1
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van der Straat R, Draijer R, Surmiak E, Butera R, Land L, Magiera-Mularz K, Musielak B, Plewka J, Holak TA, Dömling A. 1,5-Disubstituted tetrazoles as PD-1/PD-L1 antagonists. RSC Med Chem 2024; 15:1210-1215. [PMID: 38665826 PMCID: PMC11042242 DOI: 10.1039/d3md00746d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/21/2024] [Indexed: 04/28/2024] Open
Abstract
The progress in cancer survival and treatment has witnessed a remarkable transformation through the innovative approach of targeting the inhibitory immune checkpoint protein PD-1/PD-L1 complex by mAbs, e.g. pembrolizumab (Keytruda). While generating 17.2 billion U.S. dollars in revenue in 2021, the true significance of these developments lies in their ability to enhance cancer patient outcomes. Despite the proven efficacy of mAbs in inhibiting the PD-1/PD-L1 signaling pathways, they face significant challenges, including limited response rates, high production costs, missing oral bioavailability, and extended half-lives that can lead to immune-related adverse effects. A promising alternative approach involves the use of small molecules acting as PD-1/PD-L1 antagonists to stimulate PD-L1 dimerization. However, the precise mechanisms of action of these molecules remain partially understood, posing challenges to their development. In this context, our research focuses on the creation of a novel scaffold based on the Ugi tetrazole four-component reaction (UT-4CR) to develop low-molecular-weight inhibitors of PD-L1. Employing structure-based methods, we synthesized a library of small compounds using biphenyl vinyl isocyanide, leading to the discovery of a structure-activity relationship among 1,5-disubstituted tetrazole-based inhibitors. Supported by a cocrystal structure with PD-L1, these inhibitors underwent biophysical testing, including HTRF and protein NMR experiments, resulting in the identification of potent candidates with sub-micromolar PD-L1 affinities. This finding opens opportunities to the further development of a new class of PD-L1 antagonists, holding promise for improved cancer immunotherapy strategies.
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Affiliation(s)
- Robin van der Straat
- Department of Drug Design, University of Groningen 9713 AV Groningen The Netherlands
| | - Rosalie Draijer
- Department of Drug Design, University of Groningen 9713 AV Groningen The Netherlands
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University 30-387 Kraków Poland
| | - Roberto Butera
- Department of Drug Design, University of Groningen 9713 AV Groningen The Netherlands
| | - Lennart Land
- Department of Drug Design, University of Groningen 9713 AV Groningen The Netherlands
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University 30-387 Kraków Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University 30-387 Kraków Poland
| | - Jacek Plewka
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University 30-387 Kraków Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University 30-387 Kraków Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen 9713 AV Groningen The Netherlands
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackȳ University in Olomouc Olomouc Czech Republic
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2
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Donati G, Viviano M, D'Amore VM, Cipriano A, Diakogiannaki I, Amato J, Tomassi S, Brancaccio D, Russomanno P, Di Leva FS, Arosio D, Seneci P, Taliani S, Magiera-Mularz K, Musielak B, Skalniak L, Holak TA, Castellano S, La Pietra V, Marinelli L. A combined approach of structure-based virtual screening and NMR to interrupt the PD-1/PD-L1 axis: Biphenyl-benzimidazole containing compounds as novel PD-L1 inhibitors. Arch Pharm (Weinheim) 2024; 357:e2300583. [PMID: 38110703 DOI: 10.1002/ardp.202300583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Immunotherapy has emerged as a game-changing approach for cancer treatment. Although monoclonal antibodies (mAbs) targeting the programmed cell death protein 1/programmed cell death protein 1 ligand 1 (PD-1/PD-L1) axis have entered the market revolutionizing the treatment landscape of many cancer types, small molecules, although presenting several advantages including the possibility of oral administration and/or reduced costs, struggled to enter in clinical trials, suffering of water insolubility and/or inadequate potency compared with mAbs. Thus, the search for novel scaffolds for both the design of effective small molecules and possible synergistic strategies is an ongoing field of interest. In an attempt to find novel chemotypes, a virtual screening approach was employed, resulting in the identification of new chemical entities with a certain binding capability, the most versatile of which was the benzimidazole-containing compound 10. Through rational design, a small library of its derivatives was synthesized and evaluated. The homogeneous time-resolved fluorescence (HTRF) assay revealed that compound 17 shows the most potent inhibitory activity (IC50 ) in the submicromolar range and notably, differently from the major part of PD-L1 inhibitors, exhibits satisfactory water solubility properties. These findings highlight the potential of benzimidazole-based compounds as novel promising candidates for PD-L1 inhibition.
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Affiliation(s)
- Greta Donati
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Monica Viviano
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | | | | | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | | | | | | | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | | | - Valeria La Pietra
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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3
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Surmiak E, Ząber J, Plewka J, Wojtanowicz G, Kocik-Krol J, Kruc O, Muszak D, Rodríguez I, Musielak B, Viviano M, Castellano S, Skalniak L, Magiera-Mularz K, Holak TA, Kalinowska-Tłuścik J. Solubilizer Tag Effect on PD-L1/Inhibitor Binding Properties for m-Terphenyl Derivatives. ACS Med Chem Lett 2024; 15:36-44. [PMID: 38229762 PMCID: PMC10788941 DOI: 10.1021/acsmedchemlett.3c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024] Open
Abstract
Although heavily studied, the subject of anti-PD-L1 small-molecule inhibitors is still elusive. Here we present a systematic overview of the principles behind successful anti-PD-L1 small-molecule inhibitor design on the example of the m-terphenyl scaffold, with a particular focus on the neglected influence of the solubilizer tag on the overall affinity toward PD-L1. The inhibitor developed according to the proposed guidelines was characterized through its potency in blocking PD-1/PD-L1 complex formation in homogeneous time-resolved fluorescence and cell-based assays. The affinity is also explained based on the crystal structure of the inhibitor itself and its costructure with PD-L1 as well as a molecular modeling study. Our results structuralize the knowledge related to the strong pharmacophore feature of the m-terphenyl scaffold preferential geometry and the more complex role of the solubilizer tag in PD-L1 homodimer stabilization.
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Affiliation(s)
- Ewa Surmiak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Julia Ząber
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Łojasiewicza 11, 30-348 Cracow, Poland
| | - Jacek Plewka
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Grzegorz Wojtanowicz
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Justyna Kocik-Krol
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Łojasiewicza 11, 30-348 Cracow, Poland
| | - Oskar Kruc
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Łojasiewicza 11, 30-348 Cracow, Poland
| | - Damian Muszak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Ismael Rodríguez
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Łojasiewicza 11, 30-348 Cracow, Poland
| | - Bogdan Musielak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Monica Viviano
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 84085 Fisciano, Italy
| | - Sabrina Castellano
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 84085 Fisciano, Italy
| | - Lukasz Skalniak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | | | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
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4
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Kitel R, Surmiak E, Borggräfe J, Kalinowska-Tluscik J, Golik P, Czub M, Uzar W, Musielak B, Madej M, Popowicz GM, Dubin G, Holak TA. Discovery of Inhibitory Fragments That Selectively Target Spire2-FMN2 Interaction. J Med Chem 2023; 66:15715-15727. [PMID: 38039505 PMCID: PMC10726347 DOI: 10.1021/acs.jmedchem.3c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Here, we report the fragment-based drug discovery of potent and selective fragments that disrupt the Spire2-FMN2 but not the Spire1-FMN2 interaction. Hit fragments were identified in a differential scanning fluorimetry-based screen of an in-house library of 755 compounds and subsequently validated in multiple orthogonal biophysical assays, including fluorescence polarization, microscale thermophoresis, and 1H-15N HSQC nuclear magnetic resonance. Extensive structure-activity relationships combined with molecular docking followed by chemical optimization led to the discovery of compound 13, which exhibits micromolar potency and high ligand efficiency (LE = 0.38). Therefore, this fragment represents a validated starting point for the future development of selective chemical probes targeting the Spire2-FMN2 interaction.
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Affiliation(s)
- Radoslaw Kitel
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Ewa Surmiak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Jan Borggräfe
- Institute
of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian
NMR Center, School of Natural Sciences, Technical University of Munich Garching, 85748 München, Germany
| | | | - Przemyslaw Golik
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Miroslawa Czub
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Wiktor Uzar
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Prof. S.
Lojasiewicza 11, 30-348 Krakow, Poland
| | - Bogdan Musielak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
| | - Mariusz Madej
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Grzegorz M. Popowicz
- Institute
of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian
NMR Center, School of Natural Sciences, Technical University of Munich Garching, 85748 München, Germany
| | - Grzegorz Dubin
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kracow, Poland
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5
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Mikitiuk M, Barczyński J, Bielski P, Arciniega M, Tyrcha U, Hec A, Lipińska AD, Rychłowski M, Holak TA, Sitar T. IGF2 Peptide-Based LYTACs for Targeted Degradation of Extracellular and Transmembrane Proteins. Molecules 2023; 28:7519. [PMID: 38005242 PMCID: PMC10673611 DOI: 10.3390/molecules28227519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Lysosome-targeting chimeras (LYTACs) have recently been developed to facilitate the lysosomal degradation of specific extracellular and transmembrane molecular targets. However, the LYTAC particles described to date are based on glycopeptide conjugates, which are difficult to prepare and produce on a large scale. Here, we report on the development of pure protein LYTACs based on the non-glycosylated IGF2 peptides, which can be readily produced in virtually any facility capable of monoclonal antibody production. These chimeras utilize the IGF2R/CI-M6PR pathway for lysosomal shuttling and, in our illustrative example, target programmed death ligand 1 (PD-L1), eliciting physiological effects analogous to immune checkpoint blockade. Results from in vitro assays significantly exceed the effects of anti-PD-L1 antibodies alone.
