Computational Characterization of Binding of Small Molecule Inhibitors to HIV‐1 gp41

Developing orally available small molecule inhibitors of HIV‐1 fusion has attracted significant interest over many years. Frey had recently reported several synthetic compounds which are experimentally shown to inhibit cell‐cell fusion in the low micromolar range. We carried out computational study to help identify possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and to characterize structures of binding complexes. The detailed gp41‐molecule binding interactions and free energies of binding are obtained through molecular dynamics simulation and MM‐PBSA calculation. Specific molecular interactions in the gp41‐inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point for further refinement of small molecular gp41 inhibitors.     

Inhibiting HIV fusion with a beta-peptide foldamer

Linear peptides derived from the HIV gp41 C-terminus (C-peptides), such as the 36-residue Fuzeon, are potent HIV fusion inhibitors. These molecules bind to the N-peptide region of gp41 and inhibit an intramolecular protein-protein interaction that powers fusion of the viral and host cell membranes. The N-peptide region contains a surface pocket that is occupied in the post-fusion state by three alpha-helical residues found near the gp41 C-terminus: Trp628, Trp631, and Ile635-the WWI epitope. Here, we describe a set of beta3-decapeptides (betaWWI-1-4) in which the WWI epitope is presented on one face of a short 14-helix stabilized by macrodipole neutralization and side chain-side chain salt bridges. betaWWI-1-4 bind in vitro to IZN17, a validated gp41 model, and inhibit syncytia formation in cell culture. Molecules lacking a complete WWI functional epitope neither bind IZN17 nor inhibit syncytia formation. These results provide evidence that short beta-peptide 14-helices can inhibit an intramolecular protein-protein interaction in vivo. Molecules related to betaWWI-1-4 could represent starting points for the development of highly potent inhibitors or antigens effective against HIV or other viruses, including SARS, Ebola, HRSV, and influenza, that employ common fusion mechanisms.     

Development of a FRET assay for monitoring of HIV gp41 core disruption

The fusogenic core assembly of human immunodeficiency virus type 1 (HIV-1) fusion protein gp41 is a critical transformation for viral entry. Molecules that are able to intercept this process are of great therapeutic value as HIV-1 fusion inhibitors. In the search for such molecules, assay systems that can be adapted to high-throughput screens are valuable. Given that gp41 fusogenic transformation is characterized by the hexameric association of heptads located at the N and C terminal regions of the protein ectodomain, the corresponding heptad peptides (CHR and NHR), known to form the six-helix bundle core of gp41 fusion active form, are potentially useful in developing a fluorescence resonance energy transfer (FRET) system for identification of HIV fusion inhibitors. We demonstrate that by strategically placing two FRET probes on these two peptides, we are able to monitor the intermolecular co-association by fluorescence quenching between the fluorescence donor and acceptor. The utility of the system is that it should be adaptable to high-throughput screening (HTS) toward peptide or small-molecule HIV fusion inhibitors targeting the gp41 core. Herein, we report the design, synthesis, and development of a N- and C- terminal peptide FRET pair for screening of gp41 six-helix bundle disruption.     

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future.     

Cell Surface Assembly of HIV gp41 Six-Helix Bundles for Facile, Quantitative Measurements of Hetero-oligomeric Interactions

Helix-helix interactions are fundamental to many biological signals and systems and are found in homo- or heteromultimerization of signaling molecules as well as in the process of virus entry into the host. In HIV, virus-host membrane fusion during infection is mediated by the formation of six-helix bundles (6HBs) from homotrimers of gp41, from which a number of synthetic peptides have been derived as antagonists of virus entry. Using a yeast surface two-hybrid (YS2H) system, a platform designed to detect protein-protein interactions occurring through a secretory pathway, we reconstituted 6HB complexes on the yeast surface, quantitatively measured the equilibrium and kinetic constants of soluble 6HB, and delineated the residues influencing homo-oligomeric and hetero-oligomeric coiled-coil interactions. Hence, we present YS2H as a platform for the facile characterization and design of antagonistic peptides for inhibition of HIV and many other enveloped viruses relying on membrane fusion for infection, as well as cellular signaling events triggered by hetero-oligomeric coiled coils.     

