<p>Escherichia coli i Klebsiella pneumoniae su među najznačajnijim uzročnicima infekcija kod ljudi. Problem predstavljaju multirezistentni sojevi koji se javljaju ne samo u bolničkom nego i u vanbolničkom okruženju. Karbapenemi, beta-laktami sa naj&scaron;irim spektrom delovanja, spadaju u lekove poslednje linije odbrane. Rezistencija na karbapeneme među enterobakterijama je u porastu &scaron;irom sveta. Može nastati usled prisustva karbapenemaza, enzima koji degradiraju karbapeneme, ili usled hiperprodukcije AmpC cefalosporinaza ili beta-laktamaza pro&scaron;irenog spektra uz gubitak porina. Geni koji kodiraju karbapenemaze se nalaze na mobilnim genetičkim elementima koji im omogućavaju brz prenos. Najče&scaron;će karbapenemaze su KPC, NDM, VIM, IMP i OXA-48 enzimi. Detekcija sojeva koji produkuju karbapenemaze nije moguća samo na osnovu profila rezistencije izolata, s obzirom da minimalne inhibitorne koncentracije karbapenema mogu biti u referentnom opsegu. Svaki izolat sa smanjenom osetljivo&scaron;ću na karbapeneme bi trebalo ispitati kako bi se sprečilo njihovo &scaron;irenje. Detekcija karbapenemaza može da se zasniva na fenotipskim i genotipskim metodama. Ciljevi istraživanja su bili da se utvrdi postojanje rezistencije na karbapeneme kod multirezistentnih izolata Escherichia coli i Klebsiella pneumoniae iz kliničkih uzoraka, da se dokaže produkcija karbapenemaza kori&scaron;ćenjem fenotipskih i genotipskih testova, kao i da se analizira osetljivost izolata Escherichia coli i Klebsiella pneumoniae sa molekularno dokazanim karbapenemazama. Istraživanje je sprovedeno kao prospektivna studija u periodu 01.11.2013. do 01.11.2014. godine u Centru za mikrobiologiju Instituta za javno zdravlje Vojvodine u Novom Sadu. U istraživanje je bilo uključeno 300 multirezistentnih izolata Escherichia coli i Klebsiella pneumoniae konsekutivno izolovanih iz kliničkih uzoraka (krv, punktat, sekret iz donjeg respiratornog trakta, urin i sekret rana) hospitalizovanih pacijenata. Identifikacija do nivoa vrste je vr&scaron;ena klasičnim bakteriolo&scaron;kim metodama. Za ispitivanje osetljivosti kori&scaron;ćeni su disk difuziona metoda i gradijent testovi. Vrednosti minimalnih inhibitornih koncentracija su ispitane automatizovanim Vitek 2 sistemom (BioM&eacute;rieux, Francuska), a interpretacija izvr&scaron;ena u skladu sa preporukama CLSI (Clinical Laboratory Standards Institute). Za fenotipsko testiranje prisustva betalaktamaza pro&scaron;irenog spektra kori&scaron;ćen je kombinovani disk test. Za fenotipsko testiranje prisustva karbapenemaza kod sojeva rezistentnih na karbapeneme kori&scaron;ćen je kombinovani disk test i test sinergizma sa dva diska. Detekcija gena za beta-laktamaze blaCTXM, gena za karbapenemaze blaKPC, blaVIM, blaNDM, blaIMP i blaOXA-48-like izvr&scaron;ena je metodom lančane reakcije polimeraze. Genotipizacija odabranih izolata Klebsiella pneumoniae izvr&scaron;ena pomoću repetitivne lančane reakcije polimeraze kori&scaron;ćenjem DiversiLab sistema (BioM&eacute;rieux, Francuska). Od 300 multirezistetntnih izolata, bilo je 242 (80,7%) Klebsiella pneumoniae i 58 (19,3%) Escherichia coli izolovanih iz kliničkih uzoraka. Smanjenu osetljivost na bar jedan karbapenem (imipenem, meropenem, ertapenem) pokazalo je 179 (59,7%) izolata. Fenotipski test za dokazivanje produkcije betalaktamaza pro&scaron;irenog spektra bio je pozitivan kod 87/171 (50,9%) izolata. Gen blaCTX-M je dokazan kod 111/121 (91,7%) izolata. Fenotipski test za dokazivanje karbapenemaza bio je pozitivan kod 65/179 (36,3%) izolata, kod 63 (96,9%) je ukazivao na prisustvo metalo-beta laktamaza, a kod 2 (3,1%) na prisustvo karbapenemaza iz grupe A. Senzitivnost fenotipskog testa za dokazivanje karbapenemaza klase A i B iznosila je 100,0%, specifičnost 96,6%, a ukupna tačnost 97,6%. Karbapenemaze su nađene kod 79/179 (44,1%) izolata rezistentnih na karbapeneme. Gen blaNDM nađen je kod 58 (32,4%) izolata, blaOXA- 48-like kod 11 (6,1%), a blaKPC kod 2 (1,1%) izolata. Geni blaVIM i blaIMP nisu detektovani. Kod 8 (4,5%) izolata nađena su 2 gena koja kodiraju karbapenemaze, blaNDM i blaOXA-48-like. Određivanjem osetljivosti disk difuzionom metodom i automatizovanim Vitek 2 sistemom, izolati koji produkuju karbapenemaze pokazivali su smanjenu osetljivost na sve testirane beta-laktame i gentamicin, odnosno tobramicin. Visok procenat rezistenicije izolati su pokazali u odnosu na ciprofloksacin, levofloksacin i trimetoprim/sulfametoksazol. Najefikasniji antibiotski lekovi su bili amikacin, tigeciklin, fosfomicin i kolistin. Poređenjem minimalnih inhibitornih koncentracija izolata koji produkuju i izolata koji ne produkuju karbapenemaze utvrđena je statistički značajna razlika za meropenem, imipenem, ertapenem, amikacin, gentamicin. Genotipizacijom odabranih izolata Klebsiella pneumoniae kori&scaron;ćenjem DiversiLab sistema klonalno &scaron;irenje je dokazano među izolatima koji produkuju NDM i OXA-48-like karbapenemaze u okviru iste zdravstvene institucije, ali i među različitim zdravstvenim ustanovama. Među izolatima rezistentnim na karbapeneme Klebsiella pneumoniae se če&scaron;će izoluje od Escherichia coli. Kod izolata koji su pokazali smanjenu osetljivost prema bar jednom karbapenemu, karbapenemaze su detektovane u manje od polovine izolata. Kod ostalih izolata dokazane su beta-laktamaze pro&scaron;irenog spektra koje uz gubitak porina mogu uzrokovati rezistenciju na karbapeneme. Kod izolata Klebsiella pneumoniae sa dokazanim genima koji kodiraju karbapenemaze detektovani su pojedinačni blaKPC, blaNDM i blaOXA-48-like geni, kao i kombinacija gena blaNDM i blaOXA-48-like. Kod izolata Escherichia coli nađeni su samo blaNDM geni. Najefikasniji antibiotski lekovi za izolate koji produkuju karbapenemaze su amikacin, tigeciklin, fosfomicin i kolistin. Izolati sa dokazanim karbapenemazama pokazuju rezistenciju na veći broj antibiotika u odnosu na izolate koji ne produkuju karbapenemaze. Dokazano je klonalno &scaron;irenje izolata Klebsiella pneumoniae koji produkuju karbapenemaze. Testove za fenotipsku detekciju karbapenemaza bi trebalo koristiti i u rutinskim mikrobiolo&scaron;kim laboratorijama u skladu sa EUCAST (European Committee on Antimicrobial Susceptibility Testing) preporukama, a konačnu potvrdu treba izvr&scaron;iti molekularnim metodama u referentnoj laboratoriji.</p> / <p>Escherichia coli and Klebsiella pneumoniae are among the most common human pathogens. Multiresistant strains are emerging not only in hospital settings, but also in the community representing a major concern. Carbapenems, beta-lactams with the broadest spectrum of activity are considered to be antibiotics of last resort. Resistance to carbapenems among enterobacteria is spreading worldwide. It is mainly caused by carbapenemases, enzymes capable of degrading carbapenems or by hyperproduction/overexpression of AmpC betalactamases or extended spectrum betalactamases with porin loss. Carbapenemaseencoding genes are usually located on mobile genetic elements providing their fast transfer. The most common carbapenemases are KPC, NDM, VIM, IMP and OXA-48. The detection of carbapenemase-producer cannot rely only on the resistance profile as their minimal inhibitory concentration values may sometimes lay within the susceptibility range. Therefore, every multidrug-resistant isolates with lower susceptibility to carbapenems should be tested for the presence of carbapenemases in order to prevent further spreading. The detection of carbapenemases is based on phenotypic and genotypic methods. The aims of the study were to determine the occurrence of carbapenem resistance in multidrug-resistant Escherichia coli and Klebsiella pneumoniae isolated from clinical samples, to detect carbapenemase