Alexander M. Andrianov

Computational Model of the HIV-1 Subtype A V3 Loop: Study on the Conformational Mobility for Structure-Based Anti-AIDS Drug Design

Abstract The V3 loop of the HIV-1gp120 glycoprotein presenting 35-residue-long, frequently glycosylated, highly variable, and disulfide bonded structure plays the central role in the virus biology and forms the principal target for neutralizing antibodies and the major viral determinant for co-receptor binding. Here we present the computer-aided studies on the 3D structure of the HIV-1 subtype A V3 loop (SA-V3 loop) in which its structurally inflexible regions and individual amino acids were identified and the structure-function analysis of V3 aimed at the informational support for anti-AIDS drug researches was put into practice. To this end, the following successive steps were carried out: (i) using the methods of comparative modeling and simulated annealing, the ensemble of the low-energy structures was generated for the consensus amino acid sequence of the SA-V3 loop and its most probable conformation was defined basing on the general criteria widely adopted as a measure of the quality of protein structures in terms of their 3D folds and local geometry; (ii) the elements of secondary V3 structures in the built conformations were characterized and careful analysis of the corresponding data arising from experimental observations for the V3 loops in various HIV-1 strains was made; (iii) to reveal common structural motifs in the HIV-1 V3 loops regardless of their sequence variability and medium inconstancy, the simulated structures were collated with each other as well as with those of V3 deciphered by NMR spectroscopy and X-ray studies for diverse virus isolates in different environments; (iv) with the object of delving into the conformational features of the SA-V3 loop, molecular dynamics trajectory was computed from its static 3D structure followed by determining the structurally rigid V3 segments and comparing the findings obtained with the ones derived hereinbefore; and (v) to evaluate the masking effect that can occur due to interaction of the SA-V3 loop with the two virtual molecules constructed previously by tools of computational modeling and named FKBP and CycA peptides, molecular docking of V3 with these molecules was implemented and inter-atomic contacts appearing in the simulated complexes were analyzed to specify the V3 stretches keeping in touch with the ligands. As a matter of record, V3 segments 3–7, 15–20, and 28–32 containing the highly conserved and biologically meaningful residues of gp120 were shown to retain their 3D main chain shapes in all the cases of interest presenting the forward-looking targets for anti-AIDS drug researches. From the data on molecular docking, synthetic analogs of the CycA and FKBP peptides were suggested being suitable frameworks for making a reality of the V3-based anti-HIV-1 drug projects.

Immunophilins and HIV-1 V3 loop for structure-based anti-AIDS drug design.

Abstract The model of the structural complex of cyclophilin A (CycA) belonging to the immunophilins family with the HIV-MN gpl20 V3 loop was generated, and the computer-aided design of the immunophilin-derived peptide able to mask the biologically crucial V3 segments was implemented. To this end, the following problems were solved: (i) the NMR-based conformational analysis of the HIV-MN V3 loop was put into effect, and its low energy structure fitting the input experimental observations was determined; (ii) molecular docking of this V3 structure with the X-ray conformation of CycA was carried out, and the energy refining the simulated structural complex was performed; (iii) the matrix of inter-atomic distances for the amino acids of the molecules forming part of the built over-molecular ensemble was computed, the types of interactions responsible for its stabilization were analyzed, and the CycA stretch, which accounts for the binding to V3, was identified; (iv) the most probable 3D structure for this stretch in the unbound state was predicted, and its collation with the X-ray structure for the corresponding site of CycA was performed; (v) the potential energy function and its constituents were studied for the structural complex generated by molecular docking of the V3 loop with the CycA peptide offering the virtual molecule that imitates the CycA segment, making a key contribution to the interactions of the native protein with the HIV-1 principal neutralizing determinant; (vi) as a result of the studies above, the designed molecule was shown to be capable of the efficacious blockading the functionally crucial V3 sites; and (vii) based on the joint analysis of the evidence obtained previously and in the present study, the composition of the peptide cocktail presenting the promising anti-AIDS pharmacological substance was developed. The molecules simulated here by molecular modeling methods may become the first representatives of a new class of the chemical compounds (immunophilin-derived peptides) offering the looking-forward basic structures for the design of efficacious and safe antiviral agents.

