In Silico Evaluation of Hexamethylene Amiloride Derivatives as Potential Luminal Inhibitors of SARS-CoV-2 E Protein

Abstract

The coronavirus E proteins are small membrane proteins found in the virus envelope of alpha and beta coronaviruses that have a high degree of overlap in their biochemical and functional properties despite minor sequence variations. The SARS-CoV-2 E is a 75-amino acid transmembrane protein capable of acting as an ion channel when assembled in a pentameric fashion. Various studies have found that hexamethylene amiloride (HMA) can inhibit the ion channel activity of the E protein in bilayers and also inhibit viral replication in cultured cells. Here, we use the available structural data in conjunction with homology modelling to build a comprehensive model of the E protein to assess potential binding sites and molecular interactions of HMA derivatives. Furthermore, we employed an iterative cycle of molecular modelling, extensive docking simulations, molecular dynamics and leveraging steered molecular dynamics to better understand the pore characteristics and quantify the affinity of the bound ligands. Results from this work highlight the potential of acylguanidines as blockers of the E protein and guide the development of subsequent small molecule inhibitors.

Comparative genomics of spike, envelope, and nucleocapsid protein of severe acute respiratory syndrome coronavirus 2

“…E-protein is crucial for viral genome packaging and the synthesis of ion channels (IC), which are vital for virus-host contact and are frequently associated with pathogenicity 15 , 31 , 46 . We have observed one amino acid mutation of Proline (P) to Leucine (L) at the 71 st locus in the E-protein of SARS-CoV-2 (South Africa).…”

“…E-proteins are polypeptides with approximately 100 residues that are miniature components of virions but are extensively synthesized within infected cells 47,48 . They exhibit a small hydrophilic N-terminus, one or more putative terminal transmembrane (TM) domains, and a less hydrophobic C-terminal tail (15). Previously, it was demonstrated that SNPs within the TMD domain of the E-protein impaired IC function and resulted in reduced viral virulence 49 .…”

“…Asides from spike protein, SARS-CoV-2 also embodies additional structural proteins such as E-protein and N-protein. E-protein is crucial for viral genome packaging and the synthesis of ion channels (IC), which are vital for virus-host contact and are frequently associated with pathogenicity 15 , 16 . In contrast, the N-protein serves a variety of roles in the CoV virus replication.…”

Viroporins Manipulate Cellular Powerhouses and Modulate Innate Immunity

“…Thus, other ion channel inhibitors (pharmacophores), among the aromatic heterocyclic compounds that can strongly bind to proteins, were investigated, such as the spirene guanidine analogue, 2-[3-azaspiro (5,5) undecanol]-2-imidazoline (BL-1743) [ 117 ]. Other molecules, such as tauroursodeoxycholic acid as hexamethylene amiloride [ 118 ], gliclazide [ 119 ], memantine and other flavonoids such as epigallocatechin and quercetin were also effective [ 112 ].…”