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      A novel small-molecule selective activator of homomeric GIRK4 channels

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      1 , 2 , , 1 , 1 , 3 , 1 , 1 , 1 , 1 , 2 , 3 , 1 , 2 , 4 ,
      The Journal of Biological Chemistry
      American Society for Biochemistry and Molecular Biology
      Kir3 channels, drug–channel interaction, molecular docking, molecular dynamics simulations, mutagenesis, electrophysiology, ACh, acetylcholine, Ba, barium, CIBN, cryptochrome-interacting basic helix–loop–helix N-terminal fragment, CRY2, cryptochrome 2, GIRK, G protein–sensitive inwardly rectifying potassium channel, HAC15, human adrenocortical 15 cell line, HBC, helix bundle crossing, 3hi2one-G4, 3-[2-(3,4-dimethoxyphenyl)-2-oxoethyl]-3-hydroxy-1-(1-naphthylmethyl)-1,3-dihydro-2H-indol-2-one, HK, high potassium, IKACh, acetylcholine-activated inwardly rectifying K+ current, IVM, ivermectin, LK, low potassium, PA, primary aldosteronism, PIP2, phosphatidylinositol-4,5-bisphosphate, PMC, pro-opiomelanocortin, S-HLX, slide helix, TEVC, two-electrode voltage clamp, TM, transmembrane domain, TIRF, total internal reflection fluorescence, VMN, ventromedial nucleus

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          Abstract

          G protein–sensitive inwardly rectifying potassium (GIRK) channels are important pharmaceutical targets for neuronal, cardiac, and endocrine diseases. Although a number of GIRK channel modulators have been discovered in recent years, most lack selectivity. GIRK channels function as either homomeric ( i.e., GIRK2 and GIRK4) or heteromeric ( e.g., GIRK1/2, GIRK1/4, and GIRK2/3) tetramers. Activators, such as ML297, ivermectin, and GAT1508, have been shown to activate heteromeric GIRK1/2 channels better than GIRK1/4 channels with varying degrees of selectivity but not homomeric GIRK2 and GIRK4 channels. In addition, VU0529331 was discovered as the first homomeric GIRK channel activator, but it shows weak selectivity for GIRK2 over GIRK4 (or G4) homomeric channels. Here, we report the first highly selective small-molecule activator targeting GIRK4 homomeric channels, 3hi2one-G4 (3-[2-(3,4-dimethoxyphenyl)-2-oxoethyl]-3-hydroxy-1-(1-naphthylmethyl)-1,3-dihydro-2H-indol-2-one). We show that 3hi2one-G4 does not activate GIRK2, GIRK1/2, or GIRK1/4 channels. Using molecular modeling, mutagenesis, and electrophysiology, we analyzed the binding site of 3hi2one-G4 formed by the transmembrane 1, transmembrane 2, and slide helix regions of the GIRK4 channel, near the phosphatidylinositol-4,5-bisphosphate binding site, and show that it causes channel activation by strengthening channel–phosphatidylinositol-4,5-bisphosphate interactions. We also identify slide helix residue L77 in GIRK4, corresponding to residue I82 in GIRK2, as a major determinant of isoform-specific selectivity. We propose that 3hi2one-G4 could serve as a useful pharmaceutical probe in studying GIRK4 channel function and may also be pursued in drug optimization studies to tackle GIRK4-related diseases such as primary aldosteronism and late-onset obesity.

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          Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

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            Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

            Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 A in nearly half of the cases and are greater than 2 A in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.
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              Comparative protein modelling by satisfaction of spatial restraints.

              We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.
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                Author and article information

                Contributors
                Journal
                J Biol Chem
                J Biol Chem
                The Journal of Biological Chemistry
                American Society for Biochemistry and Molecular Biology
                0021-9258
                1083-351X
                04 May 2022
                June 2022
                04 May 2022
                : 298
                : 6
                : 102009
                Affiliations
                [1 ]Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, USA
                [2 ]Center for Drug Discovery, Northeastern University, Boston, Massachusetts, USA
                [3 ]Department of Physiology and Pharmacology and Sagol School of Neuroscience, School of Medicine, Tel Aviv University, Tel Aviv, Israel
                [4 ]Chemistry and Chemical Biology, College of Science, Northeastern University, Boston, Massachusetts, USA
                Author notes
                []For correspondence: Diomedes E. Logothetis; Meng Cui m.cui@ 123456northeastern.edu d.logothetis@ 123456northeastern.edu
                Article
                S0021-9258(22)00449-5 102009
                10.1016/j.jbc.2022.102009
                9194863
                35525275
                ce5fdd11-9bfe-44dd-9bb1-b19010f78c6a
                © 2022 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 7 November 2021
                : 27 April 2022
                Categories
                Research Article

                Biochemistry
                kir3 channels,drug–channel interaction,molecular docking,molecular dynamics simulations,mutagenesis,electrophysiology,ach, acetylcholine,ba, barium,cibn, cryptochrome-interacting basic helix–loop–helix n-terminal fragment,cry2, cryptochrome 2,girk, g protein–sensitive inwardly rectifying potassium channel,hac15, human adrenocortical 15 cell line,hbc, helix bundle crossing,3hi2one-g4, 3-[2-(3,4-dimethoxyphenyl)-2-oxoethyl]-3-hydroxy-1-(1-naphthylmethyl)-1,3-dihydro-2h-indol-2-one,hk, high potassium,ikach, acetylcholine-activated inwardly rectifying k+ current,ivm, ivermectin,lk, low potassium,pa, primary aldosteronism,pip2, phosphatidylinositol-4,5-bisphosphate,pmc, pro-opiomelanocortin,s-hlx, slide helix,tevc, two-electrode voltage clamp,tm, transmembrane domain,tirf, total internal reflection fluorescence,vmn, ventromedial nucleus

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