1
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Day JEH, Berdini V, Castro J, Chessari G, Davies TG, Day PJ, St Denis JD, Fujiwara H, Fukaya S, Hamlett CCF, Hearn K, Hiscock SD, Holvey RS, Ito S, Kandola N, Kodama Y, Liebeschuetz JW, Martins V, Matsuo K, Mortenson PN, Muench S, Nakatsuru Y, Ochiiwa H, Palmer N, Peakman T, Price A, Reader M, Rees DC, Rich SJ, Shah A, Shibata Y, Smyth T, Twigg DG, Wallis NG, Williams G, Wilsher NE, Woodhead A, Shimamura T, Johnson CN. Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2). J Med Chem 2024. [PMID: 38462716 DOI: 10.1021/acs.jmedchem.3c02118] [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: 03/12/2024]
Abstract
The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signaling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signaling and inhibit the proliferation of RTK-driven cancer cell lines. Here, we describe the first reported fragment-to-lead campaign against SHP2, where X-ray crystallography and biophysical techniques were used to identify fragments binding to multiple sites on SHP2. Structure-guided optimization, including several computational methods, led to the discovery of two structurally distinct series of SHP2 inhibitors binding to the previously reported allosteric tunnel binding site (Tunnel Site). One of these series was advanced to a low-nanomolar lead that inhibited tumor growth when dosed orally to mice bearing HCC827 xenografts. Furthermore, a third series of SHP2 inhibitors was discovered binding to a previously unreported site, lying at the interface of the C-terminal SH2 and catalytic domains.
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Affiliation(s)
- James E H Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joan Castro
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Philip J Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Jeffrey D St Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Hideto Fujiwara
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoshi Fukaya
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Steven D Hiscock
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoru Ito
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Navrohit Kandola
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yasuo Kodama
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - John W Liebeschuetz
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Kenichi Matsuo
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sandra Muench
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoko Nakatsuru
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Hiroaki Ochiiwa
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Nicholas Palmer
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Amanda Price
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Michael Reader
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - David C Rees
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Alpesh Shah
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoshihiro Shibata
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Tomoko Smyth
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola G Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Glyn Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola E Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Tadashi Shimamura
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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2
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O’Neill MJ, Ng CA, Aizawa T, Sala L, Bains S, Denjoy I, Winbo A, Ullah R, Shen Q, Tan CY, Kozek K, Vanags LR, Mitchell DW, Shen A, Wada Y, Kashiwa A, Crotti L, Dagradi F, Musu G, Spazzolini C, Neves R, Bos JM, Giudicessi JR, Bledsoe X, Lancaster M, Glazer AM, Roden DM, Leenhardt A, Salem JE, Earle N, Stiles R, Agee T, Johnson CN, Horie M, Skinner J, Extramiana F, Ackerman MJ, Schwartz PJ, Ohno S, Vandenberg JI, Kroncke BM. Prognostic Value of Multiplexed Assays of Variant Effect and Automated Patch-clamping for KCNH2-LQTS Risk Stratification. medRxiv 2024:2024.02.01.24301443. [PMID: 38370760 PMCID: PMC10871451 DOI: 10.1101/2024.02.01.24301443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background Long QT syndrome (LQTS) is a lethal arrhythmia condition, frequently caused by rare loss-of-function variants in the cardiac potassium channel encoded by KCNH2. Variant-based risk stratification is complicated by heterogenous clinical data, incomplete penetrance, and low-throughput functional data. Objective To test the utility of variant-specific features, including high-throughput functional data, to predict cardiac events among KCNH2 variant heterozygotes. Methods We quantified cell-surface trafficking of 18,323 variants in KCNH2 and recorded potassium current densities for 506 KCNH2 variants. Next, we deeply phenotyped 1150 KCNH2 missense variant patients, including ECG features, cardiac event history (528 total cardiac events), and mortality. We then assessed variant functional, in silico, structural, and LQTS penetrance data to stratify event-free survival for cardiac events in the study cohort. Results Variant-specific current density (HR 0.28 [0.13-0.60]) and estimates of LQTS penetrance incorporating MAVE data (HR 3.16 [1.59-6.27]) were independently predictive of severe cardiac events when controlling for patient-specific features. Risk prediction models incorporating these data significantly improved prediction of 20 year cardiac events (AUC 0.79 [0.75-0.82]) over patient-only covariates (QTc and sex) (AUC 0.73 [0.70-0.77]). Conclusion We show that high-throughput functional data, and other variant-specific features, meaningfully contribute to both diagnosis and prognosis of a clinically actionable monogenic disease.
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Affiliation(s)
- Matthew J. O’Neill
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Nashville, TN, USA
- These authors contributed equally
| | - Chai-Ann Ng
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
- These authors contributed equally
| | - Takanori Aizawa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Luca Sala
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Sahej Bains
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Isabelle Denjoy
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Annika Winbo
- Department of Physiology, University of Auckland, Auckland, New Zealand
| | - Rizwan Ullah
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qianyi Shen
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Chek-Ying Tan
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Krystian Kozek
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Loren R. Vanags
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Devyn W. Mitchell
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alex Shen
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuko Wada
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Asami Kashiwa
- Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine Kyoto, Japan
| | - Lia Crotti
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
- Department of Medicine and Surgery, University Milano Bicocca, Milan, Italy
| | - Federica Dagradi
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Giulia Musu
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Carla Spazzolini
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Raquel Neves
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - J. Martijn Bos
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - John R. Giudicessi
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Xavier Bledsoe
- Vanderbilt University School of Medicine, Medical Scientist Training Program, Nashville, TN, USA
| | - Megan Lancaster
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew M. Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M. Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Antoine Leenhardt
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Joe-Elie Salem
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Nikki Earle
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Rachael Stiles
- Department of Cardiology, Waikato Hospital, Hamilton, New Zealand
| | - Taylor Agee
- Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA
| | | | - Minoru Horie
- Department of Cardiovascular Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Jonathan Skinner
- Sydney Children’s Hospital Network, University of Sydney, Sydney, Australia
| | - Fabrice Extramiana
- Department of Cardiovascular Medicine, Hôpital Bichat, APHP, Université de Paris Cité, Paris, France
| | - Michael J. Ackerman
- Department of Molecular Pharmacology & Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN, USA
| | - Peter J. Schwartz
- IRCCS, Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milano, Italy
| | - Seiko Ohno
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Jamie I. Vandenberg
- Mark Cowley Lidwill Research Program in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Brett M. Kroncke
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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3
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de Winter JM, Molenaar JP, Yuen M, van der Pijl R, Shen S, Conijn S, van de Locht M, Willigenburg M, Bogaards SJ, van Kleef ES, Lassche S, Persson M, Rassier DE, Sztal TE, Ruparelia AA, Oorschot V, Ramm G, Hall TE, Xiong Z, Johnson CN, Li F, Kiss B, Lozano-Vidal N, Boon RA, Marabita M, Nogara L, Blaauw B, Rodenburg RJ, Küsters B, Doorduin J, Beggs AH, Granzier H, Campbell K, Ma W, Irving T, Malfatti E, Romero NB, Bryson-Richardson RJ, van Engelen BG, Voermans NC, Ottenheijm CA. KBTBD13 is an actin-binding protein that modulates muscle kinetics. J Clin Invest 2024; 134:e179111. [PMID: 38299595 PMCID: PMC10836800 DOI: 10.1172/jci179111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
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4
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Townley C, Branduardi D, Chessari G, Cons BD, Griffiths-Jones C, Hall RJ, Johnson CN, Ochi Y, Whibley S, Grainger R. Enabling synthesis in fragment-based drug discovery (FBDD): microscale high-throughput optimisation of the medicinal chemist's toolbox reactions. RSC Med Chem 2023; 14:2699-2713. [PMID: 38107176 PMCID: PMC10718589 DOI: 10.1039/d3md00495c] [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] [Received: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 12/19/2023] Open
Abstract
Miniaturised high-throughput experimentation (HTE) is widely employed in industrial and academic laboratories for rapid reaction optimisation using material-limited, multifactorial reaction condition screening. In fragment-based drug discovery (FBDD), common toolbox reactions such as the Suzuki-Miyaura and Buchwald-Hartwig cross couplings can be hampered by the fragment's intrinsic heteroatom-rich pharmacophore which is required for ligand-protein binding. At Astex, we are using microscale HTE to speed up reaction optimisation and prevent target down-prioritisation. By identifying catalyst/base/solvent combinations which tolerate unprotected heteroatoms we can rapidly optimise key cross-couplings and expedite route design by avoiding superfluous protecting group manipulations. However, HTE requires extensive upfront training, and this modern automated synthesis technique largely differs to the way organic chemists are traditionally trained. To make HTE accessible to all our synthetic chemists we have developed a semi-automated workflow enabled by pre-made 96-well screening kits, rapid analytical methods and in-house software development, which is empowering chemists at Astex to run HTE screens independently with minimal training.
