100 research outputs found
Scaffold Hopping and Bioisosteric Replacements Based on Binding Site Alignments
Bioisosteric replacements and scaffold hopping play an important role in modern drug discovery and design, as they enable the change of either a core scaffold or substitutes in a drug structure, thereby facilitating optimization of pharmacokinetic properties and patenting, while the drug retains its activity. A new knowledge-based method was developed to obtain bioisosteric or scaffold replacements based on the extensive data existing in the Protein Data Bank. The method uses all-against-all ProBiS-based protein superimposition to identify ligand fragments that overlap in similar binding sites and could therefore be considered as bioisosteric replacements. The method was demonstrated on a specific example of drug candidate â a nanomolar butyrylcholinesterase inhibitor, on which bioisosteric replacements of the three ring fragments were performed. The new molecule containing bioisosteric replacements was evaluated virtually using AutoDock Vina; a similar score for the original and the compound with replacements was obtained, suggesting that the newly designed bioisostere compound might retain the potency of the original inhibitor.
This work is licensed under a Creative Commons Attribution 4.0 International License
Computational Analysis of Structure-Activity Relationships : From Prediction to Visualization Methods
Understanding how structural modifications affect the biological activity of small molecules is one of the central themes in medicinal chemistry. By no means is structure-activity relationship (SAR) analysis a priori dependent on computational methods. However, as molecular data sets grow in size, we quickly approach our limits to access and compare structures and associated biological properties so that computational data processing and analysis often become essential. Here, different types of approaches of varying complexity for the analysis of SAR information are presented, which can be applied in the context of screening and chemical optimization projects. The first part of this thesis is dedicated to machine-learning strategies that aim at de novo ligand prediction and the preferential detection of potent hits in virtual screening. High emphasis is put on benchmarking of different strategies and a thorough evaluation of their utility in practical applications. However, an often claimed disadvantage of these prediction methods is their "black box" character because they do not necessarily reveal which structural features are associated with biological activity. Therefore, these methods are complemented by more descriptive SAR analysis approaches showing a higher degree of interpretability. Concepts from information theory are adapted to identify activity-relevant structure-derived descriptors. Furthermore, compound data mining methods exploring prespecified properties of available bioactive compounds on a large scale are designed to systematically relate molecular transformations to activity changes. Finally, these approaches are complemented by graphical methods that primarily help to access and visualize SAR data in congeneric series of compounds and allow the formulation of intuitive SAR rules applicable to the design of new compounds. The compendium of SAR analysis tools introduced in this thesis investigates SARs from different perspectives
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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
Investigating phosphate structural replacements through computational and experimental approaches
Bioisosteric replacements are used in drug design during lead generation and optimization processes with the aim to replace one functional group of a known molecule by another while retaining biological activity. The reason to use bioisosteric replacements are typically to optimize bioavailability or reducing toxicity. Phosphate groups represent a paradigm to study bioisosteric replacements. Protein-phosphate interaction plays a critical role during molecular recognition processes, and for example kinases represent one of the largest families of drug targets. However, some challenges exclude phosphate as a promising lead-like building block: i) charged phosphates do not cross molecular membranes; ii) some widely expressed proteins such as phosphatases easily hydrolyze phosphoric acid esters, which lead phosphate-containing ligands to lose their binding affinities before reaching their biological targets; iii) introduction of phosphate groups to parent scaffold is not easy.
In the first part of the thesis work, I designed and implemented a computational protocol to mine information about phosphate structural replacements deposited in the Protein Data Bank. I constructed 116, 314, 271, and 42 sets of superimposed proteins where each set contains a reference protein to either POP, AMP, ADP, or ATP as well as a certain number of non-nucleotide ligands. 929 of such ligands are under study. The chemotypes that came out as structural replacements are diverse, ranging from common phosphate isosteres such as carboxyl, amide and squaramide to more surprising moieties such as benzoxaborole and aromatic ring systems. I exemplified some novel examples and interpreted the mechanism behind them. Local structural replacements are circumstance dependent: one chemical group valid in certain set-up cannot necessarily guarantee the success of another. The data from the study is available at http://86.50.168.121/phosphates_LSR.php.
In the second part, I synthesized fifteen compounds retaining the adenosine moieties and bearing bioisosteric replacements of the phosphate at the ribose 5'-oxygen to test their stability toward human macro domain protein 1. These compounds are composed of either a squaryldiamide or an amide group as the bioisosteric replacement and/or as a linker. To these groups a variety of substituents were attached: phenyl, benzyl, pyridyl, carboxyl, hydroxy and tetrazolyl. Biological evaluation using differential scanning fluorimetry showed that four compounds stabilized human MDO1 at levels comparable to ADP and one at level comparable to AMP. Virtual screening was also run to identify MDO1 binding ligands. Among 20,000 FIMM database lead-like molecules, 39 compounds were selected for testing and eleven compounds found active based on ADPr and Poly-ADPr competition binding assay. The assay is however not well validated and a second confirmatory assay was conducted using calorimetry. To the best of my knowledge, this is the first report of non-endogenous ligands of the human MDO1.
