Targeting ACE2–RBD Interaction as a Platform for COVID-19 Therapeutics: Development and Drug-Repurposing Screen of an AlphaLISA Proximity Assay

Abstract

The COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public health emergency garnering a rapid response from scientists across the globe. Host cell invasion is initiated through direct binding of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Disrupting the spike protein–ACE2 interaction is a potential therapeutic target for treating COVID-19. We have developed a proximity-based AlphaLISA assay to measure the binding of SARS-CoV-2 spike protein receptor binding domain (RBD) to ACE2. Utilizing this assay platform, a drug-repurposing screen against 3384 small-molecule drugs and preclinical compounds was carried out, yielding 25 high-quality primary hits, of which only corilagin was validated in cherry-picking. This established AlphaLISA RBD–ACE2 platform can facilitate evaluation of biologics or small molecules that can perturb this essential viral–host interaction to further the development of interventions to address the global health pandemic.

SMMPPI: a machine learning-based approach for prediction of modulators of protein–protein interactions and its application for identification of novel inhibitors for RBD:hACE2 interactions in SARS-CoV-2

“…Figure 6 shows representative compounds from some of the scaffolds/clusters. Out of these 319 clusters, 5 clusters contain compounds similar to already known inhibitors of RBD:hACE2 or SARS-CoV2 viral growth from the two published experimental studies [ 25 , 46 ], while all the remaining 314 clusters represent the novel classes of compounds identified with potential to target RBD:hACE interaction. Cluster 120 consisting of 2 compounds shares similarity with Paredrine (4-(2-Aminopropyl)phenol) which has been used as an eye solution for dilation of pupils and controls the release of aqueous humor.…”

“…Unlike single protein targets, additional complexity associated with flat interaction interfaces of PPIs [ 4 ] and lack of a reference small molecule substrate or native ligand to guide the search strategy, pose major challenges for prediction of modulators of PPIs by docking. Availability of experimentally validated data set of 25 inhibitors for RBD_hACE and a set of 250 compounds which do not inhibit RBD_hACE2 interactions [ 25 ] gave us the opportunity to evaluate the performance of a docking approach for this PPI. Docking of these compounds on to the interaction interface of RBD using OpenEye software revealed that out of the 25 inhibitors (binders to RBD) in positive data set, 16 compounds docked to the site with docking score in the range of −2 to −3 kcal/mol, while remaining nine compounds were rejected as potential binders.…”

“…The data on experimentally characterized small molecule modulators of PPIs were retrieved from PPI modulator databases such as iPP-DB [ 23 ] and 2P2Idb v2 [ 24 ], Hanson et al. study [ 25 ]. This provided a total set of 2578 PPIMs targeting 27 different PPI families, from which redundancy was removed (for details see Supplementary Methods, see Supplementary Data available online at http://bib.oxfordjournals.org/) by clustering the chemical structures of the molecules using Butina clustering module of RDKIT based on chemical structure similarity as measured by Tanimoto score with RDK fingerprints and a clustering radius of 0.9 [ 26 ].…”

An Overview of Spike Surface Glycoprotein in Severe Acute Respiratory Syndrome–Coronavirus

“…Hanson et al, performed drug repurposing of 3384 small molecule drugs with 25 hits using a proximity-based assay that measures the binding of SARS-CoV-2 RBD and ACE2 ( Hanson et al, 2020 ). Even though the unbound states of the S protein and ACE2 lacks druggable pockets, there are well-defined pockets in the bound states for drug development.…”

A machine learning platform to estimate anti-SARS-CoV-2 activities

“…These models were developed using experimental data generated by the following assays: the SARS-CoV-2 cytopathic effect (CPE) assay and its host cell cytotoxicity counterscreen, the Spike-ACE2 protein-protein interaction (AlphaLISA) assay and its TruHit counterscreen, the angiotensin-converting enzyme 2 (ACE2) enzymatic activity assay, the 3C-like (3CL) proteinase enzymatic activity assay, the SARS-CoV pseudotyped particle entry (CoV-PPE) assay and its counterscreen, the Middle-East respiratory syndrome coronavirus (MERS-CoV) pseudotyped particle entry assay (MERS-PPE) and its counterscreen and the human fibroblast toxicity (hCYTOX) assay. Such assays represent five distinct categories: viral entry (CPE 1 and host cell cytotoxicity counterscreen 2 ), viral replication (3CL enzymatic activity), live virus infectivity (AlphaLISA, TruHit counter screen, and ACE2 enzymatic activity) 3 , in vitro infectivity (coronavirus pseudotyped particle entry, PPE, with associated counter screens for two other coronaviruses, SARS-CoV and MERS) and human fibroblast cytotoxicity (hCYTOX), respectively, as described in the National Center for Advancing Translational Sciences (NCATS) COVID-19 portal. 4 We retrieved these datasets from the NCATS COVID-19 portal.…”