This dissertation is dedicated to the research and investigation of novel enzymes and the methods used to study them, with physiological roles ranging from isoprenoid biosynthesis to neurotransmitter production. Using a combination of bioinformatics, recombinant cloning, enzymology, and proteomics, we have contributed to the understanding and exploration of several human illnesses, including malaria, cancer, and endocrine dysfunction. Our first project involved studying the enzymes responsible for N-acylarylalkylamide biosynthesis in Bombyx mori. Very little is known how these potent signaling molecules are produced in vivo, however, one possible pathway is the direct conjugation of an acyl-CoA to a corresponding arylalkylamide by the enzyme arylalkylamine N-acyltransferase (AANAT). In insects, this enzyme is responsible for controlling melanism, the inactivation of biogenic amines, the sclerotization of the insect cuticle, photoperiodism, and the penultimate intermediate in the production of melatonin. We studied a pair of AANAT enzymes from B. mori: Bm-AANAT and Bm-AANAT3. The former was found to catalyze the direct formation of long-chain acylarylalkylamines (only the second enzyme discovered to do such chemistry), while the latter exhibited potent inactivation of several amines through acetylation. We conducted a full kinetic characterization of Bm-AANAT3, including double-reciprocal plots, pH-rate profiling, dead-end inhibition, and the construction of mutants to elucidate catalytically-relevant amino acids. Our hope is that new insights and discoveries on these enzymatic pathways in model organisms will yield novel molecular targets for human health and disease. We then developed an innovative, microwave-assisted synthesis of a binding-based probe capable of enriching proteins that bind adenine ribose derivatives (AdoRs). We employed this probe in activity-based protein profiling studies to qualitatively assess the AdoR-binding proteome in three bacterial cell lines from the genus Bacillus. This proof of concept experiment demonstrated a unique subset of proteins distinctive to each species, and confirmed the efficacy of the probe tagging and subsequent enrichment. This technology can be used in clinical applications for the detection and identification of cancerous biomarkers. Finally, we successfully truncated and recombinantly-expressed 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from both P. vivax and P. falciparum. We elucidated the order of substrate binding for both of these TPP-dependent enzymes using steady-state kinetic analyses, dead-end inhibition, and intrinsic tryptophan fluorescence titrations. Both enzymes adhere to a random sequential mechanism with respect to binding of both substrates: pyruvate and D-glyceraldehyde-3-phosphate. These findings are in contrast to other TPP-dependent enzymes, which exhibit classical ordered and/or ping-pong kinetic mechanisms. A better understanding of the kinetic mechanism for these two Plasmodial enzymes could aid in the development of novel DXS-specific inhibitors that might prove useful in treatment of malaria.

<p>U ovoj doktorskoj disertaciji proučavano je građenje i termohromno&nbsp;pona&scaron;anje hloro kompleksa kobalt(II) jona u tri različita medijuma:&nbsp;amonijum-nitrat + <em>z</em>formamid (z= 2, 3, 4, 5, 6 i 20), amonijum-nitrat +&nbsp;<em>z</em>N-metilformamid (<em>z&nbsp;</em>= 3, 4, 5, 6 i 20) i amonijum-nitrat +&nbsp; <em>zN,N</em>-dimetilformamid (<em>z</em> = 3) u temperaturnom intervalu od 308,15 do&nbsp;348,15 K. Cilj ovog istraživanja je bio određivanje stabilnosti&nbsp;termohromnih kompleksa kobalta(II) koji se grade sahloridnim i&nbsp;nitratnim jonima i molekulima rastvarača, pronalaženje kvalitativne i&nbsp;kvantitativne zavisnosti konstanti stabilnosti kompleksa kobalta(II) od&nbsp;temperature i molskog odnosa komponenti ispitivanih sistema.&nbsp;Termodinamički parametri, koji karakteri&scaron;u reakcije asocijacije u&nbsp;ispitivanim sistemima izračunati su na osnovu dobijenih konstanti&nbsp;stabilnosti na različitim temperaturama. Drugi deo ovog rada obuhvata&nbsp;fizičko-hemijsku karakterizaciju ispitivanih sistema, i&nbsp; to: merenje&nbsp;gustine, provodljivosti i njihove viskoznosti. Na osnovu dobijenih&nbsp;podataka razmotrene su vrste interakcija koje se javljaju među&nbsp;česticama rastvarača i rastvorene supstance, kao i njihov uticaj na&nbsp;građenje kompleksnih&nbsp; čestica kobalta(II). Ispitivani sistemi su&nbsp;posebno interesantni, jer predstavljaju dobre medijume za ispitivanje&nbsp;termohromizma u praksi.