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Simon I, Homan EJ, Wijtmans M, Sundström M, Leurs R, De Esch IJP, Zarzycka BA. PSW-Designer: An Open-Source Computational Platform for the Design and Virtual Screening of Photopharmacological Ligands. J Chem Inf Model 2023; 63:6696-6705. [PMID: 37831965 PMCID: PMC10647043 DOI: 10.1021/acs.jcim.3c01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Indexed: 10/15/2023]
Abstract
Photoswitchable (PSW) molecules offer an attractive opportunity for the optical control of biological processes. However, the successful design of such compounds remains a challenging multioptimization endeavor, resulting in several biological target classes still relatively poorly explored by photoswitchable ligands, as is the case for G protein-coupled receptors (GPCRs). Here, we present the PSW-Designer, a fully open-source computational platform, implemented in the KNIME Analytics Platform, to design and virtually screen novel photoswitchable ligands for photopharmacological applications based on privileged scaffolds. We demonstrate the applicability of the PSW-Designer to GPCRs and assess its predictive capabilities via two retrospective case studies. Furthermore, by leveraging bioactivity information on known ligands, typical and atypical strategies for photoswitchable group incorporation, and the increasingly structural information available for biological targets, the PSW-Design will facilitate the design of novel photoswitchable molecules with improved photopharmacological properties and increased binding affinity shifts upon illumination for GPCRs and many other protein targets.
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Affiliation(s)
- Icaro
A. Simon
- Division
of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for
Molecular and Life Sciences, Vrije Universiteit
Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Evert J. Homan
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Maikel Wijtmans
- Division
of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for
Molecular and Life Sciences, Vrije Universiteit
Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Michael Sundström
- Centre
for Molecular Medicine, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Rob Leurs
- Division
of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for
Molecular and Life Sciences, Vrije Universiteit
Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J. P. De Esch
- Division
of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for
Molecular and Life Sciences, Vrije Universiteit
Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Barbara A. Zarzycka
- Division
of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for
Molecular and Life Sciences, Vrije Universiteit
Amsterdam, 1081 HZ Amsterdam, The Netherlands
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Khanfar MA, Reiner D, Hagenow S, Stark H. Design, synthesis, and biological evaluation of novel oxadiazole- and thiazole-based histamine H 3R ligands. Bioorg Med Chem 2018; 26:4034-4046. [PMID: 29960729 DOI: 10.1016/j.bmc.2018.06.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 02/06/2023]
Abstract
Histamine H3 receptor (H3R) is largely expressed in the CNS and modulation of the H3R function can affect histamine synthesis and liberation, and modulate the release of many other neurotransmitters. Targeting H3R with antagonists/inverse agonists may have therapeutic applications in neurodegenerative disorders, gastrointestinal and inflammatory diseases. This prompted us to design and synthesize azole-based H3R ligands, i.e. having oxadiazole- or thiazole-based core structures. While ligands of oxadiazole scaffold were almost inactive, thiazole-based ligands were very potent and several exhibited binding affinities in a nanomolar concentration range. Ligands combining 4-cyanophenyl moiety as arbitrary region, para-xylene or piperidine carbamoyl linkers, and/or pyrrolidine or piperidine basic heads were found to be the most active within this series of thiazole-based H3R ligands. The most active ligands were in silico screened for ADMET properties and drug-likeness. They fulfilled Lipinski's and Veber's rules and exhibited potential activities for oral administration, blood-brain barrier penetration, low hepatotoxicity, combined with an overall good toxicity profile.
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Affiliation(s)
- Mohammad A Khanfar
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany; Faculty of Pharmacy, University of Jordan, P.O Box 13140, Amman 11942, Jordan; College of Pharmacy, Alfaisal University, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - David Reiner
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Stefanie Hagenow
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Holger Stark
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Duesseldorf, Germany.
