Computer Modelling and Synthesis of Deoxy and Monohydroxy Analogues of a Ribitylaminouracil Bacterial Metabolite that Potently Activates Human T Cells

Abstract

5-(2-Oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU) is an atural productf ormedd uring bacterial synthesis of vitamin B2. It potently activates mucosal associated invariant T( MAIT) cells and has immunomodulatory,i nflammatory,a nd anticancer properties. This highly polar and unstable compound forms ar emarkablys table Schiff base with al ysine residuei nm ajor histocompatibility complex class Irelated protein (MR1) expressed in antigen-presentingc ells. Inspiredb yt he importance of the ribityl moiety of 5-OP-RU for binding to both MR1 and the Tc ell receptor (TCR) on MAIT cells, each OH was removed in silico. DFT calculations and MD simulations revealedavery stable hydrogen bond betweent he C3'ÀOH and uracil N1H, which profoundly restrictsf lexibility and positioning of each ribityl-OH, potentially impacting their interactionsw ith MR1 and TCR. By using deoxygenation strategies and kinetically controlled imine formation,f our monodeoxyribityl and four monohydroxyalkyl analogues of 5-OP-RU were synthesised as new tools for probingTcell activation mechanisms.[a] G.Scheme4.Synthesis of 4-deoxy-d-ribitylamine (32)b yB arton-McCombied eoxygenation of d-ribose (24).Scheme5.Synthesis of 5-deoxy-d-ribitylamine (40)b yC 5-tosylate reduction of d-ribose (24).

The effects of 5‐OP‐RU stereochemistry on its stability and MAIT‐MR1 axis

“…Indeed, Awad et al. reported that subtle modifications of 5‐OP‐RU, including deoxy analogues, had a profound impact on their chemical stability [18] . Thus, prior to evaluating the T cell activation, we first investigated the chemical stability of four diastereomers [ 1 a and its stereoisomers 1 c , 1 e and 1 g ] prepared from the corresponding 5‐A‐RU stereoisomers.…”

“…The ribityl group of 5‐OP‐RU is mainly recognized by TCR on MAIT cells [14] . For investigating the molecular recognition by MR1 and MAIT‐TCR, and the chemical stability, several structure‐activity relationship (SAR) studies of 5‐OP‐RU have been carried out by various approaches [17–22] . For instance, Mak et al.…”

Endoplasmic reticulum chaperones stabilize ligand-receptive MR1 molecules for efficient presentation of metabolite antigens

“…Despite chemical modifications to the natural antigen 5-OP-RU, the synthetic analog MAgA-TAMRA was still able to traffic to the ER, bind to MR1 molecules, and inhibit MAIT cell recognition of other ligands. MAgA-TAMRA helps to further define the structural limitations and ligand tolerance in the Ag binding cleft of MR1, which can accommodate a variety of small molecules (47), and it serves as a blueprint for creating new MR1 ligands customized with different payloads and functionalities for studying MR1 biology (5,48,49).…”

MR1‐dependent immune surveillance of the skin contributes to pathogenesis and is a photobiological target of UV light therapy in a mouse model of atopic dermatitis

“…5‐Amino‐6‐(2‐deoxy‐D‐ribitylamino)uracil (5‐A‐(2‐deoxy)RU) 30,67 was prepared by reduction with 4.5 eq of sodium dithionite of the 5‐nitroso‐6‐(2‐deoxy‐D‐ribitylamino)uracil precursor, 67 as previously described for 5‐A‐RU 66 and was stored at −80℃ until required for biological studies. Analysis by liquid chromatography‐mass spectrometry (LC‐MS) indicated the formation of 5‐A‐(2‐deoxy)RU (Figure ).…”