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Palazzotti D, Fiorelli M, Sabatini S, Massari S, Barreca ML, Astolfi A. Q-raKtion: A Semiautomated KNIME Workflow for Bioactivity Data Points Curation. J Chem Inf Model 2022; 62:6309-6315. [PMID: 36442071 PMCID: PMC9795488 DOI: 10.1021/acs.jcim.2c01199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recent increase of bioactivity data freely available to the scientific community and stored as activity data points in chemogenomic repositories provides a huge amount of ready-to-use information to support the development of predictive models. However, the benefits provided by the availability of such a vast amount of accessible information are strongly counteracted by the lack of uniformity and consistency of data from multiple sources, requiring a process of integration and harmonization. While different automated pipelines for processing and assessing chemical data have emerged in the last years, the curation of bioactivity data points is a less investigated topic, with useful concepts provided but no tangible tools available. In this context, the present work represents a first step toward the filling of this gap, by providing a tool to meet the needs of end-user in building proprietary high-quality data sets for further studies. Specifically, we herein describe Q-raKtion, a systematic, semiautomated, flexible, and, above all, customizable KNIME workflow that effectively aggregates information on biological activities of compounds retrieved by two of the most comprehensive and widely used repositories, PubChem and ChEMBL.
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2
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Astolfi A, Milano F, Palazzotti D, Brea J, Pismataro MC, Morlando M, Tabarrini O, Loza MI, Massari S, Martelli MP, Barreca ML. From Serendipity to Rational Identification of the 5,6,7,8-Tetrahydrobenzo[4,5]thieno[2,3- d]pyrimidin-4(3 H)-one Core as a New Chemotype of AKT1 Inhibitors for Acute Myeloid Leukemia. Pharmaceutics 2022; 14:2295. [PMID: 36365115 PMCID: PMC9698716 DOI: 10.3390/pharmaceutics14112295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 07/30/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematopoietic malignancy whose prognosis is globally poor. In more than 60% of AML patients, the PI3K/AKTs/mTOR signaling pathway is aberrantly activated because of oncogenic driver alterations and further enhanced by chemotherapy as a mechanism of drug resistance. Against this backdrop, very recently we have started a multidisciplinary research project focused on AKT1 as a pharmacological target to identify novel anti-AML agents. Indeed, the serendipitous finding of the in-house compound T187 as an AKT1 inhibitor has paved the way to the rational identification of new active small molecules, among which T126 has emerged as the most interesting compound with IC50 = 1.99 ± 0.11 μM, ligand efficiency of 0.35, and a clear effect at low micromolar concentrations on growth inhibition and induction of apoptosis in AML cells. The collected results together with preliminary SAR data strongly indicate that the 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidin-4(3H)-one derivative T126 is worthy of future biological experiments and medicinal chemistry efforts aimed at developing a novel chemical class of AKT1 inhibitors as anti-AML agents.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, “Department of Excellence 2018–2022”, University of Perugia, 06123 Perugia, Italy
| | - Francesca Milano
- Hematology and Clinical Immunology, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Deborah Palazzotti
- Department of Pharmaceutical Sciences, “Department of Excellence 2018–2022”, University of Perugia, 06123 Perugia, Italy
| | - Jose Brea
- CIMUS Research Center, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Maria Chiara Pismataro
- Department of Pharmaceutical Sciences, “Department of Excellence 2018–2022”, University of Perugia, 06123 Perugia, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, “Department of Excellence 2018–2022”, University of Perugia, 06123 Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, “Department of Excellence 2018–2022”, University of Perugia, 06123 Perugia, Italy
| | - Maria Isabel Loza
- CIMUS Research Center, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Serena Massari
- Department of Pharmaceutical Sciences, “Department of Excellence 2018–2022”, University of Perugia, 06123 Perugia, Italy
| | - Maria Paola Martelli
- Hematology and Clinical Immunology, Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, “Department of Excellence 2018–2022”, University of Perugia, 06123 Perugia, Italy
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Vo NB, Ngo QA. Synthesis, Anti‐inflammatory and Cytotoxic Activity of Novel Pyrazolo[4,3‐
c
][2,1]benzothiazine 4,4‐dioxide Derivatives. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ngoc Binh Vo
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Quoc Anh Ngo
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
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4
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de Klerk DJ, de Keijzer MJ, Dias LM, Heemskerk J, de Haan LR, Kleijn TG, Franchi LP, Heger M. Strategies for Improving Photodynamic Therapy Through Pharmacological Modulation of the Immediate Early Stress Response. Methods Mol Biol 2022; 2451:405-480. [PMID: 35505025 DOI: 10.1007/978-1-0716-2099-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Photodynamic therapy (PDT) is a minimally to noninvasive treatment modality that has emerged as a promising alternative to conventional cancer treatments. PDT induces hyperoxidative stress and disrupts cellular homeostasis in photosensitized cancer cells, resulting in cell death and ultimately removal of the tumor. However, various survival pathways can be activated in sublethally afflicted cancer cells following PDT. The acute stress response is one of the known survival pathways in PDT, which is activated by reactive oxygen species and signals via ASK-1 (directly) or via TNFR (indirectly). The acute stress response can activate various other survival pathways that may entail antioxidant, pro-inflammatory, angiogenic, and proteotoxic stress responses that culminate in the cancer cell's ability to cope with redox stress and oxidative damage. This review provides an overview of the immediate early stress response in the context of PDT, mechanisms of activation by PDT, and molecular intervention strategies aimed at inhibiting survival signaling and improving PDT outcome.