production using both phenotypic and genotypic methods and to analyze the susceptibility of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae. The study was conducted from 1st November 2013 to 1st November 2014 at the Center for Microbiology in the Institute for Public Health of Vojvodina, Novi Sad, Serbia. The study included 300 nonrepetitive multidrug-resistant strains of Escherichia coli and Klebsiella pneumoniae isolated from clinical specimen (blood, aspirates, lower respiratory tract secretions, urine and wound secretion) of hospitalized patients. Identification of isolated strains was done using conventional bacteriological methods. Antimicrobial susceptibility was tested using the disk diffusion method and MIC test strips. Minimal inhibitory concentrations were determined using Vitek 2 Compact automated system (BioM&eacute;rieux, France), interpreted according to the CLSI (Clinical and Laboratory Standards Institute) recommendations. Phenotypic testing of extended-spectrum beta-lactamases production was done using combined disk test. Phenotypic testing of carbapenemase production was done by combined disk test and double-disk synergy test. Detection of blaCTX-M, gene encoding extended-spectrum beta-lactamases and blaKPC, blaVIM, blaNDM, blaIMP i blaOXA-48-like, genes encoding carbapenemases was done using PCR. Genotyping of selected Klebsiella pneumoniae isolates was done by repPCR using DiversiLab system (BioM&eacute;rieux, France). From the total of 300 multiresistant isolates, 242 (80.7%) were Klebsiella pneumoniae and 58 (19.3%) were Escherichia coli obtained from clinical samples. Reduced susceptibility to at least one carbapenem (imipenem, meropenem, ertapenem) was found in 179 (59.7%) isolates. Phenotypic test for extended-spectrum betalactamases production was positive in 87/171 (50.9%) isolates. A total of 111/121 (91.7%) isolates harbored blaCTX-M. Phenotypic test for carbapenemase production was positive in 65/179 (36.3%) isolates, 63 (96.9%) indicating the presence of metallo-beta-lactamases and 2 (3.1%) indicating the presence of class A carbapenemases. Sensitivity of the phenotypic test for carbapenemase production of class A and B was 100.0%, specificity 96.6% and overall accuracy 97.6%. Carbapenemases were detected in 79/179 (44.1%) carbapenemresistant isolates. Gene blaNDM was found in 58 (32.4%) isolates, blaOXA-48-like in 11 (6.1%) and blaKPC in 2 (1.1%) isolates. Genes blaVIM and blaIMP were not detected. In 8 (4.5%) isolates 2 genes encoding carbapenemases were found, blaNDM and blaOXA-48-like. Using both disk diffusion method and Vitek 2 automated system for antimicrobial susceptibility testing carbapenemase-producing isolates were resistant to all beta-lactams and also to gentamicin and tobramicin respectively. Resistance rates were high for ciprofloxacin, levofloxacin and cotrimoxazole. Good activity maintained for amikacin, tigecycline, fosfomycin and colistin. Comparing minimal inhibitory concentrations of carbapenemaseproducing isolates and non-carbapenemase producers, significant difference was found for meropenem, imipenem, ertapenem, amikacin and gentamicin. Genotyping of selected Klebsiella pneumoniae isolates using DiversiLab system, revealed the clonal spread of NDM- and OXA-48-like-producers not only within one healthcare-setting, but also between different healthcare centers. Among carbapenem-resistant isolates, Klebsiella pneumoniae was found more often than Escherichia coli. Carbapenemases were detected in less than 50% of isolates resistant to at least one carbapenem. In other carbapenem resistant isolates extended-spectrum betalactamases were confirmed most likely causing carbapenem-resistance with porin deficiency or porin loss. Among carbapenemase-producing Klebsiella pneumoniae blaKPC, blaNDM and blaOXA-48-like genes were detected, as well as combination of 2 genes blaNDM and blaOXA-48-like. In carbapenemase-producing Escherichia coli only blaNDM was found. The most efficient antimicrobial drugs among tested carbapenemase-producing isolates were amikacin, tigecycline, fosfomycin and colistin. Carbapenemase-producing isolates were resistant to more antimicrobial agents compared to non-carbapenemase producers. Clonal dissemination of carbapenemase-producing Klebsiella pneumoniae was confirmed. Phenotypic detection of carbapenemase production should be done in routine microbiology laboratories according to EUCAST (European Committee on Antimicrobial Susceptibility Testing) recommendations. Final confirmation should be done by molecular methods in the reference laboratory.</p>

Les antibiotiques β-lactamines sont parmi les médicaments antimicrobiens les plus anciens et les plus utilisés. L'enzyme bactérienne β-lactamase hydrolyse l'antibiotique β-lactame en cassant la structure de base "anneau β-lactame". Pour identifier les nouvelles β-lactamases, une étude complète a été réalisée dans diverses bases de données biologiques telles que Human Microbiome Project, env_nr et NCBI nr. L'analyse a révélé que les séquences ancestrales putatives et les recherches de profil HMM jouaient un rôle important dans l'identification de la base de données homologue et métagénomique à distance dans l'enzyme β-lactamase existante comme matière noire. Les larges analyses phylogénétiques des β-lactamases existantes et nouvellement identifiées représentent les nouveaux clades dans les arbres. En outre, l'activité d'hydrolyse des antibiotiques β-lactamines de séquences nouvellement identifiées (provenant d'archées et d'humains) a été étudiée en laboratoire, ce qui montre l'activité de la β-lactamase. La deuxième phase de l'étude a été entreprise pour examiner l'évolution fonctionnelle des β-lactamases. Premièrement, des séquences de protéines ß-lactamase 1155 ont été extraites de la base de données ARG-ANNOT et des valeurs CMI la littérature correspondante. Les résultats ont révélé que l'activité fonctionnelle de la β-lactamase évoluait de manière convergente au sein de la classe moléculaire. La troisième phase de cette thèse représente le développement d'une base de données intégrative de β-lactamases. La base de données publique actuelle de β-lactamases a des informations limitées, par conséquence, une base de données intégrative a été développée. / The β-lactam antibiotics are one of the oldest and widely used antimicrobial drugs. The bacterial enzyme β-lactamase hydrolyzes the β-lactam antibiotic by breaking the core structure “β-lactam ring”. To identify the novel β-lactamases a comprehensive investigation was performed in different biological databases such as Human Microbiome Project, env_nr, and NCBI nr. The analysis revealed that putative ancestral sequences and HMM profile searches played a significant role in the identification of remote homologous and uncovered the existing β-lactamase enzyme in the metagenomic database as dark-matter. The comprehensive phylogenetic analyses of extant and newly identified β-lactamase represent the novel clades in the trees. Further, the β-lactam antibiotic hydrolysis activity of newly identified sequences (from archaea and human) was investigated in laboratory, which shows β-lactamase activity.The second phase of the investigation was undertaken to examine the functional evolution of β-lactamases. First, 1155 β-lactamase protein sequences were retrieved from ARG-ANNOT database and MIC values from the corresponding literature. The results revealed that the functional activity of β-lactamase evolved convergently within the molecular class.The third phase of this thesis presents development of an integrative β-lactamase database. The existing public database of β-lactamase has limited information, therefore, an integrative database was developed.