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Affiliation(s)
- Michał Mikitiuk
- Recepton Sp. z o.o., Trzy Lipy 3, 80-172 Gdańsk, Poland
- Department of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdansk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Jan Barczyński
- Recepton Sp. z o.o., Trzy Lipy 3, 80-172 Gdańsk, Poland
- Department of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdansk, Abrahama 58, 80-307 Gdańsk, Poland
| | | | | | | | | | - Andrea D. Lipińska
- Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-307 Gdańsk, Poland
| | - Michał Rychłowski
- Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-307 Gdańsk, Poland
| | - Tad A. Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland;
| | - Tomasz Sitar
- Recepton Sp. z o.o., Trzy Lipy 3, 80-172 Gdańsk, Poland
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6
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Rodriguez I, Kocik-Krol J, Skalniak L, Musielak B, Wisniewska A, Ciesiołkiewicz A, Berlicki Ł, Plewka J, Grudnik P, Stec M, Siedlar M, Holak TA, Magiera-Mularz K. Structural and biological characterization of pAC65, a macrocyclic peptide that blocks PD-L1 with equivalent potency to the FDA-approved antibodies. Mol Cancer 2023; 22:150. [PMID: 37679783 PMCID: PMC10483858 DOI: 10.1186/s12943-023-01853-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
Recent advances in immuno-oncology have opened up new and impressive treatment options for cancer. Notwithstanding, overcoming the limitations of the current FDA-approved therapies with monoclonal antibodies (mAbs) that block the PD-1/PD-L1 pathway continues to lead to the testing of multiple approaches and optimizations. Recently, a series of macrocyclic peptides have been developed that exhibit binding strengths to PD-L1 ranging from sub-micromolar to micromolar. In this study, we present the most potent non-antibody-based PD-1/PD-L1 interaction inhibitor reported to date. The structural and biological characterization of this macrocyclic PD-L1 targeting peptide provides the rationale for inhibition of both PD-1/PD-L1 and CD80/PD-L1 complexes. The IC50 and EC50 values obtained in PD-L1 binding assays indicate that the pAC65 peptide has potency equivalent to the current FDA-approved mAbs and may have similar activity to the BMS986189 peptide, which entered the clinical trial and has favorable safety and pharmacokinetic data. The data presented here delineate the generation of similar peptides with improved biological activities and applications not only in the field of cancer immunotherapy but also in other disorders related to the immune system.
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Affiliation(s)
- Ismael Rodriguez
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Justyna Kocik-Krol
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Aneta Wisniewska
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Agnieszka Ciesiołkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, 50-370, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, 50-370, Poland
| | - Jacek Plewka
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, Krakow, 30-387, Poland
| | - Malgorzata Stec
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, Krakow, 30-663, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, Krakow, 30-663, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow, 30-387, Poland.
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7
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Ważyńska MA, Butera R, Requesens M, Plat A, Zarganes-Tzitzikas T, Neochoritis CG, Plewka J, Skalniak L, Kocik-Krol J, Musielak B, Magiera-Mularz K, Rodriguez I, Blok SN, de Bruyn M, Nijman HW, Elsinga PH, Holak TA, Dömling A. Design, Synthesis, and Biological Evaluation of 2-Hydroxy-4-phenylthiophene-3-carbonitrile as PD-L1 Antagonist and Its Comparison to Available Small Molecular PD-L1 Inhibitors. J Med Chem 2023. [PMID: 37450644 PMCID: PMC10388299 DOI: 10.1021/acs.jmedchem.3c00254] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In search of a potent small molecular PD-L1 inhibitor, we designed and synthesized a compound based on a 2-hydroxy-4-phenylthiophene-3-carbonitrile moiety. Ligand's performance was tested in vitro and compared side-by-side with a known PD-L1 antagonist with a proven bioactivity BMS1166. Subsequently, we modified both compounds to allow 18F labeling that could be used for PET imaging. Radiolabeling, which is used in drug development and diagnosis, was applied to investigate the properties of those ligands and test them against tissue sections with diverse expression levels of PD-L1. We confirmed biological activity toward hPD-L1 for this inhibitor, comparable with BMS1166, while holding enhanced pharmacological properties.
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Affiliation(s)
- Marta A Ważyńska
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Roberto Butera
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Marta Requesens
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Annechien Plat
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Tryfon Zarganes-Tzitzikas
- Centre for Medicines Discovery, Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, NDM Research Building, Roosevelt Drive, OX3 7FZ Oxford, U.K
| | | | - Jacek Plewka
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Justyna Kocik-Krol
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicz St 11, 30-348 Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ismael Rodriguez
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicz St 11, 30-348 Krakow, Poland
| | - Simon N Blok
- Department of Nuclear Medicine and MolecularImaging, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hans W Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Philip H Elsinga
- Department of Nuclear Medicine and MolecularImaging, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palacky University in Olomouc, Olomouc 77900, Czech Republic
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8
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Nietzold F, Rubner S, Labuzek B, Golik P, Surmiak E, Del Corte X, Kitel R, Protzel C, Reppich-Sacher R, Stichel J, Magiera-Mularz K, Holak TA, Berg T. Nutlin-3a-aa: Improving the Bioactivity of a p53/MDM2 Interaction Inhibitor by Introducing a Solvent-Exposed Methylene Group. Chembiochem 2023; 24:e202300006. [PMID: 36602436 DOI: 10.1002/cbic.202300006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Nutlin-3a is a reversible inhibitor of the p53/MDM2 interaction. We have synthesized the derivative Nutlin-3a-aa bearing an additional exocyclic methylene group in the piperazinone moiety. Nutlin-3a-aa is more active than Nutlin-3a against purified wild-type MDM2, and is more effective at increasing p53 levels and releasing transcription of p53 target genes from MDM2-induced repression. X-ray analysis of wild-type MDM2-bound Nutlin-3a-aa indicated that the orientation of its modified piperazinone ring was altered in comparison to the piperazinone ring of MDM2-bound Nutlin-3a, with the exocyclic methylene group of Nutlin-3a-aa pointing away from the protein surface. Our data point to the introduction of exocyclic methylene groups as a useful approach by which to tailor the conformation of bioactive molecules for improved biological activity.
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Affiliation(s)
- Florian Nietzold
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Stefan Rubner
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Beata Labuzek
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Przemysław Golik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Xabier Del Corte
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.,Present address: Departamento de Química Orgánica I, Centro de Investigación y Estudios Avanzados "Lucio Lascaray", Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Christoph Protzel
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
| | - Regina Reppich-Sacher
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Thorsten Berg
- Institute of Organic Chemistry, Leipzig University, Johannisallee 29, 04103, Leipzig, Germany
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9
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Reyes Romero A, Kubica K, Kitel R, Rodríguez I, Magiera-Mularz K, Dömling A, Holak TA, Surmiak E. Computer- and NMR-Aided Design of Small-Molecule Inhibitors of the Hub1 Protein. Molecules 2022; 27:molecules27238282. [PMID: 36500376 PMCID: PMC9738620 DOI: 10.3390/molecules27238282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
By binding to the spliceosomal protein Snu66, the human ubiquitin-like protein Hub1 is a modulator of the spliceosome performance and facilitates alternative splicing. Small molecules that bind to Hub1 would be of interest to study the protein-protein interaction of Hub1/Snu66, which is linked to several human pathologies, such as hypercholesterolemia, premature aging, neurodegenerative diseases, and cancer. To identify small molecule ligands for Hub1, we used the interface analysis, peptide modeling of the Hub1/Snu66 interaction and the fragment-based NMR screening. Fragment-based NMR screening has not proven sufficient to unambiguously search for fragments that bind to the Hub1 protein. This was because the Snu66 binding pocket of Hub1 is occupied by pH-sensitive residues, making it difficult to distinguish between pH-induced NMR shifts and actual binding events. The NMR analyses were therefore verified experimentally by microscale thermophoresis and by NMR pH titration experiments. Our study found two small peptides that showed binding to Hub1. These peptides are the first small-molecule ligands reported to interact with the Hub1 protein.
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Affiliation(s)
- Atilio Reyes Romero
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kubica
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ismael Rodríguez
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department of Innovative Chemistry, Palackӯ University, CATRIN, Šlechtitelů 241/27, 779 00 Olomouc, Czech Republic
| | - Tad A. Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Correspondence: (T.A.H.); (E.S.)
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Correspondence: (T.A.H.); (E.S.)
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10
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Kitel R, Rodríguez I, del Corte X, Atmaj J, Żarnik M, Surmiak E, Muszak D, Magiera-Mularz K, Popowicz GM, Holak TA, Musielak B. Exploring the Surface of the Ectodomain of the PD-L1 Immune Checkpoint with Small-Molecule Fragments. ACS Chem Biol 2022; 17:2655-2663. [PMID: 36073782 PMCID: PMC9486809 DOI: 10.1021/acschembio.2c00583] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Development of small molecules targeting the PD-L1/PD-1 interface is advancing both in industry and academia, but only a few have reached early-stage clinical trials. Here, we take a closer look at the general druggability of PD-L1 using in silico hot spot mapping and nuclear magnetic resonance (NMR)-based characterization. We found that the conformational elasticity of the PD-L1 surface strongly influences the formation of hot spots. We deconstructed several generations of known inhibitors into fragments and examined their binding properties using differential scanning fluorimetry (DSF) and protein-based nuclear magnetic resonance (NMR). These biophysical analyses showed that not all fragments bind to the PD-L1 ectodomain despite having the biphenyl scaffold. Although most of the binding fragments induced PD-L1 oligomerization, two compounds, TAH35 and TAH36, retain the monomeric state of proteins upon binding. Additionally, the presence of the entire ectodomain did not affect the binding of the hit compounds and dimerization of PD-L1. The data demonstrated here provide important information on the PD-L1 druggability and the structure-activity relationship of the biphenyl core moiety and therefore may aid in the design of novel inhibitors and focused fragment libraries for PD-L1.
