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May 30, 2024;

Structural basis for antibiotic transport and inhibition in PepT2, the mammalian proton-coupled peptide transporter.

Simon Newstead, Joanne Parker, Justin Deme, Simon Lichtinger, Gabriel Kuteyi, Philip Biggin, Susan Lea
Author Information
  1. Simon Newstead: University of Oxford. ORCID
  2. Joanne Parker: University of Oxford. ORCID
  3. Justin Deme: National Cancer Institute, National Institutes of Health. ORCID
  4. Simon Lichtinger: University of Oxford. ORCID
  5. Gabriel Kuteyi: University of Oxford.
  6. Philip Biggin: University of Oxford. ORCID
  7. Susan Lea: Center for Structural Biology, Center for Cancer Research, National Cancer Institute. ORCID
PMID: 38903084 DOI: 10.21203/rs.3.rs-4435259/v1

Abstract

The uptake and elimination of beta-lactam antibiotics in the human body are facilitated by the proton-coupled peptide transporters PepT1 (SLC15A1) and PepT2 (SLC15A2). The mechanism by which SLC15 family transporters recognize and discriminate between different drug classes and dietary peptides remains unclear, hampering efforts to improve antibiotic pharmacokinetics through targeted drug design and delivery. Here, we present cryo-EM structures of the mammalian proton-coupled peptide transporter, PepT2, in complex with the widely used beta-lactam antibiotics cefadroxil, amoxicillin and cloxacillin. Our structures, combined with pharmacophore mapping, molecular dynamics simulations and biochemical assays, establish the mechanism of antibiotic recognition and the important role of protonation in drug binding and transport.

