Transition metal catalysis is a powerful tool for the construction of biologically active and pharmaceutically relevant architectures. With the challenge of continually depleting resources that this generation of scientists faces, it is becoming increasingly important to develop sustainable technologies for organic synthesis that utilize abundant and renewable feedstocks while minimizing byproduct formation and shortening the length of synthetic sequences by removing unnecessary protecting group manipulations and functionalizations. To this end, we have developed four new methods that transform inexpensive starting materials to valuable products. This dissertation covers the following key areas: 1) activation of CO2 for a mild and functional group tolerant synthesis of carboxylic acids, 2) oxidative twofold C–H bond activations as a strategy toward biaryls, 3) migratory O- to N-rearrangements in pyridines and related heterocycles for the preparation of N-alkylated heterocycles, and 4) asymmetric hydrogenations of cyclic imines and enamines en route to chiral 1,2- and 1,3-diamines and macrocyclic peptides.

Transition metal catalysis is a powerful tool for the construction of biologically active and pharmaceutically relevant architectures. With the challenge of continually depleting resources that this generation of scientists faces, it is becoming increasingly important to develop sustainable technologies for organic synthesis that utilize abundant and renewable feedstocks while minimizing byproduct formation and shortening the length of synthetic sequences by removing unnecessary protecting group manipulations and functionalizations. To this end, we have developed four new methods that transform inexpensive starting materials to valuable products. This dissertation covers the following key areas: 1) activation of CO2 for a mild and functional group tolerant synthesis of carboxylic acids, 2) oxidative twofold C–H bond activations as a strategy toward biaryls, 3) migratory O- to N-rearrangements in pyridines and related heterocycles for the preparation of N-alkylated heterocycles, and 4) asymmetric hydrogenations of cyclic imines and enamines en route to chiral 1,2- and 1,3-diamines and macrocyclic peptides.

Elucidation of the primary structure of peptides and proteins de novo by mass spectrometry (MS) has become possible with the advent of tandem MS methods. The most widely used chemical method due to Edman (Edman & Begg, 1967) has shortcomings with regard to N- terminal blocked peptides, cyclic peptides and posttranslational modifications, for example phosphorylation (Metzger, 1994). However, mass spectrometric sequencing methods are increasingly becoming applicable for a variety of peptides and proteins, including N- and C- termini modified peptides and cyclic peptides (Jegorov et al., 2003; Sabareesh & Balaram, 2006; Sabareesh et al., 2007). Further, conventional and tandem mass spectrometry have proven useful in the detection of post-translational modifications (Hansson et al., 2004; Nair et al., 2006; Mandal et al., 2007). This thesis details mass spectrometric sequencing of acyclic and cyclic peptides, involving tandem MS methods carried out using both electrospray ionization (ESI) ion trap (Esquire 3000 plus, Bruker Daltonics) and matrix assisted laser desorption and ionization time-of-flight/time-of-flight (MALDI TOF/TOF) (Ultraflex TOF/TOF, Bruker Daltonics) instruments. The peptides are either chemically synthesized or isolated from diverse natural sources. Synthetically designed peptides possessing modified N- and C- termini and peptaibols from the soil fungus Trichoderma constitute the acyclic peptides. The cyclic peptides include backbone cyclized depsipeptides from the fungus Isaria and disulfide bonded peptides from the venom of marine cone snails. Chapter 1 gives an account of various concepts of mass spectrometry, tandem mass spectrometry and peptide fragmentation chemistry, providing necessary background information for the following chapters. Chapter 2 describes the fragmentation studies of [M + H]+ and [M + Na]+ adducts of six neutral peptides with blocked N- and C- termini investigated using an electrospray ion trap mass spectrometer. The N- terminus of these synthetically designed peptides is blocked with a tertiarybutyloxycarbonyl (Boc) group and the C- terminus is esterified. These peptides do not possess sidechains that are capable of complexation and hence the backbone amide