Nuovi coniugati fra acido azelaico ed azaeterocicli: sintesi e valutazione dell'attività biologica

The well-known antiproliferative properties of the 9-hydroxystearic acid (9-HSA) on human colon cancer cells (HT-29 cell line) have inspired this thesis work in order to obtain new derivatives maintaining the C1-C8 chain of the HSA linked to an heterocyclic moiety at the C-9 carbon atom and to investigate their biological activity. First, thiazoles, thiadiazoles and benzothiazoles, that are compounds of interest in many fields for their biological activities, have been introduced through an amide bond starting from their 2-amino precursors. The products have been obtained by treatment with methyl 9-chloro-9-oxononanoate according to a Schotten-Baumann type reaction. The acylation reaction occurred at the endocyclic nitrogen atom of the heterocycle, as ascertained through NOESY-1D experiment. After, methyl 9-chloro-9-oxononanoate was reacted with indole, N-methylindole, and triptamine giving a serie of new indole derivatives. Finally, the biological activity of some compounds has been tested through assays on HT-29 cancer cells and bacterial and fungal microorganisms; docking calculations have also been performed to evaluate the possible interactions with the active site of histone deacetylase, which are molecular targets of the 9-HSA.

Sintesi di acido glucarico da d-glucosio con catalizzatori a base di oro nanoparticellare

L’utilizzo delle biomasse rappresenta oggi una delle vie più interessanti da percorrere nell’ambito di una chimica industriale maggiormente sostenibile, alternativa alla chimica tradizionale basata sulle risorse fossili. I carboidrati sono i costituenti maggioritari della biomassa e potrebbero rappresentare un’alternativa ideale al petrolio per la produzione dei building-blocks, molecole di partenza per lo sviluppo della filiera produttiva della chimica. Fra i building-blocks ottenibili dagli zuccheri vi è l’acido glucarico. I suoi usi sono molteplici ma suscita grande interesse soprattutto per la possibilità di essere utilizzato nella sintesi di diverse tipologie di polimeri. Attualmente la maggior parte dei metodi di sintesi di questa molecola prevedono l’utilizzo di ossidanti tossici o dannosi per l’ambiente come l’acido nitrico. Lo scopo di questo lavoro di tesi è stato lo studio di catalizzatori eterogenei per la sintesi di acido glucarico da D-glucosio utilizzando ossigeno puro come ossidante. Sono stati sintetizzati sistemi monometallici a base di oro e sistemi multimetallici contenenti oro ed altri metalli in lega. Tutti i catalizzatori sono stati preparati depositando i metalli sotto forma di nanoparticelle su carbone attivo. Lo studio dei catalizzatori è stato focalizzato sull’individuazione dei metalli e delle condizioni di reazione ottimali che permettano di aumentare la selettività in acido glucarico. Gli studi condotti hanno portato alla conclusione che è possibile ottenere acido glucarico a partire da D-glucosio con rese fino al 35% utilizzando catalizzatori a base di oro in presenza di ossigeno. Attualmente l’acido glucarico viene prodotto solo su piccola scala ma ulteriori sviluppi in questa direzione potrebbero aprire la strada allo sviluppo di un nuovo processo industriale per la sintesi di acido glucarico sostenibile sia da un punto di vista economico che ambientale.

Formulazioni di blend a base di acido polilattico e biochar per la termoformatura di imballaggi alimentari

In questo studio verranno descritte formulazioni di materiali innovativi, completamente biodegradabili e compostabili, a base di acido polilattico e biochar. Queste formulazioni sono state ideate per applicazioni nel settore degli imballaggi alimentari, in particolare da utilizzare nella produzione di vaschette ortofrutticole nere termoformate come alternativa alle tradizionali vaschette a base di PP e PET. È stato scelto di testare il biochar poiché rappresenta un composto ecocompatibile esattamente come la matrice polimerica utilizzata, alternativo al carbon black di origine fossile utilizzato in queste applicazioni come colorante. Varie formulazioni di PLA contenenti biochar e plasticizzanti sono state preparate con un miscelatore Brabender e trasformate in fogli tramite una pressa a doppio piatto riscaldante. Da questi film sono stati poi realizzati provini per prove di trazione e strappo. Sono state sviluppate inoltre reazioni di funzionalizzazione sul biochar allo scopo di migliorare la sua la compatibilità con la matrice polimerica rendendo la miscela più omogenea.

