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Arduini A, Fleming SJ, Xiao L, Hall AW, Akkad AD, Chaffin M, Bendinelli KJ, Tucker NR, Papangeli I, Mantineo H, Babadi M, Stegmann CM, García-Cardeña G, Lindsay ME, Klattenhoff C, Ellinor PT. Transcriptional profile of the rat cardiovascular system at single cell resolution. bioRxiv 2023:2023.11.14.567085. [PMID: 38014050 PMCID: PMC10680727 DOI: 10.1101/2023.11.14.567085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background Despite the critical role of the cardiovascular system, our understanding of its cellular and transcriptional diversity remains limited. We therefore sought to characterize the cellular composition, phenotypes, molecular pathways, and communication networks between cell types at the tissue and sub-tissue level across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We obtained high quality tissue samples under controlled conditions that reveal a level of cellular detail so far inaccessible in human studies. Methods and Results We performed single nucleus RNA-sequencing in 78 samples in 10 distinct regions including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins (PV), which produced an aggregate map of 505,835 nuclei. We identified 26 distinct cell types and additional subtypes, including a number of rare cell types such as PV cardiomyocytes and non-myelinating Schwann cells (NMSCs), and unique groups of vascular smooth muscle cells (VSMCs), endothelial cells (ECs) and fibroblasts (FBs), which gave rise to a detailed cell type distribution across tissues. We demonstrated differences in the cellular composition across different cardiac regions and tissue-specific differences in transcription for each cell type, highlighting the molecular diversity and complex tissue architecture of the cardiovascular system. Specifically, we observed great transcriptional heterogeneities among ECs and FBs. Importantly, several cell subtypes had a unique regional localization such as a subtype of VSMCs enriched in the large vasculature. We found the cellular makeup of PV tissue is closer to heart tissue than to the large arteries. We further explored the ligand-receptor repertoire across cell clusters and tissues, and observed tissue-enriched cellular communication networks, including heightened Nppa - Npr1 / 2 / 3 signaling in the sinoatrial node. Conclusions Through a large single nucleus sequencing effort encompassing over 500,000 nuclei, we broadened our understanding of cellular transcription in the healthy cardiovascular system. The existence of tissue-restricted cellular phenotypes suggests regional regulation of cardiovascular physiology. The overall conservation in gene expression and molecular pathways across rat and human cell types, together with our detailed transcriptional characterization of each cell type, offers the potential to identify novel therapeutic targets and improve preclinical models of cardiovascular disease.
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2
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Chaffin M, Papangeli I, Simonson B, Akkad AD, Hill MC, Arduini A, Fleming SJ, Melanson M, Hayat S, Kost-Alimova M, Atwa O, Ye J, Bedi KC, Nahrendorf M, Kaushik VK, Stegmann CM, Margulies KB, Tucker NR, Ellinor PT. Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. Nature 2022; 608:174-180. [PMID: 35732739 DOI: 10.1038/s41586-022-04817-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/27/2022] [Indexed: 12/22/2022]
Abstract
Heart failure encompasses a heterogeneous set of clinical features that converge on impaired cardiac contractile function1,2 and presents a growing public health concern. Previous work has highlighted changes in both transcription and protein expression in failing hearts3,4, but may overlook molecular changes in less prevalent cell types. Here we identify extensive molecular alterations in failing hearts at single-cell resolution by performing single-nucleus RNA sequencing of nearly 600,000 nuclei in left ventricle samples from 11 hearts with dilated cardiomyopathy and 15 hearts with hypertrophic cardiomyopathy as well as 16 non-failing hearts. The transcriptional profiles of dilated or hypertrophic cardiomyopathy hearts broadly converged at the tissue and cell-type level. Further, a subset of hearts from patients with cardiomyopathy harbour a unique population of activated fibroblasts that is almost entirely absent from non-failing samples. We performed a CRISPR-knockout screen in primary human cardiac fibroblasts to evaluate this fibrotic cell state transition; knockout of genes associated with fibroblast transition resulted in a reduction of myofibroblast cell-state transition upon TGFβ1 stimulation for a subset of genes. Our results provide insights into the transcriptional diversity of the human heart in health and disease as well as new potential therapeutic targets and biomarkers for heart failure.