</p> / <p>In this thesis absorption spectra of cobalt(II) chloride in three ammonium nitrate binary mixtures with organic solvents (formamide, N-methylformamide and&nbsp; <em>N,N</em>-dimethylformamide) at different temperatures (from 308.15 to 248.15 K) and compositions have been investigated in the wavelength range 400-800 nm. Influence of the temperature and composition of the mixture on complex formation between cobalt(II) and nitrate ions, chloride ions&nbsp; and/or solvent molecules have been studied. Thermodynamic parameters for cobalt(II)-ligand association in different solventswere also determined. The second part of this work involves physical-chemical characterization of the studied systems, namely: density, electrical conductivity and viscosity measurements. On the basis of the obtained&nbsp;data, the types and nature of the solute-solvent interactions that occur, as well as their impact on the cobalt(II) complex formation were discussed. In all investigated systems, complexes of cobalt(II) change the geometry and colour from pale pink to dark blueupon addition of &nbsp;chloride ions and upon heating/cooling. Hence, additional chemical energy can be stored in such system. Because the effective working temperatures match very well with that readily achievable under sunlight, these thermochromic systems present an &nbsp;example of novel materials suitable for auto-regulated protection and energy storage.</p>

Ce manuscrit décrit les travaux de doctorat réalisés au sein du laboratoire du Pr. Charette entre 2015 et 2019. Ceux-ci s’inscrivent dans deux thématiques de recherche différentes : le développement de nouvelles stratégies d’amidation et le développement de nouvelles méthodologies de cyclopropanation. La synthèse de liaisons amides est, encore aujourd’hui, un défi pour la communauté chimique. En effet, le développement de méthodologies simples, robustes, économes en atomes, et plus respectueuses de l’environnement reste l’une des priorités de recherche en chimie organique. Afin d’apporter une contribution à ce domaine, une méthodologie de synthèse d’amides a été développée en utilisant le diphénylsilane en tant qu’agent de couplage. Celui-ci est disponible commercialement, stable et peu onéreux. De plus, il ne génère qu’un siloxane et du dihydrogène gazeux en fin de réaction. La méthodologie mise au point a également pu être appliquée à la synthèse d’une série de di- et tripeptides. L’utilisation du motif cyclopropanique n’a cessé de prendre de l’ampleur dans le secteur pharmaceutique. En effet, celui-ci peut influer sur différents paramètres cruciaux dans le développement de molécules biologiquement actives. Le développement de nouvelles méthodologies de cyclopropanation est donc un domaine pertinent. La synthèse de borocyclopropanes est particulièrement intéressante : en effet, ces composés peuvent permettre de créer de la diversité structurale via une fonctionnalisation du boronate. Afin d’obtenir un procédé de synthèse de ces composés simple, robuste et plus « vert », une approche photochimique utilisant la technologie en débit continu a été favorisée. Une réaction de borocyclopropanation photorédox de styrènes a pu être mise au point ; celle-ci est réalisée sous irradiation UV-A en présence de xanthone en tant que photocatalyseur. Les études menées afin d’élucider le mécanisme ont permis de conclure que cette transformation se déroulait selon deux cycles catalytiques photorédox concomitants. Finalement, un nouveau réactif diiodé comportant une fonction ester boronique de pinacol et un groupement triméthylsilyle a été développé afin d’accéder à des cyclopropanes gem-disubstitués. Les bases d’un procédé photochimique UV-visible utilisant ce nouveau réactif ont ensuite pu être établies. Ainsi, le premier exemple d’un gem-borocyclopropyl silane dérivé du styrène a pu être synthétisé. / This manuscript describes the work carried out in Pr. Charette’s laboratory between 2015 and 2019. It can be divided into two different topics: the development of new amidation strategies and the development of new cyclopropanation methodologies. Amide synthesis is still a challenge for the scientific community nowadays. Indeed, the development of simple, robust, atom economical and environmental friendly procedures remain one of the research priority in organic chemistry. To contribute to this field, an amide synthesis methodology has been developed by using diphenylsilane as a coupling reagent. The latter is commercially available, stable and cheap. Moreover, only a siloxane and dihydrogen are generated during the reaction. The developed methodology has also been applied to the synthesis of a series of di- and tripeptides. The cyclopropane moiety has been increasingly used in pharmaceuticals. Indeed, this moiety can influence different crucial parameters in the development of bioactive molecules. The development of new cyclopropanation methodologies is therefore a relevant field. Borocyclopropane synthesis is of particular interest: as a matter of fact, these compounds can create structural diversity via boronate functionalization. In order to obtain a user-friendly, robust and greener chemical process, a photochemical approach using continuous flow technology has been favored. A photoredox borocyclopropanation of styrenes has been developed; the latter is carried out under UV-A irradiation with xanthone as a photosensitizer. Mechanistic studies have supported that this transformation proceeds according to two concurrent photoredox catalytic cycles. Finally, a new diiodo reagent bearing a pinacol boronate group and a trimethylsilyl group has been developed to access gem-disubstituted cyclopropanes. The bases of a UV-visible photochemical process using this new reagent have then been established. Thereby, the first example of a gem-borocyclopropyl silane derived from styrene has been synthesized.

