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Czestkowski W, Krzemiński Ł, Piotrowicz MC, Mazur M, Pluta E, Andryianau G, Koralewski R, Matyszewski K, Olejniczak S, Kowalski M, Lisiecka K, Kozieł R, Piwowar K, Papiernik D, Nowotny M, Napiórkowska-Gromadzka A, Nowak E, Niedziałek D, Wieczorek G, Siwińska A, Rejczak T, Jędrzejczak K, Mulewski K, Olczak J, Zasłona Z, Gołębiowski A, Drzewicka K, Bartoszewicz A. Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1. J Med Chem 2024; 67:3959-3985. [PMID: 38427954 DOI: 10.1021/acs.jmedchem.3c02255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Chitinase-3-like-1 (CHI3L1), also known as YKL-40, is a glycoprotein linked to inflammation, fibrosis, and cancer. This study explored CHI3L1's interactions with various oligosaccharides using microscale thermophoresis (MST) and AlphaScreen (AS). These investigations guided the development of high-throughput screening assays to assess interference of small molecules in binding between CHI3L1 and biotinylated small molecules or heparan sulfate-based probes. Small molecule binders of YKL-40 were identified in our chitotriosidase inhibitors library with MST and confirmed through X-ray crystallography. Based on cocrystal structures of potent hit compounds with CHI3L1, small molecule probes 19 and 20 were designed for an AS assay. Structure-based optimization led to compounds 30 and 31 with nanomolar activities and drug-like properties. Additionally, an orthogonal AS assay using biotinylated heparan sulfate as a probe was developed. The compounds' affinity showed a significant correlation in both assays. These screening tools and compounds offer novel avenues for investigating the role of CHI3L1.
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Affiliation(s)
| | | | | | - Marzena Mazur
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | - Elżbieta Pluta
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | | | | | | | | | - Rafał Kozieł
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Agnieszka Napiórkowska-Gromadzka
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | | | | | - Anna Siwińska
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | - Tomasz Rejczak
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | - Jacek Olczak
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
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2
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Balestri LI, Trivisani CI, Orofino F, Fiorucci D, Truglio GI, D’Agostino I, Poggialini F, Botta L, Docquier JD, Dreassi E. Discovery and Optimization of a Novel Macrocyclic Amidinourea Series Active as Acidic Mammalian Chitinase Inhibitors. ACS Med Chem Lett 2023; 14:417-424. [PMID: 37077400 PMCID: PMC10107916 DOI: 10.1021/acsmedchemlett.2c00472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/14/2023] [Indexed: 04/21/2023] Open
Abstract
Our research group has been involved for a long time in the development of macrocyclic amidinoureas (MCAs) as antifungal agents. The mechanistic investigation drove us to perform an in silico target fishing study, which allowed the identification of chitinases as one of their putative targets, with 1a showing a submicromolar inhibition of Trichoderma viride chitinase. In this work, we investigated the possibility to further inhibit the corresponding human enzymes, acidic mammalian chitinase (AMCase) and chitotriosidase (CHIT1), involved in several chronic inflammatory lung diseases. Thus, we first validated the inhibitory activity of 1a against AMCase and CHIT1 and then designed and synthesized new derivatives aimed at improving the potency and selectivity against AMCase. Among them, compound 3f emerged for its activity profile along with its promising in vitro ADME properties. We also gained a good understanding of the key interactions with the target enzyme through in silico studies.