Η Ecteinascidin 743 είναι ένα σπουδαίο αντικαρκινικό φάρμακο, που καταστρέφει μέσω αλκυλίωσης τα καρκινικά κυττάρα και είναι εμπορικά διαθέσιμο με το όνομα Yondelis. Χρησιμοποιείται στην Ευρώπη, τη Ρωσία και τη Νότια Κορέα για τη θεραπεία του σαρκώματος του μαλακού ιστού, δηλαδή καρκίνου των ιστών που υποστηρίζουν το σώμα, όπως οι μύες, τα αιμοφόρα αγγεία και άλλα είδη ιστών που υποστηρίζουν και προστατεύουν τα όργανα του σώματος. Η Ecteinascidin 743 βρίσκεται υπό κλινικές δοκιμές για τη θεραπεία και άλλων μορφών καρκίνου, όπως του καρκίνου του μαστού, του προστάτη, των ωοθηκών, των νεφρών, των πνευμόνων και του μελανώματος. Απομονώθηκε από το μικρό θαλάσσιο οργανισμό, Ecteinascidia turbinate, που ζει στις θάλασσες της Καραϊβικής και ανακαλύφθηκε ότι έχει αντικαρκινική δράση το 1969. Αυτό το φυσικό προϊόν αποτέλεσε πηγή έμπνευσης για την παρούσα ερευνητική εργασία, όπου στην ρετροσυνθετική του πορεία (Εικόνα 3) περιλαμβάνεται η σύνθεση ενός μορίου πιπεραζίνης, καθώς και ενός β-λακταμικού δακτυλίου. Οι β-λακτάμες χρησιμοποιούνται σήμερα ως βακτηριοκτόνα, αντιβιοτικά, αναστολείς των πρωτεασών σερίνης και αναστολείς της ακυλομεταφεράσης της χοληστερολης (acyl-CoA: cholesterol acyltransferase, ACAT), η οποία είναι υπεύθυνη κυρίως για την αθηροσκληρωτική στεφανιαία καρδιακή νόσο. Η ασθένεια αυτή αποτελεί ήδη την πιο κοινή μορφή ασθένειας που προσβάλλει την καρδιά και μία σημαντική αιτία πρόωρου θανάτου στην Ευρώπη, σε κράτη της Βαλτικής, τη Ρωσία, τη Βόρεια και Νότια Αμερική, την Αυστραλία και τη Νέα Ζηλανδία. Η αθηροσκλήρωση σχετίζεται με την στεφανιαία καρδιακή νόσο, η οποία αποδίδεται στην ανικανότητα της στεφανιαίας κυκλοφορίας να τροφοδοτεί με επαρκές αίμα το μυ της καρδιάς και τους περιβάλλοντες ιστούς. Οι παράγοντες που οδηγούν στην αθηροσκλήρωση είναι τα υψηλά επίπεδα χοληστερόλης, η υπέρταση, ο διαβήτης, το κάπνισμα, οι κακές διατροφικές συνήθειες, η παχυσαρκία και η έλλειψη σωματικής άσκησης. Οι παραπάνω δράσεις των β-λακταμών έχουν καταστήσει πολύ ενδιαφέρουσα τη στερεοεκλεκτική και εναντιοεκλεκτική σύνθεση αυτών. Ένας β-λακταμικός δακτύλιος είναι μία λακτάμη με δομή ετεροατομικού τετραμελούς δακτυλίου, που αποτελείται από τρία άτομα άνθρακα και ένα άτομο αζώτου. Ο β-λακταμικός δακτύλιος είναι μέρος της δομής μερικών κατηγοριών β- λακταμικών αντιβιοτικών, όπως οι πενικιλίνες, οι κεφαλοσπορίνες, οι κεφαμυκίνες, οι καρβαπενέμες, οι μονοβακτάμες, και οι τρινέμες. Οι ενώσεις των β-λακταμών παρασκευάστηκαν σύμφωνα με την Mannich αντίδραση μέσω σουλφινιμινών. Οι πιπεραζίνες χρησιμοποιούνται σήμερα ως μυκητοκτόνα, αγχολυτικά, αντιικά, και ανταγωνιστές του υποδοχέα της σεροτονίνης (5-HT). Η τελευταία θεραπευτική ικανότητα των πιπεραζινών είναι πλέον ένα θέμα εκτενούς επιστημονικής έρευνας και περιλαμβάνει υποδοχείς-στόχους που ανήκουν στην κατηγορία των υποδοχέων συζευγμένων με G-πρωτεΐνη (G-ptotein-coupled receptors, GPCRs). Η εκλεκτικότητα των πιπεραζινών για τις GPCRs εμφανίζεται εξαιτίας της βασικότητας. Αυξάνοντας το μέγεθος του όρθο υποκαταστάτη σε Ν-άρυλο πιπεραζίνες, αυξάνεται η ικανότητα πρόσδεσής τους και η λειτουργική τους δραστικότητα. Οι πιπεραζίνες είναι οργανικές ενώσεις, που αποτελούνται από έναν εξαμελή δακτύλιο, ο οποίος περιέχει δύο άτομα αζώτου, που βρίσκονται στις θέσεις 1 και 4 του δακτυλίου. Οι ενώσεις των πιπεραζινών παρασκευάστηκαν σύμφωνα με την Diels-Alder αντίδραση μέσω σουλφινιμινών. Οι σουλφινιμίνες αποτέλεσαν το μόριο-κλειδί για την σύνθεση όλων των τελικών επιθυμητών προϊόντων και είναι γνωστές ως πολύ καλοί πρόδρομοι αμινών, όταν αντιδράσουν με οργανομεταλλικές ενώσεις [RLi, RMgX (αντιδραστήρια οργανολιθίου, αντιδραστήρια Grignard)]. Οι οπτικώς καθαρές σουλφινιμίνες είναι σημαντικές δομικές μονάδες (building blocks) στην ασύμμετρη σύνθεση άμινο παραγώγων, και παρασκευάζονται σε πολύ καλές αποδόσεις μέσω ενός σταδίου από αρωματικές, ετεροαρωματικές και αλιφατικές αλδεΰδες. Στην παρούσα ερευνητική μελέτη συντέθηκαν νέες β-λακταμικές ενώσεις και υποκατεστημένες ενώσεις πιπεραζίνης, συμπληρώνοντας έτσι και ενισχύοντας τα ήδη υπάρχοντα δεδομένα για τις συγκεκριμένες κατηγορίες ενώσεων αφενός και, αφετέρου, παρέχοντας νέα δεδομένα για την ολική σύνθεση του φυσικού προϊόντος, Ecteinascidin 743 (σύνθεση των εξαμελών αζόξυ προϊόντων 18, 19 και 20). Η ρετροσυνθετική ανάλυση της Ecteinascidin 743, που περιγράφηκε αρχικά, δύναται να εφαρμοστεί, σύμφωνα με τα αποτελέσματα της παρούσας ερευνητικής εργασίας. / Ecteinascidin 743 is an important antitumor drug that can service a novel way of killing cancer cells, and it is sold under the brand name Yondelis. It has been approved for use in Europe, Russia and South Korea for the treatment of advanced soft tissue sarcoma, cancers of the supporting tissues of the body, such as muscles, fat, blood vessels or in any other tissues that support, surround and protect the organs of the body. Ecteinascidin 743 is undergoing clinical trials for the treatment of breast, prostate, ovarian, renal, lung, and melanoma cancers. It is isolated from the Caribbean tunicate Ecteinascidia turbinate, and was found to have anticancer activity in 1969. We were inpired by this natural product and as we can observe from its retrosynthetic analysis (Scheme 3), the synthesis of a piperazine molecule and a β-lactam ring are involved. The extreme importance of β-lactams serving not only as bactericidal and as key structural