Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission Vikram Babu Kasaragoda,1,2,3, Anabel Pacios-Michelenaa,1, Natascha Schaeferb, Fang Zhengc, Nicole Badera, Christian Alzheimerc, Carmen Villmannb, and Hermann Schindelina,3 aInstitute of Structural Biology, Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany; bInstitute for Clinical Neurobiology, University of Würzburg, 97078 Würzburg, Germany; and cInstitute of Physiology and Pathophysiology, Friedrich Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany Edited by Lily Yeh Jan, University of California, San Francisco, CA, and approved October 26, 2020 (received for review May 3, 2020) The antimalarial artemisinins have also been implicated in the combination with quinones such as mefloquine and lumefantrine, regulation of various cellular pathways including immunomodu- nowadays represent the standard drug combinations used to treat lation of cancers and regulation of pancreatic cell signaling in malaria caused by Plasmodium falciparum (9). In addition to their mammals. Despite their widespread application, the cellular speci- antiprotozoan activities, these drugs have also been pharmaco- ficities and molecular mechanisms of target recognition by artemi- logically observed to regulate the activities of a variety of mam- sinins remain poorly characterized. We recently demonstrated how malian cellular processes, some of which are deregulated in these drugs modulate inhibitory postsynaptic signaling by direct various types of cancer (10, 11). Recently, it was discovered that binding to the postsynaptic scaffolding protein gephyrin. Here, we artemisinins also modulate the differentiation of pancreatic Tα report the crystal structure of the central metabolic enzyme pyri- cells by inducing the transdifferentiation of glucagon-producing doxal kinase (PDXK), which catalyzes the production of the active Tα cells into insulin-secreting Tβ cells, thus suggesting an antidi- ′ form of vitamin B6 (also known as pyridoxal 5 -phosphate [PLP]), in abetic activity of artemisinins (7). However, two subsequent complex with artesunate at 2.4-Å resolution. Partially overlapping studies contradicted this observation, thus questioning the po- binding of artemisinins with the substrate pyridoxal inhibits PLP tential clinical application of these compounds in the treatment of biosynthesis as demonstrated by kinetic measurements. Electro- diabetes (12, 13). physiological recordings from hippocampal slices and activity mea- Until recently, in the absence of a single protein crystal BIOCHEMISTRY surements of glutamic acid decarboxylase (GAD), a PLP-dependent enzyme synthesizing the neurotransmitter γ-aminobutyric acid structure in complex with artemisinins (neither a plasmodial nor a (GABA), define how artemisinins also interfere presynaptically with mammalian protein), the detailed framework describing the target GABAergic signaling. Our data provide a comprehensive picture of recognition by these small molecules remained enigmatic. The first artemisinin-induced effects on inhibitory signaling in the brain. molecular insights into artemisinin recognition by a target protein were derived by us from crystal structures of the C-terminal domain artemisinins | pyridoxal kinase | pyridoxal phosphate (PLP) | of the moonlighting protein gephyrin (GephE) in complex with two GABA biosynthesis | inhibitory neurotransmission artemisinin derivatives, artesunate and artemether (14). Gephyrin is yridoxal 5′-phosphate (PLP) is the active form of vitamin B6. Significance PIn humans, PLP biosynthesis is catalyzed by pyridoxal kinase (PDXK), a member of the ribokinase superfamily. PDXK uti- Information processing in the central nervous system relies on lizes inactive forms of vitamin B6 (pyridoxal [PL], pyridoxine, chemical synapses where neurotransmitters such as the inhib- and pyridoxamine) and ATP as substrates, producing PLP along itory neurotransmitter γ-aminobutyric acid (GABA) are released with the byproduct ADP. The corresponding reaction proceeds at presynaptic nerve endings. GABA is synthesized by glutamic via a random substrate addition reaction mechanism (1) in which acid decarboxylase (GAD), an enzyme requiring pyridoxal 5’- PLP biosynthesis takes place by transferring the γ-phosphate of phosphate (PLP or vitamin B6) as cofactor, the latter being ATP to the 5′-OH group of the B6 vitamers, in a process assisted synthesized by pyridoxal kinase (PDXK). Here, we show that by divalent metal ions such as Zn2+ and Mg2+ (2) (Fig. 1A). PLP the antimalarial drug artemisinin inhibits PDXK and describe serves as the essential active site component for more than 160 the structural basis of this inhibition. The decrease in PLP