Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for En5hanced Presentation of HIV-1 gp41 Epitopes

Abstract

The development of an effective AIDS vaccine remains the most promising long-term strategy to combat human immunodeficiency virus (HIV)/AIDS. Here, we report favorable antigenic characteristics of vaccine candidates isolated from a combinatorial library of human rhinoviruses displaying the ELDKWA epitope of the gp41 glycoprotein of HIV-1. The design principles of this library emerged from the application of molecular modeling calculations in conjunction with our knowledge of previously obtained ELDKWA-displaying chimeras, including knowledge of a chimera with one of the best 2F5-binding characteristics obtained to date. The molecular modeling calculations identified the energetic and structural factors affecting the ability of the epitope to assume conformations capable of fitting into the complementarity determining region of the ELDKWAbinding, broadly neutralizing human mAb 2F5. Individual viruses were isolated from the library following competitive immunoselection and were tested using ELISA and fluorescence quenching experiments. Dissociation constants obtained using both techniques revealed that some of the newly isolated chimeras bind 2F5 with greater affinity than previously identified chimeric rhinoviruses. Molecular dynamics simulations of two of these same chimeras confirmed that their HIV inserts were partially preorganized for binding, which is largely responsible for their corresponding gains in binding affinity. The study illustrates the utility of combining structure-based experiments with computational modeling approaches for improving the odds of selecting vaccine component designs with preferred antigenic characteristics. The results obtained also confirm the flexibility of HRV as a presentation vehicle for HIV epitopes and the potential of this platform for the development of vaccine components against AIDS.Keywords vaccine design; monoclonal antibody 2F5; chimeric virus; reorganization free energy; protein binding

Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses

“…In an effort to produce live-virus immunogens capable of eliciting effective and cross-reactive immune responses against HIV-1, we have made a number of combinatorial libraries of chimeric viruses that display the conserved 2F5 epitope, E 662 LDKWA 667 [49,53], of the HIV-1 membrane-proximal external region (MPER; [35,42]; and this work). This region of the MPER appears to be flexible, normally assuming an extended structure in the N-terminal portion and a helical structure in the C-terminal portion, becoming more extended with β-turn conformations in the presence of 2F5 [31,43,44,54,55,56,57].…”

“…The pST-LIC plasmid was used for all of the genetic engineering. This plasmid was derived from modification of the previously used HRV-encoding p3IIST plasmid [47], whereby the sequences flanking the missing VP2 puff of the NIm-II region of HRV14 [48] were modified to have extended sticky ends to maximize the efficiency of ligation with complementary HIV-encoding DNA oligonucleotides [42]. …”

“…Graphic models were used to design combinatorial libraries in which the epitopes were connected to the HRV loop by short linkers of variable lengths and sequences, optimized to include HIV-like presentations of the epitopes (as has been done previously to generate other immunogenic presentations of HIV epitopes [35,40,41,42]). In the case of the 2F5 epitope presentations, we previously explored novel molecular dynamics simulations approaches that optimized the length, hydrophobicity, and propensity of the epitope for vaccine design [43] aiming to promote the HIV-like type 1 β-turn conformation of this epitope [44].…”

HIV-1 Gag p17 presented as virus-like particles on the E2 scaffold from Geobacillus stearothermophilus induces sustained humoral and cellular immune responses in the absence of IFNγ production by CD4+ T cells

“…Recent advances in understanding of virus assembly have led to the development of methods that chemically and irreversibly inactivate whole virions and that maintain the receptor binding activity of Envelope (Arthur et al, 1998; Lifson et al, 2004). The attractiveness of VLPs that can mimic the natural HIV virion without any risk of HIV infection led to the early development of recombinant Gag-Env particles produced in mammalian cells by recombinant vaccinia virus (Haffar et al, 1990; Haffar et al, 1992; Haffar et al, 1991; Luo, Li, and Yong Kang, 2003), or rhinovirus chimeras (Arnold et al, 1994; Lapelosa et al, 2010), yeast (Tsunetsugu-Yokota et al, 2003), or in other systems, reviewed in (Deml et al, 2005). While clearly immunogenic in eliciting Gag-specific CTL (Paliard et al, 2000) and antibodies, including some neutralizing antibodies (Ding et al, 2002), none of these approaches has elicited strong protective immunity.…”

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

“…The corresponding reorganization free energy is recognized as an important component of the binding free energy 45 and a key factor needed to understand ligand affinity and specificity. 46 We have previously shown that conformational reorganization upon binding plays a pivotal role in cases, such as epitope-antibody binding, 47,48 in which there are small variations in the binding interface and most of the variations in binding affinities are due to differences in reorganization of the binding partners. Binding reorganization effects have been shown to be important in the FKBP12 system as well.…”