units of several important antibiotics, but also as mechanism-based inhibitors of serine proteases and as inhibitors of acyl-CoA cholesterol acyltransferase (ACAT), which is mainly responsible for atherosclerotic coronary heart disease. Coronary heart disease is already the most common form of disease affecting the heart and is an important cause of premature death in Europe, the Baltic states, Russia, North and South America, Australia and New Zealand. Atherosclerosis is most commonly equated with atherosclerotic coronary artery disease, which is rendered in the failure of the artery circulation to supply with sufficient blood the heart muscle and the surrounding tissues. Risk factors for the coronary heart disease include high levels of cholesterol, hypertension, diabetes, smoking, bad diet habbits, obesity, and lack of excercise. The above activities of β-lactams have propelled strong resurgent interest toward their stereoselective and enantioselective synthesis. A β-lactam ring is a lactam with a heteroatomic four-membered ring structure, consisting of three carbon atoms and one nitrogen atom. Penicillins, cephalosporins, cephamycins, carbapenems, monobactams, and trinems are classified as b-lactam antibiotics. β-Lactams were prepared by the Mannich reaction using sulfinimines. Piperazines are used now-a-days as antifungals,antidepressants, antiviral, and serotonin receptor antagonists (5-HT). The latter therapeutic area of piperazines has been the subject of intense research and includes targets belonging to the G-Protein- Coupled Receptor (GPCR) superfamily. The selectivity of piperazines towards GPCRs has deen attributed to their basicity. Increasing the size of the ortho substituent in N-aryl piperazines resulted in an increase in binding affinity and functional potency. Piperazines are organic compounds that consists of a six-membered ring containing two opposing nitrogen atoms, at the 1 and 4 positions of the ring. Piperazines were prepared by the Diels-Alder reaction using sulfinimines. Sulfinimines are the key-compounds for the synthesis of the final desirable products described herein and excellent precursors of amines, when they react with organometallic compounds [RLi, RMgX (organolithium reagents, Grignard reagents)]. Enantiomerically pure sulfinimines representing, important building blocks in the asymmetric synthesis of amine derivatives, are prepared in high yields in one step from aromatic, heteroaromatic, and aliphatic aldehydes. In this project, novel β-lactam compounds and substituted piperazine compounds were synthesized, in order to complete and highlight the already existing data for these specific compounds classes and provide new data about the total synthesis of the natural product, Ecteinascidin 743 (synthesis of six-membered azoxy products 18, 19 and 20). The retrosynthetic analysis of Ecteinascidin 743 could be viable given the result described in Scheme 44.

La synthèse d'une nouvelle famille d'oligomères de motifs contraints de dipeptides est décrite dans ce manuscrit. Les monomères utilisés sont des motifs 3(S)-amino-5-carbonylméthyl-2,3-dihydro-1,5-benzothiazépine-4(5H)-one (DBT), acide 2-aminométhyl-phényl-acétique (AMPA) et α-amino γ-lactames. La structure secondaire de ces édifices a été étudiée par spectroscopies RMN, IR, CD et RX. Nous avons montré tout d'abord que les oligomères de DBT sont capables d'adopter des structures stables et définies en ruban. En se basant sur ces structures, nous avons conçu de nouveaux systèmes beaucoup plus versatiles qui permettent de répartir diverses fonctions (basiques, acides, aromatiques) de part et d'autre de l'axe du ruban. Une stratégie de synthèse originale a été développée à cet effet. Elle consiste en la conversion directe de séquences peptidiques, incorporant des méthionines, en oligomères d'α-amino γ-lactames. Ils sont capables, au même titre que ceux de DBT, d'adopter des structures en ruban et de pénétrer dans les cellules. Enfin une étude in vivo chez la souris a montré le fort potentiel anti-tumoral d'un bioconjugué associant des oligomères d'AMPA à un inhibiteur de la Cathepsine D, enzyme lysosomale surexprimée et sécrétée par de nombreuses tumeurs solides. / The synthesis of a new type of constrained dipeptide motif oligomers is described. Monomers used are the (3S)-amino-5-(carboxylmethyl)-2,3-dihydro-1,5-benzothiazepin-4(5H)-one (DBT), the 2-aminomethyl-phenyl-acetic acid (AMPA) and α-amino γ-lactams. The secondary structure of those architectures has been studied by NMR, IR, CD and X-ray spectroscopies. Firstly, we demonstrated that DBT oligomers are able to adopt stable and well defined ribbon like structures. Based on these structures, we designed new systems, far more versatile which are able to distribute various functions (basic, acidic, aromatic) on each side of the ribbon axis. An original strategy has been developed for this purpose. It consists in the direct conversion of peptidic sequences, incorporating methionine, in α-amino γ-lactams oligomers. They are able, as the DBT, to adopt ribbon like structures and to be internalized into cells. Finally, an in vivo study in mice showed the high anti-tumoral potency of a bioconjugate linking AMPA oligomers to an inhibitor of the cathepsin D, a lysosomal enzyme overexpressed and secreted by numerous solid tumors.