units are the sole sites of protonation and metallation. The cleavage pattern of protonated adducts is strikingly different from that of sodium adducts. While the loss of the N- terminal blocking group happens quite readily in the case of MS/MS of [M + Na]+, the cleavage of C- terminal methoxy group seems to be a facile process in the case of MS/MS of [M + H]+. Fragmentation of the protonated adducts yields only bn ions, while yn and an type ions are predominantly formed from the fragmentation of sodium adducts. The an ions arising from the fragmentation of [M + Na]+ lack the N-terminal Boc group (termed as an*). MS/MS of [M + Na]+ species also yields bn ions of substantial lower intensities, that lack the N- terminal Boc group (bn*). Comparison of the fragmentation of [M + H]+ with [M + Na]+ of the peptides chosen in this study reveal that the combined use of both protonated and sodium adducts should prove useful in de novo sequencing of peptides that possess modified N- and C- termini, particularly naturally occurring neutral peptides, for example, peptaibols. Chapter 3 describes about the ESI-MS/MS investigation of an HPLC fraction from the soil fungus Trichoderma, which aided in identification of microheterogeneous trichotoxin peptaibols in that fraction. Dramatic differences were noted between the fragmentation spectra of [M + H]+ and [M + Na]+ species. While b-type ions were noted from the former, the latter yielded a-, b-and y- type ions (the same feature was noted in the cases presented in the previous chapter). Inspection of the isotope pattern of b-ions yielded from the dissociation of H+ species, clearly revealed the presence of three microheterogeneous trichotoxin sequences; two isobars (1718 Da), each possessing one Glu residue and another completely neutral peptide (1717 Da). The microheterogeneity is due to Gly ↔ Ala, Iva ↔ Aib and Gln ↔ Glu replacements and exchanges (Iva: DIva: R-Isovaline; Aib: α-aminoisobutyric acid). The MS/MS of [M + Na]+ adduct predominantly yielded product ions from the neutral peptaibol. Further, the fragmentation patterns of H+ and Na+ adducts of two N-acetyl peptide esters were found to be very similar to that of the neutral peptaibol component. The results presented in this chapter establish that under the electrospray ion trap conditions, the fragmentation patterns of the H+ and Na+ adducts of model peptides that possess modified N- (Boc and acetyl) and C- termini are indeed very similar to that of the neutral trichotoxin. Chapter 4 delineates the applicability of liquid chromatography coupled to conventional and tandem electrospray ionization mass spectrometry (LC-ESI-MS, LC-ESI-MS/MS, LC-ESI-MS3) for the screening of novel cyclic hexadepsipeptide metabolites directly from the crude hyphal extract of the fungus Isaria. The fungal strain was grown on a solid medium (potato carrot agar), which yields aerial hyphae growing erect from the basal mycelial colony (Ravindra et al., 2004). A total of ten microheterogeneous components were identified to belong to the isariin class of cyclodepsipeptides from the LC-ESI-MS and LC-ESI-MS/MS analysis of the crude hyphal extract. Out of ten, six are determined to be new and the remaining four are previously reported isariins A-D. The primary structures of isariins A-D were from the fungi Isaria cretacea and Isaria felina (Vining & Taber 1962; Deffieux et al., 1981) and the fungal strain used in this study resembles Isaria felina (Sabareesh et al., 2007). Isariins are backbone cyclized hexadepsipeptides composed of a D-β-hydroxy acid possessing a hydrocarbon sidechain and five α-amino acids; one of the α-amino acids is a D-amino acid (Vining & Taber 1962; Deffieux et al., 1981). The detection of fragment ions due to loss of CO concomitant with the loss of H2O from the protonated precursor ion ([M + H]+) ascertained the cyclic depsipeptide nature of both the known and the new components. The fragmentation behavior of the [M + H]+ of known isariins facilitated sequence determination of the new components. Therefore, the configuration of the amino acids and the β-hydroxy acid of the new components is assumed to be same as that of the reported peptides. The microheterogeneity of the ten sequences is due to changes in the D-β-hydroxy acid (residue 1) and the adjoining α-amino acid (residue 6), whose carbonyl is linked to the hydroxyl function by an ester linkage. The number of methylene units ((-CH2)n) in the hydrocarbon