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Li GX, Chen L, Hsiao Y, Mannan R, Zhang Y, Luo J, Petralia F, Cho H, Hosseini N, Leprevost FDV, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Kumar-Sinha C, Chugh S, Le A, Ponce S, Guo S, Zhang C, Schnaubelt M, Al Deen NN, Chen F, Caravan W, Houston A, Hopkins A, Newton CJ, Wang X, Polasky DA, Haynes S, Yu F, Jing X, Chen S, Robles AI, Mesri M, Thiagarajan M, An E, Getz GA, Linehan WM, Hostetter G, Jewell SD, Chan DW, Wang P, Omenn GS, Mehra R, Ricketts CJ, Ding L, Chinnaiyan AM, Cieslik MP, Dhanasekaran SM, Zhang H, Nesvizhskii AI. Comprehensive proteogenomic characterization of rare kidney tumors. Cell Rep Med 2024:101547. [PMID: 38703764 DOI: 10.1016/j.xcrm.2024.101547] [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: 03/20/2023] [Revised: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
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Affiliation(s)
- Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanbyul Cho
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaoming Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Gad A Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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Hsiao Y, Zhang H, Li GX, Deng Y, Yu F, Kahrood HV, Steele JR, Schittenhelm RB, Nesvizhskii AI. Analysis and visualization of quantitative proteomics data using FragPipe-Analyst. bioRxiv 2024:2024.03.05.583643. [PMID: 38496650 PMCID: PMC10942459 DOI: 10.1101/2024.03.05.583643] [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] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.
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Affiliation(s)
- Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haijian Zhang
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yamei Deng
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hossein Valipour Kahrood
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Monash Genomics & Bioinformatics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Joel R. Steele
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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Perera AR, Warrier V, Sundararaman S, Hsiao Y, Ghosh S, Kularatnarajah L, Pitt JJ. Melvin is a conversational voice interface for cancer genomics data. Commun Biol 2024; 7:30. [PMID: 38182884 PMCID: PMC10770357 DOI: 10.1038/s42003-023-05688-z] [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: 07/04/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024] Open
Abstract
Melvin is a multi-modal Amazon Alexa skill that allows users to quickly explore cancer genomics data from TCGA through simple conversations.
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Affiliation(s)
- Akila R Perera
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Vinay Warrier
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shwetha Sundararaman
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yi Hsiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Soumita Ghosh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Jason J Pitt
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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Bedran G, Polasky DA, Hsiao Y, Yu F, da Veiga Leprevost F, Alfaro JA, Cieslik M, Nesvizhskii AI. Unraveling the glycosylated immunopeptidome with HLA-Glyco. Nat Commun 2023; 14:3461. [PMID: 37308510 PMCID: PMC10258777 DOI: 10.1038/s41467-023-39270-2] [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: 11/07/2022] [Accepted: 06/02/2023] [Indexed: 06/14/2023] Open
Abstract
Recent interest in targeted therapies has been sparked by the study of MHC-associated peptides (MAPs) that undergo post-translational modifications (PTMs), particularly glycosylation. In this study, we introduce a fast computational workflow that merges the MSFragger-Glyco search algorithm with a false discovery rate control for glycopeptide analysis from mass spectrometry-based immunopeptidome data. By analyzing eight large-scale publicly available studies, we find that glycosylated MAPs are predominantly presented by MHC class II. Here, we present HLA-Glyco, a comprehensive resource containing over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. This resource provides valuable insights, including high levels of truncated glycans, conserved HLA-binding cores, and differences in glycosylation positional specificity between HLA allele groups. We integrate the workflow within the FragPipe computational platform and provide HLA-Glyco as a free web resource. Overall, our work provides a valuable tool and resource to aid the nascent field of glyco-immunopeptidomics.
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Affiliation(s)
- Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Hsiao
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Javier A Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA.
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Li GX, Hsiao Y, Chen L, Mannan R, Zhang Y, Petralia F, Cho H, Hosseini N, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Leprevost FV, Le A, Ponce S, Schnaubelt M, Deen NNA, Caravan W, Houston A, Kumar-Sinha C, Wang X, Chugh S, Omenn GS, Chan DW, Ricketts C, Mehra R, Chinnaiyan A, Ding L, Cieslik M, Zhang H, Dhanasekaran SM, Nesvizhskii AI. Abstract 3127: Comprehensive proteogenomic characterization of rare kidney tumors. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) represent ~15-20% RCCs cases comprising nearly 20 different disease subtypes and a wide spectrum of clinical behavior from benign to highly aggressive course. Clinically, metastatic non-ccRCC patients, regardless of subtypes with distinct genomic aberrations, are all treated with the same standard of care therapies, underscoring the need for precision therapeutic strategies. Diagnostic challenges also exist as benign and malignant entities often display overlapping histomorphologies that current diagnostic cytokeratin markers cannot resolve. Therefore, identification of more reliable diagnostic and prognostic non-ccRCC biomarkers remains an unmet need in this field.
As part of the Clinical Tumor Analysis Consortium (CPTAC), we performed integrative analysis of multi-omics data including genomic next generation sequencing-based whole exome, whole genome, RNAseq, snRNAseq and mass spectrometry-based proteomics, post translational modifications (glycosylation and phosphorylation) and metabolomic profiles generated by CPTAC. The composition of the kidney tumor cohort (n=151) included 103 ccRCC, 15 oncocytomas, 13 papillary RCC (PRCC), 11 other rare tumors and 8 unclassified RCCs. Our multi-omic analysis revealed both unique and shared molecular features of RCC subtypes. We characterized proteogenomic, PTM and glycoproteome impact of genome instability (GI), a feature that is associated with poor prognosis in both ccRCC and non-ccRCC and affects 10-15% of cases. These analyses identified new prognostic signatures, outlier targetable kinase expression patterns, kinase-substrate relationships and differential protein glycosylation events. Glycoproteome analysis also revealed variation in cell-type specific marker expression among RCC subtypes such as FUT8 (core-fucosyltransferase) associated protein glycosylation in PRCC. Integrative analysis of snRNA-seq data predicted diverse tumor cell-of-origin and stratified RCC subtype specific proteogenomic signatures. Differential expression analysis revealed several novel diagnostic makers including MAPRE3, GPNMB, PIGR, SOSTDC1. These biomarkers were validated by IHC and their addition to existing panels results in improved diagnostic specificity. Metabolic characterization revealed RCC subtype-specific differences and increased oncometabolite SAICAR in oncocytomas that may have functional significance. The valuable proteogenomic data resource we generated contains several rare tumor types that are hard to obtain for proteogenomic characterization at the scale described here, and will certainly aid in future pan-RCC studies.
