Papers by Axel Bidon-chanal
Chemical Physics Letters, 2004
Group contributions to the hydration free energy for a series of monosubstituted alkane (CH3–(CH2... more Group contributions to the hydration free energy for a series of monosubstituted alkane (CH3–(CH2)n–X; n=0–7) derivatives have been determined from Miertus–Scrocco–Tomasi (MST) continuum calculations. Particular attention is paid to the dependence of the group contributions on the procedure used to carry out the charge normalization in the MST model. The contributions of the functional groups (X) appear to be largely
Proteins, 2006
Mycobacterium tuberculosis, the causative agent of human tuberculosis, is forced into latency by ... more Mycobacterium tuberculosis, the causative agent of human tuberculosis, is forced into latency by nitric oxide produced by macrophages during infection. In response to nitrosative stress M. tuberculosis has evolved a defense mechanism that relies on the oxygenated form of "truncated hemoglobin" N (trHbN), formally acting as NO-dioxygenase, yielding the harmless nitrate ion. X-ray crystal structures have shown that trHbN hosts a two-branched protein matrix tunnel system, proposed to control diatomic ligand migration to the heme, as the rate-limiting step in NO conversion to nitrate. Extended molecular dynamics simulations (0.1 micros), employed here to characterize the factors controlling diatomic ligand diffusion through the apolar tunnel system, suggest that O2 migration in deoxy-trHbN is restricted to a short branch of the tunnel, and that O2 binding to the heme drives conformational and dynamical fluctuations promoting NO migration through the long tunnel branch. The sim...
The balance between electrostatic and nonelectrostatic enthalpic contributions to the free energy... more The balance between electrostatic and nonelectrostatic enthalpic contributions to the free energy of solvation of a series of neutral solutes in water and n-octanol is examined by means of continuum solvation calculations based on the Miertus-Scrocco-Tomasi (MST) method. The experimental data indicate that the solvation enthalpy of hydrocarbons is very similar in water and n-octanol, and that the enthalpic contribution measured for polar compounds is larger in water than in n-octanol. According to MST calculations, the different magnitude of the solvation enthalpy found for polar compounds in the two solvents can be largely attributed to the electrostatic contribution. Moreover, the results point out that there is close resemblance between the non-electrostatic components for both hydrocarbons and polar compounds in the two solvents. Finally, the results show the power of current continuum models like MST to dissect the total free energy of solvation in entropic and enthalpic contributions and suggest that new refinements of continuum solvation models should include not only the fitting to solvation free energies, but also their enthalpic components.
Mycobacterium tuberculosis, the causative agent of human tuberculosis, encodes a haemoprotein nam... more Mycobacterium tuberculosis, the causative agent of human tuberculosis, encodes a haemoprotein named Truncated Haemoglobin N (trHbN), which in its active site transforms nitric oxide (NO) to nitrate anion. ( \textNO3-</font > )\left( {{\text{NO}}_3^ - } \right). The NO-dioxygenase activity of trHbN seems to be crucial for the bacillus, which can survive under the nitrosative stress conditions that occur upon infection of the host. As a defense mechanism against the copious amounts of NO produced by macrophages upon infection, the protein must achieve a high level of NO-dioxygenase activity to eliminate NO, but this is modulated by its efficiency in capturing O2 and NO. Migration of small diatomic ligands through the protein matrix is related to the presence of a doubly branched tunnel system connecting the surface and the haem cavity site. In this work, we have studied the mechanism that controls ligand diffusion and product egression with state-of-the-art molecular dynamics simulations. The results support a dual path mechanism for migration of O2 and NO through distinct branches of the tunnel, where migration of NO is facilitated upon binding of O2 to the haem group. Finally, egression of ( \textNO3-</font > )\left( {{\text{NO}}_3^ - } \right) is preceded by the entrance of water to the haem cavity and occurs through a different pathway. Overall, the results highlight the intimate relationship between structure, dynamical behavior and biological function of trHbN.