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Affiliation(s)
- Mark Chaffin
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA
| | - Irinna Papangeli
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Bridget Simonson
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA
| | - Amer-Denis Akkad
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Matthew C Hill
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Alessandro Arduini
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA
| | - Stephen J Fleming
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA
- Data Sciences Platform, The Broad Institute, Cambridge, MA, USA
| | - Michelle Melanson
- Center for the Development of Therapeutics, The Broad Institute, Cambridge, MA, USA
| | - Sikander Hayat
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Maria Kost-Alimova
- Center for the Development of Therapeutics, The Broad Institute, Cambridge, MA, USA
| | - Ondine Atwa
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA
| | - Jiangchuan Ye
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA
| | - Kenneth C Bedi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthias Nahrendorf
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, The Broad Institute, Cambridge, MA, USA
| | | | - Kenneth B Margulies
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Patrick T Ellinor
- Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA.
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3
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Xu Y, Baumgart SJ, Stegmann CM, Hayat S. MACA: marker-based automatic cell-type annotation for single-cell expression data. Bioinformatics 2022; 38:1756-1760. [PMID: 34935911 DOI: 10.1093/bioinformatics/btab840] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/07/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Accurately identifying cell types is a critical step in single-cell sequencing analyses. Here, we present marker-based automatic cell-type annotation (MACA), a new tool for annotating single-cell transcriptomics datasets. We developed MACA by testing four cell-type scoring methods with two public cell-marker databases as reference in six single-cell studies. MACA compares favorably to four existing marker-based cell-type annotation methods in terms of accuracy and speed. We show that MACA can annotate a large single-nuclei RNA-seq study in minutes on human hearts with ∼290K cells. MACA scales easily to large datasets and can broadly help experts to annotate cell types in single-cell transcriptomics datasets, and we envision MACA provides a new opportunity for integration and standardization of cell-type annotation across multiple datasets. AVAILABILITY AND IMPLEMENTATION MACA is written in python and released under GNU General Public License v3.0. The source code is available at https://github.com/ImXman/MACA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Xu
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
| | - Simon J Baumgart
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
| | - Christian M Stegmann
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
| | - Sikander Hayat
- Bayer-Broad Joint Precision Cardiology Lab, 75 Ames Street, Cambridge, MA 02142, USA
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4
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Pirruccello JP, Chaffin MD, Chou EL, Fleming SJ, Lin H, Nekoui M, Khurshid S, Friedman SF, Bick AG, Arduini A, Weng LC, Choi SH, Akkad AD, Batra P, Tucker NR, Hall AW, Roselli C, Benjamin EJ, Vellarikkal SK, Gupta RM, Stegmann CM, Juric D, Stone JR, Vasan RS, Ho JE, Hoffmann U, Lubitz SA, Philippakis AA, Lindsay ME, Ellinor PT. Deep learning enables genetic analysis of the human thoracic aorta. Nat Genet 2022; 54:40-51. [PMID: 34837083 PMCID: PMC8758523 DOI: 10.1038/s41588-021-00962-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/30/2021] [Indexed: 11/16/2022]
Abstract
Enlargement or aneurysm of the aorta predisposes to dissection, an important cause of sudden death. We trained a deep learning model to evaluate the dimensions of the ascending and descending thoracic aorta in 4.6 million cardiac magnetic resonance images from the UK Biobank. We then conducted genome-wide association studies in 39,688 individuals, identifying 82 loci associated with ascending and 47 with descending thoracic aortic diameter, of which 14 loci overlapped. Transcriptome-wide analyses, rare-variant burden tests and human aortic single nucleus RNA sequencing prioritized genes including SVIL, which was strongly associated with descending aortic diameter. A polygenic score for ascending aortic diameter was associated with thoracic aortic aneurysm in 385,621 UK Biobank participants (hazard ratio = 1.43 per s.d., confidence interval 1.32-1.54, P = 3.3 × 10-20). Our results illustrate the potential for rapidly defining quantitative traits with deep learning, an approach that can be broadly applied to biomedical images.
