Diarylaniline Derivatives as a Distinct Class of HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors

By using structure-based drug design and isosteric replacement, diarylaniline and 1,5-diarylbenzene-1,2-diamine derivatives were synthesized and evaluated against wild type HIV-1 and drug-resistant viral strains, resulting in the discovery of diarylaniline derivatives as a distinct class of next-generation HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) agents. The most promising compound 37 showed significant EC50 values of 0.003-0.032 μM against HIV-1 wild-type strains and of 0.005-0.604 μM against several drug-resistant strains. Current results also revealed important structure-activity relationship (SAR) conclusions for diarylanilines and strongly support our hypothesis that an NH2 group on the central benzene ring ortho to the aniline moiety is crucial for interaction with K101 of the NNRTI binding site in HIV-1 RT, likely by forming H-bonds with K101. Furthermore, molecular modeling studies with molecular mechanism/general born surface area (MM/GBSA) technology demonstrated the rationality of our hypothesis

Striking HIV-1 Entry by Targeting HIV-1 gp41. But, Where Should We Target?

HIV-1 gp41 facilitates the viral fusion through a conformational switch involving the association of three C-terminal helices along the conserved hydrophobic grooves of three N-terminal helices coiled-coil. The control of these structural rearrangements is thought to be central to HIV-1 entry and, therefore, different strategies of intervention are being developed. Herewith, we describe a procedure to simulate the folding of an HIV-1 gp41 simplified model. This procedure is based on the construction of plausible conformational pathways, which describe protein transition between non-fusogenic and fusogenic conformations. The calculation of the paths started with 100 molecular dynamics simulations of the non-fusogenic conformation, which were found to converge to different intermediate states. Those presenting defined criteria were selected for separate targeted molecular dynamics simulations, subjected to a force constant imposing a movement towards the gp41 fusogenic conformation. Despite significant diversity, a preferred sequence of events emerged when the simulations were analyzed in terms of the formation, breakage and evolution of the contacts. We pointed out 29 residues as the most relevant for the movement of gp41; also, 2696 possible interactions were reduced to only 48 major interactions, which reveals the efficiency of the method. The analysis of the evolution of the main interactions lead to the detection of four main behaviors for those contacts: stable, increasing, decreasing and repulsive interactions. Altogether, these results suggest a specific small cavity of the HIV-1 gp41 hydrophobic groove as the preferred target to small molecules

Etude par RMN et modélisation moléculaire des structures de la séquence ARN initiant la dimérisation chez VIH-1Lai et de son analogue ADN

M. Gérald Guillaumet président M. Serge Fermandjian rapporteur Mme Brigitte Hartmann rapporteur Mme Françoise Vovelle examinateur M. Jacques Paoletti examinateur M. Gérard Lancelot directeur de thèseLike all retroviruses, the human immunodeficience virus (HIV) genome is made up of two identical copies of genomic RNA. Those are related in a non-covalent way to their 5' leader. This dimerization phenomenon interferes with various key stages of the retroviral cycle life. Therefore, the dimerization inhibition represents a new way of processing against HIV. The first part of this work concerns the RNA SL1 sequence who initiating the HIV-1Lai dimerization. We were interested in the structural determination, by NMR and molecular modeling, of the species present in the dimerization process. After having isolated both RNA different dimer, we highlighted the stable dimer structure which makes it possible to advance assumptions of their relative stability. The second part of this work still concerns the study of the deoxyribose SL1 fragment. Here again, two forms of different stability may be isolate. The unstable dimer is organized in the form of "kissing-complex" and represents the first structure of this type elucidated for a DNA. The structure of stable dimer remains of type "kissing-complex" although presenting distinctions at the origin of the stability difference. The presence of the hydroxyl group distinguishing DNA from RNA explains this behavior difference. These structural investigations constitute a solid base study in the "drug-design" strategies implying the development of inhibitors likely to interfere with the dimerization phenomenon.Le génome du virus de l'immunodéficience humaine (VIH) est constitué, comme tous les rétrovirus, de deux copies identiques d'ARN génomique. Celles-ci sont liées de manière non covalente au niveau de leur région 5'-terminale. Ce phénomène de dimérisation interfère avec différentes étapes clés du cycle rétroviral. C'est pourquoi, l'inhibition de la dimérisation représente une nouvelle voie de traitement potentiel du VIH. La première partie de ce travail porte sur la séquence d'ARN SL1 initiant la dimérisation chez VIH-1Lai. Nous nous sommes intéressés à la détermination structurale, par RMN et modélisation moléculaire, des espèces présentes dans le processus de dimérisation sous forme instable. Après avoir isolé les deux différents dimère d'ARN, nous avons mis en évidence la structure du dimère stable qui permet d'avancer des hypothèses quant à leur stabilité relative. La seconde partie de ce travail porte sur l'étude du fragment désoxyribose de SL1. Là encore, deux conformères de stabilité différente sont isolables. Le dimère instable s'organise sous forme de “kissing-complex” et représente la première structure de ce type élucidée pour un ADN. La structure du dimère stable demeure de type “kissing-complex” bien que présentant des différences à l'origine du changement de stabilité. La présence du groupement hydroxyle distinguant l'ADN de l'ARN explique cette différence de comportement. Ces investigations structurales constituent une solide base d'étude dans les stratégies de “drug-design” impliquant le développement d'inhibiteurs susceptibles d'interférer avec le phénomène de dimérisation

