Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211

Danny J. Scholten, Luc Roumen, Maikel Wijtmans, Marlies C. A. Verkade-Vreeker, Hans Custers, Michael Lai, Daniela de Hooge, Meritxell Canals, Iwan J. P. de Esch, Martine J. Smit, Chris de Graaf, Rob Leurs

Research output: Contribution to journalArticleResearchpeer-review

Abstract

CXC chemokine receptor CXCR3 and/or its main three ligands CXCL9, CXCL10, and CXCL11 are highly upregulated in a variety of diseases. As such, considerable efforts have beenmade to develop small-molecule receptor CXCR3 antagonists, yielding distinct chemical classes of antagonists blocking binding and/or function of CXCR3 chemokines. Although it is suggested that these compounds bind in an allosteric fashion, thus far no evidence has been provided regarding the molecular details of their interaction with CXCR3. Using site-directed mutagenesis complemented with in silico homology modeling, we report the binding modes of two high-affinity CXCR3 antagonists of distinct chemotypes: VUF11211 [(S)-5-chloro-6-(4-(1-(4-chlorobenzyl)piperidin-4-yl)-3- ethylpiperazin-1-yl)-N-ethylnicotinamide] (piperazinyl-piperidine) with a rigid elongated structure containing two basic groups andNBI-74330 [(R)-N-(1-(3-(4-ethoxyphenyl)-4-oxo-3,4-dihydropyrido[ 2,3-d]pyrimidin-2-yl) ethyl)-2-(4-fluoro-3-(trifluoromethyl)phenyl)- N-(pyridin-3-ylmethyl)acetamide] (8-azaquinazolinone) without any basic group. Here we show that NBI-74330 is anchored in the transmembrane minor pocket lined by helices 2 (W2.60, D2.63), 3 (F3.32), and 7 (S7.39, Y7.43), whereas VUF11211 extends from the minor pocket into the major pocket of the transmembrane domains, located between residues in helices 1 (Y1.39), 2 (W2.60), 3 (F3.32), 4 (D4.60), 6 (Y6.51), and 7 (S7.39, Y7.43). Mutation of these residues did not affect CXCL11 binding significantly, confirming the allosteric nature of the interaction of these small molecules with CXCR3. Moreover, the model derived from our in silico-guided studies fits well with the already published structure-activity relationship data on these ligands. Altogether, in this study, we show overlapping, yet different binding sites for two high-affinity CXCR3 antagonists, which offer new opportunities for the structure-based design of allosteric modulators for CXCR3.

Original languageEnglish
Pages (from-to)116-126
Number of pages11
JournalMolecular Pharmacology
Volume85
Issue number1
DOIs
Publication statusPublished - Jan 2014