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Affiliation(s)
| | | | - Francesco Orofino
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Diego Fiorucci
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Giuseppina Ivana Truglio
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Ilaria D’Agostino
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Federica Poggialini
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Lorenzo Botta
- Lead
Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
- Department
of Ecological and Biological Sciences, University
of Tuscia, Largo Università s.n.c., I-01100 Viterbo, Italy
| | - Jean-Denis Docquier
- Dipartimento
di Biotecnologie Mediche, University of
Siena, Viale Bracci 16, I-53100, Siena, Italy
- Laboratoire
de Bactériologie Moléculaire, Centre d’Ingénierie
des Protéines, UR-InBioS, University
of Liège, Allée
du 6 Août, 4000 Liège, Belgium
| | - Elena Dreassi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
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3
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Characterization of Acidic Mammalian Chitinase as a Novel Biomarker for Severe Periodontitis (Stage III/IV): A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074113. [PMID: 35409795 PMCID: PMC8998681 DOI: 10.3390/ijerph19074113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022]
Abstract
Periodontitis is a chronic inflammatory condition characterized by gingival infection, periodontal pocket formation, and alveolar bone loss. Acidic mammalian chitinase (AMCase), an active chitinase enzyme, increased its expression under severe inflammation and related systemic disorders. However, AMCase expression and molecular mechanism in periodontal inflammation, have not been elucidated yet. This study was aimed to characterize AMCase in severe periodontitis patients compare to those in periodontally healthy subjects. In total, 15 periodontally healthy subjects and 15 severe (stage III/IV) periodontitis patients were enrolled with their informed consent. Tissue samples were collected and analyzed using Western blot and enzyme-linked immunosorbent assay (ELISA). AMCase protein expressions in periodontal patients were significantly more increased than those of periodontally healthy individuals. ELISA resulted in median values (first quartile to third quartile) of the periodontally healthy group 0.654 ng/mL (range, 0.644−0.827 ng/mL) and the periodontitis group 0.965 ng/mL (range, 0.886−1.165 ng/mL). AMCase was expressed significantly higher levels in periodontitis patients than in periodontally healthy individuals (p < 0.05). This suggests that AMCase may play a potential role as a biomarker for the screening and early diagnosis of severe periodontitis.
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4
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Mazur M, Włodarczyk J, Świerczyński M, Kordek R, Grzybowski MM, Olczak J, Fichna J. The Anti-Inflammatory Effect of Acidic Mammalian Chitinase Inhibitor OAT-177 in DSS-Induced Mouse Model of Colitis. Int J Mol Sci 2022; 23:ijms23042159. [PMID: 35216274 PMCID: PMC8875595 DOI: 10.3390/ijms23042159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and relapsing gastrointestinal disorders, where a significant proportion of patients are unresponsive or lose response to traditional and currently used therapies. In the current study, we propose a new concept for anti-inflammatory treatment based on a selective acidic mammalian chitinase (AMCase) inhibitor. The functions of chitinases remain unclear, but they have been shown to be implicated in the pathology of various inflammatory disorders regarding the lung (asthma, idiopathic pulmonary fibrosis) and gastrointestinal tract (IBD and colon cancer). The aim of the study is to investigate the impact of AMCase inhibitor (OAT-177) on the dextran sulfate sodium (DSS)-induced models of colitis. In the short-term therapeutic protocol, OAT-177 given intragastrically in a 30 mg/kg dose, twice daily, produced a significant (p < 0.001) anti-inflammatory effect, as shown by the macroscopic score. Additionally, OAT-177 significantly decreased TNF-α mRNA levels and MPO activity compared to DSS-only treated mice. Intraperitoneal administration of OAT-177 at a dose of 50 mg/kg caused statistically relevant reduction of the colon length. In the long-term therapeutic protocol, OAT-177 given intragastrically in a dose of 30 mg/kg, twice daily, significantly improved colon length and body weight compared to DSS-induced colitis. This is the first study proving that AMCase inhibitors may have therapeutic potential in the treatment of IBD.
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Affiliation(s)
- Marzena Mazur
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (M.M.); (J.W.); (M.Ś.)
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (M.M.G.); (J.O.)
| | - Jakub Włodarczyk
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (M.M.); (J.W.); (M.Ś.)
| | - Mikołaj Świerczyński
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (M.M.); (J.W.); (M.Ś.)
| | - Radzisław Kordek
- Department of Pathology, Faculty of Medicine, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland;
| | - Marcin M. Grzybowski
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (M.M.G.); (J.O.)
| | - Jacek Olczak
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland; (M.M.G.); (J.O.)
| | - Jakub Fichna
- Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (M.M.); (J.W.); (M.Ś.)