Solvation Effects on Molecules and Biomolecules, 2008
The enthalpic and entropic contributions to the free energy of hydration of a series of neutral s... more The enthalpic and entropic contributions to the free energy of hydration of a series of neutral solutes are analyzed by means of continuum solvation methods based on the Miertus–Scrocco–Tomasi (MST) method. Particular attention is paid to the partitioning of the enthalpic and entropic components of the hydration free energy into its electrostatic and non-electrostatic terms. The results provide a basis to design further refinements of continuum solvation models
The Journal of Physical Chemistry B, 2005
In this study, we revisit the protocol previously proposed within the framework of the Miertus-Sc... more In this study, we revisit the protocol previously proposed within the framework of the Miertus-Scrocco-Tomasi (MST) continuum model to define the cavity between the solute and solvent for predicting hydration free energies of univalent ions Luque, F. J. Chem. Phys. 1994, 182, 237]. The protocol relies on the use of a reduced cavity (around 10-15% smaller than the cavity used for neutral compounds) around the atom(s) bearing the formal charge. The suitability of this approach is examined here for a series of 47 univalent ions for which accurate experimental hydration free energies are available. Attention is also paid to the effect of the charge renormalization protocol used to correct uncertainties arising from the electron density located outside the solute cavity. The method presented here provides, with a minimum number of fitted parameters, reasonable estimates within the experimental error of the hydration free energy of ions (average relative error of 4.7%) and is able to reproduce solvation in water of both small and large ions.
The Journal of Physical Chemistry B, 2009
The increasing number of nonsymbiotic plant hemoglobins discovered in genomic studies in the past... more The increasing number of nonsymbiotic plant hemoglobins discovered in genomic studies in the past decade raises intriguing questions about their physiological role. Among them, the nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana deserves particular attention, as it combines an extremely high oxygen affinity with an internal hexacoordination of the distal histidine HisE7 to the heme iron in the absence of exogenous ligands. In order to gain insight into the structure-function relationships of the protein, the ligand binding properties of mutants of two conserved residues of the distal cavity, HisE7 --&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; Leu and PheB10 --&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; Leu, were investigated by experimental and computational studies and compared to results determined for the wild type (wt) protein. The Fe(2+)-deoxy HisE7 --&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; Leu mutant exists, as expected, in the pentacoordinated form, while a mixture of penta- and hexacoordinated forms is found for the PheB10 --&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt; Leu mutant, with an equilibrium shifted toward the pentacoordinated form with respect to the wt protein. Spectroscopic studies of the complexes of CO and CN(-) with AHb1 and its mutants show a subtle interplay of steric and electrostatic effects by distal residues on the ligand binding to the heme. Moreover, stopped-flow and flash photolysis experiments reveal substantial kinetic differences triggered by those mutations, which are particularly manifested in the enhanced geminate rebinding and bimolecular association rate. These findings are discussed in light of the drastic alterations found by molecular dynamics simulations in the nature and distribution of internal cavities in the protein matrix of the mutants, revealing an extremely large sensitivity of the protein structure to changes in distal HisE7 and PheB10 residues. Overall, data are consistent with the putative NO-dioxygenase activity attributed to AHb1.
Proteins: Structure, Function, and Bioinformatics, 2009
The influence of pressure on the equilibrium between five-(5c) and six-coordination (6c) forms in... more The influence of pressure on the equilibrium between five-(5c) and six-coordination (6c) forms in neuroglobin (Ngb) and myoglobin (Mb) has been examined by means of molecular dynamics (MD) simulations at normal and high pressure. The results show that the main effect of high pressure is to reduce the protein mobility without altering the structure in a significant manner. Moreover, our data suggest that the equilibrium between 5c and 6c states in globins is largely controlled by the structure and dynamics of the C-D region. Finally, in agreement with the available experimental data, the free energy profiles obtained from steered MD for both proteins indicate that high pressure enhances hexacoordination. In Ngb, the shift in equilibrium is mainly related to an increase in the 6c--&gt;5c transition barrier, whereas in Mb such a shift is primarily due to a destabilization of the 5c state.