Citation Format: Ginny Xiaohe Li, Yi Hsiao, Lijun Chen, Rahul Mannan, Yuping Zhang, Francesca Petralia, Hanbyul Cho, Noshad Hosseini, Anna Calinawan, Yize Li, Shankara Anand, Aniket Dagar, Yifat Geffen, Felipe V. Leprevost, Anne Le, Sean Ponce, Michael Schnaubelt, Nataly Naser Al Deen, Wagma Caravan, Andrew Houston, Chandan Kumar-Sinha, Xiaoming Wang, Seema Chugh, Gilbert S. Omenn, Daniel W. Chan, Christopher Ricketts, Rohit Mehra, Arul Chinnaiyan, Li Ding, Marcin Cieslik, Hui Zhang, Saravana M. Dhanasekaran, Alexey I. Nesvizhskii. Comprehensive proteogenomic characterization of rare kidney tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3127.
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Affiliation(s)
| | - Yi Hsiao
- 2University of Michigan, Ann Arbor, MI
| | - Lijun Chen
- 3Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rahul Mannan
- 1University of Michigan Medical School, Ann Arbor, MI
| | | | | | | | | | | | - Yize Li
- 5Washington University of St. Louis, St. Louis, MO
| | | | | | | | | | - Anne Le
- 7Johns Hopkins Medicine, Baltimore, MD
| | - Sean Ponce
- 8Johns Hopkins University, Baltimore, MD
| | | | | | | | | | | | | | | | | | | | | | | | | | - Li Ding
- 5Washington University of St. Louis, St. Louis, MO
| | | | - Hui Zhang
- 3Johns Hopkins University School of Medicine, Baltimore, MD
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Ichikawa-Kaji Y, Ishizawa F, Nishiyama R, Tachikawa H, Uemura N, Moriuchi Y, Umino K, Hsiao Y, Muramatsu H, Suzuki T, Inomata A, Honda K, Moriyasu T. Development of a detector tube for rapid detection of tadalafil in adulterated dietary supplements. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kempson J, Hou X, Sun JH, Wong M, Pawluczyk J, Li J, Krishnananthan S, Simmons EM, Hsiao Y, Li YX, Sun D, Wu DR, Meng W, Ahmad S, Negash L, Brigance R, Turdi H, Hangeland JJ, Lawrence RM, Devasthale P, Robl JA, Mathur A. Synthesis Optimization, Scale-Up, and Catalyst Screening Efforts toward the MGAT2 Clinical Candidate, BMS-963272. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James Kempson
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Xiaoping Hou
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Jung-Hui Sun
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Michael Wong
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Joseph Pawluczyk
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Jianqing Li
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | | | - Eric M. Simmons
- Chemical Development, Bristol-Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical Development, Bristol-Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Yi-Xin Li
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Dawn Sun
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Dauh-Rurng Wu
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Wei Meng
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Saleem Ahmad
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Lidet Negash
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Robert Brigance
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Huji Turdi
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Jon J. Hangeland
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - R. Michael Lawrence
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Pratik Devasthale
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Jeffrey A. Robl
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
| | - Arvind Mathur
- Discovery Chemistry, Bristol-Myers Squibb, Princeton, New Jersey 08540, United States
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Hsiao Y, Gopman DB, Mohanchandra K, Shirazi P, Lynch CS. Effect of interfacial and edge roughness on magnetoelectric control of Co/Ni microdisks on PMN-PT(011). Sci Rep 2022; 12:3919. [PMID: 35273193 PMCID: PMC8913801 DOI: 10.1038/s41598-022-06285-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 10/05/2021] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Uniform magnetic behavior within arrays of magnetoelectric heterostructures is important for the development of reliable strain-mediated microdevices. Multiple mechanisms may contribute to observed nonuniform magnetization reversal including surface roughness, non-uniform strain, and fabrication induced imperfections. Here, Co/Ni microdisks of 7 µm diameter were produced on both [Pb(Mg1/3Nb2/3)O3]1−x–[PbTiO3]x with x = 0.3 nominal composition (PMN-30PT) (011) and Si substrates, and the out-of-plane magnetization reversal was characterized using magneto-optical Kerr effect (MOKE). Coercivity variation across the microdisks within the arrays was observed on both the PMN-30PT and Si specimens with zero electric field applied. Co/Ni microdisks on a PMN-30PT substrate displayed relatively larger coercivity than those on a Si substrate due to the surface roughness effect. Quasistatic electric fields of varying magnitude were applied to the PMN-30PT substrate to assess the dependence of the coercivity on electric field induced strain. Our results indicate that while coercivity decreases with the increase of electric field induced strain, interfacial and edge roughness combine to realize a prohibitively large coercivity to overcome within the Co/Ni microdisks as well as a broad distribution of coercive field across a patterned microdisk array.
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Affiliation(s)
- Y Hsiao
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
| | - D B Gopman
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - K Mohanchandra
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
| | - P Shirazi
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
| | - C S Lynch
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA. .,Bourns College of Engineering, University California, Riverside, CA, USA.
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9
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Hang C, Ramirez A, Chan C, Hsiao Y, DelMonte AJ, Simmons EM. Mechanistic Studies of a Pd-Catalyzed Direct Arylation En Route to Beclabuvir: Dual Role of a Tetramethylammonium Cation and an Unusual Turnover-Limiting Step. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chao Hang
- Chemical Process Development, Bristol Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Antonio Ramirez
- Chemical Process Development, Bristol Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Collin Chan
- Chemical Process Development, Bristol Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical Process Development, Bristol Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Albert J. DelMonte
- Chemical Process Development, Bristol Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Eric M. Simmons
- Chemical Process Development, Bristol Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
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10
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Chen TF, Chang YC, Hsiao Y, Lee KH, Hsiao YC, Lin YH, Tu YCE, Huang HC, Chen CY, Juan HF. DockCoV2: a drug database against SARS-CoV-2. Nucleic Acids Res 2021; 49:D1152-D1159. [PMID: 33035337 PMCID: PMC7778986 DOI: 10.1093/nar/gkaa861] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 01/18/2023] Open
Abstract
The current state of the COVID-19 pandemic is a global health crisis. To fight the novel coronavirus, one of the best-known ways is to block enzymes essential for virus replication. Currently, we know that the SARS-CoV-2 virus encodes about 29 proteins such as spike protein, 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), Papain-like protease (PLpro), and nucleocapsid (N) protein. SARS-CoV-2 uses human angiotensin-converting enzyme 2 (ACE2) for viral entry and transmembrane serine protease family member II (TMPRSS2) for spike protein priming. Thus in order to speed up the discovery of potential drugs, we develop DockCoV2, a drug database for SARS-CoV-2. DockCoV2 focuses on predicting the binding affinity of FDA-approved and Taiwan National Health Insurance (NHI) drugs with the seven proteins mentioned above. This database contains a total of 3,109 drugs. DockCoV2 is easy to use and search against, is well cross-linked to external databases, and provides the state-of-the-art prediction results in one site. Users can download their drug-protein docking data of interest and examine additional drug-related information on DockCoV2. Furthermore, DockCoV2 provides experimental information to help users understand which drugs have already been reported to be effective against MERS or SARS-CoV. DockCoV2 is available at https://covirus.cc/drugs/.
