Crystalline structure of mangiferin, a C-glycosyl-substituted 9H-xanthen-9-one isolated from the stem bark of Mangifera indica

The crystalline structure of mangiferin (= 2-beta-D-glucopyranosyl-1,3,6,7-tetrahydroxy-9H-xanthen-9-one; 1), a biologically active xanthenone C-glycoside, isolated from the stem bark of Mangifera indica (Anacardiaceae), was unambiguously determined by single-crystal X-ray diffraction (XRD). The crystal structure is summarized as follows: triclinic, P1, a = 7.6575(5), b = 11.2094(8), c = 11.8749(8) angstrom, alpha = 79.967(5), beta = 87.988(4), gamma = 72.164(4)degrees, V = 955.3(1) angstrom(3), and Z = 2. The structure also shows two molecules in the asymmetric unit cell and five crystallization H2O molecules. The packing is stabilized by several intermolecular H-bonds involving either the two symmetry-independent mangiferin molecules 1a and 1b, or the H2O ones.

Antioxidant Activity and Total Phenols from the Methanolic Extract of Miconia albicans (Sw.) Triana Leaves

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Rhamnolipids and PHAs: Recent reports on Pseudomonas-derived molecules of increasing industrial interest

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Natural products from Brazilian biodiversity as a source of new models for medicinal chemistry

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Papel da hidrofobicidade na evolução de proteínas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Self-Organizing Maps of Molecular Descriptors for Sesquiterpene Lactones and Their Application to the Chemotaxonomy of the Asteraceae Family

The Asteraceae, one of the largest families among angiosperms, is chemically characterised by the production of sesquiterpene lactones (SLs). A total of 1,111 SLs, which were extracted from 658 species, 161 genera, 63 subtribes and 15 tribes of Asteraceae, were represented and registered in two dimensions in the SISTEMATX, an in-house software system, and were associated with their botanical sources. The respective 11 block of descriptors: Constitutional, Functional groups, BCUT, Atom-centred, 2D autocorrelations, Topological, Geometrical, RDF, 3D-MoRSE, GETAWAY and WHIM were used as input data to separate the botanical occurrences through self-organising maps. Maps that were generated with each descriptor divided the Asteraceae tribes, with total index values between 66.7% and 83.6%. The analysis of the results shows evident similarities among the Heliantheae, Helenieae and Eupatorieae tribes as well as between the Anthemideae and Inuleae tribes. Those observations are in agreement with systematic classifications that were proposed by Bremer, which use mainly morphological and molecular data, therefore chemical markers partially corroborate with these classifications. The results demonstrate that the atom-centred and RDF descriptors can be used as a tool for taxonomic classification in low hierarchical levels, such as tribes. Descriptors obtained through fragments or by the two-dimensional representation of the SL structures were sufficient to obtain significant results, and better results were not achieved by using descriptors derived from three-dimensional representations of SLs. Such models based on physico-chemical properties can project new design SLs, similar structures from literature or even unreported structures in two-dimensional chemical space. Therefore, the generated SOMs can predict the most probable tribe where a biologically active molecule can be found according Bremer classification.

Venomics Profiling of Thamnodynastes strigatus Unveils Matrix Metalloproteinases and Other Novel Proteins Recruited to the Toxin Arsenal of Rear-Fanged Snakes

Rear-fanged and aglyphous snakes are usually considered not dangerous to humans because of their limited capacity of injecting venom. Therefore, only a few studies have been dedicated to characterizing the venom of the largest parcel of snake fauna. Here, we investigated the venom proteome of the rear-fanged snake Thamnodynastes strigatus, in combination with a transcriptomic evaluation of the venom gland. About 60% of all transcripts code for putative venom components. A striking finding is that the most abundant type of transcript (similar to 47%) and also the major protein type in the venom correspond to a new kind of matrix metalloproteinase (MMP) that is unrelated to the classical snake venom metalloproteinases found in all snake families. These enzymes were recently suggested as possible venom components, and we show here that they are proteolytically active and probably recruited to venom from a MMP-9 ancestor. Other unusual proteins were suggested to be venom components: a protein related to lactadherin and an EGF repeat-containing transcript. Despite these unusual molecules, seven toxin classes commonly found in typical venomous snakes are also present in the venom. These results support the evidence that the arsenals of these snakes are very diverse and harbor new types of biologically important molecules.