Proteins: Structure, Function, and Bioinformatics, 2006
Mycobacterium tuberculosis, the causative agent of human tuberculosis, is forced into latency by ... more Mycobacterium tuberculosis, the causative agent of human tuberculosis, is forced into latency by nitric oxide produced by macrophages during infection. In response to nitrosative stress M. tuberculosis has evolved a defense mechanism that relies on the oxygenated form of "truncated hemoglobin" N (trHbN), formally acting as NO-dioxygenase, yielding the harmless nitrate ion. X-ray crystal structures have shown that trHbN hosts a two-branched protein matrix tunnel system, proposed to control diatomic ligand migration to the heme, as the rate-limiting step in NO conversion to nitrate. Extended molecular dynamics simulations (0.1 s), employed here to characterize the factors controlling diatomic ligand diffusion through the apolar tunnel system, suggest that O 2 migration in deoxy-trHbN is restricted to a short branch of the tunnel, and that O 2 binding to the heme drives conformational and dynamical fluctuations promoting NO migration through the long tunnel branch. The simulation results suggest that trHbN has evolved a dual-path mechanism for migration of O 2 and NO to the heme, to achieve the most efficient NO detoxification. Proteins 2006;64:457-464.
Physical Chemistry Chemical Physics, 2003
... F. Javier Luque*a, C. Curutcheta, J. Muñoz-Muriedasa, A. Bidon-Chanala, I. Soterasa, A. Morre... more ... F. Javier Luque*a, C. Curutcheta, J. Muñoz-Muriedasa, A. Bidon-Chanala, I. Soterasa, A. Morrealeb, JL Gelpíb and Modesto Orozco*b. a Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain. ...
Journal of the American Chemical Society, 2007
Truncated hemoglobin-N is believed to constitute a defense mechanism of Mycobacterium tuberculosi... more Truncated hemoglobin-N is believed to constitute a defense mechanism of Mycobacterium tuberculosis against NO produced by macrophages, which is converted to the harmless nitrate anion. This process is catalyzed very efficiently, as the enzyme activity is limited by ligand diffusion. By using extended molecular dynamics simulations we explore the mechanism that regulates ligand diffusion and, particularly, the role played by residues that assist binding of O2 to the heme group. Our data strongly support the hypothesis that the access of NO to the heme cavity is dynamically regulated by the TyrB10-GlnE11 pair, which acts as a molecular switch that controls opening of the ligand diffusion tunnel. Binding of O2 to the heme group triggers local conformational changes in the TyrB10-GlnE11 pair, which favor opening of the PheE15 gate residue through global changes in the essential motions of the protein skeleton. The complex pattern of conformational changes triggered upon O2 binding is drastically altered in the GlnE11--&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Ala and TyrB10--&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Phe mutants, which justifies the poor enzymatic activity observed experimentally for the TyrB10--&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;Phe form. The results support a molecular mechanism evolved to ensure access of NO to the heme cavity in the oxygenated form of the protein, which should warrant survival of the microorganism under stress conditions.
Journal of the American Chemical Society, 2008
The capability of Mycobacterium tuberculosis to rest in latency in the infected organism appears ... more The capability of Mycobacterium tuberculosis to rest in latency in the infected organism appears to be related to the disposal of detoxification mechanisms, which converts the nitric oxide (NO) produced by macrophages during the initial growth infection stage into a nitrate anion. Such a reaction appears to be associated with the truncated hemoglobin N (trHbN). Even though previous experimental and theoretical studies have examined the pathways used by NO and O2 to access the heme cavity, the eggression pathway of the nitrate anion is still a challenging question. In this work we present results obtained by means of classical and quantum chemistry simulations that show that trHbN is able to release rapidly the nitrate anion using an eggression pathway other than those used for the entry of both O2 and NO and that its release is promoted by hydration of the heme cavity. These results provide a detailed understanding of the molecular basis of the NO detoxification mechanism used by trHbN to guarantee an efficient NO detoxification and thus warrant survival of the microorganism under stress conditions.