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Affiliation(s)
- James P Pirruccello
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Precision Cardiology Laboratory, The Broad Institute & Bayer US LLC, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Precision Cardiology Laboratory, The Broad Institute & Bayer US LLC, Cambridge, MA, USA
| | - Elizabeth L Chou
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Division of Vascular and Endovascular Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen J Fleming
- Precision Cardiology Laboratory, The Broad Institute & Bayer US LLC, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute, Cambridge, MA, USA
| | - Honghuang Lin
- Framingham Heart Study, Boston University and National Heart, Lung, and Blood Institute, Framingham, MA, USA
- Department of Medicine, Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Mahan Nekoui
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Shaan Khurshid
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | | | - Alexander G Bick
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alessandro Arduini
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Precision Cardiology Laboratory, The Broad Institute & Bayer US LLC, Cambridge, MA, USA
| | - Lu-Chen Weng
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Amer-Denis Akkad
- Precision Cardiology Laboratory, The Broad Institute & Bayer US LLC, Cambridge, MA, USA
| | - Puneet Batra
- Data Sciences Platform, Broad Institute, Cambridge, MA, USA
| | | | - Amelia W Hall
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Carolina Roselli
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Emelia J Benjamin
- Framingham Heart Study, Boston University and National Heart, Lung, and Blood Institute, Framingham, MA, USA
- Department of Medicine, Cardiology and Preventive Medicine Sections, Boston University School of Medicine, Boston, MA, USA
- Epidemiology Department, Boston University School of Public Health, Boston, MA, USA
| | | | - Rajat M Gupta
- Department of Medicine, Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Christian M Stegmann
- Precision Cardiology Laboratory, The Broad Institute & Bayer US LLC, Cambridge, MA, USA
| | - Dejan Juric
- Harvard Medical School, Boston, MA, USA
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - James R Stone
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Boston University and National Heart, Lung, and Blood Institute, Framingham, MA, USA
- Department of Medicine, Cardiology and Preventive Medicine Sections, Boston University School of Medicine, Boston, MA, USA
- Epidemiology Department, Boston University School of Public Health, Boston, MA, USA
| | - Jennifer E Ho
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Udo Hoffmann
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Lubitz
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Anthony A Philippakis
- Data Sciences Platform, Broad Institute, Cambridge, MA, USA
- GV, Mountain View, CA, USA
| | - Mark E Lindsay
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Thoracic Aortic Center, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Division of Cardiology, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA.
- Precision Cardiology Laboratory, The Broad Institute & Bayer US LLC, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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5
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Tucker NR, Chaffin M, Bedi KC, Papangeli I, Akkad AD, Arduini A, Hayat S, Eraslan G, Muus C, Bhattacharyya RP, Stegmann CM, Margulies KB, Ellinor PT. Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis. Circulation 2020; 142:708-710. [PMID: 32795091 PMCID: PMC7424896 DOI: 10.1161/circulationaha.120.047911] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Supplemental Digital Content is available in the text.
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Affiliation(s)
- Nathan R. Tucker
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA (N.R.T., M.C., A.A., P.T.E.)
| | - Mark Chaffin
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA (N.R.T., M.C., A.A., P.T.E.)
| | - Kenneth C. Bedi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.C.B., K.B.M.)
| | - Irinna Papangeli
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA (I.P., A.-D.A., S.H., C.M.S.)
| | - Amer-Denis Akkad
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA (I.P., A.-D.A., S.H., C.M.S.)
| | - Alessandro Arduini
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA (N.R.T., M.C., A.A., P.T.E.)
| | - Sikander Hayat
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA (I.P., A.-D.A., S.H., C.M.S.)
| | - Gökcen Eraslan
- The Broad Institute of MIT and Harvard, Cambridge, MA (G.E., C.M., R.P.B.)
| | - Christoph Muus
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA (C.M.)
| | | | - Christian M. Stegmann
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA (I.P., A.-D.A., S.H., C.M.S.)
| | | | - Kenneth B. Margulies
- Perelman School of Medicine, University of Pennsylvania, Philadelphia (K.C.B., K.B.M.)
| | - Patrick T. Ellinor
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA (N.R.T., M.C., A.A., P.T.E.)