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Affiliation(s)
| | | | - Yi Hsiao
- Taiwan AI Labs, Taipei 10351, Taiwan
| | | | | | | | | | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Chien-Yu Chen
- Taiwan AI Labs, Taipei 10351, Taiwan.,Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Hsueh-Fen Juan
- Taiwan AI Labs, Taipei 10351, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
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11
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Tsukano Y, Shimizu I, Yoshida Y, Hsiao Y, Ikegami R, Hayashi Y, Suda M, Katsuumi G, Nakao M, Minamino T. Obesity associated pro-fibrotic protein augments fibrosis in heart. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Chronic sterile inflammation in visceral fat has causal roles for systemic metabolic disorders in obesity. Inflamed visceral adipose tissue secretes pro-inflammatory adipokines, and this contributes to tissue remodeling under a metabolically stressed condition. Various kinds of white adipokines are broadly studied, however, roles of brown adipose tissue (BAT) derived adipokines (BATokine) remain to be explored. In this project, we tried to characterize pathogenic role of BATokine in obesity related fibrotic disorders, especially focusing on heart failure with preserved ejection fraction (HFpEF). For this purpose, we analyzed two sets of DNA microarray data, and identified an obesity associated pro-fibrotic protein (OAFP) as a possible pathogenic BATokine. Our biobank studies showed OAFP increased in patients with diastolic dysfunction, and E/e' analyzed with cardiac echo increased in direct proportion to circulating OAFP level in humans. We generated dietary obese mice model, and found OAFP increased both in BAT and circulation. We generated a murine systemic or BAT specific OAFP knockout (KO) models, and found that obesity-induced diastolic dysfunction ameliorated in these models. Cardiac fibrosis was also suppressed by genetic depletion of OAFP. We found OAFP increased in circulation in aged humans and mice, and studies in chronologically aged mice showed this molecule increased in BAT with aging. Our results indicate that OAFP is secreted predominantly from BAT, and mediates pathogenic roles by augmenting cardiac fibrosis in dietary obesity or aging. Suppression of OAFP may become a therapy for HFpEF.
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- Y Tsukano
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - I Shimizu
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - Y Yoshida
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - Y Hsiao
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - R Ikegami
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - Y Hayashi
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - M Suda
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - G Katsuumi
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - M Nakao
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - T Minamino
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
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12
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Hsiao Y, Shimizu I, Wakasugi T, Jiao S, Watanabe T, Kashimura T, Yoshida Y, Hanawa H, Ozaki K, Minamino T. Cardiac mitofusin-1 is declined in non-responding patients with idiopathic dilated cardiomyopathy. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background/Introduction
Mitochondria are dynamic regulators of cellular metabolism and homeostasis. The dysfunction of mitochondria has long been considered a major contributor to aging and age-related diseases. The prognosis of severe heart failure is still unacceptably poor and it is urgent to establish new therapies for this critical condition. Some patients with heart failure do not respond to established multidisciplinary treatment and they are classified as “non-responders”. The outcome is especially poor for non-responders, and underlying mechanisms are largely unknown.
Purpose
Studies indicate mitochondrial dysfunction has causal roles for metabolic remodeling in the failing heart, but underlying mechanisms remain to be explored. This study tried to elucidate the role of Mitofusin-1 in a failing heart.
Methods
We examined twenty-two heart failure patients who underwent endomyocardial biopsy of intraventricular septum. Patients were classified as non-responders when their left-ventricular (LV) ejection fraction did not show more than 10% improvement at remote phase after biopsy. Fourteen patients were classified as responders, and eight as non-responders. Electron microscopy, quantitative PCR, and immunofluorescence studies were performed to explore the biological processes or molecules involved in failure to respond. In addition to studies with cardiac tissue specific knockout mice, we also conducted functional in-vitro studies with neonatal rat ventricular myocytes.
Results
Twenty-two patients with IDCM who underwent endomyocardial biopsy were enrolled in this study, including 14 responders and 8 non-responders. Transmission electron microscopy (EM) showed a significant reduction in mitochondrial size in cardiomyocytes of non-responders compared to responders. Quantitative PCR revealed that transcript of mitochondrial fusion protein, Mitofusin-1, was significantly reduced in non-responders. Studies with neonatal rat ventricular myocytes (NRVMs) indicated that the beta-1 adrenergic receptor-mediated signaling pathway negatively regulates Mitofusin-1 expression. Suppression of Mitofusin-1 resulted in a significant reduction in mitochondrial respiration of NRVMs. We generated left ventricular pressure overload model with thoracic aortic constriction (TAC) in cardiac specific Mitofusin-1 knockout model (c-Mfn1 KO). Systolic function was reduced in c-Mfn1 KO mice, and EM study showed an increase in dysfunctional mitochondria in the KO group subjected to TAC.
Conclusions
Mitofusin-1 becomes a biomarker for non-responders with heart failure. In addition, our results suggest that therapies targeting mitochondrial dynamics and homeostasis would become next generation therapy for severe heart failure patients.
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- Y Hsiao
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - I Shimizu
- Niigata University Graduate School of Medical and Dental Sciences, Division of Molecular Aging and Cell Biology, Niigata, Japan
| | - T Wakasugi
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - S Jiao
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - T Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - T Kashimura
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - Y Yoshida
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - H Hanawa
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - K Ozaki
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - T Minamino
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
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13
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Hsiao Y, Shimizu I, Yoshida Y, Ikegami R, Hayashi Y, Suda M, Katsuumi G, Wakasugi T, Nakao M, Minamino T. Circulating pro fibrotic protein promotes fibrosis in liver. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background/Introduction
Non-alcoholic steatohepatitis (NASH), driven by the obesity epidemic, has become the most common form of liver disease. Inflamed visceral adipose tissue secretes pro-inflammatory adipokines that are causal for systemic metabolic disorders. Role of adipokines in NASH, especially those from brown adipose tissues (BATokine) remain unclear.
Purpose
To show the pathogenic role of BATokine in NASH.
Methods
To identify and characterize the pathological roles of pro-fibrotic BATokine, we generated a murine obese NASH model by imposing a high fat diet in C57BL6/NCr mice, and murine systemic or BAT specific knockout (KO) models. We also conducted functional in-vitro studies with differentiated brown adipocytes.
Results
Analyzing two sets of DNA micro array data with bioinformatics, we identified a secreted form pro-fibrotic protein (sPFP) expressed in dysfunctional brown adipose tissues (BAT) in mice. Testing our biobank samples, we found this protein increased in plasma of NASH patients. We generated a murine obese NASH model by imposing a high fat diet in C57BL6/NCr mice for 9–10 months since 4 weeks of age, and found that sPFP is produced predominantly by BAT. In this model, we also found that sPFP increased in plasma. We generated a murine systemic or BAT specific sPFP knockout (KO) models and found that liver fibrosis ameliorated in these models. We also suppressed circulating sPFP with a peptide vaccine targeting this molecule, and found that sPFP vaccination therapy inhibited liver fibrosis. Next, we generated sPFP gain of function (GOF) model by the administration of plasmid encoding sPFP into skeletal muscle. Liver fibrosis augmented in sPFP-GOF model, and these results suggested that sPFP has causal role for the progression of fibrotic response in liver. In vitro studies with differentiated brown adipocytes showed that metabolic stress increased c-Fos in nuclear, and this was causal for an increase in sPFP level.
