7 research outputs found
Identification of target-specific bioisosteric fragments from ligand-protein crystallographic data
Bioisosteres are functional groups or atoms that are structurally different but that can form similar intermolecular interactions. Potential bioisosteres were identified here from analysing the X-ray crystallographic structures for sets of different ligands complexed with a fixed protein. The protein was used to align the ligands with each other, and then pairs of ligands compared to identify substructural features with high volume overlap that occurred in approximately the same region of geometric space. The resulting pairs of substructural features can suggest potential bioisosteric replacements for use in lead-optimisation studies. Experiments with 12 sets of ligand-protein complexes from the Protein Data Bank demonstrate the effectiveness of the procedure
Drug design of novel molecules using a bioisosteric and de novo techniques - a comparison
Rational drug design is an area of science that evolves continuously in order to answer contemporary demands for a decrease in novel drug discovery turnover time. Multiple drug design modalities exist which may be exploited in response to the parameters of specific drug design projects. Bioisosteric modification of existing molecules and de novo design are two such approaches, both of which were employed in parallel in this study which aimed to compare their scope and efficiency using Tricyclic Antidepressants (TCAs) and Selective Serotonin Reuptake Inhibiting (SSRIs) molecules as case studies. Results indicated that bioisosterically modified structures did not have a higher affinity for their cognate receptor when compared to the template structure while the de novo design yielded molecules that were markedly different to the template from a structural perspective, and which also bound to the cognate receptor with an affinity superior to that of the template. This study showed therefore that bioisosteric modification is of utility when minor structural variations are considered sufficiently relative to a template molecule, and could consequently be of utility in the acquisition of new patents, in the reduction of toxicity, or in the attainment of improved biological profiles. It indicated furthermore, the role of the de novo approach in the successful exploration of novel pharmacophoric space and in the generation of molecular structures with an affinity significantly greater than that of lead molecules for a target receptor.peer-reviewe
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On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine
Protein kinases are important regulatory enzymes in signal transduction and in cell regulation. Understanding inhibition mechanisms of kinases is important for the further development of new therapies for cancer and inflammatory diseases. I have developed a statistical approach based on the Mantel test to find the relationship between the shapes of ATP binding sites and their affinities for inhibitors. My shape-based dendrogram shows clustering of the kinases based on similarity in shape. I investigate the pocket in terms of conservation of surrounding amino acids and atoms in order to identify the key determinants of ligand binding. I find that the most conserved regions are the main chain atoms in the hinge region and I show that the tetrahydropyran ring of staurosporine causes induced-fit of the glycine rich loop. I apply multiple linear regression to select distances measured between the distinctive parts of residues which correlate with the binding constants. This method allows me to understand the importance of the size of the gatekeeper residue and the closure between the first glycine of the GXGXXG motif and the aspartate of the DFG loop, which act together to promote tight binding to staurosporine. I also find that the greater the number of hydrogen bonds made by the kinase around the methylamine group of staurosporine, the tighter the binding to staurosporine. The website I have developed allows a better understanding of cross reactivity and may be useful for narrowing down the options for a synthetic strategy to design kinase inhibitors.This work was supported by the Royal Thai Government
Methods for the Efficient Comparison of Protein Binding Sites and for the Assessment of Protein-Ligand Complexes
In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented.
Protein binding site comparisons are frequently used receptor-based techniques in early stages of the drug development process. Binding sites of other proteins which are similar to the binding site of the target protein can offer hints for possible side effects of a new drug prior to clinical studies. Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases.
Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. These programs are utilized to screen entire libraries of molecules for a possible ligand of a binding site and to furthermore estimate in which conformation the ligand will most likely bind. By employing this information, molecule libraries can be filtered for subsequent affinity assays and molecular structures can be refined with regard to affinity and selectivity
Development of Computational Methods to Predict Protein Pocket Druggability and Profile Ligands using Structural Data
This thesis presents the development of computational methods and tools using as input three-dimensional structures data of protein-ligand complexes. The tools are useful to mine, profile and predict data from protein-ligand complexes to improve the modeling and the understanding of the protein-ligand recognition. This thesis is divided into five sub-projects. In addition, unpublished results about positioning water molecules in binding pockets are also presented.
I developed a statistical model, PockDrug, which combines three properties (hydrophobicity, geometry and aromaticity) to predict the druggability of protein pockets, with results that are not dependent on the pocket estimation methods. The performance of pockets estimated on apo or holo proteins is better than that previously reported in the literature (Publication I).
PockDrug is made available through a web server, PockDrug-Server (http://pockdrug.rpbs.univ-paris-diderot.fr), which additionally includes many tools for protein pocket analysis and characterization (Publication II).
I developed a customizable computational workflow based on the superimposition of homologous proteins to mine the structural replacements of functional groups in the Protein Data Bank (PDB). Applied to phosphate groups, we identified a surprisingly high number of phosphate non-polar replacements as well as some mechanisms allowing positively charged replacements. In addition, we observed that ligands adopted a U-shape conformation at nucleotide binding pockets across phylogenetically unrelated proteins (Publication III).
