-CoV-2. (A) Overall structure of the spike glycoprotein (S) of SARS-CoV-2 in its homotrimeric conformation. One up and open conformation of the trimer is shown; the up position of the receptor binding domain (RBD), shown in green, is indicated by the orange circle (PDB ID 6VXX). The N-terminal domain (NTD), RBD, HR1, CH, and C-terminal domain (CD) are shown in blue, green, yellow, orange, and purple, respectively. (B) The CryoEM structure of human ACE2 in complex with the RBD of SARS-CoV-2 and B0AT1 (PDB ID 6M17). The overall structure reveals that human ACE2 forms a homodimer (orange and light-yellow) with B0AT1 (dark and light gray), which is located in the transmembrane region. The two SARS-CoV-2 RBDs are shown as dark and light green surfaces. (C) The interaction interface between RBD and ACE2 is shown (PDB ID 6M0J). The residues involved in the interaction between SARS-CoV-2 RBD and hACE2 are represented with stick models in green and orange, respectively. Alpha helix 1 (α1) of hACE2 is also labeled. (D) The overall structure of SARS-CoV-2 RBD in complex with its neutralizing antibody CR3022 (PDB ID 6W41). The Fab regions of the heavy and light chains are shown in hot pink and pink, respectively. SARS-CoV-2 RBD is shown in green. (E) Structural comparison of interfaces between SARS-CoV-2 RBD and Nab or hACE2. The interaction interfaces with the light chain of CR3022, heavy chain of CR3022, and hACE2 are shown in pink, hot pink, and orange, respectively. (F) Hinge movement of hACE2 upon binding of the enzyme inhibitor. The Apo form (PDB ID 1R42) and inhibitor-bound form (PDB ID 1R4L) are superimposed and shown in blue and red, respectively.

Figure 3

Structure of SARS-CoV-2 viral M^pro and its complex with inhibitors. (A) The crystal structure of SARS-CoV-2 M^pro. M^pro is a cysteine protease that consists of three domains and two protomers. Protomer B is shown in darker colors than protomer A and each domain is shown in different colors (sky blue, split pea, and violet represent domains 1, 2, and 3, respectively). (B) Substrate binding site of SARS-CoV-2 M^pro. The substrate binding site of M^pro is subdivided into S1, S1′, S2, and S4 (shown in bold orange). The inhibitors bind to 17 residues shown as yellow sticks (H41, S46, M49, Y56, F140, L141, N142, C145, H164, M165, E166, L167, H172, Q189, F185, T190, and Q192). The cysteine-histidine dyad (C145-H41) between domains 1 and 2 is shown in red. (C) SARS-CoV-2 M^pro in complex with its inhibitors. The structures of SARS-CoV-2 M^pro in complex with 13b (PDB ID 6Y2G, purple sticks), 11a (PDB ID 6LZ2, magenta sticks), N3 (PDB ID 7BQY, orange sticks), and x77 (PDB ID 6W63, cyan sticks) are shown. The molecular interaction of each inhibitor in the active site is shown as a surface and stick complex (D–G are 13b, 11a, N3, and x77). The γ-lactam ring that plays an important inhibitory role is shown in the yellow circle, and C-S covalent bonds with Cys145 are shown in the red circle.

Figure 4

CryoEM structure of RdRp in complex with cofactors (nsp7 and nsp8), RNA template, and remdesivir. (A) Surface representation of the CryoEM structure of SARS-CoV-2 RdRp in complex with its cofactors (two nsp8 and one nsp7) (PDB ID 6M71). nsp7 and nsp8 are shown in gray and pink, respectively. The β-hairpin, NiRAN, interface, thumb, palm, and finger of SARS-CoV-2 RdRp are shown in cyan, yellow, green, orange, purple, and blue, respectively. (B) A cartoon representation of the overall structure of SARS-CoV-2 RdRp in complex with the RNA template and its inhibitor remdesivir (PDB ID 7BV2). The RNA template and primer strand are shown in blue and red, respectively. The red arrow indicated the direction of NTP entry. (C) magnified view of remdesivir monophosphate binding region. Remdesivir covalently binds to the primer RNA strand and interacts with the template RNA.