**5. Conclusions**

and number of predicted non-target epitopes at the junction. Finally, the software designs an optimal polyepitope immunogen sequence that is calculated as a complete simple way in the

Besides, PolyCTLDesigner makes it possible to construct a sequence of the epitope fragment comprising T-helper epitopes. In the compound of the selected antigens software predicts peptide fragments with the length of 20–40 amino acid residues with the majority of overlapping T-helper epitopes restricted by the widest possible repertoire of HLA class II allomorphs. Then five C- and N-terminal amino acid residues from the initial antigen sequence are added to each of the selected fragments since it was shown that they can play significant role in binding to T-cell receptors of CD4+ T-lymphocytes [76, 77]. Fragments with T-helper epitopes are combined using [KR][KR] motif which is a cleavage site for a number of lysosomal cathepsins

More detailed information on PolyCTLDesigner software is available at http://tepredict.

We used the developed software when designing new polyepitope constructs – candidate DNA-vaccines against HIV-1. Particularly, when evaluating the influence of proteasomedependent and lysosome-dependent degradation of polyepitopes on immunogenicity of the target polyepitope construct, we designed three polyepitope HIV-1 immunogens, i.e. TСI-N1,

All three polyepitope immunogens are based on the same core sequence of polyE, while differences between immunogens lie in the use of different terminal signal sequences (**Figure 6**). Immunogen TCI-N1 comprises only the core sequence polyE. Sequence polyE of TCI-N2 immunogen includes

**Figure 6.** Design of T-cell polyepitope immunogens. polyE – common for all antigens sequence polyE designed using cytotoxic and helper T-cell epitopes of HIV-1; ER-signal – N-terminal signal peptide (in our case MRYMILGLLALAAVCSAA – the signal sequence of the adenovirus protein E3/gp19K); LAMP1 – C-terminal tyrosine-based motif of LAMP-1 glycoprotein (RKRSHAGYQTI); Ub – N-terminal ubiquitin with substitution of the C-terminal Gly to Val to prevent

TСI-N2, and TСI-N3 using cytotoxic and helper T-cell epitopes of HIV-1 [78].

constructed graph with the least length (weight).

involved in antigen processing.

216 Advances in HIV and AIDS Control

liberation of Ub cleavage by Ub hydrolases.

sourceforge.net/PolyCTLDesigner.html.

We did not set ourselves the task of covering all challenges facing designers of HIV-1 vaccine. The paper presents our experience on designing artificial polyepitope HIV-1 immunogens constructed using a broad spectrum of conservative T- and B-cell epitopes. This approach is believed to be promising for the design of new generation HIV-vaccines. In theory, it makes it possible to overcome HIV-1 antigenic variability, focuses immune responses on protective determinants, and allows to exclude from vaccine composition undesired determinants capable of inducing autoantibodies or antibodies increasing virus infectivity. The results demonstrate that completely artificial molecules designed with the use of bioinformatic and combinatorial biology methods are able to induce production of broad-spectrum neutralizing antibodies and responses of cytotoxic (CD8+ CTL) and helper (CD4+ Th) T-lymphocytes in laboratory animals and human.

It is our belief that the proposed approach can play an important and positive role in the development of HIV-1 vaccine.
