Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. We report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 G-protein coupled receptor and a series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Site-directed mutagenesis, homology modelling and docking were further used to characterize agonist binding to the human neuropeptide Y2 receptor, which is important in feeding behavior and an obesity drug target.  In a separate project, homology modelling was also used for rationalization of mutagenesis data for an integron integrase involved in antibiotic resistance. Blockade of the hERG potassium channel by various drug-like compounds, potentially causing serious cardiac side effects, is a major problem in drug development. We have used a homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations are in good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships with implications for design of new compounds. Docking, scoring, molecular dynamics, and the linear interaction energy method were also used to predict binding modes and affinities for a large set of inhibitors to HIV-1 reverse transcriptase. Good agreement with experiment was found and the work provides a validation of the methodology as a powerful tool in structure-based drug design. It is also easily scalable for higher throughput of compounds.

Materials intended for disposal of spent nuclear fuel require a particular combination of physical and chemical properties. The driving forces and mechanisms underlying the material’s behavior must be scientifically understood in order to enable modeling at the relevant time- and length-scales. The processes that determine the mechanical behavior of copper canisters and iron inserts, as well as the evolution of their mechanical properties, are strongly dependent on the properties of various defects in the bulk copper and iron alloys. The first part of the present thesis deals with precipitation in the cast iron insert. A nodular cast iron insert will be used as the inner container of the spent nuclear fuel. Precipitation is investigated by computing effective interaction energies for point defect pairs (solute–solute and vacancy–solute) in bcc iron using first-principles calculations. The main considered impurities in the iron matrix include 3sp (Si, P, S) and 3d (Cr, Mn, Ni, Cu) solute elements. By computing interaction energies possibility of formation of different second phase particles such as late blooming phases (LBPs) in the cast iron insert is evaluated. The second part is devoted to the fundamentals of dislocations and their role in plastic deformation of metals. Deformation of single-crystal copper under high strain rates is simulated by employing dislocation dynamics (DD) method to examine the effect of strain rate on mechanical properties as well as dislocation microstructure development. Creep deformation of copper canister at low temperatures is studied. The copper canister will be used in the long-term storage of spent nuclear fuel as the outer shell of the waste package to provide corrosion protection. A glide rate is derived based on the assumption that at low temperatures it is controlled by the climb rate of jogs on the dislocations. Using DD simulation creep deformation of copper at low temperatures is modeled by taking glide but not climb into account. Moreover, effective stresses acting on dislocations are computed using the data extracted from DD simulations. / <p>QC 20170428</p>

Interaction preferences in protein - DNA complexes Dávid Jakubec Abstract Interactions of proteins with DNA lie at the basis of many fundamental bio- logical processes. Despite ongoing efforts, the rules governing the recognition of specific nucleic acid sequences have still not been universally elucidated. In this work, I attempt to explore the recognition process by splitting the intricate network of contacts at the protein - DNA interface into contribu- tions of individual amino acid - nucleotide pairs. These pairs are extracted from existing high-resolution structures of protein - DNA complexes and in- vestigated by bioinformatics and computational-chemistry based methods. Criteria of specificity based on the coupling of observed geometrical prefer- ences and the respective interaction energies are introduced. The application of these criteria is used to expand the library of amino acid - nucleotide pairs potentially significant for direct sequence recognition. Electrostatic poten- tial maps are calculated for individual nucleotides as well as for selected complexes to investigate the physical basis of the observed specificity. 1