Les hypersensibilités allergiques médicamenteuses sont des pathologies mettant en jeu le système immunitaire et induites par la prise de médicaments. Notre travail s’est décomposé en quatre étapes successives : 1- Nous avons classé les β-lactamines en fonction de leurs champs moléculaires, et obtenons un dendrogramme de 4 familles, validé par les données cliniques. Nous avons également réalisé une étude de 3D-QSAR visant à connaître les parties du médicament impliquées dans la pathologie, et à prédire l’allergénicité des β-lactamines. 2- Partant de l’hypothèse que les β-lactamines sont des haptènes, nous avons étudié leur réactivité vis-à-vis d’acides aminés de type lysine et sérine. Nous avons ensuite réalisé des expériences de « docking » afin de définir les interactions entre le médicament et l’albumine sérique humaine. Nous concluons que les sites des lysines 190 et 212 sont les plus adaptés pour la fixation covalente de la drogue et avons validé cette analyse par des méthodes mixtes QM/MM. Enfin, grâce à notre logiciel SuMo, nous avons déterminé d’autres protéines candidates pour l’hapténisation. 3- S’agissant des HyperSensibilités Allergiques Immédiates, nous avons modélisé les différents partenaires que sont les IgE, la β-lactamine portée ou non par une protéine. Nous avons envisagé plusieurs modes de reconnaissance. D’autre part, nous avons analysé les modifications de la protéine, induites par la fixation de la drogue. 4- Concernant les HSA retardées, nous avons émis plusieurs scénarios de reconnaissance de la β-lactamine par le TCR. Nous avons modélisé différents complexes impliquant le TCR, le peptide hapténisé par le médicament, un ion éventuel, ainsi que le CMH, et les soumettons à des dynamiques moléculaires afin d’en étudier la pertinence. D’autre part, nous avons déterminé plusieurs peptides, issus des protéines d’hapténisation et susceptibles de présenter le médicament au TCR, via le CMH. L’ensemble des résultats obtenus est ou sera validé par des expériences in vitro et in vivo. / Drug hypersensitivity is an immune-mediated reaction to a drug. Our work was divided into four stages: 1 - We have classified β-lactam antibiotics based on their molecular fields, and obtained a dendrogram of 4 families, validated by clinical data. We also conducted a 3D-QSAR study to determine what parts of the drug are involved in the pathology and to predict the allergenicity of β- lactams. 2 - Under the assumption that β-lactam antibiotics are haptens, we studied their reactivity in comparison with lysine and serine. We then conducted "docking" experiments to define the interactions between the drug and human serum albumin. We conclude that lysine 190 and 212 are the most suitable sites for the covalent binding of the drugs. We validate this analysis by mixed QM / MM methods. Finally, thanks to our software SuMo, we have found other candidate proteins for haptenization. 3 - Regarding immediate hypersensitivity reactions, we modeled the IgE, the β-lactam and the haptenized protein. We considered several modes of recognition. Secondly, we analyzed the structural changes of the protein induced by the binding of the drug. 4 - Concerning delayed reactions, we considered different scenarios for the recognition of β-lactam by the TCR. We modeled complexes involving the TCR, the peptide haptenized by the β-lactam, a possible ion, and the MHC. We investigated them with molecular dynamics to study their relevance. On the other hand, we have identified many peptides derived from haptenization proteins and able to present the drug to the TCR through the MHC. The validity of the obtained results is or will be confirmed using experiments in vitro and in vivo.

[ES] Los fármacos pertenecientes a la familia de los ß-lactámicos son los antibióticos más usados en todo el mundo. Estudios recientes revelan que hasta un 10% de la población refiere haber presentado síntomas alérgico, esta porción de la población se considera "alérgica". En el diagnóstico de la alergia a antibióticos ß-lactámicos existen varios tipos de pruebas que sirven para orientar y confirmar la presencia de una alergia, clasificadas como ensayos in vivo e in vitro. En lo que se refiere a los ensayos in vivo, la detección de los procesos alérgicos más comunes se realiza mediante pruebas de exposición oral controladas, y pruebas intraepidérmicas e intradérmicas. No obstante, estas pruebas tienen sus limitaciones como es el riesgo de inducir reacciones alérgicas sistémicas graves. Por todo ello, su práctica requiere personal entrenado. Este requisito limitan la realización de este tipo de pruebas a centros hospitalarios especializados. La aplicación y desarrollo de técnicas de diagnóstico in vitro tiene como objetivo llegar a un diagnóstico de la alergia sin riesgos para el paciente. Entre las distintas pruebas serológicas y celulares que se pueden emplear, la detección de IgE específica es una de las más extendidas debido a que, dada su sensibilidad y especificidad, y mayor seguridad. Los sistemas de diagnóstico in vitro actuales utilizan una instrumentación analítica cara y de gran tamaño, así como materiales desechables caros, manejados por personal cualificado, por lo que este tipo de pruebas se realizan únicamente por servicios de alergia y/o análisis clínicos de grandes centros sanitarios. En consecuencia, hay una necesidad de desarrollar nuevos métodos de diagnóstico que cumplan los requisitos de sensibilidad, rapidez, sencillez, multiplexado y portabilidad, a un precio reducido para su implantación en todo tipo de laboratorios clínicos de los diferentes niveles de atención sanitaria. Por este motivo, en esta tesis doctoral se plantea como objetivo principal la puesta a punto de un inmunoensayo múltiple, utilizando la tecnología de disco compacto para la detección y cuantificación in vitro de niveles de IgE específica a un amplio espectro de antibióticos ß-lactámicos en muestras de suero humano. Las limitaciones más críticas para la determinación de IgE específica multianalito mediante métodos inmunoquímicos son las relacionados con la sensibilidad y selectividad. Por lo tanto, una parte importante de la tesis se ha centrado en la preparación y caracterización de un panel antígenos ß-lactámicos, selección de inmunoreactivos, formato y estudio de diferentes parámetros claves del inmunoensayo. Otra parte importante de la tesis se ha enfocado en abordar la mejora de la reproducibilidad de los resultados. La estrategia ha consistido en estudiar diferentes sistemas de calibración con el objetivo de estandarizar la cuantificación de los métodos in vitro de diagnóstico de este tipo de alergias. Para ello, se han evaluado las prestaciones de la calibración homóloga, heteróloga y el uso de un patrón interno, comparado sus prestaciones analíticas (relación señal ruido, sensibilidad, reproducibilidad, etc.) con el sistema de referencia. Finalmente, la validación del inmunoensayo se realizó con un conjunto de 101 muestras de suero de pacientes y controles. Los resultados obtenidos han sido comparados con los obtenidos mediante las técnicas de referencia, mostrando una mejor sensibilidad, especificidad, precisión, y linealidad. La capacidad múltiplex de la tecnología de disco compacto permitió llevar a cabo paralelamente estudios de reactividad cruzada frente a diferentes antibióticos ß-lactámicos esclareciendo el patrón de reconocimiento de los pacientes. En esta línea de trabajo, el uso de otras estrategias de conjugación de haptenos ha resultado en la mejora de la sensibilidad clínica del ensayo, identificando nuevos epítopos / [CA] Els fàrmacs que pertanyen a la família dels beta-lactams, són els antibiòtics d'us més estès a tot el món. Estudis recents posen de manifest que fins un 10% de la població ha presentat símptomes d'al·lèrgia, essent considerats població al·lèrgica als beta-lactams. En el diagnòstic de l'al·lèrgia front aquest tipus d'antibiòtics, existeixen diferents tipus de proves que serveixen per orientar i confirmar la presència d'una al·lèrgia, classificades com assajos in vivo i in vitro. Pel que fa als assajos in vivo, la detecció dels processos al·lèrgics més comuns es realitza mitjançant proves d'exposició oral controlades, i proves intra-epidèrmiques i intradèrmiques. No obstant això, aquestes proves tenen les seues limitacions com és el risc d'induir reaccions al·lèrgiques sistèmiques greus. Per tot això, la seua pràctica requereix personal entrenat. Aquests requisits limiten la realització d'aquesta mena de proves a centres hospitalaris especialitzats. L'aplicació