Nicotinic cholinergic system and COVID-19: In silico identification of interactions between α7 nicotinic acetylcholine receptor and the cryptic epitopes of SARS-Co-V and SARS-CoV-2 Spike glycoproteins

Abstract

SARS-CoV-2 is the coronavirus that originated in Wuhan in December 2019 and has spread globally. Studies have shown that smokers are less likely to be diagnosed with or be hospitalized for COVID-19 but, once hospitalized, have higher odds for an adverse outcome. We have previously presented the potential interaction between SARS-CoV-2 Spike glycoprotein and nicotinic acetylcholine receptors (nAChRs), due to a "toxin-like" epitope on the Spike glycoprotein, with homology to a sequence of a snake venom toxin. This epitope coincides with the well-described cryptic epitope for the human anti-SARS-CoV antibody CR3022. In this study, we present the molecular complexes of both SARS-CoV and SARS-CoV-2 Spike glycoproteins, at their open or closed conformations, with the model of the human α7 nAChR. We found that all studied protein complexes' interface involves a large part of the "toxin-like" sequences of SARS-CoV and SARS-CoV-2 Spike glycoproteins and toxin binding site of human α7 nAChR. Our findings provide further support to the hypothesis about the protective role of nicotine and other cholinergic agonists. The potential therapeutic role of CR3022 and other similar monoclonal antibodies with increased affinity for SARS-CoV-2 Spike glycoprotein against the clinical effects originating from the dysregulated cholinergic pathway should be further explored.

Keywords: COVID-19; CR3022; Cryptic epitope; Molecular modeling; SARS-CoV-2; Spike glycoprotein; nAChRs.

Fig. 1

SARS-COV-2 RBD epitope sequence for the CR3022 mAb. Grey-shadowed amino acids show the CR3022 interacting residue epitopes in the SARS-CoV-2 RBD. (A, Ala; D, Asp; E, Glu; F, Phe; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr).

Fig. 2

(A): Multiple amino acid sequence alignment of spike glycoprotein RBDs of SARS-CoV-2 and other SARS-related coronaviruses. Non-conserved residues among the RBDs of SARS-COV-2 and other SARS-related coronaviruses are shown in a red color font. Yellow highlighted panel indicates the highly conserved region of SARS-CoVs RBD (aa 375–395), bearing the snakes' neurotoxin-like residues, potentially resulting in binding to nAChRs and adversely affecting their function. (B): Sequence alignment of Spike glycoprotein RBDs of SARS-CoV-2 and the other human SARS-related CoVs (i.e., SARS-CoV 0C43, SARS-CoV HKU1, and MERS-CoV). Non-conserved residues are shown in red color. The red frame indicates the aa 375–395 region highly conserved in all other SARS-related CoVs but not to SARS-CoV 0C43, SARS-CoV HKU1, and MERS-CoV. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2

(A): Multiple amino acid sequence alignment of spike glycoprotein RBDs of SARS-CoV-2 and other SARS-related coronaviruses. Non-conserved residues among the RBDs of SARS-COV-2 and other SARS-related coronaviruses are shown in a red color font. Yellow highlighted panel indicates the highly conserved region of SARS-CoVs RBD (aa 375–395), bearing the snakes' neurotoxin-like residues, potentially resulting in binding to nAChRs and adversely affecting their function. (B): Sequence alignment of Spike glycoprotein RBDs of SARS-CoV-2 and the other human SARS-related CoVs (i.e., SARS-CoV 0C43, SARS-CoV HKU1, and MERS-CoV). Non-conserved residues are shown in red color. The red frame indicates the aa 375–395 region highly conserved in all other SARS-related CoVs but not to SARS-CoV 0C43, SARS-CoV HKU1, and MERS-CoV. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

(A): Sequence alignment between the SARS-CoV and SARS-CoV-2 Spike glycoproteins and Neurotoxin homolog NL1 depicting amino acids within this sequence identical or functionally equivalent to Neurotoxin homolog NL1 toxin. (B): Amino acid interactions between SARS-CoV-2 RBD and SARS-CoV neutralizing mAb CR3022. (C): Spatial amino acid interactions between SARS-CoV-2 RBD (red) and CR3022 heavy (blue) and light chain (green) through different angles. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4

Structural location of the toxin-like sequence within the SARS-CoV (A) and SARS-CoV-2 (B) Spike glycoprotein. The toxin-like sequence is illustrated in ball and stick format.

Fig. 5

The cluster of intermolecular contacts (ICs) at the interface (within the threshold distance of 5.5 Å) for the complexes between SARS-CoV S1 (A) and SARS-CoV-2 S1 (B) glycoproteins in open and closed conformation with the LBD of the human ECD of α7 nAChR.

Fig. 6

(A): HADDOCK complexes of the RBD of SARS-CoV in its open and closed state with one subunit of the pentameric extracellular domain of human α7 nAChR. (B): The interaction interface between the RBD of SARS-CoV in an open state (red color) with the extracellular domain of human α7 nAChR (cyan color). (C): The interaction interface between the RBD of SARS-CoV in a closed state (red color) with the extracellular domain of human α7 nAChR (cyan color). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7

(A): HADDOCK complexes of RBDs of SARS-CoV-2 in their open and closed state with one subunit of the pentameric extracellular domain of human α7 nAChR. (B): The interaction interface between the RBD spike of SARS-CoV-2 in the open state (red color) with the extracellular domain of human α7 nAChR (cyan color). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 8

Contacts between ³⁶⁶Cys and ³⁶⁷Tyr of SARS-CoV cryptic epitope with residues of the α7 subunit in closed (A) and open (B) state of their complexes.

Fig. 9

Contacts between ³⁸⁴Pro and ³⁸⁵Thr of SARS-CoV-2 cryptic epitope with the α7 subunit's residues in closed (A) and open (B) state of their complexes.