EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

The completion of the Human Genome Project, the growing effort on proteomics, and the Structural Genomics Initiative have recently intensified the attention being paid to reliable computer docking programs able to identify molecules that can affect the function of a macromolecule through molecular complexation. We report herein an automated computer docking program, EUDOC, for prediction of ligand-receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases. This program was evaluated from the standpoints of force field and sampling issues using 154 experimentally determined ligand-receptor complexes and four "real-life" applications of the EUDOC program. The results provide evidence for the reliability and accuracy of the EUDOC program. In addition, key principles underlying molecular recognition, and the effects of structural water molecules in the active site and different atomic charge models on docking results are discussed. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1750-1771, 2001     

Electronic factors affecting second-order NLO properties: case study of four different push-pull bis-dithiolene nickel complexes

The paper presents a detailed experimental and theoretical study of the four mixed nickel-bisdithiolene complexes [Ni(Pr(i)(2)pipdt)(dmit)] (1b, Pr(i)(2)pipdt = 1,4-diisopropyl-piperazine-3,2-dithione; dmit = 1,3-dithiolo-2-tione-4,5-dithiolato), [Ni(R(2)pipdt)(mnt)] (2b", R = 2-ethylhexyl; mnt = maleonitriledithiolato), [Ni(Pr(i)(2)timdt)(dmit)] (3b, Pr(i)(2)timdt = 1,3-diisopropyl-imidazoline-2,4,5-trithione), and [Ni(Pr(i)(2)timdt)(mnt)] (4b), and their models. All the complexes, with common (C(2)S(2))Ni(C(2)S(2)) core and two different terminal groups, are uncharged and square-planar coordinated. Previous measurements of the first molecular hyperpolarizability indicated that some of the species are potential NLO chromophores due to the pi-delocalized character of two frontier levels (HOMO and LUMO) which is asymmetrically perturbed by the combination of one push (R(2)pipdt, R(2)timdt) with one pull ligand (dmit and mnt). The X-ray structure of complex 1b is presented and its geometry is compared with those available in the literature for the four types of complexes under study. The results of electrochemical and spectroscopic measurements (oxidation and reduction potentials, IR, dipole moment, molecular absorptivities, etc.) indicate rather different responses between the pairs of complexes 1-2 and 3-4. Hence, DFT calculations on the model compounds 1a-4a, where hydrogen atoms replace the alkyl groups of R(2)pipdt and R(2)timdt, have been carried out to correlate geometries and electronic structures. Moreover, the first molecular hyperpolarizabilities have been calculated and their components have been analyzed with the simplest two-level approximation. The derived picture highlights the different roles of the two push and pull ligands, but also the peculiar perturbation of the pi-electron density induced by the terminal CS(3) grouping of the ligand dmit.     

Comparison of the performances of a particle beam LC-MS interface obtained by standard and modified skimmers

Stainless steel skimmers were made in the technical workshop of our Department and mounted on a commercial Particle Beam interface. Their performances were compared with the standard ones, using three different compounds: benzidine, caffeine and perylene. Library searchable EI spectra were collected with a high quality match and remarkable improvements in the sensitivity were obtained (detection limit of 20 pg for perylene and benzidine), probably due to their better tightness that allowed to widen the skimmer orifices without significantly compromising the ion source vacuum. Also calibration curves showed a good linearity, in the concentration range 10-200 ng/ml.     

A mass spectrometric investigation on some 3-[2-(Nitroxy)alkyl]-2H-1,3-benzoxazin-4-(3H)-one derivatives

The electron ionization mass spectrometric behaviour of ten 3-[2-(nitroxy)alkyl]-2H-1,3-benzoxazin-4-(3H)-one derivatives has been studied by means of metastable ion studies. By mass-analysed ion kinetic energy spectrometry of the related molecular ions, clear differences have been evidenced between the 5-methyl derivative and the other compounds, consisting of a highly favoured loss of NO₂ radical. The same methodology has allowed easy characterization of isomeric compounds.     

