Identification of Entry Inhibitors against Delta and Omicron Variants of SARS-CoV-2

Abstract

Entry inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed to control the outbreak of coronavirus disease 2019 (COVID-19). This study developed a robust and straightforward assay that detected the molecular interaction between the receptor-binding domain (RBD) of viral spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor in just 10 min. A drug library of 1068 approved compounds was used to screen for SARS-CoV2 entry inhibition, and 9 active drugs were identified as specific pseudovirus entry inhibitors. A plaque reduction neutralization test using authentic SARS-CoV-2 virus in Vero E6 cells confirmed that 2 of these drugs (Etravirine and Dolutegravir) significantly inhibited the infection of SARS-CoV-2. With molecular docking, we showed that both Etravirine and Dolutegravir are preferentially bound to primary ACE2-interacting residues on the RBD domain, implying that these two drug blocks may prohibit the viral attachment of SARS-CoV-2. We compared the neutralizing activities of these entry inhibitors against different pseudoviruses carrying spike proteins from alpha, beta, gamma, and delta variants. Both Etravirine and Dolutegravir showed similar neutralizing activities against different variants, with EC50 values between 4.5 to 5.8 nM for Etravirine and 10.2 to 22.9 nM for Dolutegravir. These data implied that Etravirine and Dolutegravir may serve as general spike inhibitors against dominant viral variants of SARS-CoV-2.

Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule

“…Protein–protein docking studies pointed out in the same direction . There is undoubtedly well-built support for the importance of electrostatic interactions for this process which is constantly confirmed for the latest variants, ACE2 polymorphisms, and new studied Abs. ,,,− Nevertheless, it is worth mentioning that Jawad and coauthors more recently added that the van der Waals interactions can also be critical to stabilizing the RBD-ACE2 complex even if the Coulombic interactions are the main driving force for the recognition process between the RBD and ACE2 . Some new all-atom MD works have shown that the presence of long glycans can enhance the RBD-ACE2 binding affinity .…”

Electrostatic features for the Receptor binding domain of SARS-COV-2 wildtype and its variants. Compass to the severity of the future variants with the charge-rule

“…56 There is undoubtedly well-built support for the importance of electrostatic interactions for this process which is constantly confirmed for the latest variants, ACE2 polymorphisms, and new studied Abs. 23,32,36,[57][58][59][60][61][62] Nevertheless, it is worth mentioning that Jawad and co-authors more recently added that the van der Waals interactions can also be critical to stabilizing the RBD-ACE2 complex even if the Coulombic interactions are the main driving force for the recognition process between the RBD and ACE2. 59 Although the main aspects are consistently reproduced, quantitative results for the predicted binding affinities can vary a lot as was critically discussed by Taka and colleagues.…”

Combined effect of traditional Chinese herbal-based formulations Jing Si herbal tea and Jing Si nasal drop inhibits adhesion and transmission of SARS-CoV2 in diabetic SKH-1 mice

“…The wild-type, alpha, delta, epsilon, and gamma variants of pseudotyped viral particles were obtained from RNAicore, Academia Sinica, Taiwan. The viral particles were prepared as reported earlier ( Lee et al, 2022 ). Briefly, the pseudotyped viral particles were obtained by co-transfecting Lenti-X 293T cells with transfer plasmid (pLAS2w.Nluc-T2A-RFP-C.Ppuro, 5 μg), packaging plasmid (pCMVdeltaR8.91, 4 μg), and 1 μg spike-expressing plasmid (wild type, alpha, delta, epsilon, and gamma variants of pcDNA3.1-2019-nCoV-S-d18 in a 10-cm culture dish.…”