L'objet de ce travail concernait la compréhension de l'évolution des propriétés hydrauliques des membranes céramiques d'UF/NF durant l'étape du conditionnement, et suite à un traitement alcalin. Dans un premier temps, une étude expérimentale a été réalisée par des tests de flux à l'eau pure avec 6 membranes minérales asymétriques (Na-mordenite et TiO2). Ensuite, l'évolution de la perméabilité hydraulique de ces membranes a été modélisée précisément par une fonction mathématique, mettant en évidence deux phases distinctes au cours du conditionnement : une hydratation rapide de la surface des cristaux de Na-mordenite (mésoporosité intercristalline) suivie d'une hydratation lente des pores de la Na-mordenite (microporosité intracristalline). Cette étude a également permis de montrer que la cinétique d'hydratation des micropores est proportionnelle au volume microporeux des couches actives. Dans un deuxième temps, des caractérisations physico-chimiques (DRX, MEB, DFX, adsorption N2), des mesures de propriétés électriques ainsi que des tests de mouillabilité ont été réalisés sur la phase active des membranes de Na-mordenite avant et après un traitement alcalin (filtration d'une solution de carbonate de sodium) dans le but de pouvoir comprendre/expliquer la diminution de la perméabilité hydraulique observée à la suite du traitement alcalin. Les composantes de la tension de surface (polaires et apolaires) et l'énergie d'interaction entre la surface des membranes et les molécules d'eau ont été déterminées via l'équation de Young-Dupré (théorie de Lifshitz-van der Waals des états condensés). L'ensemble des résultats obtenus a montré que la modification des propriétés hydrauliques des membranes est due à une augmentation de l'hydrophilicité de surface de la zéolithe (par la présence des micro-défauts à la surface : extraction des atomes de silicium) provoquant la formation d'une couche ultra-polaire à la surface des cristaux de Na-mordenite. / The aim of this work was to understand hydraulic properties evolution of mineral UF/NF membranes during the conditioning step and after a mild alkaline treatment. First, experimental tests by filtration of pure water were carried out to determine the membrane permeation flux. Six tubular asymetric ceramic membranes were studied (Na-mordenite and TiO2) and a mathematical modelling of the hydraulic permeability (during the conditioning step) was performed. Two separate phases were identified: a fast decrease of the permeability that was attributed to the hydration of the crystal surface of Na-mordenite (inter-crystalline mesoporosity) and then a slow decrease until the stabilization of the permeability that was attributed to the hydration of the Na-mordenite internal pores (intra-crystalline microposity). During this study, it was also shown that the kinetic of micropore hydration is directly proportional to the microporous volume of the membrane active layer. Secondly, physicochemical characterizations, electric properties and contact angle measurements were carried out on the Na-mordenite active phase before and after a mild alkaline treatment (filtration of a sodium carbonate-water solution) to understand/explain the decrease of the hydraulic permeability after the alkaline treatment. The surface tension components (polar and apolar) and the energy of interaction between water molecules and the surface of the active layer were determined via the Young-Dupré equation according to the Lifshitz-van der Waals theory of the condensed states. The whole of these results showed that the modification of the hydraulic properties of the zeolite membranes is due to an increase of the surface hydrophilicity of the surface (surface defaults: extraction of the silicon atoms), leading to the formation of an ultra-polar layer on the surface of the zeolite crystals.

<p>The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.</p><p>For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.</p><p>A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.</p><p>A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.</p><p>The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.</p>

The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions. A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands. A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding. The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

Over the last few decades, computer simulation techniques have been established as an essential tool for understanding biochemical processes. This thesis deals mainly with the application of free energy calculations to ribosomal complexes and a cardiac ion channel. The linear interaction energy (LIE) method is used to explore the energetic properties of the essential process of codon–anticodon recognition on the ribosome. The calculations show the structural and energetic consequences and effects of first, second, and third position mismatches in the ribosomal decoding center. Recognition of stop codons by ribosomal termination complexes is fundamentally different from sense codon recognition. Free energy perturbation simulations are used to study the detailed energetics of stop codon recognition by the bacterial ribosomal release factors RF1 and RF2. The calculations explain the vastly different responses to third codon position A to G substitutions by RF1 and RF2. Also, previously unknown highly specific water interactions are identified. The GGQ loop of ribosomal RFs is essential for its hydrolytic activity and contains a universally methylated glutamine residue. The structural effect of this methylation is investigated. The results strongly suggest that the methylation has no effect on the intrinsic conformation of the GGQ loop, and, thus, that its sole purpose is to enhance interactions in the ribosomal termination complex. A first microscopic, atomic level, analysis of blocker binding to the pharmaceutically interesting potassium ion channel Kv1.5 is presented. A previously unknown uniform binding mode is identified, and experimental binding data is accurately reproduced. Furthermore, problems associated with pharmacophore models based on minimized gas phase ligand conformations are highlighted. Generalized Born and Poisson–Boltzmann continuum models are incorporated into the LIE method to enable implicit treatment of solvent, in an effort to improve speed and convergence. The methods are evaluated and validated using a set of plasmepsin II inhibitors.