Coiled-coil surface presentation: an efficient HIV gp41 binding interface mimic

An efficient mimic of the gp41 N-terminal coiled-coil trimer is described. The native protein mediates fusion of viral and cellular membranes, and its function is critical for infectivity. A central event in this process is formation of a "trimer of hairpins" structure in which a C-terminal gp41 sequence binds to a hydrophobic groove on the N-terminal trimer surface. Inhibition of this interaction is a promising therapeutic strategy, but the isolated trimer is not a convenient screening target, since the exposed hydrophobic pocket causes aggregation and precipitation. The problem has been circumvented in several ways such as attachment of auxiliary scaffolding elements or covalent subunit tethering. Here we report a more efficient approach, in which purely peptidic systems comparable in size to the native trimer display the expected specificity for the C-terminal ligand. Steric matching of 2:1 alanine/cyclohexylalanine core layers promotes formation of a 1:1:1 heterotrimer, whose surface interhelical interfaces can be uniquely controlled. Two of these interfaces contain solubilizing Glu/Lys pairs, while the third presents the gp41 interface. The model system binds the C-terminal peptide, while a control complex with only half the interface does not. A variety of biophysical methods are used to characterize the complex. The ability to control complex stoichiometry with only interior core residues should permit formation of any such interface, and extension to other viral systems is underway.     

用作HIV-1融合抑制剂的多肽及其类似物

HIV-1通过其包膜糖蛋白跨膜亚基gp41介导的病毒-细胞膜融合进入和感染靶细胞.HIV-1融合抑制剂以gp41为靶点,通过阻断病毒与宿主细胞膜的融合,在感染的初始环节切断HIV-1的复制周期.2003年,首个多肽类融合抑制剂T-20获美国食品药物管理局（FDA）批准上市,但其易被体内蛋白酶降解、临床剂量大、耐受性差,且耐药性HIV-1毒株也很快出现.针对这些缺点,近年来在融合抑制剂的作用机制研究和新融合抑制剂的研发等方面取得了重要进展.以gp41不同功能区为靶点,具有高活性和更好代谢性质的多肽及多肽类似物候选分子不断被发现,成为抗HIV药物研究领域的热点之一.本文综述了多肽和类肽类融合抑制剂的研究进展,为相关的药物开发和基础研究提供参考.     

Homochiral oligopeptides generated by induced "mirror symmetry breaking" lattice-controlled polymerizations in racemic crystals of phenylalanine N-carboxyanhydride

The formation of diastereoisomeric libraries of oligopeptides through the heterogeneous polymerization of racemic crystals of phenylalanine N-carboxyanhydride (PheNCA) is reported. The diastereoisomeric compositions of the oligopeptides formed on polymerization of (R,S) crystals incorporating the deuterium-tagged S enantiomer were determined by MALDI-TOF mass spectrometry. The racemic mixtures of the oligopeptides longer than pentamers are represented primarily by diastereoisomers of homochiral sequence and with peptides containing only one heterochiral repeating unit. A mechanism comprising the following three sequential steps to account for this unusual observation is proposed: 1) formation of dimers and trimers at a partially damaged liquid/solid interface, 2) chain propagation that takes place within the bulk of the crystal through a lattice-controlled "zipper-like" mechanism between homochiral molecules arranged in a head-to-tail motif to yield crystalline antiparallel beta-sheets of alternating oligopeptide chains of homochiral sequence of opposite handedness, and 3) enantiomeric cross-inhibition that results in chain termination. Induced desymmetrization of the racemic mixtures of the formed peptides was achieved by the polymerization of the mixed quasi-racemic crystals of (R)-PheNCA, ((S)-PheNCA), and (S)-ThieNCA (3-(2-thienyl)-alanine N-carboxyanhydride) of various compositions. These experiments resulted in the formation of nonracemic libraries of oligopeptides composed of homochiral chains of (R)-Phe and copolymers of randomly distributed (S)-Phe and (S)-Thie sequences. From these findings, we propose a stochastic model for the generation of libraries of nonracemic mixtures of oligopeptides from the polymerization of host (R,S)-PheNCA with racemic mixtures of other guest NCA amino acids dissolved in limited quantities in the crystal.     