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6
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Tucker NR, Chaffin M, Fleming SJ, Hall AW, Parsons VA, Bedi KC, Akkad AD, Herndon CN, Arduini A, Papangeli I, Roselli C, Aguet F, Choi SH, Ardlie KG, Babadi M, Margulies KB, Stegmann CM, Ellinor PT. Transcriptional and Cellular Diversity of the Human Heart. Circulation 2020; 142:466-482. [PMID: 32403949 PMCID: PMC7666104 DOI: 10.1161/circulationaha.119.045401] [Citation(s) in RCA: 250] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The human heart requires a complex ensemble of specialized cell types to perform its essential function. A greater knowledge of the intricate cellular milieu of the heart is critical to increase our understanding of cardiac homeostasis and pathology. As recent advances in low-input RNA sequencing have allowed definitions of cellular transcriptomes at single-cell resolution at scale, we have applied these approaches to assess the cellular and transcriptional diversity of the nonfailing human heart. METHODS Microfluidic encapsulation and barcoding was used to perform single nuclear RNA sequencing with samples from 7 human donors, selected for their absence of overt cardiac disease. Individual nuclear transcriptomes were then clustered based on transcriptional profiles of highly variable genes. These clusters were used as the basis for between-chamber and between-sex differential gene expression analyses and intersection with genetic and pharmacologic data. RESULTS We sequenced the transcriptomes of 287 269 single cardiac nuclei, revealing 9 major cell types and 20 subclusters of cell types within the human heart. Cellular subclasses include 2 distinct groups of resident macrophages, 4 endothelial subtypes, and 2 fibroblast subsets. Comparisons of cellular transcriptomes by cardiac chamber or sex reveal diversity not only in cardiomyocyte transcriptional programs but also in subtypes involved in extracellular matrix remodeling and vascularization. Using genetic association data, we identified strong enrichment for the role of cell subtypes in cardiac traits and diseases. Intersection of our data set with genes on cardiac clinical testing panels and the druggable genome reveals striking patterns of cellular specificity. CONCLUSIONS Using large-scale single nuclei RNA sequencing, we defined the transcriptional and cellular diversity in the normal human heart. Our identification of discrete cell subtypes and differentially expressed genes within the heart will ultimately facilitate the development of new therapeutics for cardiovascular diseases.
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Affiliation(s)
- Nathan R. Tucker
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA 02114
- Masonic Medical Research Institute, Utica, NY, USA 13501
| | - Mark Chaffin
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
| | - Stephen J. Fleming
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
| | - Amelia W. Hall
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA 02114
| | - Victoria A. Parsons
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA 02114
| | - Kenneth C. Bedi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - Amer-Denis Akkad
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, 02142
| | - Caroline N. Herndon
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
| | - Alessandro Arduini
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
| | - Irinna Papangeli
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, 02142
| | - Carolina Roselli
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- University Medical Center Groningen, University of Groningen, 9712 CP, Groningen, NL
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
| | - Seung Hoan Choi
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
| | | | - Mehrtash Babadi
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
| | - Kenneth B. Margulies
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - Christian M. Stegmann
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, 02142
| | - Patrick T. Ellinor
- Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA 02114
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7
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Tucker NR, Chaffin M, Bedi KC, Papangeli I, Akkad AD, Arduini A, Hayat S, Eraslan G, Muus C, Bhattacharyya R, Stegmann CM, Margulies KB, Ellinor PT. Myocyte Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2 mediated myocarditis. medRxiv 2020. [PMID: 32511660 DOI: 10.1101/2020.04.09.20059204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a global pandemic caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 infection of host cells occurs predominantly via binding of the viral surface spike protein to the human angiotensin-converting enzyme 2 (ACE2) receptor. Hypertension and pre-existing cardiovascular disease are risk factors for morbidity from COVID-19, and it remains uncertain whether the use of angiotensin converting enzyme inhibitors (ACEi) or angiotensin receptor blockers (ARB) impacts infection and disease. Here, we aim to shed light on this question by assessing ACE2 expression in normal and diseased human myocardial samples profiled by bulk and single nucleus RNA-seq.