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Affiliation(s)
- Daniel J de Klerk
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Mark J de Keijzer
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Lionel M Dias
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Faculdade de Ciências da Saúde (FCS-UBI), Universidade da Beira Interior, Covilhã, Portugal
| | - Jordi Heemskerk
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
| | - Lianne R de Haan
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Tony G Kleijn
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Leonardo P Franchi
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas (ICB) 2, Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
- Faculty of Philosophy, Department of Chemistry, Center of Nanotechnology and Tissue Engineering-Photobiology and Photomedicine Research Group, Sciences, and Letters of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Michal Heger
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China.
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands.
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
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5
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Madkour MM, Anbar HS, El-Gamal MI. Current status and future prospects of p38α/MAPK14 kinase and its inhibitors. Eur J Med Chem 2021; 213:113216. [PMID: 33524689 DOI: 10.1016/j.ejmech.2021.113216] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 12/26/2022]
Abstract
P38α (which is also named MAPK14) plays a pivotal role in initiating different disease states such as inflammatory disorders, neurodegenerative diseases, cardiovascular cases, and cancer. Inhibitors of p38α can be utilized for treatment of these diseases. In this article, we reviewed the structural and biological characteristics of p38α, its relationship to the fore-mentioned disease states, as well as the recently reported inhibitors and classified them according to their chemical structures. We focused on the articles published in the literature during the last decade (2011-2020).
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Affiliation(s)
- Moustafa M Madkour
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hanan S Anbar
- Department of Clinical Pharmacy and Pharmacotherapeutics, Dubai Pharmacy College for Girls, Dubai, 19099, United Arab Emirates
| | - Mohammed I El-Gamal
- College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura, 35516, Egypt.
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Ahmad Saddique F, Ahmad M, Kanwal A, Aslam S, Fawad Zahoor A. Recent trends toward the synthesis of fused-benzothiazines and their derivatives. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1830420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Afshan Kanwal
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University, Faisalabad, Pakistan
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7
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Astolfi A, Kudolo M, Brea J, Manni G, Manfroni G, Palazzotti D, Sabatini S, Cecchetti F, Felicetti T, Cannalire R, Massari S, Tabarrini O, Loza MI, Fallarino F, Cecchetti V, Laufer SA, Barreca ML. Discovery of potent p38α MAPK inhibitors through a funnel like workflow combining in silico screening and in vitro validation. Eur J Med Chem 2019; 182:111624. [PMID: 31445234 DOI: 10.1016/j.ejmech.2019.111624] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 01/31/2023]
Abstract
This work describes the rational discovery of novel chemotypes of p38α MAPK inhibitors using a funnel approach consisting of several computer-aided drug discovery methods and biological experiments. Among the identified hits, four compounds belonging to different chemical families showed IC50 values lower than 10 μM. In particular, the 1,4-benzodioxane derivative 5 turned out to be a potent and efficient p38α MAPK inhibitor having IC50 = 0.07 μM, and LEexp and LipE values of 0.38 and 4.8, respectively; noteworthy, the compound had also a promising kinase selectivity profile and the capability to suppress p38α MAPK effects in human immune cells. Overall, the collected findings highlight that the applied strategy has been successful in generating chemical novelty in the inhibitor kinase field, providing suitable chemical candidates for further inhibitor optimization.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Mark Kudolo
- Department of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Jose Brea
- CIMUS Research Center, University of Santiago de Compostela, Avda de Barcelona s/n, Planta 3, Despacho1, 15782, Santiago de Compostela, Spain
| | - Giorgia Manni
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, 06100, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Deborah Palazzotti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Federica Cecchetti
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, 06100, Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Rolando Cannalire
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Maria Isabel Loza