Construction and validation of a RET TK catalytic domain by homology modeling

RET tyrosine kinase (TK) oncoproteins are potential targets for anticancer therapy. However, the search for novel RET inhibitors has been hampered by the lack of a 3D structure of the receptor. In this study, the "open" and the "closed" structure of the RET TK catalytic domain have been built by homology modeling techniques. The structures were validated by extensive docking studies with practically all the inhibitors reported in the literature and through molecular dynamics simulations of the resulting complexes. All the expected major interactions between the active domain amino acids and the inhibitors have been reproduced in their details. Furthermore, the proposed 3D models are in agreement with the results of available mutation studies. Therefore, these models could be profitably used to filter off from large libraries new potential hit compounds able to target this enzyme.     

A novel approach for characterizing protein ligand complexes: molecular basis for specificity of small-molecule Bcl-2 inhibitors

The increasing diversity of small molecule libraries has been an important source for the development of new drugs and, more recently, for unraveling the mechanisms of cellular events-a process termed chemical genetics.(1) Unfortunately, the majority of currently available compounds are mechanism-based enzyme inhibitors, whereas most of cellular activity regulation proceeds on the level of protein-protein interactions. Hence, the development of small molecule inhibitors of protein-protein interactions is important. When screening compound libraries, low-micromolar inhibitors of protein interactions can be routinely found. The enhancement of affinities and rationalization of the binding mechanism require structural information about the protein-ligand complexes. Crystallization of low-affinity complexes is difficult, and their NMR analysis suffers from exchange broadening, which limits the number of obtainable intermolecular constraints. Here we present a novel method of ligand validation and optimization, which is based on the combination of structural and computational approaches. We successfully used this method to analyze the basis for structure-activity relationships of previously selected (2) small molecule inhibitors of the antiapoptotic protein Bcl-xL and identified new members of this inhibitor family.     

二价HIV-1融合抑制剂的设计、合成与活性评价

针对人免疫缺陷病毒跨膜糖蛋白(HIV-1 gp41)N末端重复序列靶标设计二价融合抑制剂, 以C肽为模板, 通过共价交联形成类似发夹结构的相互平行的2条肽链, 研究了二价C肽分子不同连接位点与不同连接臂对抗HIV融合活性的影响. 细胞-细胞融合活性测试表明, 与单价分子相比, 所设计的基于N末端交联的C34或T20的二价分子在前体共价交联后, 活性明显提升. 基于C34或T20的N末端与C末端均存在发生协同效应的可能性, 在C34的N末端设计中β-丙氨酸为最适连接臂, 而在C末端的设计中C34C的融合活性提高最大. 单价分子CβAC34经过氧化形成二硫键连接的二价分子BiCβAC34, 融合活性从43.7 nmol/L提高到6.4 nmol/L, 表明二价抑制剂中2条C肽链间具有良好的协同效应. 本文结果表明, 针对gp41靶标设计的二价融合抑制剂能够相互协同.     

Broad distribution of energetically important contacts across an extended protein interface

Infection of cells by HIV depends upon profound structural rearrangements within the trimeric viral protein gp41. Critical to this process is the formation of a six-helix bundle in which a set of three N-terminal heptad repeat (NHR) helices assemble to form a core displaying long grooves that provide docking sites for three C-terminal heptad repeat (CHR) helices. We report experiments designed to discriminate between two alternative hypotheses regarding the source of affinity between individual CHR helices and the complementary groove: (1) affinity is dominated by interactions of a small cluster of side chains at one end of the CHR helix; or (2) affinity depends upon interactions distributed across the long CHR helix. We have employed two complementary experimental designs, and results from both favor the latter hypothesis.     

