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Docking of inhibitors to the structure of the human K‐Cl cotransporter
Author(s) -
Delpire Eric
Publication year - 2020
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2020.34.s1.06139
Subject(s) - chemistry , cotransporter , docking (animal) , stereochemistry , binding site , binding energy , crystallography , autodock , biochemistry , organic chemistry , medicine , physics , nursing , nuclear physics , sodium , in silico , gene
Following the release of the cryo‐electron microscopy structure of the human K‐Cl cotransporter, hKCC1, we used a ligand‐protein docking program (Autodock Vina from the Scripps Research Institute) to assess the binding of KCC inhibitors to the K‐Cl cotransporter. We hypothesized that the inhibitors were likely to utilize the ion permeation pathway and overlap with some of the ion binding sites. We first modeled the binding of ML077 starting from the position of the 3 ions at S Cl1 , S K , and S Cl2 . ML077 is a potent inhibitor of KCC function, as it binds rat KCC2 with an EC 50 of 560 nM. The top binding energies for the best solutions from these three positions were: −7.6, −7.6, and −8.5 kcal/mol, indicating that the compound clearly fits better in the lower portion of the permeation pathway. We observed that the ring structures of the inhibitory compound nicely fitted within the hydrophobic groove or cavity which is located at the bottom of the transporter core. Furthermore, the most distal methyl group of ML077 was conveniently positioned 3.6 Å from the side chain of Tyr216. Since this residue also coordinates the placement of K + , this data is consistent with previous report showing that the binding of ML077 is competitive with regard to K + . When we docked the stilbene derivatives DIDS and H2DIDS to the structure, we observed binding modalities with binding energy around −7.5 kcal/mol. The inhibitors were located in the groove with the nitrogen atom or sulfur atom of an isothiocyanate group placed 3.3 – 3.5 Å from Tyr 216 and one the sulfonic acid group oriented either towards the Cl − ion at S Cl2 or TM8. The second sulfonic acid group orients towards the outside of the cavity, while the second isothiocyanate group nicely fits within a lower portion of the groove. As these conformations do not involve Tyr 216 and do not seem to overlap with the bound K + , this docking is consistent with non‐competitive DIDS inhibition with regards to K + . Finally, docking of furosemide to the hKCC1 structure also preferentially placed the loop diuretic within the cavity with a possible hydrogen bond between the amine group of the ligand and the hydroxyl group of Tyr 216 (distance 1.8 Å). Involvement of the tyrosine residue in coordinating furosemide binding is also consistent with the competitive inhibition of furosemide with respect to K + . Thus, it seems that the binding of ML077, DIDS and H2DIDS, and furosemide are consistent with some older functional studies. Single site mutagenesis and functional experiments should confirm these predictions. Support or Funding Information This work was supported by NIH grant DK93501 and by grant 17CVD05 from the Leducq foundation.