sidechain of the residue 1 differs between 2 and 8 and the variability of the residue 6 is limited to Ala/Val. The ester oxygen atom was chosen as the preferable site of protonation causing ring-opening, based on the observed distribution of the fragment ions. Chapter 5 demonstrates the utility of the LC-ESI-MS and LC-ESI-MS/MS methods in the identification and characterization of six microheterogeneous backbone cyclized hexadepsipeptides, isaridins, directly from the crude hyphal extract of the fungus Isaria. Among the six components, four were found to be novel. The other two peptides, isaridins A and B were identified earlier from this laboratory (Ravindra et al., 2004). The isaridins are characterized by the presence of unusual amino acids such as N-methylated residues, β-methylproline (β-MePro) and hydroxyleucine (HyLeu) (Ravindra et al., 2004). The cyclic nature of both the known and the new peptides were confirmed from the observation of peaks due to loss of CO and H2O from the protonated precursor ion ([M + H]+). However, unlike isariins (Chapter 4), the intensity of the peak corresponding to [M + H - H2O]+ was noted to be of very low intensity, in the case of isaridins. Detection of product ion peak due to [M + H - CO2]+ suggests an additional dissociation pathway involving cleavage at the depsipeptide linkage and is supportive of the cyclic depsipeptide nature (Eckart, 1994). The sequencing of the newly detected components was enabled by understanding the fragmentation mechanism of the known isaridins. The tertiary amide nitrogens of the N-methylated residues were regarded as the preferable sites of protonation leading to ring-opening, as noted from the fragmentation spectra. The microheterogeneity in the sequences was identified using the diagnostic product ions obtained from the protonated precursor of the known isaridins. The microheterogeneity can be attributed to the variations of two residues; Pro ↔ β-MePro and N-MePhe ↔ N-MeLxx (Lxx: Leu, Ile, alloIle). The recently reported ‘isarfelins’ from the fungus Isaria felina (Guo et al., 2005) were reassigned as ‘isaridins’. The reassignment was based on very similar fragmentation profiles observed for the [M + Na]+ adduct of isaridins and isarfelins; further, the fungal strain used in this study resembles Isaria felina (Sabareesh et al., 2007). Chapter 6 presents mass spectrometric sequencing of disulfide bonded peptides from marine cone snails (conopeptides), using the MALDI LIFT MS/MS method. Lo959, a single disulfide bonded octapeptide isolated from Conus loroisii, was identified to belong to the class of contryphans (Sabareesh et al., 2006). Contryphans are small single disulfide bonded conopeptides, whose length is in the range of 7-11 residues and are rich in tryptophan. A significant feature of the contryphans is the presence of conserved DTrp (DW) at the 3rd residue within the disulfide loop (Sabareesh et al., 2006). Lo959 displays an unusual behavior under reverse phase chromatographic conditions, typical of the DW containing contryphans (Jacobsen et al., 1998). It undergoes slow conformational interconversion on the chromatographic time scale exhibiting two distinct peaks. The presence of DW at the 4th position in Lo959 was established by comparing the chromatographic profiles of natural peptide with that of two chemically synthesized peptides, one containing LW (4) and another possessing DW (4). De novo sequencing of the two peptides Ar1446 and Ar1430 from Conus araneosus established that they belonged to M-superfamily of conotoxins, in particular m-2 branch. M-superfamily conotoxins are three-disulfide bonded peptides characterized by the consensus cysteine framework, CC…C…C…CC (Corpuz et al., 2005). Ar1446 and Ar1430 are fourteen residue long peptides, each possessing three disulfide bonds. The peptides have the cysteine scaffold typical of the M-superfamily, as shown above. Specifically, the peptides belong to m-2 branch of M-superfamily, where the fourth and fifth cysteines are separated by two residues (Corpuz et al., 2005). The sequences of the peptides were derived following chemical and enzymatic modifications. The carboxamidomethylation reaction established the presence of three disulfide bonds. Indeed, the sequences were deduced from the MALDI LIFT MS/MS of [M + H]+ of the tryptic peptides. The sequences of the two peptides are almost identical and they differ only at residue 12; hydroxyproline in Ar1446, proline in Ar1430.

