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Hutchinson K, Silva DB, Bohlke J, Clausen C, Thomas AA, Bonomi M, Schlessinger A. Describing inhibitor specificity for the amino acid transporter LAT1 from metainference simulations. Biophys J 2022; 121:4476-4491. [PMID: 36369754 PMCID: PMC9748366 DOI: 10.1016/j.bpj.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/09/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
The human L-type amino acid transporter 1 (LAT1; SLC7A5) is a membrane transporter of amino acids, thyroid hormones, and drugs such as the Parkinson's disease drug levodopa (L-Dopa). LAT1 is found in the blood-brain barrier, testis, bone marrow, and placenta, and its dysregulation has been associated with various neurological diseases, such as autism and epilepsy, as well as cancer. In this study, we combine metainference molecular dynamics simulations, molecular docking, and experimental testing, to characterize LAT1-inhibitor interactions. We first conducted a series of molecular docking experiments to identify the most relevant interactions between LAT1's substrate-binding site and ligands, including both inhibitors and substrates. We then performed metainference molecular dynamics simulations using cryoelectron microscopy structures in different conformations of LAT1 with the electron density map as a spatial restraint, to explore the inherent heterogeneity in the structures. We analyzed the LAT1 substrate-binding site to map important LAT1-ligand interactions as well as newly described druggable pockets. Finally, this analysis guided the discovery of previously unknown LAT1 ligands using virtual screening and cellular uptake experiments. Our results improve our understanding of LAT1-inhibitor recognition, providing a framework for rational design of future lead compounds targeting this key drug target.
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Affiliation(s)
- Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, California
| | - Joshua Bohlke
- Department of Chemistry, University of Nebraska at Kearney, Kearney, Nebraska
| | - Chase Clausen
- Department of Chemistry, University of Nebraska at Kearney, Kearney, Nebraska
| | - Allen A Thomas
- Department of Chemistry, University of Nebraska at Kearney, Kearney, Nebraska
| | - Massimiliano Bonomi
- Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
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Venteicher B, Merklin K, Ngo HX, Chien HC, Hutchinson K, Campbell J, Way H, Griffith J, Alvarado C, Chandra S, Hill E, Schlessinger A, Thomas AA. The Effects of Prodrug Size and a Carbonyl Linker on l-Type Amino Acid Transporter 1-Targeted Cellular and Brain Uptake. ChemMedChem 2020; 16:869-880. [PMID: 33230949 DOI: 10.1002/cmdc.202000824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/23/2020] [Indexed: 11/08/2022]
Abstract
The l-type amino acid transporter 1 (LAT1, SLC7A5) imports dietary amino acids and amino acid drugs (e. g., l-DOPA) into the brain, and plays a role in cancer metabolism. Though there have been numerous reports of LAT1-targeted amino acid-drug conjugates (prodrugs), identifying the structural determinants to enhance substrate activity has been challenging. In this work, we investigated the position and orientation of a carbonyl group in linking hydrophobic moieties including the anti-inflammatory drug ketoprofen to l-tyrosine and l-phenylalanine. We found that esters of meta-carboxyl l-phenylalanine had better LAT1 transport rates than the corresponding acylated l-tyrosine analogues. However, as the size of the hydrophobic moiety increased, we observed a decrease in LAT1 transport rate with a concomitant increase in potency of inhibition. Our results have important implications for designing amino acid prodrugs that target LAT1 at the blood-brain barrier or on cancer cells.
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Affiliation(s)
- Brooklynn Venteicher
- Department of Chemistry, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
| | - Kasey Merklin
- Department of Chemistry, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
| | - Huy X Ngo
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1550 4th St, Rm RH581, San Francisco, CA 94143, USA
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1550 4th St, Rm RH581, San Francisco, CA 94143, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mt. Sinai, 1468 Madison Ave, Annenberg Building Floor 19, New York, NY 10029, USA
| | - Jerome Campbell
- Department of Chemistry, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
| | - Hannah Way
- Department of Chemistry, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
| | - Joseph Griffith
- Department of Chemistry, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
| | - Cesar Alvarado
- Department of Chemistry, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
| | - Surabhi Chandra
- Department of Biology, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
| | - Evan Hill
- Department of Psychology, University of Nebraska, at Kearney 2507 11th Ave, Copeland Hall, Kearney, NE, 68849, (USA)
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mt. Sinai, 1468 Madison Ave, Annenberg Building Floor 19, New York, NY 10029, USA
| | - Allen A Thomas
- Department of Chemistry, University of Nebraska at Kearney, 2401 11th Ave, Bruner Hall of Science, Kearney, NE 68849, USA
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