I investigated the prevalence of salt bridges at protein-ligand complexes in the PDB for five basic functional groups. The prevalence ranges from around 70% for guanidinium to 16% for tertiary ammonium cations, in this latter case appearing to be connected to a smaller volume available for interacting groups. In the absence of strong carboxylate-mediated salt bridges, the environment around the basic functional groups studied appeared enriched in functional groups with acidic properties such as hydroxyl, phenol groups or water molecules (Publication IV).
I developed a tool that allows the analysis of binding poses obtained by docking. The tool compares a set of docked ligands to a reference bound ligand (may be different molecule) and provides a graphic output that plots the shape overlap and a Jaccard score based on comparison of molecular interaction fingerprints. The tool was applied to analyse the docking poses of active ligands at the orexin-1 and orexin-2 receptors found as a result of a combined virtual and experimental screen (Publication V).
The review of literature focusses on protein-ligand recognition, presenting different concepts and current challenges in drug discovery.TÀssÀ vÀitöskirjassa esitetÀÀn tietokoneavusteisia menetelmiÀ ja työkaluja, jotka perustuvat proteiini-ligandikompleksien kolmiulotteisiin rakenteisiin. Ne soveltuvat proteiini-ligandikompleksien rakennetiedon louhimiseen, optimointiin ja ennustamiseen. Tavoitteena on parantaa sekÀ mallinnusta ettÀ kÀsitystÀ proteiini-liganditunnistuksesta. VÀitöskirjassa työkalut kuvataan viitenÀ eri alahankkeena. LisÀksi esitetÀÀn toistaiseksi julkaisemattomia tuloksia vesimolekyylien asemoinnista proteiinien sitoutumistaskuihin.
Kehitin PockDrugiksi kutsumani tilastollisen mallin, joka yhdistÀÀ kolme ominaisuutta â hydrofobisuuden, geometrian ja aromaattisuuden â proteiinitaskujen lÀÀkekehityskohteeksi soveltuvuuden ennustamista varten siten, ettĂ€ tulokset ovat riippumattomia sitoutumistaskun sijoitusmenetelmĂ€stĂ€. Apo- ja holoproteiinien taskujen ennustaminen toimii paremmin kuin alan kirjallisuudessa on aiemmin kuvattu (Julkaisu I).
PockDrug on vapaasti kÀyttÀjien saatavilla PockDrug-verkkopalvelimelta (http://pockdrug.rpbs.univ-paris-diderot.fr), jossa on lisÀksi useita työkaluja proteiinin sitoutumiskohdan analyysiin ja karakterisointiin (Julkaisu II).
Kehitin myös muokattavissa olevan tietokoneavusteisen prosessin, joka perustuu samankaltaisten proteiinien pÀÀllekkÀin asetteluun, louhiakseni Protein Data Bankista (PDB) toiminnallisten ryhmien rakenteellisia korvikkeita. TÀtÀ fosfaattiryhmiin soveltaessani tunnistin yllÀttÀvÀn paljon poolittomia fosfaattiryhmÀn korvikkeita ja joitakin positiivisesti varautuneita korvikkeita mahdollistavia mekanismeja. LisÀksi havaitsin, ettÀ ligandit omaksuivat U muotoisen konformaation fylogeneettisesti riippumattomien proteiinien nukleotidien sitoutumistaskuissa (Julkaisu III).
Tutkin PDB:n proteiini-ligandikompleksien suolasiltojen yleisyyttÀ viidelle emÀksiselle toiminnalliselle ryhmÀlle. Suolasiltojen yleisyys vaihteli guanidinium-ionin 70 prosentista tertiÀÀristen ammoniumkationien 16 prosenttiin. JÀlkimmÀisessÀ tapauksessa suolasiltojen vÀhÀisyys vaikuttaa riippuvan siitÀ, ettÀ vuorovaikuttaville ryhmille on vÀhemmÀn tilaa. MikÀli tarkastellut emÀksiset ryhmÀt eivÀt osallistuneet vahvoihin karboksylaattivÀlitteisiin suolasiltoihin, niiden ympÀristössÀ vaikutti olevan runsaasti happamia toiminnallisia ryhmiÀ, kuten hydroksi- ja fenoliryhmiÀ sekÀ vesimolekyylejÀ (Julkaisu IV).