<p>U&nbsp; radu&nbsp; je&nbsp; ispitan&nbsp; uticaj&nbsp; amida&nbsp; kao&nbsp; modela&nbsp; AOM-a (Algalne organske materije)&nbsp; na adsorpciju nitrofenola iz vodene&nbsp; sredine&nbsp; na&nbsp; aktivnom&nbsp; uglju.&nbsp; Istraţivanje&nbsp; se sastojalo&nbsp; iz&nbsp; tri&nbsp; faze:&nbsp; ispitivanje&nbsp; uticaja&nbsp; karateristika amida&nbsp; na&nbsp; adsorpciju&nbsp; nitrofenola,&nbsp; ispitivanje&nbsp; uticaja granulacije na adsorpciju nitrofenola u prisustvu amida i ispitvanje karakterisitka samih nitrofenola na adsorpciju u&nbsp; prisustvu&nbsp; amida.&nbsp; Pre&nbsp; ispitivanja&nbsp; adsorpcije&nbsp; u dvokomponentnim&nbsp; sistemima&nbsp; ispitana&nbsp; je&nbsp; adsorpcija jednokomponentnih&nbsp; sistema&nbsp; 4-nitrofenola,&nbsp; 2,4-dinitrofenola&nbsp; i&nbsp; 2,4,6-trinitrofenola,&nbsp; kao&nbsp; i&nbsp; amida&nbsp; Nmetilbenzamid,&nbsp; nikotinamida&nbsp; i&nbsp; N-benzilbenzamida&nbsp; na komercijalnim&nbsp; aktivnim&nbsp; ugljevima&nbsp; NORIT&nbsp; SA2&nbsp; i&nbsp; dve granulacije&nbsp; aktivnog&nbsp; uglja&nbsp; DARCO.&nbsp; Aktivni&nbsp; ugljevi&nbsp; su ispitani&nbsp; metodom&nbsp; FTIR&nbsp; spektroskopije,&nbsp; SEM&nbsp; analizom, analizom&nbsp; povr&scaron;ine&nbsp; adsorpcijom&nbsp; azota&nbsp; na&nbsp; niskoj temperaturi&nbsp; i&nbsp; određivanjem&nbsp; taĉke&nbsp; nultog&nbsp; naelektrisanja. Urađena&nbsp; je&nbsp; geometrijska&nbsp; optimizacija&nbsp; modela&nbsp; molekula ispitivanih nitrofenola i amida i izraĉunati su molekulski parametri.&nbsp; Uticaj&nbsp; amida&nbsp; kao&nbsp; modela&nbsp; AOM-a&nbsp; je&nbsp; ispitan kori&scaron;ćenjem&nbsp; razliĉitih&nbsp; ravnotežnih&nbsp; i&nbsp; difuzionih adsorpcionih&nbsp; modela.&nbsp; Kao&nbsp; kriterijum&nbsp; za&nbsp; određivanje najsporije&nbsp; adsorpcione&nbsp; faze&nbsp; kori&scaron;ćen&nbsp; je&nbsp; Biotov&nbsp; broj.<br />Adsorpcioni&nbsp; parametri&nbsp; dobijeni&nbsp; u&nbsp; eksperimentima&nbsp; sa dvokomponentnim&nbsp; sistemima&nbsp; su&nbsp; upoređivani&nbsp; sa parametrima dobijenim za adsorpciju samih nitrofenola.</p> / <p>In this research influence of selected amides, as a model of&nbsp; AOM&nbsp; (Algal&nbsp; organic&nbsp; matter),&nbsp; on&nbsp; adsorption&nbsp; of nitrophenols&nbsp; from&nbsp; water&nbsp; on&nbsp; activated&nbsp; carbon&nbsp; has&nbsp; been<br />investigated.&nbsp; Research&nbsp; is&nbsp; divided&nbsp; in&nbsp; three&nbsp; phases: investigation&nbsp; of&nbsp; influence&nbsp; of&nbsp; amide&nbsp; molecule characteristics&nbsp; on&nbsp; the&nbsp; adsorption&nbsp; of&nbsp; nitrophenols, investigation&nbsp; of&nbsp; granulation&nbsp; influence&nbsp; on&nbsp; nitrophenol adsorption in&nbsp; the&nbsp; presence of amide and investigation of nitrophenol characteristics that can influence adsorption in&nbsp; the&nbsp; presence&nbsp; of&nbsp; amides.