1
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Buffa V, Meyners C, Sugiarto WO, Bauder M, Gaali S, Hausch F. 1,4-Pyrazolyl-Containing SAFit-Analogues are Selective FKBP51 Inhibitors With Improved Ligand Efficiency and Drug-Like Profile. ChemMedChem 2024:e202400264. [PMID: 38818693 DOI: 10.1002/cmdc.202400264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
The FK506 binding protein 51 (FKBP51) is an appealing drug target due to its role in several diseases such as depression, anxiety, chronic pain and obesity. Towards this, selectivity versus the close homolog FKBP52 is essential. However, currently available FKBP51-selective ligands such as SAFit2 are too large and lack drug-like properties. Here, we present a structure activity relationship (SAR) analysis of the pipecolic ester moiety of SAFit1 and SAFit2, which culminated in the discovery of the 1,4-pyrazolyl derivative 23 d, displaying a binding affinity of 0.077 μM for FKBP51, reduced molecular weight (541.7 g/mol), lower hydrophobicity (cLogP=3.72) and higher ligand efficiency (LE=0.25). Cocrystal structures revealed the importance of the 1,4- and 1,3,4- substitution patterns of the pyrazole ring versus the 1,4,5 arrangement.
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Affiliation(s)
- Vanessa Buffa
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
- InfectoPharm Arzneimittel und Consilium GmbH, Von-Humboldt-Str.1, 64646, Heppenheim, Germany
| | - Christian Meyners
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
- InfectoPharm Arzneimittel und Consilium GmbH, Von-Humboldt-Str.1, 64646, Heppenheim, Germany
| | - Wisely Oki Sugiarto
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
- InfectoPharm Arzneimittel und Consilium GmbH, Von-Humboldt-Str.1, 64646, Heppenheim, Germany
| | - Michael Bauder
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
- InfectoPharm Arzneimittel und Consilium GmbH, Von-Humboldt-Str.1, 64646, Heppenheim, Germany
| | - Steffen Gaali
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804, Munich, Germany
- Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg
| | - Felix Hausch
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
- InfectoPharm Arzneimittel und Consilium GmbH, Von-Humboldt-Str.1, 64646, Heppenheim, Germany
- Center for Synthetic Biology, Technical University Darmstadt, Germany
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2
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Buffa V, Knaup FH, Heymann T, Springer M, Schmidt MV, Hausch F. Analysis of the Selective Antagonist SAFit2 as a Chemical Probe for the FK506-Binding Protein 51. ACS Pharmacol Transl Sci 2023; 6:361-371. [PMID: 36926456 PMCID: PMC10012253 DOI: 10.1021/acsptsci.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 02/16/2023]
Abstract
The FK506-binding protein 51 (FKBP51) has emerged as an important regulator of the mammalian stress response and is involved in persistent pain states and metabolic pathways. The FK506 analog SAFit2 (short for selective antagonist of FKBP51 by induced fit) was the first potent and selective FKBP51 ligand with an acceptable pharmacokinetic profile. At present, SAFit2 represents the gold standard for FKBP51 pharmacology and has been extensively used in numerous biological studies. Here we review the current knowledge on SAFit2 as well as guidelines for its use.
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Affiliation(s)
- Vanessa Buffa
- Department
of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287 Darmstadt, Germany
| | - Fabian H. Knaup
- Department
of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287 Darmstadt, Germany
| | - Tim Heymann
- Department
of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287 Darmstadt, Germany
| | - Margherita Springer
- Research
Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Mathias V. Schmidt
- Research
Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Felix Hausch
- Department
of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287 Darmstadt, Germany
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3
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Simpson LM, Glennie L, Brewer A, Zhao JF, Crooks J, Shpiro N, Sapkota GP. Target protein localization and its impact on PROTAC-mediated degradation. Cell Chem Biol 2022; 29:1482-1504.e7. [PMID: 36075213 DOI: 10.1016/j.chembiol.2022.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 12/21/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) bring a protein of interest (POI) into spatial proximity of an E3 ubiquitin ligase, promoting POI ubiquitylation and proteasomal degradation. PROTACs rely on endogenous cellular machinery to mediate POI degradation, therefore the subcellular location of the POI and access to the E3 ligase being recruited potentially impacts PROTAC efficacy. To interrogate whether the subcellular context of the POI influences PROTAC-mediated degradation, we expressed either Halo or FKBP12F36V (dTAG) constructs consisting of varying localization signals and tested the efficacy of their degradation by von Hippel-Lindau (VHL)- or cereblon (CRBN)-recruiting PROTACs targeting either Halo or dTAG. POIs were localized to the nucleus, cytoplasm, outer mitochondrial membrane, endoplasmic reticulum, Golgi, peroxisome or lysosome. Differentially localized Halo or FKBP12F36V proteins displayed varying levels of degradation using the same respective PROTACs, suggesting therefore that the subcellular context of the POI can influence the efficacy of PROTAC-mediated POI degradation.
