Identification of ligands that target the HCV-E2 binding site on CD81

Abstract

Hepatitis C is a global health problem. While many drug companies have active R&D efforts to develop new drugs for treating Hepatitis C virus (HCV), most target the viral enzymes. The HCV glycoprotein E2 has been shown to play an essential role in hepatocyte invasion by binding to CD81 and other cell surface receptors. This paper describes the use of AutoDock to identify ligand binding sites on the large extracellular loop of the open conformation of CD81 and to perform virtual screening runs to identify sets of small molecule ligands predicted to bind to two of these sites. The best sites selected by AutoLigand were located in regions identified by mutational studies to be the site of E2 binding. Thirty-six ligands predicted by AutoDock to bind to these sites were subsequently tested experimentally to determine if they bound to CD81-LEL. Binding assays conducted using surface Plasmon resonance revealed that 26 out of 36 (72 %) of the ligands bound in vitro to the recombinant CD81-LEL protein. Competition experiments performed using dual polarization interferometry showed that one of the ligands predicted to bind to the large cleft between the C and D helices was also effective in blocking E2 binding to CD81-LEL.

Target-specificity of different amyrin subunits in impeding HCV influx mechanism inside the human cells considering the quantum tunnel profiles and molecular strings of the CD81 receptor: a combined in silico and in vivo study

“…6 A). The control ligand Benzyl-salicylate scored between 0 Å to 1.759 Å as reported in established literature as well (Olaby et al 2013 ). In the case of the ligand RMSD, the same phenomena were found for both the β and δ-amyrins, where the α-amyrin fluctuation range was the highest, making it a less effective drug candidate (Fig.…”

Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop

“…Across the four hCD81 LEL molecules crystallized previously, the head subdomain shows conformational flexibility within helices C and D (consensus residues 165-172 and 180-186, respectively), adopting closed and open conformations even within the same crystal (Kitadokoro et al, 2001(Kitadokoro et al, , 2002. This variability has cast doubt on whether these conformations are physiologically relevant (Olaby et al, 2013;Rajesh et al, 2012;Holzer et al, 2008;Neugebauer et al, 2004). Using nuclear magnetic resonance (NMR), hCD81 LEL helix D appears to be disordered in solution (at pH 7.0), whereas previous energy minimization studies suggested that helix D is ordered and forming a narrow cleft with helix C (closed conformation) (Rajesh et al, 2012;Neugebauer et al, 2004).…”

Targeting of Tetraspanin CD81 with Monoclonal Antibodies and Small Molecules to Combat Cancers and Viral Diseases

“…However, a few direct CD81 binders have been identified through a virtual screening approach, such as the indole derivative 30 ( Figure 5 ) which was predicted to bind to CD81 EC2 and then experimentally confirmed as a ligand for CD81 using surface plasmon resonance (SPR). This 5-benzyloxyindole derivative is indeed a weak ligand for CD81 EC2 (K D = 2.01 × 10 −4 M) [ 149 ]. Two other synthetic molecules have been identified as CD81 binders: (i) the antihistaminic drug fexofenadine approved to treat seasonal allergic rhinitis and chronic idiopathic urticaria (a common skin allergy), and (ii) benzyl salicylate, a natural ingredient of many essential oils, largely used as a fragrance chemical (and an allergenic compound).…”