&nbsp; Adsorption&nbsp; of&nbsp; nitrophenols and&nbsp; amides&nbsp; in&nbsp; single- component&nbsp; systems&nbsp; has&nbsp; also&nbsp; been carried&nbsp; out.&nbsp; Adsorption&nbsp; kinetics&nbsp; of&nbsp; 4-nitrophenol,&nbsp; 2,4-dinitrophenol,&nbsp; 2,4,6-trinitrophenol,&nbsp; N-methylbenzamide,<br />nicotinamide&nbsp; and&nbsp; N-benzylbenzamide&nbsp; has&nbsp; also&nbsp; been investigated. Commercial activated carbons NORIT SA2 and&nbsp; two&nbsp; granulations&nbsp; of&nbsp; DARCO&nbsp; were&nbsp; used.&nbsp; Activated carbons&nbsp; were&nbsp; characterized&nbsp; using&nbsp; FTIR&nbsp; spectroscopy, SEM&nbsp; analysis,&nbsp; internal&nbsp; surface&nbsp; analysis&nbsp; using&nbsp; nitrogen adsorption&nbsp; on&nbsp; low&nbsp; temperature&nbsp; and&nbsp; determination&nbsp; of point&nbsp; of&nbsp; zero&nbsp; charge.&nbsp; Geometry&nbsp; optimization&nbsp; of nitrophenol&nbsp; and&nbsp; amide&nbsp; molecules&nbsp; has&nbsp; been&nbsp; carried&nbsp; out and different molecular parameters have been calculated. Influence&nbsp; of&nbsp; amides&nbsp; as&nbsp; AOM&nbsp; model&nbsp; has&nbsp; been investigated by using diffusion and equilibrium models. Biot number has been obtained&nbsp; in order to establish the limiting&nbsp; step&nbsp; in&nbsp; adsorption&nbsp; process.&nbsp;&nbsp; Adsorption parameters&nbsp; obtained&nbsp; in&nbsp; two-component&nbsp; adsorption systems&nbsp; were&nbsp; compared&nbsp; to&nbsp; parameters&nbsp; obtained&nbsp; for adsorption of nitrophenols alone.</p>

Title: Phosphinoferrocene amides and hydrazides Author: Hana Solařová Department: Department of Inorganic Chemistry Supervisor: doc. RNDr. Petr Štěpnička, Ph.D. Abstract: While studying functionalized phosphinoferrocene ligands, we recently turned to phosphinoferrocene carboxamides. These donors already proved to be versatile ligands for coordination chemistry and catalysis. This led us to synthesize and study the archetypal representative, 1'-(diphenylphosphino)-1-carbamoylferrocene (5), and the corresponding hydrazide 6. PPh2 COOH Fe Hdpf PPh2 CONH2 Fe 5 PPh2 CONHNH2 Fe 6 This work describes the preparation of primary amide 5 and hydrazide 6 from 1'- (diphenylphosphino)-1-ferrocenecarboxylic acid (Hdpf) via the corresponding acylbenzo- triazole derivative. The hydrazide was alternatively obtained from Hdpf methylester and hydrazine hydrate. Both newly synthesized compounds were characterized by spectroscopic methods (NMR, IR, and MS) and elemental analysis, and their crystal structures were determined by single-crystal X-ray crystallography. The amide was further utilized in the preparation of several palladium complexes, which were characterized in a similar manner including X-ray crystallography. One palladium complex was obtained also from the hydrazide. However, the hydrazide was used mainly as a...