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8
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Ayaz P, Andres D, Kwiatkowski DA, Kolbe CC, Lienau P, Siemeister G, Lücking U, Stegmann CM. Conformational Adaption May Explain the Slow Dissociation Kinetics of Roniciclib (BAY 1000394), a Type I CDK Inhibitor with Kinetic Selectivity for CDK2 and CDK9. ACS Chem Biol 2016; 11:1710-9. [PMID: 27090615 DOI: 10.1021/acschembio.6b00074] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Roniciclib (BAY 1000394) is a type I pan-CDK (cyclin-dependent kinase) inhibitor which has revealed potent efficacy in xenograft cancer models. Here, we show that roniciclib displays prolonged residence times on CDK2 and CDK9, whereas residence times on other CDKs are transient, thus giving rise to a kinetic selectivity of roniciclib. Surprisingly, variation of the substituent at the 5-position of the pyrimidine scaffold results in changes of up to 3 orders of magnitude of the drug-target residence time. CDK2 X-ray cocrystal structures have revealed a DFG-loop adaption for the 5-(trifluoromethyl) substituent, while for hydrogen and bromo substituents the DFG loop remains in its characteristic type I inhibitor position. In tumor cells, the prolonged residence times of roniciclib on CDK2 and CDK9 are reflected in a sustained inhibitory effect on retinoblastoma protein (RB) phosphorylation, indicating that the target residence time on CDK2 may contribute to sustained target engagement and antitumor efficacy.
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Affiliation(s)
- Pelin Ayaz
- Bayer Pharma AG, Drug Discovery, Lead Discovery
Berlin, Berlin, Germany
| | - Dorothee Andres
- Bayer Pharma AG, Drug Discovery, Lead Discovery
Berlin, Berlin, Germany
| | | | | | - Philip Lienau
- Bayer Pharma AG, Drug Discovery, Research Pharmacokinetics, Berlin, Germany
| | | | - Ulrich Lücking
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry, Berlin, Germany
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9
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Prinz F, Puetter V, Holton SJ, Andres D, Stegmann CM, Kwiatkowski D, Prechtl S, Petersen K, Beckmann G, Kreft B, Mumberg D, Fernández-Montalván A. Functional and Structural Characterization of Bub3·BubR1 Interactions Required for Spindle Assembly Checkpoint Signaling in Human Cells. J Biol Chem 2016; 291:11252-67. [PMID: 27030009 DOI: 10.1074/jbc.m115.702142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 11/02/2015] [Indexed: 02/02/2023] Open
Abstract
The spindle assembly checkpoint (SAC) is an essential safeguarding mechanism devised to ensure equal chromosome distribution in daughter cells upon mitosis. The proteins Bub3 and BubR1 are key components of the mitotic checkpoint complex, an essential part of the molecular machinery on which the SAC relies. In the present work we have performed a detailed functional and biochemical characterization of the interaction between human Bub3 and BubR1 in cells and in vitro Our results demonstrate that genetic knockdown of Bub3 abrogates the SAC, promotes apoptosis, and inhibits the proliferation of human cancer cells. We also show that the integrity of the human mitotic checkpoint complex depends on the specific recognition between BubR1 and Bub3, for which the BubR1 Gle2 binding sequence motif is essential. This 1:1 binding event is high affinity, enthalpy-driven and with slow dissociation kinetics. The affinity, kinetics, and thermodynamic parameters of the interaction are differentially modulated by small regions in the N and C termini of the Gle2 binding domain sequence, suggesting the existence of "hotspots" for this protein-protein interaction. Furthermore, we show that specific disruption of endogenous BubR1·Bub3 complexes in human cancer cells phenocopies the effects observed in gene targeting experiments. Our work enhances the current understanding of key members of the SAC and paves the road for the pursuit of novel targeted cancer therapies based on SAC inhibition.
