meCocan -Zu einem mechanistischen Verständnis der Wechselwirkung von SARS-CoV-2-Spike-Glykoprotein und Wirts-Heparansulfat-Proteoglykanen
Bioinformatik und Theoretische Biologie
Virologie
Zusammenfassung der Projektergebnisse
Virus-cell surface interactions are key determinants of viral tropism and pathogenesis. SARS- CoV-2 gains entry into respiratory cells following the interaction between the receptor binding domain (RBD) of the prefusion spike (S) glycoprotein and angiotensin-converting enzyme 2 (ACE2). Notably, the tissue distribution and expression levels of ACE2 do not explain the differing severity of COVID-19. Host-cell invasion by SARS-CoV-2 depends on the interaction of S glycoprotein with the heparan sulphate proteoglycans (HSPGs), co-receptors composed of a core protein with covalently attached long glycosaminoglycan chains of heparan sulphates (HS). However, it is not clear if this dependency is responsible for the host susceptibility and COVID-19 severity. Heparin, a structural analogue of HS, is a linear anionic polysaccharide chain administered intravenously as an anticoagulant to COVID-19 patients and via aerosol for the treatment of other lung diseases. Experimental data indicate that heparin acts as an antiviral agent against SARS-CoV-2 by binding the viral spike glycoprotein, but its mechanisms of action are unclear. The first goal of the project was to investigate the mechanisms by which heparin exerts its antiviral effects on the S glycoprotein and to identify mechanisms by which HSPGs, acting as host-cell co-receptors, may facilitate host cell interaction and affect host susceptibility. To address these questions, we applied molecular dynamics (MD) simulation as a “computational microscope” that allows a real-time visualization at an atomistic level of the S glycoprotein/heparin interaction and mechanism. For this purpose, we modelled the prefusion configuration of the homotrimeric spike glycoprotein in both inactive-closed and active-open conformations in the presence of zero, one or three linear polyanionic chains of heparin, performing several replica simulations of microsecond duration of each system. Our models reveal long basic groove patches on the spike head that can accommodate linear anionic polysaccharide chains. Some spike N-glycans are involved in these interactions. We identified direct and allosteric mechanisms by which heparin and HSPGs can affect the spike-host cell interaction. Guided by the simulations, we carried out biochemical tests that, in turn, corroborated the predictions. Our results provide a basis for understanding the role of HSPGs in SARS-CoV-2 pathogenesis and for the rational optimization of heparin derivatives for new antiviral therapies. For the next goals of the project, the aims were to investigate the putative evolutionary advantage given by the S1/S2 basic domain of SARS-CoV-2 S glycoprotein for HS/heparin binding and the relevance of HSPGs in spike-ACE2 receptor complex formation and stabilization. For this purpose, we performed over 15 microseconds of MD simulation of the complex of the spike head in an open conformation bound to ACE2-RBD and zero or three heparin chains. Analysis of these simulations is ongoing, but they indicate that heparin, and thus HS, while not directly affecting the spike-RBD/ACE2-RBD interface residues, does increase the spike-RBD/ACE2-RBD dynamically coupled motions. Finally, we have designed heparin derivatives with the aim of improving antiviral activity by using knowledge obtained from our simulations. Preliminary data from molecular simulations and binding measurements are promising. The results of the first part of the project have been published.
Projektbezogene Publikationen (Auswahl)
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The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms. Journal of Biological Chemistry, 298(2), 101507.
Paiardi, Giulia; Richter, Stefan; Oreste, Pasqua; Urbinati, Chiara; Rusnati, Marco & Wade, Rebecca C.