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Affiliation(s)
- Radoslaw Kitel
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ismael Rodríguez
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Xabier del Corte
- Departamento
de Química Orgánica I, Centro de Investigación
y Estudios Avanzados “Lucio Lascaray” − Facultad
de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad
7, 01006 Vitoria-Gasteiz, Spain
| | - Jack Atmaj
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Magdalena Żarnik
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ewa Surmiak
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Damian Muszak
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Katarzyna Magiera-Mularz
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Grzegorz M. Popowicz
- Institute
of Structural Biology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Tad A. Holak
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Faculty
of Chemistry, Organic Chemistry Department, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland,
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11
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Hoyer M, Crevenna AH, Kitel R, Willems K, Czub M, Dubin G, Van Dorpe P, Holak TA, Lamb DC. Analysis tools for single-monomer measurements of self-assembly processes. Sci Rep 2022; 12:4682. [PMID: 35304498 PMCID: PMC8933434 DOI: 10.1038/s41598-022-08245-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 11/29/2022] Open
Abstract
Protein assembly plays an important role throughout all phyla of life, both physiologically and pathologically. In particular, aggregation and polymerization of proteins are key-strategies that regulate cellular function. In recent years, methods to experimentally study the assembly process on a single-molecule level have been developed. This progress concomitantly has triggered the question of how to analyze this type of single-filament data adequately and what experimental conditions are necessary to allow a meaningful interpretation of the analysis. Here, we developed two analysis methods for single-filament data: the visitation analysis and the average-rate analysis. We benchmarked and compared both approaches with the classic dwell-time-analysis frequently used to study microscopic association and dissociation rates. In particular, we tested the limitations of each analysis method along the lines of the signal-to-noise ratio, the sampling rate, and the labeling efficiency and bleaching rate of the fluorescent dyes used in single-molecule fluorescence experiments. Finally, we applied our newly developed methods to study the monomer assembly of actin at the single-molecule-level in the presence of the class II nucleator Cappuccino and the WH2 repeats of Spire. For Cappuccino, our data indicated fast elongation circumventing a nucleation phase whereas, for Spire, we found that the four WH2 motifs are not sufficient to promote de novo nucleation of actin.
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Affiliation(s)
- Maria Hoyer
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians University Munich, Munich, Germany
| | - Alvaro H Crevenna
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians University Munich, Munich, Germany.,Epigenetics and Neurobiology Unit, EMBL Rome, Monterotondo, Italy
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | | | - Miroslawa Czub
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | | | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians University Munich, Munich, Germany.
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12
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Surmiak E, Magiera-Mularz K, Musielak B, Muszak D, Kocik-Krol J, Kitel R, Plewka J, Holak TA, Skalniak L. PD-L1 Inhibitors: Different Classes, Activities, and Mechanisms of Action. Int J Mol Sci 2021; 22:ijms222111797. [PMID: 34769226 PMCID: PMC8583776 DOI: 10.3390/ijms222111797] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 01/02/2023] Open
Abstract
Targeting the programmed cell death protein 1/programmed cell death 1 ligand 1 (PD-1/PD-L1) interaction has become an established strategy for cancer immunotherapy. Although hundreds of small-molecule, peptide, and peptidomimetic inhibitors have been proposed in recent years, only a limited number of drug candidates show good PD-1/PD-L1 blocking activity in cell-based assays. In this article, we compare representative molecules from different classes in terms of their PD-1/PD-L1 dissociation capacity measured by HTRF and in vitro bioactivity determined by the immune checkpoint blockade (ICB) co-culture assay. We point to recent discoveries that underscore important differences in the mechanisms of action of these molecules and also indicate one principal feature that needs to be considered, which is the eventual human PD-L1 specificity.
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13
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Reyes Romero A, Lunev S, Popowicz GM, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak TA, Dömling ASS, Groves MR. A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity. Commun Biol 2021; 4:949. [PMID: 34376783 PMCID: PMC8355244 DOI: 10.1038/s42003-021-02442-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/09/2021] [Indexed: 11/14/2022] Open
Abstract
Malate dehydrogenases (MDHs) sustain tumor growth and carbon metabolism by pathogens including Plasmodium falciparum. However, clinical success of MDH inhibitors is absent, as current small molecule approaches targeting the active site are unselective. The presence of an allosteric binding site at oligomeric interface allows the development of more specific inhibitors. To this end we performed a differential NMR-based screening of 1500 fragments to identify fragments that bind at the oligomeric interface. Subsequent biophysical and biochemical experiments of an identified fragment indicate an allosteric mechanism of 4-(3,4-difluorophenyl) thiazol-2-amine (4DT) inhibition by impacting the formation of the active site loop, located >30 Å from the 4DT binding site. Further characterization of the more tractable homolog 4-phenylthiazol-2-amine (4PA) and 16 other derivatives are also reported. These data pave the way for downstream development of more selective molecules by utilizing the oligomeric interfaces showing higher species sequence divergence than the MDH active site. Romero et al. perform NMR-based screening of 1500 fragments to identify fragments that bind at the oligomeric interface of malate dehydrogenase (MDH). Their study indicates an allosteric mechanism impacting enzymatic activity, paving the way for development of more selective molecules and a starting point for the future development of specific MDH inhibitors.
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Affiliation(s)
- Atilio Reyes Romero
- Drug Design, University of Groningen, Department of Pharmacy, Groningen, The Netherlands
| | - Serjey Lunev
- EV Biotech, Zernikelaan 8, Groningen, the Netherlands
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Vito Calderone
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Poznań, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Alexander S S Dömling
- Drug Design, University of Groningen, Department of Pharmacy, Groningen, The Netherlands
| | - Matthew R Groves
- Drug Design, University of Groningen, Department of Pharmacy, Groningen, The Netherlands.
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14
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Muszak D, Surmiak E, Plewka J, Magiera-Mularz K, Kocik-Krol J, Musielak B, Sala D, Kitel R, Stec M, Weglarczyk K, Siedlar M, Dömling A, Skalniak L, Holak TA. Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction. J Med Chem 2021; 64:11614-11636. [PMID: 34313116 PMCID: PMC8365601 DOI: 10.1021/acs.jmedchem.1c00957] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
We describe a new
class of potent PD-L1/PD-1 inhibitors based on
a terphenyl scaffold that is derived from the rigidified biphenyl-inspired
structure. Using in silico docking, we designed and
then experimentally demonstrated the effectiveness of the terphenyl-based
scaffolds in inhibiting PD-1/PD-L1 complex formation using various
biophysical and biochemical techniques. We also present a high-resolution
structure of the complex of PD-L1 with one of our most potent inhibitors
to identify key PD-L1/inhibitor interactions at the molecular level.
In addition, we show the efficacy of our most potent inhibitors in
activating the antitumor response using primary human immune cells
from healthy donors.
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Affiliation(s)
- Damian Muszak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jacek Plewka
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Kraków, Poland
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Justyna Kocik-Krol
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Dominik Sala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Malgorzata Stec
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Kazimierz Weglarczyk
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
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15
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Butera R, Ważyńska M, Magiera-Mularz K, Plewka J, Musielak B, Surmiak E, Sala D, Kitel R, de Bruyn M, Nijman HW, Elsinga PH, Holak TA, Dömling A. Design, Synthesis, and Biological Evaluation of Imidazopyridines as PD-1/PD-L1 Antagonists. ACS Med Chem Lett 2021; 12:768-773. [PMID: 34055224 PMCID: PMC8155249 DOI: 10.1021/acsmedchemlett.1c00033] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
![]()
The PD-1/PD-L1 axis
has proven to be a highly efficacious target
for cancer immune checkpoint therapy with several approved antibodies.
Also, small molecules based on a biphenyl core can antagonize PD-1/PD-L1,
leading to the in vitro formation of PD-L1 dimers. However, their
development remains challenging, as we do not yet fully understand
their mode of action. In this work, we designed a new scaffold based
on our previously solved high-resolution structures of low-molecular-weight
inhibitors bound to PD-L1. A small compound library was synthesized
using the Groebke–Blackburn–Bienaymé multicomponent
reaction (GBB-3CR), resulting in the structure–activity relationship
of imidazo[1,2-a]pyridine-based inhibitors. These
inhibitors were tested for their biological activity using various
biophysical assays giving potent candidates with low-micromolar PD-L1
affinities. An obtained PD-L1 cocrystal structure reveals the binding
to PD-L1. Our results open the door to an interesting bioactive scaffold
that could lead to a new class of PD-L1 antagonists.
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Affiliation(s)
- Roberto Butera
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Marta Ważyńska
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Katarzyna Magiera-Mularz
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Jacek Plewka
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Bogdan Musielak
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Ewa Surmiak
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Dominik Sala
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Radoslaw Kitel
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Marco de Bruyn
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Hans W. Nijman
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Philip H. Elsinga
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Tad A. Holak
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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16
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Niedziałkowski P, Bojko M, Ryl J, Wcisło A, Spodzieja M, Magiera-Mularz K, Guzik K, Dubin G, Holak TA, Ossowski T, Rodziewicz-Motowidło S. Ultrasensitive electrochemical determination of the cancer biomarker protein sPD-L1 based on a BMS-8-modified gold electrode. Bioelectrochemistry 2021; 139:107742. [PMID: 33517203 DOI: 10.1016/j.bioelechem.2021.107742] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/22/2023]
Abstract
This work describes the modification of a gold electrode with the BMS-8 compound that interacts with the Programmed Death-Ligand 1 (PD-L1), an immune checkpoint protein. The results show that we can confirm the presence of the sPD-L1 in the concentration range of 10-18 to 10-8 M using electrochemical impedance spectroscopy (EIS) with a limit of detection (LOD) of 1.87 × 10-14 M for PD-L1 (S/N = 3.3) and at a concentration of 10-14 M via cyclic voltammetry (CV). Additionally, high-resolution X-ray photoelectron spectroscopy (XPS), contact angle, and surface free energy measurements were applied to confirm the functionalization of the electrode. We investigated the selectivity of the electrode for other proteins: Programmed Death-1 (PD-1), cluster of differentiation 160 (CD160), and B- and T-lymphocyte attenuator (BTLA) at concentrations of 10-8 M. Differentiation between PD-L1 and PD-1 was achieved based on the analysis of the capacitance effect frequency dispersion at the surface of the modified Au electrode with BMS-8 after incubation at various concentrations of PD-L1 and PD-1 proteins in the range of 10-18 to 10-8 M. Significant differences were observed in the heterogeneity of PD-L1 and PD-1. The results of the quasi-capacitance studies demonstrate that BMS-8 strongly and specifically interacts with the PD-L1 protein.
