Andrea Zaliani

The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits antiinflammatory properties via suppression of cytokines

Suberoylanilide hydroxamic acid (SAHA) is a hydroxamic acid-containing hybrid polar molecule; SAHA specifically binds to and inhibits the activity of histone deacetylase. Although SAHA, like other inhibitors of histone deacetylase, exhibits antitumor effects by increasing expression of genes regulating tumor survival, we found that SAHA reduces the production of proinflammatory cytokines in vivo and in vitro. A single oral administration of SAHA to mice dose-dependently reduced circulating TNF-α, IL-1-β, IL-6, and IFN-γ induced by lipopolysaccharide (LPS). Administration of SAHA also reduced hepatic cellular injury in mice following i.v. injection of Con A. SAHA inhibited nitric oxide release in mouse macrophages stimulated by the combination of TNF-α plus IFN-γ. Human peripheral blood mononuclear cells stimulated with LPS in the presence of SAHA released less TNF-α, IL-1-β, IL-12, and IFN-γ (50% reduction at 100–200 nM). The production of IFN-γ stimulated by IL-18 plus IL-12 was also inhibited by SAHA (85% at 200 nM). However, SAHA did not affect LPS-induced synthesis of the IL-1-β precursor, the IL-1 receptor antagonist, or the chemokine IL-8. In addition, IFN-γ induced by anti-CD3 was not suppressed by SAHA. Steady-state mRNA levels for LPS-induced TNF-α and IFN-γ in peripheral blood mononuclear cells were markedly decreased, whereas IL-8 and IL-1-β mRNA levels were unaffected. Because SAHA exhibits antiinflammatory properties in vivo and in vitro, inhibitors of histone deacetylase may stimulate the expression of genes that control the synthesis of cytokines and nitric oxide or hyperacetylate other targets.

MS-WHIM Scores for Amino Acids: A New 3D-Description for Peptide QSAR and QSPR Studies

Several descriptors applied to peptide structure−activity and/or structure−property relationships have been developed in recent years. This report describes new descriptors for the natural amino acids which have been derived from the principal component analysis (PCA) applied on the MS-WHIM 3D-description matrices. MS-WHIM indexes are a collection of 36 statistical indexes aimed at extracting and condensing steric and electrostatic 3D-properties of a molecule. These new descriptors have been developed both on extended side-chain conformation and on rotamer library of natural amino acids. The method appeared to be more potent when describing a single conformation (i.e. extended) than when applied collectively on library conformation families. MS-WHIM scores, however, were shown to efficacely describe and correctly classify the natural amino acid features and to provide sound statistical models either predicting activities of two peptide sets taken as a test or correlating amino acid chemicophysical propert...

MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: A comparative 3D QSAR study in a series of steroids

The recently proposed WHIM (Weighted Holistic Invariant Molecular) approach [Todeschini,R., Lasagni, M. and Marengo, E., J. Chemometrics, 8 (1994) 263] has been applied tomolecular surfaces to derive new 3D theoretical descriptors, called MS-WHIM. To test theirreliability, a 3D QSAR study has been performed on a series of steroids, comparing the MS-WHIM description to both the original WHIM indices and CoMFA fields. The analysis of thestatistical models obtained shows that MS-WHIM descriptors provide meaningful quantitativestructure–activity correlations. Thus, the results obtained agree well with thoseachieved using CoMFA fields. The concise number of indices, the ease of their calculationand their invariance to the coordinate system make MS-WHIM an attractive tool for 3DQSAR studies.

Global 3D-QSAR methods: MS-WHIM and autocorrelation

The recently proposed MS-WHIM indices, a set of theoretical descriptors containing information about size, shape and electrostatic distribution of a molecule, have been further investigated. The main objectives of this work were: (i) to confirm the descriptive power of MS-WHIM in modelling specific biological interactions, (ii) to analyse the dependence of MS-WHIM on the type of atomic charges used for computing electrostatic potential and (iii) to compare the performances of MS-WHIM with those provided by other global 3D molecular descriptors. The spatial autocorrelation of atomic and molecular surface properties were selected for comparison purposes. WHIM-based and autocorrelation-based vectors were calculated for two molecular sets from the literature, namely a series of 18 HIV-1 reverse transcriptase inhibitors and a set of 36 sulphonamide endothelin inhibitors. PLS was adopted to derive statistical predictive models that were validated by means of cross-validation. The reported results confirmed that MS-WHIM indices are able to provide meaningful statistical correlations with biological activity. MS-WHIM descriptors are sensitive to the type of partial atomic charges applied and improved models were obtained using more accurate charges. Moreover for both the datasets, MS-WHIM results, in terms of fitting and predictive power of PLS models, were superior to those from autocorrelation. Finally, the strengths/weaknesses of global 3D-QSAR descriptors over local CoMFA-like methods, as well as the main differences between WHIM-based and autocorrelation-based vectors, are discussed.