Biomimetic Materials for Biomedical Applications

Objects with complex shape and functions have always attracted attention and interest. The morphological diversity and complexity of naturally occurring forms and patterns have been a motivation for humans to copy and adopt ideas from Nature to achieve functional, aesthetic and social value. Biomimetics is addressed to the design and development of new synthetic materials using strategies adopted by living organisms to produce biological materials. In particular, biomineralized tissues are often sophisticate composite materials, in which the components and the interfaces between them have been defined and optimized, and that present unusual and optimal chemical-physical, morphological and mechanical properties. Moreover, biominerals are generally produced by easily traceable raw materials, in aqueous media and at room pressure and temperature, that is through cheap process and materials. Thus, it is not surprising that the idea to mimic those strategies proper of Nature has been employed in several areas of applied sciences, such as for the preparation of liquid crystals, ceramic thin films computer switches and many other advanced materials. On this basis, this PhD thesis is focused on the investigation of the interaction of biologically active ions and molecules with calcium phosphates with the aim to develop new materials for the substitution and repair of skeletal tissue, according to the following lines: I. Modified calcium phosphates. A relevant part of this PhD thesis has been addressed to study the interaction of Strontium with calcium phosphates. It was demonstrated that strontium ion can substitute for calcium into hydroxyapatite, causing appreciable structural and morphological modifications. The detailed structural analysis carried out on the nanocrystals at different strontium content provided new insight into its interaction with the structure of hydroxyapatite. At variance with the behaviour of Sr towards HA, it was found that this ion inhibits the synthesis of octacalcium phosphate. However, it can substitute for calcium in this structure up to 15 atom %, in agreement with the increase of the cell parameters observed on increasing ion concentration. A similar behaviour was found for Magnesium ion, whereas Manganese inhibits the synthesis of octacalcium phosphate and it promotes the precipitation of dicalcium phosphate dehydrate. It was also found that Strontium affects the kinetics of the reaction of hydrolysis of α-TCP. It inhibits the conversion from α-TCP to hydroxyapatite. However, the resulting apatitic phase contains significant amounts of Sr2+ suggesting that the addition of Sr2+ to the composition of α-TCP bone cements could be successfully exploited for its local delivery in bone defects. The hydrolysis of α-TCP has been investigated also in the presence of increasing amounts of gelatin: the results indicated that this biopolymer accelerates the hydrolysis reaction and promotes the conversion of α-TCP into OCP, suggesting that its addition in the composition of calcium phosphate cements can be employed to modulate the OCP/HA ratio, and as a consequence the solubility, of the set cement. II. Deposition of modified calcium phosphates on metallic substrates. Coating with a thin film of calcium phosphates is frequently applied on the surface of metallic implants in order to combine the high mechanical strength of the metal with the excellent bioactivity of the calcium phosphates surface layers. During this PhD thesis, thank to the collaboration with prof. I.N. Mihailescu, head of the Laser-Surface-Plasma Interactions Laboratory (National Institute for Lasers, Plasma and Radiation Physics – Laser Department, Bucharest) Pulsed Laser Deposition has been successfully applied to deposit thin films of Sr substituted HA on Titanium substrates. The synthesized coatings displayed a uniform Sr distribution, a granular surface and a good degree of crystallinity which slightly decreased on increasing Sr content. The results of in vitro tests carried out on osteoblast-like and osteoclast cells suggested that the presence of Sr in HA thin films can enhance the positive effect of HA coatings on osteointegration and bone regeneration, and prevent undesirable bone resorption. The possibility to introduce an active molecule in the implant site was explored using Matrix Assisted Pulsed Laser Evaporation to deposit hydroxyapatite nanocrystals at different content of alendronate, a bisphosphonate widely employed in the treatments of pathological diseases associated to bone loss. The coatings displayed a good degree of crystallinity, and the results of in vitro tests indicated that alendronate promotes proliferation and differentiation of osteoblasts even when incorporated into hydroxyapatite. III. Synthesis of drug carriers with a delayed release modulated by a calcium phosphate coating. A core-shell system for modulated drug delivery and release has been developed through optimization of the experimental conditions to cover gelatin microspheres with a uniform layer of calcium phosphate. The kinetics of the release from uncoated and coated microspheres was investigated using aspirin as a model drug. It was shown that the presence of the calcium phosphate shell delays the release of aspirin and allows to modulate its action.

