Swimming into peptidomimetic chemical space using pepMMsMIMIC

pepMMsMIMIC is a novel web-oriented peptidomimetic compound virtual screening tool based on a multi-conformers three-dimensional (3D)-similarity search strategy. Key to the development of pepMMsMIMIC has been the creation of a library of 17 million conformers calculated from 3.9 million commercially available chemicals collected in the MMsINC® database. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein–protein recognition of this natural peptide using both pharmacophore and shape similarity techniques. We hope that the accessibility of pepMMsMIMIC (freely available at http://mms.dsfarm.unipd.it/pepMMsMIMIC) will encourage medicinal chemists to de-peptidize protein–protein recognition processes of biological interest, thus increasing the potential of in silico peptidomimetic compound screening of known small molecules to expedite drug development

IDENTIFICATION OF POTENTIAL SALMONELLA TYPHI BETA-LACTAMASE TEM 1 INHIBITORS USING PEPTIDOMIMETICS, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS SIMULATIONS

Objective: The purpose of this study was to identify a potential peptidomimetic S. typhi Beta-lactamase TEM 1 inhibitor to tackle the antibiotic resistance among S. typhi.Methods: The potential peptidomimetic inhibitor was identified by in silico docking of the small peptide WFRKQLKW with S. typhi Beta-lactamase TEM 1. The 3D coordinate geometry of the residues of small peptide interacting with the active site of the receptor was generated and mimics were identified using PEP: MMs: MIMIC server. All the identified mimics were docked at the active site of the receptor using Autodock 4.2 and the best-docked complex was selected on the basis of binding energy and number of H-bonds. The complex was then subjected to molecular dynamics simulations of 30 ns using AMBER 12 software package. The stereochemical stability of the Beta-lactamase TEM 1-WFRKQLKW complex was estimated with the help of Ramachandran plot using PROCHECK tool.Results: In the present study, a new potential peptidomimetic inhibitor (ZINC05839264) of Beta-lactamase TEM 1 has been identified based on antimicrobial peptide WFRKQLKW by virtual screening of the MMsINC database. The docking and molecular simulation studies revealed that the mimic binds more tightly to the active site of the receptor than the peptide. The Ramachandran plot also shows that the Beta-lactamase TEM 1-mimic complex is stereo chemically more stable than Beta-lactamase TEM 1-WFRKQLKW complex as more number of residues (93.6%) are falling under the core region of the plot in case of the former.Conclusion: The study shows that the peptidomimetic compound can act as a potential inhibitor of S. typhi Beta-lactamase TEM 1 and further it can be developed into more effective therapeutic to tackle the problem of antibiotic resistance

Chemoinformatics approaches for new drugs discovery

Chemoinformatics uses computational methods and technologies to solve chemical problems. It works on molecular structures, their representations, properties and related data. The first and most important phase in this field is the translation of interconnected atomic systems into in-silico models, ensuring complete and correct chemical information transfer. In the last 20 years the chemical databases evolved from the state of molecular repositories to research tools for new drugs identification, while the modern high-throughput technologies allow for continuous chemical libraries size increase as highlighted by publicly available repository like PubChem [http://pubchem.ncbi.nlm.nih.gov/], ZINC [http://zinc.docking.org/], ChemSpider[http://www.chemspider. com/]. Chemical libraries fundamental requirements are molecular uniqueness, absence of ambiguity, chemical correctness (related to atoms, bonds, chemical orthography), standardized storage and registration formats. The aim of this work is the development of chemoinformatics tools and data for drug discovery process. The first part of the research project was focused on accessible commercial chemical space analysis; looking for molecular redundancy and in-silico models correctness in order to identify a unique and univocal molecular descriptor for chemical libraries indexing. This allows for the 0%-redundancy achievement on a 42 millions compounds library. The protocol was implemented as MMsDusty, a web based tool for molecular databases cleaning. The major protocol developed is MMsINC, a chemoinformatics platform based on a starting number of 4 millions non-redundant high-quality annotated and biomedically relevant chemical structures; the library is now being expanded up to 460 millions compounds. MMsINC is able to perform various types of queries, like substructure or similarity search and descriptors filtering. MMsINC is interfaced with PDB(Protein Data Bank)[http://www.rcsb.org/pdb/home/home.do] and related to approved drugs. The second developed protocol is called pepMMsMIMIC, a peptidomimetic screening tool based on multiconformational chemical libraries; the screening process uses pharmacophoric fingerprints similarity to identify small molecules able to geometrically and chemically mimic endogenous peptides or proteins. The last part of this project lead to the implementation of an optimized and exhaustive conformational space analysis protocol for small molecules libraries; this is crucial for high quality 3D molecular models prediction as requested in chemoinformatics applications. The torsional exploration was optimized in the range of most frequent dihedral angles seen in X-ray solved small molecules structures of CSD(Cambridge Structural Database); by appling this on a 89 millions structures library was generated a library of 2.6 x 10 exp 7 high quality conformers. Tools, protocols and platforms developed in this work allow for chemoinformatics analysis and screening on large size chemical libraries achieving high quality, correct and unique chemical data and in-silico model

Recherche de nouveaux antipaludiques par bioinformatique structurale et chémoinformatique : application à deux cibles : PfAMA1 et PfCCT