i desenvolupament de tècniques de diagnòstic in vitro té com a objectiu arribar a un diagnòstic de l'al·lèrgia sense riscos per al pacient. Entre les diferents proves serològiques i cel·lulars que es poden emprar, la detecció d'IgE específica és una de les més esteses donada la seua sensibilitat, especificitat, i major seguretat. Els sistemes de diagnòstic in vitro actuals utilitzen una instrumentació analítica cara i de gran grandària, així com materials d'un sol ús també cars, que requereixen de personal qualificat, per la qual cosa aquest tipus de proves es realitzen únicament per serveis d'al·lèrgia i/o anàlisis clíniques de grans centres sanitaris. En conseqüència, hi ha una necessitat de desenvolupar nous mètodes de diagnòstic que complisquen els requisits de sensibilitat, rapidesa, senzillesa, multiplexatge i portabilitat, a un preu reduït per a la seua implantació en tota mena de laboratoris clínics dels diferents nivells d'atenció sanitària. Per aquest motiu, en aquesta tesi doctoral es planteja com a objectiu principal la posada a punt d'un immunoassaig múltiple, utilitzant la tecnologia de disc compacte per a la detecció i quantificació in vitro de nivells d'IgE específica a un ampli espectre d'antibiòtics ß-lactáms en mostres de sèrum humà. Les limitacions més crítiques per a la determinació d'IgE específica multianàlit mitjançant mètodes inmunoquímics estan directament relacionades amb la sensibilitat i selectivitat. Per tant, una part important de la tesi s'ha centrat en la preparació i caracterització d'un panell antígens ß-lactáms, selecció d'inmunoreactius, del format d'assaig i estudi de diferents paràmetres claus de l'immunoassaig. Una altra part important de la tesi s'ha enfocat a abordar la millora de la reproductibilitat dels resultats. L'estratègia ha consistit a estudiar diferents sistemes de calibratge amb l'objectiu d'estandarditzar la quantificació dels mètodes in vitro de diagnòstic d'aquesta mena d'al·lèrgies. Per a això, s'han avaluat les prestacions del calibratge homòleg, heteròleg i l'ús d'un patró intern, comparant les seues prestacions analítiques (relació senyal soroll, sensibilitat, reproductibilitat, etc.) amb el sistema de referència. Finalment, la validació de l'immunoassaig es va realitzar amb un conjunt de 101 mostres de sèrum de pacients i controls. Els resultats obtinguts han sigut comparats amb els obtinguts mitjançant les tècniques de referència, mostrant una millor sensibilitat, especificitat, precisió, i linealitat. La capacitat múltiplex de la tecnologia de disc compacte va permetre dur a terme paral·lelament estudis de reactivitat creuada enfront de diferents antibiòtics ß-lactáms esclarint el patró de reconeixement dels pacients. En aquesta línia de treball, l'ús d'altres estratègies de conjugació d'haptens ha resultat en la millora de la sensibilitat clínica de l'assaig, identificant nous epítops / [EN] ß-lactam antibiotics are one of the most widely used antimicrobials worldwide. However, up to 10% of the population reports having presented allergic symptoms derived from their consumption. Consequently, this portion of the population is considered "allergic". In the diagnosis of allergy to ß-lactam antibiotics there are several types of tests that serve to orient and confirm the presence of an allergy. These diagnostic methods are classified as in vivo and in vitro assays. Regarding in vivo tests, the most standardized tests are the provocation, prick and intradermal test. The aim of these assays is to observe the response produced by the different beta-lactam antibiotics in the patient after oral or cutaneous administration. Despite their wide use, these tests have their limitations, such as the risk of inducing severe systemic allergic reactions. Therefore, their practice requires specialized professionals for their indication, performance and interpretation. This requirement limit the performance of this type of test to specialized hospitals. The use and development of in vitro diagnostic techniques can overcome these disadvantages and allow the diagnosis of allergy without risks. In vitro assays are less invasive and therefore neither pose a risk of adverse reactions. Among the different serological and cellular tests that can be used, the detection of specific IgE is one of the most widespread due to its sensitivity and specificity. Current in vitro diagnostic systems use expensive and bulky analytical instrumentation and high-cost single-use materials, handled by qualified professionals. Therefore, such tests are performed only by allergy and/or clinical analysis services of hospitals or by companies specialized in clinical diagnostics. Consequently, there is a need to develop new diagnostic methods that can be implemented in all types of clinical laboratories at diverse levels of health care, meeting the requirements of sensitivity, speed, simplicity, multiplexing and portability at a reduced price. For this reason, the main objective of this doctoral thesis is the development of a multiplex immunoassay using compact disc technology for the detection and quantification of specific IgE levels to a wide variety of ß-lactam antibiotics in human serum samples. The most crucial limitations for the determination of multianalyte specific IgE by immunochemical methods are those related to sensitivity and selectivity. Hence, an important part of the thesis has been focused on the preparation and characterization of a pool of beta-lactam antigens, selection of immunoreagents, format and optimization of different critical parameters of the immunoassay. Another important aspect of the thesis has been focused on improving the reproducibility of the results. The strategy consisted of studying different calibration systems with the aim of standardizing the quantification of in vitro diagnostic tests for this type of allergy. To achieve that goal, the performance of homologous and heterologous calibration and the use of an internal standard have been evaluated, comparing their analytical performance (signal-to-noise ratio, sensitivity, reproducibility, etc.) with the reference system. Finally, the validation of the immunoassay was performed with a total of 101 serum samples from patients and controls. The results obtained have been compared with those obtained using the reference techniques, showing improved sensitivity, specificity, precision, and linearity. The multiplex capability of the compact disc technology allowed carrying out parallel cross-reactivity studies against different beta-lactam antibiotics both from the penicillin family and from other families, elucidating the recognition profile. Following this working line, the use of other hapten conjugation strategies improved clinical sensitivity of the assay by identifying new epitopes. / Juárez Rodriguez, MJ. (2022). Metodologías bioanalíticas para el diagnóstico in vitro de alergia a antibióticos ß-lactámicos [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/184011 / TESIS / Premios Extraordinarios de tesis doctorales

Tesis por compendio / [ES] El diagnóstico de alergias a antibióticos ß-lactámicos incluye el uso de pruebas in vivo no satisfactorias ya que consumen mucho tiempo y conllevan el riesgo de provocar una nueva reacción alérgica. Por otro lado, los métodos in vitro basados en la inmunodetección de IgE alérgeno-específica generan una información muy valiosa, confirmando o descartando la alergia y postulándose como una alternativa de diagnóstico segura. A pesar de ello, las pruebas in vitro actuales carecen de sensibilidad y exactitud, con un 81% de falsos negativos, lo que limita su uso diagnóstico. Esto ha desencadenado una creciente demanda de nuevas pruebas in vitro basadas en la inmunodetección de IgE, el biomarcador presente en suero más estudiado en alergia. Sin embargo, la falta de estándares de referencia de IgE alérgeno-específica ha imposibilitado la validación y estandarización de los métodos, lo que hace que los resultados de las distintas pruebas no sean comparables. Además, dicha falta de estándares de referencia hace que las concentraciones de IgE específica se calculen a partir de una curva de calibración de IgE total mediante una interpolación heteróloga, lo que ha demostrado no ser totalmente correcto. Por los motivos mencionados, en esta tesis doctoral se plantea como objetivo principal el diseño, obtención y caracterización de proteínas recombinantes con reactividad frente a antibióticos ß-lactámicos. Esta investigación comienza con la puesta a punto de un inmunoensayo en placa ELISA con