Studio della trasformazione di 1,2-propandiolo ad acido propionico

Il presente lavoro ha riguardato lo studio della trasformazione one-pot in fase gas di 1,2-propandiolo ad acido propionico, impiegando il pirofosfato di vanadile (VPP), (VO)2P2O7, e due differenti sistemi a base di bronzi di tungsteno con struttura esagonale (HTB), gli ossidi misti W1V0,3 e W1Mo0,5V0,1. Il processo richiede un catalizzatore con due differenti funzionalità: una acida, principalmente di tipo Brønsted, fornita nel VPP dai gruppi P-OH presenti sulla sua superficie, e negli HTB dai gruppi W-OH sulla loro superficie e dagli ioni H+ nei canali esagonali dell’ossido; e una ossidante, fornita nel VPP dal V, e negli HTB da V e Mo incorporati nella struttura esagonale. I risultati delle prove di reattività hanno consentito di dedurre gli aspetti principali dello schema della reazione one-pot di disidratazione-ossidazione dell’1,2-propandiolo ad acido propionico. I catalizzatori provati non possiedono la combinazione ottimale di proprietà acide e redox necessarie per ottenere elevate rese in acido propionico. Le scarse proprietà ossidanti portano a un accumulo di propionaldeide, che reagisce con l’1,2-propandiolo a dare diossolani, e inoltre dà luogo alla formazione di altri sottoprodotti. È perciò necessario incrementare le proprietà ossidanti del catalizzatore, in modo da accelerare la trasformazione della propionaldeide ad acido propionico, ed evitare quindi che le proprietà acide del catalizzatore, necessarie per compiere il primo stadio di disidratazione di 1,2-propandiolo, siano causa di reazioni parassite di trasformazione dell’aldeide stessa.

Cross-reactions vs co-sensitization evaluated by in silico motifs and in vitro IgE microarray testing

Using an in silico allergen clustering method, we have recently shown that allergen extracts are highly cross-reactive. Here we used serological data from a multi-array IgE test based on recombinant or highly purified natural allergens to evaluate whether co-reactions are true cross-reactions or co-sensitizations by allergens with the same motifs.

Besnoitia besnoiti protein disulfide isomerase (BbPDI): molecular characterization, expression and in silico modelling

Besnoitia besnoiti is an apicomplexan parasite responsible for bovine besnoitiosis, a disease with a high prevalence in tropical and subtropical regions and re-emerging in Europe. Despite the great economical losses associated with besnoitiosis, this disease has been underestimated and poorly studied, and neither an effective therapy nor an efficacious vaccine is available. Protein disulfide isomerase (PDI) is an essential enzyme for the acquisition of the correct three-dimensional structure of proteins. Current evidence suggests that in Neosporacaninum and Toxoplasmagondii, which are closely related to B. besnoiti, PDI play an important role in host cell invasion, is a relevant target for the host immune response, and represents a promising drug target and/or vaccine candidate. In this work, we present the nucleotide sequence of the B. besnoiti PDI gene. BbPDI belongs to the thioredoxin-like superfamily (cluster 00388) and is included in the PDI_a family (cluster defined cd02961) and the PDI_a_PDI_a'_c subfamily (cd02995). A 3D theoretical model was built by comparative homology using Swiss-Model server, using as a template the crystallographic deduced model of Tapasin-ERp57 (PDB code 3F8U chain C). Analysis of the phylogenetic tree for PDI within the phylum apicomplexa reinforces the close relationship among B. besnoiti, N. caninum and T. gondii. When subjected to a PDI-assay based on the polymerisation of reduced insulin, recombinant BbPDI expressed in E. coli exhibited enzymatic activity, which was inhibited by bacitracin. Antiserum directed against recombinant BbPDI reacted with PDI in Western blots and by immunofluorescence with B. besnoiti tachyzoites and bradyzoites.

Engineering Tocopherol Selectivity in alpha-TTP: A Combined In Vitro/In Silico Study

"We present a combined in vitro/in silico study to determine the molecular origin of the selectivity of a-tocopherol transfer" "protein (a-TTP) towards a-tocopherol. Molecular dynamics simulations combined to free energy perturbation calculations predict a binding free energy for a-tocopherol to a-TTP 8.26+2.13 kcal mol{1 lower than that of c-tocopherol. Our calculations show that c-tocopherol binds to a-TTP in a significantly distorted geometry as compared to that of the natural ligand. Variations in the hydration of the binding pocket and in the protein structure are found as well. We propose a mutation, A156L, which significantly modifies the selectivity properties of a-TTP towards the two tocopherols. In particular, our simulations predict that A156L binds preferentially to c-tocopherol, with striking structural similarities to the wild-type- a-tocopherol complex. The affinity properties are confirmed by differential scanning fluorimetry as well as in vitro competitive binding assays. Our data indicate that residue A156 is at a critical position for determination of the selectivity of a-TTP. The engineering of TTP mutants with modulating binding properties can have potential impact at industrial level for easier purification of single tocopherols from vitamin E mixtures coming from natural oils or synthetic processes. Moreover," "the identification of a c-tocopherol selective TTP offers the possibility to challenge the hypotheses for the evolutionary development of a mechanism for a-tocopherol selection in omnivorous animals."

