Biophysical studies of HIV-1 glycoprotein-41 interactions with peptides and small molecules - Effect of lipids and detergents

Time to consider ruling out inclusion bodies denaturing protocols for spontaneous solubilization of biologically active proteins

The formation of inclusion bodies (IBs) in microbial cell factories is a very common process occurring during recombinant protein production. Different protocols have been developed for the extraction of soluble proteins from IBs using several strategies, ranging from the use of harsh denaturing and high concentrations of chaotropic agents and reducing agents to the use of mild protocols based on the use of non-denaturing detergents. However, in recent years, the biological vision of IBs has changed and research studies have demonstrated that these protein aggregates contain biologically active and properly folded recombinant proteins. This drives us to redefine the methodologies currently used to obtain soluble protein using IB as a protein source. Hence, we propose the extraction of IB protein via the simple spontaneous solubilization of IB as a strategy broadly applicable to all kinds of recombinant proteins without the negative effects of detergents and chaotropic agents on final biological activity. We prove the wide applicability of spontaneous solubilization processes to different types of IBs and that protocols can be easily customized for each protein in terms of timing and incubation temperature by monitoring the protein activity of the solubilized fraction.

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

A targeted covalent small molecule inhibitor of HIV-1 fusion

We describe a low molecular weight covalent inhibitor targeting a conserved lysine residue within the hydrophobic pocket of HIV-1 glycoprotein-41. The inhibitor bound selectively to the hydrophobic pocket and exhibited an order of magnitude enhancement of anti-fusion activity against HIV-1 compared to its non-covalent counterpart. The findings represent a significant advance in the quest to obtain non-peptide fusion inhibitors.