Molecular characterization of COVID-19 therapeutics: luteolin as an allosteric modulator of the spike protein of SARS-CoV-2

The interactions between the receptor binding domain (RBD) of SARS-CoV-2 and the angiotensin-converting enzyme 2 (ACE2) are crucial for viral entry and subsequent replication. Given the large and featureless contact surfaces between both proteins, finding a suitable small-molecule drug that can bind and disrupt regulatory pathways has remained a challenge. A promising therapeutic alternative has been the use of small compounds that bind at the protein-protein interface or at distal "hotspots" and induce conformational changes that inhibit or stabilize protein-protein interactions (PPIs). In this work, we conduct large-scale all-atom explicit solvent simulations of the top scoring compounds from a recent large-scale high-throughput docking screening to investigate their interaction with the RBD domain of the spike (S) protein in complex with ACE2. We identify several promising candidates that exhibit a large negative free energy of binding to the RBD/ACE2 complex based on ab initio thermodynamic integration calculations. A systematic structural analysis of two glycosylation profiles of the RBD/ACE2 complex reveals the important role glycans play in modulating the binding of small-molecules. Cross correlation, fluctuation and strain analysis identify several of these compounds as effective PPI modulators that inhibit or stabilize the protein-protein interactions of RBD/ACE2 based on the glycosylation profile. Among them, luteolin, a drug currently approved for asthma, exhibits an intense allosteric effect when it binds to a previously unidentified distal binding site of the RBD domain far from the RBD and ACE2 interface which may serve as a potential target for future drug discovery.