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Affiliation(s)
- Florian Prinz
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
| | | | | | | | | | | | | | - Kirstin Petersen
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
| | | | - Bertolt Kreft
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
| | - Dominik Mumberg
- TRG Oncology, Bayer Pharma AG, Global Drug Discovery, 13353 Berlin, Germany
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10
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Ferreira de Freitas R, Eram MS, Szewczyk MM, Steuber H, Smil D, Wu H, Li F, Senisterra G, Dong A, Brown PJ, Hitchcock M, Moosmayer D, Stegmann CM, Egner U, Arrowsmith C, Barsyte-Lovejoy D, Vedadi M, Schapira M. Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor. J Med Chem 2016; 59:1176-83. [PMID: 26824386 DOI: 10.1021/acs.jmedchem.5b01772] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein methyltransferases (PMTs) are a promising target class in oncology and other disease areas. They are composed of SET domain methyltransferases and structurally unrelated Rossman-fold enzymes that include protein arginine methyltransferases (PRMTs). In the absence of a well-defined medicinal chemistry tool-kit focused on PMTs, most current inhibitors were identified by screening large and diverse libraries of leadlike molecules. So far, no successful fragment-based approach was reported against this target class. Here, by deconstructing potent PRMT inhibitors, we find that chemical moieties occupying the substrate arginine-binding site can act as efficient fragment inhibitors. Screening a fragment library against PRMT6 produced numerous hits, including a 300 nM inhibitor (ligand efficiency of 0.56) that decreased global histone 3 arginine 2 methylation in cells, and can serve as a warhead for the development of PRMT chemical probes.
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Affiliation(s)
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Holger Steuber
- Pharmaceuticals Division, Bayer Pharma AG, 13353 Berlin, Germany
| | - David Smil
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Guillermo Senisterra
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada
| | - Marion Hitchcock
- Pharmaceuticals Division, Bayer Pharma AG, 13353 Berlin, Germany
| | - Dieter Moosmayer
- Pharmaceuticals Division, Bayer Pharma AG, 13353 Berlin, Germany
| | | | - Ursula Egner
- Pharmaceuticals Division, Bayer Pharma AG, 13353 Berlin, Germany
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto , Toronto, ON M5G 1L7, Canada
| | | | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada
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11
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Drögemüller J, Stegmann CM, Mandal A, Steiner T, Burmann BM, Gottesman ME, Wöhrl BM, Rösch P, Wahl MC, Schweimer K. An autoinhibited state in the structure of Thermotoga maritima NusG. Structure 2013; 21:365-75. [PMID: 23415559 DOI: 10.1016/j.str.2012.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 11/19/2012] [Accepted: 12/21/2012] [Indexed: 01/05/2023]
Abstract
NusG is a conserved regulatory protein interacting with RNA polymerase (RNAP) and other proteins to form multicomponent complexes that modulate transcription. The crystal structure of Thermotoga maritima NusG (TmNusG) shows a three-domain architecture, comprising well-conserved amino-terminal (NTD) and carboxy-terminal (CTD) domains with an additional, species-specific domain inserted into the NTD. NTD and CTD directly contact each other, occluding a surface of the NTD for binding to RNAP and a surface on the CTD interacting either with transcription termination factor Rho or transcription antitermination factor NusE. NMR spectroscopy confirmed the intramolecular NTD-CTD interaction up to the optimal growth temperature of Thermotoga maritima. The domain interaction involves a dynamic equilibrium between open and closed states and contributes significantly to the overall fold stability of the protein. Wild-type TmNusG and deletion variants could not replace endogenous Escherichia coli NusG, suggesting that the NTD-CTD interaction of TmNusG represents an autoinhibited state.
