Structural and energetic study of cation-π-cation interactions in proteins.

Cation-π interactions of aromatic rings and positively charged groups are among the most important interactions in structural biology. The role and energetic characteristics of these interactions are well established. However, the occurrence of cation-π-cation interactions is an unexpected motif, which raises intriguing questions about its functional role in proteins. We present a statistical analysis of the occurrence, composition and geometrical preferences of cation-π-cation interactions identified in a set of non-redundant protein structures taken from the Protein Data Bank. Our results demonstrate that this structural motif is observed at a small, albeit non-negligible frequency in proteins, and suggest a preference to establish cation-π-cation motifs with Trp, followed by Tyr and Phe. Furthermore, we have found that cation-π-cation interactions tend to be highly conserved, which supports their structural or functional role. Finally, we have performed an energetic analysis of a representative subset of cation-π-cation complexes combining quantum-chemical and continuum solvation calculations. Our results point out that the protein environment can strongly screen the cation-cation repulsion, leading to an attractive interaction in 64% of the complexes analyzed. Together with the high degree of conservation observed, these results suggest a potential stabilizing role in the protein fold, as demonstrated recently for a miniature protein (Craven et al., J. Am. Chem. Soc. 2016, 138, 1543). From a computational point of view, the significant contribution of non-additive three-body terms challenges the suitability of standard additive force fields for describing cation-π-cation motifs in molecular simulations.

The boron-boron single bond in diborane(4) as a non-classical electron donor for hydrogen bonding.

An ab initio study of an isomer of diborane(4) [B(2)H(4)] has been carried out at MP2/aug-cc-pVTZ to investigate the ground-state properties of this unusual molecule, a derivative of which has been described in the recent literature. The geometric, electronic and orbital characteristics of B(2)H(4)(4) have been analyzed using AIM, NBO, and ELF methodologies. A region with a high concentration of electron density is located near and along the B-B bond, on the opposite side of this bond relative to the bridging H atoms. This site serves as an electron-donor site to electrophiles, resulting in hydrogen-bonded complexes of B(2)H(4) with proton donors HF, HNC, HCl, HCN, and HCCH, and a van der Waals complex with H(2). These complexes have C(2v) symmetry and stabilization energies that vary from 2 to 27 kJ mol(-1). The SAPT2 energy decomposition analysis shows that the relative importance of the various terms that contribute to the interaction energy depends on the strength of the interaction.

Boron-based dipolar multicomponent reactions: simple generation of substituted aziridines, oxazolidines and pyrrolidines.

New multicomponent reactions of aldehydes, isocyanides, trialkylboron reagents and dipolarophiles have been developed as an efficient route to diverse scaffolds, including aziridines, oxazolidines and poly-substituted pyrrolidines. This chemistry, inspired by a report by Hesse in 1965, is simple and involves mild conditions. Computational studies provide a basis to investigate the stereochemical features observed in the formation of oxazolidines and four-component adducts, and permit identification of potential factors that might influence the outcome of the multicomponent reaction. Thus, a rational screening of all the components and reaction parameters is made to examine the manifold mechanistic pathways and establish the practical limits for standard applications. Finally, intramolecular and solid-supported versions of these reactions bring new synthetic possibilities and practical protocols. Overall, the results describe a new family of multicomponent reactions valuable not only for organic reactivity, but also for combinatorial chemistry and drug discovery.

Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies.

The IEF-MST continuum solvation model is used to predict the hydration free energies and tautomeric preferences of a set of multifunctional compounds compiled as a blind test for computational solvation methods in the SAMPL2 contest. Computations of hydration free energies was performed using both HF/6-31G(d) and B3LYP/6-31G(d) versions of the IEF-MST model. For tautomeric preferences, the IEF-MST data was combined with the gas phase free energy differences predicted at different levels of theory ranging from MP2/6-31+G(d) to MP2/CBS+[CCSD-MP2/6-31+G(d)] levels. Comparison with the experimental data provided for hydration free energies yields a root-mean square deviation (rmsd) close to 2.3 kcal/mol, which is quite remarkable, especially considering the reduced set of training compounds used in the parametrization of the IEF-MST method. With regard to tautomerism, the lowest error in the prediction of the relative stabilities between tautomers in solution is obtained by combining MP2/CBS+[CCSD-MP2/6-31+G(d)] results with IEF-MST hydration free energies, yielding a rmsd of ca. 3.4 kcal/mol. The results illustrate the delicate balance that must be kept between the intrinsic relative stabilities in the gas phase and the differential hydration preferences in order to obtain an accurate description of the prototropic tautomerism in bioorganic compounds.

Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies.

The IEF-MST continuum solvation model is used to predict the hydration free energies of a set of 63 multifunctional compounds very recently compiled as a blind test (denoted SAMPL1) for computational solvation methods (Guthrie, J. P. J. Phys. Chem. B 2009, 113, 4501). Computations were performed using the IEF-MST versions parametrized at both HF/6-31G(d) and B3LYP/6-31G(d) levels. For direct comparison with other methods, computations were performed using the frozen geometries provided with the SAMPL1 data set, as well as the gas phase optimized geometries following the implementation of the IEF-MST model. Comparison with experimental data yields a root-mean square deviation for the whole set of compounds of 2.7 and 2.4 kcal/mol at both HF and B3LYP levels. The agreement between IEF-MST and experimental data is then quite remarkable, especially considering the reduced set of training compounds (72 data in water) used in the parametrization of the IEF-MST method.

The impact of monovalent ion force field model in nucleic acids simulations.

Different classical models for monovalent ions (typically used to neutralize proteins or nucleic acids) are available in the literature and are widely used in molecular dynamics simulations without a great knowledge of their quality, consistency with the macromolecular force field and impact on the global simulation results. In this paper the ability of several of the most popular ion models to reproduce both quantum mechanics and experimental results is examined. Artefacts due to the use of incorrect ion models in molecular dynamics simulations of concentrated solutions of NaCl and KCl in water and of a short DNA duplex in 500 mM aqueous solutions of NaCl and KCl have been analyzed. Our results allow us to discuss the robustness and reliability of different ion models and to highlight the source of potential errors arising from non-optimal models. However, it is also found that the structural and dynamic characteristics of DNA (as an example of a heavily charged macromolecule) in near-physiological conditions are quite independent of the ion model used, providing support to most already-published simulations of macromolecules.

Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams.

The reversal of the pi-facial diastereoselectivity observed in the benzyl bromide alkylation of the enolate of phenylglycinol-derived oxazolopiperidone is examined by means of theoretical calculations and experimental assays. When the angular carbon adopts an R configuration, the endo addition is intrinsically favored due to the lower torsional strain induced in the TS, but for the reaction with benzyl bromide, which affords the exo product. This reversal is attributed to the formation of a C-H...pi hydrogen bond between the C-H unit of the C8a angular position and the benzene ring of the alkylating reagent. A similar secondary interaction explains the stereochemical reversion observed in the benzyl alkylation of the enolate of oxazolopyrrolidinone. These findings point out that the delicate balance between factors that dictate the diastereoselectivity in the alkylation of chiral byciclic lactams can be unexpectedly altered by weak secondary interactions. The results presented here provide valuable guidelines to tune the selective preparation of enantiopure bioorganic and pharmaceutical compounds.

Unraveling phosphodiesterase surfaces. Identification of phosphodiesterase 7 allosteric modulation cavities.

The last findings of our group by using chemical genetic approaches have shown that PDE7 is an interesting target in neurodegenerative diseases. The following step in this travel to unravel PDE7 is the design of more selective inhibitors. In this sense we have proposed to perform an analysis of PDE7 surface to identify possible allosteric sites following by a docking study of different PDE7 inhibitors synthesized by our group. Thanks to these studies we have proved the existence of allosteric sites in PDE7 and we have been able to explain the binding modes of the employed PDE7 inhibitors.

