Modeling from Theory and Modeling from Data: Complementary or Alternative Approaches? The Case of Ionic Liquids.

In the field of ionic liquids (ILs), theory-driven modeling approaches aimed at the best fit for all available data by using a unique, and often nonlinear, model have been widely adopted to develop quantitative structure-property relationship (QSPR) models. In this context, we propose chemoinformatic and chemometric data-driven procedures that lead to QSPR soft models with local validity that are able to predict relevant physicochemical properties of ILs, such as viscosity, density, decomposition temperature, and conductivity. These models, which use readily available and easily interpretable VolSurf+ descriptors, represent an unexploited opportunity for experimentalists to model and predict the physicochemical properties of ILs in industrial R&D design.

A QSPR approach to the ecotoxicity of ionic liquids (Vibrio fischeri) using VolSurf principal properties.

Recently derived in silico structural descriptors for both IL cations and anions allowed the development of a QSPR model correlating ionic liquid structures to Vibrio fischeri toxicity using the partial least squares (PLS) approach. Interpretation of the PLS model confirmed the effect of IL cationic structural features such as the influence of cation side chain length, presence of heteroatoms, and non-aromaticity of the heterocyclic scaffold on toxicity. The PLS model also provided a quantitative evaluation of anion effects, previously not evidenced due to the structural similarity of the anions considered. A simple equation in which three descriptors (two for the cations and one for the anions) allow the prediction of Vibrio fischeri toxicity for over 8000 ILs is reported.

New potent antibacterials against Gram-positive multiresistant pathogens: effects of side chain modification and chirality in linezolid-like 1,2,4-oxadiazoles.

The effects of side chain modification and chirality in linezolid-like 1,2,4-oxadiazoles have been studied to design new potent antibacterials against Gram-positive multidrug-resistant pathogens. The adopted strategy involved a molecular modelling approach, the synthesis and biological evaluation of new designed compounds, enantiomers separation and absolute configuration assignment. Experimental determination of the antibacterial activity of the designed (S)-1-((3-(4-(3-methyl-1,2,4-oxadiazol-5-yl)phenyl)-oxazolidin-2-one-5-yl)methyl)-3-methylthiourea and (S)-1-((3-(3-fluoro-4-(3-methyl-1,2,4-oxadiazol-5-yl)phenyl)-oxazolidin-2-one-5-yl)methyl)-3-methylthiourea against multidrug resistant linezolid bacterial strains was higher than that of linezolid.

Modeling, design and synthesis of new heteroaryl ethylenes active against the MCF-7 breast cancer cell-line.

A dataset of 50 compounds was used to generate a QSAR model and to design 9 new heteroaryl ethylenes. These compounds were synthesized, tested in vitro and a significant agreement with in silico predictions observed. Studies using Laser Scanning Confocal Microscopy pointed out that the compounds may act by different mechanisms.

New linezolid-like 1,2,4-oxadiazoles active against Gram-positive multiresistant pathogens.

The synthesis and the in vitro antibacterial activity of novel linezolid-like oxadiazoles are reported. Replacement of the linezolid morpholine C-ring with 1,2,4-oxadiazole results in an antibacterial activity against Staphylococcus aureus both methicillin-susceptible and methicillin-resistant comparable or even superior to that of linezolid. While acetamidomethyl or thioacetoamidomethyl moieties in the C(5) side-chain are required, fluorination of the phenyl B ring exhibits a slight effect on an antibacterial activity but its presence seems to reduce the compounds cytotoxicity. Molecular modeling performed using two different approaches - FLAP and Amber software - shows that in the binding pose of the newly synthesized compounds as compared with the crystallographic pose of linezolid, the 1,2,4-oxadiazole moiety seems to perfectly mimic the function of the morpholinic ring, since the H-bond interaction with U2585 is retained.

Design, synthesis and in vitro antitumour activity of new heteroaryl ethylenes.

Almond and VolSurf + modelling procedures allowed the structural design of new di- and mono-heteroaryl-ethylenes. The structural modifications suggested by the molecular modelling were verified by the synthesis of the designed molecules and by the evaluation of their in vitro activities against two lung tumour cell lines, A549 and H226. 2-{(E)-2-[5'-(Dibutylamino)-2,2'-bithien-5-yl]vinyl}-1-methylquinolinium iodide exhibited in vitro antiproliferative activity two orders of magnitude higher than that of the most active compound previously synthesized in our laboratory.

