Titel Deelnemers "Korte inhoud" "Synthesis of modified nucleosides and nucleotides as potential substrates or inhibitors of viral polymerase" "Shiqiong Yang" "Virale enzymen, in het bijzonder de polymerases, zijn gekende doelwitten voor de ontwikkeling van antivirale medicijnen. Gemodificeerde nucleosiden en nucleotiden werden reeds eerder geïdentificeerd als alternatieve substraat-inhibitoren van polymerasen. In het algemeen hangt de antivirale activiteit nauw samen met de substraat specificiteit voor cellulaire en virale kinasen en, als trifosfaat, voor virale polymerasen. In het kader van het bestaande onderzoek naar gemodificeerde nucleosiden, opgebouwd uit zes-ring-suikers, werd besloten om N-methyl-D-ribopyranuronamide nucleosiden te synthetiseren en als potentiële antivirale verbindingen te evalueren. Verder werd de aandacht gericht op de synthese en evaluatie van nieuwe nucleoside-trifosfaat anlogen als substraten voor HIV-1 RT. Het onderzoek naar de leaving-group omhelst de ontwikkeling van fosforamidaat nucleotide analogen als directe substraten voor het polymerase. In deze thesis worden de experimentele methoden, de resultaten en discussie in drie hoofdstukken beschreven.In het tweede hoofdstuk wordt de synthese en karakterisatie van N-methyl-D-ribopyranuronamide beschreven. De aza-suiker gemodificeerde nucleosiden met adenine of thymine als base werden gesynthetiseerd vertrekkend van het 3-O-acetyl-1,2:5,6-di-O-isopropylidene-α-D-allofuranose in acht stappen. Concreet bestaat deze synthese uit een omlegging van een furanose suiker met een carboxamide functie op de 4-positie tot een ribopyranuronamide ring, gevolgd door een condensatie met adenine en thymine nucleobasen, gekatalyseerd door SnCl4. De N-methyl-D-ribopyranuronamide nucleosiden met adenine of thymine als base werden antiviraal inactief bevonden in concentraties lager dan 50 μg/mL and 100 μg/mL, respectievelijk.In hoofdstuk drie wordt de synthese en evaluatie vaneen serie sulf(on)aat en fosf(on)aat fosforamidaat analogen van 2'-deoxyadenosine als substraten voor HIV-1 RT beschreven. Twee synthese routes werden verkend om deze fosforamidaat producten te bekomen. Taurine, L-cysteine zuur, 3-fosfono-L-alanine, O-sulfonato-L-serine, en O-fosfo-L-serine werden onderzocht als uittredende groepen in een in vitro DNA synthese protocol, gekatalyseerd door HIV-1 RT. De fosfaat analogen functioneerden het beste en 3-fosfono-L-Ala-dAMP is een beter substraat voor het polymerisatie proces dan de hiervoor beschreven L-Asp-dAMP (uitgedrukt in een meer succesvolle DNA synthese bij een 10-voudig lagere substraat concentratie en een lagere Vmax/Km waarde). In het vierde hoofdstuk werd de invloed van de base op de incorporatie efficiëntie onderzocht door gebruik te maken van 3-fosfono-L-alanine fosforamidaat nucleotiden bestaande uit de drie overige nucleobasen (G, C en T). Primer-verlenging is base specifiek en de incorporatie efficiëntie van de primer sequentie verloopt in dalende volgorde A ≥ T = G > C. Daarnaast werd d4T monofosfaat geconjugeerd met 3-fosfono-L-alanine mono- of di-ester en werden de conjugaten geëvalueerd alssubstraat inhibitoren van HIV-1 RT. Hoewel verbinding 4.5 een goed substraat is van HIV-RT voor in vitro DNA synthese, werden gelijkaardige antivirale activiteiten tegen HIV-1 and HIV-2 waargenomen als voor d4TMP en het D4T. En werd hierbij aangetoond dat 4.5 eerder werkt als prodrug van het d4T, en dus gedefosforyleerd wordt.Samenvattend werd aangetoond dat 3-fosfono-L-alanine een uitstekende mimic is voor het pyrofosfaat gedeelte van deoxynucleoside trifosfaat, wat gebruikt kan worden in de enzymatische synthese van nucleïnezuren. Het onderzoek naar de leaving group kan worden toegepast in de verdere ontwikkeling van directe substraten voor andere virale of bacteriële polymerasen. Voor de biologische beschikbaarheid zal het nodig zijn de negatieve lading van de fosforamidaat te maskeren en vervolgens de overeenkomstige verbindingen te evalueren." "Synthesis of a 3'-C-ethynyl-β-D-ribofuranose purine nucleoside library : discovery of C7-deazapurine analogs as potent antiproliferative nucleosides" "Fabian Hulpia, Sam Noppen, Dominique Schols, Graciela Andrei, Robert Snoeck, Sandra Liekens, Peter Vervaeke, Serge Van Calenbergh" "Acyclic Phosphono Nucleosides, Nucleotides, and Oligonucleotides: Synthesis, Antiviral Evaluation, and Genetic Selection" "Min Luo" "The chemical diversification and enzymatic proliferation of artificial genetic polymers (xeno nucleic acids, XNAs) is an intriguing avenue of research, especially in view of potential applications in synthetic biology. One of the main goals in this area is to achieve the genetic reprogramming of novel microorganisms through the development of both chemical and biological tools. For this purpose, oligonucleotide analogues, showing good hybridization properties under physiological conditions (high affinity and high specificity) and higher stability than their natural congeners against degradation by cellular and serum nucleases, are attractive molecular targets. It has been reported that a number of XNAs, such as HNA, TNA, CeNA and GNA, can store genetic information and can be recognized and incorporated by engineered thermophilic polymerase mutants. One of the disadvantages of the present XNA approach is the potential instability of the phosphodiester bond in vivo. As a consequence, the information could be lost over time. The phosphonate unit is known to be a biological active mimic of the natural phosphate, while not being susceptible to enzymatic cleavage by phosphatases in vivo. In this work, we are interested in the replacement of the enzymatically labile phosphodiester bond (O-P) by a phosphonate linkage (C-P) to avoid this problem. In addition, the C-P moiety could reduce interactions with natural nucleic acids binding