Zinc catalysis in metalloproteases

A Family of [Zn6] Complexes from the Carboxylate-Bridge-Supported Assembly of [Zn2] Building Units: Synthetic, Structural, Spectroscopic, and Systematic Biological Studies

The three discrete [Zn₆] complexes [Na₃Zn₆(cpdp)₃(μ-Bz)₃(CH₃OH)₆][ZnCl₄][ZnCl₃(H₂O)]·3CH₃OH·1.5H₂O (1), [Na₃Zn₆(cpdp)₃(μ-p-OBz)₃(CH₃OH)₆]·2H₂O (2), and [Na₃Zn₆(cpdp)₃(μ-p-NO₂Bz)₃(CH₃OH)₆]Cl₃·2H₂O (3), supported by the carboxylate-based multidentate ligand N,N'-bis[2-carboxybenzomethyl]-N,N'-bis[2-pyridylmethyl]-1,3-diaminopropan-2-ol (H₃cpdp), have been successfully synthesized and fully characterized (Bz = benzoate; p-OBz = dianion of p-hydroxybenzoic acid; p-NO₂Bz = p-nitrobenzoate). The complexes have been characterized by elemental analysis, FTIR, UV-vis, NMR spectroscopy, PXRD, and thermal analysis, including single-crystal X-ray crystallography of 1 and 2. The molecular architectures of 1-3 are built from the self-assembly of their corresponding [Zn₂] units, which are interconnected to the central [Na₃(CH₃OH)₆]³⁺ core by six endogenous benzoate groups, with each linking one Zn(II) and one Na(I) ion in a μ₂:η¹:η¹-syn-anti bidentate fashion. The composition of the (cpdp^3-)₃/(Zn²⁺)₆ complexes in 1-3 has been observed to be 1:2, on the basis of the UV-vis titration and NMR spectroscopic results, which is further supported by X-ray crystallography. Systematic biological studies performed with a mice model suggested possible antidiabetic efficacy as well as anticancer activities of the complexes. When complexes 1-3 were administered intraperitoneally in mice, 1 showed a lowering in the blood glucose level, overall maintenance of the pancreatic tissue mass, restriction of DNA damage in pancreatic cells, and retention of lipid droplet (LD) frequency, whereas 2 and 3 showed hepatic tissue mass consistency by inhibiting the DNA damage in hepatic cells, prior to the exposure to a potent diabetic inducer, alloxan (ALX). Similar trends of results were observed in inhibiting the generation of reactive oxygen species (ROS) in the pancreatic and hepatic cells, as examined by spectrofluorometric methods. Thus, 1 seems to be a better compound for overall diabetic management and control, whereas 2 and 3 seem to be promising compounds for designing chemopreventive drugs against hepatic carcinoma.

Efficient routes to carbon-silicon bond formation for the synthesis of silicon-containing peptides and azasilaheterocycles

Silasubstitution, where silicon is substituted for carbon at specific sites of the substrate, has become a growing practice in medicinal chemistry. Introducing silicon into bioactive compounds provides slight physical and electronic alterations to the parent compound, which in certain instances could make the substrate a more viable candidate for a drug target. One application is in the field of protease inhibition. Various silane diol isosteres can act as potent inhibitors of aspartic and metalloproteases because of their ability to mimic the high-energy tetrahedral intermediate in peptide bond hydrolysis. In particular, since 1998, the Sieburth group has prepared a number of functionalized peptide silane diol isosteres. In a seminal study, they demonstrated that these molecules can bind to the active site of the enzymes. Inspired by these results, we initiated a study to develop a concise and straightforward route to access highly functionalized silicon diol based peptidomimetic analogs, which we describe in this Account. The synthesis of such analogs is challenging because the dipeptide mimics require the formation of two carbon-silicon bonds as well as two chiral carbon centers. Our first strategy was to assemble the two C-Si bonds from diphenylsilane through an initial regioselective hydrosilylation step of a terminal alkene, followed by lithiation of the formed alkyldiphenylsilane by a simple lithium metal reduction. Subsequent diastereoselective addition of this silyllithium species to a tert-butylsulfinimine provided a rapid method to assemble the dipeptide mimic with stereochemical control at the new chiral carbon center adjacent to the silicon. This strategy worked with a wide range of functional groups. However, there were some limitations with the more elaborate targets. In particular, we needed to exchange the phenyl groups of the diphenylsilane with aryl groups that were more labile under acidic conditions in order to introduce Si-O bonds in the end product. We demonstrated that a variety of Ar(2)SiH(2) compounds with methyl substituents on the aromatic core could effectively undergo hydrosilylation and reductive lithiation with a soluble reducing agent, lithium naphthalenide. The electron-rich aromatic groups were more acid labile and, depending on the conditions, could produce either the silane diol or the silanol. In an alternative strategy, we used a highly regioselective Rh-catalyzed sequential double hydrosilylation to form the two C-Si bonds with a single catalyst. This approach is a more efficient, atom economical way to synthesize a wider range of highly functionalized organosilanes with the added possibility of extending this method into an asymmetric protocol. By this method, various functional groups that were not previously tolerated in the lithiation protocol, including OBn, OAc, furyl, and thiophenes, could now be incorporated. Hydrosilylation of a terminal olefin and a peptide functionalized with an enamide at the C-terminus achieved the desired silane in high yields in a one pot reaction without compromising the stereochemical integrity of the peptide. As an extension of this work, we used these methods to efficiently generate a variety of chiral azasilaheterocycles, including silapiperidines and silaindolizidines.

Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation

Acutolysin A, which is isolated from the snake venom of Agkistrodon acutus, is a member of the SVMPs subfamily of the metzincin family, and it is a snake venom zinc metalloproteinase possessing only one catalytic domain. The catalytic zinc ion, in the active site, is coordinated in a tetrahedral manner with three imidazole nitrogen atoms of histidine and one oxygen atom. It is uncertain whether this oxygen atom is a water molecule or a hydroxide ion just from the three-dimensional X-ray crystal structure. The identity of the fourth ligand of zinc is theoretically determined for the first time by performing both combined quantum mechanical and molecular mechanical (QM/MM) simulation and high-level quantum mechanical calculations. All of the results obtained indicate that the fourth ligand in the active site of the reported X-ray crystal structure is a water molecule rather than a hydroxide anion. On the basis of these theoretical results, we note that the experimental observed pH dependence of the proteolytic and hemorrhagic activity of Acutolysin A can be attributed to the deprotonation of the zinc-bound water to yield a better nucleophile, the hydroxide ion. Structural analyses revealed structural details useful for the understanding of acutolysin catalytic mechanism.

A comparative study of semiempirical, ab initio, and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes

Although theoretical methods are now available which give very accurate results, often comparable to the experimental ones, modeling chemical or biological interesting systems often requires less demanding and less accurate theoretical methods, mainly due to computer limitations. Therefore, it is crucial to know the precision of such less reliable methods for relevant models and data. This has been done in this work for small zinc-active site models including O- (H(2)O and OH(-)) and N-donor (NH(3) and imidazole) ligands. Calculations using a number of quantum mechanical methods were carried out to determine their precision for geometries, coordination number relative stability, metal-ligand bond strengths, proton affinities, and interaction energies between first and second shell ligands. We have found that obtaining chemical accuracy can be as straightforward as HF geometry optimization with a double-zeta plus polarization basis followed by a B3LYP energy calculation with a triple-zeta quality basis set including diffuse and polarization functions. The use of levels as low as PM3 geometry optimization followed by a B3LYP single-point energy calculation with a double-zeta quality basis including polarization functions already yields useful trends in bond length, proton affinities or bond dissociation energies, provided that appropriate caution is taken with the optimized structures. The reliability of these levels of calculation has been successfully demonstrated for real biomimetic cases.

Thiolate exchange in [TmR]ZnSR' complexes and relevance to the mechanisms of thiolate alkylation reactions involving zinc enzymes and proteins

The zinc and cadmium thiolate complexes [TmBut]MSCH2C(O)N(H)Ph (M = Zn, Cd) may be obtained via treatment of the respective methyl complex [TmBut]MMe with PhN(H)C(O)CH2SH. The molecular structure of [TmBut]ZnSCH2C(O)N(H)Ph has been determined by X-ray diffraction, thereby demonstrating the presence of an intramolecular N-H S hydrogen bond between the amide N-H group and thiolate sulfur atom. [TmBut]ZnSCH2C(O)N(H)Ph mimics the function of the Ada DNA repair protein by undergoing alkylation with MeI to give [TmBut]ZnI and MeSCH2C(O)N(H)Ph. A series of crossover experiments and 1H NMR magnetization transfer studies establish that thiolate exchange between [TmR]ZnSR' derivatives is facile in this system, an observation that supports the previous suggestion that the alkylation of [TmPh]ZnSCH2C(O)N(H)Ph by MeI may proceed via a sequence that involves dissociation of [PhN(H)C(O)CH2S]-.