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Affiliation(s)
- Paweł Niedziałkowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Magdalena Bojko
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Jacek Ryl
- Department of Electrochemistry, Corrosion and Materials Engineering, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk 80-233, Poland
| | - Anna Wcisło
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Spodzieja
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | | | - Katarzyna Guzik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tadeusz Ossowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sylwia Rodziewicz-Motowidło
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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17
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Magiera-Mularz K, Kocik J, Musielak B, Plewka J, Sala D, Machula M, Grudnik P, Hajduk M, Czepiel M, Siedlar M, Holak TA, Skalniak L. Human and mouse PD-L1: similar molecular structure, but different druggability profiles. iScience 2020; 24:101960. [PMID: 33437940 PMCID: PMC7788105 DOI: 10.1016/j.isci.2020.101960] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
In the development of PD-L1-blocking therapeutics, it is essential to transfer initial in vitro findings into proper in vivo animal models. Classical immunocompetent mice are attractive due to high accessibility and low experimental costs. However, it is unknown whether inter-species differences in PD-L1 sequence and structure would allow for human-mouse cross applications. Here, we disclose the first structure of the mouse (m) PD-L1 and analyze its similarity to the human (h) PD-L1. We show that mPD-L1 interacts with hPD-1 and provides a negative signal toward activated Jurkat T cells. We also show major differences in druggability between the hPD-L1 and mPD-L1 using therapeutic antibodies, a macrocyclic peptide, and small molecules. Our study indicates that while the amino acid sequence is well conserved between the hPD-L1 and mPD-L1 and overall structures are almost identical, crucial differences determine the interaction with anti-PD-L1 agents, that cannot be easily predicted in silico. Mouse (m) PD-L1 interacts with human (h) PD-1 and inhibits human Jurkat T cells Small molecule and macrocyclic peptide inhibitors of hPD-L1 do not bind to mPD-L1 Atezolizumab but not durvalumab binds and blocks mouse PD-L1
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Affiliation(s)
- Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Justyna Kocik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jacek Plewka
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Dominik Sala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Monika Machula
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Przemyslaw Grudnik
- Malopolska Center of Biotechnology Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Malgorzata Hajduk
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Marcin Czepiel
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
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18
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Konieczny M, Musielak B, Kocik J, Skalniak L, Sala D, Czub M, Magiera-Mularz K, Rodriguez I, Myrcha M, Stec M, Siedlar M, Holak TA, Plewka J. Di-bromo-Based Small-Molecule Inhibitors of the PD-1/PD-L1 Immune Checkpoint. J Med Chem 2020; 63:11271-11285. [PMID: 32936638 PMCID: PMC7584369 DOI: 10.1021/acs.jmedchem.0c01260] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Immune checkpoint blockade is one
of the most promising strategies
of cancer immunotherapy. However, unlike classical targeted therapies,
it is currently solely based on expensive monoclonal antibodies, which
often inflict immune-related adverse events. Herein, we propose a
novel small-molecule inhibitor targeted at the most clinically relevant
immune checkpoint, PD-1/PD-L1. The compound is capable of disrupting
the PD-1/PD-L1 complex by antagonizing PD-L1 and, therefore, restores
activation of T cells similarly to the antibodies, while being cheap
in production and possibly nonimmunogenic. The final compound is significantly
smaller than others reported in the literature while being nontoxic
to cells even at high concentrations. The scaffold was designed using
a structure–activity relationship screening cascade based on
a new antagonist-induced dissociation NMR assay, called the weak-AIDA-NMR.
Weak-AIDA-NMR finds true inhibitors, as opposed to only binders to
the target protein, in early steps of lead compound development, and
this process makes it less time and cost consuming.
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Affiliation(s)
- Magdalena Konieczny
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Justyna Kocik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Dominik Sala
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Miroslawa Czub
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | | | - Ismael Rodriguez
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Maja Myrcha
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Malgorzata Stec
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, Krakow 30-663, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, Krakow 30-663, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Krakow 30-387, Poland
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19
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Pęcak A, Skalniak Ł, Pels K, Książek M, Madej M, Krzemień D, Malicki S, Władyka B, Dubin A, Holak TA, Dubin G. Anti-CD44 DNA Aptamers Selectively Target Cancer Cells. Nucleic Acid Ther 2020; 30:289-298. [PMID: 32379519 DOI: 10.1089/nat.2019.0833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CD44 is a type I transmembrane glycoprotein interacting with a number of extracellular components, including hyaluronic acid (HA). CD44-HA axis is involved in a variety of processes, including adhesion, migration, differentiation, trafficking, and others. CD44 is overexpressed in several cancers where binding of HA induces signal transduction leading to activation of antiapoptotic proteins and factors linked to drug resistance. As such, CD44 has been implicated in cancer growth, progression, and metastasis. It has been convincingly demonstrated that blocking CD44-HA interaction decreases cancer cell survival and metastasis. In this study, using in vitro selection, we have developed DNA aptamers recognizing a HA-binding domain of CD44 with high affinity and specificity. The aptamers bind to CD44 with nanomolar affinities and efficiently inhibit the growth of leukemic cancer cells characterized by high expression of CD44. The selectivity is demonstrated by an irrelevant effect on cells characterized by low CD44 levels. The obtained aptamers broaden the existing landscape of potential approaches to the development of antitumor strategies based on inhibition of the CD44 axis.
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Affiliation(s)
- Aleksandra Pęcak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Łukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Katarzyna Pels
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mirosław Książek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mariusz Madej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dobrosława Krzemień
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Stanisław Malicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Benedykt Władyka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Adam Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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20
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van der Vlag R, Yagiz Unver M, Felicetti T, Twarda‐Clapa A, Kassim F, Ermis C, Neochoritis CG, Musielak B, Labuzek B, Dömling A, Holak TA, Hirsch AKH. Optimized Inhibitors of MDM2 via an Attempted Protein-Templated Reductive Amination. ChemMedChem 2020; 15:370-375. [PMID: 31774938 PMCID: PMC7064911 DOI: 10.1002/cmdc.201900574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Innovative and efficient hit-identification techniques are required to accelerate drug discovery. Protein-templated fragment ligations represent a promising strategy in early drug discovery, enabling the target to assemble and select its binders from a pool of building blocks. Development of new protein-templated reactions to access a larger structural diversity and expansion of the variety of targets to demonstrate the scope of the technique are of prime interest for medicinal chemists. Herein, we present our attempts to use a protein-templated reductive amination to target protein-protein interactions (PPIs), a challenging class of drug targets. We address a flexible pocket, which is difficult to achieve by structure-based drug design. After careful analysis we did not find one of the possible products in the kinetic target-guided synthesis (KTGS) approach, however subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (Ki =0.095 μm) identified is almost as active as Nutlin-3, a potent inhibitor of the p53-MDM2 PPI.
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Affiliation(s)
- Ramon van der Vlag
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - M. Yagiz Unver
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Tommaso Felicetti
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo 106123PerugiaItaly
| | | | - Fatima Kassim
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Cagdas Ermis
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Constantinos G. Neochoritis
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
- Chemistry departmentUniversity of Crete70013HeraklionGreece
| | - Bogdan Musielak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Alexander Dömling
- Department of Pharmacy, Drug Design groupUniversity of GroningenA. Deusinglaan 1GroningenThe Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian UniversityGronostajowa 230-387KrakowPoland
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
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21
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity‐Driven Tool for the Development of Inhibitors of Protein–Protein Interactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Manuel G. Ricardo
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Ameena M. Ali
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Jacek Plewka
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Ewa Surmiak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Constantinos G. Neochoritis
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Department of ChemistryUniversity of Crete Greece
| | - Jack Atmaj
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Faculty of ChemistryJagiellonian University Krakow Poland
| | | | - Ran Zhang
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Matthew Groves
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Daniel G. Rivera
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Alexander Dömling
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
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22
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions. Angew Chem Int Ed Engl 2020; 59:5235-5241. [PMID: 31944488 DOI: 10.1002/anie.201916257] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Stapled peptides are chemical entities in-between biologics and small molecules, which have proven to be the solution to high affinity protein-protein interaction antagonism, while keeping control over pharmacological performance such as stability and membrane penetration. We demonstrate that the multicomponent reaction-based stapling is an effective strategy for the development of α-helical peptides with highly potent dual antagonistic action of MDM2 and MDMX binding p53. Such a potent inhibitory activity of p53-MDM2/X interactions was assessed by fluorescence polarization, microscale thermophoresis, and 2D NMR, while several cocrystal structures with MDM2 were obtained. This MCR stapling protocol proved efficient and versatile in terms of diversity generation at the staple, as evidenced by the incorporation of both exo- and endo-cyclic hydrophobic moieties at the side chain cross-linkers. The interaction of the Ugi-staple fragments with the target protein was demonstrated by crystallography.
