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Glycolipids Against the HIV

#B-1830


Development of the Potential Drugs for AIDS Therapy: Glycolipids Against the HIV-1 gp120 V3 Loop

Tech Area / Field

  • BIO-CHM/Biochemistry/Biotechnology
  • MED-DRG/Drug Discovery/Medicine

Status
3 Approved without Funding

Registration date
25.03.2010

Leading Institute
Institute of Bioorganic Chemistry, Belarus, Minsk

Supporting institutes

  • Belarussian Research Institute for Epidemiology and Microbiology, Belarus, Minsk\nNational Academy of Sciences of the Republic of Belarus / Institute of Informatics Problems, Belarus, Minsk

Collaborators

  • University of Quebec at Montreal / Departement de Chimie et de Biochimie, Canada, QC, Montreal\nUniversitat Leipzig / Institute of Medical Physics and Biophysics, Germany, Leipzig\nUniversity of Amsterdam / Academic Medical Center, The Netherlands, Amsterdam

Project summary

Project goal

The goals of the project are (i) to generate the high-resolution models describing the 3D structure and dynamic features for the complexes of the HIV-1 subtype A and B V3 loops with galactosylceramide (GalCer) water soluble analogs of which, versus the data of literature, may block the virus replication by specific interactions with V3, and (ii) based on the design data, to implement the computer modeling of the modified glycolipid forms capable of more efficacious (as compared to the native molecule) masking of the HIV-1 principal neutralizing determinant followed by their synthesis, testing, and selection of the basic structures presenting the most promising targets for anti-AIDS drugs development.

One needs to stress that the main task of theoretical part of the project is to obtain the structural data necessary for achieving its final point that consists in getting of the forward-looking pharmacological substances on the basis of which the efficacious and safe anti-AIDS drugs exhibiting a broadly neutralizing effect may be developed. Moreover, extensive sample material on the HIV-1 that will be collected in Belarus due to molecular-epidemiological monitoring is also of great importance for testing of the constructed and synthesized chemicals as well as for better understanding of the patterns of resistant mutations in the HIV-1 genome.

Introduction and Overview

The problem. Modern approaches to treatment of the HIV-1 infection (highly active antiretroviral therapy, or HAART) slow down its progress and transition into AIDS stage. However, due to high variability of the virus strains this process is accompanied by intensive mutations in the virus genome. This leads to drug resistance which is a major obstacle to the effective treatment. Although different antiretroviral drugs have been approved for the treatment of HIV-1, cross-resistance within each of the antiretroviral drug classes (nucleotide and nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, protease inhibitors etc.) often leads to the development of multidrug resistance (Rhee S.-Y., Fessel W.J. et al., 2005; Gonzales, M. J., Machekano R. N., Shafer R. W., 2001). This process is accompanied by structural changes of the corresponding proteins that are responsible for the HIV-1 vital activities. The potential pharmacological substances for the HIV-1 preventive maintenance and treatment designed in the project and based on blocking the structurally conserved and functionally critical V3 loop sites may also be affected by these consequences. Nevertheless, in practice only a subset of treatment-associated mutations is responsible for establishment of drug-resistance.

Past works. In spite of disappointing progress over more than a decade, studies on the design of anti-HIV-1 drugs and vaccines to protect against viral infection have still been focused on gp120 V3 loop (see, e.g., Sirois S., Sing T., Chou K.C., 2005). Comprehensive analysis of the literature makes it clear (Hartley O., Klasse P.J., Sattentau Q.J., Moore J.P., 2005; Sirois S., Sing T., Chou K.C., 2005) that relatively little is known about structural properties of V3, and available data provide one with insufficient and conflicting information on its structure. To all appearance, the ambiguity of knowledge of the V3 loop structure can be provoked by the high variability of its amino acid sequence, which stimulates the structural reconstruction of the fragment resulting in the differences of its 3D structures in various viral isolates. Collation of the V3 amino acid sequences in perse virus modifications bears witness that, in spite of intensive mutations of the primary structure, this site of gp120 is well disposed towards preserving the inpidual amino acids both in its central region and the terminal stretches. Moreover, analysis of the database of the Protein Data Bank reveals that currently it contains information on the 3D structures of a number of glycolipids including GalCer. However, there is no evidence for their water soluble analogs and structural complexes with V3 in the specified information source.

The demand. Careful analysis of the literature data on the V3 loop structures testifies to the availability of contradictions between the models of different authors, which does not allow one to answer a number of questions concerning the principles of functioning of the virus principal neutralizing determinant. Due to the absence of the X-ray data on the complexes of GalCer and its derivatives with the V3 variable loops the usage of the methods of computer modeling presents the most rational way to get the detailed information on the principles of their structural organization. Moreover, most of the published data on the HIV-1 V3 structures and drug resistance relates to the virus subtype B dominating in the North America and Western Europe, whereas the majority of infection cases in Eastern Europe including Republic of Belarus deals with the HIV-1 subtype A. Finally, a lot of new data on the HIV-1 vital activity, V3 structures, and its complexes with the promising pharmacological substances will be obtained here not only for scientific purposes but also for practical use, namely for the further AIDS prevention and treatment of real patients.

Influence to the progress. Providing scientific community with the data on the high-resolution 3D structures of the HIV-1 V3 loops and their complexes with GalCer-WSAs followed by the experimental trials of the constructed potential pharmacological substances as well as deriving the new analytical information on the HIV-1 mutations development may contribute appreciably to removal of some weak spots existing in the V3-based anti-AIDS drug studies.