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3
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Hauwert NJ, Mocking TAM, Da Costa Pereira D, Kooistra AJ, Wijnen LM, Vreeker GCM, Verweij EWE, De Boer AH, Smit MJ, De Graaf C, Vischer HF, de Esch IJP, Wijtmans M, Leurs R. Synthesis and Characterization of a Bidirectional Photoswitchable Antagonist Toolbox for Real-Time GPCR Photopharmacology. J Am Chem Soc 2018; 140:4232-4243. [PMID: 29470065 PMCID: PMC5879491 DOI: 10.1021/jacs.7b11422] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Noninvasive methods
to modulate G protein-coupled receptors (GPCRs)
with temporal and spatial precision are in great demand. Photopharmacology
uses photons to control in situ the biological properties
of photoswitchable small-molecule ligands, which bodes well for chemical
biological precision approaches. Integrating the light-switchable
configurational properties of an azobenzene into the ligand core,
we developed a bidirectional antagonist toolbox for an archetypical
family A GPCR, the histamine H3 receptor (H3R). From 16 newly synthesized photoswitchable compounds, VUF14738
(28) and VUF14862 (33) were selected as
they swiftly and reversibly photoisomerize and show over 10-fold increased
or decreased H3R binding affinities, respectively, upon
illumination at 360 nm. Both ligands combine long thermal half-lives
with fast and high photochemical trans-/cis conversion, allowing their use in real-time electrophysiology experiments
with oocytes to confirm dynamic photomodulation of H3R
activation in repeated second-scale cycles. VUF14738 and VUF14862
are robust and fatigue-resistant photoswitchable GPCR antagonists
suitable for spatiotemporal studies of H3R signaling.
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Affiliation(s)
- Niels J Hauwert
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Tamara A M Mocking
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Daniel Da Costa Pereira
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Lisa M Wijnen
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Gerda C M Vreeker
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Eléonore W E Verweij
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Albertus H De Boer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Martine J Smit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Chris De Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Henry F Vischer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
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Berlin M, Boyce CW, de Lera Ruiz M. Histamine H3 Receptor as a Drug Discovery Target. J Med Chem 2010; 54:26-53. [DOI: 10.1021/jm100064d] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michael Berlin
- Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Christopher W. Boyce
- Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Manuel de Lera Ruiz
- Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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5
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Discovery of potent and selective histamine H3 receptor inverse agonists based on the 3,4-dihydro-2H-pyrazino[1,2-a]indol-1-one scaffold. Bioorg Med Chem Lett 2010; 20:5713-7. [DOI: 10.1016/j.bmcl.2010.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/02/2010] [Accepted: 08/03/2010] [Indexed: 11/22/2022]
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6
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Walter M, von Coburg Y, Isensee K, Sander K, Ligneau X, Camelin JC, Schwartz JC, Stark H. Azole derivatives as histamine H3 receptor antagonists, Part I: Thiazol-2-yl ethers. Bioorg Med Chem Lett 2010; 20:5879-82. [DOI: 10.1016/j.bmcl.2010.07.098] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/23/2010] [Accepted: 07/25/2010] [Indexed: 11/29/2022]
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7
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Wijtmans M, Denonne F, Célanire S, Gillard M, Hulscher S, Delaunoy C, Van houtvin N, Bakker RA, Defays S, Gérard J, Grooters L, Hubert D, Timmerman H, Leurs R, Talaga P, de Esch IJP, Provins L. Histamine H3 receptor ligands with a 3-cyclobutoxy motif: a novel and versatile constraint of the classical 3-propoxy linker. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00056f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Strasser A. Molecular modeling and QSAR-based design of histamine receptor ligands. Expert Opin Drug Discov 2009; 4:1061-75. [DOI: 10.1517/17460440903264972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Rodríguez Sarmiento RM, Nettekoven MH, Taylor S, Plancher JM, Richter H, Roche O. Selective naphthalene H3 receptor inverse agonists with reduced potential to induce phospholipidosis and their quinoline analogs. Bioorg Med Chem Lett 2009; 19:4495-500. [DOI: 10.1016/j.bmcl.2009.03.100] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/18/2009] [Accepted: 03/21/2009] [Indexed: 10/21/2022]
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10
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Pierson PD, Fettes A, Freichel C, Gatti-McArthur S, Hertel C, Huwyler J, Mohr P, Nakagawa T, Nettekoven M, Plancher JM, Raab S, Richter H, Roche O, Rodríguez Sarmiento RM, Schmitt M, Schuler F, Takahashi T, Taylor S, Ullmer C, Wiegand R. 5-Hydroxyindole-2-carboxylic Acid Amides: Novel Histamine-3 Receptor Inverse Agonists for the Treatment of Obesity. J Med Chem 2009; 52:3855-68. [DOI: 10.1021/jm900409x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Alec Fettes
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Christian Freichel
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | | | - Cornelia Hertel
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Jörg Huwyler
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Peter Mohr
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Toshito Nakagawa
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Matthias Nettekoven
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Jean-Marc Plancher
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Susanne Raab
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Hans Richter
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Olivier Roche
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | | | - Monique Schmitt
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Franz Schuler
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Tadakatsu Takahashi
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Sven Taylor
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Christoph Ullmer
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
| | - Ruby Wiegand
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, CH-4070 Basel, Switzerland
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