Development of chimeric innate immune agonists as vaccine adjuvants : research data underlying the doctoral dissertation

Paradiso, Emiliano (author), Jakopin, Žiga (mentor)

This data set comprises the research data collected during doctoral studies at the Faculty of Pharmacy, University of Ljubljana, between 2022 and 2026, underpinning the doctoral dissertation "Development of chimeric innate immune agonists as vaccine adjuvants". It covers the design, synthesis, analytical characterisation and biological evaluation of covalent conjugates of innate immune receptor agonists, namely NOD1, NOD2, TLR4, TLR7 and RIG-I, together with CD1d ligands and the parent compounds against which the conjugates were compared. The computational part comprises compound libraries as SMILES and prepared three-dimensional structures, receptor structures retrieved from the Protein Data Bank and prepared for calculation, and molecular docking results obtained with Schrödinger Glide. The synthetic and analytical part comprises 1H and 13C NMR spectra in raw and processed form, HPLC and UPLC chromatograms with the corresponding raw data folders, high-resolution mass spectra, and kinetic aqueous solubility measurements of selected final compounds with their external-standard calibration curves. The biological part contains raw readouts and their statistical treatment for receptor activity in HEK-Blue and HEK-Lucia reporter cell lines, cell viability by MTS assay, cytokine profiling of stimulated human peripheral blood mononuclear cells and their cytotoxicity against K562 cells, along with adjuvant activity assessed in a murine immunisation model using ovalbumin as model antigen and antigen-specific antibody titres as readout. The data are arranged by type of evaluation, and the compounds are labelled with the internal codes of the research group's synthesis log. The accompanying README file maps these codes onto the compounds reported in the associated published articles and describes the folder structure, the instruments used, the measurement conditions and the file formats in more detail. In this form the data allow reprocessing and verification of the published results, the linking of structural and physicochemical properties of the conjugates to their biological activity, and further use in the design of conjugated agonists and vaccine adjuvants.

• Language: English
• Keywords: vaccine adjuvants, PRRs, CD1d, conjugates, α-GalCer
• Typology: 2.20 - Complete scientific database of research data
• Geographic coverage: Ljubljana (Slovenia), Zagreb (Croatia) / Ljubljana (Slovenija), Zagreb (Hrvaška)
• Temporal coverage: 2022–2026
• Organization: FFA - Faculty of Pharmacy
• Year: 2026
• PID: 20.500.12556/RUL-185743
• Data col. methods: Experiment: Laboratory; Synthesis; Simulation; Measurements and tests
• Publication date in RUL: 20.08.2026

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Title: Razvoj himernih agonistov prirojenega imunskega sistema kot adjuvansov za cepiva : raziskovalni podatki, obravnavani v doktorskem delu

Abstract

Sklop obsega raziskovalne podatke, pridobljene med doktorskim študijem na Fakulteti za farmacijo Univerze v Ljubljani med letoma 2022 in 2026, ki so podlaga doktorske disertacije »Razvoj himernih agonistov prirojenega imunskega sistema kot adjuvansov za cepiva«. Nanašajo se na načrtovanje, sintezo, analizno karakterizacijo in biološko vrednotenje kovalentnih konjugatov agonistov receptorjev prirojenega imunskega sistema, in sicer NOD1, NOD2, TLR4, TLR7 in RIG-I, ter ligandov CD1d, skupaj z izhodnimi spojinami, s katerimi so bili konjugati primerjani. Računski del podatkov zajema knjižnice spojin v zapisu SMILES in pripravljene tridimenzionalne strukture, pripravljene strukture receptorjev iz zbirke Protein Data Bank ter rezultate molekulskega sidranja s programom Schrödinger Glide. Sintezni in analizni del obsega spektre 1H in 13C NMR v surovi in obdelani obliki, kromatograme HPLC oziroma UPLC z ustreznimi surovimi mapami, spektre visokoločljivostne masne spektrometrije ter meritve kinetične topnosti izbranih končnih spojin z umeritvenimi krivuljami zunanjih standardov. Biološki del vsebuje surove odčitke in njihovo statistično obdelavo za merjenje receptorske aktivnosti v reporterskih celičnih linijah HEK-Blue in HEK-Lucia, za preverjanje viabilnosti celic s testom MTS, za profiliranje citokinov v stimuliranih humanih mononuklearnih celicah periferne krvi in za njihovo citotoksičnost proti celicam K562, poleg tega pa še podatke o adjuvantnem učinku, ovrednotenem v mišjem modelu imunizacije z ovalbuminom kot modelnim antigenom in z določanjem titrov specifičnih protiteles. Podatki so razvrščeni po vrsti vrednotenja, spojine pa označene z internimi kodami sintezne evidence raziskovalne skupine. Priložena datoteka PREBERI ME povezuje kode s spojinami iz pripadajočih objavljenih člankov ter podrobneje opisuje strukturo map, uporabljene instrumente, pogoje meritev in zapise datotek. V tej obliki podatki omogočajo ponovno obdelavo in preverbo objavljenih rezultatov, povezovanje strukturnih in fizikalno-kemijskih lastnosti konjugatov z njihovo biološko aktivnostjo ter nadaljnjo uporabo pri načrtovanju konjugiranih agonistov in adjuvansov za cepiva.

• Keywords: adjuvansi za cepiva, PRR-ji, CD1d, konjugati, α-GalCer