Project participants and their roles. Scientific team of the project includes the specialists from several areas of fundamental and applied researches: biology, medicine, chemistry, and information technologies. They came from the leading Belarusian centers, namely Institute of Bioorganic Chemistry (IBOCH), Republican Research and Practical Center for Epidemiology and Microbiology (RRPCEM), and United Institute of Informatics Problems (UIIP). The role of IBOCH is to set up the research hypotheses, generate the V3 loop structures, design and synthesize the potential anti-AIDS drugs. The role of RRPCEM is to set up the research hypotheses, collect clinical data, prepare biological probes, test constructed substances, and create a HIV sequence database. The role of UIIP professionals is mostly focused on computer modeling and HIV sequence analysis. Other activities such as testing research hypotheses and checking mathematical models are supposed to be performed jointly.

Expected Results and their Application

Specific results. Implementation of the project tasks will bring in the following specific outcomes:

  1. High-resolution 3D structure models of the HIV-1 subtype A and B V3 loops.
  2. 3D models of GalCer-WSAs structures and their complexes with the HIV-1 V3 loops.
  3. List of glycolipids most promising for synthesis.
  4. Synthesized glycolipids according to the design data.
  5. Register of glycolipids selected as a result of their testing for antiretroviral activity.
  6. List of resistant mutations in the HIV-1 genes revealed during in-vitro trials.
  7. Specified HIV-1 strains circulating in Belarus.

General results. Synthetic chemical compounds designed and tested in the project may form a new class of the molecules presenting the promising basic structures for making a reality of the protein engineering projects aimed at development of the anti-AIDS drugs for therapy of patients in Eastern Europe. Based on the results of in-vitro trials for synthesized substances and other medical products taken at different dozes, the dynamics of mutation development in separate HIV-1 genome regions and its contribution to drug resistance establishment will be analyzed.

Project consequences. In scientific area, the project will cast light on the 3D structures of GalCer-WSAs feeling a strong attraction to V3 and blocking its structurally conserved sites. In practical domain, it will provide one with the chemical compounds that may mask efficiently the biologically active stretches of the HIV-1 gp120 envelope protein. Insight into the new experimental data on the HIV-1 subtype A and its analysis for resistant mutations will afford one with important information for decision-making on identification of antiretroviral therapy failure. It may enable one to specify the time domain when one needs to switch to another treatment regimen as well as to define its elements that have to be changed. In the field of commerce, the project will supply one with the forward-looking chemicals for anti-AIDS drug development.

Application areas. They include molecular dynamics, molecular docking, statistical analysis of bioinformatics data, chemical synthesis, HIV-1 studies, and medical education.

Dissemination. Since all of the Institutions participating in the project present the leading Belarusian scientific centers in their professional areas, this secures a high level of conducted research and legal, duly organized dissemination of the results in the Republic of Belarus and worldwide.

Meeting ISTC Goals and Objectives

Meeting ISTC goals and objectives is achieved by:

  1. providing former weapons scientists for opportunities to redirect their talents and experience to a highly humanistic problem of HIV/AIDS therapy;
  2. integration of project participants into the international community of HIV research by dissemination of new data and novel results on HIV proteins structure and vital activity;
  3. supporting applied research for peaceful and extremely important purposes of human health;
  4. contributing to the solution of the problem of developing new efficient methods for HIV treatment and drug design, discovering fundamental problems concerning development of resistant mutations in HIV-1 subtypes A and B;
  5. reinforcing the transition of applied science sector to market-based economies responsive to civil needs.

Scope of Activities

Project scope. The whole bunch of project activities is naturally subpided into the three groups of actions that can be conditionally referred to as engineering, chemical and medical. The engineering wing (UIIP, IBOCH) is liable for modeling the HIV-1 V3 loop structure, developing the data analysis and statistical assessment algorithms. The biochemical wing (IBOCH) is responsible for the design and synthesis of potential drug substances. The medical wing (RPCEM) is mostly liable for in vitro testing of synthesized substances and HIV genome data acquisition. The final study of selection between potential pharmacological substances and interpretation of the results of HIV mutation analysis is performed jointly.

Project efforts. The total number of project participants is 27 with the total project effort of 5839 person*days. It includes 10 engineering participants with the total effort of 2134 person*days, 9 biochemical participants with the total effort of 2025 person*days and 8 medical with the efforts of 1680 person*days.

Project specificity. The characteristic point of this project is very large amount of computations used for potential pharmacological substance design, modeling and analysis efforts.

Role of Foreign Collaborators

Involvement of foreign collaborators is based on their genuine interests in both verifying the proposed ideas for anti-AIDS drug design and the unique collection of material on the HIV-1 subtype A resistance development. Specifically, the role of foreign collaborators is:

  1. to conduct joint expertise of the HIV-1 data including phylogenetic analysis and interpretation of mutations;
  2. to validate the intermediate project results and to provide advices on further steps;
  3. to provide help in development of methods for synthesis and analysis of the designed pharmacological substances;
  4. to participate in preparation of joint publications resulted from the project and dissemination of the results;
  5. to provide technical help and occasional, non-systematic use of lab equipment in cases of high mutual interests;
  6. it is anticipated that the collaborators will submit further proposals based on the results obtained within the project.

Technical Approach and Methodology

By comprehensive approach combining homology modeling with molecular docking structural analysis of the protein-glycolipid complexes is proposed to be implemented from the data on the X-ray conformation of GalCer and spatial structures of the HIV-1 subtype A and B V3 loop giving rise to the virus principal neutralizing determinant as well as determinants of cell tropism and syncutium formation. Because of absence of the X-ray structures for these complexes the joint employment of the methods of comparative modeling with molecular docking tools is the most rational way to get the detailed and reliable information on the principles of their structural organization. The suggested methodology providing for utilization of glycolipids as potential therapeutic agents presents an alternative to the traditional approach where antibodies elicited to V3 are commonly used to neutralize the HIV-1 infectivity and has no analogues in the literature.


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