Identification and in silico analyses of novel TGFBR1 and TGFBR2 mutations in Marfan syndrome-related disorders

Very recently, heterozygous mutations in the genes encoding transforming growth factor beta receptors I (TGFBR1) and II (TGFBR2) have been reported in Loeys-Dietz aortic aneurysm syndrome (LDS). In addition, dominant TGFBR2 mutations have been identified in Marfan syndrome type 2 (MFS2) and familial thoracic aortic aneurysms and dissections (TAAD). In the past, mutations of these genes were associated with atherosclerosis and several human cancers. Here, we report a total of nine novel and one known heterozygous sequence variants in the TGFBR1 and TGFBR2 genes in nine of 70 unrelated individuals with MFS-like phenotypes who previously tested negative for mutations in the gene encoding the extracellular matrix protein fibrillin-1 (FBN1). To assess the pathogenic impact of these sequence variants, in silico analyses were performed by the PolyPhen, SIFT, and Fold-X algorithms and by means of a 3D homology model of the TGFBR2 kinase domain. Our results showed that in all but one of the patients the pathogenic effect of at least one sequence variant is highly probable (c.722C > T, c.799A > C, and c.1460G > A in TGFBR1 and c.773T > G, c.1106G > T, c.1159G > A, c.1181G > A, and c.1561T > C in TGFBR2). These deleterious alleles occurred de novo or segregated with the disease in the families, indicating a causative association between the sequence variants and clinical phenotypes. Since TGFBR2 mutations found in patients with MFS-related disorders cannot be distinguished from heterozygous TGFBR2 mutations reported in tumor samples, we emphasize the importance of segregation analysis in affected families. In order to be able to find the mutation that is indeed responsible for a MFS-related phenotype, we also propose that genetic testing for sequence alterations in TGFBR1 and TGFBR2 should be complemented by mutation screening of the FBN1 gene.

Pseudodominant Inheritance of Goitrous Congenital Hypothyroidism Caused by TPO Mutations: Molecular and in Silico Studies

Context and Objective: Most cases of goitrous congenital hypothyroidism (CH) from thyroid dyshormonogenesis 1) follow a recessive mode of inheritance and 2) are due to mutations in the thyroid peroxidase gene (TPO). We report the genetic mechanism underlying the apparently dominant inheritance of goitrous CH in a nonconsanguineous family of French Canadian origin. Design, Setting, and Participants: Two brothers identified by newborn TSH screening had severe hypothyroidism and a goiter with increased (99m)Tc uptake. The mother was euthyroid, but the father and two paternal uncles had also been diagnosed with goitrous CH. After having excluded PAX8 gene mutations, we hypothesized that the underlying defect could be TPO mutations. Results: Both compound heterozygous siblings had inherited a mutant TPO allele carried by their mother (c.1496delC; p.Pro499Argfs2X), and from their father, one brother had inherited a missense mutation (c.1978C-->G; p.Gln660Glu) and the other an insertion (c.1955insT; p.Phe653Valfs15X). The thyroid gland of one uncle who is a compound heterozygote for TPO mutations (p.Phe653Valfs15X/p.Gln660Glu) was removed because of concurrent multiple endocrine neoplasia type 2A. Immunohistochemistry revealed normal TPO staining, implying that Gln660Glu TPO is expressed properly. Modeling of this mutant in silico suggests that its three-dimensional structure is conserved, whereas the electrostatic binding energy between the Gln660Glu TPO and its heme group becomes repulsive. Conclusion: We report a pedigree presenting with pseudodominant goitrous CH due to segregation of three different TPO mutations. Although goitrous CH generally follows a recessive mode of inheritance, the high frequency of TPO mutations carriers may lead to pseudodominant inheritance.

