Supplementary material for the article: Gruden, M.; Andjelkovic, L.; Jissy, A. K.; Stepanović, S.; Zlatar, M.; Cui, Q.; Elstner, M. Benchmarking Density Functional Tight Binding Models for Barrier Heights and Reaction Energetics of Organic Molecules. Journal of Computational Chemistry 2017, 38 (25), 2171–2185. https://doi.org/10.1002/jcc.24866

Supplementary material for:[https://doi.org/10.1002/jcc.24866]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2504

Supplementary material for the article: Gruden, M.; Andjelkovic, L.; Jissy, A. K.; Stepanović, S.; Zlatar, M.; Cui, Q.; Elstner, M. Benchmarking Density Functional Tight Binding Models for Barrier Heights and Reaction Energetics of Organic Molecules. Journal of Computational Chemistry 2017, 38 (25), 2171–2185. https://doi.org/10.1002/jcc.24866

Supplementary material for:[https://doi.org/10.1002/jcc.24866]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2504

QM/MM description of newly selected catalytic bioscavengers against organophosphorus compounds revealed reactivation stimulus mediated by histidine residue in the acyl-binding loop

© 2018 Zlobin, Mokrushina, Terekhov, Zalevsky, Bobik, Stepanova, Aliseychik, Kartseva, Panteleev, Golovin, Belogurov, Gabibov and Smirnov. Butyrylcholinesterase (BChE) is considered as an efficient stoichiometric antidote against organophosphorus (OP) poisons. Recently we utilized combination of calculations and ultrahigh-throughput screening (uHTS) to select BChE variants capable of catalytic destruction of OP pesticide paraoxon. The purpose of this study was to elucidate the molecular mechanism underlying enzymatic hydrolysis of paraoxon by BChE variants using hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. Detailed analysis of accomplished QM/MM runs revealed that histidine residues introduced into the acyl-binding loop are always located in close proximity with aspartate residue at position 70. Histidine residue acts as general base thus leading to attacking water molecule activation and subsequent SN2 inline hydrolysis resulting in BChE reactivation. This combination resembles canonical catalytic triad found in active centers of various proteases. Carboxyl group activates histidine residue by altering its pKa, which in turn promotes the activation of water molecule in terms of its nucleophilicity. Observed re-protonation of catalytic serine residue at position 198 from histidine residue at position 438 recovers initial configuration of the enzyme's active center, facilitating next catalytic cycle. We therefore suggest that utilization of uHTS platform in combination with deciphering of molecular mechanisms by QM/MM calculations may significantly improve our knowledge of enzyme function, propose new strategies for enzyme design and open new horizons in generation of catalytic bioscavengers against OP poisons

QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding Loop

Butyrylcholinesterase (BChE) is considered as an efficient stoichiometric antidote against organophosphorus (OP) poisons. Recently we utilized combination of calculations and ultrahigh-throughput screening (uHTS) to select BChE variants capable of catalytic destruction of OP pesticide paraoxon. The purpose of this study was to elucidate the molecular mechanism underlying enzymatic hydrolysis of paraoxon by BChE variants using hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. Detailed analysis of accomplished QM/MM runs revealed that histidine residues introduced into the acyl-binding loop are always located in close proximity with aspartate residue at position 70. Histidine residue acts as general base thus leading to attacking water molecule activation and subsequent SN2 inline hydrolysis resulting in BChE reactivation. This combination resembles canonical catalytic triad found in active centers of various proteases. Carboxyl group activates histidine residue by altering its pKa, which in turn promotes the activation of water molecule in terms of its nucleophilicity. Observed re-protonation of catalytic serine residue at position 198 from histidine residue at position 438 recovers initial configuration of the enzyme’s active center, facilitating next catalytic cycle. We therefore suggest that utilization of uHTS platform in combination with deciphering of molecular mechanisms by QM/MM calculations may significantly improve our knowledge of enzyme function, propose new strategies for enzyme design and open new horizons in generation of catalytic bioscavengers against OP poisons

Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations

Quantum mechanics/molecular mechanics (QM/MM) hybrid technique is emerging as a reliable computational method to investigate and characterize chemical reactions occurring in enzymes. From a drug discovery perspective, a thorough understanding of enzyme catalysis appears pivotal to assist the design of inhibitors able to covalently bind one of the residues belonging to the enzyme catalytic machinery. Thanks to the current advances in computer power, and the availability of more efficient algorithms for QM-based simulations, the use of QM/MM methodology is becoming a viable option in the field of covalent inhibitor design. In the present review, we summarized our experience in the field of QM/MM simulations applied to drug design problems which involved the optimization of agents working on two well-known drug targets, namely fatty acid amide hydrolase (FAAH) and epidermal growth factor receptor (EGFR). In this context, QM/MM simulations gave valuable information in terms of geometry (i.e., of transition states and metastable intermediates) and reaction energetics that allowed to correctly predict inhibitor binding orientation and substituent effect on enzyme inhibition. What is more, enzyme reaction modelling with QM/MM provided insights that were translated into the synthesis of new covalent inhibitor featured by a unique combination of intrinsic reactivity, on-target activity, and selectivity

Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules

Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory.Peer-reviwed version: [http://cer.ihtm.bg.ac.rs/handle/123456789/2734

RNA synthesis under prebiotic conditions : the challenge of phosphoester bond formation