The application of perfluorooctanoate to investigate trimerization of the human immunodeficiency virus-1 gp41 ectodomain by electrophoresis

The transmembrane glycoprotein gp41 of human immunodeficiency virus has been proposed to form trimer-of-hairpin during virus-cell membrane fusion. To investigate its oligomerization propensity under soluble and membrane-mimic conditions, sodium salt of perfluorooctanoate (PFO) was applied. A recombinant gp41 ectodomain devoid of disulfide linkage was overexpressed in Escherichia coli and characterized by MS and circular dichroism spectropolarimetry in PFO solution in comparison to SDS. The helical content of this ectodomain in PFO is higher than that in SDS. Notably, PFO employed in PAGE clearly conduced to the formation of trimer under the optimized condition as visualized in the gel. In addition, the proteins expressed from the two mutants in the heptad repeat (HR) domains of gp41, I62P, and N126K, were also examined by the PFO-PAGE analysis for functional ramification of molecular organization. Remarkably, the I62P mutation completely abolished the gp41 trimer formation, whereas the N126K mutation resulted in a more stable trimer. The data suggested that PFO-PAGE analysis is appropriate for evaluating the effect of mutations on the trimerization of gp41 and other fusion proteins which may be implicated in the alteration of their fusogenicity.     

Identification of a potent botulinum neurotoxin a protease inhibitor using in situ lead identification chemistry

[reaction: see text] Botulinum neurotoxins (BoNTs), etiological agents of the deadly food poisoning disease botulism, are the most toxic proteins currently known. By using in situ lead identification chemistry, we have uncovered the first class of inhibitors that displays nanomolar potency. From a 15 microM lead compound, structure-activity relationship studies were performed granting the most potent BoNT/A inhibitor reported to date that displays an inhibition constant of 300 nM.     

Purification of a recombinantly produced transmembrane protein (gp41) of HIV I

The transmembrane protein gp41, a component of the viral envelope of HIV I, and its analogue gp36 of HIV II are important antigens for the sensitive and specific detection of anti-HIV antibodies. The immunodominant region of the protein gp41, which reacts with 100% of sera of infected persons, was produced by gene technological means in Escherichia coli. The protein accumulates in the form of insoluble inclusion bodies in the bacterial cell. Purification strategies for this aggregated material depend mainly on the isolation of these "inclusion bodies" and subsequent washing procedures. Growth conditions of the recombinant E. coli cells and the method of the cell disruption are important for the efficiency of purification and the recovery of the antigen. Owing to the insolubility of the expressed antigen, a significant concentration of recombinant gp41 was possible by extracting the soluble cell components. For this purpose, mild detergent solutions and low-molarity chaotropic buffer solutions were used. After final solubilization in 8 M urea buffer at pH 12.5, further chromatographic purification steps followed. The reduction of disulphide bridges with beta-mercaptoethanol or dithiothreitol was important. Gel filtration on a Sephacryl S-200 or Superose 12 column and/or ion-exchange chromatography on a DEAE-Sepharose Fast Flow or Mono Q HR (5/5) column finally resulted in the desired purity of the antigen.     

Membrane mediated regulation in free peptides of HIV-1 gp41: minimal modulation of the hemifusion phase

Membrane-mediated structural modulation in two short fragments of the human HIV-1 envelope protein gp41 is demonstrated. Derived from the C-terminal membrane proximal external (MPE) and N-terminal fusion peptide proximal (FPP) regions, these peptides are widely separated in the primary sequence but form tertiary contacts during the intermediate (hemifusion) phase of HIV infection. The structural perturbations observed at the membrane interface offer evidence of rudimentary regulatory mechanisms operating in the free peptides which may be relevant in the biological system. No such regulatory phenomena were observed for the individual peptides in a membrane environment or between the peptides in aqueous solutions. Structure determination is made using a combination of circular and linear dichroism spectroscopy (supported by calorimetric measurements) and molecular dynamics simulations. Specifically, we show that these peptides interact locally without the conformational support of helical heptad repeat regions in native gp41 and that the modulation is not mutual with the FPP peptide operating as a primary regulator of the MPE-FPP interactions in the hemifusion phase.     

