Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin

TY - JOUR

T1 - Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats

T2 - insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin

AU - Dagil, Robert

AU - O'Shea, Charlotte

AU - Nykjær, Anders

AU - Bonvin, Alexandre M J J

AU - Kragelund, Birthe B

PY - 2013/2/8

Y1 - 2013/2/8

N2 - Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information has been available to describe the interaction with gentamicin in atomic detail, and neither have any three-dimensional structures of domains from the human megalin receptor been solved. To address this gap in our knowledge, we have solved the NMR structure of the 10th complement type repeat of human megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described (Jensen, G. A., Andersen, O. M., Bonvin, A. M., Bjerrum-Bohr, I., Etzerodt, M., Thogersen, H. C., O'Shea, C., Poulsen, F. M., and Kragelund, B. B. (2006) J. Mol. Biol. 362, 700-716) utilizing the indole side chain of Trp-1126 and the negatively charged residues Asp-1129, Asp-1131, and Asp-1133. Binding to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists.

AB - Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information has been available to describe the interaction with gentamicin in atomic detail, and neither have any three-dimensional structures of domains from the human megalin receptor been solved. To address this gap in our knowledge, we have solved the NMR structure of the 10th complement type repeat of human megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described (Jensen, G. A., Andersen, O. M., Bonvin, A. M., Bjerrum-Bohr, I., Etzerodt, M., Thogersen, H. C., O'Shea, C., Poulsen, F. M., and Kragelund, B. B. (2006) J. Mol. Biol. 362, 700-716) utilizing the indole side chain of Trp-1126 and the negatively charged residues Asp-1129, Asp-1131, and Asp-1133. Binding to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists.

KW - Amino Acid Motifs

KW - Gentamicins

KW - Humans

KW - Low Density Lipoprotein Receptor-Related Protein-2

KW - Molecular Docking Simulation

KW - Nuclear Magnetic Resonance, Biomolecular

KW - Protein Binding

KW - Protein Structure, Tertiary

KW - Repetitive Sequences, Amino Acid

KW - Structure-Activity Relationship

U2 - 10.1074/jbc.M112.434159

DO - 10.1074/jbc.M112.434159

M3 - Journal article

C2 - 23275343

SN - 0021-9258

VL - 288

SP - 4424

EP - 4435

JO - The Journal of Biological Chemistry

JF - The Journal of Biological Chemistry

IS - 6

ER -