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Affiliation(s)
- Johanna Drögemüller
- Lehrstuhl Biopolymere und Forschungszentrum für Biomakromoleküle, Universität Bayreuth, Universitätsstrasse 30, Bayreuth, Germany
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12
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Stegmann CM, Seeliger D, Sheldrick GM, de Groot BL, Wahl MC. The thermodynamic influence of trapped water molecules on a protein-ligand interaction. Acta Crystallogr A 2010. [DOI: 10.1107/s0108767310099599] [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: 11/10/2022] Open
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13
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Stegmann CM, Lührmann R, Wahl MC. The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein. PLoS One 2010; 5:e10013. [PMID: 20368803 PMCID: PMC2848857 DOI: 10.1371/journal.pone.0010013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 03/08/2010] [Indexed: 12/02/2022] Open
Abstract
Background The removal of introns from pre-mRNA is carried out by a large macromolecular machine called the spliceosome. The peptidyl-prolyl cis/trans isomerase PPIL1 is a component of the human spliceosome and binds to the spliceosomal SKIP protein via a binding site distinct from its active site. Principal Findings Here, we have studied the PPIL1 protein and its interaction with SKIP biochemically and by X-ray crystallography. A minimal linear binding epitope derived from the SKIP protein could be determined using a peptide array. A 36-residue region of SKIP centred on an eight-residue epitope suffices to bind PPIL1 in pull-down experiments. The crystal structure of PPIL1 in complex with the inhibitor cyclosporine A (CsA) was obtained at a resolution of 1.15 Å and exhibited two bound Cd2+ ions that enabled SAD phasing. PPIL1 residues that have previously been implicated in binding of SKIP are involved in the coordination of Cd2+ ions in the present crystal structure. Employing the present crystal structure, the determined minimal binding epitope and previously published NMR data [1], a molecular docking study was performed. In the docked model of the PPIL1·SKIP interaction, a proline residue of SKIP is buried in a hydrophobic pocket of PPIL1. This hydrophobic contact is encircled by several hydrogen bonds between the SKIP peptide and PPIL1. Conclusion We characterized a short, linear epitope of SKIP that is sufficient to bind the PPIL1 protein. Our data indicate that this SKIP peptide could function in recruiting PPIL1 into the core of the spliceosome. We present a molecular model for the binding mode of SKIP to PPIL1 which emphasizes the versatility of cyclophilin-type PPIases to engage in additional interactions with other proteins apart from active site contacts despite their limited surface area.
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Affiliation(s)
- Christian M. Stegmann
- Max-Planck-Institut für biophysikalische Chemie, Zelluläre Biochemie/Makromolekulare Röntgenkristallographie, Göttingen, Germany
- Max-Planck-Institut für biophysikalische Chemie, AG Strukturbiochemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Reinhard Lührmann
- Max-Planck-Institut für biophysikalische Chemie, Zelluläre Biochemie/Makromolekulare Röntgenkristallographie, Göttingen, Germany
| | - Markus C. Wahl
- Max-Planck-Institut für biophysikalische Chemie, Zelluläre Biochemie/Makromolekulare Röntgenkristallographie, Göttingen, Germany
- Max-Planck-Institut für biophysikalische Chemie, AG Strukturbiochemie, Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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14
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Jin R, Sikorra S, Stegmann CM, Pich A, Binz T, Brunger AT. Structural and biochemical studies of botulinum neurotoxin serotype C1 light chain protease: implications for dual substrate specificity. Biochemistry 2007; 46:10685-93. [PMID: 17718519 DOI: 10.1021/bi701162d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clostridial neurotoxins are the causative agents of the neuroparalytic disease botulism and tetanus. They block neurotransmitter release through specific proteolysis of one of the three soluble N-ethylmaleimide-sensitive-factor attachment protein receptors (SNAREs) SNAP-25, syntaxin, and synaptobrevin, which constitute part of the synaptic vesicle fusion machinery. The catalytic component of the clostridial neurotoxins is their light chain (LC), a Zn2+ endopeptidase. There are seven structurally and functionally related botulinum neurotoxins (BoNTs), termed serotype A to G, and tetanus neurotoxin (TeNT). Each of them exhibits unique specificity for their target SNAREs and peptide bond(s) they cleave. The mechanisms of action for substrate recognition and target cleavage are largely unknown. Here, we report structural and biochemical studies of BoNT/C1-LC, which is unique among BoNTs in that it exhibits dual specificity toward both syntaxin and SNAP-25. A distinct pocket (S1') near the active site likely achieves the correct register for the cleavage site by only allowing Ala as the P1' residue for both SNAP-25 and syntaxin. Mutations of this SNAP-25 residue dramatically reduce enzymatic activity. The remote alpha-exosite that was previously identified in the complex of BoNT/A-LC and SNAP-25 is structurally conserved in BoNT/C1. However, mutagenesis experiments show that the alpha-exosite of BoNT/C1 plays a less stringent role in substrate discrimination in comparison to that of BoNT/A, which could account for its dual substrate specificity.