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Affiliation(s)
- Chloe Townley
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Davide Branduardi
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Gianni Chessari
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Benjamin D Cons
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Richard J Hall
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Yuji Ochi
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Stuart Whibley
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rachel Grainger
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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5
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Williams RB, Alam Afsar MN, Tikunova S, Kou Y, Fang X, Somarathne RP, Gyawu RF, Knotts GM, Agee TA, Garcia SA, Losordo LD, Fitzkee NC, Kekenes-Huskey PM, Davis JP, Johnson CN. Human disease-associated calmodulin mutations alter calcineurin function through multiple mechanisms. Cell Calcium 2023; 113:102752. [PMID: 37245392 PMCID: PMC10330910 DOI: 10.1016/j.ceca.2023.102752] [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: 12/17/2022] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
Calmodulin (CaM) is a ubiquitous, calcium-sensing protein that regulates a multitude of processes throughout the body. In response to changes in [Ca2+], CaM modifies, activates, and deactivates enzymes and ion channels, as well as many other cellular processes. The importance of CaM is highlighted by the conservation of an identical amino acid sequence in all mammals. Alterations to CaM amino acid sequence were once thought to be incompatible with life. During the last decade modifications to the CaM protein sequence have been observed in patients suffering from life-threatening heart disease (calmodulinopathy). Thus far, inadequate or untimely interaction between mutant CaM and several proteins (LTCC, RyR2, and CaMKII) have been identified as mechanisms underlying calmodulinopathy. Given the extensive number of CaM interactions in the body, there are likely many consequences for altering CaM protein sequence. Here, we demonstrate that disease-associated CaM mutations alter the sensitivity and activity of the Ca2+-CaM-enhanced serine/threonine phosphatase calcineurin (CaN). Biophysical characterization by circular dichroism, solution NMR spectroscopy, stopped-flow kinetic measurements, and MD simulations provide mechanistic insight into mutation dysfunction as well as highlight important aspects of CaM Ca2+ signal transduction. We find that individual CaM point mutations (N53I, F89L, D129G, and F141L) impair CaN function, however, the mechanisms are not the same. Specifically, individual point mutations can influence or modify the following properties: CaM binding, Ca2+ binding, and/or Ca2+kinetics. Moreover, structural aspects of the CaNCaM complex can be altered in manners that indicate changes to allosteric transmission of CaM binding to the enzyme active site. Given that loss of CaN function can be fatal, as well as evidence that CaN modifies ion channels already associated with calmodulinopathy, our results raise the possibility that altered CaN function contributes to calmodulinopathy.
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Affiliation(s)
- Ryan B Williams
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Md Nure Alam Afsar
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Svetlana Tikunova
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Yongjun Kou
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Xuan Fang
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Radha P Somarathne
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Rita F Gyawu
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Garrett M Knotts
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Taylor A Agee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Sara A Garcia
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Luke D Losordo
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A.
| | - Christopher N Johnson
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A; Vanderbilt Center for Arrhythmia Research and Therapeutics, Nashville TN 37232, U.S.A.
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6
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Taylor CJ, Felton KC, Wigh D, Jeraal MI, Grainger R, Chessari G, Johnson CN, Lapkin AA. Accelerated Chemical Reaction Optimization Using Multi-Task Learning. ACS Cent Sci 2023; 9:957-968. [PMID: 37252348 PMCID: PMC10214532 DOI: 10.1021/acscentsci.3c00050] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/31/2023]
Abstract
Functionalization of C-H bonds is a key challenge in medicinal chemistry, particularly for fragment-based drug discovery (FBDD) where such transformations require execution in the presence of polar functionality necessary for protein binding. Recent work has shown the effectiveness of Bayesian optimization (BO) for the self-optimization of chemical reactions; however, in all previous cases these algorithmic procedures have started with no prior information about the reaction of interest. In this work, we explore the use of multitask Bayesian optimization (MTBO) in several in silico case studies by leveraging reaction data collected from historical optimization campaigns to accelerate the optimization of new reactions. This methodology was then translated to real-world, medicinal chemistry applications in the yield optimization of several pharmaceutical intermediates using an autonomous flow-based reactor platform. The use of the MTBO algorithm was shown to be successful in determining optimal conditions of unseen experimental C-H activation reactions with differing substrates, demonstrating an efficient optimization strategy with large potential cost reductions when compared to industry-standard process optimization techniques. Our findings highlight the effectiveness of the methodology as an enabling tool in medicinal chemistry workflows, representing a step-change in the utilization of data and machine learning with the goal of accelerated reaction optimization.
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Affiliation(s)
- Connor J. Taylor
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
- Innovation
Centre in Digital Molecular Technologies, Yusuf Hamied Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
| | - Kobi C. Felton
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Daniel Wigh
- Innovation
Centre in Digital Molecular Technologies, Yusuf Hamied Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Mohammed I. Jeraal
- Cambridge
Centre for Advanced Research and Education in Singapore Ltd., 1 Create Way, CREATE Tower #05-05, 138602, Singapore
| | - Rachel Grainger
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Christopher N. Johnson
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Alexei A. Lapkin
- Innovation
Centre in Digital Molecular Technologies, Yusuf Hamied Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United
Kingdom
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore Ltd., 1 Create Way, CREATE Tower #05-05, 138602, Singapore
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7
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Scoleri VP, Ingram J, Johnson CN, Jones ME. Top predator restricts the niche breadth of prey: effects of assisted colonization of Tasmanian devils on a widespread omnivorous prey. Proc Biol Sci 2023; 290:20222113. [PMID: 36919429 PMCID: PMC10015323 DOI: 10.1098/rspb.2022.2113] [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] [Indexed: 03/16/2023] Open
Abstract
Few landscape-scale experiments test the effects of predators on the abundance and distribution of prey across habitat gradients. We use the assisted colonization of a top predator, the Tasmanian devil (Sarcophilus harrisii), to test the impacts of predation on the abundance, habitat use and temporal activity of a widespread prey species, the omnivorous common brushtail possum (Trichosurus vulpecula). Before introduction of devils to Maria Island, Tasmania, Australia, in 2012, possums were abundant in open grasslands as well as forests. Predation by devils caused high mortality of possums in grasslands, but individuals with access to trees had a higher survival probability. Possum abundance declined across the whole island from 2012-2016, as possums disappeared almost completely from grasslands and declined in drier forests with more open understorey. Abundance remained stable in wet forests, which are not preferred habitat for possums but provide better refuge from devils. Abundance and habitat use of possums remained unchanged at a control site on the adjacent Tasmanian mainland, where the devil population was low and stable. This study demonstrates how spatial variation in predator-caused mortality can limit both abundance and habitat breadth in generalist prey species, excluding them entirely from certain habitats.
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Affiliation(s)
- Vincent P Scoleri
- School of Natural Sciences, University of Tasmania, Sandy Bay 7005, Australia
| | - Janeane Ingram
- School of Geography, Planning and Spatial Sciences, University of Tasmania, Sandy Bay 7005, Australia
| | - Christopher N Johnson
- School of Natural Sciences, University of Tasmania, Sandy Bay 7005, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Sandy Bay 7005, Australia
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Sandy Bay 7005, Australia
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8
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Taylor CJ, Pomberger A, Felton KC, Grainger R, Barecka M, Chamberlain TW, Bourne RA, Johnson CN, Lapkin AA. A Brief Introduction to Chemical Reaction Optimization. Chem Rev 2023; 123:3089-3126. [PMID: 36820880 PMCID: PMC10037254 DOI: 10.1021/acs.chemrev.2c00798] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
From the start of a synthetic chemist's training, experiments are conducted based on recipes from textbooks and manuscripts that achieve clean reaction outcomes, allowing the scientist to develop practical skills and some chemical intuition. This procedure is often kept long into a researcher's career, as new recipes are developed based on similar reaction protocols, and intuition-guided deviations are conducted through learning from failed experiments. However, when attempting to understand chemical systems of interest, it has been shown that model-based, algorithm-based, and miniaturized high-throughput techniques outperform human chemical intuition and achieve reaction optimization in a much more time- and material-efficient manner; this is covered in detail in this paper. As many synthetic chemists are not exposed to these techniques in undergraduate teaching, this leads to a disproportionate number of scientists that wish to optimize their reactions but are unable to use these methodologies or are simply unaware of their existence. This review highlights the basics, and the cutting-edge, of modern chemical reaction optimization as well as its relation to process scale-up and can thereby serve as a reference for inspired scientists for each of these techniques, detailing several of their respective applications.
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Affiliation(s)
- Connor J Taylor
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Alexander Pomberger
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Kobi C Felton
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Rachel Grainger
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Magda Barecka
- Chemical Engineering Department, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Chemistry and Chemical Biology Department, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, 138602 Singapore
| | - Thomas W Chamberlain
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Richard A Bourne
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Alexei A Lapkin
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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9
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Hamer RP, Andersen GE, Hradsky BA, Troy SN, Gardiner RZ, Johnson CN, Jones ME. <i>Corrigendum to</i>: Differing effects of productivity on home-range size and population density of a native and an invasive mammalian carnivore. Wildlife Res 2022. [DOI: 10.1071/wr20134_co] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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10
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Hamer RP, Gardiner RZ, Proft KM, Johnson CN, Jones ME. Correction to: ‘A triple threat: high population density, high foraging intensity and flexible habitat preferences explain high impact of feral cats on prey’ (2021) by Hamer
et al.. Proc Biol Sci 2022; 289:20221985. [DOI: 10.1098/rspb.2022.1985] [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: 11/17/2022] Open
Affiliation(s)
- Rowena P. Hamer
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
- Tasmanian Land Conservancy, Hobart, Tasmania 7005, Australia
| | - Riana Z. Gardiner
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Kirstin M. Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | | | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
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11
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Szulcek R, Johnson CN, Pearson JT, Sequeira V. Editorial: Bridging Techniques: Basic Science of Molecules, Cellular Systems, and Whole-Organ Physiology. Front Physiol 2022; 13:879396. [PMID: 35399270 PMCID: PMC8987352 DOI: 10.3389/fphys.2022.879396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Robert Szulcek
- Laboratory of in Vitro Modeling Systems of Pulmonary and Thrombotic Diseases, Institute of Physiology, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Heart Center Berlin, Berlin, Germany
| | | | - James Todd Pearson
- Department of Cardiac Physiology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
- Monash Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, VIC, Australia
| | - Vasco Sequeira
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
- *Correspondence: Vasco Sequeira
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12
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Abstract
Fragment-based drug discovery (FBDD) continues to evolve and make an impact in the pharmaceutical sciences. We summarize successful fragment-to-lead studies that were published in 2020. Having systematically analyzed annual scientific outputs since 2015, we discuss trends and best practices in terms of fragment libraries, target proteins, screening technologies, hit-optimization strategies, and the properties of hit fragments and the leads resulting from them. As well as the tabulated Fragment-to-Lead (F2L) programs, our 2020 literature review identifies several trends and innovations that promise to further increase the success of FBDD. These include developing structurally novel screening fragments, improving fragment-screening technologies, using new computer-aided design and virtual screening approaches, and combining FBDD with other innovative drug-discovery technologies.