Local Structural Properties of the V3 Loop of Thailand HIV-1 Isolate

Abstract The model of locally accurate conformation for the HIV-Thailand principal neutralizing determinant (PND) located within the V3 loop of the virus envelope protein gp 120 was built in terms of NMR spectroscopy data. To this end, the NMR-based conformational analysis of synthetic molecule representing the peptide copy of the fragment under study was carried out using the published sequential d connectivity data and values of spin-spin coupling constants. As a result, (i) the local structure for the V3 loop from Thailand isolate was determined, (ii) the conformations of its irregular segments were analyzed, and the secondary structure elements identified, (iii) the ensemble of conformers matching the experimental and theoretical data was derived for the stretch forming the neutralizing epitope of the HIV-Thailand PND, (iv) to estimate the probability of realizing each of these conformers in solution, the results obtained were collated with the X-ray data for corresponding segments in synthetic molecules imitating the central region of the HIV-MN PND as well as for homologous segments 39–44 in Bence-Jonce REI protein (BJRP), 41–46 in immunoglobulin λ (Igλ), and 50–55 in β-chain of horse hemoglobin (HH), (v) to find the conserved structural motifs inside diverse HIV-1 isolates, the structure determined was compared with the one derived earlier for the HIV-MN PND from NMR spectroscopy data, (vi) on the basis of all data obtained, the 3D structure model describing the set of biologically relevant conformations, which may present different antigenic determinants to the immune system in various HIV-1 isolates, was proposed for the immunogenic crown of the V3 loop. The results obtained are discussed in conjunction with the data on the structure for the HIV-1 PND reported in literature.

Structure and polymorphism of the principal neutralization site of Thailand HIV-1 isolate

Abstract Refining the geometric parameters for the ensemble of conformers, derived earlier in terms of NMR-spectroscopy data for the immunogenic tip of Thailand HIV-1 isolate, was carried out by quantum chemical methods. As a result, (i) the energy characteristics of initial structures were significanly improved, (ii) their relative locations on the scale of formation heats were determined, and (iii) the energy barriers between conformers under study were computed. On the basis of all data obtained, the high resotion 3D structure model, describing the set of stable conformers and containing the biologically active conformation, was proposed for neutralizing epitope of Thailand HIV-1 isolate. The following major conclusions were made based on the analysis of simulated conformations: i) the Gly-Pro-Gly-Gln-Val-Phe stretch forming the immunogenic crown of Thailand HIV-1 isolate exhibits the properties characteristic for metastable oligopeptide that constitutes in solution the dominant structure with other conformations admissible; (ii) three structures out of five NMR-based starting models form the cluster of conformers which adequately describes general conformational features of this functionally important site of gp120; (iii) two structures residing in this cluster are found to be well-ground for implementing the function of immunoreactive conformation of the stretch of interest; (iv) in spite of this observation, the “global” structure which gives rise to inverse γ-turn in the central Gly-Pro-Gly crest of Thailand HIV-1 gp120 is proposed to be the most probable conformation responsible for the formation of viral antigen-antibody complex in particular case under study.

