Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes

In this work a computational study of the mechanism of inhibition of cruzain, rhodesain, and cathepsin L cysteine proteases by the dipeptidyl nitroalkene Cbz-Phe-Ala-CH=CH-NO₂ has been carried out by means of molecular dynamics simulations with hybrid QM/MM potentials. The free-energy surfaces confirmed that the inhibition takes place by the formation of a covalent bond between the protein and the β-carbon atom of the inhibitor. According to the results, the tested inhibitor should be a much more efficient inhibitor of cruzain than of rhodesain, and little activity would be expected against cathepsin L, in total correspondence with the available experimental data. The origin of these differences may lie in the different stabilizing electrostatic interactions established between the inhibitor and the residues of the active site and S2 pocket of these enzymes. These results may be useful for the rational design of new dipeptidyl nitroalkenes with higher and more selective inhibitory activity against cysteine proteases.     

Electrospray Ionization Based Methods for the Generation of Polynuclear Oxo- and Hydroxo Group 6 Anions in the Gas-Phase

Electrospray ionization (ESI) of the Lindqvist (n-Bu₄N)₂[M₆O₁₉] (M = Mo, W) polyoxometalates provides a straightforward entry for the generation of an assortment of oxo- and hydroxo anions in the gas-phase. In particular, the series of oxo dianions of general formula [(MO₃) _n O]²⁻ (n = 2–6; M = Mo, W), monoanions, namely [(MO₃) _n O]⁻ (n = 1, 2) and [(MO₃) _n ]⁻ (n = 1, 2), and the hydroxo [(MO₃) _n (OH)]⁻ (n = 1–6) species can be readily generated in the gas-phase upon varying the solvent composition as well as the ionisation conditions (typically the U_c cone voltage). Complementary tandem mass experiments (collision induced dissociation and ion–molecule reactions) are also used aimed to investigate the consecutive dissociation of these species and their intrinsic gas-phase reactivity towards methanol. Special emphasis is paid to some of the key factors of these group 6 anions related to the gas-phase activation of methanol, such as molecular composition, open vs closed shell electronic nature and cluster size.     

Inside Cover: A Synthetic Lectin for O‐Linked β‐N‐Acetylglucosamine (Angew. Chem. Int. Ed. 10/2009)

Carbohydrates are slippery customers in water. Camouflaged by solvent‐mimicking hydroxy groups, they make challenging targets, even for natural receptors. In their Communication on page 1775 ff., A. P. Davis and co‐workers describe a synthetic receptor that is remarkably effective for the important β‐N‐acetylglucosaminyl (β‐GlcNAC) unit. The affinities of the receptor are good and its selectivities are excellent, even by the standards of natural carbohydrate‐binding proteins.

     

Stereoselectivity behavior of the AZ28 antibody catalyzed oxy-Cope rearrangement

Catalytic antibodies are very interesting not only because of the rate enhancement of the reactions that they catalyze but also because of the selectivities they can achieve that are sometimes not present in natural enzyme processes. We have selected the study of the stereoselectivity of the matured AZ28 that catalyzes an oxy-Cope rearrangement. For this particular case, the presence of a chiral center in the substrate provokes the existence of two different enantiomers, R and S. Furthermore, it is also possible to locate two different orientations for the hydroxyl group in the central ring of the substrate in the transition state, equatorial and axial, rendering two different conformers. In this paper we present the free energy profiles obtained for different substrate isomers in the cavity created by the matured catalytic antibody. Our simulations have reproduced the stereoselectivity of the matured AZ28, differentiating between the axial or equatorial orientations and preferentially stabilizing the S forms, at a qualitative level. Finally, the inclusion of the substrate-CA interactions in a flexible molecular model has allowed us to observe the different pattern of interactions that are related to different interaction energies, which seem to be crucial in the stereoselectivity behavior of the catalytic antibody.     

Total variation and Cheeger sets in Gauss space

The aim of this paper is to study the isoperimetric problem with fixed volume inside convex sets and other related geometric variational problems in the Gauss space, in both the finite and infinite dimensional case. We first study the finite dimensional case, proving the existence of a maximal Cheeger set which is convex inside any bounded convex set. We also prove the uniqueness and convexity of solutions of the isoperimetric problem with fixed volume inside any convex set. Then we extend these results in the context of the abstract Wiener space, and for that we study the total variation denoising problem in this context.     

Some Qualitative Properties for the Total Variation Flow

We prove the existence of a finite extinction time for the solutions of the Dirichlet problem for the total variation flow. For the Neumann problem, we prove that the solutions reach the average of its initial datum in finite time. The asymptotic profile of the solutions of the Dirichlet problem is also studied. It is shown that the profiles are nonzero solutions of an eigenvalue-type problem that seems to be unexplored in the previous literature. The propagation of the support is analyzed in the radial case showing a behaviour entirely different to the case of the problem associated with the p-Laplacian operator. Finally, the study of the radially symmetric case allows us to point out other qualitative properties that are peculiar of this special class of quasilinear equations.     

