José Luis Gelpí

Role of Pre-A Motif in Nitric Oxide Scavenging by Truncated Hemoglobin, HbN, of Mycobacterium tuberculosis

Mycobacterium tuberculosis truncated hemoglobin, HbN, is endowed with a potent nitric-oxide dioxygenase activity and has been found to relieve nitrosative stress and enhance in vivo survival of a heterologous host, Salmonella enterica Typhimurium, within the macrophages. These findings implicate involvement of HbN in the defense of M. tuberculosis against nitrosative stress. The protein carries a tunnel system composed of a short and a long tunnel branch that has been proposed to facilitate diatomic ligand migration to the heme and an unusual Pre-A motif at the N terminus, which does not contribute significantly to the structural integrity of the protein, as it protrudes out of the compact globin fold. Strikingly, deletion of Pre-A region from the M. tuberculosis HbN drastically reduces its ability to scavenge nitric oxide (NO), whereas its insertion at the N terminus of Pre-A lacking HbN of Mycobacterium smegmatis improved its nitric-oxide dioxygenase activity. Titration of the oxygenated adduct of HbN and its mutants with NO indicated that the stoichiometric oxidation of protein is severalfold slower when the Pre-A region is deleted in HbN. Molecular dynamics simulations show that the excision of Pre-A motif results in distinct changes in the protein dynamics, which cause the gate of the tunnel long branch to be trapped into a closed conformation, thus impeding migration of diatomic ligands toward the heme active site. The present study, thus, unequivocally demonstrates vital function of Pre-A region in NO scavenging and unravels its unique role by which HbN might attain its efficient NO-detoxification ability.

Continuum solvation models: Dissecting the free energy of solvation

The most usual self-consistent reaction field (SCRF) continuum models for the description of solvation within the quantum mechanical (QM) framework are reviewed, trying to emphasize their common roots as well as the inherent approximations assumed in the calculation of the free energy of solvation. Particular attention is also paid to the specific features involved in the development of current state-of-the-art QM SCRF continuum models. This is used to discuss the need to maintain a close correspondence between each SCRF formalism and the specific details entailing its parametrization, as well as the need to be cautious in analyzing the balance between electrostatic and non-electrostatic contributions to the solvation free energy between different SCRF models. Finally, special emphasis is given to the post-processing of the free energy of solvation to derive parameters providing a compact picture of the ability of a molecule to interact with different solvents, which can be of particular interest in biopharmaceutical studies.

Synthesis, Structural Analysis, and Biological Evaluation of Thioxoquinazoline Derivatives as Phosphodiesterase 7 Inhibitors

PDE7 inhibitors regulate pro‐inflammatory and immune T‐cell functions, and are a potentially novel class of drugs particularly useful for treatment of a wide variety of immune and inflammatory disorders. Structural optimization of thioxoquinazoline derivatives led to new compounds with very interesting profiles as PDE7 or PDE7/PDE4 dual inhibitors, which may be further developed as new drugs for inflammatory and neurological diseases.

Ligand-induced changes in the binding sites of proteins

Classical molecular interaction potentials, in conjunction with other theoretical techniques, are used to analyze the dependence of the binding sites of representative proteins on the bound ligand. It is found that the ligand bound introduces in general small structural perturbations at the binding site of the protein. However, such small structural changes can lead to important alterations in the recognition pattern of the protein. The impact of these findings in docking procedures is discussed.

Unconventional interactions between water and heterocyclic nitrogens in protein structures

We report an unusual interaction in which a water molecule approaches the heterocyclic nitrogen of tryptophan and histidine along an axis that is roughly perpendicular to the aromatic plane of the side chain. The interaction is distinct from the well‐known conventional aromatic hydrogen‐bond, and it occurs at roughly the same frequency in protein structures. Calculations indicate that the water–indole interaction is favorable energetically, and we find several cases in which such contacts are conserved among structural orthologs. The indole–water interaction links side chains and peptide backbone in turn regions, connects the side chains in β‐sheets, and bridges secondary elements from different domains. We suggest that the water–indole interaction can be indirectly responsible for the quenching of tryptophan fluorescence that is observed in the folding of homeodomains and, possibly, many other proteins. We also observe a similar interaction between water and the imidazole nitrogens of the histidine side chain. Taken together, these observations suggest that the unconventional water–indole and water–imidazole interactions provide a small but favorable contribution to protein structures. Proteins 2004.

Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools.

Thienylhalomethylketones, whose chemical, biological, and pharmaceutical data are here reported, are the first irreversible inhibitors of GSK-3beta described to date. Their inhibitory activity is likely related to the cysteine residue present in the ATP-binding site, which is proposed as a relevant residue for modulation of GSK-3 activity. The good cell permeability of the compounds allows them to be used in different cell models. Overall, the results presented here support the potential use of halomethylketones as pharmacological tools for the study of GSK-3beta functions and suggest a new mechanism for GSK-3beta inhibition that may be considered for further drug design.

Partitioning of Free Energies of Solvation into Fragment Contributions: Applications in Drug Design

It is recognised that solvation influences the activity of therapeutic agents at two different levels [1–6]: i) the binding with the receptor, and ii) the bioavailability of the drug in the organism. These aspects are complementary in drug discovery in the sense that lead optimisation should ideally concentrate on compounds having tight binding affinity and favorable ADME (absorption, distribution, metabolism, excretion) properties.