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Affiliation(s)
- Luke M Simpson
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Lorraine Glennie
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jin-Feng Zhao
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Crooks
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Natalia Shpiro
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gopal P Sapkota
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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4
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Voll AM, Meyners C, Taubert MC, Bajaj T, Heymann T, Merz S, Charalampidou A, Kolos J, Purder PL, Geiger TM, Wessig P, Gassen NC, Bracher A, Hausch F. Makrozyklische FKBP51‐Liganden enthüllen einen transienten Bindungsmodus mit erhöhter Selektivität. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andreas M. Voll
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Christian Meyners
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Martha C. Taubert
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Thomas Bajaj
- Research Group Neurohomeostasis Department of Psychiatry and Psychotherapy University of Bonn Venusberg Campus 1 53127 Bonn Deutschland
| | - Tim Heymann
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Stephanie Merz
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Anna Charalampidou
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Jürgen Kolos
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Patrick L. Purder
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Thomas M. Geiger
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
| | - Pablo Wessig
- Universität Potsdam Institut für Chemie Karl-Liebknecht-Straße 24–25 14476 Potsdam Deutschland
| | - Nils C. Gassen
- Research Group Neurohomeostasis Department of Psychiatry and Psychotherapy University of Bonn Venusberg Campus 1 53127 Bonn Deutschland
| | - Andreas Bracher
- Max-Planck-Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Felix Hausch
- Department Chemistry and Biochemistry Clemens-Schöpf-Institute Technical University Darmstadt Alarich-Weiss Straße 4 64287 Darmstadt Deutschland
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5
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Voll AM, Meyners C, Taubert MC, Bajaj T, Heymann T, Merz S, Charalampidou A, Kolos J, Purder PL, Geiger TM, Wessig P, Gassen NC, Bracher A, Hausch F. Macrocyclic FKBP51 Ligands Define a Transient Binding Mode with Enhanced Selectivity. Angew Chem Int Ed Engl 2021; 60:13257-13263. [PMID: 33843131 PMCID: PMC8252719 DOI: 10.1002/anie.202017352] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/14/2021] [Indexed: 12/28/2022]
Abstract
Subtype selectivity represents a challenge in many drug discovery campaigns. A typical example is the FK506 binding protein 51 (FKBP51), which has emerged as an attractive drug target. The most advanced FKBP51 ligands of the SAFit class are highly selective vs. FKBP52 but poorly discriminate against the homologs and off-targets FKBP12 and FKBP12.6. During a macrocyclization pilot study, we observed that many of these macrocyclic analogs have unanticipated and unprecedented preference for FKBP51 over FKBP12 and FKBP12.6. Structural studies revealed that these macrocycles bind with a new binding mode featuring a transient conformation, which is disfavored for the small FKBPs. Using a conformation-sensitive assay we show that this binding mode occurs in solution and is characteristic for this new class of compounds. The discovered macrocycles are non-immunosuppressive, engage FKBP51 in cells, and block the cellular effect of FKBP51 on IKKα. Our findings provide a new chemical scaffold for improved FKBP51 ligands and the structural basis for enhanced selectivity.