Synthesis and NLO properties of new trans 2-(thiophen-2-yl)vinyl heteroaromatic iodides.

The synthesis and characterisation of new trans 2-(thiophen-2-yl)vinyl pyridinium, imidazolium and quinoilinium iodides is reported together with their solvatochromic shifts and EFISH characterization. 2-{(E)-2-[5'-(dibutylamino)-2,2'-bithien-5-yl]vinyl}-1-methyl pyridinium and quinolinium iodides display high µ.ß(vec) values up to 1200 × 10(-48) esu. The promising non-linear optical (NLO) properties of this new family of chromophores, which can be further improved by the design of highly efficient systems exploiting the donor and acceptor properties of both heteroaromatic rings and substituents, make them suitable candidates for second harmonic generation imaging with interesting biological applications.

OPLS-DA as a suitable method for selecting a set of gene transcripts discriminating RAS- and PTPN11-mutated cells in acute lymphoblastic leukaemia.

OPLS discriminant analysis (OPLS-DA) was successfully applied for the selection of a limited number of gene transcripts necessary to discriminate PTPN11 and RAS mutated cells in acute lymphoblastic leukaemia (ALL) patients. The original set of 273 variables with VIP (1) values higher than 2.0 in the OPLS-DA model could be further reduced to 200 by elimination of less informative variables in the PCA class models adopted for SIMCA classification. The above 200 transcripts not only achieve a satisfactory discrimination accuracy between PTPN11 and RAS mutated cells but also indicate clearly that wild type samples belong to none of the mutated class models. In this list it was possible to identify candidate genes that could be involved in the molecular mechanisms discriminating PTPN11 and RAS mutations in ALL. Among them CBFA2T2, a member of the "ETO" family, is known because of its homology and association with the product of RUNX1-CBFA2T1 gene fusion generated by t(8;21) translocation, one frequent cause of acute myeloid leukemia.

Design, synthesis and biological evaluation of trans 2-(thiophen-2-yl)vinyl heteroaromatic iodides.

A modeling approach based on physico-chemical and pharmacokinetic properties, called Volsurf+, was used to design new trans 2-(thiophen-2-yl)vinyl heteroaromatic iodides with antiproliferative activity. The synthesis and in vitro antitumor tests on two cell lines (MCF-7 and LNCap) confirmed Volsurf predicted activity values. An Almond model, derived to have an overall structural insight on the above compounds, supported the validity of Volsurf and provided guidelines for the synthesis of new compounds.

N-benzoxazol-2-yl-N'-1-(isoquinolin-3-yl-ethylidene)-hydrazine, a novel compound with antitumor activity, induces radicals and dissipation of mitochondrial membrane potential.

The novel compound N-benzoxazol-2-yl-N'-1-(isoquinolin-3-yl-ethylidene)-hydrazine (EPH136) has been shown to exhibit antitumor activity in vitro and in vivo. A COMPARE analysis showed that the patterns of cellular effects of EPH136 are not related to any of 175 standard antitumor agents with a known mechanism of action. In order to help identify the mechanism of action we employed a bioinformatics approach called partial least squares modelling in latent variables in which the expression levels of approximately 8,000 genes in each of 56 untreated NCI panel cell lines were correlated with the respective IC(50) values of each cell line following treatment with EPH136. The 60 genes found to be most important for the antiproliferative effect of EPH136 are involved in nucleoside, nucleotide, nucleic acid binding and metabolism, developmental processes, protein modification and metabolism. In addition, using a DNA microarray we measured the expression of approximately 5,000 known genes following treatment of HT-29 colon carcinoma cells with a two-fold IC(50) concentration of EPH136. The genes that were up-regulated more than two-fold compared to untreated controls belong to the same classes as found by the bioinformatic approach. Many of these proteins are regulated by oxidation/reduction and so we concluded that formation of radicals may be involved in the mechanism of action. We show here that EPH136 leads to generation of oxygen radicals, swelling of mitochondria and dissipation of the mitochondrial membrane potential. The antiproliferative activity of EPH136 was prevented by the radical scavenger N-acetylcysteine. Cells with elevated glutathione exhibited resistance to EPH136. In summary, the mechanism of the novel experimental anticancer drug EPH136 is generation of radicals and dissipation of the mitochondrial membrane potential.