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Affiliation(s)
- Manuel G Ricardo
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Ameena M Ali
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Department of Chemistry, University of, Crete, Greece
| | - Jack Atmaj
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ran Zhang
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Daniel G Rivera
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
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23
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Musielak B, Kocik J, Skalniak L, Magiera-Mularz K, Sala D, Czub M, Stec M, Siedlar M, Holak TA, Plewka J. CA-170 - A Potent Small-Molecule PD-L1 Inhibitor or Not? Molecules 2019; 24:molecules24152804. [PMID: 31374878 PMCID: PMC6695792 DOI: 10.3390/molecules24152804] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
CA-170 is currently the only small-molecule modulator in clinical trials targeting PD-L1 and VISTA proteins – important negative checkpoint regulators of immune activation. The reported therapeutic results to some extent mimic those of FDA-approved monoclonal antibodies overcoming the limitations of the high production costs and adverse effects of the latter. However, no conclusive biophysical evidence proving the binding to hPD-L1 has ever been presented. Using well-known in vitro methods: NMR binding assay, HTRF and cell-based activation assays, we clearly show that there is no direct binding between CA-170 and PD-L1. To strengthen our reasoning, we performed control experiments on AUNP-12 – a 29-mer peptide, which is a precursor of CA-170. Positive controls consisted of the well-documented small-molecule PD-L1 inhibitors: BMS-1166 and peptide-57.
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Affiliation(s)
- Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Justyna Kocik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Dominik Sala
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Miroslawa Czub
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Malgorzata Stec
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, Wielicka 265, 30-663 Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
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24
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Muszak D, Łabuzek B, Brela MZ, Twarda-Clapa A, Czub M, Musielak B, Surmiak E, Holak TA. The synthesis and characterization of tetramic acid derivatives as Mdm2-p53 inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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25
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Basu S, Yang J, Xu B, Magiera-Mularz K, Skalniak L, Musielak B, Kholodovych V, Holak TA, Hu L. Design, Synthesis, Evaluation, and Structural Studies of C2-Symmetric Small Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction. J Med Chem 2019; 62:7250-7263. [PMID: 31298541 DOI: 10.1021/acs.jmedchem.9b00795] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A series of C2-symmetric inhibitors was designed and evaluated for inhibitory activity against the programmed cell death-1/programmed death-ligand 1(PD-1/PD-L1) protein-protein interaction (PPI) in a homogenous time-resolved fluorescence (HTRF) assay and PD-1 signaling in cell-based coculture assays. C2-symmetric inhibitors 2a (LH1306) and 2b (LH1307) exhibited IC50 values of 25 and 3.0 nM, respectively, in the HTRF assay. While 2a was ∼3.8-fold more potent than previously reported inhibitor 1a, 2b could not be differentiated from 1b due to their high potency and the limit of our HTRF assay conditions. In one cell-based coculture PD-1 signaling assay, 2a and 2b were 8.2- and 2.8-fold more potent in inhibiting PD-1 signaling than 1a and 1b, respectively. NMR and X-ray cocrystal structural studies provided more structural insights into the interaction between 2b and PD-L1; 2b binds to PD-L1 at the PD-1 binding site and induces the formation of a more symmetrically arranged PD-L1 homodimer than that previously reported for other inhibitors.
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Affiliation(s)
| | | | | | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
| | | | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry , Jagiellonian University , Gronostajowa 2 , 30-387 Krakow , Poland
| | - Longqin Hu
- The Cancer Institute of New Jersey , New Brunswick , New Jersey 08901 , United States
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26
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Kocik J, Machula M, Wisniewska A, Surmiak E, Holak TA, Skalniak L. Helping the Released Guardian: Drug Combinations for Supporting the Anticancer Activity of HDM2 (MDM2) Antagonists. Cancers (Basel) 2019; 11:cancers11071014. [PMID: 31331108 PMCID: PMC6678622 DOI: 10.3390/cancers11071014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/13/2019] [Accepted: 07/16/2019] [Indexed: 01/22/2023] Open
Abstract
The protein p53, known as the “Guardian of the Genome”, plays an important role in maintaining DNA integrity, providing protection against cancer-promoting mutations. Dysfunction of p53 is observed in almost every cancer, with 50% of cases bearing loss-of-function mutations/deletions in the TP53 gene. In the remaining 50% of cases the overexpression of HDM2 (mouse double minute 2, human homolog) protein, which is a natural inhibitor of p53, is the most common way of keeping p53 inactive. Disruption of HDM2-p53 interaction with the use of HDM2 antagonists leads to the release of p53 and expression of its target genes, engaged in the induction of cell cycle arrest, DNA repair, senescence, and apoptosis. The induction of apoptosis, however, is restricted to only a handful of p53wt cells, and, generally, cancer cells treated with HDM2 antagonists are not efficiently eliminated. For this reason, HDM2 antagonists were tested in combinations with multiple other therapeutics in a search for synergy that would enhance the cancer eradication. This manuscript aims at reviewing the recent progress in developing strategies of combined cancer treatment with the use of HDM2 antagonists.
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Affiliation(s)
- Justyna Kocik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland
| | - Monika Machula
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland
| | - Aneta Wisniewska
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland.
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27
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Affiliation(s)
- Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ewa Surmiak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Tad A. Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
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28
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Neochoritis CG, Kazemi Miraki M, Abdelraheem EMM, Surmiak E, Zarganes-Tzitzikas T, Łabuzek B, Holak TA, Dömling A. Design of indole- and MCR-based macrocycles as p53-MDM2 antagonists. Beilstein J Org Chem 2019; 15:513-520. [PMID: 30873235 PMCID: PMC6404402 DOI: 10.3762/bjoc.15.45] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/14/2019] [Indexed: 01/02/2023] Open
Abstract
Macrocycles were designed to antagonize the protein–protein interaction p53-MDM2 based on the three-finger pharmacophore F19W23L25. The synthesis was accomplished by a rapid, one-pot synthesis of indole-based macrocycles based on Ugi macrocyclization. The reaction of 12 different α,ω-amino acids and different indole-3-carboxaldehyde derivatives afforded a unique library of macrocycles otherwise difficult to access. Screening of the library for p53-MDM2 inhibition by fluorescence polarization and 1H,15N HSQC NMR measurements confirm MDM2 binding.
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Affiliation(s)
- Constantinos G Neochoritis
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Maryam Kazemi Miraki
- Chemistry Department, Tarbiat Modares University, P.O. Box 14155-4838, Tehran, Iran
| | - Eman M M Abdelraheem
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tryfon Zarganes-Tzitzikas
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Beata Łabuzek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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Skalniak L, Twarda-Clapa A, Neochoritis CG, Surmiak E, Machula M, Wisniewska A, Labuzek B, Ali AM, Krzanik S, Dubin G, Groves M, Dömling A, Holak TA. A fluorinated indole-based MDM2 antagonist selectively inhibits the growth of p53 wt osteosarcoma cells. FEBS J 2019; 286:1360-1374. [PMID: 30715803 DOI: 10.1111/febs.14774] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/15/2018] [Accepted: 01/31/2019] [Indexed: 12/14/2022]
Abstract
The p53 protein is engaged in the repair of DNA mutations and elimination of heavily damaged cells, providing anticancer protection. Dysregulation of p53 activity is a crucial step in carcinogenesis. This dysregulation is often caused by the overexpression of negative regulators of p53, among which MDM2 is the most prominent one. Antagonizing MDM2 with small molecules restores the activity of p53 in p53 wild-type (p53wt ) cells and thus provides positive outcomes in the treatment of p53wt cancers. Previously, we have reported the discovery of a panel of fluoro-substituted indole-based antagonists of MDM2. Here, we demonstrate the biological activity and stereoselectivity of the most active compound from this series. Both enantiomers of the esterified form of the compound, as well as its corresponding carboxylic acids, were found active in fluorescence polarization (FP) assay, nuclear magnetic resonance (NMR) and microscale thermophoresis (MST) assay, with Ki and KD values around 1 μm. From these four compounds, the esterified enantiomer (R)-5a was active in cells, which was evidenced by the increase of p53 levels, the induced expression of p53-target genes (CDKN1A and MDM2), the selective induction of cell cycle arrest, and selective growth inhibition of p53wt U-2 OS and SJSA-1 compared to p53del SAOS-2 cells. The analysis of the crystal structure of human MDM2 in complex with the compound (R)-6a (carboxylic acid of the active (R)-5a compound) revealed the classical three-finger binding mode. Altogether, our data demonstrate the activity of the compound and provide the structural basis for further structure optimization.
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Affiliation(s)
- Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | | | | | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Monika Machula
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | | | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ameena M Ali
- Department of Drug Design, University of Groningen, The Netherlands
| | - Sylwia Krzanik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Drug Design, University of Groningen, The Netherlands
| | | | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
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Pustuła M, Czub M, Łabuzek B, Surmiak E, Tomala M, Twarda-Clapa A, Guzik K, Popowicz GM, Holak TA. NMR fragment-based screening for development of the CD44-binding small molecules. Bioorg Chem 2018; 82:284-289. [PMID: 30396062 DOI: 10.1016/j.bioorg.2018.10.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
Abstract
The cell-surface protein CD44, a primary receptor for hyaluronic acid (HA), is one of the most promising targets for cancer therapies. It is prominently involved in the process of tumor growth and metastasis. The possibility of modulating the CD44-HA interaction with a pharmacological inhibitor is therefore of great importance, yet until now there are only few small molecules reported to bind to CD44. Here, we describe the results of the NMR fragment-based screening conducted against CD44 by which we found eight new hit compounds that bind to the receptor with the affinity in milimolar range. The NMR-based characterization revealed that there are two possible binding modes for these compounds, and for some of them the binding is no longer possible in the presence of hyaluronic acid. This could provide an interesting starting point for the development of new high-affinity ligands targeting the CD44-HA axis.