Conclusions
Our results suggest that one of the BATokines, sPFP, contributes for the progression of fibrotic responses in obese-NASH model. Inhibition of sPFP may become a therapy for NASH or obesity related fibrotic disorders.
Funding Acknowledgement
Type of funding source: None
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Affiliation(s)
- Y Hsiao
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - I Shimizu
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - Y Yoshida
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - R Ikegami
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - Y Hayashi
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - M Suda
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - G Katsuumi
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - T Wakasugi
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - M Nakao
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
| | - T Minamino
- Niigata University Graduate School of Medical and Dental Sciences, Department of Cardiovascular Biology and Medicine, Niigata, Japan
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14
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Hsiao Y, Su BH, Tseng YJ. Current development of integrated web servers for preclinical safety and pharmacokinetics assessments in drug development. Brief Bioinform 2020; 22:5881374. [PMID: 32770190 DOI: 10.1093/bib/bbaa160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/27/2022] Open
Abstract
In drug development, preclinical safety and pharmacokinetics assessments of candidate drugs to ensure the safety profile are a must. While in vivo and in vitro tests are traditionally used, experimental determinations have disadvantages, as they are usually time-consuming and costly. In silico predictions of these preclinical endpoints have each been developed in the past decades. However, only a few web-based tools have integrated different models to provide a simple one-step platform to help researchers thoroughly evaluate potential drug candidates. To efficiently achieve this approach, a platform for preclinical evaluation must not only predict key ADMET (absorption, distribution, metabolism, excretion and toxicity) properties but also provide some guidance on structural modifications to improve the undesired properties. In this review, we organized and compared several existing integrated web servers that can be adopted in preclinical drug development projects to evaluate the subject of interest. We also introduced our new web server, Virtual Rat, as an alternative choice to profile the properties of drug candidates. In Virtual Rat, we provide not only predictions of important ADMET properties but also possible reasons as to why the model made those structural predictions. Multiple models were implemented into Virtual Rat, including models for predicting human ether-a-go-go-related gene (hERG) inhibition, cytochrome P450 (CYP) inhibition, mutagenicity (Ames test), blood-brain barrier penetration, cytotoxicity and Caco-2 permeability. Virtual Rat is free and has been made publicly available at https://virtualrat.cmdm.tw/.
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15
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Hansen KB, Hsiao Y, Xu F, Rivera N, Clausen A, Kubryk M, Krska S, Rosner T, Simmons B, Balsells J, Ikemoto N, Sun Y, Spindler F, Malan C, Grabowski EJJ, Armstrong JD. Correction to “Highly Efficient Asymmetric Synthesis of Sitagliptin”. J Am Chem Soc 2020; 142:13622. [DOI: 10.1021/jacs.0c06041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Kuo TH, Kuei MS, Hsiao Y, Chung HH, Hsu CC, Chen HJ. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Typings of Edible Oils through Spectral Networking of Triacylglycerol Fingerprints. ACS Omega 2019; 4:15734-15741. [PMID: 31572877 PMCID: PMC6761802 DOI: 10.1021/acsomega.9b02433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Adulteration of edible oils by the manufacturers has been found frequently in modern societies. Due to the complexity of the chemical contents in edible oils, it is challenging to quantitatively determine the extent of adulteration and prove the authenticity of edible oils. In this study, a robust and simple MALDI-TOF-MS platform for rapid fingerprinting of triacylglycerols (TAGs) in edible oils was developed, where spectral similarity analysis was performed to quantitatively reveal correlations among edible oils in the chemical level. Specifically, we proposed oil networking, a spectral similarity-based illustration, which enabled reliable classifications of tens of commercial edible oils from vegetable and animal origins. The strategy was superior to traditional multivariate statistics due to its high sensitivity in probing subtle changes in TAG profiles, as further demonstrated by the success in determination of the adulterated lard in a food fraud in Taiwan. Finally, we showed that the platform allowed quantitative assessment of the binary mixture of olive oil and canola oil, which is a common type of olive oil adulteration in the market. Overall, these results suggested a novel strategy for chemical fingerprint-based quality control and authentication of oils in the food industry.
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Affiliation(s)
- Ting-Hao Kuo
- Department
of Chemistry, Institute of Food
Science and Technology, and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Min-Shan Kuei
- Department
of Chemistry, Institute of Food
Science and Technology, and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Yi Hsiao
- Department
of Chemistry, Institute of Food
Science and Technology, and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Hsiang Chung
- Department
of Chemistry, Institute of Food
Science and Technology, and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Chih Hsu
- Department
of Chemistry, Institute of Food
Science and Technology, and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Hong-Jhang Chen
- Department
of Chemistry, Institute of Food
Science and Technology, and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
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17
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Fox RJ, Cuniere NL, Bakrania L, Wei C, Strotman NA, Hay M, Fanfair D, Regens C, Beutner GL, Lawler M, Lobben P, Soumeillant MC, Cohen B, Zhu K, Skliar D, Rosner T, Markwalter CE, Hsiao Y, Tran K, Eastgate MD. C–H Arylation in the Formation of a Complex Pyrrolopyridine, the Commercial Synthesis of the Potent JAK2 Inhibitor, BMS-911543. J Org Chem 2018; 84:4661-4669. [DOI: 10.1021/acs.joc.8b02383] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Richard J. Fox
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Nicolas L. Cuniere
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Lopa Bakrania
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Carolyn Wei
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Neil A. Strotman
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael Hay
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Dayne Fanfair
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Christopher Regens
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Gregory L. Beutner
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael Lawler
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Paul Lobben
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Maxime C. Soumeillant
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Benjamin Cohen
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Keming Zhu
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Dimitri Skliar
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Thorsten Rosner
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Chester E. Markwalter
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Kristy Tran
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin D. Eastgate
- Chemical Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
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18
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Strotman NA, Soumeillant MC, Zhu K, Markwalter CE, Wei CS, Hsiao Y, Eastgate MD. Effects of Multiple Catalyst Deactivation Pathways and Continuous Ligand Recycling on the Kinetics of Pd-Catalyzed C–N Coupling Reactions. J Org Chem 2018; 84:4653-4660. [PMID: 30336032 DOI: 10.1021/acs.joc.8b02214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neil A. Strotman
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Maxime C. Soumeillant
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Keming Zhu
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Chester E. Markwalter
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Carolyn S. Wei
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin D. Eastgate
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
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19
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Bien J, Davulcu A, DelMonte AJ, Fraunhoffer KJ, Gao Z, Hang C, Hsiao Y, Hu W, Katipally K, Littke A, Pedro A, Qiu Y, Sandoval M, Schild R, Soltani M, Tedesco A, Vanyo D, Vemishetti P, Waltermire RE. The First Kilogram Synthesis of Beclabuvir, an HCV NS5B Polymerase Inhibitor. Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00214] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jeffrey Bien
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Akin Davulcu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Albert J. DelMonte
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Kenneth J. Fraunhoffer
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Zhinong Gao
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Chao Hang
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Wenhao Hu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Kishta Katipally
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Adam Littke
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Aghogho Pedro
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Yuping Qiu
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Maria Sandoval
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Richard Schild
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Michelle Soltani
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Anthony Tedesco
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Dale Vanyo
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Purushotham Vemishetti
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
| | - Robert E. Waltermire
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, P.O. Box 191, New Brunswick, New Jersey 08903, United States
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20
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Zhuang Z, Yu CB, Chen G, Wu QF, Hsiao Y, Joe CL, Qiao JX, Poss MA, Yu JQ. Ligand-Enabled β-C(sp 3)-H Olefination of Free Carboxylic Acids. J Am Chem Soc 2018; 140:10363-10367. [PMID: 30029574 DOI: 10.1021/jacs.8b06527] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An acetyl-protected aminoethyl phenyl thioether has been developed to promote C(sp3)-H activation. Significant ligand enhancement is demonstrated by the realization of the first Pd(II)-catalyzed olefination of C(sp3)-H bonds of free carboxylic acids without using an auxiliary. Subsequent lactonization of the olefinated product via 1,4 addition provided exclusively monoselectivity in the presence of multiple β-C-H bonds. The product γ-lactone can be readily opened to give either the highly valuable β-olefinated or γ-hydroxylated aliphatic acids. Considering the challenges in developing Heck couplings using alkyl halides, this reaction offers a useful alternative.