- Correspondence: ; Tel.: +48-42-272-57-07
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5
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Yang M, Shrestha SK, Soh Y, Heo SM. Effects of aloe-emodin on alveolar bone in Porphyromonas gingivalis-induced periodontitis rat model: a pilot study. J Periodontal Implant Sci 2022; 52:383-393. [DOI: 10.5051/jpis.2104060203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/27/2022] [Accepted: 04/04/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Ming Yang
- Department of Periodontology, School of Dentistry, Jeonbuk National University, Jeonju, South Korea
- Department of Periodontology, School of Dentistry, Beihua University, Jilin, China
| | - Saroj K Shrestha
- Department of Dental Pharmacology, School of Dentistry, Jeonbuk National University, Jeonju, South Korea
| | - Yunjo Soh
- Laboratory of Pharmacology, School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju, South Korea
| | - Seok-Mo Heo
- Department of Periodontology, School of Dentistry, Jeonbuk National University, Jeonju, South Korea
- Research Institute of Clinical Medicine of Jeonbuk National University, Jeonju, South Korea
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6
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Chitinases and Chitinase-Like Proteins as Therapeutic Targets in Inflammatory Diseases, with a Special Focus on Inflammatory Bowel Diseases. Int J Mol Sci 2021; 22:ijms22136966. [PMID: 34203467 PMCID: PMC8268069 DOI: 10.3390/ijms22136966] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 11/17/2022] Open
Abstract
Chitinases belong to the evolutionarily conserved glycosyl hydrolase family 18 (GH18). They catalyze degradation of chitin to N-acetylglucosamine by hydrolysis of the β-(1-4)-glycosidic bonds. Although mammals do not synthesize chitin, they possess two enzymatically active chitinases, i.e., chitotriosidase (CHIT1) and acidic mammalian chitinase (AMCase), as well as several chitinase-like proteins (YKL-40, YKL-39, oviductin, and stabilin-interacting protein). The latter lack enzymatic activity but still display oligosaccharides-binding ability. The physiologic functions of chitinases are still unclear, but they have been shown to be involved in the pathogenesis of various human fibrotic and inflammatory disorders, particularly those of the lung (idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, sarcoidosis, and asthma) and the gastrointestinal tract (inflammatory bowel diseases (IBDs) and colon cancer). In this review, we summarize the current knowledge about chitinases, particularly in IBDs, and demonstrate that chitinases can serve as prognostic biomarkers of disease progression. Moreover, we suggest that the inhibition of chitinase activity may be considered as a novel therapeutic strategy for the treatment of IBDs.
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7
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Koralewski R, Dymek B, Mazur M, Sklepkiewicz P, Olejniczak S, Czestkowski W, Matyszewski K, Andryianau G, Niedziejko P, Kowalski M, Gruza M, Borek B, Jedrzejczak K, Bartoszewicz A, Pluta E, Rymaszewska A, Kania M, Rejczak T, Piasecka S, Mlacki M, Mazurkiewicz M, Piotrowicz M, Salamon M, Zagozdzon A, Napiorkowska-Gromadzka A, Bartlomiejczak A, Mozga W, Dobrzański P, Dzwonek K, Golab J, Nowotny M, Olczak J, Golebiowski A. Discovery of OATD-01, a First-in-Class Chitinase Inhibitor as Potential New Therapeutics for Idiopathic Pulmonary Fibrosis. J Med Chem 2020; 63:15527-15540. [PMID: 33078933 DOI: 10.1021/acs.jmedchem.0c01179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chitotriosidase (CHIT1) and acidic mammalian chitinase (AMCase) are the enzymatically active chitinases that have been implicated in the pathology of chronic lung diseases such as asthma and interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF) and sarcoidosis. The clinical and preclinical data suggest that pharmacological inhibition of CHIT1 might represent a novel therapeutic approach in IPF. Structural modification of an advanced lead molecule 3 led to the identification of compound 9 (OATD-01), a highly active CHIT1 inhibitor with both an excellent PK profile in multiple species and selectivity against a panel of other off-targets. OATD-01 given orally once daily in a range of doses between 30 and 100 mg/kg showed significant antifibrotic efficacy in an animal model of bleomycin-induced pulmonary fibrosis. OATD-01 is the first-in-class CHIT1 inhibitor, currently completed phase 1b of clinical trials, to be a potential treatment for IPF.
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Affiliation(s)
- Robert Koralewski
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Barbara Dymek
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Marzena Mazur
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Sylwia Olejniczak
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | | | - Gleb Andryianau
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Piotr Niedziejko
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Michal Kowalski
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Mariusz Gruza
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Bartłomiej Borek
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Karol Jedrzejczak
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Elżbieta Pluta
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Magdalena Kania
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Tomasz Rejczak
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Sylwia Piasecka
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Michal Mlacki
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Michał Piotrowicz
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Magdalena Salamon
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | | | - Aneta Bartlomiejczak
- Structural Biology Center, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Witold Mozga
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Dobrzański
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Karolina Dzwonek
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Jakub Golab
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland.,Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland
| | - Marcin Nowotny
- Structural Biology Center, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jacek Olczak
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Adam Golebiowski
- OncoArendi Therapeutics SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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