abstract: Peptides offer great promise as targeted affinity ligands, but the space of possible peptide sequences is vast, making experimental identification of lead candidates expensive, difficult, and uncertain. Computational modeling can narrow the search by estimating the affinity and specificity of a given peptide in relation to a predetermined protein target. The predictive performance of computational models of interactions of intermediate-length peptides with proteins can be improved by taking into account the stochastic nature of the encounter and binding dynamics. A theoretical case is made for the hypothesis that, because of the flexibility of the peptide and the structural complexity of the target protein, interactions are best characterized by an ensemble of possible bound configurations rather than a single “lock and key” fit. A model incorporating these factors is proposed and evaluated. A comprehensive dataset of 3,924 peptide-protein interface structures was extracted from the Protein Data Bank (PDB) and descriptors were computed characterizing the geometry and energetics of each interface. The characteristics of these interfaces are shown to be generally consistent with the proposed model, and heuristics for design and selection of peptide ligands are derived. The curated and energy-minimized interface structure dataset and a relational database containing the detailed results of analysis and energy modeling are made publicly available via a web repository. A novel analytical technique based on the proposed theoretical model, Virtual Scanning Probe Mapping (VSPM), is implemented in software to analyze the interaction between a target protein of known structure and a peptide of specified sequence, producing a spatial map indicating the most likely peptide binding regions on the protein target. The resulting predictions are shown to be superior to those of two other published methods, and support the validity of the stochastic binding model. / Dissertation/Thesis / Ph.D. Bioengineering 2010

This thesis describes the design, synthesis and application of artificial metalloenzymes for transition metal catalysed reactions not performed by natural enzymes. Unique cysteine containing protein templates were covalently modified with transition metal ligand complexes that generate catalytic activity, which allows for the use of virtually any protein template. SCP-2L was selected as template for the linear hydrophobic tunnel that traverses the protein, which has high affinity for linear aliphatic molecules. The use of catalysts based on this protein to induce increased activity in the biphasic hydroformylation of linear α-olefins is investigated in this work. For this purpose, unique cysteine containing mutants of SCP-2L were modified with phosphine ligands by application of a novel bioconjugation procedure. Application of rhodium adducts of the phosphine modified protein constructs led to up to a 100 fold increase of the turn over numbers was measured compared to a Rh/TPPTS model system which is used in industry. Furthermore, good selectivity towards the linear product was observed. If it can be confirmed that the found catalytic results truly are the result of substrate encapsulation by the protein scaffold, this system represents the first rationally designed artificial metalloenzyme which exploits the shape selectivity of the protein scaffold to direct the outcome of a catalytic reaction. In addition, a study was performed for the development of enantioselective artificial metalloenzymes. Nitrogen ligands were covalently introduced in SCP-2L and the obtained conjugates were applied in the copper catalysed Diels-Alder and Michael addition reaction. A promising 25% ee was found for the Diels-Alder reaction between azachalcone and cyclopentadiene using one of the created constructs. Further development of these catalyst systems with the use of both synthetic (e.g. optimisation of ligand structure) and biomolecular tools (e.g. optimisation of protein environment) for optimisation can lead to very efficient and enantioselective conversions in the future.

abstract: The late first row transition metals, being inexpensive and environmentally benign, have become very attractive for sustainable catalyst development. However, to overcome the detrimental one electron redox processes exhibited by these metals, the employment of redox non-innocent chelates turned out to be very useful. The Trovitch group has designed a series of pentadentate bis(imino)pyridine ligands (pyridine diimine, PDI) that are capable of binding the metal center beyond their 3-N,N,N core and also possess coordination flexibility. My research is focused on developing PDI-supported manganese catalysts for organic transformations and renewable fuel production. The thesis presents synthesis and characterization of a family of low valent (PDI)Mn complexes. Detailed electronic structure evaluation from spectroscopic and crystallographic data revealed electron transfer from the reduced metal center to the accessible ligand orbitals. One particular (PDI)Mn variant, (5-Ph2PPrPDI)Mn has been found to be the most efficient carbonyl hydrosilylation catalyst reported till date, achieving a maximum turnover frequency of up to 4950 min-1. This observation demanded a thorough investigation of the operative mechanism. A series of controlled stoichiometric reactions, detailed kinetic analysis, and relevant intermediate isolation suggest a mechanism that involves oxidative addition, carbonyl insertion, and reductive elimination. Noticing such remarkable efficiency of the (PDI)Mn system, it has been tested for application in renewable fuel generation. A modest efficiency for H2 production at an apparent pH of 8.4 have been achieved using a cationic Mn complex, [(Ph2PPrPDI)Mn(CO)]Br. Although, a detailed mechanistic investigation remained challenging due to complex instability, a set of relevant Mn(-I) intermediates have been isolated and characterized thoroughly. The dissertation also includes synthesis, characterization, and electronic structure evaluation of a series of Triphos supported iron complexes. Using this pincer chelate and either 2,2’-bipyridine (bpy) or 1,3,5,7-cyclooctatetraene (COT), a set of electronically interesting complexes have been isolated. Detailed electronic structure investigation using spectroscopy, magnetometry, crystallography, and DFT calculations revealed redox non-innocent behavior in the Bpy and COT ligands. Additionally, CO binding to the (Triphos)Fe system followed by reaction with borohydride reagents allowed for the isolation of some catalytically relevant and reactive iron hydride complexes. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