factors by changing the surface electrostatic potential of the relevant XNA polymer. Almost 20 years after the discovery of the broad antiviral activity spectrum of the first acyclic nucleoside phosphonate, several structural analogues have become important drugs in the treatment of DNA virus and retrovirus infections. Acyclic nucleoside phosphonates (ANPs) represent an important class of antiviral nucleoside derivatives. In addition, acyclic nucleosides are structurally simplified analogues of naturally occurring nucleosides due to the reduced number of stereocentres, and they should therefore serve in principle as ideal building blocks as initial proof of concept. On this basis, we aim at exploring chemical synthetic methods for the preparation of acyclic phosphonate oligonucleotides (aPhoNA) for further hybridization and in vivo studies, as well as screening polymerases suitable for this particular modification in order to identify potential candidates for directed enzyme evolution. In addition, novel prodrugs of ANPs were synthesized and evaluated against a range of retro- and DNA viruses." "Milestones in the discovery of antiviral agents: nucleosides and nucleotides" "Erik De Clercq" "A chemoenzymatic synthesis of carbocyclic nucleosides and nucleotides" "M Mahler, B Riechardt, Jan Balzarini, C Meier" "Nucleoside Derivatives of 2,6-Diaminopurine Antivirals: Base-Modified Nucleosides with Broad-Spectrum Antimicrobial Properties" "Elisabetta Groaz, Jef Rozenski" "The plethora of viral outbreaks experienced in the last decade, together with the widespread distribution of many re-emerging and newly emerging viruses, emphasize the urgent need for novel broad-spectrum antivirals as tools for early intervention in case of future epidemics. Non-natural nucleosides have been at the forefront for the treatment of infectious diseases for many years and still represent one of the most successful classes of antiviral molecules on the market. In the attempt to explore the biologically relevant chemical space of this class of antimicrobials, we describe herein the development of novel base-modified nucleosides by converting previously identified 2,6-diaminopurine antivirals into the corresponding D/L ribonucleosides, acyclic nucleosides and prodrug derivatives. A phenotypic screening against viruses belonging to different families (Flaviviridae, Coronaviridae, Retroviridae) and against a panel of Gram-positive and Gram-negative bacteria, allowed to identify a few interesting molecules with broad-spectrum antimicrobial activities." "Synthesis and biological evaluation of pyrimidine nucleosides and nucleoside phosphonates" "Sara Van Poecke" "An Overview of Marketed Nucleoside and Nucleotide Analogs." "Steven De Jonghe, Piet Herdewyn" "Nucleos(t)ide chemistry has been the subject of intense research, mainly because of the promising antiviral and antitumoral activity associated with this compound class. Numerous analogs have been synthesized over the past decades, yielding a number of derivatives that have reached the status of marketed drugs. Herein, an overview of the nucleos(t)ide analogs that have received marketing approval is given. The review is divided into several sections, including antiviral and antitumoral nucleoside analogs as well as nucleoside analogs that have received marketing approval in other therapeutic areas. © 2022 Wiley Periodicals LLC." "Ten paths to the discovery of antivirally active nucleoside and nucleotide analogues" "Erik De Clercq" "Nucleoside and nucleotide analogues have proven to be an effective approach toward the development of antiviral compounds. This approach has so far yielded a number of clinically useful antiviral drugs, such as BVDU (brivudin), (val)aciclovir, cidofovir, adefovir dipivoxil, and tenofovir disoproxil fumarate, and current perspectives justify the further development of other nucleoside analogues, such as FV-100, and that of the DAPy-based nucleotide analogues, the 5-aza analogue of cidofovir, and prodrug derivatives thereof." "Pan-pathway based interaction profiling of FDA-approved nucleoside and nucleobase analogs with enzymes of the human nucleotide metabolism" "Jan Balzarini" "To identify interactions a nucleoside analog library (NAL) consisting of 45 FDA-approved nucleoside analogs was screened against 23 enzymes of the human nucleotide metabolism using a thermal shift assay. The method was validated with deoxycytidine kinase; eight interactions known from the literature were detected and five additional interactions were revealed after the addition of ATP, the second substrate. The NAL screening gave relatively few significant hits, supporting a low rate of ""off target effects."" However, unexpected ligands were identified for two catabolic enzymes guanine deaminase (GDA) and uridine phosphorylase 1 (UPP1). An acyclic guanosine prodrug analog, valaciclovir, was shown to stabilize GDA to the same degree as the natural substrate, guanine, with a ΔT(agg) around 7°C. Aciclovir, penciclovir, ganciclovir, thioguanine and mercaptopurine were also identified as ligands for GDA. The crystal structure of GDA with valaciclovir bound in the active site was determined, revealing the binding of the long unbranched chain of valaciclovir in the active site of the enzyme. Several ligands were identified for UPP1: vidarabine, an antiviral nucleoside analog, as well as trifluridine, idoxuridine, floxuridine, zidovudine, telbivudine, fluorouracil and thioguanine caused concentration-dependent stabilization of UPP1. A kinetic study of UPP1 with vidarabine revealed that vidarabine was a mixed-type competitive inhibitor with the natural substrate uridine. The unexpected ligands identified for UPP1 and GDA imply further metabolic consequences for these nucleoside analogs, which could also serve as a starting point for future drug design."