GLOBAL AND LOCAL STRUCTURAL PROPERTIES OF THE PRINCIPAL NEUTRALIZING DETERMINANT OF THE HIV-1 ENVELOPE PROTEIN GP120

The model of spatial structure for the principal neutralizing determinant (PND) of the HIV-1 envelope protein gp120 is proposed in terms of two-dimensional nuclear Overhauser effect (NOE) spectroscopy data. To build the model, the NMR-based theoretical conformational analysis of synthetic PND peptides of length 40, 24, and 12 residues is carried out. The modeling of the molecular spatial structures is performed by a new approach to research of conformationally mobile peptides using the algorithms of the restrained molecular mechanics method developed earlier. The following major conclusions are made based on the analysis of the simulated peptide conformations: i) there is not unique PND structure in solution, ii) there are seven different PND structures each of which agrees with the experimental data and stereochemical criteria used in computing its spatial model, iii) the PND is characterized by irregular conformation containing a number of reverse turns, iv) all of the selected conformations are conserved in the Gly-Pro-Gly-Arg-Ala-Phe stretch, the most probable viral immunodominant epitope. These data allow to suppose that binding properties of this site are determined by the structural motif which forms the conformation of a double beta-turn and appears common for all hexapeptide structures.

3D Structure Model of the Principal Neutralizing Epitope of Minnesota HIV-1 Isolate

Abstract A hierarchical procedure, using a “bottom-up” strategy and combining (i) a probabilistic approach for estimating all possible starting structures, (ii) restrained molecular mechanics algorithms for preliminary selection of all energetically preferred conformers, as well as (iii) quantum chemical computations for refining their geometry, was used to study the structural properties of the HIV-MN neutralizing epitope in terms of NMR spectroscopy data. As a result, only one of initial structures matching the experimental and theoretical data was found to be well-ground for implementing the function of immunoreactive conformation of the virus immunogenic crown. The geometric parameters of this structure in water solution were shown to correspond to a double β-turn conformation similar to that revealed in crystal for synthetic molecules imitating the central region of the HIV-MN V3 loop. The following conclusion was drawn from the comparative analysis of simulated structure with the one computed previously: the HIV-MN immunogenic tip has some inherent conformational flexibility that manifests at the alterations of hexapeptide environment and leads to the structural transitions changing the local conformation of the stretch of interest but retaining its spatial main chain fold. As a matter of record, the high resolution 3D structure model for the HIV-MN principal neutralization site was constructed, and its geometric parameters were compared with the corresponding characteristics of conformers derived earlier for describing the conformational features of immunogenic tip of gp120 from Thailand HIV-1 isolate. The results are discussed in the light of literature data on HIV-1 neutralizing epitope structure.

Dual Spatial Folds and Different Local Structures of the HIV-1 Immunogenic Crown in Various Virus Isolates

Abstract Local and global structural properties of the HIV-1 principal neutralizing epitope were studied in terms of NMR spectroscopy data reported in literature for the HIV-Haiti and HIV-RF isolates. To this effect, the NMR-based method comprising a probabilistic model of protein conformation in conjunction with the molecular mechanics and quantum chemical computations was used for determining the ensembles of conformers matching the NMR requirements and energy criteria. As a matter of record, the high resolution 3D structure models were constructed for the HIV-Haiti and HIV-RF immuno- genic crowns, and their geometric parameters were collated with the ones of conformers derived previously for describing the conformational features of immunogenic tip of gp120 from Thailand and MN HIV-1 strains. The HIV-1 neutralization site was demonstrated to constitute in water solution highly flexible system sensitive to its environment. This inference is completely valid for the geometric space of dihedral angles where statistically significant differences in local structures of simulated conformers have been found for all virus isolates of interest. In spite of this fact, the stretch analyzed was shown to manifest a certain conservatism in the space of atomic coordinates, building up in four HIV-1 isolates two spatial folds similar to those observed in crystal for the V3 loop peptides bound to different neutralizing Fabs. The results are discussed in the light of literature data on HIV-1 neutralizing epitope structure.

Discovery of novel promising targets for anti-AIDS drug developments by computer modeling: application to the HIV-1 gp120 V3 loop.