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Affiliation(s)
- Andreas M. Voll
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Christian Meyners
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Martha C. Taubert
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Thomas Bajaj
- Research Group NeurohomeostasisDepartment of Psychiatry and PsychotherapyUniversity of BonnVenusberg Campus 153127BonnGermany
| | - Tim Heymann
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Stephanie Merz
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Anna Charalampidou
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Jürgen Kolos
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Patrick L. Purder
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Thomas M. Geiger
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
| | - Pablo Wessig
- Universität PotsdamInstitut für ChemieKarl-Liebknecht-Strasse 24–2514476PotsdamGermany
| | - Nils C. Gassen
- Research Group NeurohomeostasisDepartment of Psychiatry and PsychotherapyUniversity of BonnVenusberg Campus 153127BonnGermany
| | - Andreas Bracher
- Max-Planck-Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Felix Hausch
- Department Chemistry and BiochemistryClemens-Schöpf-InstituteTechnical University DarmstadtAlarich-Weiss Strasse 464287DarmstadtGermany
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6
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Bauder M, Meyners C, Purder PL, Merz S, Sugiarto WO, Voll AM, Heymann T, Hausch F. Structure-Based Design of High-Affinity Macrocyclic FKBP51 Inhibitors. J Med Chem 2021; 64:3320-3349. [PMID: 33666419 DOI: 10.1021/acs.jmedchem.0c02195] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The FK506-binding protein 51 (FKBP51) emerged as a key player in several diseases like stress-related disorders, chronic pain, and obesity. Linear analogues of FK506 called SAFit were shown to be highly selective for FKBP51 over its closest homologue FKBP52, allowing the proof-of-concept studies in animal models. Here, we designed and synthesized the first macrocyclic FKBP51-selective ligands to stabilize the active conformation. All macrocycles retained full FKBP51 affinity and selectivity over FKBP52 and the incorporation of polar functionalities further enhanced affinity. Six high-resolution crystal structures of macrocyclic inhibitors in complex with FKBP51 confirmed the desired selectivity-enabling binding mode. Our results show that macrocyclization is a viable strategy to target the shallow FKBP51 binding site selectively.
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Affiliation(s)
- Michael Bauder
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Christian Meyners
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Patrick L Purder
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Stephanie Merz
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Wisely Oki Sugiarto
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Andreas M Voll
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Tim Heymann
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Felix Hausch
- Department Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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7
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Sreekanth V, Zhou Q, Kokkonda P, Bermudez-Cabrera HC, Lim D, Law BK, Holmes BR, Chaudhary SK, Pergu R, Leger BS, Walker JA, Gifford DK, Sherwood RI, Choudhary A. Chemogenetic System Demonstrates That Cas9 Longevity Impacts Genome Editing Outcomes. ACS CENTRAL SCIENCE 2020; 6:2228-2237. [PMID: 33376784 PMCID: PMC7760466 DOI: 10.1021/acscentsci.0c00129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Indexed: 06/02/2023]
Abstract
Prolonged Cas9 activity can hinder genome engineering as it causes off-target effects, genotoxicity, heterogeneous genome-editing outcomes, immunogenicity, and mosaicism in embryonic editing-issues which could be addressed by controlling the longevity of Cas9. Though some temporal controls of Cas9 activity have been developed, only cumbersome systems exist for modifying the lifetime. Here, we have developed a chemogenetic system that brings Cas9 in proximity to a ubiquitin ligase, enabling rapid ubiquitination and degradation of Cas9 by the proteasome. Despite the large size of Cas9, we were able to demonstrate efficient degradation in cells from multiple species. Furthermore, by controlling the Cas9 lifetime, we were able to bias the DNA repair pathways and the genotypic outcome for both templated and nontemplated genome editing. Finally, we were able to dosably control the Cas9 activity and specificity to ameliorate the off-target effects. The ability of this system to change the Cas9 lifetime and, therefore, bias repair pathways and specificity in the desired direction allows precision control of the genome editing outcome.
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Affiliation(s)
- Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qingxuan Zhou
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Heysol C. Bermudez-Cabrera
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Benjamin K. Law
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Benjamin R. Holmes
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts 02142, United States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Santosh K. Chaudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Rajaiah Pergu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Brittany S. Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - James A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - David K. Gifford
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts 02142, United States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Richard I. Sherwood
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht 3584 CT, The Netherlands
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
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8
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Madsen D, Jørgensen FP, Palmer D, Roux ME, Olsen JV, Bols M, Schoffelen S, Diness F, Meldal M. Design and Combinatorial Development of Shield-1 Peptide Mimetics Binding to Destabilized FKBP12. ACS COMBINATORIAL SCIENCE 2020; 22:156-164. [PMID: 32027120 DOI: 10.1021/acscombsci.9b00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of computational design, a focused one-bead one-compound library has been prepared on microparticle-encoded PEGA1900 beads consisting of small tripeptides with a triazole-capped N-terminal. The library was screened towards a double point-mutated version of the human FKBP12 protein, known as the destabilizing domain (DD). Inspired by the decoded library hits, unnatural peptide structures were screened in a novel on-bead assay, which was useful for a rapid structure evaluation prior to off-bead resynthesis. Subsequently, a series of 19 compounds were prepared and tested using a competitive fluorescence polarization assay, which led to the discovery of peptide ligands with low micromolar binding affinity towards the DD. The methodology represents a rapid approach for identification of a novel structure scaffold, where the screening and initial structure refinement was accomplished using small quantities of library building blocks.