Design and synthesis of trans 2-(furan-2-yl)vinyl heteroaromatic iodides with antitumour activity.

A new molecular modelling approach based on physico-chemical and pharmacokinetic properties, called Volsurf plus, was used to design new heterocyclic compounds with antiproliferative activity. The synthesis and in vitro antitumour tests on a breast carcinoma cell line (MCF7) confirmed VOLSURF predicted activity values.

Identification of genes involved in the sensitivity to antitumour drug 17-allylamino,17-demethoxygeldanamycin (17AAG).

In the present study we analysed the gene expression database provided by the National Cancer Institute in an attempt to correlate activity profiles of geldanamycin, 17AAG and 11 other analogues in 60 human tumor cell lines with their gene expression profiles determined by the cDNA microarray technique. On the basis of the activity profiles two classes of geldanamycin analogues could be distinguished, having geldanamycin and 17AAG, respectively, as prototype compounds (denominated as gelda-like and 17AAG-like classes). Application of the "soft" statistical methodology of PLS (partial least squares modelling in latent variables or projections to latent structures) allowed us to evaluate the influence of each gene expression target in determining the therapeutical responses. The transcript encoding the translocating chain-associated membrane protein (TRAM) showed a significant statistical correlation with activity profiles of 17AAG. In order to validate the role of TRAM in determining sensitivity to 17AAG we induced a selective knocking-down of this transcript by the RNA interference methodology in H226 non-small cell lung carcinoma cell line. The efficiency of double-stranded RNA oligonucleotides (short-interfering RNAs, siRNAs) was determined by measuring TRAM mRNA levels by quantitative real-time RT-PCR at different times (24-72 hours) after siRNA lipotransfection. A significant increase in chemosensitivity to 17AAG was observed in siRNA-silenced cells. Although a number of factors may affect tumour sensitivity to 17AAG the present methodology allowed us to dissect out a single parameter which may be partly responsible for its activity.

Design, synthesis, and biological evaluation of 4-alkyliden-beta lactams: new products with promising antibiotic activity against resistant bacteria.

The design, synthesis, and antibacterial activity of 4-alkyliden-azetidin-2-ones as new antimicrobial agents against multidrug-resistant pathogens is reported. 4-Alkyliden-azetidin-2-ones were easily obtained using an original protocol starting from 4-acetoxy-azetidinones and diazoesters. Parent compounds were further elaborated to obtain a small library of 4-alkylidene derivatives. A molecular modeling approach using GRID descriptors based on the concept of VRS identified attractive drug candidates and contributed to the rationalization of functional group effects in QSARs. The in vitro antibacterial activity of the new agents was evaluated against 43 recent clinical isolates of antibiotic-susceptible and -resistant Gram-positive and Gram-negative pathogens by determining their minimum inhibitory concentrations (MICs). The most active compound showed MIC values ranging from 0.25 to 32 mg/L against some of the bacterial species tested. Interestingly, some compounds demonstrated similar activity against methicillin-susceptible and -resistant strains of Staphylococcus aureus suggesting possible alternative mechanisms of action of these agents, supported by citotoxicity and preliminary scanning electron microscopy studies.

Genome-based identification of diagnostic molecular markers for human lung carcinomas by PLS-DA.

Partial least squares discriminant analysis (PLS-DA) provides a sound statistical basis for the selection of a limited number of gene transcripts most effective in discriminating different lung tumoral histotypes. The potentialities of the PLS-DA approach are pointed out by its ability to identify genes which, according to current knowledge, are considered molecular markers for colon cancer diagnostics and classification. Indeed application of PLS-DA to in vivo data allowed identification of a set of genes able to discriminate primary lung tumours from colon metastases.

Structure-based rationalization of antitumor drugs mechanism of action by a MIF approach.

Structural patterns for antitumor drugs, evidenced by means of a molecular interaction field (MIF) approach using grid independent descriptors (GRIND), resembled closely those of a previous independent pharmacological classification based on their antitumor mechanism of action. For topoisomerase II inhibitors, antimitotic agents and DNA antimetabolites, systematic structural patterns were evidenced by MIF and the structural features of "outliers" in these classes corresponded to peculiar pharmacological mechanisms of action supported by literature evidences. Alkylating agents and DNA/RNA antimetabolites, interacting with a large variety of targets by different molecular mechanisms, did not exhibit clustering in the structure-based MIF approach. Moreover MIFS were able to point out similarities between drugs which, in spite of apparent dramatic differences in chemical structure, exhibit the same pharmacological behaviour.