Splenic immunity and atherosclerosis: a glimpse into a novel paradigm?

International audienceThe chemical shift calculation, a tool for nucleic acids structure validation. The large majority of analytical NMR methods in chemistry or biochemistry are based on the quality of the chemical shift dispersion. The purpose of this work is to show that theoretical chemical shift back calculation starting from structures can be used to select molecular modeling structures in order to differentiate several conformational possibilities. Here we report the result of the chemical shift calculation carried out on two original structures corresponding to two DNA 'kissing complexes'. The 46 nucleotides sequence corresponds to the RNA deoxyribose analogous implied in the HIV-1 Lai dimerization process. It is interesting to note that, even in cases we are very far from the classical helical structure (loop-loop interaction, AA base pairing, base stacking, misappariement...), the theoretical chemical shift is in very good agreement with the experimental chemical shift (±0.25 ppm). The satisfactory results obtained enable us to conclude that the comparison of the proton chemical shifts is an invaluable tool making it possible to select or to validate oligonucleotides structures. © 2001 Académie des sciences / Éditions scientifiques et médicales Elsevier SAS NMR / chemical shift calculation / DNA / nucleic acids / kissing complexLa grande majorité des analyses de spectres RMN en chimie ou en biochimie repose sur la qualité en dispersion de leur déplacement chimique. L'objectif de ce travail est de montrer que le calcul en retour du déplacement chimique théorique à partir de structures peut être utilisé pour sélectionner des structures issues de la modélisation moléculaire, afin de différencier plusieurs possibilités conformationnelles. Nous présentons ici le résultat du calcul de déplacement chimique effectué sur deux structures originales : deux kissing complexes d'ADN de 46 nucléotides, analogue désoxyribose de la séquence d'ARN impliquée dans le phénomène de dimérisation du virus d'HIV-1 Lai. Il est remarquable de constater que, même dans des cas très éloignés de la structure hélicoïdale (interaction boucle-boucle, paire AA, stacking, mésappariement…), le déplacement chimique théorique est en bon accord avec le déplacement chimique expérimental (±0,25 ppm). Les résultats satisfaisants obtenus nous permettent de conclure que la comparaison des dépla-cements chimiques du proton est un outil précieux permettant de sélectionner ou de valider des structures d'oligonucléo-tides. © 2001 Académie des sciences / Éditions scientifiques et médicales Elsevier SAS RMN / calcul du déplacement chimique / ADN / acide nucléiques / kissing complexe

Etude par RMN et modélisation moléculaire des structures de la séquence ARN initiant la dimérisation chez VIH-1Lai et de son analogue ADN

ORLEANS-BU Sciences (452342104) / SudocSudocFranceF

Etude du processus d'entrée du VIH-1 par modélisation moléculaire (application à la conception de nouveaux inhibiteurs potentiels)

PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement.