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9
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Argüello‐Velasco RO, Sánchez‐Muñoz GK, Viveros‐Ceballos JL, Ordóñez M, Kafarski P. A Straightforward Synthesis of Six‐Membered‐Ring Heterocyclic α‐Aminophosphonic Acids from
N
‐Acyliminium Ions. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rubén Oswaldo Argüello‐Velasco
- Centro de Investigaciones Químicas‐IICBAUniversidad Autónoma del Estado de Morelos Avenue Universidad 1001 62209 Cuernavaca Morelos Mexico
| | - Grecia Katherine Sánchez‐Muñoz
- Centro de Investigaciones Químicas‐IICBAUniversidad Autónoma del Estado de Morelos Avenue Universidad 1001 62209 Cuernavaca Morelos Mexico
| | - José Luis Viveros‐Ceballos
- Centro de Investigaciones Químicas‐IICBAUniversidad Autónoma del Estado de Morelos Avenue Universidad 1001 62209 Cuernavaca Morelos Mexico
| | - Mario Ordóñez
- Centro de Investigaciones Químicas‐IICBAUniversidad Autónoma del Estado de Morelos Avenue Universidad 1001 62209 Cuernavaca Morelos Mexico
| | - Pawel Kafarski
- Department of Bioorganic ChemistryWroclaw University of Science and Technology Wybrzeże Wyspiańskiego 27 50‐370 Wrocław Poland
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10
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Jørgensen FP, Madsen D, Meldal M, Olsen JV, Petersen M, Granhøj J, Bols M. Synthesis of Shld Derivatives, Their Binding to the Destabilizing Domain, and Influence on Protein Accumulation in Transgenic Plants. J Med Chem 2019; 62:5191-5216. [PMID: 31059249 DOI: 10.1021/acs.jmedchem.9b00497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 35 analogues of Shld with modifications in the A-residue and the C-residues were prepared and investigated for binding to FKBP and GFP accumulation in transgenic plants. The modifications investigated explored variations that were supposedly inside or outside the receptor binding site with the latter being important by influencing the overall polarity of the compounds in order to improve the absorption in plants. The binding of the new compounds to the destabilizing domain was determined using a fluorescence polarization competition assay, and the GFP expression in engineered Arabidopsis thaliana was studied. The results showed that modifications of the C-building block phenol with acidic, basic, and neutral groups led to better ligands with some being better than Shld in the plant. Generally small, polar substituents showed the best GFP accumulation.
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Affiliation(s)
- Frederik Præstholm Jørgensen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Daniel Madsen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Morten Meldal
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Jacob Valdbjørn Olsen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Morten Petersen
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Jeppe Granhøj
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
| | - Mikael Bols
- Departments of Chemistry and Biology , University of Copenhagen , Universitetsparken 5 , 2100 Copenhagen Ø, Denmark
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Kolos JM, Voll AM, Bauder M, Hausch F. FKBP Ligands-Where We Are and Where to Go? Front Pharmacol 2018; 9:1425. [PMID: 30568592 PMCID: PMC6290070 DOI: 10.3389/fphar.2018.01425] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/19/2018] [Indexed: 12/24/2022] Open
Abstract
In recent years, many members of the FK506-binding protein (FKBP) family were increasingly linked to various diseases. The binding domain of FKBPs differs only in a few amino acid residues, but their biological roles are versatile. High-affinity ligands with selectivity between close homologs are scarce. This review will give an overview of the most prominent ligands developed for FKBPs and highlight a perspective for future developments. More precisely, human FKBPs and correlated diseases will be discussed as well as microbial FKBPs in the context of anti-bacterial and anti-fungal therapeutics. The last section gives insights into high-affinity ligands as chemical tools and dimerizers.
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Affiliation(s)
| | | | | | - Felix Hausch
- Department of Chemistry, Institute of Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
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