Mass spectrometry strategies applied to the characterization of proline-rich peptides from secretory parotid granules of pig (Sus scrofa)

Basic proline-rich proteins (bPRPs) are a class of proteins widely present in saliva of humans and other mammals. They are synthesized as preproproteins and enzymatically cleaved into small peptides before secretion from the salivary glands. Recently, we characterized two proline-rich peptides (SP-A and SP-B) in parotid secretory granules of pig (Sus Scrofa) that are derived from three isoforms of a PRP proprotein (Swiss-Prot data bank: Q95JC9-1, Q95JC9-2 and Q95JC9-3). Together the coding regions for SP-A and SP-B, which are repeated many times, account for 52-70% of the coding regions of the PRP proproteins. This study was undertaken to identify peptides encoded by unassigned regions of the PRP proproteins. RP-HPLC-ESI-IT-MS analysis of enriched granule preparations from pig parotid glands by two different analytical strategies identified ten new proline-rich peptides derived from the three proproteins. Together with the coding regions for SP-A and SP-B already identified it was possible to assign 68-75% of the proproteins coding regions. The peptide sequences indicated a number of unusual proteolytic cleavage sites suggesting the presence of unknown proprotein convertases.     

Nested set complexes of Dowling lattices and complexes of Dowling trees

Given a finite group G and a natural number n, we study the structure of the complex of nested sets of the associated Dowling lattice (Proc. Internat. Sympos., 1971, pp. 101–115) and of its subposet of the G-symmetric partitions which was recently introduced by Hultman (, 2006), together with the complex of G-symmetric phylogenetic trees . Hultman shows that the complexes and are homotopy equivalent and Cohen–Macaulay, and determines the rank of their top homology. An application of the theory of building sets and nested set complexes by Feichtner and Kozlov (Selecta Math. (N.S.) 10, 37–60, 2004) shows that in fact is subdivided by the order complex of . We introduce the complex of Dowling trees and prove that it is subdivided by the order complex of . Application of a theorem of Feichtner and Sturmfels (Port. Math. (N.S.) 62, 437–468, 2005) shows that, as a simplicial complex, is in fact isomorphic to the Bergman complex of the associated Dowling geometry. Topologically, we prove that is obtained from by successive coning over certain subcomplexes. It is well known that is shellable, and of the same dimension as . We explicitly and independently calculate how many homology spheres are added in passing from to . Comparison with work of Gottlieb and Wachs (Adv. Appl. Math. 24(4), 301–336, 2000) shows that is intimely related to the representation theory of the top homology of . Research partially supported by the Swiss National Science Foundation, project PP002-106403/1.     

Analytical Method Performance Evaluation (AMPE)--a software tool for analytical method validation

A Windows-based software tool [Analytical Method Performance Evaluation (AMPE)] was developed to support the validation of analytical methods. The software implements standard statistical approaches commonly adopted in validation studies to estimate analytical method performance (limits of detection and quantitation, accuracy, specificity, working range, and linearity of responses) according to ISO 5725. In addition, AMPE proposes the application of innovative and unique approaches for the assessment of analytical method performance. Specifically, AMPE proposes the use of difference-based indexes to quantify the agreement between measurements and reference values, the use of pattern indexes to quantify methods bias with respect to specific external variables, and the application of fuzzy logic to aggregate into synthetic indicators the information collected independently via the different performance statistics traditionally estimated in validation studies. Aggregated measures are particularly useful for methods comparison, when more than one method is available for a specific analysis and it may be of interest to identify the best performing one taking into account, simultaneously, the information available from different performance statistics. Illustrative examples of the type of outputs expected from AMPE-based validation sessions are given. The extensive data handling capabilities and the wide range of statistics supplied in the software package makes AMPE suitable for specific needs that may arise in different validation studies. The installation package, complete with a fully documented help file, is distributed free of charge to interested users along with input files exemplary of the type of entry data required to run validation data analyses.     

Multivariate optimization approach for the analysis of butyltin compounds in mussel tissues by gas chromatography-mass spectrometry

The derivatization with NaBEt(4) for the determination of butyltin compounds in mussel tissues (Mytilus galloprovincialis) by GC-MS was optimized using a central composite design. The effects of NaBEt(4) concentration, pH and acetate buffer concentration on the derivatization efficiency were considered. Solid-phase extraction with Florisil cartridges was performed, demonstrating that the clean-up drastically reduces the background and improves the sensitivity. The good accuracy of the method was verified on a certified reference material (ERM 477); the figures of merit for all the three analytes, evaluated under optimum conditions, were satisfactory. The optimized derivatization procedure was applied to the determination of the analytes in mussels exposed to tributyltin (TBT). All considered tissues showed considerable accumulation of TBT, especially gills.