Interplay between Ionization and Tautomerism in Bioactive β-Enamino Ester-Containing Cyclic Compounds: Study of Annulated 1,2,3,6-Tetrahydroazocine Derivatives

Depending on the chemical scaffold, the bioactive species could reflect the interplay between ionization and tautomerism, often complicated by the possibility to populate different conformational states in the case of flexible ligands. In this context, theoretical methods can be valuable to discern the role of these factors, as shown here for β-enamino esters of 1,2,3,6 tetrahydroazocino fused ring systems, some of which had proven to be suitable scaffolds for designing novel acetylcholinesterase inhibitors. The compounds investigated herein form two clusters with distinctive experimental pKa values (i.e., α,β-diesters and β-esters ranging within 6.1-7.3 and 8.2-9.0 pKa intervals, respectively), which implies a drastic difference in the most populated species at physiological conditions. While chemoinformatic tools did not provide a consistent description of the actual pKa values, the theoretical analysis performed for the protonated and neutral species of these compounds revealed a marked change in the tautomeric preference of the tetrahydroazocine moiety upon (de)protonation. Excellent agreement between calculated and experimental pKa values was found when the tautomeric preference of protonated and neutral species was considered. Overall, this study highlights the potential use of high-level computational methods to disclose the mutual influence between ionization, tautomerism and conformational preferences in multifunctional (bio)organic compounds

Searching for selective scaffolds against Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase

Malaria is a parasitic disease caused by Plasmodium spp., being one of the major causes of death worldwide with two-hundred million new infections and hundreds of thousands of deaths in 2015. Despite the important advances in its prevention and treatment, its resistance to current drug therapies is still a serious risk in its eradication. There is urgency in finding novel targets and drugs operating by novel mechanisms, avoiding cross-resistance to classical antimalarials. In this context, the bifunctional enzyme Glucose-6- phosphate dehydrogenase 6-phosphogluconolactonase appears to be a promising therapeutic target due to its crucial role in regulating the PPP pathway (pentose phosphate pathway), which is the major source of redox potential in Plasmodium falciparum. In the last few years, our group detected a specific mutation between the human and the Plasmodium falciparum form in the binding site of Glucose-6-phosphate (G6P), the endogenous ligand of Glucose-6-phosphate dehydrogenase (G6PD). This mutation involves the substitution of an Arginine (human) by an Aspartate (parasite), which allowed us to create a validated in-house homology model of PfG6PD. Based on this result, the group has focused their efforts, through different molecular modelling techniques, in the discovery of selective scaffolds against PfG6PD. Current efforts address the development of a complete structural model of the bifunctional enzyme, which may offer novel opportunities to develop molecules capable of inhibiting this relevant enzyme

Enantioselective Synthesis of Spiro[indolizidine-1,3 '-oxindoles]

A three-step procedure for the enantioselective synthesis of spiro[indolizidine-1,3'-oxindoles], consisting of a stereoselective cyclocondensation reaction between (S)-tryptophanol and a prochiral or racemic 5-oxoester, bromination of the resulting oxazolopiperidone lactam, and a final stereoselective spirocyclization, is reported

Desarrollos metodológicos en la exploración de la especie bioactiva en fármacos: Búsqueda de agentes antimaláricos