The V3 loop on gp120 from HIV-1 is a focus of many research groups involved in anti-AIDS drug studies, because this region of the protein determines the preference of the virus for T-lymphocytes or primary macrophages. Although the V3 loop governs cell tropism and, for this reason, exhibits one of the most attractive targets for anti-HIV-1 drug developments, its high sequence variability is a major complicating factor. Nevertheless, the data on the spatial arrangement of V3 obtained here for different HIV-1 subtypes by computer modeling clearly show that, despite a wide range of 3D folds, this functionally important site of gp120 forms at least three structurally invariant segments, which contain residues critical for cell tropism. It is evident that these conserved V3 segments represent potential HIV-1 vulnerable spots and, therefore, provide a blueprint for the design of novel, potent and broad antiviral agents able to stop the HIVs spread.

Computational anti-AIDS drug design based on the analysis of the specific interactions between immunophilins and the HIV-1 gp120 V3 loop. Application to the FK506-binding protein.

Abstract The object of the study was to model the structural complex of the FK506-binding protein (FKBP) with the CRK peptide imitating the central region of the HIV-1 V3 loop, as well as to define the FKBP stretch giving rise to the binding site for V3 the synthetic copy of which, on the assumption of preserving the spatial peptide structure in the free state, can be considered as a promising applicant for the role of antiviral drug. To this end, the following successive steps were carried out: (i) the NMR-based conformational analysis of CRK was put into practice, and, in the light of the results derived, the best energy CRK structure meeting the requirements of the input NMR data was identified; (ii) molecular docking of the CRK structure with the X-ray FKBP conformation was implemented, and energy refining the simulated structural complex was realized; (iii) the matrix of distances between amino acids of the ligand and receptor was computed to specify the FKBP stretch keeping in touch with CRK followed by analyzing the types of interactions stabilizing the over-molecular ensemble; (iv) 3D structure of this stretch in the unbound status referred to as the FKBP peptide was predicted, and its collation with the X-ray conformation of the identical FKBP site was performed; (v) the potential energy function and its constituents were studied for the structural complex generated by molecular docking of the CRK molecule with the FKBP peptide; and (vi) from all evidence, the virtual FKBP-derived peptide was submitted to be utilized as a prospective structural framework in the anti-HIV-1 drug design. Summing up the results obtained, the following principal conclusion was drawn: a high affinity of the V3 loop peptide to the FKBP is based on the principle of “mirror similarity” that implies the near resemblance of 3D structures for the two individual fragments of the receptor and ligand, which, most likely, accounts for recognizing the immunophilin by V3 and determines the specificity of their efficacious interactions arising from the experimental observations.

Human immunodeficiency virus-1 gp120 V3 loop for anti-acquired immune deficiency syndrome drug discovery: computer-aided approaches to the problem solving

Introduction: The V3 loop on gp120 from HIV-1 is a focus of many research groups involved in anti-AIDS drug development because this region of the protein is the principal target for neutralizing antibodies and determines the preference of the virus for T-lymphocytes or primary macrophages. Areas covered: This review summarizes findings related to the 3D structure, conformational mobility, function, antigenicity and immunogenicity of the HIV-1 V3 loop. Particular consideration is given to the V3 loop core sequence Gly-Pro-Gly-Arg/Gln-Ala-Phe, which forms the HIV-1 gp120 immunogenic tip, the role of which has not been completely determined in the virus pathogenesis. New computer-aided approaches for designing potential HIV-1 entry inhibitors are illustrated by a series of examples in which promising basic structures for the V3-based anti-AIDS drug researches have been constructed. Special focus is given to recent studies aimed at defining the structurally conservative V3 sites that may present the HIV-1 weak points most suitable for therapeutic intervention. Finally, the article also discusses how this information can be used to develop novel, potent and broad anti-AIDS agents. Expert opinion: Data on the structure and function of the HIV-1 V3 loop prove convincingly that, in spite of disappointing progress > 20 years, this mysterious site of gp120 (comprising at least three structural motifs recurring in various viral isolates) still remains one of the most attractive targets for the anti-AIDS drug development.