ABSTRACT
Rationale: The pulmonary surfactant protein A (SP-A) plays an immune protective role by binding to the cell membrane of immune cells and by opsonizing infectious agents such as bacteria, fungi and viruses through glycoprotein and lipid binding domains. SARS-CoV-2 enters airway epithelial cells through its Spike glycoprotein (S protein) that binds the Angiotensin Converting Enzyme 2 (ACE2) on the cell surface. Using in silico methods we aimed to predict whether human SP-A could bind the S protein and whether this could interfere with SARS-CoV-2 - ACE2 binding. Methods: We assessed binding sites, the relative binding affinity of the interactions, and the protein chains and residues involved using ZDOCK and a novel software “Polar+” .We then compared these binding parameters between S protein - ACE2 and S protein-SP-A binding. We hypothesized that SP-A competes for the same binding site of the S protein with ACE2. We applied the “Polar+” to determine the best binding sites between the proteins.This process involved electronegativity and topologically oriented molecular pruning, calculation of electronic force-fields and electrostatic binding combined with protein-protein docking, geometric fitting and assessment of protein glycosylation sites. Results: We established the parameters of ACE2-S protein binding (left panel in figure) and found that SP-A potentially binds to the S protein with an affinity similar to that of ACE2. However, our data suggested that SP-A most likely binds to the fusion portion of the S2 chain of the S protein. This part is responsible for viral entry into the host cell (right panel in figure). Conclusions: Our study supports the use of quantum computing and the Polar+ algorithm for studying protein-protein interactions. Based on our findings we speculate that SP-A while does not compete with ACE2 for S protein binding, could still interfere with viral entry to the cell through hindering the membrane fusion process. These findings are important in understanding SARS-CoV-2 biology and warrant studies in experimental biological systems.
ABSTRACT
Rationale: Surfactant protein D (SP-D) is a major immune protective molecule produced in the respiratory epithelium. SP-D binds to specific pathogen surfaces through its carbohydrate recognition (lectin) domain, that helps in their neutralization and clearance by phagocytes. SP-D also acts as an anti-inflammatory molecule. We hypothesized that SP-D plays a protective role in COVID-19. Methods: Polar+, a novel quantum computing algorithm for molecular pruning, and classical in silico modeling were used to investigate potential binding sites between SP-D and SARS CoV2. Electronegativity and topologically oriented molecular pruning, calculation of electronic force-fields and electrostatic binding combined with protein-protein docking, geometric fitting and assessment of protein glycosylation sites were employed. SP-D-/- mouse lung was used to study expression of the SARS-CoV-2 viral entry molecules TMPRSS2 and ACE2. Plasma from COVID-19 patients was studied for SP-D leakage, cytokine levels and lipid mediators. Results: We found that SP-D potentially binds to the same SARS CoV-2 glycoprotein (S protein) that it utilizes to bind the cellular receptor, ACE2, with high affinity. However, SP-D binds to subunit 2, instead of subunit 1 (that ACE2 utilizes). Additional studies will need to determine if SP-D binding affects S protein and ACE2 interactions. We also found that SP-D-/- mice had increased expression of the TMRSS2 gene in the lung and that both TMPRSS2 and ACE2 mRNA levels were increased during lung injury, amplified by the lack of SP-D. SP-D leakage from the lung to the circulation was significantly increased in COVID- 19 patients and correlated with expression of pro-neutrophilic inflammatory markers. Conclusions: We speculate that SP-D aids in the protection from SARS CoV2 infection by both acting as a potential natural decoy to prevent coronavirus entry into airway epithelial cells and by attenuating the expression of the viral entry receptor TMPRSS2. Oxidative lung injury results in SP-D leak into the circulation denoting disease severity in COVID-19 patients. (AH) .