L'importance industrielle et économique de la catalyse en fait aujourd'hui un des thèmes le plus étudiés dans la recherche. La récupération de catalyseurs est très important, particulièrement lorsque l'on utilise des métaux coûteux (Rh, Ir, Pt, Ru, etc.), tant d'un point de vue économique, qu'environnemental ou sanitaire. Notre équipe a entamé depuis quelques années un programme de recherche sur l'utilisation de polymères cœur-coquille, de taille et de composition bien définie, comportant un cœur hydrophobe et fonctionnalisé par des ligands et une chevelure hydrophile en périphérie pour le confinement des objets en milieu aqueux. Ces polymères sont construits pour fonctionner comme des nanoréacteurs en conditions biphasiques. Seuls des nanoréacteurs possédant des ligands monophosphine avaient été synthétisés jusqu'ici. La première application de ces nanoréacteurs catalytiques a été réalisée, avec succès, en hydroformylation de l'octène en conditions biphasiques. Dans cette thèse, nous nous sommes intéressés, dans un premier temps, à continuer l'étude physicochimique de ces nanoréacteurs et à les utiliser en catalyse d'hydrogénation. Dans un deuxième temps, nous avons synthétisé de nouveaux polymères cœur-coquille contenant des ligands bidentes, soit ferrocénique (PS), soit des ligands nixantphos (PP). Nous présentons donc la synthèse de ligands possédant des groupements styryles polymérisables ainsi que leur incorporation dans les polymères cœur-coquille amphiphiles réticulés au cœur par polymérisation radicalaire contrôlée. La stratégie de synthèse des polymères est convergente : la chevelure hydrophile périphérique est d'abord synthétisée dans l'eau puis un deuxième bloc hydrophobe est ajouté. Les chaînes s'assemblent spontanément en micelles. Enfin, l'ajout d'un agent réticulant donne lieu à la réticulation totale au cœur pour former la micelle réticulée. Enfin, les premiers résultats de l'utilisation de ces nouveaux nanoréacteurs en chimie de coordination et en catalyse (hydroformylation, hydrogénation) seront présentés. / The industrial and economic importance of catalysis makes it one of the most studied topics in research today. Recovery of catalysts is very important, especially when expensive metals (Rh, Ir, Pt, Ru, etc.) are used, on the economic, environmental and sanitary points of view. Our team has recently started a research program on the use of core-shell polymers of well-defined size and composition, comprising a hydrophobic and ligand-functionalized core and a hydrophilic shell at the periphery for their confinement in an aqueous medium. These macromolecules are constructed to function as nanoreactors under biphasic conditions. Only nanoreactors with monophosphine ligands had been synthesized prior to this thesis, and successfully applied to the hydroformylation of 1-octene under biphasic conditions. In this thesis, we were initially interested in continuing the physicochemical study of these nanoreactors and in using them in catalyzed hydrogenations. Secondly, we have synthesized novel core-shell polymers containing bidentate ligands, either ferrocene-based (PS) or nixantphos-based (PP) ligands. We therefore present the synthesis of ligands possessing polymerizable styryl groups as well as their incorporation in the amphiphilic and core-cross-linked core-shell polymers by controlled radical polymerization. The polymer synthetic strategy is convergent: the peripheral hydrophilic shell was first synthesized in water and then a second hydrophobic block was added. The chains spontaneously assemble as micelles. Finally, the addition of a crosslinking agent gives rise to total core-cross-linking to form the core-cross-linked micelle (CCM). Finally, the first results of the use of these new nanoreactors in coordination chemistry and in catalysis (hydroformylation, hydrogenation) will be presented.

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Tridentate benzimidazole-based ligands, bis((1H-benzimidazol-2-yl)methyl)sulfide (BNSN) and bis((1H-benzimidazol-2-yl)methyl)amine (BNNN), along with dinonylnaphthalene sulfonic acid (DNNSA) as a synergist, were investigated as potential selective extractants for Ni2+ from base metals in a solvent extraction system using 2-octanol/Shellsol 2325 (8:2) as diluent and modifier. However, extraction studies show a lack of pH-metric separation of the later 3d metal ions with bis((1-octylbenzimidazol-2-yl)methyl)sulfide (BONSN) and bis((1- decylbenzimidazol-2-yl)methyl)amine (BDNNN) as extractants, but extractions occurred in the low pH range with an opportunity for back extraction. This investigation suggested that tridentate ligands (at least those of the nature investigated here) are not feasible extractants for separation of base metal ions due to their lack of stereochemical “tailor-making.”