- CIMUS Research Center, University of Santiago de Compostela, Avda de Barcelona s/n, Planta 3, Despacho1, 15782, Santiago de Compostela, Spain
| | - Francesca Fallarino
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, 06100, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Stefan A Laufer
- Department of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
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8
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Bartolini D, Bührmann M, Barreca ML, Manfroni G, Cecchetti V, Rauh D, Galli F. Co-crystal structure determination and cellular evaluation of 1,4-dihydropyrazolo[4,3-c] [1,2] benzothiazine 5,5-dioxide p38α MAPK inhibitors. Biochem Biophys Res Commun 2019; 511:579-586. [DOI: 10.1016/j.bbrc.2019.02.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 12/17/2022]
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9
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Abrahams A, Mouchet N, Gouault N, Lohézic Le Dévéhat F, Le Roch M, Rouaud I, Gilot D, Galibert MD. Integrating targeted gene expression and a skin model system to identify functional inhibitors of the UV activated p38 MAP kinase. Photochem Photobiol Sci 2018; 15:1468-1475. [PMID: 27748490 DOI: 10.1039/c6pp00283h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The stress-activated p38α MAP Kinase is an integral and critical component of the UV-induced inflammatory response. Despite the advances in recent years in the development of p38 kinase inhibitors, validation of these compounds in the diseased models remains limited. Based on the pharmacological profile of p38α inhibitor lead compound, SB203580, we synthesized a series of pyrrole-derivatives. Using UV-irradiated human skin punch-biopsies and cell cultures, we identified and validated the inhibitory activity of the derivatives by quantitatively measuring their effect on the expression of p38α target genes using real-time PCR. This approach not only identified pyrrole-2 as a unique derivative of this series that specifically inhibited the UV-activated p38α kinase, but also documented the skin permeation, bioavailability and reversible properties of this derivative in a 3D structure. The successful skin permeation of pyrrole-2 and its impact on AREG, COX-2 and MMP-9 gene expression demonstrates its potential use in modulating inflammatory processes in the skin. This study underscored the importance of using adapted biological models to identify accurate bioactive compounds.
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Affiliation(s)
- Amaal Abrahams
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France and University of Cape Town, Department of Human Biology, Cape Town, South Africa
| | - Nicolas Mouchet
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France
| | - Nicolas Gouault
- University of Rennes1, France and CNRS UMR6226, Sciences Chimiques de Rennes, France
| | | | - Myriam Le Roch
- University of Rennes1, France and CNRS UMR6226, Sciences Chimiques de Rennes, France
| | - Isabelle Rouaud
- University of Rennes1, France and CNRS UMR6226, Sciences Chimiques de Rennes, France
| | - David Gilot
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France
| | - Marie-Dominique Galibert
- CNRS UMR6290, Institut de Génétique et Développement de Rennes, France. and University of Rennes1, France and CHU-Pontchaillou, Rennes, France
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Etsè KS, Dassonneville B, Zaragoza G, Demonceau A. One-pot, Pd/Cu-catalysed synthesis of alkynyl-substituted 3-ylidene-dihydrobenzo[d]isothiazole 1,1-dioxides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.01.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Xiang J, Zhang Z, Fu R, Ternansky RJ, Gladstone PL, Allan AL, Donate F, Parry G, Juarez J, Mazar AP, Bai X. The discovery of kinase inhibitors by a combination of diversity-oriented synthesis and selective screening. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00351f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An efficient strategy for the discovery of kinase inhibitors by a combination of diversity-oriented synthesis and selective screening was presented.
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Affiliation(s)
- Jinbao Xiang
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University
- The School of Pharmaceutical Sciences and The College of Chemistry
- Jilin University
- Changchun
- PR China
| | - Zhuoqi Zhang
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University
- The School of Pharmaceutical Sciences and The College of Chemistry
- Jilin University
- Changchun
- PR China
| | - Renzhong Fu
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University
- The School of Pharmaceutical Sciences and The College of Chemistry
- Jilin University
- Changchun
- PR China
| | | | | | | | | | | | | | | | - Xu Bai
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University
- The School of Pharmaceutical Sciences and The College of Chemistry
- Jilin University
- Changchun
- PR China
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