1
|
Ren F, Aliper A, Chen J, Zhao H, Rao S, Kuppe C, Ozerov IV, Zhang M, Witte K, Kruse C, Aladinskiy V, Ivanenkov Y, Polykovskiy D, Fu Y, Babin E, Qiao J, Liang X, Mou Z, Wang H, Pun FW, Ayuso PT, Veviorskiy A, Song D, Liu S, Zhang B, Naumov V, Ding X, Kukharenko A, Izumchenko E, Zhavoronkov A. A small-molecule TNIK inhibitor targets fibrosis in preclinical and clinical models. Nat Biotechnol 2024:10.1038/s41587-024-02143-0. [PMID: 38459338 DOI: 10.1038/s41587-024-02143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/16/2024] [Indexed: 03/10/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an aggressive interstitial lung disease with a high mortality rate. Putative drug targets in IPF have failed to translate into effective therapies at the clinical level. We identify TRAF2- and NCK-interacting kinase (TNIK) as an anti-fibrotic target using a predictive artificial intelligence (AI) approach. Using AI-driven methodology, we generated INS018_055, a small-molecule TNIK inhibitor, which exhibits desirable drug-like properties and anti-fibrotic activity across different organs in vivo through oral, inhaled or topical administration. INS018_055 possesses anti-inflammatory effects in addition to its anti-fibrotic profile, validated in multiple in vivo studies. Its safety and tolerability as well as pharmacokinetics were validated in a randomized, double-blinded, placebo-controlled phase I clinical trial (NCT05154240) involving 78 healthy participants. A separate phase I trial in China, CTR20221542, also demonstrated comparable safety and pharmacokinetic profiles. This work was completed in roughly 18 months from target discovery to preclinical candidate nomination and demonstrates the capabilities of our generative AI-driven drug-discovery pipeline.
Collapse
Affiliation(s)
- Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai, China
- Insilico Medicine AI Limited, Abu Dhabi, UAE
| | - Alex Aliper
- Insilico Medicine AI Limited, Abu Dhabi, UAE
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Jian Chen
- Department of Clinical Pharmacology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Heng Zhao
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Sujata Rao
- Insilico Medicine US Inc., New York, NY, USA
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Department of Nephrology, University Clinic RWTH Aachen, Aachen, Germany
| | - Ivan V Ozerov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Klaus Witte
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Chris Kruse
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Yan Ivanenkov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Yanyun Fu
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | | | - Junwen Qiao
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Xing Liang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Zhenzhen Mou
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Hui Wang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Frank W Pun
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Pedro Torres Ayuso
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, PA, USA
| | | | - Dandan Song
- Department of Clinical Pharmacology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Sang Liu
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Bei Zhang
- Insilico Medicine Shanghai Ltd., Shanghai, China
| | - Vladimir Naumov
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Xiaoqiang Ding
- Division of Nephrology, Zhongshan Hospital Shanghai Medical College, Fudan University, Shanghai, China
| | - Andrey Kukharenko
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Evgeny Izumchenko
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Alex Zhavoronkov
- Insilico Medicine AI Limited, Abu Dhabi, UAE.
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong SAR, China.
- Insilico Medicine US Inc., New York, NY, USA.
- Insilico Medicine Canada Inc, Montreal, Quebec, Canada.
