I am currently responsible of a Start-Up unit funded by the Italian Association for Cancer Research. My present research mainly involve the usage of different chemoinformatic and computer-aided drug design techniques for the discovery of new anticancer therapeutics.
Beyond the application on anticancer drug design my research interests also involve: - The world of chemoinformatics and in particular virtual screenings, QSAR, CADD and other in silico techniques. - The curation of large collection of chemical compounds (see CoCoCo: Commercial Compound Collection) - Computational chemistry in a broad sense, i.e. ab-initio, DFT, QM/MM, molecular mechanics, molecular dynamics etc. In addition I still keep an eye of interest on particular topics that comes from my past scientific background: - Stereochemistry: molecular chirality, supramolecular chemistry - Chiral separations: enantioselective recognition mechanisms - Reaction mechanisms, stability of organic compounds and quantitative structure-property relationship.
Abstract: An application of molecular dynamics and molecular mechanics Poisson-Boltzmann surface area techniques to the prediction of protein kinase inhibitor selectivity is presented. A highly active and selective ERK2 inhibitor was placed in equivalent orientations in five different protein kinases (SRC, LCK, GSK3, JNK3 and Aurora-A). Binding free energies were then computed with the molecular mechanics Poisson-Boltzmann surface area approach using 15 nanosecond fully solvated molecular dynamics trajectories of the corresponding protein-ligand complexes. The results show correlation with experimentally determined selectivities and provide useful insights into the underlying structural determinants for selectivity.
Abstract: Cytochrome P450 aromatase catalyzes the conversion of androgen substrates into estrogens. Aromatase inhibitors (AIs) have been used as first-line drugs in the treatment of estrogen-dependent breast cancer in postmenopausal women. However, the search for new, more potent, and selective AIs still remains necessary to avoid the risk of possible resistances and reduce toxicity and side effects of current available drugs. The publication of a high resolution X-ray structure of human aromatase has opened the way to structure-based virtual screening to identify new small-molecule inhibitors with structural motifs different from all known AIs. In this context, a high-throughput docking protocol was set up and led to the identification of nanomolar AIs with new core structures.
Abstract: In the last few decades, virtual screening has proved to be able to guide the selection of new hit compounds with predefined biological activity. However, the usage of these computational techniques is often associated with resource- and time-consuming preparation protocols. In this work we present Commercial Compound Collection (CoCoCo), a suite of free and ready-to-use chemical databases to help setting up in silico screening projects. CoCoCo collects molecular structural information of commercial compounds from various chemical vendors by merging them in a unique, non-redundant format. CoCoCo databases are prepared with transparent and straightforward routines based on state-of-the-art computational tools that introduce comprehensive structural information about tautomers, stereoisomers and conformational states of each compound. CoCoCo suite is especially conceived as a set of valuable tools that may help a wide range of researchers who wish to initiate their own project in the field of computational drug design. CoCoCo suite is available free of charge at the website .
Abstract: In the drug discovery process, accurate methods of computing the affinity of small molecules with a biological target are strongly needed. This is particularly true for molecular docking and virtual screening methods, which use approximated scoring functions and struggle in estimating binding energies in correlation with experimental values. Among the various methods, MM-PBSA and MM-GBSA are emerging as useful and effective approaches. Although these methods are typically applied to large collections of equilibrated structures of protein-ligand complexes sampled during molecular dynamics in water, the possibility to reliably estimate ligand affinity using a single energy-minimized structure and implicit solvation models has not been explored in sufficient detail. Herein, we thoroughly investigate this hypothesis by comparing different methods for the generation of protein-ligand complexes and diverse methods for free energy prediction for their ability to correlate with experimental values. The methods were tested on a series of structurally diverse inhibitors of Plasmodium falciparum DHFR with known binding mode and measured affinities. The results showed that correlations between MM-PBSA or MM-GBSA binding free energies with experimental affinities were in most cases excellent. Importantly, we found that correlations obtained with the use of a single protein-ligand minimized structure and with implicit solvation models were similar to those obtained after averaging over multiple MD snapshots with explicit water molecules, with consequent save of computing time without loss of accuracy. When applied to a virtual screening experiment, such an approach proved to discriminate between true binders and decoy molecules and yielded significantly better enrichment curves.