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This thesis entitled “Design and Access to Disallowed and Unusual Conformers of Peptides in Crystals and in Solution: Structural Consequences of the Imidate and Thioimidate Isosteres for the Peptide bond” is divided into eight chapters. Imidate Modification The range of disallowed dihedral angles for residues in peptides is governed by their local steric and electrostatic clashes. Rare tolerances of violations in these angles are attributed to distortions in both local and global bond characteristics of the peptides. Discerning the origins of such disallowed angles and the consequent distortions in body of the peptides is essential, for a complete understanding of the protein fold, to improve the crystal database for validation of rare but acceptable residue conformations and for validation and improvement of theoretical models that evaluate the interactions that define the Ramachandran space. Unlike for the ordered secondary structures such as β-sheets α-helices and β-turns currently there are no models for residues constrained in disallowed folds. We reasoned that residues may be stabilized in disallowed folds in peptides if a neighbouring group and The range of disallowed dihedral angles ( , ψ) for residues in peptides is governed by their hence its local unfavorable clashes can be selectively modified to a motif that favors such space Steric clashes of the type H•••Xi±n involving the backbone amide hydrogen (H) contribute to ~60% of disallowed ,ψspace. Conversion of an amide to an imidate (A→I) will remove the corresponding H and hence the steric clashes related to it in peptides. Importantly, this will introduce an H-bond acceptor N (of imidate) in place of an H-bond donor NH (of amide), which will allow formation of unusual H-bonding interactions between the imidate N and the neighbouring Hs and hence constrain residues in otherwise inaccessible dihedral angles. The conversion of A→I is challenging owing to difficulties in selective synthesis, stability and purification of the imidate motif. We address all these concerns by the selective conversion of a backbone amide in peptides to the relatively stable cyclic 5,6-dihydro-4H-1,3-oxazine imidate isostere, by an intra¬molecular nucleophilic cyclo-O-alkylation reaction. Chapter 1:SectionB: Autocyclo-O-Alkylation of N-(3-Bromopropyl)amides into 2-Alkyl-5,6-Dihydro-4H-1,3-Oxazinehydrobromides We are describing the reactivity of N-(3-bromopropyl)amides that are precursors for 2-peptide-5,6-dihydro-4H-1,3-oxazine. The starting materials, 3-bromopropylamides, were synthesized in good yields by coupling the corresponding carboxylic acids and anhydrides with 3-bromopropylaminehydrobromide using standard mixed anhydride peptide coupling protocol. N-(3-bromopropyl)-acylamides are unstable during the isolation. Time-dependent 1H NMR of all the acetamides revealed that they underwent clean auto-cyclization to form the corresponding 2-alkyl-5,6-dihydro-4H-1,3-oxazine hydrobromides following first order rate. The salts were easily isolated in high purity by trituration of the mixtures with ether. The t1/2 of autocycliation of decreased upon increase in electron density on the R-carbon. Notably, the tert-butyl substituent cyclized significantly faster than acetamide which have enolizable hydrogens at the R-carbon. Thus, the cyclization rate is affected predominantly by the inductive effect of the R-carbon substituents. The formamide remained stable and unchanged due to the poor electron-donating ability of hydrogen. Chapter 1: Section C: Intramolecular Hydrogen Bond Assistance Improves Autocyclization in N-(3-Bromopropyl)amides The autocyclisation do not go to 100% completion. This is because the released hydrobromic acid quenches the nucleophilicity of amide carbonyl oxygen. In order to scavenge hydro bromic acid, we used 1 equivalent of DIEA base is acting only acid scavenger which conformed by unaffecting the reaction rate upon increasing equivalents of DIEA. We found that autocyclisation of N-(3-bromopropyl)amides rates in peptides involved in intramolecular backbone H-bonding interactions improve the autocyclization rates significantly than unstructured (random coil) peptides. Even with in the ordered structures the rate depends on the proximity of H-bonding distances as well as the H-bond acceptor strength. Half-life of autocyclisation in various peptide secondary structures are determined from time variant 1H NMR studies performed at 60 mM peptide concentration in CDCl3 at 32 oC. Chapter 2: Section A: Synthesis and Isolation of 5,6 Dihydro-4H-1,3-Oxazine Containing Peptidomimetics We have introduced 5,6-Dihydro-4H-1,3-oxazine as the imidate isostere at C-terminus of a number of peptides through NaH (base) mediated intramolecular cyclo-O-alkylation of N-(3-bromopropyl)amides. The amide to imidate (A→I) modification reaction is faster (1-5.5 h), Exhibiting no electronic and structural effects under these conditions. The side product NaBr can be easily separated by filtration