Ondansetron and Granisetron Binding Orientation in the 5-HT<sub>3</sub> Receptor Determined by Unnatural Amino Acid Mutagenesis

Duffy, N; Lester, Henry A.; Dougherty, Dennis A.

doi:10.1021/cb300246j

Cited by 36 publications

(31 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the structure 2YME the equivalent residue (R55) makes a cation-π interaction with granisetron and this interaction is supported by both the effect we report here and by previous findings that showed preserving the charge in R92K mutants does not affect granisetron binding (Duffy et al., 2012, Kesters et al., 2013, Thompson et al., 2005). In sharp contrast, the much smaller change in affinity shown by tropisetron suggest that interactions at R92 are less important.…”

Section: Discussionsupporting

confidence: 88%

The binding orientations of structurally-related ligands can differ; A cautionary note

et al. 2017

View full text Add to dashboard Cite

Crystal structures can identify ligand-receptor interactions and assist the development of novel therapeutics, but experimental challenges sometimes necessitate the use of homologous proteins. Tropisetron is an orthosteric ligand at both 5-HT3 and α7 nACh receptors and its binding orientation has been determined in the structural homologue AChBP (pdbid: 2WNC). Co-crystallisation with a structurally-related ligand, granisetron, reveals an almost identical orientation (pdbid; 2YME). However, there is a >1000-fold difference in the affinity of tropisetron at 5-HT3 versus α7 nACh receptors, and α7 nACh receptors do not bind granisetron. These striking pharmacological differences prompt questions about which receptor the crystal structures most closely represent and whether the ligand orientations are correct. Here we probe the binding orientation of tropisetron and granisetron at 5-HT3 receptors by in silico modelling and docking, radioligand binding on cysteine-substituted 5-HT3 receptor mutants transiently expressed in HEK 293 cells, and synthetic modification of the ligands. For 15 of the 23 cysteine substitutions, the effects on tropisetron and granisetron were different. Structure-activity relationships on synthesised derivatives of both ligands were also consistent with different orientations, revealing that contrary to the crystallographic evidence from AChBP, the two ligands adopt different orientations in the 5-HT3 receptor binding site. Our results show that even quite structurally similar molecules can adopt different orientations in the same binding site, and that caution may be needed when using homologous proteins to predict ligand binding.

show abstract

Section: Discussionsupporting

confidence: 88%

The binding orientations of structurally-related ligands can differ; A cautionary note

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Drug-like molecules with widely differing structures have been studied, including quaternary ammonium ions (acetylcholine) and protonated amines, including primary (glycine, GABA, serotonin), secondary (epibatidine, cytidine, varenicline) and tertiary (nicotine). In addition, more complex cations such as granisetron, ondansetron, 9 and the guanidinium toxin tetrodotoxin (TTX) 10 have shown linear fluorination plots. In contrast, a study of another guanidinium compound, meta-chlorophenyl biguanide (mCPBG) binding to the 5-HT 3 (serotonin) receptor showed behavior that was difficult to interpret.…”

Section: Introductionmentioning

confidence: 99%

Cation–π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation

Davis

Dougherty

2015

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4+ and NMe4+ to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the “fluorination strategy” to study cation-π interactions in vivo.

show abstract

“…The map quality was particularly good at the ligand-binding site allowing us to model sidechains and the setron orientation. Setrons bind within the canonical neurotransmitter binding [31][32][33] . In each setron-5-HT3AR complex, the essential pharmacophore of setron is placed in a similar orientation: the basic amine is at the deep-end of the pocket in the principal subunit; the defining aromatic moiety interacts with residues in the complementary subunit; and the carbonyl-based linker, between the two groups, is essentially coplanar with the aromatic ring.…”

Section: Cryo-em Structures Of Setron-5-ht3ar Complexesmentioning

confidence: 99%

High-resolution Structures of multiple 5-HT_3AR-setron complexes reveal a novel mechanism of competitive inhibition

Basak

Kumar

Ramsey

et al. 2020

Preprint

View full text Add to dashboard Cite

Serotonin receptors (5-HT3AR) play a crucial role in regulating gut movement, and are the principal target of setrons, a class of high-affinity competitive antagonists, used in the management of nausea and vomiting associated with radiation and chemotherapies. Structural insights into setron-binding poses and their inhibitory mechanisms are just beginning to emerge. Here, we present high-resolution cryo-EM structures of full-length 5-HT3AR in complex with palonosetron, ondansetron, and alosetron. Each structure reveals a distinct interaction fingerprint between the setron and binding-pocket residues that may underlie their diverse affinities. In addition, setrons elicit varying degrees of conformational change throughout the channel that, quite surprisingly, lie along the channel activation pathway, suggesting a novel mechanism of competitive inhibition.Molecular dynamic simulations were used to assess binding-poses and the drug-target interaction dynamics. Together, this study provides a molecular basis for setron binding affinities and their inhibitory effects.

show abstract

Ondansetron and Granisetron Binding Orientation in the 5-HT₃ Receptor Determined by Unnatural Amino Acid Mutagenesis

Cited by 36 publications

References 29 publications

The binding orientations of structurally-related ligands can differ; A cautionary note

The binding orientations of structurally-related ligands can differ; A cautionary note

Cation–π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation

High-resolution Structures of multiple 5-HT_3AR-setron complexes reveal a novel mechanism of competitive inhibition

Contact Info

Product

Resources

About

Ondansetron and Granisetron Binding Orientation in the 5-HT3 Receptor Determined by Unnatural Amino Acid Mutagenesis

Cited by 36 publications

References 29 publications

The binding orientations of structurally-related ligands can differ; A cautionary note

The binding orientations of structurally-related ligands can differ; A cautionary note

Cation–π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation

High-resolution Structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition

Contact Info

Product

Resources

About

Ondansetron and Granisetron Binding Orientation in the 5-HT₃ Receptor Determined by Unnatural Amino Acid Mutagenesis

High-resolution Structures of multiple 5-HT_3AR-setron complexes reveal a novel mechanism of competitive inhibition