Structures of SARS-CoV-2 RNA-Binding Proteins and Therapeutic Targets

Abstract

Background: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemic has resulted in thousands of infections and deaths worldwide. Several therapies are currently undergoing clinical trials for the treatment of SARS-CoV-2 infection. However, the development of new drugs and the repositioning of existing drugs can only be achieved after the identification of potential therapeutic targets within structures, as this strategy provides the most precise solution for developing treatments for sudden epidemic infectious diseases.

Summary: In the current investigation, crystal and cryo-electron microscopy structures encoded by the SARS-CoV-2 genome were systematically examined for the identification of potential drug targets. These structures include nonstructural proteins (Nsp-9; Nsp-12; and Nsp-15), nucleocapsid (N) proteins, and the main protease (Mpro). Key Message: The structural information reveals the presence of many potential alternative therapeutic targets, primarily involved in interaction between N protein and Nsp3, forming replication-transcription complexes (RTCs) which might be a potential drug target for effective control of current SARS-CoV-2 pandemic. RTCs consist of 16 nonstructural proteins (Nsp1-16) that play the most essential role in the synthesis of viral RNA. Targeting the physical linkage between the envelope and single-stranded positive RNA, a process facilitated by matrix proteins may provide a good alternative strategy. Our current study provides useful information for the development of new lead compounds against SARS-CoV-2 infections.

Keywords: Inhibitors; Mpro; Nsp-15; Nsp-9; Nsp12; Targets.

Fig. 1

Structure of SARS-CoV-2 and its genome organization [40, 92, 93, 94]. N protein is a major facilitator of viral replication within host cells, where it interacts with viral RNA during replication to form the virion after attachment to Nsp3 of the RTCs. RNA also interacts with M proteins via N. RTCs facilitate viral RNA replication. SARS-CoV-2, severe acute respiratory syndrome coronavirus-2; RTC, replication-transcription complex; Nsp, nonstructural protein; S, spike, E, envelope; M, matrix; EM, electron microscopy.

Fig. 2

Structural organization of N proteins. a RNA-binding location and residues involved in interactions. b Structural components of N proteins (basic finger and palm) that facilitate RNA binding. Surface representation of RNA binding (c) N-terminal tail residues N48, N49, T50, and A51 (d). G phosphate moiety recognition residues T55, A56, and R89. N, nucleocapsid proteins; G, guanosine.

Fig. 3

Domain organization of Nsp15 (a) Catalytic residues are indicated by blue circles (H235, H250, K290, T341, Y343, and S294). b RNA (PDB ID: 4u37) binding to the NendoU catalytic domain. RNA was docked using the HDOCK webserver [95]. Nsp, nonstructural protein.

Fig. 4

a Structure of Nsp9. b β2–3- and β3–4-loops are glycine rich and integral for RNA-binding. β2–3-and β3–4-loops are glycine rich and are involved in RNA-binding. c Secondary structure of Nsp9. Nsp, nonstructural protein.

Fig. 5

Domain organization of M^pro. a The 3 domains are shown as domain I (residues 8–101), domain II (residues 102–184), and domain III (residues 201–303). b Dimers. Catalytic residues (C145 and H41) are circled. In SARS-CoV-2, T285 is replaced by A285 (black balls) and Ile286 is replaced by leucine. SARS-CoV-2, severe acute respiratory syndrome coronavirus-2

Fig. 6

Structure assembly of Nsp12-Nsp7-Nsp8 complex in SARS-CoV-2. a Organization of SARS-CoV-2 domains. b Zn binding residues. c Complex structure containing active site residues for RNA template access and remdesivir (F88). SARS-CoV-2, severe acute respiratory syndrome coronavirus-2; Nsp, nonstructural protein.