References

  1. Pharm Res. 2013 Apr;30(4):1017-25 [PMID: 23224978]
  2. Nature. 2014 Mar 6;507(7490):68-72 [PMID: 24572366]
  3. Front Mol Biosci. 2022 Jul 11;9:917725 [PMID: 35898305]
  4. EMBO Rep. 2014 Aug;15(8):886-93 [PMID: 24916388]
  5. Bioinformatics. 2020 Mar 1;36(6):1765-1771 [PMID: 31697312]
  6. Expert Opin Drug Metab Toxicol. 2009 Aug;5(8):887-905 [PMID: 19519280]
  7. J Chem Phys. 2008 Sep 28;129(12):124105 [PMID: 19045004]
  8. EMBO J. 2011 Jan 19;30(2):417-26 [PMID: 21131908]
  9. Xenobiotica. 2008 Jul;38(7-8):1022-42 [PMID: 18668438]
  10. Protein Pept Lett. 2012 Mar;19(3):282-7 [PMID: 21933132]
  11. J Biol Chem. 2002 Mar 1;277(9):7287-92 [PMID: 11751927]
  12. Mol Pharm. 2017 Dec 4;14(12):4685-4693 [PMID: 29111754]
  13. Drug Metab Pharmacokinet. 2008;23(6):464-8 [PMID: 19122341]
  14. Peptides. 2012 Nov;38(1):89-93 [PMID: 22940668]
  15. PLoS One. 2017 Mar 6;12(3):e0173126 [PMID: 28264013]
  16. Drug Discov Today. 2021 Feb;26(2):551-560 [PMID: 33197621]
  17. EMBO J. 2012 Aug 15;31(16):3411-21 [PMID: 22659829]
  18. Nephrol Dial Transplant. 2000;15 Suppl 6:11-3 [PMID: 11143972]
  19. J Mol Biol. 1993 Dec 5;234(3):779-815 [PMID: 8254673]
  20. Pflugers Arch. 2004 Feb;447(5):610-8 [PMID: 12905028]
  21. Br J Pharmacol. 1995 Dec;116(7):3021-7 [PMID: 8680738]
  22. Commun Chem. 2022 Feb 24;5(1):23 [PMID: 36697632]
  23. J Biol Chem. 1999 Jan 29;274(5):2773-9 [PMID: 9915809]
  24. Am J Physiol Renal Physiol. 2003 May;284(5):F885-92 [PMID: 12676733]
  25. Gastroenterology. 1986 Mar;90(3):577-82 [PMID: 3943689]
  26. J Struct Biol X. 2020 Nov 07;4:100040 [PMID: 33294840]
  27. J Pharmacol Exp Ther. 1998 Aug;286(2):1037-42 [PMID: 9694966]
  28. Structure. 2018 Mar 6;26(3):467-476.e4 [PMID: 29429879]
  29. Pharm Res. 1999 Jan;16(1):55-61 [PMID: 9950279]
  30. J Biol Chem. 2022 Feb;298(2):101505 [PMID: 34929170]
  31. J Chem Theory Comput. 2015 Aug 11;11(8):3696-713 [PMID: 26574453]
  32. Sci Adv. 2021 Aug 25;7(35): [PMID: 34433568]
  33. PLoS One. 2012;7(10):e47780 [PMID: 23110099]
  34. IUCrJ. 2019 Jan 01;6(Pt 1):5-17 [PMID: 30713699]
  35. Mol Pharm. 2010 Oct 4;7(5):1747-56 [PMID: 20735088]
  36. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544 [PMID: 29872004]
  37. J Pharm Pharmacol. 2008 May;60(5):543-85 [PMID: 18416933]
  38. J Chem Theory Comput. 2023 Jun 13;19(11):3251-3275 [PMID: 37167319]
  39. Nature. 2020 May;581(7808):316-322 [PMID: 32433612]
  40. Nat Struct Mol Biol. 2014 Aug;21(8):728-31 [PMID: 25064511]
  41. Sci Adv. 2021 Nov 05;7(45):eabk3259 [PMID: 34730990]
  42. Elife. 2024 Jul 23;13: [PMID: 39042711]
  43. Structure. 2022 Jul 7;30(7):1035-1041.e3 [PMID: 35580608]
  44. Physiology (Bethesda). 2006 Apr;21:93-102 [PMID: 16565475]
  45. J Chem Theory Comput. 2012 Aug 14;8(8):2938-48 [PMID: 26592132]
  46. Protein Sci. 2021 Jan;30(1):70-82 [PMID: 32881101]
  47. EMBO Rep. 2013 Sep;14(9):804-10 [PMID: 23867627]
  48. Biochem Biophys Res Commun. 2009 Nov 6;389(1):112-6 [PMID: 19703419]
  49. Trends Biochem Sci. 2023 Sep;48(9):801-814 [PMID: 37355450]
  50. Annu Rev Nutr. 1996;16:99-119 [PMID: 8839921]
  51. Biomol Ther (Seoul). 2023 Mar 1;31(2):141-147 [PMID: 36788654]
  52. Trends Pharmacol Sci. 2019 Oct;40(10):790-800 [PMID: 31519459]
  53. Biochem Soc Trans. 2020 Apr 29;48(2):337-346 [PMID: 32219385]
  54. Nat Commun. 2013;4:2502 [PMID: 24060756]
  55. Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):804-809 [PMID: 30602453]
  56. J Physiol. 2006 Jul 1;574(Pt 1):149-66 [PMID: 16627568]
  57. Mol Pharmacol. 2002 Jan;61(1):214-21 [PMID: 11752223]
  58. Nature. 1994 Apr 7;368(6471):563-6 [PMID: 8139693]
  59. J Biol Chem. 2015 Dec 11;290(50):29931-40 [PMID: 26483552]
  60. Eur J Pharm Biopharm. 2005 Jan;59(1):17-24 [PMID: 15567297]
  61. FEMS Microbiol Rev. 2008 Mar;32(2):149-67 [PMID: 18194336]
  62. Biochim Biophys Acta. 1996 Apr 26;1280(2):173-7 [PMID: 8639691]
  63. J Med Chem. 2006 Jul 13;49(14):4286-96 [PMID: 16821788]
  64. AAPS J. 2013 Apr;15(2):581-8 [PMID: 23435786]
  65. Commun Chem. 2022 Sep 5;5(1):105 [PMID: 36697714]
  66. Eur J Pharmacol. 2009 Jun 10;612(1-3):9-14 [PMID: 19371738]
  67. Cell Chem Biol. 2016 Feb 18;23(2):299-309 [PMID: 27028887]
  68. J Am Chem Soc. 2019 Feb 13;141(6):2404-2412 [PMID: 30644743]
  69. J Chem Inf Model. 2017 Sep 25;57(9):2203-2221 [PMID: 28786670]
  70. J Biol Chem. 1995 Mar 24;270(12):6456-63 [PMID: 7896779]
  71. Am J Physiol. 1997 Nov;273(5):F706-11 [PMID: 9374833]
  72. Nat Methods. 2020 Dec;17(12):1214-1221 [PMID: 33257830]
  73. Molecules. 2023 Jan 24;28(3): [PMID: 36770817]
  74. Drug Metab Dispos. 2006 Apr;34(4):547-55 [PMID: 16434549]
  75. Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):13182-13187 [PMID: 29180426]
  76. Nat Rev Drug Discov. 2015 Aug;14(8):543-60 [PMID: 26111766]
  77. Trends Microbiol. 2006 Sep;14(9):413-20 [PMID: 16876996]
  78. Acta Crystallogr D Biol Crystallogr. 2015 Jan 1;71(Pt 1):136-53 [PMID: 25615868]
  79. J Chem Phys. 2007 Jan 7;126(1):014101 [PMID: 17212484]
  80. J Mol Microbiol Biotechnol. 2016;26(5):312-9 [PMID: 27438044]
  81. Protein Sci. 2020 Jan;29(1):315-329 [PMID: 31724275]
  82. FEBS Lett. 2014 Feb 14;588(4):560-5 [PMID: 24440353]
  83. J Comput Chem. 2014 Oct 15;35(27):1997-2004 [PMID: 25130509]

Grants

  1. /Wellcome Trust
Journal Article Preprint

Word Cloud

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