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The most used approaches in structure-based drug design possess peculiar characteristics with advantages and limitations, and thus the management of complementary data from various techniques is of particular interest to synergistically achieve the development of effective enzyme inhibitors. In this Letter, we describe the application of experimental and computational techniques to study the interactions between human carbonic anhydrases and sulfonamide inhibitors. In particular, a series of affinity-labeled carbonic anhydrase inhibitors containing sulfonamido photoprobes was designed and synthesized, and one of these compounds, a benzophenone derivative, was chosen as a model photoprobe/inhibitor. A photoaffinity labeling method followed by mass spectrometry analysis was then applied to elucidate the inhibitor binding site, and a comparison with X-ray crystallography and molecular dynamics simulation data was carried out, highlighting that to have a comprehensive view of the protein/inhibitor complex stabilization all three kinds of experiments are necessary.

Despite its high chemical value, most of lignin is nowadays burnt as low value fuel. It is therefore important to find innovative applications for its use. Copper compounds are used as plant protec...

The influenza virus PA endonuclease is an attractive target for development of novel anti-influenza virus therapeutics. Reported PA inhibitors chelate the divalent metal ion(s) in the enzyme's catalytic site, which is located in the N-terminal part of PA (PA-Nter). In this work, a series of 2-hydroxybenzamide-based compounds have been synthesized and biologically evaluated in order to identify the essential pharmacophoric motif, which could be involved in functional sequestration of the metal ions (probably Mg(2+)) in the catalytic site of PA. By using HL(1), H2L(2), and HL(3) as model ligands with Mg(2+) ions, we isolated and fully characterized a series of complexes and tested them for inhibitory activity toward PA-Nter endonuclease. H2L(2) and the corresponding Mg(2+) complex showed an interesting inhibition of the endonuclease activity. The crystal structures of the uncomplexed HL(1) and H2L(2) and of the isolated magnesium complex [Mg(L(3))2(MeOH)2]·2MeOH were solved by X-ray diffraction analysis. Furthermore, the speciation models for HL(1), H2L(2), and HL(3) with Mg(2+) were obtained, and the formation constants of the complexes were measured. Preliminary docking calculations were conducted to investigate the interactions of the title compounds with essential amino acids in the PA-Nter active site. These findings supported the "two-metal" coordination of divalent ions by a donor triad atoms chemotype as a powerful strategy to develop more potent PA endonuclease inhibitors.

The synthesis, the characterization, and the X-ray structures of cis- and trans-Pt(II) complexes with α-(4-pyridyl)benzhydrol are reported. The crystal organization of several solvates is presented and compared with particular regard to the role of the hydrogen bond in the formation of the supramolecular architecture and how this is regulated by the presence of guest solvent molecules. It is shown that these networks are flexible as a response to the insertion of small molecules. trans-Complexes reproduce the “venetian blinds” pattern observed for the palladium analogs [Bacchi, A.; Bosetti, E.; Carcelli, M.; Pelagatti, P.; Rogolino, D.; Pelizzi, G.Inorg. Chem. 2005, 44, 431 and Bacchi, A.; Bosetti, E.; Carcelli, M.CrystEngComm 2005, 7, 527], while cis-complexes persistently give supramolecular rectangles assisted by the concomitant presence of OH···OH hydrogen bonds and edge-to-face interactions between aromatic rings inside the rectangles. These rectangles are packed by taking advantage of OH···Cl intera...

Most active and selective strand transfer HIV-1 integrase (IN) inhibitors contain chelating functional groups that are crucial feature for the inhibition of the catalytic activities of the enzyme. In particular, diketo acids and their derivatives can coordinate one or two metal ions within the catalytic core of the enzyme. The present work is intended as a contribution to elucidate the mechanism of action of the HIV-IN inhibitors by studying the coordinative features of H₂L¹ (L-708,906), an important member of the diketo acids family of inhibitors, and H₂L₂, a model for S-1360, another potent IN inhibitor. Magnesium(II) and manganese(II) complexes of H₂L¹ and H₂L² were isolated and fully characterized in solution and in the solid state. The crystal structures of the manganese complex [Mn(HL₂)₂(CH₃OH)₂]·2CH₃OH were solved by X-ray diffraction analysis. Moreover, the speciation models for H₂L₂ with magnesium(II) and manganese(II) ions were performed and the formation constants of the complexes were measured. M(HL₂)₂ (M = Mg²+, Mn²+) was the most abundant species in solution at physiological pH. All the synthesized compounds were tested for their anti-IN activity, showing good results both for the ligand and the corresponding complexes. From analysis of the speciation models and of the biological data we can conclude that coordination of both metal cofactors could not be strictly necessary and that inhibitors can act as complexes and not only as free ligands.