Diante da ausência de tratamentos eficazes para a esclerose múltipla (EM) e sabendo que compostos animais têm sido usados como protótipos para o desenvolvimento de novas drogas, avaliamos o efeito do Tnp, um peptídeo cíclico inédito e com potencial antiinflamatório derivado do veneno de Thalassophryne nattereri, na encefalomielite autoimune experimental (EAE), um modelo representativo da EM. Demonstramos que o Tnp em distintos esquemas de tratamento por mecanismos também dependentes de IL-10 consegue diminuir a intensidade dos sintomas clínicos e adiar o pico de aparecimento dos sintomas graves na EAE por suprimir DC convencionais e propiciar DC plasmocitóides; por bloquear a infiltração de leucócitos e a reativação de clones Th1, Th17, microglia e macrófagos no SNC; por favorecer o aumento de células reguladoras e ainda por ultrapassar a BHE e alcançar o órgão alvo. O Tnp atenua a neuroinflamação e previne a desmielinização, refletindo assim na melhoria dos sinais clínicos na EAE, tornando-se um importante candidato para o tratamento da EM. / Given the lack of effective treatments for multiple sclerosis (MS) and knowing that venomous have been used as prototype for the development of new drugs here we evaluated the effect of the Tnp, a described antiinflammatory cyclic peptide identified in the venom of Thalassophryne nattereri, on experimental autoimmune encephalomyelitis (EAE), a representative model of MS. We found that distinct treatments of Tnp by mechanisms also dependent on IL-10 significantly reduced the clinical severity of EAE. Tnp was related with: suppression of the activation state of conventional DC and the emergence of plasmacytoid DC; blocking the leukocyte infiltration and the reactivation of Th1, Th17, microglia cells and macrophages in the CNS; increasing of regulatory cells and also Tnp can overcome the BBB and reach the target organ. Tnp can reduce the severity of symptoms and delay the peak of onset of severe symptoms. These results shed light on the role of Tnp a small molecule in the regulation of inflammation and provides a new therapeutic opportunity for the treatment of MS.

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This PhD thesis is the result of the combination of experimental and computational techniques with the aim of understanding the mechanism of action of de novo cyclic decapeptides with high antimicrobial activity. By experimental techniques the influence of the replacement of the phenylalanine for tryptophan residue in their antimicrobial activity was tested and the stability in human serum was also analyzed, in order to evaluate their potential therapeutic application as antitumor agents. On the other hand, the interaction amongst the peptide BPC194 c(KKLKKFKKLQ), the best candidate from the whole library of cyclic peptides, and a model anionic membrane was simulated. The results showed a structure-function relationship derived from the stable conformation of the peptides involved in the membrane permeabilization. As a result, a rational design was performed being BPC490 the peptide with best antimicrobial activity compared with the best active peptide from the original library. / Aquesta tesi doctoral resulta de la combinació d’estudis mitjançant tècniques experimentals i computacionals amb l’objectiu d’entendre el mecanisme d’acció de "de novo" decapèptids cíclics amb elevada activitat antimicrobiana. Experimentalment, es va avaluar la influència de la substitució dels residus de fenilalanina per triptòfan en la seva activitat antimicrobiana i també la seva estabilitat sèrum humà, per tal de valorar la seva possible aplicació terapèutica envers el càncer. Per altra banda, es va simular la interacció del pèptid BPC194 c(KKLKKFKKLQ), millor candidat de la biblioteca de pèptids cíclics, amb models aniònics de bicapa lipídica. Els resultats van posar en manifest una relació estructura-funció derivada de la conformació estable dels pèptids que participen directament en la permeabilització de la membrana. Es va procedir doncs al disseny racional de nous pèptids cíclics sent el pèptid BPC490 el que va presentar una millor activitat bacteriana en comparació amb el pèptid més actiu de la llibreria original.