Pressure and temperature as tools for investigating the role of individual non-covalent interactions in enzymatic reactions Sulfolobus solfataricus carboxypeptidase as a model enzyme

Sulfolobus solfataricus carboxypeptidase, (CPSso), is a heat- and pressure-resistant zinc-metalloprotease. Thanks to its properties, it is an ideal tool for investigating the role of non-covalent interactions in substrate binding. It has a broad substrate specificity as it can cleave any N-blocked amino acid (except for N-blocked proline). Its catalytic and kinetic mechanisms are well understood, and the hydrolytic reaction is easily detectable spectrophotometrically. Here, we report investigations on the pressure- and temperature-dependence of the kinetic parameters (turnover number and Michaelis constant) of CPSso using several benzoyl- and 3-(2-furyl)acryloyl-amino acids as substrates. This approach enabled us to study these parameters in terms of individual rate constants and establish that the release of the free amino acid is the rate-limiting step, making it possible to dissect the individual non-covalent interactions participating in substrate binding. In keeping with molecular docking experiments performed on the 3D model of CPSso available to date, our results show that both hydrophobic and energetic interactions (i.e., stacking and van der Waals) are mainly involved, but their contribution varies strongly, probably due to changes in the conformational state of the enzyme.

Polarizing a Hydrophobic Cavity for the Efficient Binding of Organic Guests: The Case of Calix[6]tren, a Highly Efficient and Versatile Receptor for Neutral or Cationic Species

The host-guest properties of calix[6]tren 1 have been evaluated. The receptor is based on a calix[6]arene that is covalently capped at the narrow rim by a tren unit. As a result, the system presents a concave hydrophobic cavity with, at its bottom, a grid-like nitrogenous core. Despite its well-defined cavity and opening to the outside at the large rim, 1 did not behave as a good receptor for neutral molecules in chloroform. However, it exhibited efficient endo-complexation of ammonium guests. By contrast, the per-protonated host, 1.4H(+), behaved as a remarkable receptor for small organic molecules. The complexation is driven by a strong charge-dipole interaction and hydrogen bonds between the polar guest and the tetracationic cap of the calixarene. Finally, coordination of Zn(2+) to the tren core led to the asymmetrization of calixarene cavity and to the strong but selective endo-binding of neutral ligands. This study emphasizes the efficiency of a receptor presenting a concave hydrophobic cavity that is polarized at its bottom. The resulting combination of charge-dipole, hydrogen bonding, CH-pi, and van der Waals interactions highly stabilizes the supramolecular architectures. Also, importantly, the tren cap allows the tuning of the polarization, offering either a basic (1), a highly charged and acidic (1.4H(+)), or a coordination (1.Zn(2+)) site. As a result, the system proved to be highly versatile, tunable, and interconvertible in solution by simple addition of protons, bases, or metal ions.

The molecular structure of the tris(2-mercapto-1-tolylimidazolyl)hydroborato zinc(2-mercapto-1-tolylimidazole) complex, {[Tmp-Tol]Zn(mimp-Tol)}[ClO4]: intermolecular N–H⋯OClO3versus intramolecular N–H⋯S hydrogen bonding interactions of the mercaptoimidazole ligand

The molecular structure of the tris(2-mercapto-1-tolylimidazolyl)hydroborato complex [[Tm(p-Tol)]Zn(mim(p-Tol))][ClO(4)].3MeCN has been determined by X-ray diffraction, thereby demonstrating that the mim(p-Tol) ligand exhibits a N-H...O hydrogen bond with the [ClO(4)](-) counterion, [[Tm(p-Tol)]Zn(mim(p-Tol))...(OClO(3))], rather than hydrogen bond with a sulfur of the [Tm(p-Tol)] ligand. DFT calculations on a series of related complexes, namely [[Tm(Me)]Zn(mim(Me))](+), [[Tm(Me)]Zn(mim(Me))]...(OClO(3))], [[Tm(Me)]Zn(mim(Me))]...[O(H)Me]](+), and [[Tm(Me)]Zn(mim(Me))]...(NCMe)](+) demonstrate that an intramolecular N-H...S hydrogen bond within [[Tm(Me)]Zn(mim(Me))](+) is also less favored than the corresponding hydrogen bonding interactions with MeCN, MeOH, and [ClO(4)](-). The inability of the sulfur atoms of [Tm(R)] ligand to act as an effective hydrogen bond acceptor is in marked contrast to the ability of sulfur atoms in thiolate ligands to participate in the formation of N-H...S hydrogen bonds, an observation that reflects the "thione"versus"thiolate" nature of the [Tm(R)] ligand.