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Affiliation(s)
- Zhe Zhuang
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Chang-Bin Yu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Gang Chen
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Qing-Feng Wu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Yi Hsiao
- Chemical and Synthetic Development , Bristol-Myers Squibb , 1 Squibb Drive , New Brunswick , New Jersey 08903 , United States
| | - Candice L Joe
- Chemical and Synthetic Development , Bristol-Myers Squibb , 1 Squibb Drive , New Brunswick , New Jersey 08903 , United States
| | - Jennifer X Qiao
- Discovery Chemistry , Bristol-Myers Squibb Company , P.O. Box 4000, Princeton , New Jersey 08543 , United States
| | - Michael A Poss
- Discovery Chemistry , Bristol-Myers Squibb Company , P.O. Box 4000, Princeton , New Jersey 08543 , United States
| | - Jin-Quan Yu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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21
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Beutner G, Carrasquillo R, Geng P, Hsiao Y, Huang EC, Janey J, Katipally K, Kolotuchin S, La Porte T, Lee A, Lobben P, Lora-Gonzalez F, Mack B, Mudryk B, Qiu Y, Qian X, Ramirez A, Razler TM, Rosner T, Shi Z, Simmons E, Stevens J, Wang J, Wei C, Wisniewski SR, Zhu Y. Adventures in Atropisomerism: Total Synthesis of a Complex Active Pharmaceutical Ingredient with Two Chirality Axes. Org Lett 2018; 20:3736-3740. [PMID: 29909639 DOI: 10.1021/acs.orglett.8b01218] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A strategy to prepare compounds with multiple chirality axes, which has led to a concise total synthesis of compound 1A with complete stereocontrol, is reported.
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Affiliation(s)
- Gregory Beutner
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Ronald Carrasquillo
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Peng Geng
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Yi Hsiao
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Eric C Huang
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Jacob Janey
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Kishta Katipally
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Sergei Kolotuchin
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Thomas La Porte
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Andrew Lee
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Paul Lobben
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Federico Lora-Gonzalez
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Brendan Mack
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Boguslaw Mudryk
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Yuping Qiu
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Xinhua Qian
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Antonio Ramirez
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Thomas M Razler
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Thorsten Rosner
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Zhongping Shi
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Eric Simmons
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Jason Stevens
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Jianji Wang
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Carolyn Wei
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Steven R Wisniewski
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
| | - Ye Zhu
- Chemical & Synthetic Development , Bristol-Myers Squibb Company , 1 Squibb Drive , New Brunswick , New Jersey 08901 , United States
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22
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Simmons EM, Mudryk B, Lee AG, Qiu Y, Razler TM, Hsiao Y. Development of a Kilogram-Scale Process for the Enantioselective Synthesis of 3-Isopropenyl-cyclohexan-1-one via Rh/DTBM-SEGPHOS-Catalyzed Asymmetric Hayashi Addition Enabled by 1,3-Diol Additives. Org Process Res Dev 2017. [DOI: 10.1021/acs.oprd.7b00253] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric M. Simmons
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Boguslaw Mudryk
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Andrew G. Lee
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yuping Qiu
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Thomas M. Razler
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
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23
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Chen K, Risatti C, Simpson J, Soumeillant M, Soltani M, Bultman M, Zheng B, Mudryk B, Tripp JC, La Cruz TE, Hsiao Y, Conlon DA, Eastgate MD. Preparation of the HIV Attachment Inhibitor BMS-663068. Part 2. Strategic Selections in the Transition from an Enabling Route to a Commercial Synthesis. Org Process Res Dev 2017. [DOI: 10.1021/acs.oprd.7b00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ke Chen
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Christina Risatti
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - James Simpson
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Maxime Soumeillant
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michelle Soltani
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael Bultman
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Bin Zheng
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Boguslaw Mudryk
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Jonathan C. Tripp
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Thomas E. La Cruz
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - David A. Conlon
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin D. Eastgate
- Chemical & Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
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24
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Gallagher WP, Soumeillant M, Chen K, Fox RJ, Hsiao Y, Mack B, Iyer V, Fan J, Zhu J, Beutner G, Silverman SM, Fanfair DD, Glace AW, Freitag A, Sweeney J, Ji Y, Blackmond DG, Eastgate MD, Conlon DA. Preparation of the HIV Attachment Inhibitor BMS-663068. Part 7. Development of a Regioselective Ullmann–Goldberg–Buchwald Reaction. Org Process Res Dev 2017. [DOI: 10.1021/acs.oprd.7b00191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- William P. Gallagher
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Maxime Soumeillant
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Ke Chen
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Richard J. Fox
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Yi Hsiao
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Brendan Mack
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Vidya Iyer
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Junying Fan
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Jason Zhu
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Gregory Beutner
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Steven M. Silverman
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Dayne D. Fanfair
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Andrew W. Glace
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Adam Freitag
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Jason Sweeney
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Yining Ji
- The Scripps Research Institute, 50550 N. Torrey Pines Road, La Jolla, California, United States
| | - Donna G. Blackmond
- The Scripps Research Institute, 50550 N. Torrey Pines Road, La Jolla, California, United States
| | - Martin D. Eastgate
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - David A. Conlon
- Chemical & Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
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25
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Affiliation(s)
- Gregory L. Beutner
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Yi Hsiao
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Thomas Razler
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - Eric M. Simmons
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
| | - William Wertjes
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903-0191, United States
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26
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Chen G, Zhuang Z, Li GC, Saint-Denis TG, Hsiao Y, Joe CL, Yu JQ. Ligand-Enabled β-C-H Arylation of α-Amino Acids Without Installing Exogenous Directing Groups. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610580] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gang Chen
- Department of Chemistry; The Scripps Research Institute (TSRI); 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Zhe Zhuang
- Department of Chemistry; The Scripps Research Institute (TSRI); 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Gen-Cheng Li
- Department of Chemistry; The Scripps Research Institute (TSRI); 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Tyler G. Saint-Denis