In the present PhD thesis we studied the solid-phase peptide synthesis of antimicrobial peptides derived from the lead peptides BP100 and BPC194. First, peptides derived from BP100 containing D-amino acids at different positions of the sequences were prepared. Moreover, peptidotriazoles derived from BP100 were also synthesized containing the triazole ring at the side-chain of different amino acids. Then, we proceeded to perform studies for the synthesis of multivalent peptides derived from BPC194. To achieve this objective, the synthesis of cyclic peptides containig a triazole ring at amino acids side-chain with different elongations was carried out. Finally, we prepared various carbopeptides containing 2 and 4 units of BP100 and/or its derivatives. The evaluation of the biological activity allowed the identification of active sequences against the economically important phytopathogenic bacteria and fungi and not toxic against eukaryotic cells. / En aquesta tesi doctoral es va estudiar la preparació en fase sòlida de pèptids antimicrobians derivats dels pèptids lead BP100 i BPC194. En primer lloc, es varen preparar derivats del pèptid lineal BP100 incorporant D aminoàcids en diferents posicions de la seqüència. A més, també es varen sintetitzar derivats d'aquest pèptid lead incorporant un anell de triazole a la cadena lateral de diferents aminoàcids. Posteriorment, es va procedir a l'estudi de la síntesi dd pèptids multivalents derivats de BPC194. Per aconseguir aquest objectiu es va portar a terme la síntesi de pèptids cíclics incorporant un anell de triazole a la cadena lateral d’aminoàcids amb diferents allargades de cadena. Finalment, va procedir a la preparació de carbopèptids contenint 2 i 4 unitats de BP100 i/o derivats. L’avaluació de l’activitat biològica dels pèptids sintetitzats va permetre idenficar seqüències actives enfront de bacteris fitopatògens i fongs i poc tòxiques enfront cèl•lules eucariotes.

The first part of the thesis describes the synthesis and application of functional magnetic polymer beads. The traditional suspension polymerization approach was used to synthesize polystyrene-iron oxide (Fe 3 O 4 ) based magnetic beads. The beads were coupled to different surface functional groups. The Fe 3 O 4 particles were encapsulated into a polystyrene shell. The surface functional groups were generated by graft-polymerization with functional monomers. The average size of the beads was in the range of 100-500 μm. Chemical tests showed that the beads were stable in strong acid, strong base and polar solvent. The beads had a fast response to an external magnetic field. A self-emulsion-polymerization approach was developed to synthesize smaller magnetic beads with the - OH groups on the surface. A modified approach based on traditional suspension-polymerization was developed to synthesize acid-durable beads with more Fe 3 O 4 encapsulated inside the beads. A novel emulsion-suspension polymerization method was successfully developed to synthesize much smaller magnetic beads ( A new peptide synthesis approach was developed using functional magnetic beads as the resin for solid phase synthesis. In this application, synthesized magnetic beads were further modified by a two-step reaction. The amino group was anchored onto the surface of these beads, followed by coupling with the Rink amide linker. The resulting beads were used as the resin to synthesize several model peptides. The peptides were successfully synthesized, and the sequences were confirmed by mass spectrometry analysis. The yields of the peptides were comparable to those obtained from commercial Rink amide resin. The second part of the thesis describes the synthesis and mass spectrometry analysis of two series of model peptides. One series has the linear (non-cyclic) structure, A n K, KA n , P n K, and AcA n K. The other series contains cyclic peptides, c-Ac-DAKAK and c-Ac-DADapAK. All peptides were synthesized using solid phase peptide synthesis. The relative proton affinities of the model peptides were measured using the collision induced dissociation experiments using a triple quadrupole mass spectrometer. It was found that the effective proton affinity of a cyclic peptide was significantly reduced compared to a linear analogue. The reduced proton affinity implies an increased lipophilicity of the peptide.