A thiazole-containing tripodal ligand: synthesis, characterization, and interactions with metal ions and matrix metalloproteinases

A new tripodal ligand, tris[2-(((2-thiazolyl)methylidene)amino)ethyl]amine (Tatren), has been synthesized and characterized by NMR, IR, and UV-visible absorbance spectroscopy and elemental analysis. Tatren forms stable complexes with transition metal ions (Zn(2+), 1; Mn(2+), 2; Co(2+), 3) and the alkaline earth metal ions (Ca(2+), 4; Mg(2+), 5). Single-crystal X-ray structures of 1, 2, and 5 revealed six-coordinate chelate complexes with formula [M(Tatren)](ClO(4))(2) in which the metal centers are coordinated by three thiazolyl N atoms and three acyclic imine N atoms. Crystals of 1, 2, and 5 are monoclinic, P2(1)/c space group. Crystals of 4 are triclinic, P space group. The Ca(2+) complex is eight-coordinate with all N atoms of Tatren and one water molecule coordinated to the metal ion. Spectrophotometric titrations show that formation constants for the chelates of metal ions are >1 in methanol. Free Tatren inhibits the catalytic domain of matrix metalloproteinase-13 (MMP-13, collagenase-3) with K(i) = 3.5 +/- 0.6 microM. Molecular mechanics-based docking calculations suggest that one leg of Tatren coordinates to the catalytic Zn(2+) in MMPs-2, -9, and -13 with significant hydrogen bonding to backbone amide groups. High-level DFT calculations suggest that, in the absence of nonbonded interactions between Tatren and the enzyme, the most stable first coordination sphere of the catalytic Zn(2+) is achieved with three imidazolyl groups from His residues and two imine N atoms from one leg of Tatren. While complexes (1-3) do not inhibit MMP-13 to a significant extent, 4 does (K(i) = 30 +/- 10 microM). Hence, this study shows that tripodal chelating ligands of this class and their Ca(2+) complexes have potential as active-site inhibitors for MMPs.     

Clustering files of chemical structures using the fuzzy k-means clustering method

This paper evaluates the use of the fuzzy k-means clustering method for the clustering of files of 2D chemical structures. Simulated property prediction experiments with the Starlist file of logP values demonstrate that use of the fuzzy k-means method can, in some cases, yield results that are superior to those obtained with the conventional k-means method and with Ward's clustering method. Clustering of several small sets of agrochemical compounds demonstrate the ability of the fuzzy k-means method to highlight multicluster membership and to identify outlier compounds, although the former can be difficult to interpret in some cases.     

Structural and energetic effects in the molecular recognition of amino acids by 18-crown-6

Absolute 18-crown-6 (18C6) affinities of five amino acids (AAs) are determined using guided ion beam tandem mass spectrometry techniques. The AAs examined in this work include glycine (Gly), alanine (Ala), lysine (Lys), histidine (His), and arginine (Arg). Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AAs as well as the proton bound complexes comprised of these species, (AA)H(+)(18C6). The proton affinities (PAs) of Gly and Ala are lower than the PA of 18C6, whereas the PAs of Lys, His, and Arg exceed that of 18C6. Therefore, the collision-induced dissociation (CID) behavior of the (AA)H(+)(18C6) complexes differs markedly across these systems. CID of the complexes to Gly and Ala produces H(+)(18C6) as the dominant and lowest energy pathway. At elevated energies, H(+)(AA) was produced in competition with H(+)(18C6) as a result of the relatively favorable entropy change in the formation of H(+)(AA). In contrast, CID of the complexes to the protonated basic AAs results in the formation of H(+)(AA) as the only direct CID product. H(+)(18C6) was not observed, even at elevated energies, as a result of unfavorable enthalpy and entropy change associated with its formation. Excellent agreement between the measured and calculated (AA)H(+)-18C6 bond dissociation energies (BDEs) is found with M06 theory for all complexes except (His)H(+)(18C6), where theory overestimates the strength of binding. In contrast, B3LYP theory significantly underestimates the (AA)H(+)-18C6 BDEs in all cases. Among the basic AAs, Lys exhibits the highest binding affinity for 18C6, suggesting that the side chains of Lys residues are the preferred binding site for 18C6 complexation in peptides and proteins. Gly and Ala exhibit greater 18C6 binding affinities than Lys, suggesting that the N-terminal amino group provides another favorable binding site for 18C6. Trends in the 18C6 binding affinities among the five AAs examined here exhibit an inverse correlation with the polarizability and proton affinity of the AA. Therefore, the ability of the N-terminal amino group to compete for 18C6 complexation is best for Gly and should become increasing less favorable as the size of the side chain substituent increases.     

