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Bojko M, Węgrzyn K, Sikorska E, Ciura P, Battin C, Steinberger P, Magiera-Mularz K, Dubin G, Kulesza A, Sieradzan AK, Spodzieja M, Rodziewicz-Motowidło S. Peptide-based inhibitors targeting the PD-1/PD-L1 axis: potential immunotherapeutics for cancer. Transl Oncol 2024; 42:101892. [PMID: 38359715 PMCID: PMC10877416 DOI: 10.1016/j.tranon.2024.101892] [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: 09/29/2023] [Revised: 12/20/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The PD-1/PD-L1 complex belongs to the group of inhibitory immune checkpoints and plays a critical role in immune regulation. The PD-1/PD-L1 axis is also responsible for immune evasion of cancer cells, and this complex is one of the main targets of immunotherapies used in oncology. Treatment using immune checkpoint inhibitors is mainly based on antibodies. This approach has great therapeutic potential; however, it also has major drawbacks and can induce immune-related adverse events. Thus, there is a strong need for alternative, non-antibody-based therapies using small molecules, peptides, or peptidomimetics. In the present study, we designed, synthesized, and evaluated a set of PD-1-targeting peptides based on the sequence and structure of PD-L1. The binding of these peptides to PD-1 was investigated using SPR and ELISA. We also assessed their ability to compete with PD-L1 for binding to PD-1 and their inhibitory properties against the PD-1/PD-L1 complex at the cellular level. The best results were obtained for the peptide PD-L1(111-127)(Y112C-I126C), named (L11), which displaced PD-L1 from binding to PD-1 in the competitive assay and inhibited the formation of the PD-1/PD-L1 complex. The (L11) peptide also exhibited strong affinity for PD-1. NMR studies revealed that (L11) does not form a well-defined secondary structure; however, MD simulation indicated that (L11) binds to PD-1 at the same place as PD-L1. After further optimization of the structure, the peptide inhibitor obtained in this study could also be used as a potential therapeutic compound targeting the PD-1/PD-L1 axis.
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Affiliation(s)
- Magdalena Bojko
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Katarzyna Węgrzyn
- University of Gdańsk, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Emilia Sikorska
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Piotr Ciura
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Claire Battin
- Medical University of Vienna, Institute of Immunology, Division of Immune Receptors and T cell Activation, Lazarettgasse 19, 1090 Vienna, Austria
| | - Peter Steinberger
- Medical University of Vienna, Institute of Immunology, Division of Immune Receptors and T cell Activation, Lazarettgasse 19, 1090 Vienna, Austria
| | - Katarzyna Magiera-Mularz
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Kraków, Poland
| | - Grzegorz Dubin
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Adam Kulesza
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K Sieradzan
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Marta Spodzieja
- University of Gdańsk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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2
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Domingo-Contreras E, Tormo JR, Gonzalez-Menendez V, Mackenzie TA, Martín-Serrano J, Magiera-Mularz K, Kitel R, Reyes F, Genilloud O, Fernández-Godino R, Ramos MC, Castillo F. Discovery of bioactive natural products of microbial origin as inhibitors of the PD-1/PD-L1 protein-protein interaction. Int J Biol Macromol 2024; 264:130458. [PMID: 38423421 DOI: 10.1016/j.ijbiomac.2024.130458] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024]
Abstract
The PD-1/PD-L1 protein-protein interaction (PPI) controls an adaptive immune resistance mechanism exerted by tumor cells to evade immune responses. The large-molecule nature of current commercial monoclonal antibodies against this PPI hampers their effectiveness by limiting tumor penetration and inducing severe immune-related side effects. Synthetic small-molecule inhibitors may overcome such limitations and have demonstrated promising clinical translation, but their design is challenging. Microbial natural products (NPs) are a source of small molecules with vast chemical diversity that have proved anti-tumoral activities, but which immunotherapeutic properties as PD-1/PD-L1 inhibitors had remained uncharacterized so far. Here, we have developed the first cell-based PD-1/PD-L1 blockade reporter assay to screen NPs libraries. In this study, 6000 microbial extracts of maximum biosynthetic diversity were screened. A secondary metabolite called alpha-cyclopiazonic acid (α-CPA) of a bioactive fungal extract was confirmed as a new PD-1/PD-L1 inhibitor with low micromolar range in the cellular assay and in an additional cell-free competitive assay. Thermal denaturation experiments with PD-1 confirmed that the mechanism of inhibition is based on its stabilization upon binding to α-CPA. The identification of α-CPA as a novel PD-1 stabilizer proves the unprecedented resolution of this methodology at capturing specific PD-1/PD-L1 PPI inhibitors from chemically diverse NP libraries.
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Affiliation(s)
- Elisabeth Domingo-Contreras
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - José R Tormo
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Victor Gonzalez-Menendez
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Thomas A Mackenzie
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Jesús Martín-Serrano
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa Str 2, 30-387 Krakow, Poland
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa Str 2, 30-387 Krakow, Poland
| | - Fernando Reyes
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Rosario Fernández-Godino
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain
| | - Maria C Ramos
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain.
| | - Francisco Castillo
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Granada, Spain.
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3
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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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4
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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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5
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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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6
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Zhang H, Zhou S, Plewka J, Wu C, Zhu M, Yu Q, Musielak B, Wang X, Awadasseid A, Magiera-Mularz K, Wu Y, Zhang W. Design, Synthesis, and Antitumor Activity Evaluation of 2-Arylmethoxy-4-(2,2'-dihalogen-substituted biphenyl-3-ylmethoxy) Benzylamine Derivatives as Potent PD-1/PD-L1 Inhibitors. J Med Chem 2023; 66:10579-10603. [PMID: 37496104 DOI: 10.1021/acs.jmedchem.3c00731] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Novel 2-arylmethoxy-4-(2,2'-dihalogen-substituted biphenyl-3-ylmethoxy) benzylamine derivatives were designed, synthesized, and evaluated in vitro and in vivo against cancers as PD-1/PD-L1 inhibitors. Through the computer-aided structural optimization and the homogeneous time-resolved fluorescence (HTRF) assay, compound A56 was found to most strongly block the PD-1/PD-L1 interaction with an IC50 value of 2.4 ± 0.8 nM and showed the most potent activity. 1H NMR titration results indicated that A56 can tightly bind to the PD-L1 protein with KD < 1 μM. The X-ray diffraction data for the cocrystal structure of the A56/PD-L1 complex (3.5 Å) deciphered a novel binding mode in detail, which can account for its most potent inhibitory activity. Cell-based assays further demonstrated the strong ability of A56 as an hPD-1/hPD-L1 blocker. Especially in an hPD-L1 MC38 humanized mouse model, A56 significantly inhibited tumor growth without obvious toxicity, with a TGI rate of 55.20% (50 mg/kg, i.g.). In conclusion, A56 is a promising clinical candidate worthy of further development.
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Affiliation(s)
- Hua Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shijia Zhou
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jacek Plewka
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Caiyun Wu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Mengyu Zhu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qimeng Yu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Xiao Wang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Annoor Awadasseid
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Katarzyna Magiera-Mularz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
- Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
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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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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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12
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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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13
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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: 25] [Impact Index Per Article: 8.3] [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] [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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14
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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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15
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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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16
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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: 37] [Impact Index Per Article: 9.3] [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: 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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17
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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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18
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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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19
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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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20
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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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21
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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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22
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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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23
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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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24
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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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