About

Olga Boudker, PhD, is a Professor of Biochemistry and Biophysics at Weill Cornell Medicine. Her lab studies membrane transporters with particular interest in how the structural dynamics of these proteins underlies their function. Her research focuses on understanding the mechanisms of membrane transporters, which are essential for various cellular processes. She is involved in exploring the structural biology of these proteins to elucidate their functional mechanisms, contributing to the broader understanding of cellular transport systems.

Research topics

• Biology
• Biochemistry
• Chemistry
• Cell biology
• Biophysics

Selected publications

• Abstract A029: Structure-guided design of SLC1A1/EAAT3-selective inhibitors reveals a metabolic vulnerability in kidney cancer

  Cancer Research · 2026-03-13

  article

  Abstract Background: SLC1A1/EAAT3 is a trimeric Na+-coupled transporter that imports aspartate, glutamate, and, to a lesser extent, cysteine. ccRCC and other cancers, such as hematologic malignancies and lung cancer, are metabolically dependent on these substrates for nucleotide synthesis, TCA cycle anaplerosis, and glutathione production, which drives an oncogenic dependence on SLC1A1. However, the lack of potent, subtype-selective SLC1A1 inhibitors has limited therapeutic targeting. Methods: We determined high-resolution cryo-EM structures of human SLC1A1 bound to the bicyclic imidazo[1,2-a]pyridine-3-amine inhibitor, 3e, and used these data to guide medicinal chemistry. New analogs were prioritized using in silico docking, thermal-shift binding assays, and SLC1A1-dependent cytotoxicity screens in RCC cell lines. On-target activity was tested using SLC1A1 drug-resistant mutants, impedance-based transport assays in inducible SLC1A1/2/3 HEK293 cells, and metabolic rescue with cell-permeable aspartate, glutamate, and glutathione. Results: The 2.5–2.8 Å cryo-EM maps show that 3e occupies a lipid-embedded allosteric cavity between the scaffold and transport domains, accessible only in an inward-facing apo state. Compound 3e, together with a bound sterol, wedges these domains apart, disfavors Na+ binding, and arrests the elevator-like translocation of SLC1A1. The non-conserved residue, F99, and the conserved T402 residue are critical for inhibitor engagement, and SLC1A1 F99M and T402I mutants remain functional but are resistant to 3e and its analogs in RCC cells, confirming on-target inhibition. Structure-activity studies yielded two optimized 3e analogs, PBJ1 and PBJ2, which retain SLC1A1 selectivity over SLC1A2/3, display improved cancer cell killing in multiple RCC lines, and deplete glutathione and TCA intermediates. Supplementation with methyl-aspartate, methyl-glutamate, or glutathione restores cell fitness, linking PBJ1/PBJ2 cytotoxicity to blockade of SLC1A1-mediated amino acid uptake. Conclusions: Our work defines a previously unrecognized, apo-state allosteric pocket in SLC1A1, establishes F99 as one structural determinant of subtype selectivity, and delivers PBJ1 and PBJ2 as next-generation, on-target probes that exploit an aspartate–glutamate dependency in kidney cancer. These findings provide a mechanistic foundation and chemical tools for developing SLC1A1-directed therapies in RCC. Citation Format: Pooneh Koochaki, Biao Qiu, Jesse A. Coker, Alexander Earsley, Nancy S. Wang, Todd Romigh, Christopher M. Goins, Shaun R. Stauffer, Olga Boudker, Abhishek A. Chakraborty. Structure-guided design of SLC1A1/EAAT3-selective inhibitors reveals a metabolic vulnerability in kidney cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Kidney Cancer Research: From Molecular Insights to Therapeutic Breakthroughs; 2026 Mar 13-16; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(5_Suppl_2):Abstract nr A029.

  PublisherDOI

• BPS2026 – Cryo-EM structure reveals Na-dependent mechanism of human OCA2

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• Structure-guided optimization of SLC1A1/EAAT3-selective inhibitors targeting renal cancer metabolism

  The EMBO Journal · 2026-04-22

  articleOpen access

  Renal cell carcinomas (RCCs) depend on the trimeric sodium-coupled aspartate and glutamate transporter, SLC1A1/EAAT3; however, pharmacologically targeting SLC1A1 is challenging. Here we determined a cryo-EM structure of human SLC1A1 bound to compound 3e, a recently described SLC1A1-selective bicyclic imidazo[1,2 α]pyridine-3-amine (BIA) inhibitor with an unclear mechanism of action. 3e binds a membrane-embedded allosteric pocket accessible only in the apo state, when SLC1A1 is unbound to substrate and sodium, and likely prevents sodium and substrate binding. Moreover, by forming a wedge between the trimerization domain and the substrate-binding transport domain, alongside a cholesterol moiety from the lipid bilayer, 3e blocks SLC1A1's elevator-like movements that support the transport cycle. Mutations in this binding pocket abolish the 3e interaction and counteract 3e's cytotoxicity in RCC cells, confirming on-target activity and explaining SLC1A1 selectivity. The subsequent design of two new SLC1A1-selective BIA derivatives, PBJ1 and PBJ2, was directed by the SLC1A1-3e structures; both inhibited SLC1A1-dependent aspartate, glutamate, and cysteine metabolism and showed enhanced cytotoxicity.