through celite. No side products were observed and there is no need of further purification to get pure 1,3-oxazines in quantitative yields in all the peptidomimetics. Using this synthetic protocol we have synthesised a variety of 1,3-oxazine containing peptide analogues including aliphatic, branched aliphatic, polar side chains and larger peptides. We show that the retention of configuration at Cαof peptides during the base mediated cyclo-O-alkylation reaction. that the C5i.structures are more populated at Aib due to operation of The Thorpe-Ingold effect. The strength of hydrogen bonding interaction in C5i structure is similar to those of the highly buried backbone hydrogen bonding interaction found in the middle of a model 310-helical peptide as indicated by DMSO titration experiments. Chapter 3: Section A: Consequences of "Disallowed" Conformations on Constrained β-Turn Peptides Here we are describe the consequence of disallowed conformations the on a C-terminus of a type-II β-turn. We choose stereochemically constrained Type-II β-turn Pro-Aib dipeptide analogue which is the ideal model to mirror the structural effects of introducing the A→I modification at the C-terminus. The imidate containing peptidomimetic crystallised in dichloromethane and hexane mixture. Analysis of crystal structure revealed that Aib NH is involved in 3-centered H-bonding interactions with the N of oxazine and N of proline. This constrains Aib in a conformation that is natively disallowed to it. The (, ) angles of Aib residue fall in the (180,0) region which is strictly disallowed for natural peptides due to steric clashes involving the back bone amide N-H. More importantly there are two C•••O interactions which are accomidated in the crystal structures. Both oxygen‟s were place in staggered orientation of the Pro oxygen (OPro) between the two β-CH3 groups of Aib, which is again strictly disallowed in natural peptides due to strong C•••Oi-1 hard sphere clashes. However no vdW space violations are observed between these atoms. Chapter 3: Section B: Conformational Effects of “Disallowed Aib on a 310-Helical peptide In order to investigate the origins and consequences of “disallowed” conformations on a folded helical peptide body, the conformationally stable peptide sequence Boc-Leu1-Aib2-Ala3-Leu4-Aib5-Ala6-Phe7-Aib8-OMe (310-helix-OMe)was chosen which is known to adopt 310-helix in crystal structure. Analyses of the ROESY spectra, DMSO titration experiments, and CD spectra of 310-helix-OMe and its Oxa analogue reveal that their solution conformations are identical to those of the crystal structure of 310-helix-OMeSix sequential i+3→i intramolecular backbone H-bonds stabilize the 310-helical peptide fold in both peptides in solvents of varying polarity. The N-terminal and central segments of the helical molecules are quite structurally rigid and are not deformed. The presence of the disallowed Aib*8 residue in Oxa analogue has a clear conformational effect mainly on the residue Phe7. It looks like the Phe7 amide H is involved in shielding, the Aib*8 amide H through a bifurcated hydrogen bonding interactions with the nitrogen of oxazine and carbonyl oxygen of Ala6 residue. Maximum structural distortion effect on the registers closest to the putative imidate bond. Our results show that “disallowed folds need not denature order in the peptide fold”. Chapter 4: Synthetic Methods for Introducing the A → I Modification anywhere along the Peptide Chain Here we describe the incorporation of imidate isostere in the middle of any peptide sequence. In Oxa selectivity is towards 5-exo-cyclo-O-alkylation in 1 : 4. In Thi it is towards 6-exo-cyclo-S-alkylation in 3 : 1 ratio. This is because of better nucleophile of sulphur (S). We saw that Thi is stable to peptide coupling, N-and C-terminus protection, deprotection conditions and can be easily incorporated in middle of peptide. Chapter 5: Section A: Cis-trans Isomerism in the X-Pro Peptide Bond In tertiary amides like X-Pro peptides having high propensity to access cis conformations due to similar environment in both cis and trans around the Cof X. X-Pro peptide bonds, constrained in s-cis conformations are prevalently found in the turn regions of peptides with the residue „X‟ in the i+1position and Pro at the i+2position of the β¬turn. These types of turns are termed as the type VI β-turns. For better understanding of the molecular recognition at specific cis X-Pro peptide bonds in biological events, the structure and dynamics of various constrained cis X-Pro peptide bond analogues with varying steric and electronic perturbations have been studied. Many models have been developed for stabilizing cis conformer by perturbation of molecular recognition surface of proline by employing steric and electronic interaction. In biological functions proline molecular recognition surface and cis X-Pro peptide bond more important. There is need of novel method for stabilizing X-Pro peptide bond in cis conformer without modifying the pyrolidine ring in proline. Chapter 