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Affiliation(s)
- Iwan J. P. de Esch
- Division
of Medicinal Chemistry, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Daniel A. Erlanson
- Frontier
Medicines, 151 Oyster
Point Blvd., South San Francisco, California 94080, United States
| | - Wolfgang Jahnke
- Novartis
Institutes for Biomedical Research, Chemical
Biology and Therapeutics, 4002 Basel, Switzerland
| | - Christopher N. Johnson
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Louise Walsh
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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13
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Cunningham CX, Aandahl Z, Jones ME, Hamer R, Johnson CN. Regional patterns of continuing decline of the eastern quoll†. Aust Mammalogy 2022. [DOI: 10.1071/am22010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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McGregor H, Moseby K, Johnson CN, Legge S. Effectiveness of thermal cameras compared to spotlights for counts of arid zone mammals across a range of ambient temperatures. Aust Mammalogy 2022. [DOI: 10.1071/am20040] [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: 11/23/2022]
Abstract
Effective monitoring of mammal species is critical to their management. Thermal cameras may enable more accurate detection of nocturnal mammals than visual observation with the aid of spotlights. We aimed to measure improvements in detection provided by thermal cameras, and to determine how these improvements depended on ambient temperatures and mammal species. We monitored small to medium sized mammals in central Australia, including small rodents, bettongs, bilbies, European rabbits, and feral cats. We conducted 20 vehicle-based camera transects using both a spotlight and thermal camera under ambient temperatures ranging from 10°C to 35°C. Thermal cameras resulted in more detections of small rodents and medium sized mammals. There was no increased benefit for feral cats, likely due to their prominent eyeshine. We found a strong relationship between increased detections using thermal cameras and environmental temperature: thermal cameras detected 30% more animals than conventional spotlighting at approximately 15°C, but produced few additional detections above 30°C. Spotlighting may be more versatile as it can be used in a greater range of ambient temperatures, but thermal cameras are more accurate than visual surveys at low temperatures, and can be used to benchmark spotlight surveys.
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15
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Jones ME, Bain GC, Hamer RP, Proft KM, Gardiner RZ, Dixon KJ, Kittipalawattanapol K, Zepeda de Alba AL, Ranyard CE, Munks SA, Barmuta LA, Burridge CP, Johnson CN, Davidson NJ. Research supporting restoration aiming to make a fragmented landscape ‘functional’ for native wildlife. Eco Management Restoration 2021. [DOI: 10.1111/emr.12504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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Williams RB, Johnson CN. A Review of Calcineurin Biophysics with Implications for Cardiac Physiology. Int J Mol Sci 2021; 22:ijms222111565. [PMID: 34768996 PMCID: PMC8583826 DOI: 10.3390/ijms222111565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/20/2022] Open
Abstract
Calcineurin, also known as protein phosphatase 2B, is a heterodimeric serine threonine phosphatase involved in numerous signaling pathways. During the past 50 years, calcineurin has been the subject of extensive investigation. Many of its cellular and physiological functions have been described, and the underlying biophysical mechanisms are the subject of active investigation. With the abundance of techniques and experimental designs utilized to study calcineurin and its numerous substrates, it is difficult to reconcile the available information. There have been a plethora of reports describing the role of calcineurin in cardiac disease. However, a physiological role of calcineurin in healthy cardiomyocyte function requires clarification. Here, we review the seminal biophysical and structural details that are responsible for the molecular function and inhibition of calcineurin. We then focus on literature describing the roles of calcineurin in cardiomyocyte physiology and disease.
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Affiliation(s)
- Ryan B. Williams
- Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA;
| | - Christopher N. Johnson
- Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA;
- Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Correspondence:
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17
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Chessari G, Hardcastle IR, Ahn JS, Anil B, Anscombe E, Bawn RH, Bevan LD, Blackburn TJ, Buck I, Cano C, Carbain B, Castro J, Cons B, Cully SJ, Endicott JA, Fazal L, Golding BT, Griffin RJ, Haggerty K, Harnor SJ, Hearn K, Hobson S, Holvey RS, Howard S, Jennings CE, Johnson CN, Lunec J, Miller DC, Newell DR, Noble MEM, Reeks J, Revill CH, Riedinger C, St Denis JD, Tamanini E, Thomas H, Thompson NT, Vinković M, Wedge SR, Williams PA, Wilsher NE, Zhang B, Zhao Y. Structure-Based Design of Potent and Orally Active Isoindolinone Inhibitors of MDM2-p53 Protein-Protein Interaction. J Med Chem 2021; 64:4071-4088. [PMID: 33761253 DOI: 10.1021/acs.jmedchem.0c02188] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 12/16/2022]
Abstract
Inhibition of murine double minute 2 (MDM2)-p53 protein-protein interaction with small molecules has been shown to reactivate p53 and inhibit tumor growth. Here, we describe rational, structure-guided, design of novel isoindolinone-based MDM2 inhibitors. MDM2 X-ray crystallography, quantum mechanics ligand-based design, and metabolite identification all contributed toward the discovery of potent in vitro and in vivo inhibitors of the MDM2-p53 interaction with representative compounds inducing cytostasis in an SJSA-1 osteosarcoma xenograft model following once-daily oral administration.
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Affiliation(s)
- Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Ian R Hardcastle
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Jong Sook Ahn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Burcu Anil
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Elizabeth Anscombe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Ruth H Bawn
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Luke D Bevan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Timothy J Blackburn
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Ildiko Buck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Celine Cano
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Benoit Carbain
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Juan Castro
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Ben Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sarah J Cully
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Jane A Endicott
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Lynsey Fazal
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Bernard T Golding
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Roger J Griffin
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Karen Haggerty
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Suzannah J Harnor
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Stephen Hobson
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Steven Howard
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Claire E Jennings
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - John Lunec
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Duncan C Miller
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - David R Newell
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Martin E M Noble
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Judith Reeks
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Charlotte H Revill
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Christiane Riedinger
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Jeffrey D St Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Emiliano Tamanini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Huw Thomas
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Neil T Thompson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Mladen Vinković
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Stephen R Wedge
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Pamela A Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola E Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Bian Zhang
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Yan Zhao
- Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
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18
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Bradshaw CJ, Johnson CN, Llewelyn J, Weisbecker V, Strona G, Saltré F. Relative demographic susceptibility does not explain the extinction chronology of Sahul's megafauna. eLife 2021; 10:63870. [PMID: 33783356 PMCID: PMC8043753 DOI: 10.7554/elife.63870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
The causes of Sahul’s megafauna extinctions remain uncertain, although several interacting factors were likely responsible. To examine the relative support for hypotheses regarding plausible ecological mechanisms underlying these extinctions, we constructed the first stochastic, age-structured models for 13 extinct megafauna species from five functional/taxonomic groups, as well as 8 extant species within these groups for comparison. Perturbing specific demographic rates individually, we tested which species were more demographically susceptible to extinction, and then compared these relative sensitivities to the fossil-derived extinction chronology. Our models show that the macropodiformes were the least demographically susceptible to extinction, followed by carnivores, monotremes, vombatiform herbivores, and large birds. Five of the eight extant species were as or more susceptible than the extinct species. There was no clear relationship between extinction susceptibility and the extinction chronology for any perturbation scenario, while body mass and generation length explained much of the variation in relative risk. Our results reveal that the actual mechanisms leading to the observed extinction chronology were unlikely related to variation in demographic susceptibility per se, but were possibly driven instead by finer-scale variation in climate change and/or human prey choice and relative hunting success.
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Affiliation(s)
- Corey Ja Bradshaw
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
| | - Christopher N Johnson
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia.,Dynamics of Eco-Evolutionary Pattern, University of Tasmania, Hobart, Australia
| | - John Llewelyn
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
| | - Vera Weisbecker
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia.,College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Giovanni Strona
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Frédérik Saltré
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
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19
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Proft KM, Bateman BL, Johnson CN, Jones ME, Pauza M, Burridge CP. The effects of weather variability on patterns of genetic diversity in Tasmanian bettongs. Mol Ecol 2021; 30:1777-1790. [PMID: 33590590 DOI: 10.1111/mec.15847] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 12/01/2022]
Abstract
While the effects of climate (long-term, prevailing weather) on species abundance, range and genetic diversity have been widely studied, short-term, localized variations in atmospheric conditions (i.e., weather) can also rapidly alter species' geographical ranges and population sizes, but little is known about how they affect genetic diversity. We investigated the relationship between weather and range-wide genetic diversity in a marsupial, Bettongia gaimardi, using dynamic species distribution models (SDMs). Genetic diversity was lower in parts of the range where the weather-based SDM predicted high variability in probability of B. gaimardi occurrence during 1950-2009. This is probably an effect of lower population sizes and extinction-recolonization cycles in places with highly variable weather. Spatial variation in genetic diversity was also better predicted by mean probabilities of B. gaimardi occurrence from weather- than climate-based SDMs. Our results illustrate the importance of weather in driving population dynamics and species distributions on decadal timescales and thereby in affecting genetic diversity. Modelling the links between changing weather patterns, species distributions and genetic diversity will allow researchers to better forecast biological impacts of climate change.
