An Overview of the Crystallized Structures of the SARS-CoV-2

Abstract

Many research teams all over the world focus their research on the SARS-CoV-2, the new coronavirus that causes the so-called COVID-19 disease. Most of the studies identify the main protease or 3C-like protease (M^pro/3CL^pro) as a valid target for large-spectrum inhibitors. Also, the interaction of the human receptor angiotensin-converting enzyme 2 (ACE2) with the viral surface glycoprotein (S) is studied in depth. Structural studies tried to identify the residues responsible for enhancement/weaken virus-ACE2 interactions or the cross-reactivity of the neutralizing antibodies. Although the understanding of the immune system and the hyper-inflammatory process in COVID-19 are crucial for managing the immediate and the long-term consequences of the disease, not many X-ray/NMR/cryo-EM crystals are available. In addition to 3CL^pro, the crystal structures of other nonstructural proteins offer valuable information for elucidating some aspects of the SARS-CoV-2 infection. Thus, the structural analysis of the SARS-CoV-2 is currently mainly focused on three directions-finding M^pro/3CL^pro inhibitors, the virus-host cell invasion, and the virus-neutralizing antibody interaction.

Keywords: COVID-19; Coronavirus; Inhibitors; Molecular docking; Protein Data Bank; Spike.

Fig. 1

The flow of the selection of the crystal structures retrieved from the PDB. *To be published

Fig. 2

The multiple sequence alignment of 3CL^pro of CoVs of different origin (using the Clustal Omega program). The Cys145 of SARS-CoV-2 3CL^pro that interact with the compounds 11a and 11b is shown in black background along with the Cys145-His41 catalytic dyad highly conserved in 3CL^pro from CoVs [42, 44, 59, 65, 66]; in green are marked the cluster of Ser with high affinity for small molecule inhibitors [44, 55]; in green it is shown the GSCGS motif essential for starting the catalysis; in light blue are marked the Glu-His residues critical for substrate binding by means of steric effect; in yellow background is marked the triad Arg-Tyr-Asp that forms a partial negative charge cluster that, by a conserved water molecule, mediates the interaction with Cys-His catalytic dyad; in brown are shown the residues involved in the glutamine substrate recognition—the conserved His and the conserved Tyr and Phe that interacts with by the phenolic hydroxyl group with His and employs a steric effect to restrain the rotation of His, respectively; in bold-underline are marked the Glu and Ser residues that are demonstrated to be essential in the dimer interactions in SARS-CoV-2 [60]; with dot “.” are marked the semi-conservative replacements; with colon “:” are marked the conservative replacements; with “*” are marked the identities of the residues

Fig. 3

The phylogenetic tree (cladogram) of seven 3CL^pro sequences of CoVs with different origin. feline infectious peritonitis virus (FIPV), porcine epidemic diarrhea virus (PEDV), HCoV-NL63, SARS-CoV-2, SARS-CoV, HCoV-HKU1, and coronavirus (strain A59) MHV-A59; performed by Clustal Omega program

Fig. 4

The interactions of SARS-CoV-2 nucleocapsid (N) (PDB ID 6M3M) with the inhibitor PJ34. a 3D display of PJ34 interaction as ligand with the 6M3M residues; b 2D interactions diagram; the molecular docking results were visualized by Dassault Systèmes BIOVA program—Discovery Studio Modeling Environment, Release 2017, San Diego: Dassault Systèmes, 2016 (https://accelrys.com)

Fig. 5

The multiple sequence alignment of SARS-CoV-2 nucleocapsid (N) (PDB ID 6M3M) and HCoV-OC43 (PDB ID 4KXJ) sequences (using the Clustal Omega program). The residues that interact with the compound PJ34 are shown in gray background, according to molecular docking results for 6M3M and according to Lin et al. findings 4KXJ; are considered all types of interactions—van der Waals, hydrogen bonds, carbon hydrogen bonds, and hydrophobic interactions; the striking differences between the two N sequences observed by the Kang et al. are marked in yellow background; the AMP-binding residues are underlined; in red is marked the Tyr residue whose mutation Y110A leads to a significant decrease of Kd for RNA binding [33]; with dot “.” are marked the semi-conservative replacements; with colon “:” are marked the conservative replacements; with “*” are marked the identities of the residues

Fig. 6

The multiple sequence alignment of spike (S) S1/S2 cleavage site sequences using the Clustal Omega program. The S1/S2 sequences are bolded and the basic arginine and lysine residues are marked in red [93]

Fig. 7

The multiple sequence alignment of spike (S) S2′ cleavage site sequences using the Clustal Omega program. The S1/S2 sequences are bolded and the basic arginine and lysine residues are marked in red [93]; in yellow background are marked the cysteine residues that form an internal disulfide bond (C840 and C851) and the residues that form a salt bridge that reinforces the previous disulfide bond (K835-D848); in light blue is shown the lysine (K854) that form a salt bridge with the aspartic acid (D614) (not shown) [, –109]

Fig. 8

The phylogenetic tree (cladogram) of the CoVs Spike (S) sequences of CoVs with different origin. feline infectious peritonitis virus (FIPV), porcine epidemic diarrhea virus (PEDV), HCoV-NL63, SARS-CoV-2, SARS-CoV, HCoV-HKU1, and coronavirus (strain A59) MHV-A59; performed by Clustal Omega program

Fig. 9

The crystal structures co-crystallized with neutralizing antibodies. The epitopes of the SARS-CoV-2 spike are NTD (N terminal domain), RBD (receptor binding domain, quaternary epitopes, and ectodomain; there are indicated the PDB entries and in parenthesis the neutralizing antibody; * the most potent neutralizing antibodies from convalescent patients according to Liu et al. work [16]

Fig. 10

The multiple sequence alignment of nsp9 sequences using the Clustal Omega program. The N-finger (in red) and GXXXG motif (grey background) are important for dimerization. The conserved residues of N-finger are underlined