Modélisation moléculaire des modifications post-translationnelles dans Bcl-xL et des sels de céténiminium

In recent years, computation chemistry plays important role in order to understand and give insight on structural properties of systems (protein, small molecules etc.) by mimicking their environment. This dissertation consists of two main topics, namely understanding impact of Bcl-xL deamidation by means of molecular dynamics (MD) simulations and investigation of keteniminium salt (KI) by quantum mechanical (QM) methods. Investigation of post-translational modifications (PTMs) gains importance to understand their roles on structure and functions of proteins. Deamidation, one of the post-translational modifications is a crucial switch used for regulating the biological function of anti-apoptotic Bcl-xL. In the first part of the thesis, deamidation-induced conformational changes in Bcl-xL were explored to gain insight into its loss of function by performing molecular dynamics (MD) simulations. The outcomes of this study will provide a unique perspective on the underlying mechanism of Bcl-xL deamidation-induced cell death.Keteniminium salt, nitrogen analog of ketene is widely used intermediate for the synthesis of various scaffolds/substances due to its higher electrophilicity, reactivity and regioselectivity. In the second part of the thesis, keteniminium salt was scrutinized from formation to its involved reactions by means of DFT study. Experimentally observed reactivity differences in the [2 + 2] cycloaddition and electrocyclization reactions were rationalized via a range of different analysis techniques. The outcomes of this study are expected to contribute to the understanding of formation and reactivity differences of keteniminium salt and aid synthetic applications.Ces dernières années, la chimie computationnelle a joué un rôle important dans la compréhension et la compréhension des propriétés structurelles des systèmes (protéines, petites molécules, etc.) en imitant leur environnement. Cette thèse se compose de deux sujets principaux, à savoir la compréhension de l'impact de la désamidation Bcl-xL au moyen de simulations de dynamique moléculaire (MD) et l'étude du sel de céténiminium (KI) par des méthodes de mécanique quantique (QM). L'étude des modifications post-traductionnelles (PTM) gagne en importance pour comprendre leurs rôles sur la structure et les fonctions des protéines. La désamidation, l'un des PTM, est un commutateur crucial utilisé pour réguler la fonction biologique de Bcl-xL anti-apoptotique. Dans la première partie de la thèse, les changements conformationnels induits par la désamidation dans Bcl-xL ont été explorés pour mieux comprendre sa perte de fonction en effectuant des simulations MD. Les résultats de cette étude fourniront une perspective unique sur le mécanisme sous-jacent de la mort cellulaire induite par la désamidation Bcl-xL. Le sel de céténiminium, analogue azoté du cétène, est un intermédiaire largement utilisé pour la synthèse de divers échafaudages/substances en raison de son électrophilie, de sa réactivité et de sa régiosélectivité plus élevée. Dans la deuxième partie de la thèse, céténiminium a été scruté de la formation à ses réactions impliquées au moyen d'une étude DFT. Les différences de réactivité observées expérimentalement dans les réactions de cycloaddition [2 + 2] et d'électrocyclisation ont été rationalisées via une gamme de techniques d'analyse différentes. Les résultats de cette étude devraient contribuer à la compréhension des différences de formation et de réactivité du céténiminium et faciliter les applications synthétiques

Impact of deamidation on the structure and function of anti-apoptotic Bcl-xL.

Bcl-xL is an anti-apoptotic mitochondrial trans-membrane protein, known to play a crucial role in the survival of tumor cells. The deamidation of Bcl-xL is a pivotal switch that regulates its biological function. The potential impact of deamidation on the structure and dynamics of Bcl-xL is directly linked to the intrinsically disordered region (IDR), which is the main site for post-translational modifications (PTMs). In this study, we explored deamidation-induced conformational changes in Bcl- xL to gain insight into its loss of function by performing microsecond-long molecular dynamics (MD) simulations. MD simulation outcomes showed that the IDR motion and interaction patterns have changed notably upon deamidation. Principal component analysis (PCA) demonstrates significant differences between wild type and deamidated Bcl-xL and suggests that deamidation affects the structure and dynamics of Bcl-xL. Differences in contact patterns and essential dynamics in the binding groove (BG) are clear indications of deamidation-induced allosteric affects

Impact of Deamidation on the Structure and Function of Antiapoptotic Bcl-x L

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Computational studies on cinchona alkaloid-catalyzed asymmetric organic reactions