detección quimioluminiscente para la cuantificación de IgE específica. El ensayo desarrollado permitió determinar IgE específica por debajo de 0.1 IU/mL (0.24 ng/mL), permitiendo así la identificación de pacientes alérgicos con una mayor sensibilidad, utilizando solo 25 ¿L de muestra (suero). El inmunoensayo mostró una buena sensibilidad (64.6%), así como una excelente especificidad (100%), que mejoran significativamente el carácter predictivo de las pruebas in vitro existentes. A continuación, se abordó la obtención y caracterización de proteínas recombinantes similares a las IgE específicas de los ß-lactámicos utilizando la metodología Phage Display. La primera aproximación se trata de una proteína formada por dos nanoanticuerpos que mimetiza el comportamiento de una IgE específica. De esta manera, se obtuvieron proteínas recombinantes en las que uno de los nanoanticuerpos reconoce selectivamente un determinante antigénico de un antibiótico ß-lactámico, mientras que el otro reconoce específicamente al parátopo de un anticuerpo detector anti-IgE. Estas construcciones resultaron ser estables y funcionales. El papel de estas proteínas recombinantes como calibrador homólogo se estudió determinando la concentración de IgE específica a penicilina G presente en suero mediante un ensayo quimioluminiscente. El método desarrollado duplicaba la sensibilidad clínica (66%) frente al método de referencia (28%), mientras que mantenía una especificidad clínica del 100%. Alcanzado este punto, la tesis se centró en la producción de IgE específica recombinante utilizando como material de partida el ADN de un paciente alérgico a amoxicilina y penicilina G. A partir del material genético aislado, mediante Phage Display, ingeniería de anticuerpos y métodos de expresión en células de insecto se consiguió producir una IgE específica recombinante. De esta manera, se obtuvo un producto biológico que cumple con los requisitos para su adopción como material de referencia en ensayos in vitro. Igualmente, se utilizó como calibrador homólogo para la determinación de IgE específica a amoxicilina. Se alcanzó un límite de detección de 0.05 IU/mL con el que se conseguía un aumento de la sensibilidad clínica (73%) que cuadruplicaba al método de referencia (16%), manteniendo la especificidad clínica en el 100%. / [CA] El diagnòstic d'al·lèrgies a antibiòtics ß-lactàmics inclou l'ús de proves in vivo no satisfactòries, ja que consumeixen molt de temps i comporten el risc de provocar una nova reacció al·lèrgica. D'altra banda, els mètodes in vitro basats en la immunodetecció d'IgE al·lergen-específica generen una informació molt valuosa, confirmant o descartant l'al·lèrgia i postulant-se com una alternativa de diagnòstic segura. Tanmateix, a les proves in vitro actuals hi ha una manca de sensibilitat i exactitud, amb un 81% de falsos negatius, cosa que en limita l'ús diagnòstic. Tot això ha desembocat en una demanda creixent de noves proves in vitro basades en la immunodetecció d'IgE, el biomarcador present en sèrum més estudiat en al·lèrgia. No obstant això, la manca d'estàndards de referència d'IgE al·lergen-específica ha impossibilitat la validació i estandardització dels mètodes, cosa que fa que els resultats de les diferents proves no siguen comparables. A més, aquesta manca d'estàndards de referència fa que les concentracions d'IgE específica es calculen a partir d'una corba de calibratge d'IgE total mitjançant una interpolació heteròloga, un mètode que ha demostrat no ser totalment correcte ja que no es pren en consideració la interacció entre el determinant antigènic i la IgE específica. Pels motius mencionats, en aquesta tesi doctoral es planteja com a objectiu principal el disseny, l'obtenció i la caracterització de proteïnes recombinants amb reactivitat davant dels antibiòtics ß-lactàmics. Aquesta investigació comença amb la posada a punt d'un immunoassaig en placa ELISA amb detecció quimioluminiscent per a la quantificació d'IgE específica. L'assaig desenvolupat va permetre determinar IgE específica per baix de 0.1 IU/mL (0.24 ng/mL), el que permet la identificació de pacients al·lèrgics amb més sensibilitat, utilitzant només 25 ¿L de mostra (sèrum). L'immunoassaig mostra una bona sensibilitat (64.6%), així com una excel·lent especificitat (100%), que milloren significativament el caràcter predictiu de les proves in vitro existents. A continuació, es va abordar l'obtenció i la caracterització de proteïnes recombinants similars a les IgE específiques dels ß-lactàmics utilitzant la metodologia Phage Display. La primera aproximació és una proteïna formada per dos nanoanticossos que mimetitza el comportament d'una IgE específica. D'aquesta manera, es van obtenir proteïnes recombinants en què un dels nanoanticossos reconeix selectivament un determinant antigènic d'un antibiòtic ß-lactàmic, mentre que l'altre reconeix específicament el paràtop d'un anticòs detector anti-IgE (Omalizumab). Aquestes construccions van resultar estables i funcionals. El paper d'aquestes proteïnes recombinants com a calibrador homòleg es va estudiar determinant la concentració d'IgE específica a penicil·lina G present en sèrum mitjançant un assaig quimioluminiscent. El mètode desenvolupat duplicava la sensibilitat clínica (66%) respecte del mètode de referència (28%), mentre que mantenia una especificitat clínica del 100%. Assolit aquest punt, la tesi es va centrar en la producció d'IgE específica recombinant utilitzant com a material de partida l'ADN d'un pacient al·lèrgic a amoxicil·lina i penicil·lina G. En combinació amb la metodologia Phage Display, enginyeria d'anticossos i mètodes d'expressió en cèl·lules d'insecte, es va aconseguir produir una IgE específica recombinant. D'aquesta manera, es va obtenir un producte biològic que compleix els requisits per ser adoptat com a material de referència en assajos in vitro. Igualment, es va utilitzar com a calibrador homòleg per a la determinació d'IgE específica a amoxicil·lina. Es va assolir un límit de detecció de 0.05 IU/mL amb què s'aconseguia un augment de la sensibilitat clínica (73%) que quadriplicava al mètode de referència (16%), mantenint l'especificitat clínica al 100%. / [EN] The diagnosis of ß-lactam antibiotics allergy involves using unsatisfactory in vivo tests that are time-consuming and carry the risk of triggering a new allergic reaction. On the other hand, in vitro methods based on allergen-specific IgE immunodetection generate precious information, confirming or ruling out allergies and postulating themselves as a safe diagnostic alternative. Despite this, current in vitro tests lack sensitivity and accuracy, with 81% false negatives limiting their diagnostic use. This has led to a growing demand for new in vitro tests based on the immunodetection of IgE, the most studied biomarker in serum allergy. However, the lack of reference standards for allergen-specific IgE has made it impossible to validate and standardize methods, which means that the results of the different tests are not comparable. Furthermore, this lack of reference standards means that specific IgE concentrations are calculated from a total IgE calibration curve by heterologous interpolation, which has been shown not to be entirely correct. For the reasons mentioned above, the main objective of this doctoral thesis is to design, obtain and characterize recombinant proteins with reactivity against ß-lactam antibiotics. This research begins with developing an ELISA immunoassay with chemiluminescent detection for quantifying specific IgE. The assay developed allowed the determination of specific IgE below 0.1 IU/mL (0.24 ng/mL), thus allowing the identification of allergic patients with greater sensitivity, using only 25 µL of sample (serum). The immunoassay showed good sensitivity (64.6%) and excellent specificity (100%), significantly improving the predictive character of existing in vitro tests. Next, the obtaining and characterizing recombinant proteins similar to ß-lactam-specific IgE was approached using the Phage Display methodology. The first approach deals with a protein consisting of two single-domain antibodies that mimics the behavior of a specific IgE. In this way, recombinant proteins were obtained in which one of the nanobodies selectively recognizes an antigenic determinant of a ß-lactam antibiotic, while the other specifically recognizes the paratope of an anti-IgE detector antibody. These constructs were found to be stable and functional. The role of these recombinant proteins as a homologous calibrator was studied by determining the concentration of penicillin G-specific IgE present in serum by employing a chemiluminescent assay. The developed method doubled the clinical sensitivity (66%) compared to the reference method (28%), while maintaining a clinical specificity of 100%. At this point, the thesis focused on the production of recombinant specific IgE using as starting material the DNA of a patient allergic to amoxicillin and penicillin G. in combination with the Phage Display, antibody engineering and expression methods in insect cells, a recombinant-specific IgE was produced. In this way, a biological product was obtained that meets the requirements for its adoption as reference material in in vitro assays. Likewise, it was used as a homologous calibrator for the determination of specific IgE to amoxicillin. A detection limit of 0.05 IU/mL was achieved, which increased clinical sensitivity (73%) fourfold compared to the reference method (16%), while maintaining clinical specificity at 100%. / This work was supported by CSIC 2007-348, ANII FMV 2019_156321, and ANII FMV 2018_148245. P.Q.