5: Section B: Biasing the cis/trans Equilibrium in X Pro Peptides using Reverse ni → ni-1 * Interactions Here we present our findings that peptidomimetics containing the 5,6-dihydro-4H-1,3¬oxazine (Oxa) and 5,6-dihydro-4H-1,3-thiazine (Thi) functional groups at the C-terminus of Pro selectively and remotely stabilize the s-cis rotamers of the preceding pyrrolyl (Xaa-Pro) 3° amide bonds, while conserving these recognition elements. The cis/trans equilibrium of Xaa-Pro peptide bonds is shifted significantly in favor of the satirically disfavored cis isomers in these peptidomimetics (upto ~90%). We also provide evidence for the influence of an unusual n→ πi-1 * interaction in the cis, and the n)(n repulsion in the trans, conformers of these molecules to beat the origin of such the origin of such cis stabilization. Chapter 6: Steric Interactions in the cis Piv-Pro Peptide Bond The inaccessibility of cis Piv-Pro rotamer in any peptide is believed to be because the steric clashes between substituents on CX and CPro are unavoidable in this conformer. Here we access the cisPiv-Pro conformer in crystal structure of Piv-Pro-Aib-OMe and that it is sufficiently flexible to undergo bond distortions and avoid all steric clashes between substituents on CPiv and CPro . It is however the unavoidable distortions in the dihedral angle of the Prothe cisPiv-Proconformer. The cisPiv -Pro conformer is indeed accessible, if such distortions are accommodated in the peptide. Chapter 7: Steric and Electronic Interactions in the cis Isomer of Piv-Pro Peptide Bond in Solution We have studied the electronic and steric interactions and the conformational equilibrium in two sets of homologous peptides, X-Pro-Aib-OMe (which contain Aib) and X-Pro-NH-Me, where X is acetyl, propionyl, isobutyryl and pivaloyl, in solvents of varying polarities consisting of carbontetrachloride, chloroform or dimethylsulfoxide, by means of their 1H and 13C-NMR, and FT-IR spectra. Formation of n * interactions between the carbonyls that flank the Aib residue, influences the alleviation of steric interactions that are believed to preclude access to the cis conformer of the Piv-Pro peptide bond. The cis Piv-Pro conformer is observable in the Aib containing peptides, at ambient conditions by FT-IR and at temperatures as low as 273 K by NMR. We estimate that the steric interactions contribute < 0.5 kcal/mol to the conformational free energy of X-Pro peptide bond isomerism, irrespective of the steric bulk on the acyl (X) group. The relative strengths of intramolecular hydrogen bonding interactions involving the X-Pro peptide motif in different conformers of these peptides influence their relative conformational stabilities. Chapter 8: Remote Effect of Oxa and Thi Functional Groups on cis-trans Isomerism at X-Pro Peptide Bonds The C5a interaction at Pro residue occurs in the transition states for the intramolecular acid catalysis of cis → trans isomerization in peptidyl prolyl isomerases (PPIs) and enables the decrease in transition energy barrier for the isomerization process. We show that the NPro….HAib interactions in C5a structures can be remotely effected in order to control in equilibrium constant values of the cis/trans isomerism (Kc/t) in X-Pro¬Aib-Oxa and Thi containing peptides. By this method we observed improvement in Kc/t values from 0.18 in esters to 0.56 in Thi and 0.66 in Oxa containing peptides. Analyses of the ROESY spectra, DMSO titration experiments, variable temperature experiments and FT-IR spectra of R-CO-Pro-Aib-Oxa (R = Me, Et, iPr) and its Thi analogues reveals that both interactions (C5a and C5i) are persistent in cis and trans conformers of this peptidomimetics. (for structural formula pl. see the abstract.)

A series of chiral phosphinoferrocene amides was prepared by the condensation either of 1'- (diphenylphosphino)ferrocene-1-carboxylic acid (Hdpf) or its planar-chiral 1,2-isomers and amino acid methyl esters in the presence of peptide coupling agents. The resulting phosphinoamides were tested as ligands in Cu-catalyzed asymmetric conjugate additions of diethylzinc to chalcones and in Pd-mediated asymmetric allylic substitution reactions of 1,3- diphenylallyl acetate with the respective nucleophile (alkylation, amination and etherification). The catalytic tests were focused on an optimization of the reaction parameters (solvent, temperature, base, metal/ligand ratio) and on survey of various substrates. Compounds based on Hdpf proved to be better ligands in both catalytic reactions than their planar chiral analogues. In order to rationalize the influence of the ligand structure on the reaction course and also to interpret the catalytic results, several model complexes were prepared and structurally characterized. Other three series of non-chiral complexes were prepared from the corresponding (η6 - arene)ruthenium(II) precursor and Hdpf-glycine conjugates; the neutral complexes of the type [(arene)RuCl2(Hdpf-Gly(R)-κP)] (arene = benzene, p-cymene, hexamethyl-benzene; R = OMe, NH2, OH) as well as two...

