What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2

Abstract

We compared the electrostatic properties of the spike proteins (S-proteins) of three coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, and their interactions with photosensitizers (PSs), octacationic octakis(cholinyl)zinc phthalocyanine (Zn-PcChol8+) and monocationic methylene blue (MB). We found a major common PS binding site at the connection of the S-protein stalk and head. The molecules of Zn-PcChol8+ and MB also form electrostatic encounter complexes with large area of negative electrostatic potential at the head of the S-protein of SARS-CoV-2, between fusion protein and heptad repeat 1 domain. The top of the SARS-CoV spike head demonstrates a notable area of electrostatic contacts with Zn-PcChol8+ and MB that corresponds to the N-terminal domain. The S-protein protomers of SARS-CoV-2 in “open” and “closed” conformations demonstrate different ability to attract PS molecules. In contrast with Zn-PcChol8+, MB possesses the ability to penetrate inside the pocket formed as a result of SARS-CoV-2 receptor binding domain transition into the “open” state. The existence of binding site for cationic PSs common to the S-proteins of SARS-CoV, SARS-CoV-2, and MERS-CoV creates prospects for the wide use of this type of PSs to combat the spread of coronaviruses.

Infectivity and Morphology of Bovine Coronavirus Inactivated In Vitro by Cationic Photosensitizers

“…PSs used in this study were monocationic 3,7-bis-(Dimethylamino)-phenazathionium chloride C16H18ClN3S (methylene blue, Samaramedprom, Samara, Russia) and octacationic octakis(cholinyl)zinc phthalocyanine (Zn-PcChol 8+ , Organic Intermediates and Dyes Institute, Moscow, Russia). The stick models with equipotential electrostatic surfaces of MB, with a total charge of +1, and Zn-PcChol 8+ with a total charge of +8, are shown in Figure 1 , in accordance with our previous study [ 22 , 27 ].…”

“…Recently, we showed that both dyes, monocationic MB and octacationic Zn-PcChol 8+ , possess an affinity for negatively charged regions of coronavirus spikes, the main region of which is located at the connection of the S-protein stalk and the head on the linker between the HR1 and HR2 domains, adjacent to HR2 [ 22 ]. Incubation of BCoV for 10 min using these dyes leads to a deterioration in the resolution of spikes ( Figure 2 ) during electron microscopy, negatively contrasting with uranyl acetate.…”

“…Large, single-strand RNA bearing enveloped coronaviruses are potential sensitive targets to reactive oxygen species generated by various PSs [ 20 , 21 ]. Recently, we have shown the existence of a negatively charged binding site for cationic PSs at the connection of the S-protein stalk and the head adjacent to the HR2 domain, which is common to the S-proteins of SARS-CoV, SARS-CoV-2, and MERS-CoV [ 22 ], all of which belong to the same with BCoV genus Betacoronavirus. One of these water-soluble cationic PSs, octakis (cholinyl) zinc phthalocyanine (Zn-PcChol 8+ ), in combination with far red light irradiation, was able to completely destroy the infectivity of SARS-CoV-2 in suspensions with the initial titer 4.75–5.00 Log 10 TCID50/mL [ 23 ].…”

“…In contrast to Zn-PcChol 8+ , with very low “dark” antiviral activity against SARS-CoV-2 [ 23 ], MB 50 % inhibitory concentration (IC50) against 10 2 TCID50 of SARS-CoV-2 was found to be 0.22 μg/mL [ 25 ]—that is about 0.7 µM. In our model experiments [ 22 ], MB was able to penetrate inside the pocket of the S-protein head formed by the transition of the receptor binding domain (RBD) into the “open” state. The binding of MB to the RBD domain of the model S-protein [ 22 ] corresponds to the dark antiviral effect of this PS, which is capable of reducing SARS-CoV-2 infectivity in a Vero E6 cell culture [ 25 ].…”

“…In our model experiments [ 22 ], MB was able to penetrate inside the pocket of the S-protein head formed by the transition of the receptor binding domain (RBD) into the “open” state. The binding of MB to the RBD domain of the model S-protein [ 22 ] corresponds to the dark antiviral effect of this PS, which is capable of reducing SARS-CoV-2 infectivity in a Vero E6 cell culture [ 25 ]. The existence of the binding site for cationic PSs, which is common to the S-proteins of SARS-CoV, SARS-CoV-2, and MERS-CoV, creates prospects for the wide use of this type of PSs to combat the spread of coronaviruses.…”