-C. acknowledges financial support from Generalitat Valenciana through the research staff training program (GVA ACIF/2018/173). This research was also funded by Agencia Estatal de Investigación (PID2019-110713RB-I00, FEDER), program UPV-La FE 2019 (P105 VALBIOAL), and PROMETEO/ 2020/094 / Quintero Campos, P. (2022). Diseño, obtención y caracterización de proteínas recombinantes a partir de determinantes antigénicos asociadas a reacciones alérgicas a ß-lactámicos [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/191429 / Compendio

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Dans ce mémoire, je présente mes études sur la synthèse, la caractérisation et l’évaluation biologique de différentes séries d’analogues du D-heptapeptide appelé 101.10, un modulateur négatif allostérique du récepteur de l’interleukine-1β (IL-1β). Sachant que les peptides ont généralement de faibles propriétés pharmacologiques, le but de ce projet portait sur l’examen des structures nécessaires à la bioactivité, la conformation tridimensionnelle de ces derniers afin d’améliorer la droguabilité du peptide parent. Les stratégies d’optimisation du 101.10 utilisées furent : la coupure N- et C-terminale; la substitution par la proline, α-amino-γ-lactame (Agl), β-amino-γ-lactame (Bgl) et α-amino-β-hydroxy-γ-lactame (Hgl); et la rigidification du squelette à l’aide d’un bicycle, l’indolozidin-2-one (I2aa). Afin de clarifier certaines relations de structure-activité, quelques modifications furent apportées au peptide, incluant l’échange de la thréonine pour la valine, la permutation de la stéréochimie de certains résidus clés ainsi que le remplacement de certaines chaînes latérales par un méthyle. Pour pallier aux difficultés de reproductibilité des résultats avec des échantillons provenant de différentes sources, des études sur l’identité du contre-anion et la pureté du peptide furent conduites. Afin d’évaluer l’effet des modifications sur la conformation aqueuse et l’activité biologique du peptide, des analyses de dichroïsme circulaire et des tests in vitro mesurant l’inhibition de certains effets de l’IL-1β furent effectués. Ces essais cellulaires comportaient l’inhibition de la prolifération de cellules immunes et de l’activation des voies de signalisation inflammatoires du facteur nucléaire κB (NF-κB) et de la protéine kinase activée par mitogène (MAPK), toutes deux stimulées par l’IL-1β. La compilation de ces données a permis de déceler certaines tendances entre la structure, la conformation et l’activité anti-IL-1β des peptidomimétiques. / In this thesis, I present my studies toward the synthesis, characterisation and biological evaluation of different series of analogues of the D-heptapeptide called 101.10, a negative allosteric modulator of the interleukin-1β (IL-1β) receptor. Considering that peptides generally exhibit poor pharmacological properties, the objective of this project consisted in: the examination of the peptidic structures essential to elicit bioactivity; the investigation of the three-dimensional arrangement of these moieties; and the improvement of the “drug-like” properties of the parent peptide. The optimisation strategies that were used include: N- and C-terminal truncation; positional scanning using monocycles such as proline, α-amino-γ-lactam (Agl), β-amino-γ-lactam (Bgl) and α-amino-β-hydroxy-γ-lactam (Hgl); and backbone rigidification with indolizidin-2-one (I2aa). Moreover, in order to validate certain structure-activity relationships, further modifications were performed on the peptide: substitution of threonine for valine, exchange of stereochemistry, and substitution of certain side-chain for a methyl group. Lastly, due to divergent behaviour between peptide samples obtained from different sources, studies on the identity of the counter-anion and on the sample purity were conducted. In order to evaluate the influence of these modifications on the aqueous conformation and on the biological activity of the peptide, circular dichroism analyses and in vitro tests measuring the inhibition of certain IL-1β-mediated effects were performed. These cellular assays comprised the inhibition of IL-1β-stimulated proliferation of immune cells, as well as activation of the inflammatory pathways of nuclear factor κB (NF-κB) and mitogen-activated protein kinase (MAPK) pathways. Compiling these data revealed certain trends existing between the structure, conformation and anti-IL-1β activity of the peptidomimetics.

L’augmentation et la dissémination de la résistance aux β-lactamines chez les bacilles à Gram négatif, particulièrement les Entérobactéries, les bactéries du genre Pseudomonas et Acinetobacter, représentent un problème majeur de santé publique. Les infections nosocomiales causées par ces bactéries multi-résistantes (BMR) ont conduit à une augmentation de la mortalité, de la morbidité et du coût de traitement. L’utilisation abusive et non contrôlée de ces antibiotiques a grandement contribué à la large diffusion de cette résistance. Ainsi, face à cette préoccupation mondiale et suite à de nombreuses recommandations, plusieurs études épidémiologiques et moléculaires ont été rapportées afin de contrôler et de surveiller la diffusion et la dissémination des BMR. Contrairement à de nombreuses régions dans le monde, il existe peu d’informations concernant la caractérisation moléculaire des gènes de résistance aux β-lactamines des bacilles à Gram négatif isolés en Tunisie et surtout en Libye. C’est dans cette optique que ce projet de Thèse de Doctorat s’articule avec comme objectifs: (i) mettre en évidence la prévalence des bacilles à Gram négatifs multi-résistants isolés aux niveaux des hôpitaux tunisiens et libyens (ii) identifier le support génétique de la résistance aux β-lactamines de ces souches cliniques (iii) étudier la diversité clonale des souches multi-résistantes par typage moléculaire. / The increase and spread of β-lactam resistance in gram negative bacteria especially Enterobacteriaceae, Pseudomonas and Acinetobacter (E.P.A) species have become a major concern worldwide. The hospital-acquired infections caused by MDR bacteria have led to an increase in mortality, morbidity and cost of treatment. The frequent misuse of antibiotic drug has greatly contributed to worldwide dissemination of antibiotics resistance. Front of this worldwide concern, and various recommendations, several epidemiological and molecular studies have been reported in order to control the spread and the dissemination of these MDR. Unlike many parts of the world, there is little information concerning the molecular characterization of the β-lactam resistance genes of Gram-negative bacilli isolated in Tunisia and especially in Libya. Therefore, it is in this context that the project of this thesis was conducted with essential objectives: (i) highlight the prevalence of multi-resistant Gram negative bacilli isolated in Tunisian and Libyan hospitals (ii) identify the genetic support of resistance to β-lactams of these clinical strains (iii) study the clonal diversity of the multi-resistant strains by molecular typing (iii) study the molecular epidemiology of these BMRs in these countries in order to control the decision-making process of the treatment and the rapid identification of epidemics by implementing appropriate control measures for the spread of infections and especially developing new tools and software for the diagnosis and monitoring of potential MDR bacteria in Mediterranean countries.