Enolate formation by proton abstraction from an sp3-hybridized carbon atom situated next to a carbonyl or carboxylate group is an abundant process in nature. Since the corresponding nonenzymatic process in water is slow and unfavorable due to high intrinsic free energy barriers and high substrate pKa s, enzymes catalyzing such reaction steps must overcome both kinetic and thermodynamic obstacles. Computer simulations were used to study enolate formation catalyzed by glyoxalase I (GlxI) and 3-oxo-Δ5-steroid isomerase (KSI). The results, which reproduce experimental kinetic data, indicate that for both enzymes the free energy barrier reduction originates mainly from the balancing of substrate and catalytic base pKas. This was found to be accomplished primarily by electrostatic interactions. The results also suggest that the remaining barrier reduction can be explained by the lower reorganization energy in the preorganized enzyme compared to the solution reaction. Moreover, it seems that quantum effects, arising from zero-point vibrations and proton tunnelling, do not contribute significantly to the barrier reduction in GlxI. For KSI, the formation of a low-barrier hydrogen bond between the enzyme and the enolate, which is suggested to stabilize the enolate, was investigated and found unlikely. The low pKa of the catalytic base in the nonpolar active site of KSI may possibly be explained by the presence of a water molecule not detected by experiments. The hemoglobin-degrading aspartic proteases plasmepsinI and plasmepsin II from Plasmodium falciparum have emerged as putative drug targets against malaria. A series of C2- symmetric compounds with a 1,2-dihydroxyethylene scaffold were investigated for plasmepsin affinity, using computer simulations and enzyme inhibition assays. The calculations correctly predicted the stereochemical preferences of the scaffold and the effect of chemical modifications. Calculated absolute binding free energies reproduced experimental data well. As these inhibitors have down to subnanomolar inhibition constants of the plasmepsins and no measurable affinity to human cathepsin D, they constitute promising lead compounds for further drug development.

Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. Homology modeling, docking, molecular dynamics simulations and free-energy calculations are used here for quantitative characterization of ligand binding to proteins. By combining computational tools, valuable contributions have been made for pharmaceutically relevant areas: a neglected tropical disease, an ion channel anti-drug-target, and GPCR drug-targets. We report three compounds inhibiting cruzain, the main cysteine protease of the protozoa causing Chagas’ disease. The compounds were found through an extensive virtual screening study and validated with experimental enzymatic assays. The compounds inhibit the enzyme in the μM-range and are therefore valuable in further lead optimization studies. A high-resolution crystal structure of the BRICHOS domain is reported, together with molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry studies. This work revealed a plausible mechanism for how the chaperone activity of the domain may operate. Rationalization of structure-activity relationships for a set of analogous blockers of the hERG potassium channel is given. A homology model of the ion channel was used for docking compounds and molecular dynamics simulations together with the linear interaction energy method employed for calculating the binding free-energies. The three-dimensional coordinates of two GPCRs, 5HT1B and 5HT2B, were derived from homology modeling and evaluated in the GPCR Dock 2013 assessment. Our models were in good correlation with the experimental structures and all of them placed among the top quarter of all models assessed.  Finally, a computational method, based on molecular dynamics free-energy calculations, for performing alanine scanning was validated with the A2A adenosine receptor bound to either agonist or antagonist. The calculated binding free-energies were found to be in good agreement with experimental data and the method was subsequently extended to non-alanine mutations. With extensive experimental mutation data, this scheme is a valuable tool for quantitative understanding of ligand binding and can ultimately be used for structure-based drug design.

