Rational design of ASCT2 inhibitors using an integrated experimental-computational approach

By R. Garibsingh, E. Ndaru, A. Garaeva, Yue-Hua Shi, L. Zielewicz, Paul Zakrepine, Massimiliano Bonomi, D. Slotboom, C. Paulino, C. Grewer and 1 more. 2021

60 citations recorded by the source corpus.

Significance The glutamine transporter ASCT2 is an emerging therapeutic target for various cancer types. Here, we use an integrated computational and experimental approach to develop unique ASCT2 inhibitors targeting a conformational state useful for rational drug design. We apply computational chemistry tools such as molecular docking and molecular dynamics simulations, in combination with structure determination with cryo-electron microscopy and synthetic chemistry, to design multiple ASCT2 inhibitors. Our results reveal a unique mechanism of stereospecific inhibition of ASCT2 and highlight the utility of combining state-of-the-art computational and experimental approaches in characterizing challenging human membrane protein targets. ASCT2 (SLC1A5) is a sodium-dependent neutral amino acid transporter that controls amino acid homeostasis in peripheral tissues. In cancer, ASCT2 is up-regulated where it modulates intracellular glutamine levels, fueling cell proliferation. Nutrient deprivation via ASCT2 inhibition provides a potential strategy for cancer therapy. Here, we rationally designed stereospecific inhibitors exploiting specific subpockets in the substrate binding site using computational modeling and cryo-electron microscopy (cryo-EM). The final structures combined with molecular dynamics simulations reveal multiple pharmacologically relevant conformations in the ASCT2 binding site as well as a previously unknown mechanism of stereospecific inhibition. Furthermore, this integrated analysis guided the design of a series of unique ASCT2 inhibitors. Our results provide a framework for future development of cancer therapeutics targeting nutrient transport via ASCT2, as well as demonstrate the utility of combining computational modeling and cryo-EM for solute carrier ligand discovery.

Subfields: Biochemistry, Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Diego del Alamo
2. Jens Meiler
3. Davide Sala
4. Hassane S. Mchaourab

In Molecular Biology

1. Diego del Alamo
2. Jens Meiler
3. Davide Sala
4. Hassane S. Mchaourab
5. Björn Wallner
6. David Baker

Citations in the corpus

• Sampling alternative conformational states of transporters and receptors with AlphaFold2 (2022, background): “…characterized in the literature ( Drew and Boudker, 2016 ), including rocking-bundle (LAT1, Yan et al., 2019 ; Yan et al., 2021 ; ZnT8, Xue et al., 2020 ), rocker-switch (MCT1, Wang et al., 2021 ; STP10, Bavnhøj et al., 2021 ), and elevator (ASCT2, Garibsingh et al., 2021 ; Garaeva et al., 2019 ).”