Lipid markers of "geometrical" radical stress: synthesis of monotrans cholesteryl ester isomers and detection in human plasma

Heteroatom-centered free radicals are able to transform cis unsaturated fatty acids to the thermodynamically more stable, but unnatural, trans configuration. The "geometrical" radical stress can be estimated in biological samples using trans fatty acid isomers as lipid markers. Regioselectivity is an important feature of the "geometrical" radical stress, because the supramolecular organization of the polyunsaturated fatty acid moieties of phospholipids can lead to preferential monotrans isomer formation. The regioisomer recognition is a crucial step, which is helped by appropriate molecular libraries available through radical-based synthetic methodologies. Cholesteryl linoleate and arachidonate esters are interesting targets for their biochemical connection with membrane phospholipid turnover and their well-known roles in cardiovascular health. The synthesis of monotrans isomers of PUFA cholesteryl esters was achieved by a thiyl radical-catalyzed cis-trans isomerization. Valuable NMR, IR, and Raman spectroscopic data have been collected for promising application in metabolomics and lipidomics. The identification of monotrans cholesteryl ester isomers was carried out in human plasma by GC, Raman, and IR analyses, demonstrating for the first time the presence of specific regiosiomers connected to free radical stress. This work helps to highlight the chemical biology approach for the access to molecular libraries applicable to biomarker development, and the cis-trans isomerization as a relevant process to be integrated in the puzzling scenario of free radical-mediated lipid modifications.     

The Glu143 Residue Might Play a Significant Role in T20 Peptide Binding to HIV-1 Receptor gp41: An In Silico Study

Despite the enormous efforts made to develop other fusion inhibitors for HIV, the enfuvirtide (known as T20) peptide is the only approved HIV-1 inhibitory drug so far. Investigating the role of potential residues of the T20 peptide’s conformational dynamics could help us to understand the role of potential residues of the T20 peptide. We investigated T20 peptide conformation and binding interactions with the HIV-1 receptor (i.e., gp41) using MD simulations and docking techniques, respectively. Although the mutation of E143 into alanine decreased the flexibility of the E143A mutant, the conformational compactness of the mutant was increased. This suggests a potential role of E143 in the T20 peptide’s conformation. Interestingly, the free energy landscape showed a significant change in the wild-type T20 minimum, as the E143A mutant produced two observed minima. Finally, the docking results of T20 to the gp41 receptor showed a different binding interaction in comparison to the E143A mutant. This suggests that E143 residue can influence the binding interaction with the gp41 receptor. Overall, the E143 residue showed a significant role in conformation and binding to the HIV-1 receptor. These findings can be helpful in optimizing and developing HIV-1 inhibitor peptides.     

A multi-functional peptide as an HIV-1 entry inhibitor based on self-concentration, recognition, and covalent attachment

HIV entry is mediated by the envelope glycoproteins gp120 and gp41. The gp41 subunit contains several functional domains: the N-terminal heptad repeat (NHR) domains fold a triple stranded coiled-coil forming a meta-stable prefusion intermediate. The C-terminal heptad repeat (CHR) subsequently folds onto the hydrophobic grooves of the NHR coiled-coil to form a stable 6-helix bundle, which juxtaposes the viral and cellular membranes for fusion. A conserved salt bridge between Lys(574) in NHR and Asp(632) in CHR plays an essential role in the formation of the six-helix bundle. A multi-functional peptide inhibitor for anti-HIV derived from the CHR of gp41 has been designed. It bears a cholesterol group (Chol) at the C-terminal through which the inhibitor can anchor in the cell membrane, and carries an isothiocyanate (NCS) group at the side chain of Asp(632) through which the inhibitor can bind to target covalently at Lys(574) in NHR. The dual functionalized peptide (NCS-C34-Chol) shows high antiviral activity in vitro and in vivo. The inhibitor reacts specifically and rapidly to NHR from gp41. In addition, it exhibits better stability under the digestion of the Proteinase K than C34 and T20.