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A High-Throughput Screen Identifies DYRK1A Inhibitor ID-8 That

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A High-Throughput Screen Identifies DYRK1A Inhibitor ID-8 That BASIC RESEARCH www.jasn.org A High-Throughput Screen Identifies DYRK1A inhibitor ID-8 that Stimulates Human Kidney Tubular Epithelial Cell Proliferation Maria B. Monteiro,1 Susanne Ramm,1,2 Vidya Chandrasekaran,1 Sarah A. Boswell,1 Elijah J. Weber,3 Kevin A. Lidberg,3 Edward J. Kelly,3 and Vishal S. Vaidya1,2,4 1Harvard Program in Therapeutic Science, Harvard Medical School Laboratory of Systems Pharmacology, Boston, Massachusetts; 2Renal Division, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts; 3Department of Pharmaceutics, University of Washington, Seattle, Washington; and 4Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts ABSTRACT Background The death of epithelial cells in the proximal tubules is thought to be the primary cause of AKI, but epithelial cells that survive kidney injury have a remarkable ability to proliferate. Because proximal tubular epithelial cells play a predominant role in kidney regeneration after damage, a potential approach to treat AKI is to discover regenerative therapeutics capable of stimulating proliferation of these cells. Methods We conducted a high-throughput phenotypic screen using 1902 biologically active compounds to identify new molecules that promote proliferation of primary human proximal tubular epithelial cells in vitro. Results The primary screen identified 129 compounds that stimulated tubular epithelial cell proliferation. A secondary screen against these compounds over a range of four doses confirmed that eight resulted in a significant increase in cell number and incorporation of the modified thymidine analog EdU (indicating actively proliferating cells), compared with control conditions. These eight compounds also stimulated tubular cell proliferation in vitro after damage induced by hypoxia, cadmium chloride, cyclosporin A, or polymyxin B. ID-8, an inhibitor of dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A), was the top candidate identified as having a robust proproliferative effect in two-dimensional culture models as well as a microphysiologic, three-dimensional cell culture system. Target engagement and genetic knockdown studies and RNA sequencing confirmed binding of ID-8 to DYRK1A and upregulation of cyclins and other cell cycle regulators, leading to epithelial cell proliferation. Conclusions We have identified a potential first-in-class compound that stimulates human kidney tubular epithelial cell proliferation after acute damage in vitro. J Am Soc Nephrol 29: ccc–ccc, 2018. doi: https://doi.org/10.1681/ASN.2018040392 AKI affects one in five hospitalized patients world- the surviving epithelial cells are responsible for wide and its incidence is currently increasing.1,2 repopulating the tubule through a process of AKI is associated with substantial morbidity and mortality and is recognized as a leading cause of Received April 16, 2018. Accepted September 20, 2018. 3,4 CKD. M.B.M. and S.R. contributed equally to this work. The death of epithelial cells in the proximal tu- Published online ahead of print. Publication date available at 5 bules is thought to be the primary cause of AKI www.jasn.org. as these cells serve as sensors, effectors, and targets Correspondence: Dr. Vishal S. Vaidya, Harvard Institutes of 6 of injury. However, they also have a remarkable Medicine, Room 562, 77 Avenue Louis Pasteur, Boston, MA ability to proliferate and repair tubules after dam- 02115. Email: [email protected] age. During tissue repair after kidney injury, Copyright © 2018 by the American Society of Nephrology J Am Soc Nephrol 29: ccc–ccc, 2018 ISSN : 1046-6673/2912-ccc 1 BASIC RESEARCH www.jasn.org dedifferentiation, proliferation, and redifferentiation.7 Re- Significance Statement cent evidence also shows that the AKI-to-CKD transition is triggered by the incomplete repair of the renal tubules after One potential therapeutic strategy for treating AKI, apart from injury, which may eventually lead to interstitial renal fibrosis.8 supportive care, dialysis, and transplantation, is stimulating the Therefore, we hypothesized that discovery of new therapeu- proliferation of proximal tubular epithelial cells. The authors de- fi scribe use of high-throughput screening to identify ID-8, an inhibitor tics that promote ef cient tubular epithelial cell proliferation of dual-specificity tyrosine-phosphorylation-regulated kinase 1A may allow regression of kidney injury, thereby preventing (DYRK1A), as a first-in-class compound that stimulates kidney tu- AKI and the development of fibrosis, and halting progression bular epithelial cell proliferation after different types of acute to CKD. damage in two- and three-dimensional in vitro models. They