Progettazione e sintesi di nuovi derivati azetidinonici biologicamente attivi

In this PhD-thesis new synthetic approaches towards new azetidinone derivatives are described. In particular, 4-alkyliden-β-lactams were used as starting materials for the preparation of new biologically active compounds. The carbapenem Thienamycin has got a broad spectrum of activity as antibiotic. It has got 3 stereocenters and apart of one epimer, all isomers have been synthesized. Using the 4-alkyliden-β-lactam benzilyc ester as precursor, we developed a synthesis for this missing epimer, which is described in chapter II. Biological tests in order to establish its biological activity are under way. The Hunsdiecker-Borodine reaction was extensively studied for the preparation of the mono halogenated and – surprisingly – the dihalogenated derivative from the 4-alkyliden-azetidinone carboxylic acid. The herein described synthetic procedures allowed the preparation of chloro-, bromo- and iodo derivatives in good to excellent yield. Furthermore, the reaction mechanism was investigated by NMR-experiments and is described in detail in chapter III. In chapter IV, synthetic approaches towards new β-lactam derivatives for inhibition of the histone deacetylase enzymes (HDACs) are reported. In collaboration with the company Sigma-Tau (Rome), 14 new β-lactams were synthesized. The new β-lactams were evaluated for the activity showing a promising activityparticulary, 10 of the β-lactams synthesized were evaluated for the in vitro inhibitory activity against the 11 human HDACs isoforms and they showed a selective inhibition of HDAC6 or HDAC8 in micromolar range. Finally, preliminary studies were conducted for the employment of 4-alkyliden-β-lactams as precursors for the synthesis of chiral β-amino acids by an opening of the β-lactam ring. In chapter V is described the ring opening reaction catalyzed by the enzyme lipase Cal-B. Preliminary results have shown that the enzyme not only catalyzes the ring opening of the β-lactam precursor, moreover, it leads to the formation of a cyclic dimer by the reaction of two molecules of β-amino acid obtained.

Sensitivity enhancement in NMR by using parahydrogen induced polarization

Enhancing the sensitivity of nuclear magnetic resonance measurements via hyperpolarization techniques like parahydrogen induced polarization (PHIP) is of high interest for spectroscopic investigations. Parahydrogen induced polarization is a chemical method, which makes use of the correlation between nuclear spins in parahydrogen to create hyperpolarized molecules. The key feature of this technique is the pairwise and simultaneous transfer of the two hydrogen atoms of parahydrogen to a double or triple bond resulting in a population of the Zeeman energy levels different from the Boltzmann equation. The obtained hyperpolarization results in antiphase peaks in the NMR spectrum with high intensities. Due to these strong NMR signals, this method finds arnlot of applications in chemistry e.g. the characterization of short-lived reaction intermediates. Also in medicine it opens up the possibility to boost the sensitivity of medical diagnostics via magnetic labeling of active contrast agents. Thus, further examination and optimization of the PHIP technique is of significant importance in order to achieve the highest possible sensitivity gain.rnrnIn this work, different aspects concerning PHIP were studied with respect to its chemical and spectroscopic background. The first part of this work mainly focused on optimizing the PHIP technique by investigating different catalyst systems and developing new setups for the parahydrogenation. Further examinations facilitated the transfer of the generated polarization from the protons to heteronuclei like 13C. The second part of this thesis examined the possibility to transfer these results to different biologically active compounds to enable their later application in medical diagnostics. Onerngroup of interesting substances is represented by metabolites or neurotransmitters in mammalian cells. Other interesting substances are clinically relevant drugs like a barbituric acid derivative or antidepressant drugs like citalopram which were investigated with regard to their applicability for the PHIP technique and the possibility to achievernpolarization transfer to 13C nuclei. The last investigated substrate is a polymerizable monomer whose polymer was used as a blood plasma expander for trauma victims after the first half of the 20th century. In this case, the utility of the monomer for the PHIP technique as a basis for later investigations of a polymerization reaction using hyperpolarized monomers was examined.rnrnHence, this thesis covers the optimization of the PHIP technology, hereby combining different fields of research like chemical and spectroscopical aspects, and transfers the results to applications of real biologally acitve compounds.