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Affiliation(s)
- Rongsheng Jin
- Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305, USA
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15
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Burnett JC, Ruthel G, Stegmann CM, Panchal RG, Nguyen TL, Hermone AR, Stafford RG, Lane DJ, Kenny TA, McGrath CF, Wipf P, Stahl AM, Schmidt JJ, Gussio R, Brunger AT, Bavari S. Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons. J Biol Chem 2006; 282:5004-5014. [PMID: 17092934 DOI: 10.1074/jbc.m608166200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An efficient research strategy integrating empirically guided, structure-based modeling and chemoinformatics was used to discover potent small molecule inhibitors of the botulinum neurotoxin serotype A light chain. First, a modeled binding mode for inhibitor 2-mercapto-3-phenylpropionyl-RATKML (K(i) = 330 nM) was generated, and required the use of a molecular dynamic conformer of the enzyme displaying the reorientation of surface loops bordering the substrate binding cleft. These flexible loops are conformationally variable in x-ray crystal structures, and the model predicted that they were pivotal for providing complementary binding surfaces and solvent shielding for the pseudo-peptide. The docked conformation of 2-mercapto-3-phenylpropionyl-RATKML was then used to refine our pharmacophore for botulinum serotype A light chain inhibition. Data base search queries derived from the pharmacophore were employed to mine small molecule (non-peptidic) inhibitors from the National Cancer Institute's Open Repository. Four of the inhibitors possess K(i) values ranging from 3.0 to 10.0 microM. Of these, NSC 240898 is a promising lead for therapeutic development, as it readily enters neurons, exhibits no neuronal toxicity, and elicits dose-dependent protection of synaptosomal-associated protein (of 25 kDa) in a primary culture of embryonic chicken neurons. Isothermal titration calorimetry showed that the interaction between NSC 240898 and the botulinum A light chain is largely entropy-driven, and occurs with a 1:1 stoichiometry and a dissociation constant of 4.6 microM.
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Affiliation(s)
- James C Burnett
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Gordon Ruthel
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Christian M Stegmann
- Howard Hughes Medical Institute (HHMI) and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and the Stanford Synchrotron Radiation Laboratory, Stanford University, School of Medicine, Stanford, California 94305, and the
| | - Rekha G Panchal
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Tam L Nguyen
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Ann R Hermone
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Robert G Stafford
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Douglas J Lane
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Tara A Kenny
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Connor F McGrath
- Target Structure-based Drug Discovery Group, SAIC-Frederick, Inc., and the National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Peter Wipf
- Combinatorial Chemistry Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Andrea M Stahl
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - James J Schmidt
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702
| | - Rick Gussio
- Information Technology Branch, Developmental Therapeutics Program, National Cancer Institute-Frederick, Frederick, Maryland 21702
| | - Axel T Brunger
- Howard Hughes Medical Institute (HHMI) and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and the Stanford Synchrotron Radiation Laboratory, Stanford University, School of Medicine, Stanford, California 94305, and the.
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702.
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