SONHICA (SIMPLE OPTIMIZED NON-HIERARCHICAL CLUSTER ANALYSIS) : A NEW TOOL FOR ANALYSIS OF MOLECULAR CONFORMATIONS

We describe a new clustering program, SONHICA (Simple Optimized Non‐HIerarchical Cluster Analysis), developed to analyze large data sets of molecular conformations. Unlike traditional clustering methods, SONHICA does not make use of an overall index, like a distance, to evaluate similarity between objects. Each descriptor variable is compared individually on the basis of a preset threshold value. This assures high control and sensitivity over the input variables. In addition, periodic and nonperiodic descriptors, such as dihedral angles and interatomic distances, can easily be used together. SONHICA generates clusters with the highest possible density and all pairs of objects within a cluster are similar. These features make SONHICA particularly suitable for the analysis of data sets which tend to form globular clusters. This method was applied to the analysis of a modified linear tetrapeptide, ITF1697, under investigation for its anti‐ischemic properties, and a cyclic pentapeptide, BQ123, a potent antagonist of endothelin A. On the basis of the results presented here, SONHICA appears to be an interesting new tool in the field of the clustering methods applied to the analysis of molecular conformations.

Solvation enthalpies as descriptors of structure--in vitro percutaneous permeation relationship of benzoxazinones regioisomers.

The aim of this work was to correlate the in vitro human skin permeability, expressed as the permeability coefficient (Kp), and some physicochemical parameters of a new series of benzoxazinones. The in vitro human skin permeability of 14 substances, including regioisomers with CH3, OH, OCH3, and Cl groups in different positions on the aromatic ring, was determined. The modified Franz diffusion cell method was used. The Kp values were in the range 0.14-8.24 cm/h, showing a strong dependence on the position and type of substituent. Physicochemical descriptors usually referred in literature, such as log P, molecular weight and volume (MV), hydrogen bond donor (Hd) and acceptor activity (Ha), and molecular refractivity were considered, with the addition of solvation enthalpy (delta deltaHsolv). Delta deltaHsolv is defined as the difference between formation enthalpies in water and octanol. The algorithm with the best correlation between Kp and physicochemical descriptors was calculated, taking into account the differences observed among the regioisomers. The algorithm obtained with delta deltaHsolv had a good correlation (r2 = 0.749, F = 16.43, P = 0.0005), comparable with the equation, proposed by Potts and Guy, based on MV, Hd and Ha (r2 = 0.830, F = 16.3, P = 0.0004).

FTree query construction for virtual screening: a statistical analysis.

FTrees (FT) is a known chemoinformatic tool able to condense molecular descriptions into a graph object and to search for actives in large databases using graph similarity. The query graph is classically derived from a known active molecule, or a set of actives, for which a similar compound has to be found. Recently, FT similarity has been extended to fragment space, widening its capabilities. If a user were able to build a knowledge-based FT query from information other than a known active structure, the similarity search could be combined with other, normally separate, fields like de-novo design or pharmacophore searches. With this aim in mind, we performed a comprehensive analysis of several databases in terms of FT description and provide a basic statistical analysis of the FT spaces so far at hand. Vendors’ catalogue collections and MDDR as a source of potential or known “actives”, respectively, have been used. With the results reported herein, a set of ranges, mean values and standard deviations for several query parameters are presented in order to set a reference guide for the users. Applications on how to use this information in FT query building are also provided, using a newly built 3D-pharmacophore from 57 5HT-1F agonists and a published one which was used for virtual screening for tRNA-guanine transglycosylase (TGT) inhibitors.

New conformationally constrained Xxx-Pro bicyclic mimetics

Conformationally constrained peptidomimetics of the Lys-Pro sequence have been obtained using a new polycyclic structure. Bicyclic compounds containing a dioxopiperazine-thiazolidine fused ring have been synthesised starting from N-lysyl-4-ethoxycarbonylthiazolidine-2-carboxylic acid. The carboxyl group in either position 2 or 4 of the thiazolidine ring was reacted with the N-terminal amino group, giving different regioisomers. NMR and computer modelling were used to study the configuration of isomers and the lysine side-chain orientation with respect to the pseudoproline ring.