Modification and structure-activity relationship of a small molecule HIV-1 inhibitor targeting the viral envelope glycoprotein gp120

This paper describes selected modification and structure-activity relationship of the small molecule HIV-1 inhibitor, 4-benzoyl-1-[(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)oxoacetyl]-2-(R)-methylpiperazine (BMS-378806). The results revealed: i) that both the presence and configuration (R vs. S) of the 3-methyl group on the piperazine moiety are important for the antiviral activity, with the 3-(R)-methyl derivatives showing the highest activity; ii) that the electronegativity of the C-4 substituent on the indole or azaindole ring seems to be important for the activity, with a small, electron-donating group such as a fluoro or a methoxy group showing enhanced activity, while a nitro group diminishes the activity; iii) that the N-1 position of the indole ring is not eligible for modification without losing activity; and iv) that bulky groups around the C-4 position of the indole or azaindole ring diminish the activity, probably due to steric hindrance in the binding. We found that a synthetic bivalent compound with two BMS-378806 moieties being tethered by a spacer demonstrated about 5-fold enhanced activity in an nM range against HIV-1 infection than the corresponding monomeric inhibitor. But the polyacrylamide-based polyvalent compounds did not show inhibitory activity at up to 200 nM.     

Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site

The selective proteolytic activation of the HIV-1 envelope glycoprotein gp160 by furin and other precursor convertases (PCs) occurs at the carboxyl side of the sequence Arg508-Glu-Lys-Arg511 (site 1), in spite of the presence of another consensus sequence: Lys500-Ala-Lys-Arg503 (site 2). We report on the solution structural analysis of a 19-residue synthetic peptide, p498, which spans the two gp160-processing sites 1 and 2, and is properly digested by furin at site 1. A molecular model is obtained for p498, by means of molecular dynamics simulations, from NMR data collected in trifluoroethanol/water. The peptide N-terminal side presents a 9-residue helical segment, enclosing the processing site 2; the C-terminal segment can be described as a loop exposing the processing site 1. A hypothesis for the docking of p498 onto the catalytic domain of human furin, modeled by homology and fitting previous site-directed mutagenesis studies, is also presented. p498 site 1 is shown to have easy access to the furin catalytic site, unlike the nonphysiological site 2. Finally, on the basis of available data, we suggest a possible structural motif required for the gp160-PCs recognition.     

Synergistic Effect by Combining a gp120-Binding Protein and a gp41-Binding Antibody to Inactivate HIV-1 Virions and Inhibit HIV-1 Infection

Acquired immune deficiency syndrome (AIDS) has prevailed over the last 30 years. Although highly active antiretroviral therapy (HAART) has decreased mortality and efficiently controlled the progression of disease, no vaccine or curative drugs have been approved until now. A viral inactivator is expected to inactivate cell-free virions in the absence of target cells. Previously, we identified a gp120-binding protein, mD1.22, which can inactivate laboratory-adapted HIV-1. In this study, we have found that the gp41 N-terminal heptad repeat (NHR)-binding antibody D5 single-chain variable fragment (scFv) alone cannot inactivate HIV-1 at the high concentration tested. However, D5 scFv in the combination could enhance inactivation activity of mD1.22 against divergent HIV-1 strains, including HIV-1 laboratory-adapted strains, primary HIV-1 isolates, T20- and AZT-resistant strains, and LRA-reactivated virions. Combining mD1.22 and D5 scFv exhibited synergistic effect on inhibition of infection by divergent HIV-1 strains. These results suggest good potential to develop the strategy of combining a gp120-binding protein and a gp41-binding antibody for the treatment of HIV-1 infection.     

Oligosaccharide and glycoprotein microarrays as tools in HIV glycobiology; glycan-dependent gp120/protein interactions.

Defining HIV envelope glycoprotein interactions with host factors or binding partners advances our understanding of the infectious process and provides a basis for the design of vaccines and agents that interfere with HIV entry. Here we employ carbohydrate and glycoprotein microarrays to analyze glycan-dependent gp120-protein interactions. In concert with new linking chemistries and synthetic methods, the carbohydrate arrays combine the advantages of microarray technology with the flexibility and precision afforded by organic synthesis. With these microarrays, we individually and competitively determined the binding profiles of five gp120 binding proteins, established the carbohydrate structural requirements for these interactions, and identified a potential strategy for HIV vaccine development.     