5-imino-1,2,4-thiadiazoles: first small molecules as substrate competitive inhibitors of glycogen synthase kinase 3.

Cumulative evidence strongly supports that glycogen synthase kinase-3 (GSK-3) is a pathogenic molecule when it is up-dysregulated, emerging as an important therapeutic target in severe unmet human diseases. GSK-3 specific inhibitors might be promising effective drugs for the treatment of devastating pathologies such as neurodegenerative diseases, stroke, and mood disorders. As GSK-3 has the ability to phosphorylate primed substrates, small molecules able to bind to this site should be perfect drug candidates, able to partially block the activity of the enzyme over some specific substrates. Here, we report substituted 5-imino-1,2,4-thiadiazoles as the first small molecules able to inhibit GSK-3 in a substrate competitive manner. These compounds are cell permeable, able to decrease inflammatory activation and to selectively differentiate neural stem cells. Overall, 5-imino-1,2,4-thiadiazoles are presented here as new molecules able to decrease neuronal cell death and to increase endogenous neurogenesis blocking the GSK-3 substrate site.

Effect of phosphodiesterase 7 (PDE7) inhibitors in experimental autoimmune encephalomyelitis mice. Discovery of a new chemically diverse family of compounds.

Phosphodiesterase (PDE) 7 is involved in proinflammatory processes, being widely expressed both on lymphocytes and on certain brain regions. Specific inhibitors of PDE7 have been recently reported as potential new drugs for the treatment of neurological disorders because of their ability to increase intracellular levels of cAMP and thus to modulate the inflammatory process, as a neuroprotective well-established strategy. Multiple sclerosis is an unmet disease in which pathologies on the immune system, T-cells, and specific neural cells are involved simultaneously. Therefore, PDE7 inhibitors able to interfere with all these targets may represent an innovative therapy for this pathology. Here, we report a new chemically diverse family of heterocyclic PDE7 inhibitors, discovered and optimized by using molecular modeling studies, able to increase cAMP levels in cells, decrease inflammatory activation on primary neural cultures, and also attenuate the clinical symptoms in the experimental autoimmune encephalomyelitis (EAE) mouse model. These results led us to propose the use of PDE7 inhibitors as innovative therapeutic agents for the treatment of multiple sclerosis.

Exploring the binding sites of glycogen synthase kinase 3. Identification and characterization of allosteric modulation cavities.

Glycogen synthase kinase 3 (GSK-3) is an important drug target for human severe unmet diseases. Discovery and/or design of allosteric kinase modulators are gaining importance in this field not only for the increased selectivity of this kind of compounds but also for the subtle modulation of the target. This last point is of utmost importance for the GSK-3 inhibition as a therapeutic approach. GSK-3 activity is completely necessary for life, and only the aberrant overactivity found in the pathologies should be inhibited with its inhibitors treatment. We performed here a search for the druggable sites on the enzyme using the fpocket algorithm with the aim to provide allosteric potential binding sites on it and new clues for further drug discoveries. Moreover, our results allowed us to determine the binding sites of different GSK-3 ATP noncompetitive inhibitors, such as manzamine A and the new small molecule VP 0.7, providing evidence for potential allosteric inhibition of GSK-3.

Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions.

A complete derivation of polarizable intermolecular potentials based on high-level, gas-phase quantum-mechanical calculations is proposed. The importance of appreciable accuracy together with inherent simplicity represents a significant endeavor when enhancement of existing force fields for biological systems is sought. Toward this end, symmetry-adapted perturbation theory (SAPT) can provide an expansion of the total interaction energy into physically meaningful e.g. electrostatic, induction and van der Waals terms. Each contribution can be readily compared with its counterpart in classical force fields. Since the complexity of the different intermolecular terms cannot be fully embraced using a minimalist description, it is necessary to resort to polyvalent expressions capable of encapsulating overlooked contributions from the quantum-mechanical expansion. This choice results in consistent force field components that reflect the underlying physical principles of the phenomena. This simplified potential energy function is detailed and definitive guidelines are drawn. As a proof of concept, the methodology is illustrated through a series of test cases that include the interaction of water and benzene with halide and metal ions. In each case considered, the total energy is reproduced accurately over a range of biologically relevant distances.