The relevance of carbohydrate hydrogen-bonding cooperativity effects: a cooperative 1,2-trans-diaxial diol and amido alcohol hydrogen-bonding array as an efficient carbohydrate-phosphate binding motif in nonpolar media

Carbohydrates with suitably positioned intramolecularly hydrogen-bonded hydroxyl and amide groups have the potential to act as efficient bidentate phosphate binders by taking advantage of sigma- and/or ,sigma,pi-H-bonding cooperativity in nonpolar solvents. Donor-donor 1,2-trans-diaxial amido alcohol (1) and diol (3), in which one of the donor centres is cooperative, are very efficient carbohydrate-phosphate binding motifs. We have proven and quantified the key role of hydrogen-bonding centres indirectly involved in complexation, which serve to generate an intramolecular H-bond (six-membered cis H-bond) in 1 and 3. This motif enhances the donor nature of the H-bonding centres that are directly involved in complexation. A comparison of the thermodynamic parameters of the complexes formed between phosphate and a cooperative (1-Phos) or anti-cooperative (2-Phos) bidentate H-bonded motif of a carbohydrate has allowed us to quantify the energetic advantage of H-bonding cooperativity in CDCl3 and CDCl3/CCl4 (1:1.3) (Delta Delta G degrees=-2.2 and -2.0 kcal mol(-1), respectively). The solvent dependences of the entropy and enthalpy contributions to binding provide a valuable example of the delicate balance between entropy and enthalpy that can arise for a single process, providing effective cooperative binding in terms of Delta G degrees.     

Preparation and properties of the full series of cuboidal clusters [Mo(x)W4-xSe4(H2O)12]n+ (n = 4-6) and their derivatives

Hydrothermal reactions between incomplete cuboidal cluster aqua complexes [M3Q4(H2O)9]4+ and M(CO)6 (M = Mo, W; Q = S, Se) offer easy access to the corresponding cuboidal clusters M4Q4. The complete series of homometal and mixed Mo/W clusters [Mo(x)W4-xQ4(H2O)12]n+ (x = 0-4, n = 4-6) has been prepared. Upon oxidation of the mixed-metal clusters, it is the W atom which is lost, allowing selective preparation of new trinuclear clusters [Mo2WSe4(H2O)9]4+ and [MoW2Se4(H2O)9]4+. The aqua complexes were converted by ligand exchange reactions into dithiophosphato and thiocyanato complexes, and crystal structures of [W4S4((EtO)2PS2)6], [MoW3S4((EtO)2PS2)6], [Mo4Se4((EtO)2PS2)6], [W4Se4((i-PrO)2PS2)6], and (NH4)6[W4Se4(NCS)12]-4H20 were determined. Cyclic voltammetry was performed on [Mo(x)W4-xCO4(H2O)12]n+, showing reversible redox waves 6+/5+ and 5+/4+. The lower oxidation states are more difficult to access as the number of W atoms increases. The [Mo2WSe4(H2O)9]4+ and [MoW2Se4(H2O)9]4+ species were derivatized into [Mo2WSe4(acac)3(py)3]+ and [MoW2Se4(acac)3(py)3]+, which were also studied by CV. When appropriate, the products were also characterized by FAB-MS and NMR (31P, 1H) data.     

A family of oxo-chalcogenide molybdenum and tungsten complexes, (n-Bu4N)2[M2O2(mu-Q)2(1,3-dithiole-2-thione-4,5-dithiolate)2] (M = Mo, W; Q = S, Se): new synthetic entries, structure, and gas-phase behavior

A new series of complexes with the general formula (n-Bu4N)2[M2O2(micro-Q)2(dmit)2] (where M = Mo, W; Q = S, Se; dmit = 1,3-dithiole-2-thione-4,5-dithiolate) have been prepared. Fragmentation of the trinuclear cluster (n-Bu4N)2[Mo3(micro3-S)(micro-S2)3(dmit)3] in the presence of triphenylphosphine (PPh3) gives the dinuclear compound (n-Bu4N)2[Mo2O2(micro-S)2(dmit)2] [(n-Bu4N)2[2]], which is formed via oxidation in air from the intermediate (n-Bu4N)2[Mo3(micro3-S)(micro-S)3(dmit)3] [(n-Bu4N)2[1]] complex. Ligand substitution of the molybdenum sulfur bridged [Mo2O2(micro-S)2(dimethylformamide)6]2+ dimer with the sodium salt of the dmit dithiolate also affords the dianionic compound (n-Bu4N)2[2]. The whole series, (n-Bu4N)2[Mo2O2(micro-Se)2(dmit)2] [(n-Bu4N)2[3]], (n-Bu4N)2[W2O2(micro-S)2(dmit)2] [(n-Bu4N)2[4]], (n-Bu4N)2[W2O2(micro-Se)2(dmit)2] [(n-Bu4N)2[5]], and (n-Bu4N)2[Mo2O2(micro-S)2(dmid)2] [(n-Bu4N)2[6]; dmid = 1,3-dithiole-2-one-4,5-dithiolate], has been synthesized by the excision of the polymeric (Mo3Q7Br4)x phases with PPh3 or 1,2-bis(diphenylphosphanyl)ethane in acetonitrile followed by the dithiolene incorporation and further degradation in air. Direct evidence of the presence of the intermediates with the formula [M3Q4(dmit)3]2- (M = Mo, W; Q = S, Se) has been obtained by electrospray ionization mass spectrometry. The crystal structures of (n-Bu4N)2[1], (PPh4)2[Mo2O2(micro-S)2(dmit)2] [(PPh4)2[2]; PPh4 = tetraphenylphosphonium], (n-Bu4N)2[2], (n-Bu4N)2[4], (PPh4)2[W2O2(micro-Se)2(dmit)2] [(PPh4)2[5]], and (n-Bu4N)2[6] have been determined. A detailed study of the gas-phase behavior for compounds (n-Bu4N)2[2-6] shows an identical fragmentation pathway for the whole family that consists of a partial breaking of the two dithiolene ligands followed by the dissociation of the dinuclear cluster.