Foram isoladas de Piper scutifolium e P. corcovadensis seis amidas, incluindo a piperovatina, piperlonguminina, isopiperlonguminina e corcovadina, duas inéditas (scutifoliamida A e scutifoliamida B), além de duas aristolactamas (piperolactama C e stigmalactama). A partir de P. tuberculatum foram isoladas as amidas piplartina e pelitorina e os ésteres (E)-3,4,5-trimetoxicinamato de etila (11) e 3,4,5- trimetoxidiidrocinamato de etila (12), esse último obtido pela primeira vez de origem natural. Em função da atividade biológica apresentada pelas amidas isoladas, foram sintetizadas 5-fenil-pentadienamidas e 3-cinamamidas com diferentes substituintes nos anéis aromáticos e na porção amídica. Os extratos, produtos naturais isolados e sintéticos foram submetidos a ensaios de atividade antifúngica frente Cladosporium cladosporioides e C. sphaerospermum, antimicrobiana frente à Candida albicans, C. krusei, C. parapsilosis e Cryptococcus neoformans, inibidora de acetilcolinesterase, carrapaticida frente à Boophilus microplus e citotóxica frente a linhagens tumorais humanas. Para a atividade antifúngica contra C. cladosporioides e C. sphaerospermum foi constatada maior atividade para as N-isobutil e N-pentilamidas sem substituintes no anel aromático. As N-isobutilamidas foram mais ativas como inibidores de acetilcolinesterase; contra B. microplus grande atividade foi apresentada por piperovatina, e os ensaios de citotoxicidade indicaram que o grupo 5,6-dihidropiridin- 2(1H)-ona é fundamental para a atividade. As plântulas de P. corcovadensis apresentaram em sua composição predominantemente piperovatina e assim foram utilizadas para estudos com incorporação de acetato de sódio-[1-14C] e L-fenilalanina - [U-14C] na mesma. As plântulas e calos obtidos para P. scutifolium não apresentaram produção significativa de metabólitos secundários. O estudo do metabolismo fenilpropanoídico de P. regnellii resultou no isolamento parcial da enzima responsável pela conversão de conocarpano em eupomatenóide-6. / Six amides were isolated from Piper scutifolium and P. corcovadensis including piperovatine, piperlonguminine, isopiperlonguminine and corcovadine, the new scutifoliamide A and scutifoliamide B and also two aristolactams (piperolactam C and stigmalactam). From P. tuberculatum the amides piplartine and pellitorine and two esters, ethyl (E)-3,4,5-trimethoxycinnamate (11) and ethyl 3,4,5- trimethoxydihydrocinnamate (12) were isolated, this last one obtained for the first time from natural sources. Due to the biological activity observed for the natural amides, 5- phenyl-pentadienamides and 3-cinnamamides having different substituents in the aromatic ring and amide moietis were synthesized. Extracts, isolated and synthetic compounds were assayed against Cladosporium cladosporioides, C. sphaerospermum, Candida albicans, C. krusei, C. parapsilosis and Cryptococcus neoformans, inhibitory of acetylcholinesterase, against the tick Boophilus microplus and citotoxic against human cell lines. A higher activity was observed against C. cladosporioides and C. sphaerospermum for N-isobutylamides and N-pentylamides having no substituents in the aromatic ring. N-isobutylamides were very active inhibitors of acetylcholinesterase; piperovatin was the most active against B. microplus and 5,6-dihydropyridin-2(1H)-one moiety was essential as the citotoxicity is concerned. Plantlets of P. corcovadensis contained piperovatine as major compound and thus were used as model for incorporation of sodium acetate-[1-14C] and L-phenylalanine-[U-14C]. The production of secondary metabolites in plantlets and callus of P. scutifolium was not significant. The studies of phenylpropanoid metabolism in P. regnellii was addressed to partial purification and characterization of the enzyme involved in the conversion of conocarpan to eupomatenoid-6.