Cite this

Scholten, D. J., Roumen, L., Wijtmans, M., Verkade-Vreeker, M. C. A., Custers, H., Lai, M., ... Leurs, R. (2014). Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211. Molecular Pharmacology, 85(1), 116-126. https://doi.org/10.1124/mol.113.088633
Scholten, Danny J. ; Roumen, Luc ; Wijtmans, Maikel ; Verkade-Vreeker, Marlies C. A. ; Custers, Hans ; Lai, Michael ; de Hooge, Daniela ; Canals, Meritxell ; de Esch, Iwan J. P. ; Smit, Martine J. ; de Graaf, Chris ; Leurs, Rob. / Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211. In: Molecular Pharmacology. 2014 ; Vol. 85, No. 1. pp. 116-126.
@article{54d041304e434158bb3db49604f6c61b,
title = "Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211",
abstract = "CXC chemokine receptor CXCR3 and/or its main three ligands CXCL9, CXCL10, and CXCL11 are highly upregulated in a variety of diseases. As such, considerable efforts have beenmade to develop small-molecule receptor CXCR3 antagonists, yielding distinct chemical classes of antagonists blocking binding and/or function of CXCR3 chemokines. Although it is suggested that these compounds bind in an allosteric fashion, thus far no evidence has been provided regarding the molecular details of their interaction with CXCR3. Using site-directed mutagenesis complemented with in silico homology modeling, we report the binding modes of two high-affinity CXCR3 antagonists of distinct chemotypes: VUF11211 [(S)-5-chloro-6-(4-(1-(4-chlorobenzyl)piperidin-4-yl)-3- ethylpiperazin-1-yl)-N-ethylnicotinamide] (piperazinyl-piperidine) with a rigid elongated structure containing two basic groups andNBI-74330 [(R)-N-(1-(3-(4-ethoxyphenyl)-4-oxo-3,4-dihydropyrido[ 2,3-d]pyrimidin-2-yl) ethyl)-2-(4-fluoro-3-(trifluoromethyl)phenyl)- N-(pyridin-3-ylmethyl)acetamide] (8-azaquinazolinone) without any basic group. Here we show that NBI-74330 is anchored in the transmembrane minor pocket lined by helices 2 (W2.60, D2.63), 3 (F3.32), and 7 (S7.39, Y7.43), whereas VUF11211 extends from the minor pocket into the major pocket of the transmembrane domains, located between residues in helices 1 (Y1.39), 2 (W2.60), 3 (F3.32), 4 (D4.60), 6 (Y6.51), and 7 (S7.39, Y7.43). Mutation of these residues did not affect CXCL11 binding significantly, confirming the allosteric nature of the interaction of these small molecules with CXCR3. Moreover, the model derived from our in silico-guided studies fits well with the already published structure-activity relationship data on these ligands. Altogether, in this study, we show overlapping, yet different binding sites for two high-affinity CXCR3 antagonists, which offer new opportunities for the structure-based design of allosteric modulators for CXCR3.",
author = "Scholten, {Danny J.} and Luc Roumen and Maikel Wijtmans and Verkade-Vreeker, {Marlies C. A.} and Hans Custers and Michael Lai and {de Hooge}, Daniela and Meritxell Canals and {de Esch}, {Iwan J. P.} and Smit, {Martine J.} and {de Graaf}, Chris and Rob Leurs",
year = "2014",
month = "1",
doi = "10.1124/mol.113.088633",
language = "English",
volume = "85",
pages = "116--126",
journal = "Molecular Pharmacology",
issn = "1521-0111",
publisher = "ACS Books",
number = "1",

}

Scholten, DJ, Roumen, L, Wijtmans, M, Verkade-Vreeker, MCA, Custers, H, Lai, M, de Hooge, D, Canals, M, de Esch, IJP, Smit, MJ, de Graaf, C & Leurs, R 2014, 'Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211', Molecular Pharmacology, vol. 85, no. 1, pp. 116-126. https://doi.org/10.1124/mol.113.088633

Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211. / Scholten, Danny J.; Roumen, Luc; Wijtmans, Maikel; Verkade-Vreeker, Marlies C. A.; Custers, Hans; Lai, Michael; de Hooge, Daniela; Canals, Meritxell; de Esch, Iwan J. P.; Smit, Martine J.; de Graaf, Chris; Leurs, Rob.

In: Molecular Pharmacology, Vol. 85, No. 1, 01.2014, p. 116-126.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Identification of overlapping but differential binding sites for the high-affinity CXCR3 antagonists NBI-74330 and VUF11211

AU - Scholten, Danny J.

AU - Roumen, Luc

AU - Wijtmans, Maikel

AU - Verkade-Vreeker, Marlies C. A.

AU - Custers, Hans

AU - Lai, Michael

AU - de Hooge, Daniela

AU - Canals, Meritxell

AU - de Esch, Iwan J. P.

AU - Smit, Martine J.