Synthesis of new bioactive β-lactam compounds

New biologically active β-lactams were designed and synthesized, developing novel antibiotics and enzymatic inhibitors directed toward specific targets. Within a work directed to the synthesis of mimetics for RGD (Arg-Gly-Asp) sequence able to interact with αvβ3 and α5β1-type integrins, new activators were developed and their Structure-Activity Relationships (SAR) analysis deepened, enhancing their activity range towards the α4β1 isoform. Moreover, to synthesize novel compounds active both against bacterial infections and pulmonary conditions of cystic fibrosis patients, new β-lactam candidates were studied. Among the abundant library of β-lactams prepared, mainly with antioxidant and antibacterial double activities, it was identified a single lead to be pharmacologically tested in vivo. Its synthesis was optimized up to the gram-scale, and pretreatment method and HPLC-MS/MS analytical protocol for sub-nanomolar quantifications were developed. Furthermore, replacement of acetoxy group in 4-acetoxy-azetidinone derivatives was studied with different nucleophiles and in aqueous media. A phosphate group was introduced and the reactivity exploited using different hydroxyapatites, obtaining biomaterials with multiple biological activities. Following the same kind of reactivity, a small series of molecules with a β-lactam and retinoic hybrid structure was synthesized as epigenetic regulators. Interacting with HDACs, two compounds were respectively identified as an inhibitor of cell proliferation and a differentiating agent on steam cells. Additionally, in collaboration with Professor L. De Cola at ISIS, University of Strasbourg, some new photochemically active β-lactam Pt (II) complexes were designed and synthesized to be used as bioprobes or theranostics. Finally, it was set up and optimized the preparation of new chiral proline-derived α-aminonitriles through an enantioselective Strecker reaction, and it was developed a chemo-enzymatic oxidative method for converting alcohols to aldehydes or acid in a selective manner, and amines to relative aldehydes, amides or imines. Moreover, enzymes and other green chemistry methodologies were used to prepare Active Pharmaceutical Ingredients (APIs).