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Affiliation(s)
- Marcin Pustuła
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Mirosława Czub
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Beata Łabuzek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marcin Tomala
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Aleksandra Twarda-Clapa
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Katarzyna Guzik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
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Skalniak L, Kocik J, Polak J, Skalniak A, Rak M, Wolnicka-Glubisz A, Holak TA. Prolonged Idasanutlin (RG7388) Treatment Leads to the Generation of p53-Mutated Cells. Cancers (Basel) 2018; 10:cancers10110396. [PMID: 30352966 PMCID: PMC6266412 DOI: 10.3390/cancers10110396] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022] Open
Abstract
The protein p53 protects the organism against carcinogenic events by the induction of cell cycle arrest and DNA repair program upon DNA damage. Virtually all cancers inactivate p53 either by mutations/deletions of the TP53 gene or by boosting negative regulation of p53 activity. The overexpression of MDM2 protein is one of the most common mechanisms utilized by p53wt cancers to keep p53 inactive. Inhibition of MDM2 action by its antagonists has proved its anticancer potential in vitro and is now tested in clinical trials. However, the prolonged treatment of p53wt cells with MDM2 antagonists leads to the development of secondary resistance, as shown first for Nutlin-3a, and later for three other small molecules. In the present study, we show that secondary resistance occurs also after treatment of p53wt cells with idasanutlin (RG7388, RO5503781), which is the only MDM2 antagonist that has passed phase II and entered phase III clinical trials, so far. Idasanutlin strongly activates p53, as evidenced by the induction of p21 expression and potent cell cycle arrest in all the three cell lines tested, i.e., MCF-7, U-2 OS, and SJSA-1. Notably, apoptosis was induced only in SJSA-1 cells, while MCF-7 and U-2 OS cells were able to restore the proliferation upon the removal of idasanutlin. Moreover, idasanutlin-treated U-2 OS cells could be cultured for long time periods in the presence of the drug. This prolonged treatment led to the generation of p53-mutated resistant cell populations. This resistance was generated de novo, as evidenced by the utilization of monoclonal U-2 OS subpopulations. Thus, although idasanutlin presents much improved activities compared to its precursor, it displays the similar weaknesses, which are limited elimination of cancer cells and the generation of p53-mutated drug-resistant subpopulations.
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Affiliation(s)
- Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
| | - Justyna Kocik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
| | - Justyna Polak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
| | - Anna Skalniak
- Department of Endocrinology, Medical Faculty, Jagiellonian University Medical College, Kopernika 17, 31-501 Krakow, Poland.
| | - Monika Rak
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
| | - Agnieszka Wolnicka-Glubisz
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
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Shaabani S, Huizinga HPS, Butera R, Kouchi A, Guzik K, Magiera-Mularz K, Holak TA, Dömling A. A patent review on PD-1/PD-L1 antagonists: small molecules, peptides, and macrocycles (2015-2018). Expert Opin Ther Pat 2018; 28:665-678. [PMID: 30107136 DOI: 10.1080/13543776.2018.1512706] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION The protein-protein interaction PD1/PD-L1 is an important immune checkpoint and several recently approved monoclonal antibodies show promising anti cancer activities in the clinical practice. However, only a small percentage of cancer patients benefit from PD1/PD-L1 directed mAbs. Moreover, some patients experience immune related side effects upon treatment with these mAbs. Recently, several atomic-resolution structures of human PD1/PD-L1, and small molecules, peptides and mAbs with PD-L1 and PD1 open the field for structure based drug design. Small molecules and peptides targeting PD1/PD-L1 promise to enhance tumor activity while showing less immune related side effects. AREAS COVERED We reviewed the small molecules classes and peptides targeting PD1/PD-L1. EXPERT OPINION Currently approved PD1/PD-L1 directed therapeutics show room for improvement. Three classes of non mAb small molecule classes have been discovered so far: (cyclic) peptides as direct competitive PD1/PD-L1 antagonists; small molecules disrupting PD1/PD-L1 and inducing a PD-L1 dimerization; and a small molecule class of unknown mode-of-action. An example of the later group CA-170 is currently investigated in a Phase 1 trial in patients with advanced solid tumors and lymphomas. Potential advantages of small molecules over mAbs include high distribution and better tumor penetration, improved PK/PD, less side effects and oral bioavailability.
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Affiliation(s)
- Shabnam Shaabani
- a Department of Drug Design , University of Groningen , Groningen , The Netherlands
| | - Harmen P S Huizinga
- a Department of Drug Design , University of Groningen , Groningen , The Netherlands
| | - Roberto Butera
- a Department of Drug Design , University of Groningen , Groningen , The Netherlands
| | - Ariana Kouchi
- a Department of Drug Design , University of Groningen , Groningen , The Netherlands
| | - Katarzyna Guzik
- b Faculty of Chemistry , Jagiellonian University , Cracow , Poland
| | | | - Tad A Holak
- b Faculty of Chemistry , Jagiellonian University , Cracow , Poland
| | - Alexander Dömling
- a Department of Drug Design , University of Groningen , Groningen , The Netherlands
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Twarda-Clapa A, Labuzek B, Krzemien D, Musielak B, Grudnik P, Dubin G, Holak TA. Crystal structure of the FAS1 domain of the hyaluronic acid receptor stabilin-2. Acta Crystallogr D Struct Biol 2018; 74:695-701. [PMID: 29968679 DOI: 10.1107/s2059798318007271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/14/2018] [Indexed: 11/11/2022]
Abstract
Recent research has identified a potential role of the hyaluronic acid receptor stabilin-2 (Stab2) in cancer metastasis. Stab2 belongs to a group of scavenger receptors and is responsible for the clearance of more than ten ligands, including hyaluronic acid (HA). In vivo experiments on mice have shown that the absence of Stab2, or its blocking by an antibody, effectively opposes cancer metastasis, which is accompanied by an increase in the level of circulating HA. Knowledge of ligand recognition and signal transduction by Stab2 is limited and no three-dimensional structures of any protein fragments of this receptor have been solved to date. Here, a high-resolution X-ray structure of the seventh FAS1 domain of Stab2 is reported. This structure provides the first insight into the Stab2 structure.
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Affiliation(s)
| | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland
| | | | - Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland
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Konstantinidou M, Zarganes-Tzitzikas T, Magiera-Mularz K, Holak TA, Dömling A. Immune Checkpoint PD-1/PD-L1: Is There Life Beyond Antibodies? Angew Chem Int Ed Engl 2018; 57:4840-4848. [PMID: 29178534 PMCID: PMC6280658 DOI: 10.1002/anie.201710407] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/21/2017] [Indexed: 12/27/2022]
Abstract
The PD-1/PD-L1 interaction has emerged as a significant target in cancer immunotherapy. Current medications include monoclonal antibodies, which have shown impressive clinical results in the treatment of several types of tumors. The cocrystal structure of human PD-1 and PD-L1 is expected to be a valuable starting point for the design of novel inhibitors, along with the recent crystal structures with monoclonal antibodies, small molecules, and macrocycles.
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Affiliation(s)
- Markella Konstantinidou
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen (The Netherlands)
| | - Tryfon Zarganes-Tzitzikas
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen (The Netherlands)
| | | | - Tad A. Holak
- Jagiellonian University Ingardena 3, 30-060 Krakow (Poland), Max Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152 Martinsried (Germany)
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen (The Netherlands)
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35
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Zak KM, Grudnik P, Magiera K, Dömling A, Dubin G, Holak TA. Structural Biology of the Immune Checkpoint Receptor PD-1 and Its Ligands PD-L1/PD-L2. Structure 2018; 25:1163-1174. [PMID: 28768162 DOI: 10.1016/j.str.2017.06.011] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/23/2017] [Accepted: 06/16/2017] [Indexed: 12/30/2022]
Abstract
Cancer cells can avoid and suppress immune responses through activation of inhibitory immune checkpoint proteins, such as PD-1, PD-L1, and CTLA-4. Blocking the activities of these proteins with monoclonal antibodies, and thus restoring T cell function, has delivered breakthrough therapies against cancer. In this review, we describe the latest work on structural characterization of the checkpoint proteins, their interactions with cognate ligands and with therapeutic antibodies. Structures of the extracellular portions of these proteins reveal that they all have a similar modular structure, composed of small domains similar in topology to the domains found in antibodies. Structural basis for blocking the PD-1/PD-L1 interaction by small molecules is illustrated with the compound BMS-202 that binds to and induces dimerization of PD-L1.
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Affiliation(s)
- Krzysztof M Zak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV 9713 Groningen, the Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland; Max Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152 Martinsried, Germany.
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Konstantinidou M, Zarganes-Tzitzikas T, Magiera-Mularz K, Holak TA, Dömling A. Der Immuncheckpoint PD-1/PD-L1: Gibt es Therapieoptionen jenseits der Antikörper? Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Markella Konstantinidou
- Department of Drug Design; University of Groningen; A. Deusinglaan 1 9713 AV Groningen Niederlande
| | | | | | - Tad A. Holak
- Fakultät für Chemie; Jagiellonen-Universität; Ingardena 3 30-060 Krakau Polen
- Max-Planck-Institut für Biochemie; Am Klopferspitz 18a 82152 Martinsried Deutschland
| | - Alexander Dömling
- Department of Drug Design; University of Groningen; A. Deusinglaan 1 9713 AV Groningen Niederlande
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Tomala MD, Magiera-Mularz K, Kubica K, Krzanik S, Zieba B, Musielak B, Pustula M, Popowicz GM, Sattler M, Dubin G, Skalniak L, Holak TA. Identification of small-molecule inhibitors of USP2a. Eur J Med Chem 2018. [PMID: 29529503 DOI: 10.1016/j.ejmech.2018.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
USP2a is a deubiquitinating protease that rescues its target proteins from destruction by the proteasome by reversing the process of protein ubiquitination. USP2a shows oncogenic properties in vivo and has been found to be a specific activator of cyclin D1. Many types of cancers are addicted to cyclin D1 expression. Targeting USP2a is a promising strategy for cancer therapy but little progress has been made in the field of inhibition of USP2a. Using NMR-based fragment screening and biophysical binding assays, we have discovered small molecules that bind to USP2a. Iterations of fragment combination and structure-driven design identified two 5-(2-thienyl)-3-isoxazoles as the inhibitors of the USP2a-ubiquitin protein-protein interaction. The affinity of these molecules for the catalytic domain of USP2a parallels their ability to interfere with USP2a binding to ubiquitin in vitro. Altogether, our results establish the 5-(2-thienyl)-3-isoxazole pharmacophore as an attractive starting point for lead optimization.