Os receptores nucleares constituem uma superfamília de fatores de transcrição regulados pela interação com hormônios. Esta superfamília inclui, por exemplo, os receptores de hormônio tireoidiano, estrogênio, androgênio, glicocorticóide e mineralocorticóide. Neste trabalho, empregamos técnicas de biologia estrutura e bioinformática para estudar as interações entre alguns dos membros da família de receptores nucleares e seus respectivos ligantes. Para o receptor de hormônio tireoidiano, foi demonstrado, através da análise das estruturas cristalográficas das duas isoformas do receptor ligados aos tiromimético Triac, que os componentes entálpicos visíveis nas estruturas não explicam a seletividade do ligante. Dados de dinâmica molecular confirmaram que a seletividade do hormônio tem um importante componente entrópico. Empregando a técnica de dinâmica molecular, estudamos a ligação do receptor de mineralocorticóide humano à aldosterona, ao cortisol, à espironolactona e à cortisona e simulamos ainda o efeito da mutação S810L, conhecida por converter a atividade antagonista da cortisona e da espironolactona em agonista. A análise das simulações revelou um perfil de ligações de hidrogênio similar na ligação do receptor selvagem ao cortisol e à aldosterona. A cortisona perde, por conta da inserção de uma hidroxila na posição 11, uma ligação de hidrogênio importante com a Asn770 e, por isso, tem menor energia potencial de ligação. A espironolactona perde a mesma ligação de hidrogênio ao mesmo tempo em que aumenta o número de contatos de van der Waals pela inserção do grupo tioacetil na posição 7. A mutação S810L simulada no complexo com cortisona, cortisol e espironolactona não interfere no padrão de ligações de hidrogênio estabelecidas entre o receptor e os ligantes, mas altera a mobilidade de uma das regiões propostas como rota de dissociação. Propomos, portanto, que a mutação interfere na cinética de dissociação dos ligantes e não no padrão de interações estabelecidas no equilíbrio. Simulações de dissociação induzida do ligante confirmam esta proposição. Na última etapa, utilizamos os modelos experimentalmente determinados para o receptor ativado por proliferadores peroxissomais gama para a busca de novos ligantes através da técnica de docking molecular. Neste trabalho, utilizamos uma base de dados com aproximadamente um milhão de compostos. Destes, quatro foram selecionados após o docking molecular e testados experimentalmente. Um dos compostos testados se mostrou ativo neste receptor, apresentando uma atividade de 60-70% da atividade da rosiglitazona, conhecido agonista total do PPARg. / Nuclear receptors are a superfamily of hormone-regulated transcriptional factors. This superfamily includes, for example, the receptor for thyroid hormone, estrogen, androgen, gluco and mineralocorticoid. In this work, we used structural biology and bioinformatic tools to study the interactions between some members of the nuclear receptor superfamily and its respective ligands. We showed by the analysis of the crystal structures of both thyroid hormone receptor isoforms bound to the thyromimetic Triac that the enthalpic components visible in the structures do not explain the ligand selectivity. Molecular dynamics simulation data confirmed later that the hormone selectivity has an important entropic component. Using the molecular dynamics simulation, we studied, in a second stage, the interaction between the human mineralocorticoid receptor bound to aldosterone, cortisol, spironolactone and cortisone and also simulated the effects of the mutations S810L, known to convert the antagonist properties of spironolactone and cortisone in an agonist activity. The analysis of the simulations showed a similar profile in hydrogen bonds established between the wild type receptor bound to cortisol and aldosterone. Cortisone looses an important hydrogen bond with Asn770 because of the insertion of a carbonyl group in the 11 position and shows a decreased binding potential energy. Spironolactone loses the same interaction but has an increased number of van der Waals contacts because of the insertion of a tioacetyl group in the 7 position. The mutant S810L simulated in complex with cortisol, cortisone and spironolactone showed that the mutation do not interfere with the hydrogen bond profile established between the receptor and the ligands but changes the mobility of a region in the receptor previously proposed as a ligand dissociation route. Ligand unbinding simulations through steered molecular dynamics (SMD) confirm that aldosterone and cortisol unbind differentially and the mutation S810L alters the unbinding profile. We then propose that the mutation changes the kinetics of ligand association/dissociation without changing the profile of the interactions established in the equilibrium. In the last stage, we used the experimentally determined structural model of the peroxissome proliferator-activated receptor gamma to search for novel ligands using the molecular docking technique. For this work, we used a database containing about 1 million compounds. Among those, four compounds were selected after the docking computation and experimentally tested. One of these compounds was found to be active in the receptor, showing about 60-70% of the agonistic activity of rosiglitzone, a known PPARg total agonist.

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