Structural basis of anti-SARS-CoV-2 activity of HCQ: specific binding to N protein to disrupt its interaction with nucleic acids and LLPS. (29th November 2021)

• Record Type: Journal Article
• Authors: Dang, Mei; Song, Jianxing
• Is Part Of: QRB discovery. Volume 2(2021)
• Publication Date: 2021-11-29
• Subjects: Hydroxychloroquine -- liquid–liquid phase separation -- NMR spectroscopy -- nucleocapsid protein -- SARS-CoV-2; Biophysics -- Periodicals; 571.4
• DOI: 10.1017/qrd.2021.12
• Languages: English
• ISSNs: 2633-2892

Abstract

Abstract: HCQ specifically binds CTD to inhibit its interaction with nucleic acid. ( a ) (I) Superimposition of HSQC spectra of CTD in the free state (blue) and in the presence of HCQ at 1:7.5 (CTD:HCQ) (red). (II) Zoom of HSQC spectra of CTD in the absence (blue) and in presence of HCQ at 1:0.925 (cyan); 1:1.86 (black); 1:3.75 (green); 1:7.5 (red). The assignments of the significantly perturbed residues are labelled. ( b ) Residue-specific chemical shift difference (CSD) of CTD in the presence of HCQ at 1:3.75 (blue) and 1:7.5 (red) (CTD:HCQ). The significantly perturbed residues are labelled, which are defined as those with the CSD values at 1:7.5 > 0.093 (average value + one standard deviation) (cyan line). ( c ) Superimposition of HSQC spectra of CTD only in the presence of HCQ at 1:7.5 (red) and with additional addition of S2m at 1:1 (CTD:S2m) (blue). Abstract: SARS-CoV-2 nucleocapsid (N) protein plays the essential roles in key steps of the viral life cycle, thus representing a top drug target. Functionality of N protein including liquid–liquid phase separation (LLPS) depends on its interaction with nucleic acids. Only the variants with N proteins functional in binding nucleic acids might survive and spread in evolution and indeed, the residues critical for binding nucleic acids are highly conserved. Hydroxychloroquine (HCQ) was shown to prevent the transmission in a large-scale clinical study in Singapore but so far, no specific SARS-CoV-2 protein was experimentally identified to be targeted by HCQ. Here by NMR, we unambiguously decode that HCQ specifically binds NTD and CTD of N protein with Kd of 112.1 and 57.1 μM, respectively to inhibit their interaction with nucleic acid, as well as to disrupt LLPS. Most importantly, HCQ-binding residues are identical in SARS-CoV-2 variants and therefore HCQ is likely effective to different variants. The results not only provide a structural basis for the anti-SARS-CoV-2 activity of HCQ, but also renders HCQ to be the first known drug capable of targeting LLPS. Furthermore, the unique structure of the HCQ-CTD complex suggests a promising strategy for design of better anti-SARS-CoV-2 drugs from HCQ.