[spa] La presente tesis doctoral se divide, de forma general, en dos principales vertientes, una de carácter metodológica y otra de carácter aplicada. La primera de ellas se ha focalizado en la caracterización de la especie bioactiva, comprendiendo en particular el estudio metodológico necesario para identificar tanto el estado de ionización (pKa) como la diversidad conformacional de ligandos tipo fármaco, pasando por aspectos tautoméricos. Para ello, se han utilizado diversas metodologías. En primer lugar, la aproximación Multinivel, anteriormente implementada en el grupo, se ha aplicado a una conjunto de 50 moléculas, siendo por tanto una muestra más grande en comparación con anteriores estudios del grupo. En concreto, se ha concentrado en la correcta estimación del coste conformacional para acceder a la conformación bioactiva, lo que ha permitido ver que la penalización conformacional es de forma general relativamente baja (< 2,0 kcal/mol), así como determinar el término entálpico y entrópico de dicho coste, detectando el mayor impacto del primero y la importancia de tomar en consideración el segundo. En segundo lugar, se han probado diferentes esquemas computacionales basados principalmente en métodos de mecánica cuántica, que combinan diversos niveles de teoría así como bases de distinta flexibilidad así como cálculos en fase gas con modelos continuos de solvatación. Ello ha permitido obtener una estimación muy exacta del valor de pKa de diferentes tipos de moléculas, lo que ha supuesto correlacionar el estado de ionización con el grado de actividad de un grupo de nuevos análogos huprina-reína. Finalmente, ambas metodologías se han combinado para poder examinar el efecto de las modificaciones estructurales introducidas en una serie de derivados éster de tetrahidroazocinas, donde se ha examinado el impacto de un equilibrio entre formas tautoméricas sobre el estado de ionización, y a su vez sobre su especie bioactiva en condiciones fisiológicas. En la segunda de ellas, se han centrado esfuerzos en la búsqueda de nuevas estructuras con capacidad de inhibir de forma selectiva el enzima Glucosa-6-fosfato deshidrogenasa de Plasmodium falciparum (PfG6PD). Concretamente, el estudio se ha basado en un modelo de homología de secuencia, que puso de relieve la existencia de una diferencia fundamental, correspondiente al cambio de Arg750 en el enzima humana por Asp en PfG6PD, lo cual permitió diseñar una serie de análogos de sustrato con actividad inhibidores frente a este enzima. Siguiendo dichos estudios, gracias al uso de diferentes técnicas de computacionales, se ha realizado una búsqueda de nuevas estructuras tipo fármaco con potencial actividad inhibidora frente a PfG6PD. En particular, se ha conseguido determinar un potencial modo de unión de dos compuestos descritos en la literatura con actividad submicromolar, y por otro lado, la combinación de métodos de cribado virtual y técnicas farmacológicas han permitido avanzar en la selección de diferentes compuestos con una prometedora actividad frente a la cepa DD2 de P. falciparum y potencial actividad frente PfG6PD.[eng] The present doctoral thesis is focused, in a general way, on two major aims, one dealing with methodological refinement to address the identification of the bioactive species, and the other consisting in the application of drug-design techniques to the development of antimalarial compounds. The methodological studies have been focused on the characterization of the bioactive species, comprising both the identification of the ionization state (pKa) and the analysis of the conformational flexibility of drug-like ligands, including also tautomeric equilibria. To this end, a variety of computational techniques have been exploited and refined. First, the Multilevel methodology, previously implemented in the group, has been applied to set of 50 molecules, which enlarges the sample considered in former studies. In particular, this study has addressed the correct estimation of the conformational cost required to access the bioactive conformation, which has allowed to conclude that the conformational penalty is generally relatively low (<2.0 kcal/mol), as well as to decompose the conformational cost into its enthalpic and entropic contributions, detecting the greater impact of the enthalpic contribution in most cases, as well as the need to take into account the entropic component. Secondly, different schemes based mainly on quantum mechanics methods, which combine distinct levels of theory and basis sets with gas phase calculations and solvation models, have been tested to predict the pKa value of different molecules. This has enabled to identify approaches well suited to provide accurate estimates of pKa of a series of huprine-rhein hybrid compounds, providing a basis to rationalize the differences in biological activity. Finally, the two methodological appraoches have been used to examine the effect of chemical differences in a series of ester derivatives of tetrahydroazocines, examining the impact of tautomerism on the ionization state, and in turn on the nature of the bioactive species in physiological conditions. In the second one, efforts have been focused in the search of new structures able to selectively inhibit the enzyme Glucose-6-phosphate dehydrogenase of Plasmodium falciparum (PfG6PD). In particular, this study was based on a structural model obtained from homology modeling that revealed a fundamental difference in the binding site, corresponding to the replacement of Arg750 in the human enzyme by Asp in PfG6PD. The relevance of this difference was validated via the design of subtrate analogs with inhibitory activity against PfG6PD. Following these studies, thanks to the use of different computational techniques, it has been possible to determine a potential binding mode of compounds with submicromolar potency reported in the literature. Finally, the combination of virtual screening methods and pharmacological techniques have allowed us to find compounds with a promising activity against P. falciparum DD2 strain and potential activity against PfG6PD

Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model

Within the scope of SAMPL7 challenge for predicting physical properties, the Integral Equation Formalism of the Miertus-Scrocco-Tomasi (IEFPCM/MST) continuum solvation model has been used for the blind prediction of n-octanol/water partition coefficients and acidity constants of a set of 22 and 20 sulfonamide-containing compounds, respectively. The log P and pKa were computed using the B3LPYP/6-31G(d) parametrized version of the IEFPCM/MST model. The performance of our method for partition coefficients yielded a root-mean square error of 1.03 (log P units), placing this method among the most accurate theoretical approaches in the comparison with both globally (rank 8th) and physical (rank 2nd) methods. On the other hand, the deviation between predicted and experimental pKa values was 1.32 log units, obtaining the second best-ranked submission. Though this highlights the reliability of the IEFPCM/MST model for predicting the partitioning and the acid dissociation constant of drug-like compounds compound, the results are discussed to identify potential weaknesses and improve the performance of the method

Holistic approach to anti-knock agents: A high-throughput screening of aniline-like compounds

The increasing concerns about greenhouse gas emissions are encouraging the search for efficient combustion technologies for transportation. A valuable strategy consists of tailoring the properties of fuels through addition of additives that might increase the octane number subject to the classification, labeling and packaging regu- lation of fuel quality. In this context, we present an integrated approach involving a high-throughput screening that relies on selected physicochemical factors of aniline-like compounds, measurements of structural resem- blance and susceptibility to participate in chemical reactions with radical species, in conjunction with production viability as well as environmental and toxicological risks. This process led to a final set of representative com- pounds that were chosen to explore their behavior as anti-knock additives. The suitability of these compounds was determined through assays performed to determine the impact on fuel volatility and RON booster efficiency in conjunction with a critical assessment of their eco/toxicological risk estimated by means of a safety index. This holistic strategy led to the identification of N-methyl-p-anisidine, N',N'-diethyl-2-methyl-p-phenylenediamine and N-nitroso-diphenylamine as promising anti-knock additives. This approach is proposed as an alternative strategy to the unsupervised experimental screening of fuel additives

Prediction of toluene/water partition coefficients in the SAMPL9 blind challenge: assessment of machine learning and IEF-PCM/MST continuum solvation models

In recent years the use of partition systems other than the widely used biphasic n-octanol/water has received increased attention to gain insight into the molecular features that dictate the lipophilicity of compounds. Thus, the difference between n-octanol/water and toluene/water partition coefficients has proven to be a valuable descriptor to study the propensity of molecules to form intramolecular hydrogen bonds and exhibit chameleon-like properties that modulate solubility and permeability. In this context, this study reports the experimental toluene/water partition coefficients (log Ptol/w) for a series of 16 drugs that were selected as an external test set in the framework of the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) blind challenge. This external set has been used by the computational community to calibrate their methods in the current edition (SAMPL9) of this contest. Furthermore, the study also investigates the performance of two computational strategies for the prediction of log Ptol/w. The first relies on the development of two machine learning (ML) models, which are built up by combining the selection of 11 molecular descriptors in conjunction with either the multiple linear regression (MLR) or the random forest regression (RFR) model to target a dataset of 252 experimental log Ptol/w values. The second consists of the parametrization of the IEF-PCM/MST continuum solvation model from B3LYP/6-31G(d) calculations to predict the solvation free energies of 163 compounds in toluene and benzene. The performance of the ML and IEF-PCM/MST models has been calibrated against external test sets, including the compounds that define the SAMPL9 log Ptol/w challenge. The results are used to discuss the merits and weaknesses of the two computational approaches