Design, synthesis and in vitro antitumor activity of new trans 2-[2-(heteroaryl)vinyl]-1,3-dimethylimidazolium iodides.

The design, the synthesis, and the in vitro antitumor activities of trans 2-[2-(heteroaryl)vinyl]-1,3-dimethylimidazolium iodides versus MCF7 (human mammary carcinoma) and LNCap (prostate carcinoma) cell lines are reported. The design indicates trans 2-[2-[5-(2-chlorophenyl)furan-2-yl]vinyl]-1, 3-dimethylimidazolium iodide 5 and trans 2-[2-[5-(4-bromophenyl)furan-2-yl]vinyl]-1, 3-dimethylimidazolium iodide 6 as highly active compounds in the series. The synthesis of the above new derivatives and in vitro antitumor tests, confirm their significant antiproliferative and cytotoxic activities.

A bioinformatic approach to the identification of candidate genes for the development of new cancer diagnostics.

A multivariate analysis of the National Cancer Institute gene expression database is reported here. The soft independent modelling of a class analogy approach achieved cell line classification according to histological origin. With the PCA method, based on the expression of 9605 genes and ESTs, classification of colon, leukaemia, renal, melanoma and CNS cells could be performed, but not of lung, breast and ovarian cells. Another multivariate procedure, called partial least squares discriminant analysis (PLS-DA), provides bioinformatic clues for the selection of a limited number of gene transcripts most effective in discriminating different tumoral histotypes. Among them it is possible to identify candidates in the development of new diagnostic tests for cancer detection and unknown genes deserving high priority in further studies. In particular, melan-A, acid phosphatase 5, dopachrome tautomerase, S100-beta and acid ceramidase were found to be among the most important genes for melanoma. The potential of the present bioinformatic approach is exemplified by its ability to identify differentiation and diagnostic markers already in use in clinical settings, such as protein S-100, a prognostic parameter in patients with metastatic melanoma and a screening marker for melanoma metastasis.

In vitro antitumor activities of 2,6-di-[2-(heteroaryl)vinyl]pyridines and pyridiniums.

The in vitro antitumor activities of 2,6-di-[2-(heteroaryl)vinyl]pyridines versus the standard National Cancer Institute 60 cell lines panel and of 2,6-di-[2-(heteroaryl)vinyl] pyridinium cations versus MCF7 (human mammary carcinoma) and LNCap (prostate carcinoma) cell lines are reported. Antiproliferative effects in both series are particularly evident for MCF7 mammary adenocarcinoma cells. Multivariate analysis of DNA microarray data for responsive tumor cell lines suggest a mechanistic pathway involving polyamine biosynthesis and prolactin signal transduction.

Acid catalyzed transesterification as a route to poly(3-hydroxybutyrate-co-epsilon-caprolactone) copolymers from their homopolymers.

Copolymers of (R)-3-hydroxybutyric acid (HB) and epsilon-caprolactone (CL) with a composition ranging from 28 to 81 mol % of HB were synthesized by transesterification of the corresponding homopolymers in solution in the presence of 4-toluenesulfonic acid. The copolyesters were characterized with regard to their molecular weights, thermal properties, molar compositions, and average block length of repeating units by gel permeation chromatography (GPC), differential scanning calorimetry, (1)H NMR, and (13)C NMR, respectively. Random and microblock copolymers could be obtained depending on experimental conditions, with weight-average molecular weights of up to 20,000. The glass transition temperature decreased from 2 to -42 degrees C as the CL content was increased from 0 to 72 mol %. The melting temperature (T(m)) of the PCL phase decreased from 70 to 46 degrees C as the HB content changed from 0 to 47 mol %, while the T(m) of the PHB phase decreased from 177 degrees C to 163 degrees C as the CL content changed from 0 to 72 mol %. Matrix-assisted laser desorption ionization time-of-flight mass spectra of GPC fractionated samples allowed us to ascertain that copolymers rich in HB units have mostly hydroxyl and carboxyl end groups, while copolymers rich in CL units have mostly tosyl and carboxyl end groups.