Abstract: Design of irreversible inhibitors is an emerging and relatively less explored strategy for the design of protein kinase inhibitors. In this paper, we present a computational workflow that was specifically conceived to assist such design. The workflow takes the form of a multi-step procedure that includes: the creation of a database of already known reversible inhibitors of protein kinases, the selection of the most promising scaffolds that bind one or more desired kinase templates, the modification of the scaffolds by introduction of chemically reactive groups (suitable cysteine traps) and the final evaluation of the reversible and irreversible protein-ligand complexes with molecular dynamics simulations and binding free energy predictions. Most of these steps were automated. In order to prove that this is viable, the workflow was tested on a database of known inhibitors of ERK2, a protein kinase possessing a cysteine in the ATP site. The modeled ERK2-ligand complexes and the values of the estimated binding free energies of the putative ligands provide useful indicators of their aptitude to bind reversibly and irreversibly to the protein kinase. Moreover, the computational data are used to rank the ligands according to their computed binding free energies and their ability to bind specific protein residues in the reversible and irreversible complexes, thereby providing a useful decision-making tool for each step of the design. In this work we present the overall procedure and the first proof of concept results.
Abstract: A comprehensive review of chemoinformatic techniques and studies applied to the field of enantioselective molecular recognition is presented. Several approaches such as enantiophores/pharmacophore modelling, QSPRs, CoMFA and other insightful data mining procedures are discussed. The review focuses on the central role of chemoinformatic approaches on the establishment of connections between available experimental data, mainly HPLC separation data, and these algorithms that describe properties of chiral molecules. The general overview of the aforementioned calculations account for a use of these techniques as a valuable strategy to achieve reliable prediction systems, infer the mechanisms of chiral recognition, generate insight for the conception of new chiral receptors and corroborate and assist experimental techniques such as chiral LC. Moreover, it is pointed out that computer methods in this field promise a wide range of applications for both academia and industry, ranging from enantioselective reactions, drug discovery and analysis of high-throughput screenings, to analytical and semi-preparative separations or large-scale production of enantiopure compounds.
Abstract: A computational application to predict, probe and interpret the activities of a series of congeneric compounds inhibiting extracellular signal-regulated kinase 2 protein kinase is presented. The study shows that molecular dynamics coupled with molecular mechanics Poisson-Boltzmann solvent accessible surface area free energy estimation is a suitable tool for investigating the experimental binding activities of ligands to protein kinases. Computed and experimental binding activities were found to be significantly correlated. Moreover, the interpretation of the X-ray co-crystal structure in conjunction with computational results shows that the hinge region of the protein insure the principal binding site via multiple hydrogen bonding interactions, whereas fine-modulation of biological activities along the series is accomplished through the combination of weak and strong interactions that compete with water. These are located in the substituent moieties of the ligands interfacing with the DFG motif, the sugar region and the hydrophobic pocket of extracellular signal-regulated kinase 2. The study suggests that a wider interaction framework that is well beyond the hinge region is required to predict and rationalize at molecular level the experimental biological activities of congeneric compound series.
Abstract: Binding estimation after refinement (BEAR) is a novel automated computational procedure suitable for correcting and overcoming limitations of docking procedures such as poor scoring function and the generation of unreasonable ligand conformations. BEAR makes use of molecular dynamics simulation followed by MM-PBSA and MM-GBSA binding free energy estimates as tools to refine and rescore the structures obtained from docking virtual screenings. As binding estimation after refinement relies on molecular dynamics, the entire procedure can be tailored to the needs of the end-user in terms of computational time and the desired accuracy of the results. In a validation test, binding estimation after refinement and rescoring resulted in a significant enrichment of known ligands among top scoring compounds compared with the original docking results. Binding estimation after refinement has direct and straightforward application in virtual screening for correcting both false-positive and false-negative hits, and should facilitate more reliable selection of biologically active molecules from compound databases.