| |
Collapse
|
2
|
Li J, Pan C, Tang C, Tan W, Zhang W, Guan J. miR-184 targets TP63 to block idiopathic pulmonary fibrosis by inhibiting proliferation and epithelial-mesenchymal transition of airway epithelial cells. J Transl Med 2021; 101:142-154. [PMID: 32989231 PMCID: PMC7815506 DOI: 10.1038/s41374-020-00487-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 08/23/2020] [Accepted: 08/26/2020] [Indexed: 11/09/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) of epithelium and airway epithelial cell proliferation disorder are key events in idiopathic pulmonary fibrosis (IPF) pathogenesis. During EMT, epithelial cell adhesion molecules (EpCAM, such as E-cadherin) are downregulated, cytokeratin cytoskeletal transforms into vimentin-based cytoskeleton, and the epithelial cells acquire mesenchymal morphology. In the present study, we show abnormal upregulation of tumor protein p63 (TP63) and downregulation of miR-184 in IPF. Transforming growth factor beta 1 (TGF-β1) stimulation of BEAS-2B and A549 cell lines significantly increased the protein levels of Tp63, alpha-smooth muscle actin (α-SMA), and vimentin, but decreased EpCAM protein levels, and promoted viability of both BEAS-2B and A549 cell lines. TP63 knockdown in BEAS-2B and A549 cell lines significantly attenuated above-described TGF-β1-induced fibrotic changes. miR-184 targeted TP63 3'-UTR to inhibit Tp63 expression. miR-184 overexpression within BEAS-2B and A549 cell lines also attenuated TGF-β1-induced fibrotic changes. miR-184 overexpression attenuated bleomycin-induced pulmonary fibrosis in mice. Moreover, TP63 overexpression aggravated TGF-β1-stimulated fibrotic alterations within BEAS-2B and A549 cells and significantly reversed the effects of miR-184 overexpression, indicating miR-184 relieves TGF-β1-stimulated fibrotic alterations within BEAS-2B and A549 cells by targeting TP63, while TP63 overexpression reversed miR-184 cellular functions. In conclusion, the miR-184/TP63 axis modulates the TGF-β1-induced fibrotic alterations in epithelial cell lines and bleomycin-induced pulmonary fibrosis in mice. Therefore, these results confirm that the miR-184/TP63 axis is involved in IPF progression.
Collapse
Affiliation(s)
- Jianmin Li
- Department of Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, PR China
| | - Chanyuan Pan
- Department of Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, PR China
| | - Chao Tang
- Department of Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, PR China
| | - Wenwen Tan
- Department of Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, PR China
| | - Weiwei Zhang
- Department of Traditional Chinese Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan, PR China
| | - Jing Guan
- Department of Science and Education, The First Hospital of Changsha, Changsha, 410008, Hunan, PR China.
| |
Collapse
|
3
|
Niu R, Liu Y, Zhang Y, Zhang Y, Wang H, Wang Y, Wang W, Li X. iTRAQ-Based Proteomics Reveals Novel Biomarkers for Idiopathic Pulmonary Fibrosis. PLoS One 2017; 12:e0170741. [PMID: 28122020 PMCID: PMC5266322 DOI: 10.1371/journal.pone.0170741] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 01/10/2017] [Indexed: 12/31/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a gradual lung disease with a survival of less than 5 years post-diagnosis for most patients. Poor molecular description of IPF has led to unsatisfactory interpretation of the pathogenesis of this disease, resulting in the lack of successful treatments. The objective of this study was to discover novel noninvasive biomarkers for the diagnosis of IPF. We employed a coupled isobaric tag for relative and absolute quantitation (iTRAQ)-liquid chromatography–tandem mass spectrometry (LC–MS/MS) approach to examine protein expression in patients with IPF. A total of 97 differentially expressed proteins (38 upregulated proteins and 59 downregulated proteins) were identified in the serum of IPF patients. Using String software, a regulatory network containing 87 nodes and 244 edges was built, and the functional enrichment showed that differentially expressed proteins were predominantly involved in protein activation cascade, regulation of response to wounding and extracellular components. A set of three most significantly upregulated proteins (HBB, CRP and SERPINA1) and four most significantly downregulated proteins (APOA2, AHSG, KNG1 and AMBP) were selected for validation in an independent cohort of IPF and other lung diseases using ELISA test. The results confirmed the iTRAQ profiling results and AHSG, AMBP, CRP and KNG1 were found as specific IPF biomarkers. ROC analysis indicated the diagnosis potential of the validated biomarkers. The findings of this study will contribute in understanding the pathogenesis of IPF and facilitate the development of therapeutic targets.