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Affiliation(s)
- Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Christopher N Johnson
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Matthew Pauza
- Biosecurity Tasmania, Department of Primary Industries, Parks, Water and Environment, Hobart, Tasmania, Australia
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20
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Wheatley R, Buettel JC, Brook BW, Johnson CN, Wilson RP. Accidents alter animal fitness landscapes. Ecol Lett 2021; 24:920-934. [PMID: 33751743 DOI: 10.1111/ele.13705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 08/27/2020] [Revised: 10/13/2020] [Accepted: 01/25/2021] [Indexed: 01/08/2023]
Abstract
Animals alter their habitat use in response to the energetic demands of movement ('energy landscapes') and the risk of predation ('the landscape of fear'). Recent research suggests that animals also select habitats and move in ways that minimise their chance of temporarily losing control of movement and thereby suffering slips, falls, collisions or other accidents, particularly when the consequences are likely to be severe (resulting in injury or death). We propose that animals respond to the costs of an 'accident landscape' in conjunction with predation risk and energetic costs when deciding when, where, and how to move in their daily lives. We develop a novel theoretical framework describing how features of physical landscapes interact with animal size, morphology, and behaviour to affect the risk and severity of accidents, and predict how accident risk might interact with predation risk and energetic costs to dictate movement decisions across the physical landscape. Future research should focus on testing the hypotheses presented here for different real-world systems to gain insight into the relative importance of theorised effects in the field.
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Affiliation(s)
- Rebecca Wheatley
- School of Natural Sciences and the Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Jessie C Buettel
- School of Natural Sciences and the Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Barry W Brook
- School of Natural Sciences and the Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Christopher N Johnson
- School of Natural Sciences and the Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania, Australia
| | - Rory P Wilson
- Department of Biosciences, Swansea University, Swansea, UK
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21
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Hamer RP, Gardiner RZ, Proft KM, Johnson CN, Jones ME. A triple threat: high population density, high foraging intensity and flexible habitat preferences explain high impact of feral cats on prey. Proc Biol Sci 2021; 288:20201194. [PMID: 33402069 DOI: 10.1098/rspb.2020.1194] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 01/25/2023] Open
Abstract
Alien mammalian carnivores have contributed disproportionately to global loss of biodiversity. In Australia, predation by the feral cat and red fox is one of the most significant causes of the decline of native vertebrates. To discover why cats have greater impacts on prey than native predators, we compared the ecology of the feral cat to a marsupial counterpart, the spotted-tailed quoll. Individual prey are 20-200 times more likely to encounter feral cats, because of the combined effects of cats' higher population densities, greater intensity of home-range use and broader habitat preferences. These characteristics also mean that the costs to the prey of adopting anti-predator behaviours against feral cats are likely to be much higher than adopting such behaviours in response to spotted-tailed quolls, due to the reliability and ubiquity of feral cat cues. These results help explain the devastating impacts of cats on wildlife in Australia and other parts of the world.
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Affiliation(s)
- Rowena P Hamer
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia.,Tasmanian Land Conservancy, Hobart, Tasmania 7005, Australia
| | - Riana Z Gardiner
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Kirstin M Proft
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Christopher N Johnson
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
| | - Menna E Jones
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7005, Australia
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22
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Hamer RP, Andersen GE, Hradsky BA, Troy SN, Gardiner RZ, Johnson CN, Jones ME. Differing effects of productivity on home-range size and population density of a native and an invasive mammalian carnivore. Wildl Res 2021. [DOI: 10.1071/wr20134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Morris SD, Johnson CN, Brook BW. Roughing it: terrain is crucial in identifying novel translocation sites for the vulnerable brush-tailed rock-wallaby ( Petrogale pencillata). R Soc Open Sci 2020; 7:201603. [PMID: 33489291 PMCID: PMC7813239 DOI: 10.1098/rsos.201603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Translocations-the movement of species from one place to another-are likely to become more common as conservation attempts to protect small isolated populations from threats posed by extreme events such as bushfires. The recent Australian mega-fires burnt almost 40% of the habitat of the brush-tailed rock-wallaby (Petrogale pencillata), a threatened species whose distribution is already restricted, primarily due to predation by invasive species. This chronic threat of over-predation, coupled with the possible extinction of the genetically distinct southern population (approx. 40 individuals in the wild), makes this species a candidate for a conservation translocation. Here, we use species distribution models to identify translocation sites for the brush-tailed rock-wallaby. Our models exhibited high predictive accuracy, and show that terrain roughness, a surrogate for predator refugia, is the most important variable. Tasmania, which currently has no rock-wallabies, showed high suitability and is fox-free, making it a promising candidate site. We outline our argument for the trial translocation of rock-wallaby to Maria Island, located off Tasmania's eastern coast. This research offers a transparent assessment of the translocation potential of a threatened species, which can be adapted to other taxa and systems.
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Affiliation(s)
- Shane D. Morris
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Christopher N. Johnson
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Barry W. Brook
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania 7001, Australia
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24
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Jahnke W, Erlanson DA, de Esch IJP, Johnson CN, Mortenson PN, Ochi Y, Urushima T. Fragment-to-Lead Medicinal Chemistry Publications in 2019. J Med Chem 2020; 63:15494-15507. [PMID: 33226222 DOI: 10.1021/acs.jmedchem.0c01608] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fragment-based drug discovery (FBDD) has grown and matured to a point where it is valuable to keep track of its extent and details of application. This Perspective summarizes successful fragment-to-lead stories published in 2019. It is the fifth in a series that started with literature published in 2015. The analysis of screening methods, optimization strategies, and molecular properties of hits and leads are presented in the hope of informing best practices for FBDD. Moreover, FBDD is constantly evolving, and the latest technologies and emerging trends are summarized. These include covalent FBDD, FBDD for the stabilization of proteins or protein-protein interactions, FBDD for enzyme activators, new screening technologies, and advances in library design and chemical synthesis.
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Affiliation(s)
- Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States of America
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yuji Ochi
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Tatsuya Urushima
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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25
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Bolam FC, Mair L, Angelico M, Brooks TM, Burgman M, Hermes C, Hoffmann M, Martin RW, McGowan PJ, Rodrigues AS, Rondinini C, Westrip JR, Wheatley H, Bedolla‐Guzmán Y, Calzada J, Child MF, Cranswick PA, Dickman CR, Fessl B, Fisher DO, Garnett ST, Groombridge JJ, Johnson CN, Kennerley RJ, King SR, Lamoreux JF, Lees AC, Lens L, Mahood SP, Mallon DP, Meijaard E, Méndez‐Sánchez F, Percequillo AR, Regan TJ, Renjifo LM, Rivers MC, Roach NS, Roxburgh L, Safford RJ, Salaman P, Squires T, Vázquez‐Domínguez E, Visconti P, Woinarski JC, Young RP, Butchart SH. How many bird and mammal extinctions has recent conservation action prevented? Conserv Lett 2020. [DOI: 10.1111/conl.12762] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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] Open
Affiliation(s)
- Friederike C. Bolam
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Louise Mair
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Marco Angelico
- Global Mammal Assessment Program, Department of Biology and Biotechnologies Sapienza University of Rome Rome Italy
| | - Thomas M. Brooks
- IUCN Gland Switzerland
- World Agroforestry Center (ICRAF) University of The Philippines Los Baños Laguna Philippines
- Institute for Marine & Antarctic Studies University of Tasmania Hobart Tasmania Australia
| | | | | | | | | | - Philip J.K. McGowan
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Ana S.L. Rodrigues
- CEFE Univ. Montpellier, CNRS, EPHE, IRD, Univ. Paul Valéry Montpellier 3 Montpellier France
| | - Carlo Rondinini
- Global Mammal Assessment Program, Department of Biology and Biotechnologies Sapienza University of Rome Rome Italy
| | - James R.S. Westrip
- Global Species Programme IUCN (International Union for Conservation of Nature) Cambridge UK
| | | | | | - Javier Calzada
- Department of Integrated Sciences University of Huelva Huelva Spain
| | - Matthew F. Child
- South African National Biodiversity Institute Pretoria South Africa
- Mammal Research Institute University of Pretoria Pretoria South Africa
| | | | - Christopher R. Dickman
- School of Life and Environmental Sciences University of Sydney Sydney Australia
- Threatened Species Recovery Hub National Environmental Science Program Brisbane Australia
| | - Birgit Fessl
- Charles Darwin Research Station Charles Darwin Foundation Galapagos Ecuador
| | - Diana O. Fisher
- School of Biological Sciences University of Queensland Brisbane Australia
| | - Stephen T. Garnett
- Threatened Species Recovery Hub National Environmental Science Program Brisbane Australia
- Research Institute for the Environment and Livelihoods Charles Darwin University Casuarina Australia
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation University of Kent Canterbury UK