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

In silico target fishing for rationalized ligand discovery exemplified on constituents of Ruta graveolens

The identification of targets whose interaction is likely to result in the successful treatment of a disease is of growing interest for natural product scientists. In the current study we performed an exemplary application of a virtual parallel screening approach to identify potential targets for 16 secondary metabolites isolated and identified from the aerial parts of the medicinal plant RUTA GRAVEOLENS L. Low energy conformers of the isolated constituents were simultaneously screened against a set of 2208 pharmacophore models generated in-house for the IN SILICO prediction of putative biological targets, i. e., target fishing. Based on the predicted ligand-target interactions, we focused on three biological targets, namely acetylcholinesterase (AChE), the human rhinovirus (HRV) coat protein and the cannabinoid receptor type-2 (CB (2)). For a critical evaluation of the applied parallel screening approach, virtual hits and non-hits were assayed on the respective targets. For AChE the highest scoring virtual hit, arborinine, showed the best inhibitory IN VITRO activity on AChE (IC (50) 34.7 muM). Determination of the anti-HRV-2 effect revealed 6,7,8-trimethoxycoumarin and arborinine to be the most active antiviral constituents with IC (50) values of 11.98 muM and 3.19 muM, respectively. Of these, arborinine was predicted virtually. Of all the molecules subjected to parallel screening, one virtual CB (2) ligand was obtained, i. e., rutamarin. Interestingly, in experimental studies only this compound showed a selective activity to the CB (2) receptor ( Ki of 7.4 muM) by using a radioligand displacement assay. The applied parallel screening paradigm with constituents of R. GRAVEOLENS on three different proteins has shown promise as an IN SILICO tool for rational target fishing and pharmacological profiling of extracts and single chemical entities in natural product research.

Modeling of human P450 oxidoreductase structure by in silico mutagenesis and MD simulation

P450 oxidoreductase (POR) is the obligate electron donor for microsomal cytochrome P450s and mutations in POR cause several metabolic disorders. We have modeled the structure of human P450 oxidoreductase by in silico amino acid replacements in the rat POR crystal structure. The rat POR has 94% homology with human POR and 38 amino acids were replaced to make its sequence identical to human POR. Several rounds of molecular dynamic simulations refined the model and removed structural clashes from side chain alterations of replaced amino acids. This approach has the advantage of keeping the cofactor contacts and structural features of the core enzyme intact which could not be achieved by homology based approaches. The final model from our approach was of high quality and compared well with experimentally determined structures of other PORs. This model will be used for analyzing the structural implications of mutations and polymorphisms in human POR.

Predictive oncology: a review of multidisciplinary, multiscale in silico modeling linking phenotype, morphology and growth.

Empirical evidence and theoretical studies suggest that the phenotype, i.e., cellular- and molecular-scale dynamics, including proliferation rate and adhesiveness due to microenvironmental factors and gene expression that govern tumor growth and invasiveness, also determine gross tumor-scale morphology. It has been difficult to quantify the relative effect of these links on disease progression and prognosis using conventional clinical and experimental methods and observables. As a result, successful individualized treatment of highly malignant and invasive cancers, such as glioblastoma, via surgical resection and chemotherapy cannot be offered and outcomes are generally poor. What is needed is a deterministic, quantifiable method to enable understanding of the connections between phenotype and tumor morphology. Here, we critically assess advantages and disadvantages of recent computational modeling efforts (e.g., continuum, discrete, and cellular automata models) that have pursued this understanding. Based on this assessment, we review a multiscale, i.e., from the molecular to the gross tumor scale, mathematical and computational "first-principle" approach based on mass conservation and other physical laws, such as employed in reaction-diffusion systems. Model variables describe known characteristics of tumor behavior, and parameters and functional relationships across scales are informed from in vitro, in vivo and ex vivo biology. We review the feasibility of this methodology that, once coupled to tumor imaging and tumor biopsy or cell culture data, should enable prediction of tumor growth and therapy outcome through quantification of the relation between the underlying dynamics and morphological characteristics. In particular, morphologic stability analysis of this mathematical model reveals that tumor cell patterning at the tumor-host interface is regulated by cell proliferation, adhesion and other phenotypic characteristics: histopathology information of tumor boundary can be inputted to the mathematical model and used as a phenotype-diagnostic tool to predict collective and individual tumor cell invasion of surrounding tissue. This approach further provides a means to deterministically test effects of novel and hypothetical therapy strategies on tumor behavior.

Properties of plant food allergens: In silico studies

International Comparative Medicine Symposium. Allergology. Revisión de métodos computacionales para determinar propiedades de alergenos alimentarios de plantas