Excretion of L-xylulose is the hallmark of pentosuria, the fourth of Garrod’s inborn errors of metabolism, yet the molecular basis for L-xylulose formation remains unknown. Here, by projecting coevolutionary data for 511,114 orthogroups across 1,929 eukaryotic genomes onto metabolic maps, we screen for unmapped genes in human metabolism. Among these, we show that the DUF1907 domain of C11orf54 catalyzes formation of L-xylulose by establishing a zinc-coordinated Michaelis complex with β-keto-L-gulonate (BKG). The identification of BKG decarboxylase completes the pentose pathway, in which pentose sugars are produced by decarboxylation of nonphosphorylated hexose precursors. The pathway was present in the unicellular ancestor of animals and is conserved in all deuterostomes, in contrast to the alternative L-ascorbate (vitamin C) biosynthesis pathway. An increased flux toward pentoses may have represented an evolutionary tradeoff, favoring energy metabolism and redox cofactor balance at the expense of ascorbate biosynthesis in organisms, such as humans and other Haplorhini primates, where dietary vitamin C intake prevents scurvy.

Transthyretin (TTR) is an amyloidogenic homotetramer involved in the transport of thyroxine in blood and cerebrospinal fluid. To date, more than 130 TTR point mutations are known to destabilise the TTR tetramer, leading to its extracellular pathological aggregation accumulating in several organs, such as heart, peripheral and autonomic nerves, and leptomeninges. Tolcapone is an FDA-approved drug for Parkinson’s disease that has been repurposed as a TTR stabiliser. We characterised 3-O-methyltolcapone and two newly synthesized lipophilic analogues, which are expected to be protected from the metabolic glucuronidation that is responsible for the lability of tolcapone in the organism. Immunoblotting assays indicated the high degree of TTR stabilisation, coupled with binding selectivity towards TTR in diluted plasma of 3-O-methyltolcapone and its lipophilic analogues. Furthermore, in vitro toxicity data showed their several-fold improved neuronal and hepatic safety compared to tolcapone. Calorimetric and structural data showed that both T4 binding sites of TTR are occupied by 3-O-methyltolcapone and its lipophilic analogs, consistent with an effective TTR tetramer stabilisation. Moreover, in vitro permeability studies showed that the three compounds can effectively cross the blood-brain barrier, which is a prerequisite for the inhibition of TTR amyloidogenesis in the cerebrospinal fluid. Our data demonstrate the relevance of 3-O-methyltolcapone and its lipophilic analogs as potent inhibitors of TTR amyloidogenesis.

The pathological aggregation of α-synuclein (syn) is a hallmark of Parkinson’s disease (PD) and related synucleinopathies. In the present study, we report a supramolecular strategy to reduce syn aggregation and its associated cellular toxicity using a panel of rationally designed anionic calix[4]­arenes. Among them, CLXP1, a tetraphosphonato derivative with a rigid, preorganized cavity, emerged as a potent inhibitor of syn aggregation in a validated yeast model of PD based on syn overexpression. CLXP1 significantly improved cell viability by reducing the formation of toxic intracellular inclusions of syn and restoring multiple dysregulated molecular pathways while preserving mitochondrial morphology and redox and lipid homeostasis and enhancing autophagic clearance. NMR analyses revealed that CLXP1 interacts with key residues of the N-terminal domain of syn, critically involved in membrane anchoring and oligomerization, supporting a model in which this interaction stabilizes the α-helical, membrane-bound conformation of syn, thereby preventing its progression toward toxic oligomeric species. These findings highlight the potential of supramolecular host–guest chemistry to selectively target intrinsically disordered proteins and provide a promising scaffold for the development of new modulators of protein aggregation.

Transthyretin (TTR) is an amyloidogenic homotetramer involved in the transport of thyroxine in blood and cerebrospinal fluid. To date, more than 130 TTR point mutations are known to destabilise the TTR tetramer, leading to its extracellular pathological aggregation accumulating in several organs, such as heart, peripheral and autonomic nerves, and leptomeninges. Tolcapone is an FDA-approved drug for Parkinson’s disease that has been repurposed as a TTR stabiliser. We characterised 3-O-methyltolcapone and two newly synthesized lipophilic analogues, which are expected to be protected from the metabolic glucuronidation which is responsible of the lability of tolcapone in the organism. Immunoblotting assays indicated the high degree of TTR stabilisation, coupled with binding selectivity towards TTR in diluted plasma of 3-O-methyltolcapone and its lipophilic analogues. Furthermore, in-vitro toxicity data showed their several-fold improved neuronal and hepatic safety compared to tolcapone. Calorimetric and structural data showed that both T4 binding sites of TTR are occupied by 3-O-methyltolcapone and its lipophilic analogs, consistent with an effective TTR tetramer stabilisation. Moreover, in-vitro permeability studies showed that the three compounds can effectively cross the blood-brain barrier, which is a prerequisite for the inhibition of TTR amyloidogenesis in the cerebrospinal fluid. Our data demonstrate the relevance of 3-O-methyltolcapone and its lipophilic analogs as potent inhibitors of TTR amyloidogenesis.

Metabolic networks and enzyme-molecule connections are still being elucidated. Here, through systematic analysis of gene loss and gain across the eukaryotic tree, mapped onto metabolic networks, we build a coevolutionary framework of human metabolism. Using this information, we identify unmapped genes in metabolic pathways, leading to the discovery of C11orf54 as the long-missing decarboxylase of the glucuronate/pentose pathway. These findings provide insights into an alternative route for sugar conversion in humans and other metazoans and its connection to L-ascorbate (vitamin C) biosynthesis. More broadly, our approach offers a framework for mapping missing enzymes across species.