Synthese und Charakterisierung von Polymeren mit peptidischen Seitenketten

Die Forschung im Bereich der Drug Delivery-Systeme konzentriert sich auf biokompatible und wenig immunogene Trägermoleküle. Eine Klasse vielversprechender Trägersysteme stellen Peptid basierte Polymere dar, die neben einer hohen Biokompatibilität auch eine Sensitivität gegenüber externen Einflüssen aufweisen. Der zwitterionische Charakter von Aminosäuren und Peptiden verhindert die Adsorption von Serumproteinen und ein „antifouling“ Verhalten kann festgestellt werden, sodass diese Moleküle für den Einsatz als Wirkstoffträgersystem sehr geeignet scheinen. In Kombination mit einer bürstenartigen Struktur entstehen Systeme mit einer einzigartigen Peptidarchitektur, die sich durch eine hohe Dichte funktioneller Gruppen für Konjugationsreaktionen auszeichnen und deren formabhängige Zellaufnahme sie besonders attraktiv für die Anwendung als „Nanocarrier“ macht.rnrnDas zwitterionische Poly-(ε-N-Methacryloyl-L-Lysin) (Mw = 721,000 g∙mol 1) wurde durch freie radikalische Polymerisation dargestellt und seine Konformation in Abhängigkeit von Ionenstärke und pH-Wert untersucht. Die Biokompatibilität des Systems konnte durch Toxizitätstests und dynamische Lichtstreuung in humanem Blutserum nachgewiesen werden. Zusammen mit der vernachlässigbaren unspezifischen Aufnahme in dendritische Zellen aus Knochenmark erfüllt das System damit alle Bedingungen, die an ein polymeres Wirkstoffträgersystem gestellt werden. Darüber hinaus können Komplexe des Polymers mit DNA in Gegenwart von divalenten Metallionen für die Gentransfektion verwendet werden.rnrnDurch Kopplung von ε-N-Methacryloyl-L-Lysin mit der Elastin-ähnlichen Polypeptid Pentasequenz Valin-Prolin-Glycin-Glycin-Glycin konnte ein Hexapeptid-Makromonomer dargestellt werden, welches anschließend mittels „grafting through“ Polymerisation zur Polymerbürste umgesetzt wurde. Die wurmartige Struktur der Polymerbürsten wurde in AFM-Aufnahmen gezeigt und eine hohe Kettensteifigkeit der Polymerbürsten über dynamische und statische Lichtstreuung nachgewiesen. Zirkulardichroismus-Messungen lieferten Informationen über struktur-, salz- und temperaturabhängige Veränderungen der Konformation. Toxizitätstests und dynamische Lichtstreuung in humanem Blutserum bestätigten die erwartete Biokompatibilität.rnrnBasierend auf zwei Elastin-ähnlichen Polypeptiden mit ähnlicher Peptidsequenz wurden insgesamt vier unterschiedliche Makromonomere mit jeweils 20 Pentapeptid-Wiederholungseinheiten dargestellt. Über anschließende „grafting through“ Polymerisation entstanden molekulare Bürstenmoleküle mit variierenden externen funktionellen Gruppen, die für zukünftige Konjugationsreaktionen verwendet werden können. Der Einfluss von Ionenstärke und Temperatur auf die Konformation der Makromonomere und Polymere wurde mittels Zirkulardichroismus- und Trübungskurven-Messungen untersucht und ein starker Einfluss der hohen Seitenkettendichte auf das Verhalten der Polymerbürsten wurde festgestellt. Über dynamische Lichtstreuung konnte ein von den externen funktionellen Gruppen abhängiges Aggregationsverhalten in humanem Blutserum nachgewiesen werden.rnrnDie in dieser Arbeit synthetisierten Polymerbürsten mit peptidischen Seitenketten stellen damit biokompatible und vielversprechende Trägersysteme für die Konjugation mit Biomolekülen dar, die zukünftig als Drug Delivery-Systeme ihren Einsatz finden können.rn

New synthetic strategies towards indolizines and pyrroles

Indolizines and pyrroles are considered as “privileged” structures since their skeletons were found in many biologically active natural products and they possess a wide range of pharmaceutical properties. Syntheses of these small drug-like molecules are very important in medicinal chemistry. However, most existent methodologies are usually limited to specific substitution patterns or require impractical starting materials or expensive catalysts. Therefore, developing new methodologies for the synthesis of indolizines and pyrroles from commercially available or readily accessible sources is highly desirable.rnIn this PhD thesis, several methods has been described for the synthesis of indolizines and pyrroles. In the first part, indolizines carrying substituents in positions 1-3 were synthesized via a formal [3+2]-cycloaddition of pyridinium ylides and nitroalkenes. Pyridinium salts were prepared by N-alkylation of pyridines with cyanohydrin triflates which could be prepared from corresponding aldehydes via a Strecker reaction followed by O-triflylation. Nitroalkenes were simply prepared from the corresponding aldehydes and nitroalkanes in a nitroaldol condensation. Overall, this modular approach allows to construct the indolizine framework with various substitution patterns starting from a pyridine, two different aldehydes and a nitroalkane. In contrast to reported methods, the produced indolizines do not have to contain an electron-withdrawing group.rnIt has also been found that nitrile-stabilized 2-alkylpyridinium ylides cyclize to unstable 2-aminoindolizines via an intramolecular 5-exo-dig cyclization. Using an in situ acetylation of the amino group, N-protected 2-aminoindolizines could be synthesized. As a less common substitution pattern, indolizines carrying substituents in positions 5–8 were synthesized from enones and 2-(1H-pyrrol-1-yl)nitriles obtained from α-aminonitriles using a modified Paal-Knorr pyrrole synthesis. The decoration of the pyridine unit in the indolizine skeleton has been achieved by a one-pot conjugate addition/cycloaromatization sequence.rnIn the second part of the thesis, the diversity-oriented synthesis of pyrroles from 3,5-diaryl substituted 2H-pyrrole-2-carbonitriles (cyanopyrrolines) obtained in a cyclocondensation of enones with aminoacetonitrile hydrochloride is being discussed. 2,4-Di-, 2,3,5-trisubstituted pyrroles, pyrrole-2-carbonitriles and 2,2’-bipyrroles were synthesized in a one- or two-step protocol. While the microwave-assisted thermal elimination of HCN from cyanopyrrolines gave 2,4-disubstituted pyrroles, DDQ-oxidation of the same intermediates furnished pyrrole-2-carbonitriles. Furthermore, 2,3,5-trisubstituted pyrroles were obtained via a C-2-alkylation of the deprotonated cyanopyrrolines followed by the elimination of HCN. Finally, it has also been found that tetraaryl substituted 2,2’-bipyrroles could be synthesized by the oxidative dimerization of cyanopyrrolines using copper (II) acetate at 100 °C.rn