Collapse
Affiliation(s)
- Rui Niu
- Department of Respiratory Medicine, Second Hospital of Shandong University, Shandong, China
| | - Ying Liu
- Operating Room, Tianjin Chest Hospital, Tianjin, China
| | - Ying Zhang
- Department of Respiratory Medicine, Second Hospital of Shandong University, Shandong, China
| | - Yuan Zhang
- Department of Evidence-based Medicine, Second Hospital of Shandong University, Shandong, China
| | - Hui Wang
- Department of Respiratory Medicine, Second Hospital of Shandong University, Shandong, China
| | - Yongbin Wang
- Department of Respiratory Medicine, Second Hospital of Shandong University, Shandong, China
| | - Wei Wang
- Department of Respiratory Medicine, Second Hospital of Shandong University, Shandong, China
- * E-mail: (WW); (XL)
| | - Xiaohui Li
- Department of Nursing, Second Hospital of Shandong University, Shandong, China
- * E-mail: (WW); (XL)
| |
Collapse
|
4
|
CD4(+)CD25(hi)Foxp3(+) Cells Exacerbate Bleomycin-Induced Pulmonary Fibrosis. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:2008-2020. [PMID: 27317904 DOI: 10.1016/j.ajpath.2016.03.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/16/2016] [Accepted: 03/23/2016] [Indexed: 01/20/2023]
Abstract
Idiopathic pulmonary fibrosis is a fatal lung disease with a median survival of 2 to 5 years. A decade of studies has downplayed inflammation contributing to its pathogenesis. However, these studies preceded the discovery of regulatory T cells (Tregs) and all of their functions. On the basis of human studies demonstrating Tregs can decrease graft-versus-host disease and vasculitides, there is consideration of their use to treat idiopathic pulmonary fibrosis. We hypothesized that Treg therapy would attenuate the fibroplasia involved in a preclinical murine model of pulmonary fibrosis. IL-2 complex was used in vivo to expand CD4(+)CD25(hi)Foxp3(+) cells in the lung during intratracheal bleomycin challenge; however, this unexpectedly led to an increase in lung fibrosis. More important, this increase in fibrosis was a lymphocyte-dependent process. We corroborated these results using a CD4(+)CD25(hi)Foxp3(+) cellular-based therapy. Mechanistically, we demonstrated that CD4(+)CD25(hi)Foxp3(+) cells undergo alterations during bleomycin challenge and the IL-2 complex had no effect on profibrotic (eg, transforming growth factor-β) or type 17 immune response cytokines; however, there was a marked down-regulation of the type 1 and augmentation of the type 2 immune response cytokines from the lungs. Collectively, our animal studies show that a specific lung injury can induce Treg alterations, which can augment pulmonary fibrosis.
Collapse
|
5
|
Kim HJ, Tashkin DP, Gjertson DW, Brown MS, Kleerup E, Chong S, Belperio JA, Roth MD, Abtin F, Elashoff R, Tseng CH, Khanna D, Goldin JG. Transitions to different patterns of interstitial lung disease in scleroderma with and without treatment. Ann Rheum Dis 2016; 75:1367-71. [PMID: 26757749 DOI: 10.1136/annrheumdis-2015-208929] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/11/2015] [Indexed: 11/04/2022]
Abstract
OBJECTIVES The aim is to investigate whether the 12-month quantitative changes in high-resolution CT (HRCT) measures of interstitial lung disease (ILD) are different, and to understand how they change, in patients with scleroderma-related ILD who receive drug therapy versus placebo. METHODS HRCT images were acquired at baseline and at 12 months in 83 participants in Scleroderma Lung Study I, a clinical trial comparing treatment with oral cyclophosphamide versus placebo. A computer-aided model was used to quantify the extent of fibrotic reticulation, ground glass and honeycomb patterns and quantitative ILD (QILD: sum of these patterns) in the whole lung and the lung zone (upper, middle or lower) of maximal disease involvement. RESULTS Mean QILD score decreased by 3.9% in the cyclophosphamide group while increasing by 4.2% in the placebo group in the most severe zone (p=0.01) and decreased by 3.2% in the cyclophosphamide group while increasing by 2.2% in the placebo group in the whole lung (p=0.03). Transitional probabilities demonstrated greater changes from a fibrotic to either a ground glass or normal pattern in the cyclophosphamide group and the reverse in the placebo group. CONCLUSIONS Changes in quantitative HRCT measures of ILD provide a sensitive indication of disease progression and response to treatment. TRIAL REGISTRATION NUMBER NCT00004563; Post-results.