| | - Christopher N. Johnson
- School of Natural Sciences and ARC Centre for Australian Biodiversity & Heritage University of Tasmania Tasmania Australia
| | | | - Sarah R.B. King
- Natural Resource Ecology Laboratory Colorado State University Fort Collins Colorado
| | | | - Alexander C. Lees
- Department of Natural Sciences Manchester Metropolitan University Manchester UK
- Cornell Lab of Ornithology Cornell University Ithaca New York
| | - Luc Lens
- Department of Biology, Terrestrial Ecology Unit Ghent University Ghent Belgium
| | - Simon P. Mahood
- Research Institute for the Environment and Livelihoods Charles Darwin University Casuarina Australia
- Wildlife Conservation Society Phnom Penh Cambodia
| | - David P. Mallon
- Department of Natural Sciences Manchester Metropolitan University Manchester UK
- IUCN Species Survival Commission Gland Switzerland
| | - Erik Meijaard
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation University of Kent Canterbury UK
- Borneo Futures Bandar Seri Begawan Brunei Darussalam
| | - Federico Méndez‐Sánchez
- Grupo de Ecología y Conservación de Islas, A.C. Ensenada Baja California, Mexico
- Centro de Investigaciones Biológicas del Noroeste, S.C. La Paz Baja California, Mexico
| | | | - Tracey J. Regan
- The Arthur Rylah Institute for Environmental Research Department of Environment Land Water and Planning Heidelberg Victoria Australia
- School of BioSciences University of Melbourne Parkville Victoria Australia
| | - Luis Miguel Renjifo
- Department of Ecology and Territory Pontificia Universidad Javeriana Bogotá Colombia
| | | | - Nicolette S. Roach
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
- Global Wildlife Conservation Austin Texas
| | | | | | | | - Tom Squires
- Department of Natural Sciences Manchester Metropolitan University Manchester UK
| | - Ella Vázquez‐Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología Universidad Nacional Autónoma de México Mexico City Mexico
| | - Piero Visconti
- International Institute for Applied System Analysis Laxenburg Austria
- Centre for Biodiversity and Environment Research University College London London UK
| | - John C.Z. Woinarski
- Threatened Species Recovery Hub National Environmental Science Program Brisbane Australia
- Research Institute for the Environment and Livelihoods Charles Darwin University Casuarina Australia
| | | | - Stuart H.M. Butchart
- BirdLife International Cambridge UK
- Department of Zoology University of Cambridge Cambridge UK
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Day PJ, Berdini V, Castro J, Chessari G, Davies TG, Day JE, Fukaya S, Hamlett C, Hearn K, Hiscock S, Holvey R, Ito S, Kodama Y, Matsuo K, Nakatsuru Y, Palmer N, Price A, Shimamura T, Denis JD, Wallis NG, Williams G, Johnson CN. Abstract 1039: Fragment-based drug discovery to identify small molecule allosteric inhibitors of SHP2. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1039] [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: 11/16/2022]
Abstract
Abstract
The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signalling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Recent advances have shown that genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signalling and inhibits proliferation of RTK-driven cancer cell lines. SHP2 is now understood to act upstream of RAS and plays a role in KRAS-driven cancers, an area of research which is rapidly growing. Considering that RTK deregulation often leads to a wide range of cancers and the newly appreciated role of SHP2 in KRAS-driven cancers, SHP2 inhibitors are therefore a promising therapeutic approach.
SHP2 contains two N-terminal tandem SH2 domains (N-SH2, C-SH2), a catalytic phosphatase domain and a C-terminal tail. SHP2 switches between “open” active and “closed” inactive forms due to autoinhibitory interactions between the N-SH2 domain and the phosphatase domain. Historically, phosphatases were deemed undruggable as there had been no advancements with active site inhibitors. We hypothesised that fragment screening would be highly applicable and amenable to this target to enable alternative means of inhibition through identification of allosteric binding sites. Here we describe the first reported fragment screen against SHP2.
Using our fragment-based PyramidTM approach, screening was carried out on two constructs of SHP2; a closed autoinhibited C-terminal truncated form (phosphatase and both SH2 domains), as well as the phosphatase-only domain. A combination of screening methods such as X-ray crystallography and NMR were employed to identify fragment hits at multiple sites on SHP2, including the tunnel-like allosteric site reported by Chen et al, 2016. Initial fragment hits had affinities for SHP2 in the range of 1mM as measured by ITC. Binding of these hits was improved using structure-guided design to generate compounds which inhibit SHP2 phosphatase activity and are promising starting points for further optimization.
Citation Format: Philip J. Day, Valerio Berdini, Juan Castro, Gianni Chessari, Thomas G. Davies, James E. Day, Satoshi Fukaya, Chris Hamlett, Keisha Hearn, Steve Hiscock, Rhian Holvey, Satoru Ito, Yasuo Kodama, Kenichi Matsuo, Yoko Nakatsuru, Nick Palmer, Amanda Price, Tadashi Shimamura, Jeffrey D.St. Denis, Nicola G. Wallis, Glyn Williams, Christopher N. Johnson. Fragment-based drug discovery to identify small molecule allosteric inhibitors of SHP2 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1039.
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Affiliation(s)
- Philip J. Day
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | - Juan Castro
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | | | - James E. Day
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | - Chris Hamlett
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Keisha Hearn
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Steve Hiscock
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Rhian Holvey
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Satoru Ito
- 2Taiho Pharmaceutical Co., Ltd, Tsukuba, Japan
| | | | | | | | - Nick Palmer
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | - Amanda Price
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
| | | | | | | | - Glyn Williams
- 1Astex Pharmaceuticals, Inc., Cambridge, United Kingdom
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Trembinski DJ, Bink DI, Theodorou K, Sommer J, Fischer A, van Bergen A, Kuo CC, Costa IG, Schürmann C, Leisegang MS, Brandes RP, Alekseeva T, Brill B, Wietelmann A, Johnson CN, Spring-Connell A, Kaulich M, Werfel S, Engelhardt S, Hirt MN, Yorgan K, Eschenhagen T, Kirchhof L, Hofmann P, Jaé N, Wittig I, Hamdani N, Bischof C, Krishnan J, Houtkooper RH, Dimmeler S, Boon RA. Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. Nat Commun 2020; 11:2039. [PMID: 32341350 PMCID: PMC7184724 DOI: 10.1038/s41467-020-15995-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 04/07/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) contribute to cardiac (patho)physiology. Aging is the major risk factor for cardiovascular disease with cardiomyocyte apoptosis as one underlying cause. Here, we report the identification of the aging-regulated lncRNA Sarrah (ENSMUST00000140003) that is anti-apoptotic in cardiomyocytes. Importantly, loss of SARRAH (OXCT1-AS1) in human engineered heart tissue results in impaired contractile force development. SARRAH directly binds to the promoters of genes downregulated after SARRAH silencing via RNA-DNA triple helix formation and cardiomyocytes lacking the triple helix forming domain of Sarrah show an increase in apoptosis. One of the direct SARRAH targets is NRF2, and restoration of NRF2 levels after SARRAH silencing partially rescues the reduction in cell viability. Overexpression of Sarrah in mice shows better recovery of cardiac contractile function after AMI compared to control mice. In summary, we identified the anti-apoptotic evolutionary conserved lncRNA Sarrah, which is downregulated by aging, as a regulator of cardiomyocyte survival.
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Affiliation(s)
- D Julia Trembinski
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Diewertje I Bink
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands
| | - Kosta Theodorou
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Janina Sommer
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Ariane Fischer
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Anke van Bergen
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands
| | - Chao-Chung Kuo
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Christoph Schürmann
- Institute for Cardiovascular Physiology, Medical Faculty, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Matthias S Leisegang
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Institute for Cardiovascular Physiology, Medical Faculty, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Ralf P Brandes
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Institute for Cardiovascular Physiology, Medical Faculty, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Tijna Alekseeva
- Georg Speyer Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Boris Brill
- Georg Speyer Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Astrid Wietelmann
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Christopher N Johnson
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, USA
| | | | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Stanislas Werfel
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Institute of Pharmacology and Toxicology, Technical University Munich, Munich, Germany
- Department of Nephrology, Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Munich, Germany
| | - Stefan Engelhardt
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Institute of Pharmacology and Toxicology, Technical University Munich, Munich, Germany
| | - Marc N Hirt
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kaja Yorgan
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Eschenhagen
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Luisa Kirchhof
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Patrick Hofmann
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Nicolas Jaé
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Ilka Wittig
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
- Functional Proteomics, Medical School, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Nazha Hamdani
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands
- Department of Cardiovascular Physiology, Ruhr University Bochum, Bochum, Germany
| | - Corinne Bischof
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Jaya Krishnan
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, the Netherlands
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Reinier A Boon
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
- German Center for Cardiovascular Research (DZHK), Berlin, Germany.
- Department of Physiology, VU University Medical Center, Amsterdam, the Netherlands.