Previously, we synthesized a series of beta-diketo acid metal complexes as novel HIV-1 integrase (IN) inhibitors (J. Med. Chem. 2006, 46, 4248-4260). Herein, a further extension of this study is reported. First, detailed docking studies were performed in order to investigate the mode of binding in the active site of the free ligands and of their metal complexes. Second, a series of potentiometric measurements were conducted for two diketo acids chosen as model ligands, with Mn(2+) and Ca(2+), in order to outline a speciation model. Third, we designed and synthesized a new set of complexes with different stoichiometries and tested them in an in vitro assay specific for IN. Finally, we obtained the first X-ray structure of a metal complex with HIV-1 IN inhibition activity. Analysis of these results supports the hypothesis that the diketo acids could act as complexes and form complexes with the metal ions on the active site of the enzyme.

A series of natural amino acid (alanine, valine, phenylalanine, and isoleucine) amides have been synthesized and fully characterized. They have been used as supporting ligands in the Ru(II)-catalyzed asymmetric transfer hydrogenation (ath) of acetophenone in the presence of i-PrOH/KOH. Secondary amides impart high reactivity to the corresponding Ru(II) complexes, with TOFs up to 1680 h-1 and ee's up to 47%. The amino acid and the substituents of the amide nitrogen govern the activity and the enantioselectivity of the catalytic processes. The precatalysts obtained by reacting (l)-phenylalanine p-anisidineamide and (l)-valine o-anisidineamide with [Ru(p-cymene)Cl2]2 have been isolated and characterized as the half-sandwich complexes [(η6-p-cymene)Ru(κ2-N,N‘-aminoamidato)Cl] (10 and 11, respectively). An ESI-MS study conducted on the acetophenone reduction catalyzed by 11 has led to the detection of the organometallic intermediates involved in the catalytic cycle: the precatalyst 11, the 16e- complex [(η6-p...

A family of organic-inorganic wheel-and-axle diols (Pd(LOH)(2)Cl(2), Pd(LOH)(2)(CH(3))Cl, Pd(LOH)(2)(CH(3)COO)(2), LOH = alpha-(4-pyridyl)benzhydrol) and several corresponding solvates are synthesized and characterized by single-crystal X-ray diffraction analysis. Their structures are compared to investigate the factors governing the modes of solid state association, the propensity to clathration, and the structural basis of guest inclusion. In all the complexes, the palladium coordination is a slightly distorted square. The LOH ligands coordinate Pd(2+) by means of the 4-pyridyl ring. In the chloride complexes solvation occurs with a 1:2 host/guest ratio by hydrogen bonding between the terminal -OH groups of the complex diol and one acceptor atom on the guest, and it is further assisted by guest stacking between host aryl rings. All solvates are organized in layers with practically invariant metrics, while the layers may be assembled in different arrangements. The structures of the nonsolvate compounds are related to the metrics of the solvate forms by rotation of the complex molecules within the layer plane. In all cases the nonsolvates are completely converted into the corresponding crystalline solvate forms by exposure to the vapor of the guest, and conversely they are quantitatively recovered from the solvate upon removal of the guest by mild conditions. On the basis of the structural data, it is proposed that the solvation/desolvation process proceeds by a concerted rotation of the complex molecules in the layer plane. The structural analysis of Pd(LOH)(2)(CH(3)COO)(2) and of its tetrahydrofuran monosolvate form suggests that the first step of the solid/gas solvation process may imply the clathration of 1 mol of guest between the aryl rings, which successively triggers the collective reorientation of the host molecules.

A series of zerovalent palladium complexes Pd(NN)(alkene) of bi- or tridentate nitrogen ligands of the general formula 6-R‘ ‘-C5H3N-(C(R‘)NR)-2 (R‘ ‘ = H, Me, CHNR‘; R‘ = H, Me; R = alkyl, aryl, or amino group) and dimethylfumarate (dmfu) have been prepared and were subsequently employed as precatalysts in the homogeneous stereoselective semihydrogenation of 1-phenyl-1-propyne. An X-ray structure of Pd(C5H4N-(C(Me)Ni-Pr)-2)(dmfu) was obtained. Whereas only relative small changes in substituents apply, the various complexes show very different stabilities under hydrogenation conditions. The complex Pd(C5H4N-(C(H)N(CH2)2OH)-2)(dmfu) exhibits a good selectivity for the (Z)-alkene but decomposes just before full conversion of the alkyne, whereas the complex Pd(C5H4N-(C(H)Ni-Pr)-2)(dmfu) exhibits a good selectivity and stability under hydrogenation conditions and is a suitable catalyst for the stereoselective hydrogenation of 1-phenyl-1-propyne to (Z)-1-phenyl-1-propene.