Tautomerization in the formation and collision-induced dissociation of alkali metal cation-cytosine complexes

Noncovalent interactions between alkali metal cations and the various low-energy tautomeric forms of cytosine are investigated both experimentally and theoretically. Threshold collision-induced dissociation (CID) of M(+)(cytosine) complexes with Xe is studied using guided ion beam tandem mass spectrometry, where M(+) = Li(+), Na(+), and K(+). In all cases, the only dissociation pathway observed corresponds to endothermic loss of the intact cytosine molecule. The cross-section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for the M(+)(cytosine) complexes after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Ab initio calculations are performed at the MP2(full)/6-31G* level of theory to determine the structures of the neutral cytosine tautomers, the M(+)(cytosine) complexes, and the TSs for unimolecular tautomerization. The molecular parameters derived from these structures are employed for the calculation of the unimolecular rates for tautomerization and the thermochemical analysis of the experimental data. Theoretical BDEs of the various M(+)(cytosine) complexes and the energy barriers for the unimolecular tautomerization of these complexes are determined at MP2(full)/6-311+G(2d,2p) level of theory using the MP2(full)/6-31G* optimized geometries. In addition, BDEs for the Li(+)(cytosine) complexes are also determined at the G3 level of theory. Based upon the tautomeric mixture generated upon thermal vaporization of cytosine, calculated M(+)-cytosine BDEs and barriers to tautomerization for the low-energy tautomeric forms of M(+)(cytosine), and measured thresholds for CID of M(+)(cytosine) complexes, we conclude that tautomerization occurs during both complex formation and CID.     

Treatment of Malignant Melanoma by High-Peak-Power 1064 nm Irradiation Followed by Photodynamic Therapy

Irradiation of B16 pigmented melanoma subcutaneously transplanted in C57 mice with a single 650 mj pulse (10 ns) of 1064 nm light from a Q-switched Nd: YAG laser caused instantaneous bleaching of the pigmented tissue. Visual and histological examination of the resulting gray-colored tumor revealed the breakdown of melanosomes with no detectable alteration of the normal and tumor-overlying skin. Histological examination of the irradiated tumor showed some degree of vascular damage; the depth of the photodamage was not affected by the successive delivery of three consecutive light pulses. The bleached tumor grew at a modestly slower rate but the high-peak-power (HPP) laser treatment did not affect the tumor concentration of a photodynamic sensitizer Si(IV)-naphthalocyanine (isoBO-SiNc) intravenously injected 24 h before Nd : YAG irradiation. Treatment of the B16 pigmented melanoma by photodynamic therapy (PDT: 1 mg/kg isoBO-SiNc, 300 mW/cm², 520 J/cm²) from a 774 nm diode laser immediately after the 1064 nm irradiation resulted in a 16 day delay of tumor regrowth, which was markedly longer than the delay (ca 6 days) obtained after PDT under identical conditions without the preirradia-tion. Thus, pretreatment of pigmented tumors with HPP 1064 nm light appears to enhance their susceptibility to conventional PDT. The tumor response was further enhanced by repeating the combined HPP/PDT treatment at an interval of 10 days (regrowth delay: 27 days), as well as by applying hyperthermia immediately after HPP/PDT (regrowth delay: ca 34 days).     

Five-coordinate Fe(III)NO and Fe(II)CO porphyrinates: where are the electrons and why does it matter?