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Foster CN, Banks SC, Cary GJ, Johnson CN, Lindenmayer DB, Valentine LE. Animals as Agents in Fire Regimes. Trends Ecol Evol 2020; 35:346-356. [DOI: 10.1016/j.tree.2020.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/17/2019] [Accepted: 01/15/2020] [Indexed: 01/08/2023]
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Andersen GE, McGregor HW, Johnson CN, Jones ME. Activity and social interactions in a wide-ranging specialist scavenger, the Tasmanian devil (Sarcophilus harrisii), revealed by animal-borne video collars. PLoS One 2020; 15:e0230216. [PMID: 32203534 PMCID: PMC7089560 DOI: 10.1371/journal.pone.0230216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 09/29/2019] [Accepted: 02/24/2020] [Indexed: 01/15/2023] Open
Abstract
Observing animals directly in the field provides the most accurate understanding of animal behaviour and resource selection. However, making prolonged observation of undisturbed animals is difficult or impossible for many species. To overcome this problem for the Tasmanian devil (Sarcophilus harrisii), a cryptic and nocturnal carnivore, we developed animal-borne video collars to investigate activity patterns, foraging behaviour and social interactions. We collected 173 hours of footage from 13 individual devils between 2013 and 2017. Devils were active mostly at night, and resting was the most common behaviour in all diel periods. Devils spent more time scavenging than hunting and exhibited opportunistic and flexible foraging behaviours. Scavenging occurred mostly in natural vegetation but also in anthropogenic vegetation and linear features (roads and fence lines). Scavenging frequency was inversely incremental with size e.g. small carcasses were scavenged most frequently. Agonistic interactions with conspecifics occurred most often when devils were traveling but also occurred over carcasses or dens. Interactions generally involved vocalisations and brief chases without physical contact. Our results highlight the importance of devils as a scavenger in the Tasmanian ecosystem, not just of large carcasses for which devils are well known but in cleaning up small items of carrion in the bush. Our results also show the complex nature of intraspecific interactions, revealing greater detail on the context in which interactions occur. In addition, this study demonstrates the benefits of using animal-borne imaging in quantifying behaviour of elusive, nocturnal carnivores not previously seen using conventional field methods.
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Affiliation(s)
| | - Hugh W. McGregor
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Christopher N. Johnson
- School of Natural Sciences, University of Tasmania, Hobart, Australia
- School of Natural Sciences and Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Australia
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30
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Affiliation(s)
- Georgina E. Andersen
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tasmania7001Australia
| | - Christopher N. Johnson
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tasmania7001Australia
- School of Biological Sciences and Australian research Council Centre for Australian Biodiversity and Heritage University of Tasmania Hobart Tasmania Australia
| | - Menna E. Jones
- School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tasmania7001Australia
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31
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Cunningham CX, Johnson CN, Jones ME. A native apex predator limits an invasive mesopredator and protects native prey: Tasmanian devils protecting bandicoots from cats. Ecol Lett 2020; 23:711-721. [DOI: 10.1111/ele.13473] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/15/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Calum X. Cunningham
- School of Natural Sciences University of Tasmania Hobart Tasmania 7001 Australia
| | - Christopher N. Johnson
- School of Natural Sciences University of Tasmania Hobart Tasmania 7001 Australia
- Australian Research Council Centre for Australian Biodiversity and Heritage University of Tasmania Hobart Tasmania 7001 Australia
| | - Menna E. Jones
- School of Natural Sciences University of Tasmania Hobart Tasmania 7001 Australia
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32
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de Winter JM, Molenaar JP, Yuen M, van der Pijl R, Shen S, Conijn S, van de Locht M, Willigenburg M, Bogaards SJ, van Kleef ES, Lassche S, Persson M, Rassier DE, Sztal TE, Ruparelia AA, Oorschot V, Ramm G, Hall TE, Xiong Z, Johnson CN, Li F, Kiss B, Lozano-Vidal N, Boon RA, Marabita M, Nogara L, Blaauw B, Rodenburg RJ, Küsters B, Doorduin J, Beggs AH, Granzier H, Campbell K, Ma W, Irving T, Malfatti E, Romero NB, Bryson-Richardson RJ, van Engelen BG, Voermans NC, Ottenheijm CA. KBTBD13 is an actin-binding protein that modulates muscle kinetics. J Clin Invest 2020; 130:754-767. [PMID: 31671076 PMCID: PMC6994151 DOI: 10.1172/jci124000] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/24/2019] [Indexed: 11/17/2022] Open
Abstract
The mechanisms that modulate the kinetics of muscle relaxation are critically important for muscle function. A prime example of the impact of impaired relaxation kinetics is nemaline myopathy caused by mutations in KBTBD13 (NEM6). In addition to weakness, NEM6 patients have slow muscle relaxation, compromising contractility and daily life activities. The role of KBTBD13 in muscle is unknown, and the pathomechanism underlying NEM6 is undetermined. A combination of transcranial magnetic stimulation-induced muscle relaxation, muscle fiber- and sarcomere-contractility assays, low-angle x-ray diffraction, and superresolution microscopy revealed that the impaired muscle-relaxation kinetics in NEM6 patients are caused by structural changes in the thin filament, a sarcomeric microstructure. Using homology modeling and binding and contractility assays with recombinant KBTBD13, Kbtbd13-knockout and Kbtbd13R408C-knockin mouse models, and a GFP-labeled Kbtbd13-transgenic zebrafish model, we discovered that KBTBD13 binds to actin - a major constituent of the thin filament - and that mutations in KBTBD13 cause structural changes impairing muscle-relaxation kinetics. We propose that this actin-based impaired relaxation is central to NEM6 pathology.
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Affiliation(s)
| | - Joery P. Molenaar
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Neurology, Rijnstate Hospital, Arnhem, Netherlands
| | - Michaela Yuen
- Department of Physiology, Amsterdam University Medical Center, Netherlands
- Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Australia
| | - Robbert van der Pijl
- Department of Physiology, Amsterdam University Medical Center, Netherlands
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Shengyi Shen
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Stefan Conijn
- Department of Physiology, Amsterdam University Medical Center, Netherlands
| | | | - Menne Willigenburg
- Department of Physiology, Amsterdam University Medical Center, Netherlands
| | | | - Esmee S.B. van Kleef
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Saskia Lassche
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Malin Persson
- Department of Kinesiology and Physical Education, McGill University, Montreal, Canada
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Dilson E. Rassier
- Department of Kinesiology and Physical Education, McGill University, Montreal, Canada
| | - Tamar E. Sztal
- School of Biological Sciences, Monash University, Melbourne, Australia
| | | | - Viola Oorschot
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Melbourne, Australia
| | - Georg Ramm
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Melbourne, Australia
- Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Thomas E. Hall
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Zherui Xiong
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Christopher N. Johnson
- Division of Clinical Pharmacology, Center for Arrhythmia Research and Therapeutics and Center for Structural Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Frank Li
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Balazs Kiss
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | | | - Reinier A. Boon
- Department of Physiology, Amsterdam University Medical Center, Netherlands
| | - Manuela Marabita
- Venetian Institute of Molecular Medicine, Department of Biomedical Sciences, University of Padova, Italy
| | - Leonardo Nogara
- Venetian Institute of Molecular Medicine, Department of Biomedical Sciences, University of Padova, Italy
| | - Bert Blaauw
- Venetian Institute of Molecular Medicine, Department of Biomedical Sciences, University of Padova, Italy
| | - Richard J. Rodenburg
- Department of Pediatrics, Radboud University Medical Centre, Translational Metabolic Laboratory, Nijmegen, Netherlands
| | - Benno Küsters
- Department of Pathology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jonne Doorduin
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Ken Campbell
- Department of Physiology and Division of Cardiovascular Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Weikang Ma
- BioCAT, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Thomas Irving
- BioCAT, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Edoardo Malfatti
- Service Neurologie Médicale, Centre de Référence Maladies Neuromusculaire Paris-Nord CHU Raymond-Poincaré, U1179 UVSQ-INSERM Handicap Neuromusculaire: Physiologie, Biothérapie et Pharmacologie Appliquées, UFR des Sciences de la Santé Simone Veil, Université Versailles-Saint-Quentin-en-Yvelines, Garches, France
| | - Norma B. Romero
- Sorbonne Université, Myology Institute, Neuromuscular Morphology Unit, Center for Research in Myology, GH Pitié-Salpêtrière Paris, France
- Centre de Référence de Pathologie Neuromusculaire Paris-Est, GHU Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Baziel G.M. van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicol C. Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Coen A.C. Ottenheijm
- Department of Physiology, Amsterdam University Medical Center, Netherlands
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
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Abstract
This Perspective, the fourth in an annual series, summarizes fragment-to-lead (F2L) success stories published during 2018. Topics such as target class, screening methods, physicochemical properties, and ligand efficiency are discussed for the 2018 examples as well as for the combined 111 F2L examples covering 2015-2018. While the overall properties of fragments and leads have remained constant, a number of new trends are noted, for example, broadening of target class coverage and application of FBDD to covalent inhibitors. Moreover, several studies make use of fragment hits that were previously described in the literature, illustrating that fragments are versatile starting points that can be optimized to structurally diverse leads. By focusing on success stories, the hope is that this Perspective will identify and inform best practices in fragment-based drug discovery.
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Affiliation(s)
- Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, 4002 Basel, Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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McGregor H, Read J, Johnson CN, Legge S, Hill B, Moseby K. Edge effects created by fenced conservation reserves benefit an invasive mesopredator. Wildl Res 2020. [DOI: 10.1071/wr19181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
ContextFenced reserves from which invasive predators are removed are increasingly used as a conservation management tool, because they provide safe havens for susceptible threatened species, and create dense populations of native wildlife that could act as a source population for recolonising the surrounding landscape. However, the latter effect might also act as a food source, and promote high densities of invasive predators on the edges of such reserves.
AimsOur study aimed to determine whether activity of the feral cat is greater around the edges of a fenced conservation reserve, Arid Recovery, in northern South Australia. This reserve has abundant native rodents that move through the fence into the surrounding landscape.
MethodsWe investigated (1) whether feral cats were increasingly likely to be detected on track transects closer to the fence over time as populations of native rodents increased inside the reserve, (2) whether native rodents were more likely to be found in the stomachs of cats caught close to the reserve edge, and (3) whether individual cats selectively hunted on the reserve fence compared with two other similar fences, on the basis of GPS movement data.