Antiestrogenic and anticancer activities of peptides derived from the active site of alpha-fetoprotein

Cyclo[EKTOVNOGN] (AFPep), a cyclic 9-amino acid peptide derived from the active site of alpha-fetoprotein, has been shown to prevent carcinogen-induced mammary cancer in rats and inhibit the growth of ER+ human breast cancer xenografts in mice. Recently, studies using replica exchange molecular dynamics predicted that the TOVN region of AFPep might form a dynamically stable putative Type I beta-turn, and thus be biologically active without additional amino acids. The studies presented in this paper were performed to determine whether TOVN and other small analogs of AFPep would inhibit estrogen-stimulated cancer growth and exhibit a broad effective-dose range. These peptides contained nine or fewer amino acids, and were designed to bracket or include the putative pharmacophoric region (TOVN) of AFPep. Biological activities of these peptides were evaluated using an immature mouse uterine growth inhibition assay, a T47D breast cancer cell proliferation assay, and an MCF-7 breast cancer xenograft assay. TOVN had very weak antiestrogenic activity in comparison to AFPep's activity, whereas TOVNO had antiestrogenic and anticancer activities similar to AFPep. OVNO, which does not form a putative Type I beta-turn, had virtually no antiestrogenic and anticancer activities. A putative proteolytic cleavage product of AFPep, TOVNOGNEK, significantly inhibited E2-stimulated growth in vivo and in vitro over a wider dose range than AFPep or TOVNO. We conclude that TOVNO has anticancer potential, that TOVNOGNEK is as effective as AFPep in suppressing growth of human breast cancer cells, and that it does so over a broader effective-dose range.

Snake C-type lectin-like proteins and platelet receptors

Snake venoms are complex mixtures of biologically active proteins and peptides. Many affect haemostasis by activating or inhibiting coagulant factors or platelets, or by disrupting endothelium. Snake venom components are classified into various families, such as serine proteases, metalloproteinases, C-type lectin-like proteins, disintegrins and phospholipases. Snake venom C-type lectin-like proteins have a typical fold resembling that in classic C-type lectins such as the selectins and mannose-binding proteins. Many snake venom C-type lectin-like proteins have now been characterized, as heterodimeric structures with alpha and beta subunits that often form large molecules by multimerization. They activate platelets by binding to VWF or specific receptors such as GPIb, alpha2beta1 and GPVI. Simple heterodimeric GPIb-binding molecules mainly inhibit platelet functions, whereas multimeric ones activate platelets. A series of tetrameric snake venom C-type lectin-like proteins activates platelets by binding to GPVI while another series affects platelet function via integrin alpha2beta1. Some act by inducing VWF to bind to GPIb. Many structures of these proteins, often complexed with their ligands, have been determined. Structure-activity studies show that these proteins are quite complex despite similar backbone folding. Snake C-type lectin-like proteins often interact with more than one platelet receptor and have complex mechanisms of action.