also in vitro In vitro phenotypic high-throughput screens (HTS) have provide evidence that ID-8 is able to bind DYRK1A in primary human proximal tubular epithelial cells and stimulate proliferation enabled the discovery of mitogenic small-molecule drugs that after injury by upregulating cell cycle mediators. This early-stage promote proliferation of pancreatic b cells and hepatocytes as discovery study identifies ID-8 as a potential therapeutic candidate potential therapeutics for diabetes and liver disease.9,10 We to stimulate regeneration and repair of epithelial cells in the kidney therefore conducted HTS to identify compounds that can after acute damage. stimulate kidney tubular epithelial cell proliferation. Primary human proximal tubular epithelial cells (HPTECs) have pre- (full medium, see Supplemental Material for a detailed de- in vitro viously been characterized as a relevant model scription). On day 1, full medium was replaced with for studying kidney cell damage and recovery in both two- DMEM/Ham-F12 GlutaMAX medium containing only peni- dimensional (2D) culture models and a three-dimensional (3D) cillin/streptomycin (free medium) to deprive cells of growth 11 in vitro microphysiologic system (MPS). These systems retain signals and increase their sensitivity to proliferative stimuli. many features of the differentiated kidney proximal tubular On day 3, cells were treated in duplicates with 11 mM dilutions epithelium, such as polar architecture; junctional assembly; of the Selleck library or with a panel of controls—full medium expression and activity of transporters; the ability to respond (positive control), free medium (negative control), or 0.1 mM to physiologic stimuli, stress, and toxicity; and the ability to digoxin (toxic control)—using a Seiko Compound Transfer 11,12 perform critical biochemical synthetic activities. We Robot. The 11 mM concentration was on the basis of previous screened primary HPTECs against the Selleck Bioactive Com- studies that performed similar assays.9,14,15 After treatment, pound Library, which contains structurally diverse, medici- live-cell imaging was performed using digital phase contrast to nally active, and cell-permeable FDA-approved compounds, generate a baseline cell count at 0 hour. On day 5, cells were active pharmaceutical and chemotherapeutic agents, and a fixed and permeabilized, and nuclei were stained and counted small number of natural products. Serial rounds of phenotypic at 48 hours (Operetta High-Content Imaging System; fi HTS identi ed ID-8 (1-[4-Methoxyphenyl]-2-methyl-3-nitro- PerkinElmer). 1 fi H-indol-6-ol), an inhibitor of the dual-speci city tyrosine- Raw images were automatically analyzed for nuclei segmen- 13 phosphorylation-regulated kinase 1A (DYRK1A) that induces tation, nuclei/cell counting, and cell area (Columbus 2.4.2 epithelial cell proliferation after injury in 2D and 3D culture Software; PerkinElmer). Proliferation rate or normalized cell systems. Wepropose that this compound may have the potential count (NCC) was calculated on the basis of nuclei counts at day to be developed into a therapeutic for AKI. 5normalizedto(1) live-cell count at day 3 (0 hour), (2) cell area at day 5, and (3) mean of eight free medium–treated control wells on each plate. Cells treated with library com- METHODS pounds or with the panel of controls were assigned as pro- liferating if NCC.1, nonproliferating if NCC=1, or dying if Cell Culture NCC,1. The assay robustness, reproducibility, and variability Primary HPTECs (Biopredic International, Saint-Grégoire, were evaluated by determining the Z-values across multiple fi France) from three different unique donors and NIH/3T3 - replicates using the panel of controls. broblasts (American Type Culture Collection no. CRL-1658) were used. Detailed methods are described in Supplemental Secondary Screen Material. Compounds with an average NCC.1.1 in the primary screen were taken forward to secondary screening. As in the primary Primary Screen screen, primary HPTECs were seeded in full medium. On day A primary screen of 1902 compounds was performed at the 1, full medium was replaced with free medium. On day 3, cells Institute of Chemistry and Cell Biology, Longwood Facility, were treated in triplicate with the selected compounds using a Harvard Medical School. Primary HPTECs were automatically D300 drug dispenser (Hewlett Packard) at 1, 3, 10, and 30 mM seeded in 96-well plates (WellMate; Thermo Scientific) in for 48 hours. After treatment, cells were counted as in the DMEM/Ham-F12 GlutaMAX medium (Thermo Scientific) primary screen. On day 5, 4 hours before fixing the cells, the supplemented with penicillin/streptomycin, hydrocortisone, modified thymidine analog EdU (Click-iT EdU Plus; Invitro- EGF, insulin-transferrin-selenium, and triiodothyronine gen) was added to
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