HIV cell entry

The earliest opportunity to block virus replication is to prevent the virus from entering the host cell. When HIV enters a host cell its surface glycoprotein gp120 attaches to the CD4 receptor and one of two cellular coreceptors: CCR5 or CXCR4. The occurrence of CXCR4-using HIV-1 variants often indicates an advanced stage of infection and accelerated disease progression. Several antiviral drugs that target these coreceptors are currently being developed.
In this project we tested viral variants for their cell entry efficiency depending on the receptor and coreceptor concentration on the cell surface and presence and concentration of entry inhibitors. We developed quantitative methods for analyzing single cell data from flow cytometry and fluorescence microscopy. Based on the single-cell data we constructed regression models of the viral cell entry phenotype. The models describe a spectrum of virus phenotypes beyond the binary tropism classification.
Our phenotype representation comprises several determinants of the virus cell entry including virus response to entry inhibitors. We are currently developing a predictive model of this representation of the virus cell entry phenotype that has a potential of assisting the application of entry inhibitor-based patient therapies.

Bozek K, Eckhardt M, Sierra S, Kaiser R, Kräusslich HG, Müller B, Lengauer T. An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data. Retrovirology 2012 Jul 25;9:60.

Bozek K, Thielen A, Sierra S, Kaiser R, Lengauer T. V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV. PLoS One. 2009 Oct 9;4(10):e7387.

HIV-host co-evolution

Human immunodeficiency viruses (HIV-1 and HIV-2) entered the human population through several cross-species transmission events of simian immunodeficiency virus (SIV). SIV infection has been reported for more than 35 African monkey species, however monkeys naturally infected with SIV do not develop disease.
In this work I did a comparative analysis of HIV-interacting genes in primates and corresponding HIV/SIV genomes. I identified specific host factors being under positive selection in primates which might reflect evolution in response to various infections. These genetic polymorphisms can influence host susceptibility to the disease and indicate a potential contribution of a gene to the HIV/SIV infection.
I also compared the strength of positive selection in host proteins with the evolutionary rates of the interacting virus genes. I found a significant correlation between the amount of evolutionary change in the interacting host and virus genes which suggests reciprocal evolutionary effects between host and pathogen.

Bozek K, Lengauer T. Positive selection of HIV host factors and the evolution of lentivirus genes. BMC Evol Biol. 2010 Jun 18;10:186.

SIV/HIV capsid - primate TRIM5α interaction

In collaboration with the group of Prof. Tatsuo Shioda at the Department of Viral Infection, Osaka University we have been working on the structural and genetic determinants of the primate TRIM5α - SIV/HIV capsid interaction. TRIM5α is a host restriction factor capable of blocking infection by binding the virus capsid protein in a species-specific manner. Understanding the determinants of this interaction has potential theurapeutic interest. We have been analyzing inhibitory capacities of different viral and primate protein variants.

Kono K, Bozek K, Domingues FS, Shioda T, Nakayama EE. Impact of a single amino acid in the variable region 2 of the Old World monkey TRIM5alpha SPRY (B30.2) domain on anti-human immunodeficiency virus type 2 activity. Virology. 2009 May 25;388(1):160-8. Epub 2009 Apr 1.

Kuroishi A, Bozek K, Shioda T, Nakayama EE.A single amino acid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5alpha. Retrovirology. 2010 Jul 7;7:58.

Bozek K, Nakayama EE, Kono K, Shioda T. Electrostatic potential of human immunodeficiency virus type 2 and rhesus macaque simian immunodeficiency virus capsid proteins. Front Microbiol. 2012 Jun 5;3:206

Structural descriptor of HIV V3 loop

Understanding HIV coreceptor usage is essential both in patient treatment with entry inhibitors as well as for monitoring disease progression. Coreceptor usage is predominantly encoded in the third highly variable loop (V3 loop) of the viral gp120 protein. As an alternative to the costly phenotypic assays that measure viral coreceptor usage in vivo, computational methods (e.g. geno2pheno, WebPSSM) can be used to predict viral phenotype based on the V3 loop sequence. Existing prediction are based on binary representation of the V3 sequence that does not encode biochemical similarities among amino acids and provide limited insights into the molecular determinants of coreceptor usage.
In this project we used the crystalized structure of the HIV gp120 protein to build a numerical descriptor of the V3 loop. The descriptor encodes the physicochemical properties of the loop together with their locations in the protein structure. The descriptor allows for structure-based prediction of HIV tropism and identification of structural and physicochemical properties of the V3 loop that are crucial for coreceptor usage. Prediction software is available as a server application.

Bozek K, Lengauer T, Sierra S, Kaiser R, Domingues FS. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage. PLoS Comput Biol. 2013;9(3):e1002977