pro- distinct human enzymatic activities (3) catalyzing crucial cellular duction reduces the amount of GABA being produced, which, processes such as detoxification reactions and multiple metabolic in turn, impacts the efficacy of GABAergic transmission. This processes including amino acid, carbohydrate, and lipid metab- study combined with our previous data sheds light on how olism. PLP-dependent enzymes also participate in neurotrans- artemisinins can influence inhibitory synaptic transmissions mitter biosynthesis including the inhibitory neurotransmitters both presynaptically, as described here, and postsynaptically. γ-aminobutyric acid (GABA) and glycine (4–6), which are syn- Author contributions: V.B.K., A.P.M., N.S., F.Z., C.A., C.V., and H.S. designed research; thesized by glutamic acid decarboxylase (GAD) and serine V.B.K., A.P.M., N.S., F.Z., N.B., and C.V. performed research; V.B.K., A.P.M., N.S., F.Z., hydroxymethyl transferase (SHMT), respectively. Vitamin B6 N.B., C.V., and H.S. analyzed data; and V.B.K., C.A., C.V., and H.S. wrote the paper. deficiency has been implicated in multiple neurological, psychi- The authors declare no competing interest. atric, and internal disorders possibly including even diabetes, This article is a PNAS Direct Submission. cancer, and autism (3), thus underpinning the importance of a Published under the PNAS license. finely tuned PLP biosynthesis. 1V.B.K. and A.P.M. contributed equally to this work. Recently, PDXK was identified as one of the mammalian 2Present address: Neurobiology Division, Medical Research Council Laboratory of Molec- targets of the antimalarial drug artemisinin (7). Artemisinin- ular Biology, Cambridge CB2 0QH, United Kingdom. containing plant extracts have been used in traditional Chinese 3To whom correspondence may be addressed. Email: [email protected] or medicine for the treatment of malaria (8). Chemically, these small [email protected]. molecules are sesquiterpene lactones with an unusual endoper- This article contains supporting information online at https://www.pnas.org/lookup/suppl/ oxide bridge. Artemisinin and its semisynthetic derivatives arte- doi:10.1073/pnas.2008695117/-/DCSupplemental. mether and artesunate (collectively referred to as artemisinins), in First published December 14, 2020. www.pnas.org/cgi/doi/10.1073/pnas.2008695117 PNAS | December 29, 2020 | vol. 117 | no. 52 | 33235–33245 Downloaded by guest on September 27, 2021 A + + PTA laxodiryP etahpsohp-'5laxodiryP PDA CH CH 3 B 0.20 C 3 D H H O O 0.15 O CH3 O CH3 ) -1 O O OH 0.10 H H H H Vel (s O O H3C O 0.05 H3C O O 0.00 0 100 200 300 400 500 O Pyridoxal ( M) Artemisinin Artesunate E 0.15 F 120 **** **** Artemisinin 100 0.10 Artesunate 80 Vel (s-1) 60 0.05 40 % Inhibition 20 0.00 WT 0 1234 Artesunate Artemisinin log Inhibitor M) Fig. 1. Biochemical basis of PDXK inhibition by artemisinins. (A) Schematic representation of the reaction catalyzed by PDXK. (B) Michaelis–Menten curve derived for the enzymatic activity of recombinantly purified PDXK. (C and D) Chemical structures of artemisinin (C) and artesunate (D). (E) Enzymatic activity of wild-type PDXK (WT-PDXK) in the absence and presence of artemisinin derivatives at a concentration of 1.5 mM (artesunate) and 156 μM (artemisinin), respectively. Data are presented as mean ± SEM (P values are *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001) (one-way ANOVA test). (F) Inhibition curves of PDXK by artemisinin and artesunate used to derive the corresponding IC50 values. the principal scaffolding protein at inhibitory postsynaptic speciali- PLP production in the presence of artemisinins with Ki values in zations and also catalyzes the final two steps of the evolutionarily the high micromolar range. Electrophysiological recordings and conserved molybdenum cofactor (Moco) biosynthesis (15–17). measurements of GABA biosynthesis suggest that artemisinins exert Structures of the GephE–artemisinin complexes demonstrated that their effect by down-regulating the activity of PLP-dependent en- artemisinins specifically target the universal receptor binding pocket zymes such as GAD. Taken together, our data define the molecular of this moonlighting protein, without altering its enzymatic activity, basis for the inhibition of PDXK by artemisinins and their conse- thus inhibiting critical interactions of gephyrin with GABA type A quences at the presynaptic terminals of inhibitory postsynapses and receptors (GABAARs) and glycine receptors (GlyRs). As an im- extend our current understanding of the artemisinin-induced mod- portant functional consequence, artemisinins modulate inhibitory ulation of inhibitory neurotransmission beyond gephyrin. neurotransmission in a gephyrin-dependent