Aptamers are a class of bioreceptors used in analytical tools dedicated to molecular diagnostics due to their ability to perform structural reorganization upon target binding. However, there is a lack of methodologies allowing to rationalize their structure in order to improve their transduction efficiency. We chose here, a three-strand DNA structure as probe anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to Ampicillin (AMP). Using a set of computational techniques, we investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates for the first time the ability of computational investigations to drive, in-silico, the design of aptasensors

DockSurf: A molecular modeling software for the prediction of protein/surface adhesion.

The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces have yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structure as a molecular docking problem with a homogenous plan as the target. To this extent we propose a new software, DockSurf which aims to quickly propose reliable protein/surface structure. Our approach considers the conformational exploration with Euler\u27s angles, which provide a cartography instead of a unique structure. Interaction energies were derived from QM computations for a set of small molecules that describe protein atom-types, and implemented in a DLVO potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community

Rational design of peptides active against the Gram positive bacteria Staphylococcus aureus

n an attempt to increase the antimicrobial activity of the insect defensin from Anopheles gambiae, which is active against Staphylococcus aureus at low concentration, hybrid defensins were designed by combining conserved sequence regions and variable regions of insect defensins. Their activity against S. aureus strains sensitive and resistant to conventional antibiotics was evaluated, and the toxicity of the most active molecules was tested. The three-dimensional structure of Anopheles gambiae defensin and five hybrids were determined by NMR and molecular modelling. This strategy led to the design of two chimeric defensins with increased activity compared with the native molecule, but one of them appears to be toxic to mice at a rather low concentration. The structure of the CS motif, which is a characteristic of insect defensin, is sensitive to sequence modifications, in particular in the N-terminal loop. The existence of the CS is most probably a prerequisite for the stability and the activity of the molecule, but is not sufficient by itself since the hybrid displaying the best defined structure is not active against the tested strains. The analysis of the structure, in relation with the activity and the toxicity data, underlines the importance of turns and of the N-terminal loop. Residues located in the turns contributing to the preservation of positive electrostatic areas at the surface of the molecules seem particularly important for the activity of the molecule, while residues involved in the N-terminal loop are both involved in the modulation of the activity and the toxicity of the molecule

NMR Solution Structure of the Archaebacterial Chromosomal Protein MC1 Reveals a New Protein Fold ‡

International audienceThe three-dimensional structure of methanogen chromosomal protein 1 (MC1), a chromosomal protein extracted from the archaebacterium Methanosarcina sp. CHTI55, has been solved using (1)H NMR spectroscopy. The small basic protein MC1 contains 93 amino acids (24 basic residues against 12 acidic residues). The main elements of secondary structures are an alpha helix and five beta strands, arranged as two antiparallel beta sheets (a double one and a triple one) packed in an orthogonal manner forming a barrel. The protein displays a largely hydrophilic surface and a very compact hydrophobic core made up by side chains at the interface of the two beta sheets and the helix side facing the interior of the protein. The MC1 solution structure shows a globular protein with overall dimensions in the range of 34-40 A, which potentially corresponds to a DNA-binding site of 10-12 base pairs. The presumed DNA-binding site is located on the sequence comprising residues K62-P82, which is formed by a part of strands II2 and II3 belonging to the triple-stranded antiparallel beta sheet and a loop flanked by prolines P68 and P76. The tryptophan W74 that is expected to play a key role in the DNA-binding according to photocross-linking experiments was found completely exposed to the solvent, in a good position to interact with DNA. The overall fold of MC1, characterized by its linking beta-beta-alpha-beta-beta-loop-beta, is different from other known DNA-binding proteins. Its structure suggests a different DNA-binding mode than those of the histone-like proteins HU or HMGB. Thus, MC1 may be classified as a member of a new family