Interactions of HIV-1 proteins gp120 and Nef with cellular partners define a novel allosteric paradigm

During the course of infection, a subset of HIV-1 proteins interacts with multiple cellular partners, sometimes in a hierarchical or sequential way. These proteins include those associated with the initial infection event, with the preparation of the cell for the replicative cycle of the virus and with the exit of new virions from the infected cell. It appears that the interactions of viral proteins with multiple cellular partners are mediated by the occurrence of ligand-induced conformational changes that direct the binding of these proteins to subsequent partners. Two of the most studied HIV-1 proteins that are known to interact with different cellular partners are gp120 and Nef. Here we discuss the interactions of these two proteins with their cellular partners and present new results indicating that the conformational changes undergone by these proteins define a novel allosteric paradigm. In the traditional view, conformational changes are thought to occur between well defined structural conformations of a protein. In gp120 and Nef, those changes involve conformations characterized by the presence of large regions devoid of stable secondary or tertiary structure. Those unstructured regions contain the binding determinants for subsequent partners and only become functionally competent by ligand-induced structuring or un-structuring of those regions. By switching binding epitopes between structured and unstructured conformations the binding affinity can be modulated by several orders of magnitude, thus effectively precluding binding against unwanted partners. A better understanding of these interactions would lead to improved strategies for inhibitor design against these viral targets.     

Use of the quartz crystal microbalance to monitor ligand-induced conformational rearrangements in HIV-1 envelope protein gp120

We evaluated the potential of a quartz crystal microbalance with dissipation monitoring (QCM-D) to provide a sensitive, label-free method for detecting the conformational rearrangement of glycoprotein gp120 upon binding to different ligands. This glycoprotein is normally found on the envelope of the HIV-1 virus and is involved in viral entry into host cells. It was immobilized on the surface of the sensing element of the QCM-D and was exposed to individual solutions of several different small-molecule inhibitors as well as to a solution of a soluble form of the host cell receptor to which gp120 binds. Instrument responses to ligand-triggered changes were in qualitative agreement with conformational changes as suggested by other biophysical methods.

Theoretical studies on the S-N interactions in sulfoximine

The potential energy surface of sulfoximines has been searched using ab initio MO and Density Functional Calculations. The electronic structures of the isomers of sulfoximine have been studied using HF/6-31+G*, MP2(full)/6-31+G* and B3LYP/6-31+G* levels. Final energies of these molecules have been calculated at the high accuracy G2 and CBS-Q levels. Though a formal SN double bond is generally considered between sulfur and nitrogen in these systems, theoretical studies do not show any π interaction between them. S-N rotational barriers, bond dissociation energies, atomic charge analysis, and NBO analysis all indicate only a single bond across S-N with a very strong ionic interaction.     

NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41

Due to the inherently flexible nature of a protein–protein interaction surface, it is difficult both to inhibit the association with a small molecule, and to predict how it might bind to the surface. In this study, we have examined small molecules that mediate the interaction between a WWI motif on the C-helix of HIV-1 glycoprotein-41 (gp41) and a deep hydrophobic pocket contained in the interior N-helical trimer. Association between these two components of gp41 leads to virus–cell and cell–cell fusion, which could be abrogated in the presence of an inhibitor that binds tightly in the pocket. We have studied a comprehensive combinatorial library of α-helical peptidomimetics, and found that compounds with strongly hydrophobic side chains had the highest affinity. Computational docking studies produced multiple possible binding modes due to the flexibility of both the binding site and the peptidomimetic compounds. We applied a transferred paramagnetic relaxation enhancement experiment to two selected members of the library, and showed that addition of a few experimental constraints enabled definitive identification of unique binding poses. Computational docking results were extremely sensitive to side chain conformations, and slight variations could preclude observation of the experimentally validated poses. Different receptor structures were required for docking simulations to sample the correct pose for the two compounds. The study demonstrated the sensitivity of predicted poses to receptor structure and indicated the importance of experimental verification when docking to a malleable protein–protein interaction surface.     

Synthesis and biological evaluation of peptide mimics derived from first extracellular loop of CCR5 toward HIV-1

Peptide mimics derived from the first extracellular loop of CCR5 bearing non-peptide spacers in place of Ala-Ala-Ala sequence in the peptide moiety were synthesized, and the effects of these compounds on the inhibition against HIV-1 were examined. Compound 2b having m-aminophenoxyacetic acid derivative as a non-peptide spacer significantly inhibited HIV-1.     

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 HIV's spread.     