Journal of Medicinal Chemistry, 2008
A novel series of donepezil-tacrine hybrids designed to simultaneously interact with the active, ... more A novel series of donepezil-tacrine hybrids designed to simultaneously interact with the active, peripheral and midgorge binding sites of acetylcholinesterase (AChE) have been synthesized and tested for their ability to inhibit AChE, butyrylcholinesterase (BChE), and AChE-induced A aggregation. These compounds consist of a unit of tacrine or 6-chlorotacrine, which occupies the same position as tacrine at the AChE active site, and the 5,6-dimethoxy-2-[(4-piperidinyl)methyl]-1-indanone moiety of donepezil (or the indane derivative thereof), whose position along the enzyme gorge and the peripheral site can be modulated by a suitable tether that connects tacrine and donepezil fragments. All of the new compounds are highly potent inhibitors of bovine and human AChE and BChE, exhibiting IC 50 values in the subnanomolar or low nanomolar range in most cases. Moreover, six out of the eight hybrids of the series, particularly those bearing an indane moiety, exhibit a significant A antiaggregating activity, which makes them promising anti-Alzheimer drug candidates.
Journal of Computer-Aided Molecular Design, 2010
Knowledge of the 3D structure of the binding groove of major histocompatibility (MHC) molecules, ... more Knowledge of the 3D structure of the binding groove of major histocompatibility (MHC) molecules, which play a central role in the immune response, is crucial to shed light into the details of peptide recognition and polymorphism. This work reports molecular modeling studies aimed at providing 3D models for two class I and two class II MHC alleles from Salmo salar (Sasa), as the lack of experimental structures of fish MHC molecules represents a serious limitation to understand the specific preferences for peptide binding. The reliability of the structural models built up using bioinformatic tools was explored by means of molecular dynamics simulations of their complexes with representative peptides, and the energetics of the MHC-peptide interaction was determined by combining molecular mechanics interaction energies and implicit continuum solvation calculations. The structural models revealed the occurrence of notable differences in the nature of residues at specific positions in the binding groove not only between human and Sasa MHC proteins, but also between different Sasa alleles. Those differences lead to distinct trends in the structural features that mediate the binding of peptides to both class I and II MHC molecules, which are qualitatively reflected in the relative binding affinities. Overall, the structural models presented here are a valuable starting point to explore the interactions between MHC receptors and pathogen-specific interactions and to design vaccines against viral pathogens.
Journal of Chemical Theory and Computation, 2006
We present a simple method for compression and management of very large molecular dynamics trajec... more We present a simple method for compression and management of very large molecular dynamics trajectories. The approach is based on the projection of the Cartesian snapshots collected along the trajectory into an orthogonal space defined by the eigenvectors obtained by diagonalization of the covariance matrix. The transformation is mathematically exact when the number of eigenvectors equals 3N-6 (N being the number of atoms), and in practice very accurate even when the number of eigenvectors is much smaller, permitting a dramatic reduction in the size of trajectory files. In addition, we have examined the ability of the method, when combined with interpolation, to recover dense samplings (snapshots collected at a high frequency) from more sparse (lower frequency) data as a method for further data compression. Finally, we have investigated the possibility of using the approach when extrapolating the behavior of the system to times longer than the original simulation period. Overall our results suggest that the method is an attractive alternative to current approaches for including dynamic information in static structure files such as those deposited in the Protein Data Bank.