Lopuksi kehitin työkalun, joka mahdollistaa telakoinnista saatujen sitoutumisasentojen analyysin. Työkalu vertaa telakoitua ligandisarjaa sitoutuneeseen vertailuligandiin, joka voi olla eri molekyyli. Graafisena tulosteena saadaan diagrammi ligandien muotojen samankaltaisuudesta ja molekyylivuorovaikutusten sormenjĂ€lkiin perustuvasta Jaccard-pistemÀÀrĂ€stĂ€. Työkalua sovellettiin oreksiini-1- ja oreksiini-2-reseptoreille yhdistetyllĂ€ virtuaalisella ja kokeellisella seulonnalla löydettyjen aktiivisten ligandien sitoutumisasentojen analyysiin (Julkaisu V).Cette thĂšse prĂ©sente le dĂ©veloppement de mĂ©thodes et dâoutils informatiques basĂ©s sur la structure tridimensionnelle des complexes protĂ©ine-ligand. Ces diffĂ©rentes mĂ©thodes sont utilisĂ©es pour extraire, optimiser et prĂ©dire des donnĂ©es Ă partir de la structure des complexes afin dâamĂ©liorer la modĂ©lisation et la comprĂ©hension de la reconnaissance entre une protĂ©ine et un ligand. Ce travail de thĂšse est divisĂ© en cinq projets. En complĂ©ment, une Ă©tude sur le positionnement des molĂ©cules dâeau dans les sites de liaisons a aussi Ă©tĂ© dĂ©veloppĂ©e et est prĂ©sentĂ©e.
Dans une premiĂšre partie un modĂšle statistique, PockDrug, a Ă©tĂ© mis en place. Il combine trois propriĂ©tĂ©s de poches protĂ©iques (lâhydrophobicitĂ©, la gĂ©omĂ©trie et lâaromaticitĂ©) pour prĂ©dire la druggabilitĂ© des poches protĂ©iques, si une poche protĂ©ique peut lier une molĂ©cule drug-like. Le modĂšle est optimisĂ© pour sâaffranchir des diffĂ©rentes mĂ©thodes dâestimation de poches protĂ©iques. La qualitĂ© des prĂ©dictions, est meilleure Ă la fois sur des poches estimĂ©es Ă partir de protĂ©ines apo et holo et est supĂ©rieure aux autres modĂšles de la littĂ©rature (Publication I). Le modĂšle PockDrug est disponible sur un serveur web, PockDrug-Server (http://pockdrug.rpbs.univ-paris-diderot.fr) qui inclus dâautres outils pour lâanalyse et la caractĂ©risation des poches protĂ©iques.
Dans un second temps un protocole, basĂ© sur la superposition de protĂ©ines homologues a Ă©tĂ© dĂ©veloppĂ© pour extraire des replacements structuraux de groupements chimiques fonctionnels Ă partir de la Protein Data Bank (PDB). AppliquĂ© aux phosphates, un grand nombre de remplacements non-polaires ont Ă©tĂ© identifiĂ© pouvant notamment ĂȘtre chargĂ©s positivement. Quelques mĂ©canismes de remplacements ont ainsi pu ĂȘtre analysĂ©. Nous avons, par exemple, observĂ© que le ligand adopte une configuration en forme U dans les sites de liaison des nuclĂ©otides indĂ©pendamment de la phylogĂ©nĂ©tique des protĂ©ines (Publication III).
Dans une quatriĂšme partie, la prĂ©valence des ponts salins de cinq groupements chimiques basiques a Ă©tĂ© Ă©tudiĂ© dans les complexes protĂ©ine-ligand. Ainsi le pourcentage de pont salin fluctue de 70% pour le guanidinium Ă 16% pour lâamine tertiaire qui a le plus faible volume disponible autour de lui pour accueillir un group pouvant interagir. Lâabsence dâacide fort comme lâacide carboxylique pour former un pont salin est remplacĂ© par un milieu enrichis en groupement chimiques fonctionnels avec des propriĂ©tĂ©s acides comme lâhydroxyle, le phĂ©nol ou encore les molĂ©cules dâeau (Publication IV).
Dans un dernier temps un outil permettant lâanalyse des poses de ligand obtenues par une mĂ©thode dâancrage molĂ©culaire a Ă©tĂ© dĂ©veloppĂ©. Cet outil compare ces poses Ă un ligand de rĂ©fĂ©rence, qui peut ĂȘtre une molĂ©cule diffĂ©rente en combinant lâinformation du chevauchement de forme de la pose et du ligand de rĂ©fĂ©rence et un score de Jaccard basĂ© sur une comparaison des empreintes dâinteraction molĂ©culaires du ligand de rĂ©fĂ©rence et de la pose. Cette mĂ©thode a Ă©tĂ© utilisĂ© dans lâanalyse des rĂ©sultats dâancrage molĂ©culaires pour des ligands actifs pour les rĂ©cepteurs aux orexine 1 et 2. Ces ligands actifs ont Ă©tĂ© trouvĂ©s Ă partir de rĂ©sultats combinant un criblage virtuel et expĂ©rimental.
La revue de la littĂ©rature associĂ©e est focalisĂ©e sur la reconnaissance molĂ©culaire dâun ligand pour une protĂ©ine et prĂ©sente diffĂšrent concepts et challenges pour la recherche de nouveaux mĂ©dicaments