Abstract: A simple method for the prediction of whether or not a racemate can be separated on a Whelk-O1 chiral stationary phase has been developed. In this approach, molecules are represented by counting the number of atom types of the neighbors spheres of the chiral center. A decision tree is then used to decide based on a few of these atom count descriptors whether a given racemate can be separated. High values of correct prediction were obtained, namely with more than 94% for training sets and of about 90% for cross-validation results. The same rate of correct prediction was also obtained on an external data set. The descriptors can be rapidly and easily retrieved by just counting the atom types around the chiral center by inspecting the chemical diagram of the molecule. Furthermore, the decision tree model can be applied through the use of a small set of rules that eventually predicts whether or not a racemate is separated. Due to its computational simplicity, the procedure is of interest for experimentalists that need to make rapid assessment of the separation without having to program or input complex formulas.
Abstract: A combination of the enantiophore concept described in a previous study and a quantitative structure enantioselective relationship (QSER) based on partial least squares (PLS) analysis is presented. In the present study, a comprehensive approach for describing the enantioselective binding properties of the Whelk-O1 chiral HPLC receptor is achieved using molecular descriptors calculated by the GRID program. The GRID descriptors allow us to describe the molecules in terms of their ability to form favorable interactions with independent chemical groups (probes) that can be related to receptor sites. For each molecule, we compute 120 enantiophore descriptors representing the energy contributions from all possible pairwise combinations of probes. The overall procedure was simplified by considering only the most energetically favorable locations and converting selected grid-point energies into alignment-independent descriptors. By using a training set of 143 diverse chiral compounds, an optimal PLS model requiring seven components was chosen by using the cross-validation method resulting in a correlation coefficient R2= 0.88 and a cross validated correlation coefficient Q2= 0.85. An interpretation of the model is proposed based upon a visual inspection of the regression coefficient plots. From these plots, the influence of particular molecular features for selective binding of solutes was estimated and used to outline the chiral recognition sites in the Whelk-O1 receptor. The predictive power of our model has been estimated by means of an external data set emphasizing the suitability of the procedure also for predictive aims.
Abstract: The synthesis of a limited series of non-racemic atropisomeric 1-(2-(4-methyl-2-thioxothiazol-3(2H)-yl)phenyl)-3-(hetero)aryl-(thio)ureas is described. Using NMR titration experiments monitoring the shift of the two NH of the (thio)urea and the C-5 hydrogen of the heterocycle, the binding constants for some optically pure (thio)-ureas with the enantiomers of N-protected amino acid tetrabutylammonium salts were determined in CD3CN. The obtained enantioselectivities were modest. Contrary to what was expected on the basis of the NH acidity in thiourea versus urea group, the association constants were smaller with the thiourea than with the corresponding urea. X-ray data, DFT calculations, and NMR provided the explanation of that unexpected behavior: the urea presents a pre-organized (Z,Z) conformation suitable for a double hydrogen bond with the carboxylate anion, the thiourea presents a (Z,E) conformation, which must be reorganized in a constrained (Z,Z) conformation in the complex. An intramolecular hydrogen bond between one NH and the thiocarbonyl group of the heterocycle, which is present in the thiourea and absent in the urea, might also contribute to the smaller K(ass) for the thiourea. The possible implication of these observations in the field of bifunctional organocatalysis is briefly discussed.
Abstract: When they were independently tested, the enantiomers of N,N'-bis(salicylidene)-trans-1,2-cyclohexanediamine showed a large difference in adsorption on new chiral selectors using microbatch technology. Surprisingly, when these enantiomers were applied on the same supports as a racemic mixture, no discrimination was observed even though suitable adsorption existed. When a mixture enriched in one enantiomer (scalemic mixture) was applied, the resulting supernatant contained the racemic form and the enantiomer in excess was adsorbed on the support together with a part of racemate. This behavior, which militates in favor of a strong heterochiral dimer formation in the racemate, was revealed using microbatch technology but remained hidden on classical column chromatography on chiral support. Molecular dynamics calculations corroborate this hypothesis, showing a favorite binding mode of the heterochiral dimer, which is stabilized by various inter- and intramolecular interactions. Our findings may be considered as a new limitation of microbatch technology, but they may have some inference in case of chiral amplification using the N,N'-bis(salicylidene)-trans-1,2-cyclohexanediamine enantiomers as chiral ligands.