- Department of Chemistry; The Scripps Research Institute (TSRI); 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Yi Hsiao
- Chemical and Synthetic Development; Bristol-Myers Squibb; 1 Squibb Drive New Brunswick NJ 08903 USA
| | - Candice L. Joe
- Chemical and Synthetic Development; Bristol-Myers Squibb; 1 Squibb Drive New Brunswick NJ 08903 USA
| | - Jin-Quan Yu
- Department of Chemistry; The Scripps Research Institute (TSRI); 10550 North Torrey Pines Road La Jolla CA 92037 USA
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27
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Chen G, Zhuang Z, Li GC, Saint-Denis TG, Hsiao Y, Joe CL, Yu JQ. Ligand-Enabled β-C-H Arylation of α-Amino Acids Without Installing Exogenous Directing Groups. Angew Chem Int Ed Engl 2017; 56:1506-1509. [PMID: 28052530 DOI: 10.1002/anie.201610580] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [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: 10/28/2016] [Indexed: 11/09/2022]
Abstract
Herein we report acid-directed β-C(sp3 )-H arylation of α-amino acids enabled by pyridine-type ligands. This reaction does not require the installation of an exogenous directing group, is scalable, and enables the preparation of Fmoc-protected unnatural amino acids in three steps. The pyridine-type ligands are crucial for the development of this new C(sp3 )-H arylation.
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Affiliation(s)
- Gang Chen
- Department of Chemistry, The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Zhe Zhuang
- Department of Chemistry, The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Gen-Cheng Li
- Department of Chemistry, The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Tyler G Saint-Denis
- Department of Chemistry, The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Yi Hsiao
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, NJ, 08903, USA
| | - Candice L Joe
- Chemical and Synthetic Development, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, NJ, 08903, USA
| | - Jin-Quan Yu
- Department of Chemistry, The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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28
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Degnan AP, Tora GO, Huang H, Conlon DA, Davis CD, Hanumegowda UM, Hou X, Hsiao Y, Hu J, Krause R, Li YW, Newton AE, Pieschl RL, Raybon J, Rosner T, Sun JH, Taber MT, Taylor SJ, Wong MK, Zhang H, Lodge NJ, Bronson JJ, Macor JE, Gillman KW. Discovery of Indazoles as Potent, Orally Active Dual Neurokinin 1 Receptor Antagonists and Serotonin Transporter Inhibitors for the Treatment of Depression. ACS Chem Neurosci 2016; 7:1635-1640. [PMID: 27744678 DOI: 10.1021/acschemneuro.6b00337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 11/28/2022] Open
Abstract
Combination studies of neurokinin 1 (NK1) receptor antagonists and serotonin-selective reuptake inhibitors (SSRIs) have shown promise in preclinical models of depression. Such a combination may offer important advantages over the current standard of care. Herein we describe the discovery and optimization of an indazole-based chemotype to provide a series of potent dual NK1 receptor antagonists/serotonin transporter (SERT) inhibitors to overcome issues of ion channel blockade. This effort culminated in the identification of compound 9, an analogue that demonstrated favorable oral bioavailability, excellent brain uptake, and robust in vivo efficacy in a validated depression model. Over the course of this work, a novel heterocycle-directed asymmetric hydrogenation was developed to facilitate installation of the key stereogenic center.
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Affiliation(s)
- Andrew P. Degnan
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - George O. Tora
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Hong Huang
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - David A. Conlon
- Chemical
Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903, United States
| | - Carl D. Davis
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Umesh M. Hanumegowda
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Xiaoping Hou
- Department of Chemical Synthesis, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Yi Hsiao
- Chemical
Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903, United States
| | - Joanna Hu
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Rudolph Krause
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Yu-Wen Li
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Amy E. Newton
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Rick L. Pieschl
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Joseph Raybon
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Thorsten Rosner
- Chemical
Development, Bristol-Myers Squibb Company, New Brunswick, New Jersey 08903, United States
| | - Jung-Hui Sun
- Department of Chemical Synthesis, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Matthew T. Taber
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Sarah J. Taylor
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Michael K. Wong
- Department of Chemical Synthesis, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Huiping Zhang
- Department of Chemical Synthesis, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, United States
| | - Nicholas J. Lodge
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Joanne J. Bronson
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - John E. Macor
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
| | - Kevin W. Gillman
- Research and Development, Bristol-Myers Squibb Company, Wallingford, Connecticut 06492, United States
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29
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Qiao JX, Fraunhoffer KJ, Hsiao Y, Li YX, Wang C, Wang TC, Poss MA. Synthesis of Fmoc-Protected Arylphenylalanines (Bip Derivatives) via Nonaqueous Suzuki-Miyaura Cross-Coupling Reactions. J Org Chem 2016; 81:9499-9506. [DOI: 10.1021/acs.joc.6b01965] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jennifer X. Qiao
- Discovery Chemistry, ‡Chemical and Synthetic
Development,
and §Pharmaceutical Candidate
Optimization, Research and Development, Bristol-Myers Squibb Company, P.O. Box
4000, Princeton, New Jersey 08543-4000, United States
| | - Kenneth J. Fraunhoffer
- Discovery Chemistry, ‡Chemical and Synthetic
Development,
and §Pharmaceutical Candidate
Optimization, Research and Development, Bristol-Myers Squibb Company, P.O. Box
4000, Princeton, New Jersey 08543-4000, United States
| | - Yi Hsiao
- Discovery Chemistry, ‡Chemical and Synthetic
Development,
and §Pharmaceutical Candidate
Optimization, Research and Development, Bristol-Myers Squibb Company, P.O. Box
4000, Princeton, New Jersey 08543-4000, United States
| | - Yi-Xin Li
- Discovery Chemistry, ‡Chemical and Synthetic
Development,
and §Pharmaceutical Candidate
Optimization, Research and Development, Bristol-Myers Squibb Company, P.O. Box
4000, Princeton, New Jersey 08543-4000, United States
| | - Chunlei Wang
- Discovery Chemistry, ‡Chemical and Synthetic
Development,
and §Pharmaceutical Candidate
Optimization, Research and Development, Bristol-Myers Squibb Company, P.O. Box
4000, Princeton, New Jersey 08543-4000, United States
| | - Tammy C. Wang
- Discovery Chemistry, ‡Chemical and Synthetic
Development,
and §Pharmaceutical Candidate
Optimization, Research and Development, Bristol-Myers Squibb Company, P.O. Box
4000, Princeton, New Jersey 08543-4000, United States
| | - Michael A. Poss
- Discovery Chemistry, ‡Chemical and Synthetic
Development,
and §Pharmaceutical Candidate
Optimization, Research and Development, Bristol-Myers Squibb Company, P.O. Box
4000, Princeton, New Jersey 08543-4000, United States
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30
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Ji Y, Plata RE, Regens CS, Hay M, Schmidt M, Razler T, Qiu Y, Geng P, Hsiao Y, Rosner T, Eastgate MD, Blackmond DG. Mono-Oxidation of Bidentate Bis-phosphines in Catalyst Activation: Kinetic and Mechanistic Studies of a Pd/Xantphos-Catalyzed C-H Functionalization. J Am Chem Soc 2015; 137:13272-81. [PMID: 26461028 DOI: 10.1021/jacs.5b01913] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Kinetic, spectroscopic, crystallographic, and computational studies probing a Pd-catalyzed C-H arylation reaction reveal that mono-oxidation of the bis-phosphine ligand is critical for the formation of the active catalyst. The bis-phosphine mono-oxide is shown to be a hemilabile, bidentate ligand for palladium. Isolation of the oxidative addition adduct, with structural elucidation by X-ray analysis, showed that the mono-oxide was catalytically competent, giving the same reaction rate in the productive reaction as the Pd(II)/xantphos precursor. A dual role for the carboxylate base in both catalyst activation and reaction turnover was demonstrated, along with the inhibiting effect of excess phosphine ligand. The generality of the role of phosphine mono-oxide complexes in Pd-catalyzed coupling processes is discussed.