Journal of Biological Chemistry, 2009
Mycobacterium tuberculosis truncated hemoglobin, HbN, is endowed with a potent nitric-oxide dioxy... more 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. The abbreviations used are: NOD, nitric-oxide dioxygenase; trHb, truncated hemoglobin; MD, molecular dynamics; ILS, implicit ligand sampling; r.m.s.d., root-mean square deviation. Downloaded from FIGURE 7. Structural flexibility of the Pre-A region in M. tuberculosis HbN. A, plot of cross-r.m.s.d. (Å) determined for backbone atoms between snapshots (taken every 100 ps) collected along the 100-ns trajectory for the M. tuberculosis HbN (cross-r.m.s.d. values were computed using the ptraj module of AMBER and plotted using R software). B, arrangement of charged residues in Pre-A region found in (top left) the x-ray crystallographic structure 1idr and four representative snapshots taken as the closest members to the centroid of the structural clusters depicted above (ordered from left to right and top to bottom; see also Fig. supplemental S4).
Current Pharmaceutical Design, 2010
Dual binding site acetylcholinesterase inhibitors have recently emerged as a new class of anti-Al... more Dual binding site acetylcholinesterase inhibitors have recently emerged as a new class of anti-Alzheimer agents with potential to positively modify the course of the disease. These compounds exhibit a multifunctional pharmacological profile arising from interaction with several biological targets involved upstream and downstream in the neurodegenerative cascade of Alzheimer&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s disease (AD). The primary target of these compounds is the enzyme acetylcholinesterase (AChE). Interaction of dual binding site AChE inhibitors with AChE results in a potent inhibitory activity of AChE and AChE-induced β-amyloid peptide (Aβ) aggregation. Some dual binding site AChE inhibitors take on added value a significant ability to additionally inhibit the enzymes butyrylcholinesterase and BACE-1, involved in the co-regulation of the hydrolysis of the neurotransmitter acetylcholine and in Aβ formation, respectively. The structural determinants which mediate the interaction of dual binding site AChE inhibitors with these three important enzymes for AD treatment are herein reviewed.
Chemico-Biological Interactions, 2010
Two novel families of dual binding site acetylcholinesterase (AChE) inhibitors have been develope... more Two novel families of dual binding site acetylcholinesterase (AChE) inhibitors have been developed, consisting of a tacrine or 6-chlorotacrine unit as the active site interacting moiety, either the 5,6-dimethoxy-2-[(4-piperidinyl)methyl]-1-indanone fragment of donepezil (or the indane derivative thereof) or a 5-phenylpyrano[3,2-c]quinoline system, reminiscent to the tryciclic core of propidium, as the peripheral site interacting unit, and a linker of suitable length as to allow the simultaneous binding at both sites. These hybrid compounds are all potent and selective inhibitors of human AChE, and more interestingly, are able to interfere in vitro both formation and aggregation of the -amyloid peptide, the latter effects endowing these compounds with the potential to modify Alzheimer's disease progression.
Bioorganic & Medicinal Chemistry, 2005
A new series of donepezil-tacrine hybrid related derivatives have been synthesised as dual acetyl... more A new series of donepezil-tacrine hybrid related derivatives have been synthesised as dual acetylcholinesterase inhibitors that could bind simultaneously to the peripheral and catalytic sites of the enzyme. These new hybrids combined a tacrine, 6-chlorotacrine or acridine unit as catalytic binding site and indanone (the heterocycle present in donepezil) or phthalimide moiety as peripheral binding site of the enzyme, connected through a different linker tether length. One of the synthesised compounds emerged as a potent and selective AChE inhibitor, which is able to displace propidium in a competition assay. These results seem to confirm the ability of this inhibitor to bind simultaneously to both sites of the enzyme and make it a promising lead for developing diseasemodifying drugs for the future treatment of AlzheimerÕs disease. To gain insight into the molecular determinants that modulate the inhibitory activity of these compounds, a molecular modelling study was performed to explore their binding to the enzyme.
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Papers by Axel Bidon-chanal