Abstract: ChirBase database has been employed to mine the chemical structures of compounds resolved on common commercial chiral stationary phases (CSP). Different data sets were produced. The molecular fingerprint (enantiophore) strategy was then applied over these data sets. Enantiophores are identified by analyzing and mapping the three-dimensional common structural features shared by the ligand molecules imported from ChirBase. Such lists of encoded ligand enantiophores allowed us to generate 3D maps of the molecular interacting fragments, which are supposed to act reciprocally with each CSP. Results show that each CSP is combined with different preferential enantiophore counterparts in the ligand. These differences may be well related to the particular behavior of a given CSP to separate different families of compounds. As expected, supramolecular cellulosic or amylosic CSPs show generalist behavior by resolving a wide range of racemates. On the other hand, molecular CSPs based on a well-defined chiral receptor (such as Whelk-O1 or Chirobiotic T) appear to be more specific and thus specially adapted for more restrictive families of compounds. In addition, enantiophore analyses confirm that the supramolecular CSPs can combine multiple potential binding sites and so offer numerous enantioselective mechanisms toward a ligand. Inversely, on molecular CSPs, the ligand must respect strict geometrical constraints to make possible the chiral discrimination. Additional applications of the methodology are discussed as well.
Abstract: A combination of molecular mechanics and first principles calculations was used to explore the enantioselectivity of receptors, taking into account experimental data from the CHIRBASE database. Interactions between the Whelk-O1 HPLC chiral stationary phase with the complete series of 1-(4-halogeno-phenyl)-1-ethylamine derivative racemates were studied. The objective was to extract information from the interactions between the chiral Whelk-O1 stationary phase and the enantiomers, hence probing the origin of the enantioselective behavior. Calculations correctly reproduce the elution orders and reasonably describe the experimental enantioselectivities and retention factors. Different binding modes were observed for the first eluted enantiomer complexes, whereas the second eluted show only one prevalent diastereomeric binding fashion. Natural bond orbital (NBO) analysis was used on the global minima bound-complexes to quantify donor-acceptor interactions among chiral stationary phase and ligand moieties. Intermolecular hydrogen bonding was found to be the essential energetic interaction for all systems studied. CH-pi, aromatic stacking and various charge transfer interactions were found to be smaller in magnitude but still important for the global enantioselective behavior. The three-point interaction model is discussed, pointing out the difficulty of its application for the qualitative prediction of elution orders (absolute configurations).
Abstract: The review covers examples in which chiral HPLC, as a source of pure enantiomers, has been combined with classical methods (X-ray, vibrational circular dichroism (VCD), enzymatic resolutions, nuclear magnetic resonance (NMR) techniques, optical rotation, circular dichroism (CD)) for the on- or off-line determination of absolute configuration of enantiomers. Furthermore, it is outlined that chiral HPLC, which associates enantioseparation process and classical purification process, opens new perspectives in the classical determination of absolute configuration by chemical correlation or chemical interconversion methods. The review also contains a discussion about the various approaches to predict the absolute configuration from the retention behavior of the enantiomers on chiral stationary phases (CSPs). Some examples illustrate the advantages and limitations of molecular modeling methods and the use of chiral recognition models. The assumptions underlying some of these methods are critically analyzed and some possible emerging new strategies are outlined.
Abstract: Internal rotations of the methyl group in ortho-substituted and 2,6-disubstituted toluenes in their ground state have been investigated by means of various ab initio quantum chemistry methods. Computed barriers at the Hartree-Fock (HF) level using medium sized basis sets agreed reasonably with experimental results in the case of the studied ortho-substituted toluenes. However, this agreement worsens when using very large basis sets. Furthermore, the determination of the conformation and barriers of more weakly hindered methyl groups, that is, for 2,6-dihalogenotoluenes or toluene itself, necessitates high level correlated computations, because of a possible failure of HF calculations in this case. Density functional theory (DFT) techniques required, in several cases, much more extended basis sets than the post-HF Møller-Plesset perturbation (MP2, MP4) ones, to insure the convergence of the computed barriers. Non-negligible variations of the computed barriers when using different DFT functionals are observed for some systems.