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Affiliation(s)
- Yining Ji
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - R Erik Plata
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Christopher S Regens
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael Hay
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael Schmidt
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Thomas Razler
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yuping Qiu
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Peng Geng
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Yi Hsiao
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Thorsten Rosner
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin D Eastgate
- Chemical Development, Bristol-Myers Squibb , One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Donna G Blackmond
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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31
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Chen YS, Cheng MJ, Hsiao Y, Chan HY, Hsieh SY, Chang CW, Liu TW, Chang HS, Chen IS. Chemical Constituents of the Endophytic FungusHypoxylonsp. 12F0687 Isolated from TaiwaneseIlex formosana. Helv Chim Acta 2015. [DOI: 10.1002/hlca.201500048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hsiao Y, Cheng MJ, Chang HS, Wu MD, Hsieh SY, Liu TW, Lin CH, Yuan GF, Chen IS. Six new metabolites produced byColletotrichum aotearoa09F0161, an endophytic fungus isolated fromBredia oldhamii. Nat Prod Res 2015; 30:251-8. [DOI: 10.1080/14786419.2015.1054285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Huang R, Lee S, Lai C, Hsiao Y, Ting H. Acute effects of obstructive sleep apnea on autonomic nervous system, arterial stiffness and heart rate in newly diagnosed untreated patients. Sleep Med 2013. [DOI: 10.1016/j.sleep.2013.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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34
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Wei CS, Davies GHM, Soltani O, Albrecht J, Gao Q, Pathirana C, Hsiao Y, Tummala S, Eastgate MD. The Impact of Palladium(II) Reduction Pathways on the Structure and Activity of Palladium(0) Catalysts. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210252] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Wei CS, Davies GHM, Soltani O, Albrecht J, Gao Q, Pathirana C, Hsiao Y, Tummala S, Eastgate MD. The Impact of Palladium(II) Reduction Pathways on the Structure and Activity of Palladium(0) Catalysts. Angew Chem Int Ed Engl 2013; 52:5822-6. [DOI: 10.1002/anie.201210252] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Indexed: 11/09/2022]
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36
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Leahy DK, Fan Y, Desai LV, Chan C, Zhu J, Luo G, Chen L, Hanson RL, Sugiyama M, Rosner T, Cuniere N, Guo Z, Hsiao Y, Gao Q. Efficient and Scalable Enantioselective Synthesis of a CGRP Antagonist. Org Lett 2012; 14:4938-41. [DOI: 10.1021/ol302262q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David K. Leahy
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yu Fan
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Lopa V. Desai
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Collin Chan
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jason Zhu
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Guanglin Luo
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ling Chen
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ronald L. Hanson
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Masano Sugiyama
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Thorsten Rosner
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Nicolas Cuniere
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Zhiwei Guo
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yi Hsiao
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Qi Gao
- Chemical Development and Drug Product Science and Technology, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States, and Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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37
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Ortiz A, Young IS, Sawyer JR, Hsiao Y, Singh A, Sugiyama M, Corbett RM, Chau M, Shi Z, Conlon DA. Synthetic approaches to a chiral 4-amino-3-hydroxy piperidine with pharmaceutical relevance. Org Biomol Chem 2012; 10:5253-7. [DOI: 10.1039/c2ob25411e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Wang CC, Hsiao Y, Lee CC, Chao TC, Wang CC, Tung CJ. Monte Carlo simulations of therapeutic proton beams for relative biological effectiveness of double-strand break. Int J Radiat Biol 2011; 88:158-63. [PMID: 21823821 DOI: 10.3109/09553002.2011.611214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE The relative biological effectiveness (RBE) values relative to (60)Co for the induction of double-strand breaks (DSB) were calculated for therapeutic proton beams. RBE-weighted absorbed doses were determined at different depths in a water phantom for proton beams. MATERIALS AND METHODS The depth-dose distributions and the fluence spectra for primary protons and secondary particles were calculated using the FLUKA (FLUktuierende KAskade) MC (Monte Carlo) transport code. These spectra were combined with the MCDS (Monte Carlo damage simulation) code to simulate the spectrum-averaged yields of clustered DNA lesions. RBE for the induction of DSB were then determined at different depths in a water phantom for the unmodulated and modulated proton beams. RESULTS The maximum RBE for the induction of DSB at 1 Gy absorbed dose was found about 1.5 at 0.5 cm distal to the Bragg peak maximum for an UNMODULATED 160 MeV proton beam. The RBE-weighted absorbed dose extended the biologically effective range of the proton beam by 1.9 mm. The corresponding maximum RBE value was inversely proportional to the proton beam energy, reaching a value of about 1.9 for 70 MeV proton beam. For a modulated 160 MeV proton beam, the RBE weightings were more pronounced near the spread-out Bragg peak (SOBP) distal edge. CONCLUSIONS It was demonstrated that a fast MCDS code could be used to simulate the DNA damage yield for therapeutic proton beams. Simulated RBE for the induction of DSB were comparable to RBE measured in vitro and in vivo. Depth dependent RBE values in the SOBP region might have to be considered in certain treatment situations.