Key resultsWe found that (1) detection rates of feral cats on the edges of a fenced reserve increased through time as populations of native rodents increased inside the reserve, (2) native rodents were far more likely to be found in the stomach of cats collected at the reserve edge than in the stomachs of cats far from the reserve edge, and (3) GPS tracking of cat movements showed a selection for the reserve fence edge, but not for similar fences away from the reserve.
ConclusionsInvasive predators such as feral cats are able to focus their movements and activity to where prey availability is greatest, including the edges of fenced conservation reserves. This limits the capacity of reserves to function as source areas from which animals can recolonise the surrounding landscape, and increases predation pressure on populations of other species living on the reserve edge.
ImplicationsManagers of fenced conservation reserves should be aware that increased predator control may be critical for offsetting the elevated impacts of feral cats attracted to the reserve fence.
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Watts ET, Johnson CN, Carver S, Butler C, Harvey AM, Cameron EZ. Maternal protectiveness in feral horses: responses to intraspecific and interspecific sources of risk. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2019.10.018] [Citation(s) in RCA: 6] [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: 11/28/2022]
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Stobo-Wilson AM, Brandle R, Johnson CN, Jones ME. Management of invasive mesopredators in the Flinders Ranges, South Australia: effectiveness and implications. Wildl Res 2020. [DOI: 10.1071/wr19237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
ContextSignificant resources have been devoted to the control of introduced mesopredators in Australia. However, the control or removal of one pest species, such as, for example, the red fox (Vulpes vulpes), may inadvertently benefit other invasive species, namely feral cats (Felis catus) and rabbits (Oryctolagus cuniculus), potentially jeopardising native-species recovery.
AimsTo (1) investigate the impact of a large-scale, long-term fox-baiting program on the abundance of foxes, feral cats and introduced and native prey species in the Flinders Ranges, South Australia, and (2) determine the effectiveness of a short time period of cat removal in immediately reducing feral cat abundance where foxes are absent.
MethodsWe conducted an initial camera-trap survey in fox-baited and unbaited sites in the Flinders Ranges, to quantify the impact of fox baiting on the relative abundance of foxes, feral cats and their prey. We then conducted a secondary survey in sites where foxes were absent, following an intensive, but short, time period of cat removal, in which 40 cats were shot and killed.
Key resultsNo foxes were detected within baited sites, but were frequently detected in unbaited sites. We found a corresponding and significant increase in several native prey species in fox-baited sites where foxes were absent. Feral cats and rabbits were also more frequently detected within baited sites, but fox baiting did not singularly predict the abundance of either species. Rather, feral cats were less abundant in open habitat where foxes were present (unbaited), and rabbits were more abundant within one predominantly open-habitat site, where foxes were absent (fox-baited). We found no effect of short-term cat removal in reducing the local abundance of feral cats. In both camera-trap surveys, feral cat detections were positively associated with rabbits.
ConclusionsLong-term fox baiting was effective in fox removal and was associated with a greater abundance of native and introduced prey species in the Flinders Ranges. To continue to recover and conserve regional biodiversity, effective cat control is required.
ImplicationsOur study showed fox removal has likely resulted in the local release of rabbits and an associated increase in cats. Because feral cat abundance seemingly fluctuated with rabbits, we suggest rabbit control may provide an alternative and more effective means to reduce local feral cat populations than short-term removal programs.
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Ng D, Carver S, Gotame M, Karmasharya D, Karmacharya D, Man Pradhan S, Narsingh Rana A, Johnson CN. Canine distemper in Nepal's Annapurna Conservation Area - Implications of dog husbandry and human behaviour for wildlife disease. PLoS One 2019; 14:e0220874. [PMID: 31805044 PMCID: PMC6894829 DOI: 10.1371/journal.pone.0220874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/18/2019] [Accepted: 11/08/2019] [Indexed: 11/19/2022] Open
Abstract
Dogs are often commensal with human settlements. In areas where settlements are adjacent to wildlife habitat, the management of dogs can affect risk of spillover of disease to wildlife. We assess dog husbandry practices, and measure the prevalence of Canine Distemper Virus (CDV) in dogs, in 10 villages in Nepal's Annapurna Conservation Area (ACA), an important region for Himalayan wildlife. A high proportion (58%) of owned dogs were allowed by their owners to roam freely, and many village dogs originated from urban areas outside the region. CDV antibodies, indicating past exposure, were detected in 70% of dogs, and 13% were positive for P-gene, suggesting current circulation of CDV. This is the first detection of canine distemper virus in a National Park in Nepal Himalaya. Dogs were generally in good condition, and none exhibited clinical signs of CDV infection, which suggests that infections were asymptomatic. CDV exposure varied with village location and age of dogs, but this variation was minor, consistent with high rates of movement of dogs across the region maintaining high seroprevalence. Residents reported the occurrence of several species of wild carnivores in or close to villages. These results suggest a high potential for transmission of CDV from village dogs to wild carnivores in ACA. We suggest that control of dog immigration, along with vaccination and neutering of dogs could mitigate the risk of CDV spillover into wild carnivore populations.
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Affiliation(s)
- Debby Ng
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Australia
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Wren LM, Jiménez-Jáimez J, Al-Ghamdi S, Al-Aama JY, Bdeir A, Al-Hassnan ZN, Kuan JL, Foo RY, Potet F, Johnson CN, Aziz MC, Carvill GL, Kaski JP, Crotti L, Perin F, Monserrat L, Burridge PW, Schwartz PJ, Chazin WJ, Bhuiyan ZA, George AL. Genetic Mosaicism in Calmodulinopathy. Circ Genom Precis Med 2019; 12:375-385. [PMID: 31454269 DOI: 10.1161/circgen.119.002581] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND CaM (calmodulin) mutations are associated with congenital arrhythmia susceptibility (calmodulinopathy) and are most often de novo. In this report, we sought to broaden the genotype-phenotype spectrum of calmodulinopathies with 2 novel calmodulin mutations and to investigate mosaicism in 2 affected families. METHODS CaM mutations were identified in 4 independent cases by DNA sequencing. Biochemical and electrophysiological studies were performed to determine functional consequences of each mutation. RESULTS Genetic studies identified 2 novel CaM variants (CALM3-E141K in 2 cases; CALM1-E141V) and one previously reported CaM pathogenic variant (CALM3-D130G) among 4 probands with shared clinical features of prolonged QTc interval (range 505-725 ms) and documented ventricular arrhythmia. A fatal outcome occurred for 2 of the cases. The parents of all probands were asymptomatic with normal QTc duration. However, 2 of the families had multiple affected offspring or multiple occurrences of intrauterine fetal demise. The mother from the family with recurrent intrauterine fetal demise exhibited the CALM3-E141K mutant allele in 25% of next-generation sequencing reads indicating somatic mosaicism, whereas CALM3-D130G was present in 6% of captured molecules of the paternal DNA sample, also indicating mosaicism. Two novel mutations (E141K and E141V) impaired Ca2+ binding affinity to the C-domain of CaM. Human-induced pluripotent stem cell-derived cardiomyocytes overexpressing mutant or wild-type CaM showed that both mutants impaired Ca2+-dependent inactivation of L-type Ca2+ channels and prolonged action potential duration. CONCLUSIONS We report 2 families with somatic mosaicism associated with arrhythmogenic calmodulinopathy, and demonstrate dysregulation of L-type Ca2+ channels by 2 novel CaM mutations affecting the same residue. Parental mosaicism should be suspected in families with unexplained fetal arrhythmia or fetal demise combined with a documented CaM mutation.
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Affiliation(s)
- Lisa M Wren
- From the Department of Pharmacology (L.M.W., F.P., P.W.B., A.L.G.), Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Juan Jiménez-Jáimez
- Cardiology Department (J.J.-J.), Virgen de las Nieves Hospital, Granada, Spain
| | - Saleh Al-Ghamdi
- Cardiac Sciences Department, Section of Pediatric Cardiology, King Abdulaziz Cardiac Center, Ministry of National Guard Health Affairs, Riyadh (S.A.-G.)
| | - Jumana Y Al-Aama
- Department of Genetic Medicine, Faculty of Medicine (J.Y.A.-A.), King Abdulaziz University, Jeddah.,Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders (J.Y.A.-A., A.B.), King Abdulaziz University, Jeddah
| | - Amnah Bdeir
- Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders (J.Y.A.-A., A.B.), King Abdulaziz University, Jeddah
| | - Zuhair N Al-Hassnan
- The Cardiovascular Genetics Program, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia (Z.N.A.-H.)
| | - Jyn L Kuan
- Department of Cardiology, National University Heart Center and Cardiovascular Research Institute, National University of Singapore (J.L.K., R.Y.F.)
| | - Roger Y Foo
- Department of Cardiology, National University Heart Center and Cardiovascular Research Institute, National University of Singapore (J.L.K., R.Y.F.)
| | - Franck Potet
- From the Department of Pharmacology (L.M.W., F.P., P.W.B., A.L.G.), Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Christopher N Johnson
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN (C.N.J., W.J.C.)
| | - Miriam C Aziz
- Department of Neurology (M.C.A., G.L.C.), Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Gemma L Carvill
- Department of Neurology (M.C.A., G.L.C.), Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Juan-Pablo Kaski
- Institute of Cardiovascular Science, University College London, United Kingdom (J.-P.K.)
| | - Lia Crotti
- Department of Medicine and Surgery, University of Milano-Bicocca (L.C.).,IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy (L.C., P.J.S.).,Cardiology Department, Health in Code SL, A Coruña, Spain (L.M.)