Electrospray ionization mass spectrometry (ESI-MS) with induced collision energy was used to carry out a comprehensive study on the interaction energies between cations and anions of dicationic ionic liquids. The influence of the anion ([Br]-, [NO3]-, [BF4]-, [SCN]- and [Cl]-) and the size of alkyl chain (n = 4,6,8 and 10) in the interaction energy of ionic liquids derived from the 1, n-bis (3-methylimidazolyl-1-yl) alkane with n = 4,6,8 and 10, in the gas phase was investigated. Three experiments were carried out to determine the cation-anion interaction energy: (i) ESI-MS of binary (1:1) mixtures of ionic liquids with different anions or cations; (Ii) ESI-MS of ionic liquid individually with variation of the applied collision energy and determination of the center of mass energy (Ecm) using the relation between the intensity of the precursor ion and the sum of the ions; (iii) the rate of variation of the intensity of the precursor ion as a function of collision energy at different concentrations of all ionic liquids was obtained. From this correlation, the cation-anion dissociation constant of the dicationic ionic liquids was obtained. The results showed the appearance of mixed species (example: [Bis-C8(MIM)22XY]- and [C8(MIM)XY]-) in the binary mixtures. The application of the induced collision energy in the mixtures allowed estimating which anion interacts more effectively with the cation. Also for this experiments, the dicationic ionic liquids with the anions [Cl]-, [Br]- and [NO3]- presented higher cation-anion interaction energy. The increasing order of interaction energy was [BF4]- <[SCN]- <[NO3]- <[Br]- <[Cl]-. The Ecm values for ionic liquids with different anions did not indicate trends in the interaction energy in relation to structural factors such as ionic radius and molecular volume. Thus, for the anions, it was found that the interaction increases in the following order: [SCN]- <[Cl]- <[NO3]- <[Br]- <[BF4]-. On the other hand, increasing the size of the spacer alkyl chain caused an increase in cation-anion interaction energy. As the concentration of the ionic liquid increased, an increase in the precursor ion intensity was observed. / A espectrometria de massa com ionização por electrospray (ESI-MS) com energia de colisão induzida foi utilizada para realizar um estudo compreensivo sobre as energias de interação entre cátions e ânions de líquidos iônicos dicatiônicos. Foi avaliada a influência do ânion ([Br]-, [NO3]-, [BF4]-, [SCN]- e [Cl]-) e o tamanho da cadeia alquílica espaçadora (n=4,6,8 e 10) na energia de interação dos líquidos iônicos dicatiônicos, derivados do 1,n-bis(3-metilimidazolil-1-íneo)alcano em fase gasosa. Três experimentos foram realizados para a determinação da energia de interação cátion-ânion: (i) ESI-MS de misturas binárias (1:1) de líquidos iônicos com diferentes ânions ou cátions; (ii) ESI-MS de cada líquido iônico individualmente com variação da energia de colisão aplicada e determinação da energia de centro de massa (Ecm) usando a relação entre intensidade do íon precursor e somatório dos íons. (iii) Por fim, foi obtida a taxa de variação da intensidade do íon precursor em função energia de colisão de todos os líquidos iônicos. A partir desta correlação, foi obtida a constante de dissociação cátion-ânion dos líquidos iônicos dicatiônicos. Os resultados mostraram o aparecimento de espécies mistas (exemplo: [Bis-C8(MIM)22XY]- e [C8(MIM)XY]-) nos experimentos das misturas. A aplicação da energia de colisão induzida nas misturas também permitiu estimar qual ânion interage mais efetivamente com o cátion. Ainda para este experimentos, os líquidos iônicos dicatiônicos com os ânions [Cl]-, [Br]- e [NO3]- apresentaram maior energia de interação cátion-ânion. A escala em ordem crescente de energia de interação foi [BF4]-< [SCN]- < [NO3]- < [Br]- < [Cl]-. Os valores de Ecm para os líquidos iônicos com diferentes ânions não indicou tendências na energia de interação em relação fatores estruturais tais como raio iônico e volume molecular. Dessa forma, para os ânions, foi encontrado que a interação aumenta na seguinte ordem: [SCN]-<[Cl]-<[NO3]-<[Br]-<[BF4]-. Por outro lado, o aumento do tamanho da cadeia alquílica espaçadora causou um aumento na energia de interação cátion-ânion. Com o aumento da concentração do líquido iônico, foi observado um aumento na intensidade do íon precursor.