Theoretical studies on tautomerism of tetrazole 5-thion

Detailed investigation of the tautomerism of all possible forms of tetrazole thion (A and E) and its tetrazole forms (B–D) induced by proton transfer in the gas phase, in a continuum solvent, and in a microhydrated environment with 1 explicit water molecule was carried out by calculations at MP2, QCISD, CBS-Q, CBS-QB3, and density functional theory (DFT). It was found that in the gas phase and solvent tetrazole thion (form A) is the most stable isomer. In addition variation of dipole moments was studied in the gas phase and in the solvent. Water molecule was gradually put in different regions in the vicinity of five isomers. It was found that water can forms different hydrogen bonding with molecule.     

HIV-1逆转录酶抑制剂2-氨基6-苯磺酰基苄腈及其类似物活性OSAR研究

首先利用半经验AM I量子化学方法计算了54个2-氨基-6-苯磺酰基苄腈及其类似物的物理化学、电子结构、指示变量等共28个参数,然后使用偏最小二乘,穷举回归和混沌遗传乘法训练的人工神经网络方法建立了这些参数和其抑制H IV-1逆转录酶活性之间的定量构效关系模型,为设计、合成更高生物活性的该类化合物提供了理论参考。     

Theoretical studies on the hydride transfer between 1-methyl-1,4-dihydronicotinamide and its corresponding pyridinium salt

MNDO and AMI studies were performed to investigate the degenerate hydride transfer reaction between 1-methyl-l,4-dihydronicotinamide and the 1-methylnicotinamide cation, a model system for a novel brain-targeted delivery system and for the NAD⁺ (ai) NADH interconversion. Four initial approach vectors were selected. These involved an endo orientation in which the carbamoyl groups are with respect to one another (cis H_S- ), an endo orientation with the carbamoyl groups (cis H_S-si), an exo configuration with the carbamoyl groups syn (trans H_S- ) and an exo configuration with the carbamoyl groups (trans H_S- ). The cis H_S- approach generated the transition state with the lowest energy. The optimized structure indicated that a linear hydride transfer occurred. A more detailed study examined the cis H_S- approach from a 100A separation to the transition state. The data indicated the formation of an intermediate induced dipole-charge complex which altered the trajectory of the two species. Closer approach yielded the transition state. The energy of activation for this reaction was calculated to be 30.7 kcal/mol using the MNDO approximation and 9.3 kcal/mol usihg the AMI method. Finally, while the linear transition state was found to be the most stable conformation, bending of the C-H-C bond by ± 30° only modestly increased (3–4 kcal/mol) the energy of the system.     

Theoretical studies on ammonia oxide and its unimolecular reactions

The unimolecular reactions of ammonia oxide H₃NO, isomerization and dehydrogenation, are investigated by ab initio MO calculations with the 4-31G basis set. The geometries and energies of the reactant, transition states and products have been determined on the singlet potential energy surface. The reaction ergodography along the intrinsic reaction coordinate (IRC) for the two reactions have been performed. The vibrational frequency correlation diagram of the two reactions are analyzed along the IRC.     

Theoretical studies on the heats of formation and the interactions among the difluoroamino groups in polydifluoroaminocubanes

The heats of formation (HOFs) were calculated for a series of polydifluoroaminocubanes by using density functional theory (DFT), Hartree-Fock, and MP2 method with 6-31G basis set as well as semiempirical methods. The cubane skeleton was not broken in the process of designing isodesmic reactions; i.e., the cubane skeleton was chosen for a reference compound. The contribution of difluoroamino group to the heat of formation deviates from group additivity. The semiempirical MO (MNDO, AM1, and PM3) methods did not produce accurate and reliable results for the HOFs of the title compounds. The relationship between HOFs and molecular structures was discussed. It was found that the HOFs decreased dramatically initially and then gradually with each difluoroamino group attached to the cubane skeleton. The distance between difluoroamino groups influences the values of HOFs. The interacting energies of polydifluoroaminocubanes are in the range 14-20 kJ/mol. The interaction of neighbor difluoroamino groups discords with the group additivity. The average interaction energy between the nearest-neighbor NF(2) group in the most stable conformer of octadifluoroaminocubane is 13.94 kJ/mol at the B3LYP/6-31G level. The NF(2) group can rotate freely around the C-N bond. The relative stability of the title compounds was accessed on the basis of the calculated HOFs, the energy gaps between the frontier orbitals, and the bond order of C-NF(2). These results provide basic information for the molecular design of novel high energetic density materials.