Induction effects in metal cation-benzene complexes.

The role of polarization in the stabilization of a series of biologically relevant alkali and alkaline-earth metal cations (Li(+), Na(+), K(+), Mg(2+) and Ca(2+)) with the pi-electron distribution of benzene is examined by means of MP2 computations using Sadlej's basis set. In all cases a full description of the energy profile for the approach of the metal cation along the axis normal to the molecular plane of benzene has been performed. Analysis of the different contributions to the interaction energy, performed within the framework of the symmetry-adapted perturbation theory (SAPT), illustrates the important role of the induction component in the definition of the geometrical and energetic properties of the pathway leading to the formation of cation-pi complex. Finally, the ability of classical polarization models based on models of implicitly and explicitly interacting distributed isotropic polarizabilities to describe the induction term has been examined and discussed in the context of the generation of new polarizable force fields.

Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.

The main thrust of this investigation is the development of models of distributed atomic polarizabilities for the treatment of induction effects in molecular mechanics simulations. The models are obtained within the framework of the induced dipole theory by fitting the induction energies computed via a fast but accurate MP2/Sadlej-adjusted perturbational approach in a grid of points surrounding the molecule. Particular care is paid in the examination of the atomic quantities obtained from models of implicitly and explicitly interacting polarizabilities. Appropriateness and accuracy of the distributed models are assessed by comparing the molecular polarizabilities recovered from the models and those obtained experimentally and from MP2/Sadlej calculations. The behavior of the models is further explored by computing the polarization energy for aromatic compounds in the context of cation-π interactions and for selected neutral compounds in a TIP3P aqueous environment. The present results suggest that the computational strategy described here constitutes a very effective tool for the development of distributed models of atomic polarizabilities and can be used in the generation of new polarizable force fields.

Benzoderivatives of nucleic acid bases as modified DNA building blocks.

The tautomeric properties of benzoderivatives of the canonical nucleic acid bases have been studied by using different computational approaches. Attention has been paid to the impact of the benzene group in altering the tautomeric preferences of the canonical bases both in the gas phase and in aqueous solution. To this end, relative solvation free energies of the tautomers determined from Self-Consistent Reaction Field continuum calculations and Monte Carlo-Free Energy Perturbation are combined with gas-phase tautomerization free energies determined from quantum mechanical calculations. The results provide a detailed picture of the tautomeric preferences of the benzoderivatives of nucleic acid bases. This information is used to examine the recognition properties of the preferred tautomers of the benzo-fused derivatives, paying particular attention to the ability to form Watson-Crick hydrogen-bonding and stacking interactions as well as to the hydrophobic nature of the modified bases. The implications of present results on the potential use of benzo-fused bases as potential building blocks in modified DNA duplexes are examined.

On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates.

The origin of the diastereoselective alkylation of enolates of oxazolopiperidones is studied by means of theoretical calculations and experimental assays. For the unsubstituted oxazolopiperidone, the alkylation with methyl chloride is predicted to afford mainly the exo product, a finding further corroborated from the analysis of the experimental outcome obtained in the reaction of the racemic oxazolopiperidone. However, such a preference can be drastically altered by the presence of substituents attached to the fused ring. In particular, when the angular carbon adopts an R configuration in a phenylglycinol-derived oxazolopiperidone, the presence of a phenyl ring at position 3 forces the pseudo-planarity of the bicyclic lactam, and the diastereoselectivity is dictated by the internal torsional strain induced in the enolate. However, when the angular carbon adopts an S configuration, the preference for the exo alkylation stems from the intermolecular steric hindrance between the enolate and the alkylating reagent. Interestingly, the intramolecular hydrogen bond formed between the phenyl ring and the carbonyl oxygen in the enolate largely reduces the difference in stability of the two TSs compared to the unsubstituted oxazolopiperidone.