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Affiliation(s)
- Chun-Ching Wang
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan
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39
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Chao TC, Huang YS, Hsu FY, Hsiao Y, Lee CC, Tung CJ. Cellular dosimetry and microdosimetry for internal electron emitters. Radiat Prot Dosimetry 2011; 143:248-252. [PMID: 21169288 DOI: 10.1093/rpd/ncq386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Radiobiological descriptions of cellular dosimetry and microdosimetry require both radiation dose and radiation quality. The lineal energy, defined as a ratio of the energy deposition by a particle in the biological target and the mean chord length of this target, is generally adopted to characterise the radiation quality. Most microdosimetry applications assume that the cell nucleus is the target region. Therefore, the lineal energy is obtained for the source (S) to target (T) geometry, T ← S, where S = cell surface, cytoplasm, cell nucleus and T = cell nucleus. The definition of lineal energy is based on the approximation that the particle mean pathlength is equal to target mean chord length. This approximation is valid for crossers of external irradiations. In the case of starters, insiders and stoppers of internal sources, particle pathlengths are always shorter than target chord lengths. Thus, the lineal energy does not reflect the specific energy deposition along particle path. In the present work, the specific energy deposition in a target is calculated using three distance parameters, i.e. target mean chord length, particle mean pathlength in the target and particle individual pathlength in the target. Monte Carlo calculations are performed for electrons of various energies and cells of different sizes. Results are analysed and discussed.
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Affiliation(s)
- T C Chao
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Kweishan 333, Taiwan
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Chiu L, Chen S, Hsiao Y, Lu S, Chiu A. UP-1.101: Comparison of Transrectal Ultrasound Guided Biopsy of the Prostate and Transurethral Resection of the Prostate in the Diagnosis of Prostate Cancer in Patients with Moderate Lower Urinary Tract Symptoms. Urology 2009. [DOI: 10.1016/j.urology.2009.07.548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hansen KB, Hsiao Y, Xu F, Rivera N, Clausen A, Kubryk M, Krska S, Rosner T, Simmons B, Balsells J, Ikemoto N, Sun Y, Spindler F, Malan C, Grabowski EJJ, Armstrong JD. Highly Efficient Asymmetric Synthesis of Sitagliptin. J Am Chem Soc 2009; 131:8798-804. [DOI: 10.1021/ja902462q] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karl B. Hansen
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Yi Hsiao
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Feng Xu
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Nelo Rivera
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Andrew Clausen
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Michele Kubryk
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Shane Krska
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Thorsten Rosner
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Bryon Simmons
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Jaume Balsells
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Nori Ikemoto
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Yongkui Sun
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Felix Spindler
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Christophe Malan
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Edward J. J. Grabowski
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
| | - Joseph D. Armstrong
- Department of Process Research, Merck Research Laboratory, Rahway, New Jersey 07065, and Solvias AG, P.O. Box 4002, Basel, Switzerland
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Lee M, Hsiao Y, Chao T, Tu S. SU-FF-T-485: Monte Carlo Simulation for DNA Damage in Gold Nanoparticle Solution. Med Phys 2009. [DOI: 10.1118/1.3181983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Razler TM, Hsiao Y, Qian F, Fu R, Khan RK, Doubleday W. A Preparatively Convenient Ligand-Free Catalytic PEG 2000 Suzuki−Miyaura Coupling. J Org Chem 2008; 74:1381-4. [DOI: 10.1021/jo802277z] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas M. Razler
- The Department of Process Research and Development and the Department of Biopharmaceutics Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903
| | - Yi Hsiao
- The Department of Process Research and Development and the Department of Biopharmaceutics Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903
| | - Feng Qian
- The Department of Process Research and Development and the Department of Biopharmaceutics Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903
| | - Ruiling Fu
- The Department of Process Research and Development and the Department of Biopharmaceutics Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903
| | - Rana Kashif Khan
- The Department of Process Research and Development and the Department of Biopharmaceutics Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903
| | - Wendel Doubleday
- The Department of Process Research and Development and the Department of Biopharmaceutics Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903
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Tu S, Hsieh H, Lee M, Low C, Hsiao Y. SU-GG-J-173: Study of CT Number Dependence On Hardware Settings and Post Image Processing in Micro CT Systems. Med Phys 2008. [DOI: 10.1118/1.2961722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Hsiao Y, Lien H, Hsieh F, Liang W. SPARC in breast tumors of different histological types: defined its role in patients' outcome and nodal status. EJC Suppl 2008. [DOI: 10.1016/s1359-6349(08)70425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Hsiao Y, Stewart R, Olivera G, Ruchala K, Li X. SU-FF-T-332: Monte Carlo Simulation of Tomotherapy: Derivation of a Dual Source Model for Treatment Planning. Med Phys 2006. [DOI: 10.1118/1.2241254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Clausen AM, Dziadul B, Cappuccio KL, Kaba M, Starbuck C, Hsiao Y, Dowling TM. Identification of Ammonium Chloride as an Effective Promoter of the Asymmetric Hydrogenation of a β-Enamine Amide. Org Process Res Dev 2006. [DOI: 10.1021/op050232o] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew M. Clausen
- Merck & Co., Inc., Process Research & Development (Process Research), P.O. Box 2000, Rahway, New Jersey 07065, U.S.A
| | - Brianne Dziadul
- Merck & Co., Inc., Process Research & Development (Process Research), P.O. Box 2000, Rahway, New Jersey 07065, U.S.A
| | - Kristine L. Cappuccio
- Merck & Co., Inc., Process Research & Development (Process Research), P.O. Box 2000, Rahway, New Jersey 07065, U.S.A
| | - Mahmoud Kaba
- Merck & Co., Inc., Process Research & Development (Process Research), P.O. Box 2000, Rahway, New Jersey 07065, U.S.A
| | - Cindy Starbuck
- Merck & Co., Inc., Process Research & Development (Process Research), P.O. Box 2000, Rahway, New Jersey 07065, U.S.A
| | - Yi Hsiao
- Merck & Co., Inc., Process Research & Development (Process Research), P.O. Box 2000, Rahway, New Jersey 07065, U.S.A
| | - Thomas M. Dowling
- Merck & Co., Inc., Process Research & Development (Process Research), P.O. Box 2000, Rahway, New Jersey 07065, U.S.A
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Yang M(M, Thompson R, Hsiao Y, Hall G. Characterization and Control of Impurities in the Synthesis of an Amino Acid Drug Candidate. J LIQ CHROMATOGR R T 2006. [DOI: 10.1080/10826070500451897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | | | - Yi Hsiao
- a Merck Research Laboratories , Rahway, New Jersey, USA
| | - Gene Hall
- b Department of Chemistry, Rutgers , The State University of New Jersey , Piscataway, New Jersey, USA
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