AU - de Graaf, Chris

AU - Leurs, Rob

PY - 2014/1

Y1 - 2014/1

N2 - CXC chemokine receptor CXCR3 and/or its main three ligands CXCL9, CXCL10, and CXCL11 are highly upregulated in a variety of diseases. As such, considerable efforts have beenmade to develop small-molecule receptor CXCR3 antagonists, yielding distinct chemical classes of antagonists blocking binding and/or function of CXCR3 chemokines. Although it is suggested that these compounds bind in an allosteric fashion, thus far no evidence has been provided regarding the molecular details of their interaction with CXCR3. Using site-directed mutagenesis complemented with in silico homology modeling, we report the binding modes of two high-affinity CXCR3 antagonists of distinct chemotypes: VUF11211 [(S)-5-chloro-6-(4-(1-(4-chlorobenzyl)piperidin-4-yl)-3- ethylpiperazin-1-yl)-N-ethylnicotinamide] (piperazinyl-piperidine) with a rigid elongated structure containing two basic groups andNBI-74330 [(R)-N-(1-(3-(4-ethoxyphenyl)-4-oxo-3,4-dihydropyrido[ 2,3-d]pyrimidin-2-yl) ethyl)-2-(4-fluoro-3-(trifluoromethyl)phenyl)- N-(pyridin-3-ylmethyl)acetamide] (8-azaquinazolinone) without any basic group. Here we show that NBI-74330 is anchored in the transmembrane minor pocket lined by helices 2 (W2.60, D2.63), 3 (F3.32), and 7 (S7.39, Y7.43), whereas VUF11211 extends from the minor pocket into the major pocket of the transmembrane domains, located between residues in helices 1 (Y1.39), 2 (W2.60), 3 (F3.32), 4 (D4.60), 6 (Y6.51), and 7 (S7.39, Y7.43). Mutation of these residues did not affect CXCL11 binding significantly, confirming the allosteric nature of the interaction of these small molecules with CXCR3. Moreover, the model derived from our in silico-guided studies fits well with the already published structure-activity relationship data on these ligands. Altogether, in this study, we show overlapping, yet different binding sites for two high-affinity CXCR3 antagonists, which offer new opportunities for the structure-based design of allosteric modulators for CXCR3.

AB - CXC chemokine receptor CXCR3 and/or its main three ligands CXCL9, CXCL10, and CXCL11 are highly upregulated in a variety of diseases. As such, considerable efforts have beenmade to develop small-molecule receptor CXCR3 antagonists, yielding distinct chemical classes of antagonists blocking binding and/or function of CXCR3 chemokines. Although it is suggested that these compounds bind in an allosteric fashion, thus far no evidence has been provided regarding the molecular details of their interaction with CXCR3. Using site-directed mutagenesis complemented with in silico homology modeling, we report the binding modes of two high-affinity CXCR3 antagonists of distinct chemotypes: VUF11211 [(S)-5-chloro-6-(4-(1-(4-chlorobenzyl)piperidin-4-yl)-3- ethylpiperazin-1-yl)-N-ethylnicotinamide] (piperazinyl-piperidine) with a rigid elongated structure containing two basic groups andNBI-74330 [(R)-N-(1-(3-(4-ethoxyphenyl)-4-oxo-3,4-dihydropyrido[ 2,3-d]pyrimidin-2-yl) ethyl)-2-(4-fluoro-3-(trifluoromethyl)phenyl)- N-(pyridin-3-ylmethyl)acetamide] (8-azaquinazolinone) without any basic group. Here we show that NBI-74330 is anchored in the transmembrane minor pocket lined by helices 2 (W2.60, D2.63), 3 (F3.32), and 7 (S7.39, Y7.43), whereas VUF11211 extends from the minor pocket into the major pocket of the transmembrane domains, located between residues in helices 1 (Y1.39), 2 (W2.60), 3 (F3.32), 4 (D4.60), 6 (Y6.51), and 7 (S7.39, Y7.43). Mutation of these residues did not affect CXCL11 binding significantly, confirming the allosteric nature of the interaction of these small molecules with CXCR3. Moreover, the model derived from our in silico-guided studies fits well with the already published structure-activity relationship data on these ligands. Altogether, in this study, we show overlapping, yet different binding sites for two high-affinity CXCR3 antagonists, which offer new opportunities for the structure-based design of allosteric modulators for CXCR3.

UR - http://www.scopus.com/inward/record.url?scp=84890653833&partnerID=8YFLogxK

U2 - 10.1124/mol.113.088633

DO - 10.1124/mol.113.088633

M3 - Article

VL - 85

SP - 116

EP - 126

JO - Molecular Pharmacology

JF - Molecular Pharmacology

SN - 1521-0111

IS - 1

ER -