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Affiliation(s)
- Marcin D Tomala
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | | | - Katarzyna Kubica
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Sylwia Krzanik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Bartosz Zieba
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Marcin Pustula
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
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38
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Estrada-Ortiz N, Neochoritis CG, Twarda-Clapa A, Musielak B, Holak TA, Dömling A. Artificial Macrocycles as Potent p53-MDM2 Inhibitors. ACS Med Chem Lett 2017; 8:1025-1030. [PMID: 29057045 PMCID: PMC5641952 DOI: 10.1021/acsmedchemlett.7b00219] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/20/2017] [Indexed: 11/28/2022] Open
Abstract
Based on a combination of an Ugi four component reaction and a ring closing metathesis, a library of novel artificial macrocyclic inhibitors of the p53-MDM2 interaction was designed and synthesized. These macrocycles, alternatively to stapled peptides, target for the first time the large hydrophobic surface area formed by Tyr67, Gln72, His73, Val93, and Lys94 yielding derivatives with affinity to MDM2 in the nanomolar range. Their binding affinity with MDM2 was evaluated using fluorescence polarization (FP) assay and 1H-15N two-dimensional HSQC nuclear magnetic resonance experiments.
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Affiliation(s)
- Natalia Estrada-Ortiz
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, Groningen 9700AV, The Netherlands
| | | | - Aleksandra Twarda-Clapa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska Centre
of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Department of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Krakow, Poland
| | - Tad A. Holak
- Malopolska Centre
of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
- Department of Chemistry, Jagiellonian University, Ingardena
3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, Groningen 9700AV, The Netherlands
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39
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Magiera-Mularz K, Skalniak L, Zak KM, Musielak B, Rudzinska-Szostak E, Berlicki Ł, Kocik J, Grudnik P, Sala D, Zarganes-Tzitzikas T, Shaabani S, Dömling A, Dubin G, Holak TA. Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint. Angew Chem Int Ed Engl 2017; 56:13732-13735. [PMID: 28881104 DOI: 10.1002/anie.201707707] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 11/05/2022]
Abstract
Blockade of the immunoinhibitory PD-1/PD-L1 pathway using monoclonal antibodies has shown impressive results with durable clinical antitumor responses. Anti-PD-1 and anti-PD-L1 antibodies have now been approved for the treatment of a number of tumor types, whereas the development of small molecules targeting immune checkpoints lags far behind. We characterized two classes of macrocyclic-peptide inhibitors directed at the PD-1/PD-L1 pathway. We show that these macrocyclic compounds act by directly binding to PD-L1 and that they are capable of antagonizing PD-L1 signaling and, similarly to antibodies, can restore the function of T-cells. We also provide the crystal structures of two of these small-molecule inhibitors bound to PD-L1. The structures provide a rationale for the checkpoint inhibition by these small molecules, and a description of their small molecule/PD-L1 interfaces provides a blueprint for the design of small-molecule inhibitors of the PD-1/PD-L1 pathway.
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Affiliation(s)
- Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Krzysztof M Zak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Ewa Rudzinska-Szostak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Justyna Kocik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Dominik Sala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Tryfon Zarganes-Tzitzikas
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV, 9713, Groningen, The Netherlands
| | - Shabnam Shaabani
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV, 9713, Groningen, The Netherlands
| | - Alexander Dömling
- Department for Drug Design, University of Groningen, A. Deusinglaan 9, AV, 9713, Groningen, The Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland.,Max Planck Institute for Biochemistry, Am Klopferspitz 18a, 82152, Martinsried, Germany
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40
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Magiera-Mularz K, Skalniak L, Zak KM, Musielak B, Rudzinska-Szostak E, Berlicki Ł, Kocik J, Grudnik P, Sala D, Zarganes-Tzitzikas T, Shaabani S, Dömling A, Dubin G, Holak TA. Bioactive Macrocyclic Inhibitors of the PD-1/PD-L1 Immune Checkpoint. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707707] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Katarzyna Magiera-Mularz
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Krzysztof M. Zak
- Malopolska Centre of Biotechnology; Jagiellonian University; Gronostajowa 7a 30-387 Krakow Poland
- Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Bogdan Musielak
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Ewa Rudzinska-Szostak
- Department of Bioorganic Chemistry; Faculty of Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry; Faculty of Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Justyna Kocik
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology; Jagiellonian University; Gronostajowa 7a 30-387 Krakow Poland
- Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Dominik Sala
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
| | - Tryfon Zarganes-Tzitzikas
- Department for Drug Design; University of Groningen; A. Deusinglaan 9 AV 9713 Groningen The Netherlands
| | - Shabnam Shaabani
- Department for Drug Design; University of Groningen; A. Deusinglaan 9 AV 9713 Groningen The Netherlands
| | - Alexander Dömling
- Department for Drug Design; University of Groningen; A. Deusinglaan 9 AV 9713 Groningen The Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology; Jagiellonian University; Gronostajowa 7a 30-387 Krakow Poland
- Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Tad A. Holak
- Department of Organic Chemistry; Faculty of Chemistry; Jagiellonian University; Ingardena 3 30-060 Krakow Poland
- Max Planck Institute for Biochemistry; Am Klopferspitz 18a 82152 Martinsried Germany
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41
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Peche VS, Holak TA, Burgute BD, Kosmas K, Kale SP, Wunderlich FT, Elhamine F, Stehle R, Pfitzer G, Nohroudi K, Addicks K, Stöckigt F, Schrickel JW, Gallinger J, Schleicher M, Noegel AA. Erratum to: Ablation of cyclase-associated protein 2 (CAP2) leads to cardiomyopathy. Cell Mol Life Sci 2017; 74:4045. [PMID: 28852764 DOI: 10.1007/s00018-017-2630-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Vivek S Peche
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Tad A Holak
- Max-Planck-Institute of Biochemistry, 82152, Martinsried, Germany.,Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland
| | - Bhagyashri D Burgute
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Kosmas Kosmas
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany
| | - Sushant P Kale
- Department of Neurology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - F Thomas Wunderlich
- Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Max-Planck-Institute of Neurological Research, Cologne, Germany
| | - Fatiha Elhamine
- Institute of Vegetative Physiology, University of Cologne, Cologne, Germany
| | - Robert Stehle
- Institute of Vegetative Physiology, University of Cologne, Cologne, Germany
| | - Gabriele Pfitzer
- Institute of Vegetative Physiology, University of Cologne, Cologne, Germany
| | - Klaus Nohroudi
- Institute of Anatomy I, University of Cologne, Cologne, Germany
| | - Klaus Addicks
- Institute of Anatomy I, University of Cologne, Cologne, Germany
| | - Florian Stöckigt
- Department of Medicine-Cardiology, University of Bonn, Bonn, Germany
| | - Jan W Schrickel
- Department of Medicine-Cardiology, University of Bonn, Bonn, Germany
| | - Julia Gallinger
- Institute for Anatomy and Cell Biology, Ludwig-Maximilians University, 80336, Munich, Germany
| | - Michael Schleicher
- Institute for Anatomy and Cell Biology, Ludwig-Maximilians University, 80336, Munich, Germany
| | - Angelika A Noegel
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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42
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Skalniak L, Zak KM, Guzik K, Magiera K, Musielak B, Pachota M, Szelazek B, Kocik J, Grudnik P, Tomala M, Krzanik S, Pyrc K, Dömling A, Dubin G, Holak TA. Small-molecule inhibitors of PD-1/PD-L1 immune checkpoint alleviate the PD-L1-induced exhaustion of T-cells. Oncotarget 2017; 8:72167-72181. [PMID: 29069777 PMCID: PMC5641120 DOI: 10.18632/oncotarget.20050] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/25/2017] [Indexed: 02/07/2023] Open
Abstract
Antibodies targeting the PD-1/PD-L1 immune checkpoint achieved spectacular success in anticancer therapy in the recent years. In contrast, no small molecules with cellular activity have been reported so far. Here we provide evidence that small molecules are capable of alleviating the PD-1/PD-L1 immune checkpoint-mediated exhaustion of Jurkat T-lymphocytes. The two optimized small-molecule inhibitors of the PD-1/PD-L1 interaction, BMS-1001 and BMS-1166, developed by Bristol-Myers Squibb, bind to human PD-L1 and block its interaction with PD-1, when tested on isolated proteins. The compounds present low toxicity towards tested cell lines and block the interaction of soluble PD-L1 with the cell surface-expressed PD-1. As a result, BMS-1001 and BMS-1166 alleviate the inhibitory effect of the soluble PD-L1 on the T-cell receptor-mediated activation of T-lymphocytes. Moreover, the compounds were effective in attenuating the inhibitory effect of the cell surface-associated PD-L1. We also determined the X-ray structures of the complexes of BMS-1001 and BMS-1166 with PD-L1, which revealed features that may be responsible for increased potency of the compounds compared to their predecessors. Further development may lead to the design of an anticancer therapy based on the orally delivered immune checkpoint inhibition.
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Affiliation(s)
- Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Krzysztof M Zak
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Katarzyna Guzik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Magdalena Pachota
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bozena Szelazek
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Justyna Kocik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Przemyslaw Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Marcin Tomala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
| | - Sylwia Krzanik
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Krzysztof Pyrc
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-060 Krakow, Poland
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43
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Madhavachary R, Abdelraheem EMM, Rossetti A, Twarda-Clapa A, Musielak B, Kurpiewska K, Kalinowska-Tłuścik J, Holak TA, Dömling A. Two-Step Synthesis of Complex Artificial Macrocyclic Compounds. Angew Chem Int Ed Engl 2017; 56:10725-10729. [PMID: 28691783 DOI: 10.1002/anie.201704426] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/23/2017] [Indexed: 11/08/2022]
Abstract
The design and synthesis of head-to-tail linked artificial macrocycles using the Ugi-reaction has been developed. This synthetic approach of just two steps is unprecedented, short, efficient and works over a wide range of medium (8-11) and macrocyclic (≥12) loop sizes. The substrate scope and functional group tolerance is exceptional. Using this approach, we have synthesized 39 novel macrocycles by two or even one single synthetic operation. The properties of our macrocycles are discussed with respect to their potential to bind to biological targets that are not druggable by conventional, drug-like compounds. As an application of these artificial macrocycles we highlight potent p53-MDM2 antagonism.