Protonation and reactivity towards carbon dioxide of the mononuclear tetrahedral zinc and cobalt hydroxide complexes, [Tp(Bu)t(,Me)]ZnOH and [Tp(Bu)t(,Me)]CoOH: comparison of the reactivity of the metal hydroxide function in synthetic analogues of carbonic anhydrase

The tris(3-tert-butyl-5-methylpyrazolyl)hydroborato zinc hydroxide complex [Tp(Bu)t(,Me)]ZnOH is protonated by (C(6)F(5))(3)B(OH(2)) to yield the aqua derivative [[Tp(Bu)t(,Me)]Zn(OH(2))][HOB(C(6)F(5))(3)], which has been structurally characterized by X-ray diffraction, thereby demonstrating that protonation results in a lengthening of the Zn-O bond by ca. 0.1 A. The protonation is reversible, and treatment of [[Tp(Bu)t(,Me)]Zn(OH(2))](+) with Et(3)N regenerates [Tp(Bu)t(,Me)]ZnOH. Consistent with the notion that the catalytic hydration of CO(2) by carbonic anhydrase requires deprotonation of the coordinated water molecule, [[Tp(Bu)t(,Me)]Zn(OH(2))](+) is inert towards CO(2), whereas [Tp(Bu)t(,Me)]ZnOH is in rapid equilibrium with the bicarbonate complex [Tp(Bu)t(,Me)]ZnOC(O)OH under comparable conditions. The cobalt hydroxide complex [Tp(Bu)t(,Me)]CoOH is likewise protonated by (C(6)F(5))(3)B(OH(2)) to yield the aqua derivative [[Tp(Bu)t(,Me)]Co(OH(2))][HOB(C(6)F(5))(3)], which is isostructural with the zinc complex. The aqua complexes [[Tp(Bu)t(,Me)]M(OH(2))][HOB(C(6)F(5))(3)] (M = Zn, Co) exhibit a hydrogen bonding interaction between the metal aqua and boron hydroxide moieties. This hydrogen bonding interaction may be viewed as analogous to that between the aqua ligand and Thr-199 at the active site of carbonic anhydrase. In addition to the structural similarities between the zinc and cobalt complexes, [Tp(Bu)t(,Me)ZnOH] and [Tp(Bu)()t(,Me)]CoOH, and between [[Tp(Bu)t(,Me)]Zn(OH(2))](+) and [[Tp(Bu)t(,Me)]Co(OH(2))](+), DFT (B3LYP) calculations demonstrate that the pK(a) value of [[Tp]Zn(OH(2))](+) is similar to that of [[Tp]Co(OH(2))](+). These similarities are in accord with the observation that Co(II) is a successful substitute for Zn(II) in carbonic anhydrase. The cobalt hydroxide [Tp(Bu)()t(,Me)]CoOH reacts with CO(2) to give the bridging carbonate complex [[Tp(Bu)t(,Me)]Co](2)(mu-eta(1),eta(2)-CO(3)). The coordination mode of the carbonate ligand in this complex, which is bidentate to one cobalt center and unidentate to the other, is in contrast to that in the zinc counterpart [[Tp(Bu)t(,Me)]Zn](2)(mu-eta(1),eta(1)-CO(3)), which bridges in a unidentate manner to both zinc centers. This difference in coordination modes concurs with the suggestion that a possible reason for the lower activity of Co(II)-carbonic anhydrase is associated with enhanced bidentate coordination of bicarbonate inhibiting its displacement.

Mutational analysis of catalytic sites of the cell wall lytic N-acetylmuramoyl-L-alanine amidases CwlC and CwlV

The Bacillus subtilis CwlC and the Bacillus polymyxa var. colistinus CwlV are the cell wall lytic N-acetylmuramoyl-l-alanine amidases in the CwlB (LytC) family. Deletion in the CwlC amidase from the C terminus to residue 177 did not change the amidase activity. However, when the deletion was extended slightly toward the N terminus, the amidase activity was entirely lost. Further, the N-terminal deletion mutant without the first 19 amino acids did not have the amidase activity. These results indicate that the N-terminal half (residues 1-176) of the CwlC amidase, the region homologous to the truncated CwlV (CwlVt), is a catalytic domain. Site-directed mutagenesis was performed on 20 highly conserved amino acid residues within the catalytic domain of CwlC. The amidase activity was lost completely on single amino acid substitutions at two residues (Glu-24 and Glu-141). Similarly, the substitution of the two glutamic acid residues (E26Q and E142Q) of the truncated CwlV (CwlV1), which corresponded to Glu-24 and Glu-141 of CwlC, was critical to the amidase activity. The EDTA-treated CwlV1 did not have amidase activity. The amidase activity of the EDTA-treated CwlV1 was restored by the addition of Zn2+, Mn2+, and Co2+ but not by the addition of Mg2+ and Ca2+. These results suggest that the amidases in the CwlB family are zinc amidases containing two glutamic acids as catalytic residues.