  PublisherDOI

• BPS2026 – Discovery of novel VGLUT inhibitors through structure-based virtual screening, molecular dynamics simulations, and experimental validation

  Biophysical Journal · 2026-02-01

  articleSenior author
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• BPS2026 – The altered stoichiometry of a non-inactivating mutant suggests the assembly sequence of the mechanosensitive channel MSCs

  Biophysical Journal · 2026-02-01

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• BPS2026 – Force field refinement at a sodium-binding site in glutamate transporters: Bridging MD simulations and cryo-EM structures

  Biophysical Journal · 2026-02-01

  articleSenior author
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• BPS2026 – Structural basis of uncoupling in a CLC transporter

  Biophysical Journal · 2026-02-01

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• Structural basis of excitatory amino acid transporter 3 substrate recognition

  Proceedings of the National Academy of Sciences · 2025-04-18 · 4 citations

  articleOpen accessSenior authorCorresponding

  Excitatory amino acid transporters (EAATs) reside on cell surfaces and uptake substrates, including L-glutamate, L-aspartate, and D-aspartate, using ion gradients. Among five EAATs, EAAT3 is the only isoform that can efficiently transport L-cysteine, a substrate for glutathione synthesis. Recent studies suggest that EAAT3 also transports the oncometabolite R-2-hydroxyglutarate (R-2HG). Here, we examined the structural basis of substrate recognition by determining the cryogenic electron microscopy (cryo-EM) structures of EAAT3 bound to different substrates. We found that L-cysteine binds to EAAT3 in thiolate form, and EAAT3 recognizes different substrates by fine-tuning local conformations of the coordinating residues. However, using purified human EAAT3, we could not observe R-2HG binding or transport. Imaging of EAAT3 bound to L-cysteine revealed several conformational states, including an outward-facing state with a semi-open gate and a disrupted sodium-binding site. These structures demonstrate that the full gate closure, coupled with the binding of the last sodium ion, occurs after substrate binding. Furthermore, we observed that different substrates affect how the transporter distributes between a fully outward-facing conformation and intermediate occluded states on a path to the inward-facing conformation, suggesting that translocation rates are substrate-dependent.

  PublisherOA PDFDOI

• Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters

  Nature Structural & Molecular Biology · 2025-08-25 · 3 citations

  articleOpen accessSenior authorCorresponding

  Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to changing environments and needs. The bases of such diversification and, thus, principles of ion coupling are unexplored. Here, using phylogenetics and ancestral protein reconstruction, we investigated sodium-coupled transport in prokaryotic glutamate transporters, a mechanism ubiquitous across life domains and critical to neurotransmitter recycling in humans by excitatory amino acid transporters from the solute carrier 1 family. By inferring ancestral prokaryotic transporter sequences during a change in the ion-coupling mechanism, we found an evolutionary transition from sodium-dependent to independent substrate binding and transport. Structural and functional experiments on ancestral transporters suggest that the transition involved allosteric mutations, rendering sodium binding dispensable without affecting the ion-binding sites. Allosteric tuning of transporters’ energy landscapes might be a widespread route of their functional diversification. Reddy et al. used ancestral protein reconstruction, cryo-electron microscopy and functional assays to elucidate how a secondary active transporter evolved to harness the energy of sodium gradients to power the concentrative uptake of its substrate.

  PublisherOA PDFDOI

• Human EAAT3 with sodium bound at inward facing state

  2025-06-17

  datasetSenior author
  PublisherDOI

Recent grants

• The structural dynamics of a glutamate transporter homologue

  NIH · $4.3M · 2014–2022

• Conformational Ensemble of Glutamate Transporters: Structure and IonicModulation

  NIH · $3.8M · 2009–2021

• NIH Grant S10RR026970

  NIH · $266k · 2012

Frequent coauthors

• Didar Ciftci

  Harvard University Press

  78 shared

• Gerard H. M. Huysmans

  Cornell University

  78 shared

• Scott C. Blanchard

  St. Jude Children's Research Hospital

  73 shared

• Xiaoyu Wang

  Cornell College

  62 shared

• Biao Qiu

  Howard Hughes Medical Institute

  46 shared

• Yun Huang

  Howard Hughes Medical Institute

  33 shared

• Krishna D. Reddy

  31 shared

• Simon Scheuring

  Weill Cornell Medicine

  27 shared

Labs

• Boudker LabPI