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Affiliation(s)
- Rudrakshula Madhavachary
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Eman M M Abdelraheem
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Arianna Rossetti
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | | | - Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland
| | | | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland
| | - Alexander Dömling
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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44
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Madhavachary R, Abdelraheem EMM, Rossetti A, Twarda-Clapa A, Musielak B, Kurpiewska K, Kalinowska-Tłuścik J, Holak TA, Dömling A. Two-Step Synthesis of Complex Artificial Macrocyclic Compounds. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Eman M. M. Abdelraheem
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
- Chemistry Department; Faculty of Science; Sohag University; Sohag 82524 Egypt
| | - Arianna Rossetti
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
| | | | - Bogdan Musielak
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | | | - Tad A. Holak
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | - Alexander Dömling
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
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45
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Guzik K, Zak KM, Grudnik P, Magiera K, Musielak B, Törner R, Skalniak L, Dömling A, Dubin G, Holak TA. Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1. J Med Chem 2017; 60:5857-5867. [PMID: 28613862 DOI: 10.1021/acs.jmedchem.7b00293] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Blockade of the PD-1/PD-L1 immune checkpoint pathway with monoclonal antibodies has provided significant advances in cancer treatment. The antibody-based immunotherapies carry a number of disadvantages such as the high cost of the antibodies, their limited half-life, and immunogenicity. Development of small-molecule PD-1/PD-L1 inhibitors that could overcome these drawbacks is slow because of the incomplete structural information for this pathway. The first chemical PD-1/PD-L1 inhibitors have been recently disclosed by Bristol-Myers Squibb. Here we present NMR and X-ray characterization for the two classes of these inhibitors. The X-ray structures of the PD-L1/inhibitor complexes reveal one inhibitor molecule located at the center of the PD-L1 homodimer, filling a deep hydrophobic channel-like pocket between two PD-L1 molecules. Derivatives of (2-methyl-3-biphenylyl)methanol exhibit the structures capped on one side of the channel, whereas the compounds based on [3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methylphenyl]methanol induce an enlarged interaction interface that results in the open "face-back" tunnel through the PD-L1 dimer.
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Affiliation(s)
- Katarzyna Guzik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Krzysztof M Zak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Przemyslaw Grudnik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Ricarda Törner
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department for Drug Design, University of Groningen , A. Deusinglaan 9, AV 9713 Groningen, The Netherlands
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7a, 30-387 Krakow, Poland
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46
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Twarda-Clapa A, Krzanik S, Kubica K, Guzik K, Labuzek B, Neochoritis CG, Khoury K, Kowalska K, Czub M, Dubin G, Dömling A, Skalniak L, Holak TA. 1,4,5-Trisubstituted Imidazole-Based p53–MDM2/MDMX Antagonists with Aliphatic Linkers for Conjugation with Biological Carriers. J Med Chem 2017; 60:4234-4244. [DOI: 10.1021/acs.jmedchem.7b00104] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Aleksandra Twarda-Clapa
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Sylwia Krzanik
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Katarzyna Kubica
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Katarzyna Guzik
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Beata Labuzek
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Constantinos G. Neochoritis
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Kareem Khoury
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Kaja Kowalska
- Max Plank Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Miroslawa Czub
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Grzegorz Dubin
- Faculty
of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Cracow, Poland
| | - Alexander Dömling
- Department
of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Lukasz Skalniak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
- Max Plank Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Cracow, Poland
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47
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Magiera K, Tomala M, Kubica K, De Cesare V, Trost M, Zieba BJ, Kachamakova-Trojanowska N, Les M, Dubin G, Holak TA, Skalniak L. Lithocholic Acid Hydroxyamide Destabilizes Cyclin D1 and Induces G 0/G 1 Arrest by Inhibiting Deubiquitinase USP2a. Cell Chem Biol 2017; 24:458-470.e18. [PMID: 28343940 PMCID: PMC5404848 DOI: 10.1016/j.chembiol.2017.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 09/26/2016] [Accepted: 03/01/2017] [Indexed: 12/29/2022]
Abstract
USP2a is a deubiquitinase responsible for stabilization of cyclin D1, a crucial regulator of cell-cycle progression and a proto-oncoprotein overexpressed in numerous cancer types. Here we report that lithocholic acid (LCA) derivatives are inhibitors of USP proteins, including USP2a. The most potent LCA derivative, LCA hydroxyamide (LCAHA), inhibits USP2a, leading to a significant Akt/GSK3β-independent destabilization of cyclin D1, but does not change the expression of p27. This leads to the defects in cell-cycle progression. As a result, LCAHA inhibits the growth of cyclin D1-expressing, but not cyclin D1-negative cells, independently of the p53 status. We show that LCA derivatives may be considered as future therapeutics for the treatment of cyclin D1-addicted p53-expressing and p53-defective cancer types.
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Affiliation(s)
- Katarzyna Magiera
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Marcin Tomala
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Katarzyna Kubica
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Bartosz J Zieba
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Neli Kachamakova-Trojanowska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland
| | - Marcin Les
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
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48
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Shaabani S, Neochoritis CG, Twarda-Clapa A, Musielak B, Holak TA, Dömling A. Scaffold hopping via ANCHOR.QUERY: β-lactams as potent p53-MDM2 antagonists †. Medchemcomm 2017; 8:1046-1052. [PMID: 29034069 DOI: 10.1039/c7md00058h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the pharmacophore-based virtual screening platform ANCHOR.QUERY, we morphed our recently described Ugi-4CR scaffold towards a β-lactam scaffold with potent p53-MDM2 antagonizing activities. 2D-HSQC and FP measurements confirm potent MDM2 binding. Molecular modeling studies are used to understand the observed SAR in the β-lactam series.
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Affiliation(s)
- S Shaabani
- Department of Drug Design, University of Groningen, The Netherlands.,Faculty of Chemistry, Shahid Beheshti University, Tehran, Iran
| | - C G Neochoritis
- Department of Drug Design, University of Groningen, The Netherlands
| | - A Twarda-Clapa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - B Musielak
- Department of Chemistry, Jagiellonian University, Krakow, Poland
| | - T A Holak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Chemistry, Jagiellonian University, Krakow, Poland
| | - A Dömling
- Department of Drug Design, University of Groningen, The Netherlands
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49
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Surmiak E, Twarda-Clapa A, Zak KM, Musielak B, Tomala MD, Kubica K, Grudnik P, Madej M, Jablonski M, Potempa J, Kalinowska-Tluscik J, Dömling A, Dubin G, Holak TA. A Unique Mdm2-Binding Mode of the 3-Pyrrolin-2-one- and 2-Furanone-Based Antagonists of the p53-Mdm2 Interaction. ACS Chem Biol 2016; 11:3310-3318. [PMID: 27709883 DOI: 10.1021/acschembio.6b00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The p53 pathway is inactivated in almost all types of cancer by mutations in the p53 encoding gene or overexpression of the p53 negative regulators, Mdm2 and/or Mdmx. Restoration of the p53 function by inhibition of the p53-Mdm2/Mdmx interaction opens up a prospect for a nongenotoxic anticancer therapy. Here, we present the syntheses, activities, and crystal structures of two novel classes of Mdm2-p53 inhibitors that are based on the 3-pyrrolin-2-one and 2-furanone scaffolds. The structures of the complexes formed by these inhibitors and Mdm2 reveal the dimeric protein molecular organization that has not been observed in the small-molecule/Mdm2 complexes described until now. In particular, the 6-chloroindole group does not occupy the usual Trp-23 pocket of Mdm2 but instead is engaged in dimerization. This entirely unique binding mode of the compounds opens new possibilities for optimization of the Mdm2-p53 interaction inhibitors.
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Affiliation(s)
- Ewa Surmiak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Aleksandra Twarda-Clapa
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Krzysztof M. Zak
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Bogdan Musielak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marcin D. Tomala
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Katarzyna Kubica
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Przemyslaw Grudnik
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Mariusz Madej
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Mateusz Jablonski
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Jan Potempa
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | | | - Alexander Dömling
- Faculty
of Mathematics and Natural Sciences, Department of Pharmacy, University of Groningen, 9713AV Groningen, The Netherlands
| | - Grzegorz Dubin
- Faculty
of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Tad A. Holak
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
- Malopolska
Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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50
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Surmiak E, Neochoritis CG, Musielak B, Twarda-Clapa A, Kurpiewska K, Dubin G, Camacho C, Holak TA, Dömling A. Rational design and synthesis of 1,5-disubstituted tetrazoles as potent inhibitors of the MDM2-p53 interaction. Eur J Med Chem 2016; 126:384-407. [PMID: 27907876 DOI: 10.1016/j.ejmech.2016.11.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/10/2016] [Accepted: 11/12/2016] [Indexed: 11/30/2022]
Abstract
Using the computational pharmacophore-based ANCHOR.QUERY platform a new scaffold was discovered. Potent compounds evolved inhibiting the protein-protein interaction p53-MDM2. An extensive SAR study was performed based on our four-point pharmacophore model, yielding derivatives with affinity to MDM2 in the nanomolar range. Their binding affinity with MDM2 was evaluated using both fluorescence polarization (FP) assay and 2D-NMR-HSQC experiments.
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Affiliation(s)
- Ewa Surmiak
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design Department, University of Groningen, 9713AV Groningen, The Netherlands
| | - Bogdan Musielak
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Aleksandra Twarda-Clapa
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Katarzyna Kurpiewska
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Carlos Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Biomedical Science Tower 3, Pittsburgh, PA 15260, USA
| | - Tad A Holak
- Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department of Pharmacy, Drug Design Department, University of Groningen, 9713AV Groningen, The Netherlands.
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