Collapse
Affiliation(s)
- Hyun J Kim
- Department of Radiological Science, Center for Computer Vision Imaging Biomarker, David Geffen School of Medicine at UCLA, Los Angeles, California, USA Department of Biostatistics, Fielding School of Public Health at UCLA, Los Angeles, California, USA
| | - Donald P Tashkin
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - David W Gjertson
- Department of Radiological Science, Center for Computer Vision Imaging Biomarker, David Geffen School of Medicine at UCLA, Los Angeles, California, USA Department of Biostatistics, Fielding School of Public Health at UCLA, Los Angeles, California, USA
| | - Matthew S Brown
- Department of Radiological Science, Center for Computer Vision Imaging Biomarker, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Eric Kleerup
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Semin Chong
- Department of Radiology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - John A Belperio
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Michael D Roth
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Fereidoun Abtin
- Department of Radiological Science, Center for Computer Vision Imaging Biomarker, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Robert Elashoff
- Department of Biostatistics, Fielding School of Public Health at UCLA, Los Angeles, California, USA Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Chi-Hong Tseng
- Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Dinesh Khanna
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan G Goldin
- Department of Radiological Science, Center for Computer Vision Imaging Biomarker, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| |
Collapse
|
6
|
Delaveri A, Rapti A, Poulou M, Fylaktou E, Tsipi M, Roussos C, Makrythanasis P, Kanavakis E, Tzetis M. BTNL2 gene SNPs as a contributing factor to sarcoidosis pathogenesis in a cohort of Greek patients. Meta Gene 2014; 2:619-30. [PMID: 25606445 PMCID: PMC4287805 DOI: 10.1016/j.mgene.2014.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 07/08/2014] [Accepted: 07/11/2014] [Indexed: 12/13/2022] Open
Abstract
Sarcoidosis is a multisystemic granulomatous disease of unknown etiology that primarily affects adults between the ages of 20 and 40 years old. It is characterized by the activation of Th1 lymphocytes resulting in the production of inflammatory cytokines and the formation of noncaseating epithelioid cell granulomas in affected tissues. The lungs and lymphatic system are the ones most frequently affected. The disease usually presents spontaneous remission in the first two years and, in a few patients, the disease progresses to pulmonary fibrosis or other fatal complications depending on the affected organ. The pathogenesis of sarcoidosis is still not clearly defined, and is considered an interaction between the environment and risk alleles in many genes. The present case control study consisted of 146 Greek patients with sarcoidosis and 90 healthy volunteers from the same ethnic group. The coding and neighboring intronic regions of the BTNL2 gene were sequenced and risk alleles were compared amongst the two groups. Thirty-seven different variants were detected from which 12 were synonymous substitutions and 25 non-synonymous. With the help of in silico tools (SIFT, PolyPhen, PROVEAN, PMut and EX_SKIP), 13 variants were classified as possible pathological risk variants including 4 novel ones. The most common risk variants contributing to phenotypic modulation of sarcoidosis were p.S360G and p.S334L, with the latter contributing to a more severe disease stage with extra-pulmonary manifestations such as skin granulomas and relapses being more common. Thirteen pathological risk variants were discovered in BTNL2 gene in sarcoidosis patients. The common risk variant p.S360G was found in cases (37.67%) and controls (30%). The 2nd most common variant p.S334L was found in cases (16.43%) and controls (12.22%). Six novel variants were detected with 4 deemed pathological. Coinheritance of common and novel variants affected the final clinical phenotype.
Collapse
Affiliation(s)
- Aikaterini Delaveri
- Department of Medical Genetics, Medical School, University of Athens, Greece
| | - Aggeliki Rapti
- 2nd Department of Respiratory Medicine, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Myrto Poulou
- Department of Medical Genetics, Medical School, University of Athens, Greece
| | - Eirini Fylaktou
- Department of Medical Genetics, Medical School, University of Athens, Greece
| | - Maria Tsipi
- Department of Medical Genetics, Medical School, University of Athens, Greece
| | - Charis Roussos
- 2nd Department of Respiratory Medicine, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Periklis Makrythanasis
- Department of Medical Genetics, Medical School, University of Athens, Greece ; Department of Genetic Medicine and Development, University of Geneva, Switzerland
| | - Emmanuel Kanavakis
- Department of Medical Genetics, Medical School, University of Athens, Greece ; Research Institute for the Study of Genetic and Malignant Disorders in Childhood, "Aghia Sophia, Children's Hospital," Athens, Greece
| | - Maria Tzetis
- Department of Medical Genetics, Medical School, University of Athens, Greece
| |
Collapse
|