Structural pharmacology of SV2A reveals an allosteric modulation mechanism in the major facilitator superfamily

Shabareesh Pidathala, Xiao Chen, Yaxin Dai, Long N. Nguyen, Christoph Gorgulla, Yiming Niu, Fangyu Liu () and Chia-Hsueh Lee ()
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Shabareesh Pidathala: St. Jude Children’s Research Hospital, Department of Structural Biology
Xiao Chen: St. Jude Children’s Research Hospital, Department of Structural Biology
Yaxin Dai: St. Jude Children’s Research Hospital, Department of Structural Biology
Long N. Nguyen: National University of Singapore, Department of Biochemistry, Yong Loo Lin School of Medicine
Christoph Gorgulla: St. Jude Children’s Research Hospital, Department of Structural Biology
Yiming Niu: The Rockefeller University, Laboratory of Chromosome and Cell Biology
Fangyu Liu: UT Southwestern Medical Center, Department of Pharmacology
Chia-Hsueh Lee: St. Jude Children’s Research Hospital, Department of Structural Biology

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract The synaptic vesicle glycoprotein 2A (SV2A), a member of the major facilitator superfamily (MFS), is a key target for antiseizure medications and a biomarker for synaptic density imaging. Despite its clinical importance, the mechanisms underlying SV2A ligand binding and modulation remain poorly understood. Here, we report sub-3 Å resolution cryo-electron microscopy (cryo-EM) structures of human SV2A in its apo form and in complex with FDA-approved antiseizure medication levetiracetam; PET imaging tracer UCB-J; experimental antiseizure drug padsevonil; and allosteric modulator UCB1244283. We find that levetiracetam and UCB-J induce vestibule occlusion, a hallmark conformational transition of MFS transporters that had not been observed in previous SV2A structures. UCB1244283 binds to an allosteric site and enhances orthosteric ligand engagement by stabilizing the occluded state and slowing ligand dissociation. Notably, padsevonil occupies both orthosteric and allosteric sites, functionally precluding modulation. These findings uncover an allosteric mechanism of regulation and provide a structural framework for the development of modulators targeting SV2A and related MFS transporters.

Date: 2025
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DOI: 10.1038/s41467-025-65781-1

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