Recent years have seen dramatic growth in our understanding of the biological roles of nitric oxide (NO). Yet, the fundamental underpinnings of its reactivities with transition metal centers in proteins and enzymes, the stabilities of their structures, and the relationships between structure and reactivity remains, to a significant extent, elusive. This is especially true for the so-called ferric heme nitrosyls ([FeNO](6) in the Enemark-Feltham scheme). The Fe-CO and C-O bond strengths in the isoelectronic ferrous carbonyl complexes are widely recognized to be inversely correlated and sensitive to structural, environmental, and electronic factors. On the other hand, the Fe-NO and N-O bonds in [FeNO](6) heme complexes exhibit seemingly inconsistent behavior in response to varying structure and environment. This report contains resonance Raman and density functional theory results that suggest a new model for FeNO bonding in five-coordinate [FeNO](6) complexes. On the basis of resonance Raman and FTIR data, a direct correlation between the nu(Fe)(-)(NO) and nu(N)(-)(O) frequencies of [Fe(OEP)NO](ClO(4)) and [Fe(OEP)NO](ClO(4)).CHCl(3) (two crystal forms of the same complex) has been established. Density functional theory calculations show that the relationship between Fe-NO and N-O bond strengths is responsive to FeNO electron density in three molecular orbitals. The highest energy orbital of the three is sigma-antibonding with respect to the entire FeNO unit. The other two comprise a lower-energy, degenerate, or nearly degenerate pair that is pi-bonding with respect to Fe-NO and pi-antibonding with respect to N-O. The relative sensitivities of the electron density distributions in these orbitals are shown to be consistent with all published indicators of Fe-N-O bond strengths and angles, including the examples reported here.     

Determination of chlorantraniliprole residues in crops by liquid chromatography coupled with atmospheric pressure chemical ionization mass spectrometry/mass spectrometry

An analytical method is presented for the determination of chlorantraniliprole residues in crops. Chlorantraniliprole residues were extracted from crop matrixes with acetonitrile after a water soak. The extracts were passed through a strong anion-exchange (SAX) SPE cartridge stacked on top of a reversed-phase (RP) polymer cartridge. After both cartridges were rinsed and vacuum-dried, the SAX cartridge was removed, and chlorantraniliprole was eluted from the RP polymer cartridge with acetonitrile. The acetonitrile eluate was evaporated to dryness, reconstituted, and analyzed using an LC/MS/MS instrument equipped with an atmospheric pressure chemical ionization source. The method was successfully validated at 0.010, 0.10, and 10 mg/kg for the following crop matrixes: potatoes, sugar beets (tops), lettuce, broccoli, soybeans, soybean forage, tomatoes, cucumbers, oranges, apples, pears, peaches, almonds (nutmeat), rice grain, wheat grain, wheat hay, corn stover, alfalfa forage, cottonseed, grapes, and corn grain. The average recoveries from all crop samples fortified at the method LOQ ranged from 91 to 108%, with an overall average recovery of 97%. The average recoveries from all crop samples fortified at 10 times the method LOQ ranged from 89 to 115%, with an overall average recovery of 101%. For all of the fortified control samples analyzed in this study, the overall average recovery was 99%.     

Mass spectrometry guided in situ proteolysis to obtain crystals for X-ray structure determination

A strategy for increasing the efficiency of protein crystallization/structure determination with mass spectrometry has been developed. This approach combines insights from limited proteolysis/mass spectrometry and crystallization via in situ proteolysis. The procedure seeks to identify protease-resistant polypeptide chain segments from purified proteins on the time-scale of crystal formation, and subsequently crystallizing the target protein in the presence of the optimal protease at the right relative concentration. We report our experience with 10 proteins of unknown structure, two of which yielded high-resolution X-ray structures. The advantage of this approach comes from its ability to select only those structure determination candidates that are likely to benefit from application of in situ proteolysis, using conditions most likely to result in formation of a stable proteolytic digestion product suitable for crystallization.     

Modeling metal cation-phosphate interactions in nucleic acids in the gas phase via alkali metal cation-triethyl phosphate complexes

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations, Na+, K+, Rb+, and Cs+, to triethyl phosphate (TEP). The primary and lowest energy dissociation pathway in all cases is the endothermic loss of the neutral TEP ligand. Theoretical electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory are used to determine the structures, molecular parameters, and theoretical estimates for the BDEs of these complexes. For the complexes to Rb+ and Cs+, theoretical calculations were performed using hybrid basis sets in which the effective core potentials and valence basis sets of Hay and Wadt were used to describe the alkali metal cation, while the standard basis sets were used for all other atoms. The agreement between theory and experiment is excellent for the complexes to Na+ and K+ and is somewhat less satisfactory for the complexes to the heavier alkali metal cations, Rb+ and Cs+, where effective core potentials were used to describe the cation. The trends in the binding energies are examined. The binding of alkali metal cations to triethyl phosphate is compared with that to trimethylphosphate.     

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.