Altogether, this thesis highlights the versatility of molecular recognition processes that accompanies chemical replacements in compounds; this in turns shows the limits of the concepts of molecular similarity and classical bioisosterism that are based on the conservation of molecular interactions.BioisosteeristÀ korvausta kÀytetÀÀn lÀÀkeainekehityksessÀ johtolankamolekyylien tuottamisessa ja optimoinnissa. Tarkoitus on vaihtaa molekyylin funktionaalinen ryhmÀ toiseksi biologisen aktiivisuuden muuttumatta. YleensÀ tavoitteena on parantaa biologista hyötyosuutta tai vÀhentÀÀ toksisuutta. FosfaattiryhmÀÀ on tÀssÀ työssÀ kÀytetty esimerkkiryhmÀnÀ bioisosteerisiÀ korvauksia tutkittaessa.
VÀitöskirjatyön ensimmÀisessÀ osassa suunnittelin ja toteutin tiedonlouhintaprotokollan etsiÀkseni Protein Data Bank -tietokannasta korvaavia rakenteita fosfaattiryhmÀlle. Kokosin 116, 314, 271 ja 42 proteiiniryhmÀÀ, joissa kussakin on vertailumolekyylinÀ fosfaattiryhmÀn sisÀltÀvÀ POP, AMP, ADP tai ATP, ja lisÀksi ei-nukleotidisiÀ ligandeja. YhteensÀ 929 ei-nukleotidistÀ ligandia tutkittiin. NiistÀ löydettiin monipuolisesti fosfaattiryhmÀn korvaavia rakenteita, muun muassa yleisesti tunnettuja fosfaatin bioisosteerejÀ kuten karboksyyli, amidi ja squaramidi, mutta myös erikoisempia ryhmiÀ kuten bentsoksaboroli ja aromaattisia rengasrakenteita. TyössÀni esittelen muutamia uusia rakenteita ja tulkitsen niiden vaikutusmekanismeja. Rakenteiden korvaaminen riippuu tilanteesta; yhteen tapaukseen sopiva korvaava ryhmÀ ei vÀlttÀmÀttÀ toimi toisessa.
Työn toisessa osassa syntetisoin 15 adenosiiniyhdistettÀ, joiden riboosiosan 5'-hapessa oleva fosfaattiryhmÀ on korvattu vaihtelevalla bioisosteerisellÀ ryhmÀllÀ. BioisosteerisenÀ ryhmÀnÀ tai linkkerinÀ oli joko squaramidi- tai amidiryhmÀ. Yhdisteiden vakaus testattiin ihmisen MDO1-makrodomeeniproteiinin kanssa.Julkaisussa virheellinen verkkoaineiston ISBN 978-951-51-0045-0
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
Design and selection of novel C1s inhibitors by in silico and in vitro approaches
The complement system is associated with various diseases such as inflammation or autoimmune diseases. Complement-targeted drugs could provide novel therapeutic intervention against the above diseases. C1s, a serine protease, plays an important role in the CS and could be an attractive target since it blocks the system at an early stage of the complement cascade. Designing C1 inhibitors is particularly challenging since known inhibitors are restricted to a narrow bioactive chemical space in addition selectivity over other serine proteases is an important requirement. The typical architecture of a small molecule inhibitor of C1s contains an amidine (or guanidine) residue, however, the discovery of non-amidine inhibitors might have high value, particularly if novel chemotypes and/or compounds displaying improved selectivity are identified. We applied various virtual screening approaches to identify C1s focused libraries that lack the amidine/guanidine functionalities, then the in silico generated libraries were evaluated by in vitro biological assays. While 3D structure-based methods were not suitable for virtual screening of C1s inhibitors, and a 2D similarity search did not lead to novel chemotypes, pharmacophore model generation allowed us to identify two novel chemotypes with submicromolar activities. In three screening rounds we tested altogether 89 compounds and identified 20 hit compounds (<10 ΌM activities; overall hit rate: 22.5%). The highest activity determined was 12 nM (1,2,4-triazole), while for the newly identified chemotypes (1,3-benzoxazin-4-one and thieno[2,3-d][1,3]oxazin-4-one) it was 241 nM and 549 nM, respectively. © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/)
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Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose.
We introduce the QuanSA method for inducing physically meaningful field-based models of ligand binding pockets based on structure-activity data alone. The method is closely related to the QMOD approach, substituting a learned scoring field for a pocket constructed of molecular fragments. The problem of mutual ligand alignment is addressed in a general way, and optimal model parameters and ligand poses are identified through multiple-instance machine learning. We provide algorithmic details along with performance results on sixteen structure-activity data sets covering many pharmaceutically relevant targets. In particular, we show how models initially induced from small data sets can extrapolatively identify potent new ligands with novel underlying scaffolds with very high specificity. Further, we show that combining predictions from QuanSA models with those from physics-based simulation approaches is synergistic. QuanSA predictions yield binding affinities, explicit estimates of ligand strain, associated ligand pose families, and estimates of structural novelty and confidence. The method is applicable for fine-grained lead optimization as well as potent new lead identification
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