Remarkable progress in the area of asymmetric organocatalysis has been achieved in the last decades. Cinchona alkaloids and their derivatives have emerged as powerful organocatalysts owing to their reactivities leading to high enantioselectivities. The widespread usage of cinchona alkaloids has been attributed to their nontoxicity, ease of use, stability, cost effectiveness, recyclability, and practical utilization in industry. The presence of tunable functional groups enables cinchona alkaloids to catalyze a broad range of reactions. Excellent experimental studies have extensively contributed to this field, and highly selective reactions were catalyzed by cinchona alkaloids and their derivatives. Computational modeling has helped elucidate the mechanistic aspects of cinchona alkaloid catalyzed reactions as well as the origins of the selectivity they induce. These studies have complemented experimental work for the design of more efficient catalysts. This Account presents recent computational studies on cinchona alkaloid catalyzed organic reactions and the theoretical rationalizations behind their effectiveness and ability to induce selectivity. Valuable efforts to investigate the mechanisms of reactions catalyzed by cinchona alkaloids and the key aspects of the catalytic activity of cinchona alkaloids in reactions ranging from pharmaceutical to industrial applications are summarized. Quantum mechanics, particularly density functional theory (DFT), and molecular mechanics, including ONIOM, were used to rationalize experimental findings by providing mechanistic insights into reaction mechanisms. B3LYP with modest basis sets has been used in most of the studies; nonetheless, the energetics have been corrected with higher basis sets as well as functionals parametrized to include dispersion M05-2X, M06-2X, and M06-L and functionals with dispersion corrections. Since cinchona alkaloids catalyze reactions by forming complexes with substrates via hydrogen bonds and long-range interactions, the use of split valence triple-ζ basis sets including diffuse and polarization functions on heavy atoms and polarization functions on hydrogens are recommended. Most of the studies have used the continuum-based models to mimic the condensed phase in which organocatalysts function; in some cases, explicit solvation was shown to yield better quantitative agreement with experimental findings. The conformational behavior of cinchona alkaloids is also highlighted as it is expected to shed light on the origin of selectivity and pave the way to a comprehensive understanding of the catalytic mechanism. The ultimate goal of this Account is to provide an up-to-date overlook on cinchona alkaloid catalyzed chemistry and provide insight for future studies in both experimental and theoretical fields

Theoretical insight into the regioselective ring-expansions of bicyclic aziridinium ions

Transient bicyclic aziridinium ions are known to undergo ring-expansion reactions, paving the way to functionalized nitrogen-containing heterocycles. In this study, the regioselectivity observed in the ring-expansion reactions of 1-azoniabicyclo[n.1.0]alkanes was investigated from a computational viewpoint to study the ring-expansion pathways of two bicyclic systems with different ring sizes. Moreover, several nucleophiles leading to different experimental results were investigated. The effect of solvation was taken into account using both explicit and implicit solvent models. This theoretical rationalization provides valuable insight into the observed regioselectivity and may be used as a predictive tool in future studies

Formation of Keteniminium Salts: Mechanistic Aspects and Substituent Effects

Keteniminium salts (KIs) are versatile intermediates in synthetic organic chemistry. Elucidation of the mechanistic aspects of KI formation reactions facilitates the design of KI intermediates that give access to complex compounds. In this study, in order to provide a comprehensive understanding of KI formation, various mechanisms were investigated using a density functional theory approach. Particularly, Ghosez’s KI formation mechanism, by activation of an amide with triflic anhydride, was extensively elaborated, since this procedure occurs under mild conditions and is, by far, the most frequently used method. Moreover, a broad range of substituents was examined to give insight on their potential contributions to the ease of formation of KIs. The effect of substituents on the reactivity of the corresponding starting amides was inspected by means of energetics, population analysis, frontier molecular orbitals (FMO) and reactivity descriptors. Computed data shows that electron donating groups lower the activation barrier by increasing the electron density of the amide carbonyl oxygen. Additionally, distortion/interaction model also confirmed the energetic outcomes. In addition, investigation of KI reactivity using FMO, and reactivity descriptors displayed that KI reactivity is inversely correlated with amide reactivity. Lastly, experimental outcomes are in line with computational predictions. We suggest that the reactivity of the amide has a crucial impact on the ease of KI formation and the reactivity of the corresponding KIs. This study gives pivotal insights into mechanistic aspects of KI formation and the role of the substituents

PBP-A, a cyanobacterial DD-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to Escherichia coli.

Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) in bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family of enzymes sharing close structural and phylogenetic proximity to class A β-lactamases. With the long-term aim of converting PBP-A into a β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such a new PBP and observed growth defect associated with the enzyme activity. To further explore the molecular origins of this harmful effect, we decided to characterize deeper the activity of PBP-A both in vitro and in vivo. We found that PBP-A is an enzyme endowed with DD-carboxypeptidase and DD-endopeptidase activities, featuring high specificity towards muropeptides amidated on the D-iso-glutamyl residue. We also show that a low promiscuous activity on non-amidated peptidoglycan deteriorates E. coli's envelope, which is much higher under acidic conditions where substrate discrimination is mitigated. Besides expanding our knowledge of the biochemical activity of PBP-A, this work also highlights that promiscuity may depend on environmental conditions and how it may hinder rather than promote enzyme evolution in nature or in the laboratory

PBP-A, a cyanobacterial dd-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to Escherichia coli

AbstractPenicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) in bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family of enzymes sharing close structural and phylogenetic proximity to class A β-lactamases. With the long-term aim of converting PBP-A into a β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such a new PBP and observed growth defect associated with the enzyme activity. To further explore the molecular origins of this harmful effect, we decided to characterize deeper the activity of PBP-A both in vitro and in vivo. We found that PBP-A is an enzyme endowed with dd-carboxypeptidase and dd-endopeptidase activities, featuring high specificity towards muropeptides amidated on the d-iso-glutamyl residue. We also show that a low promiscuous activity on non-amidated peptidoglycan deteriorates E. coli’s envelope, which is much higher under acidic conditions where substrate discrimination is mitigated. Besides expanding our knowledge of the biochemical activity of PBP-A, this work also highlights that promiscuity may depend on environmental conditions and how it may hinder rather than promote enzyme evolution in nature or in the laboratory.</jats:p