Human malaria is caused by five parasitic species of the genus Plasmodium, P. falciparum being the most deadly. Drug resistance of some parasite strains has been reported for commercial drugs. Vector mosquitoes are resistant to perythroid insecticides and no successful vaccine is available. This disease is a public and economic health issue for developing countries. My PhD projects investigate new treatments for malaria, by targeting two new proteins. Apicomplexa parasites have developed a unique invasion mechanism involving a tight interaction formed between the host cell and the parasite surfaces called Moving Junction. The structural and functional characterization of the AMA1-RON2 complex pave the way for the design of low molecular weight compounds capable of disrupting the AMA1-RON2 assembly and thereby invasion. The parasite also needs phospholipids to build its membrane during the erythrocytic cycle. There are six times more phospholipids in infected erythrocytes compared to healthy ones. Our strategy is to inhibit the de novo Kennedy pathway and more precisely its rate-limiting step catalysed by the enzyme PfCCT. Filters were used for ligand-based (LBVS) and structure-based virtual screening (SBVS) of commercial chemical databases that I have prepared. For each project, molecules were selected in terms of their docking scores and their interactions with key active site residues. By combining structural bioinformatics and cheminformatics, we identified potential inhibitors of the two protein targets.Le paludisme est causé par cinq espèces du genre Plasmodium, P. falciparum étant le plus mortel. Des résistances de certaines souches du parasite ont été rapportées pour tous les médicaments mis sur le marché. Les moustiques vecteurs du parasite sont résistants aux insecticides et aucun vaccin n'est disponible. Cette maladie est un problème économique et de santé publique pour les pays en voie de développement. Mes travaux de thèses visent à identifier de nouveaux traitements contre le paludisme, en ciblant deux nouvelles protéines. Les Apicomplexes ont développé un mécanisme unique d'invasion, impliquant une interaction forte entre la cellule hôte et la surface du parasite, appelée jonction mobile. La caractérisation structurale et fonctionnelle du complexe AMA1-RON2 a ouvert la voie à la découverte de petites molécules capables d'empêcher l'interaction AMA1-RON2 et de ce fait, l'invasion. Le parasite a aussi besoin de phospholipides pour construire sa membrane durant le cycle érythrocytaire. Il y a six fois plus de phospholipides dans les érythrocytes infectés que dans les érythrocytes sains. Notre stratégie est d'inhiber la voie de synthèse de novo Kennedy et plus précisément, son étape limitante catalysée par la PfCCT. Des filtres basés sur le ligand (LBVS) et sur la structure (SBVS) ont été utilisés pour tester virtuellement les chimiothèques commerciales que j'ai préparées. Pour chaque projet, des molécules ont été sélectionnées pour leurs scores de docking et les interactions qu'elles établissent avec les résidus clés de la protéine. En combinant la bioinformatique structurale et la chémoinformatique, nous avons identifié des inhibiteurs potentiels des deux cibles protéiques

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.Bioisosteeristä korvausta käytetään lääkeainekehityksessä johtolankamolekyylien tuottamisessa ja optimoinnissa. Tarkoitus on vaihtaa molekyylin funktionaalinen ryhmä toiseksi biologisen aktiivisuuden muuttumatta. Yleensä tavoitteena on parantaa biologista hyötyosuutta tai vähentää toksisuutta. Fosfaattiryhmää on tässä työssä käytetty esimerkkiryhmänä bioisosteerisiä korvauksia tutkittaessa. Väitöskirjatyön ensimmäisessä osassa suunnittelin ja toteutin tiedonlouhintaprotokollan etsiäkseni Protein Data Bank -tietokannasta korvaavia rakenteita fosfaattiryhmälle. Kokosin 116, 314, 271 ja 42 proteiiniryhmää, joissa kussakin on vertailumolekyylinä fosfaattiryhmän sisältävä POP, AMP, ADP tai ATP, ja lisäksi ei-nukleotidisiä ligandeja. Yhteensä 929 ei-nukleotidistä ligandia tutkittiin. Niistä löydettiin monipuolisesti fosfaattiryhmän korvaavia rakenteita, muun muassa yleisesti tunnettuja fosfaatin bioisosteerejä kuten karboksyyli, amidi ja squaramidi, mutta myös erikoisempia ryhmiä kuten bentsoksaboroli ja aromaattisia rengasrakenteita. Työssäni esittelen muutamia uusia rakenteita ja tulkitsen niiden vaikutusmekanismeja. Rakenteiden korvaaminen riippuu tilanteesta; yhteen tapaukseen sopiva korvaava ryhmä ei välttämättä toimi toisessa. Työn toisessa osassa syntetisoin 15 adenosiiniyhdistettä, joiden riboosiosan 5'-hapessa oleva fosfaattiryhmä on korvattu vaihtelevalla bioisosteerisellä ryhmällä. Bioisosteerisenä ryhmänä tai linkkerinä oli joko squaramidi- tai amidiryhmä. Yhdisteiden vakaus testattiin ihmisen MDO1-makrodomeeniproteiinin kanssa.Julkaisussa virheellinen verkkoaineiston ISBN 978-951-51-0045-0