La caractérisation de la formation de la liaison phosphodiester dans des conditions abiotiques est un enjeu majeur dans l’étude des origines de la vie. Cette liaison est présente dans de nombreux composés biologiques primordiaux pour le vivant [1], en particulier entant que liaison reliant les nucléotides de l’ARN et de l’ADN. Ainsi, en plus d’être apparue très tôt dans le processus évolutif, la liaison phosphodiester est au centre de l’hypothèse du monde à ARN [2], considéré comme l’un des scénarios les plus crédibles pour l’apparition de la vie sur Terre.Nous nous sommes intéressés à la réaction de phosphorylation entre un phosphate -mono ou dianionique et un méthanol. Malgré un nombre important d’études, les mécanismes de celle-ci n’ont toujours pas été clairement identifiés. Les barrières d’énergies étudiées sont élevées (entre 30-50kcal/mol) [3] et trop proches en énergie [4], rendant l’identification du chemin réactionnel difficilement accessible expérimentalement. Les études théoriques sont ainsi une approche complémentaire voire nécessaire pour une meilleure compréhension de la réaction et l’identification des étapes clefs à l’origine de ces hautes barrières, peu compatibles avec un scénario abiotique.Nous avons choisi d’utiliser la dynamique moléculaire ab initio [5]. Au contraire des calculs d’énergie au niveau quantique faits en phase gaz ou en solvant implicite, cette approche permet d’étudier les interactions avec le solvant, jusqu’ici négligées dans la littérature, et l’accès direct au paysage d’énergie libre (et non d’énergie), seul probant à température finie. L’inconvénient majeur reste un temps de calcul très conséquent; par conséquent, la description quantique est assurée par la Density Functional Tight Binding (DFTB) [6], une méthode semi-empirique qui rend les simulations plus accessibles en coût de calcul. Par ailleurs, l’étude des barrières d’énergie a nécessité l’emploi de méthodes d’échantillonnage avancé que sont la Métadynamique [7] et l’Umbrella Sampling [8]. Lors de cette thèse, nous avons étudié en détail et démontré l’importance des transferts de proton au cours de cette réaction. Même si les barrières expérimentales ne sont que qualitativement reproduites par notre approche, cette étude suggère que le mécanisme le plus favorable serait de type SN1 avec présence d’un intermédiaire métaphosphate.[1] Kitadai, N. Maruyama, S. Origins of building blocks of life: A Review. Geoscience Frontiers 9, 1117–1153. (2018). [2] Orgel, L. E. Prebiotic chemistry and the origin of the RNA World. Critical Reviews in Biochemistry and Molecular Biology 39, 99-123. (2004).[3] Hassan, H. A. et al. Effect of Protonation on the Mechanism of Phosphate Monoester Hydrolysis and Comparison with the Hydrolysis of Nucleoside Triphosphate in Biomolecular Motors. Biophysical Chemistry 230, 27 35. (2017).[4] Petrović, D., Szeler, K. & Kamerlin, S. C. L. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chemical Communications 54, 3077-3089.(2018).[5] Tuckerman, M. E. Ab initio molecular dynamics : basic concepts, current trends and novel applications. Journal of Physics : Condensed Matter 14, 1297-1355. (2002).[6] Gruden, M. et al. Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules. Journal of Computational Chemistry38, 2171-2185. (2017).[7] Barducci, A., Bonomi, M. S & S Parrinello, M. Metadynamics. Wiley Interdisciplinary Reviews : Computational Molecular Science 1, 826-843. (2011).[8] Torrie, G. M. & Valleau, J. Nonphysical sampling distributions in Monte Carlo free energy estimation : Umbrella Sampling. Journal of Computational Chemistry 23, 187.(1977).Characterizing the formation of the phosphodiester bond under abiotic conditions represents a major challenge when it comes to study the origins of life. This bond exists in many biological compounds that are primordial to any living organism [1], and in particular the bond linking nucleotides in RNA and DNA. Then, in addition to having emerged very early in the evolutionary process, the phosphodiester bond appears to be central in the RNA world hypothesis [2], which is considered as one of the most credible scenarios regarding the appearance of life on Earth. In this thesis, we are interested in the phosphorylation reaction between a phosphate -mono or diprotonated- and a methanol. Despite a large number of studies, the mechanisms at stake in this reaction have not yet been clearly identified. The energy barriers studied are high (between 30-50kcal/mol) [3] and very close in energy [4], making the identification of the reaction path difficult to be achieved experimentally. Thus, theoretical studies form a complementary and relatively necessary tool for a better understanding of the reaction, as well as the identification of the key steps at the origin of these high barriers, hardly compatible with an abiotic scenario. We have chosen to use ab initio Molecular Dynamics [5]. In contrast to quantum level energy calculations done in gas phase or implicit solvent, this approach allows to study the interactions with the solvent, so far neglected in the literature, and open a direct access to the free energy landscape (and not energy), which is the only conclusive data at Rinite temperature. The major drawback of this approach remains a very high computational time ; consequently, the quantum description is provided by the Density Functional Tight Binding (DFTB) [6], a semi-empirical method which makes the simulations more realistic in terms of computational cost. Moreover, the analysis of energy barriers has required advanced sampling methods such as Metadynamics [7] and Umbrella Sampling [8]. During this thesis, we have studied in detail proton transfers during phosphorylation, and demonstrated the importance of this phenomenon. Even if the experimental barriers are only qualitatively reproduced by our approach, this study suggests that the most favorable mechanism would be of the SN1 type with the presence of a metaphosphate intermediate. [1] Kitadai, N. & Maruyama, S. Origins of building blocks of life: A Review. Geoscience Frontiers 9, 1117–1153. (2018). [2] Orgel, L. E. Prebiotic chemistry and the origin of the RNA World. Critical Reviews in Biochemistry and Molecular Biology 39, 99-123. (2004). [3] Hassan, H. A. et al. Effect of Protonation on the Mechanism of Phosphate Monoester Hydrolysis and Comparison with the Hydrolysis of Nucleoside Triphosphate in Biomolecular Motors. Biophysical Chemistry 230, 27–35. (2017). [4] Petrović, D., Szeler, K. & Kamerlin, S. C. L. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chemical Communications 54, 3077-3089. (2018). [5] Tuckerman, M. E. Ab initio molecular dynamics : basic concepts, current trends and novel applications. Journal of Physics : Condensed Matter 14, 1297-1355. (2002). [6] Gruden, M. et al. Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules. Journal of Computational Chemistry 38, 2171-2185. (2017). [7] Barducci, A., Bonomi, M. S & S Parrinello, M. Metadynamics. Wiley Interdisciplinary Reviews : Computational Molecular Science 1, 826-843. (2011). [8] Torrie, G. M. S & S Valleau, J. Nonphysical sampling distributions in Monte Carlo freeenergy estimation : Umbrella Sampling. Journal of Computational Chemistry 23, 187. (1977)