| | - Francesca Perin
- Pediatric Cardiology Division (F.P.), Virgen de las Nieves Hospital, Granada, Spain
| | | | - Paul W Burridge
- From the Department of Pharmacology (L.M.W., F.P., P.W.B., A.L.G.), Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Peter J Schwartz
- IRCCS Istituto Auxologico Italiano, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy (L.C., P.J.S.)
| | - Walter J Chazin
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN (C.N.J., W.J.C.)
| | - Zahurul A Bhuiyan
- Unité de Recherche Cardiogénétique, Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland (Z.A.B.)
| | - Alfred L George
- From the Department of Pharmacology (L.M.W., F.P., P.W.B., A.L.G.), Northwestern University Feinberg School of Medicine, Chicago, IL
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Johnson CN, Pattanayek R, Potet F, Rebbeck RT, Blackwell DJ, Nikolaienko R, Sequeira V, Le Meur R, Radwański PB, Davis JP, Zima AV, Cornea RL, Damo SM, Györke S, George AL, Knollmann BC. The CaMKII inhibitor KN93-calmodulin interaction and implications for calmodulin tuning of Na V1.5 and RyR2 function. Cell Calcium 2019; 82:102063. [PMID: 31401388 DOI: 10.1016/j.ceca.2019.102063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 04/27/2019] [Revised: 07/15/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
Abstract
Here we report the structure of the widely utilized calmodulin (CaM)-dependent protein kinase II (CaMKII) inhibitor KN93 bound to the Ca2+-sensing protein CaM. KN93 is widely believed to inhibit CaMKII by binding to the kinase. The CaM-KN93 interaction is significant as it can interfere with the interaction between CaM and it's physiological targets, thereby raising the possibility of ascribing modified protein function to CaMKII phosphorylation while concealing a CaM-protein interaction. NMR spectroscopy, stopped-flow kinetic measurements, and x-ray crystallography were used to characterize the structure and biophysical properties of the CaM-KN93 interaction. We then investigated the functional properties of the cardiac Na+ channel (NaV1.5) and ryanodine receptor (RyR2). We find that KN93 disrupts a high affinity CaM-NaV1.5 interaction and alters channel function independent of CaMKII. Moreover, KN93 increases RyR2 Ca2+ release in cardiomyocytes independent of CaMKII. Therefore, when interpreting KN93 data, targets other than CaMKII need to be considered.
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Affiliation(s)
- Christopher N Johnson
- Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37240, USA; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
| | - Rekha Pattanayek
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
| | - Franck Potet
- Department of Pharmacology Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology and Biophysics University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel J Blackwell
- Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | - Roman Nikolaienko
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University, Maywood IL, 60153, USA
| | - Vasco Sequeira
- Department of Translational Science Universitätsklinikum, Würzburg, Germany
| | - Remy Le Meur
- Department of Biochemistry, Vanderbilt University, Nashville TN 37204, USA
| | - Przemysław B Radwański
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jonathan P Davis
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Aleksey V Zima
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University, Maywood IL, 60153, USA
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology and Biophysics University of Minnesota, Minneapolis, MN 55455, USA
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA
| | - Sandor Györke
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Alfred L George
- Department of Pharmacology Feinberg School of Medicine, Northwestern University, Chicago IL, 60611, USA
| | - Björn C Knollmann
- Center for Arrhythmia Research and Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37240, USA
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Walweel K, Gomez-Hurtado N, Oo YW, Beard NA, Dos Remedios C, Johnson CN, Chazin WJ, van Helden DF, Knollmann BC, Laver DR. Calmodulin Mutants Linked to Catecholaminergic Polymorphic Ventricular Tachycardia Fail to Inhibit Human RyR2 Channels. J Am Coll Cardiol 2019; 70:115-117. [PMID: 28662798 DOI: 10.1016/j.jacc.2017.04.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/11/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
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VanWagner MJ, Krebs NM, Corser W, Johnson CN. Liposomal bupivacaine reduces opioid consumption and length of stay in patients undergoing primary total hip arthroplasty. Hip Int 2019; 29:276-281. [PMID: 29808726 DOI: 10.1177/1120700018778240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Optimising postoperative pain management after total hip arthroplasty (THA) has been associated with improved patient outcomes. However, conclusions regarding the role of liposomal bupivacaine (LB) during THA remain mixed. The purpose of this study was to determine whether substituting a standard intraoperative wound infiltrate with LB as part of a multimodal pain management protocol would decrease subsequent opioid consumption and overall length of hospital stay in patients undergoing primary THA. METHODS Data was retrospectively collected on 170 consecutive patients who underwent primary THA at a single institution from January 2014 to October 2014. Outcomes from the first 85 patients who received intraoperative LB were compared to the prior 85 patients who received a standard intraoperative "cocktail" without LB. The remainder of the multimodal pain management protocol was identical between groups. RESULTS Total continuous and categorical postoperative hospital opioid consumption rates in the LB subgroup were significantly lower than the non-LB subgroup ( p < 0.001). The use of LB was associated with a relative reduction in opioid consumption on the day of surgery ( p = 0.001), postoperative day 1 ( p < 0.001), postoperative day 2 ( p < 0.001) and postoperative day 3 ( p < 0.001). Patients who received LB had decreased length of stay ( p = 0.001) and were discharged on lower doses of opioids. CONCLUSION Substituting to LB from a standard wound infiltrate during primary THA, in addition to our standard multimodal pain management protocol, resulted in significantly lower postoperative opioid consumption and decreased length of stay.
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Affiliation(s)
- Michael J VanWagner
- 1 Department of Orthopaedic Surgery, McLaren Macomb Medical Center, Mount Clemens, MI, USA
| | - Nathan M Krebs
- 1 Department of Orthopaedic Surgery, McLaren Macomb Medical Center, Mount Clemens, MI, USA
| | - William Corser
- 2 Michigan State University, College of Osteopathic Medicine, East Lansing, MI, USA
| | - Christopher N Johnson
- 1 Department of Orthopaedic Surgery, McLaren Macomb Medical Center, Mount Clemens, MI, USA.,3 Ortho Northeast, Parkview Cancer Institute, Fort Wayne, IN, USA
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Affiliation(s)
| | - Christopher N. Johnson
- School of Natural Sciences, University of Tasmania, Hobart, Australia
- Australian Research Council Centre for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Australia
| | - Menna E. Jones
- School of Natural Sciences, University of Tasmania, Hobart, Australia
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Abstract
Modification of voltage-gated Na+ channel (NaV ) function by intracellular Ca2+ has been a topic of much controversy. Early studies relied on measuring NaV function in the absence or presence of intracellular Ca2+ , and generated seemingly disparate results. Subsequent investigations revealed the mechanism(s) of Ca2+ -driven NaV modulation are complex and involve multiple accessory proteins. The Ca2+ -sensing protein calmodulin (CaM) has a central role in tuning NaV function to [Ca2+ ]i , but the mechanism has been obscured by other proteins (such as fibroblast growth factors (FGF) or CaM-dependent kinase II (CaMKII)) that can also modify channel function or exert an influence in a Ca2+ -dependent manner. Significant progress has been made in understanding the architecture of full-length ion channels and the structural and biophysical details of NaV -accessory protein interactions. Interdisciplinary structure-function studies are beginning to resolve the effect each interaction has on NaV gating. Carefully designed structure-guided or strategically selected disease-associated mutations are able to impair NaV -accessory protein interactions without altering other properties of channel function. Recently CaM was found to engage part of NaV 1.5 that is required for channel inactivation with high affinity. Careful impairment of this interaction disrupted NaV 1.5's ability to recover from inactivation. Such results support a paradigm of CaM-facilitated recovery from inactivation (CFRI). How NaV -CaM, CaMKII and FGF/fibroblast growth factor homologous factor interactions affect the timing or function of CFRI in cardiomyocytes remain open questions that are discussed herein. Moreover whether CFRI dysfunction or premature activation underlie certain NaV channelopathies are important questions that will require further investigation.
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Affiliation(s)
- Christopher N Johnson
- The Ohio State Wexner Medical Centre, Dorothy M. Davis Heart & Lung Research Institute, Columbus, OH, USA.,Vanderbilt Centre for Arrhythmia Research and Therapeutics, Division of Clinical Pharmacology, Nashville, TN, USA
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Grainger R, Heightman TD, Ley SV, Lima F, Johnson CN. Enabling synthesis in fragment-based drug discovery by reactivity mapping: photoredox-mediated cross-dehydrogenative heteroarylation of cyclic amines. Chem Sci 2019; 10:2264-2271. [PMID: 30881651 PMCID: PMC6385880 DOI: 10.1039/c8sc04789h] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [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: 10/26/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
In fragment-based drug discovery (FBDD), a weakly binding fragment hit is elaborated into a potent ligand by bespoke functionalization along specific directions (growth vectors) from the fragment core in order to complement the 3D structure of the target protein. This structure-based design approach can present significant synthetic challenges, as growth vectors often originate on sp2 or sp3 ring carbons which are not the most synthetically accessible points on the fragment. To address this issue and expedite synthesis in FBDD, we established a nanogram-to-gram workflow for the development of enabling synthetic transformations, such as the direct C-H functionalization of heterocycles. This novel approach deploys high-throughput experimentation (HTE) in 1536-well microtiter plates (MTPs) facilitated by liquid handling robots to screen reaction conditions on the nanomolar scale; subsequently the reaction is upscaled in a continuous flow to generate gram-quantities of the material. In this paper, we disclose the use of this powerful workflow for the development of a photoredox-mediated cross-dehydrogenative coupling of fragments and medicinally relevant heterocyclic precursors via Minisci-type addition of α-amino radicals to electron-deficient heteroarenes. The optimized reaction conditions were employed on the milligram-scale on a diverse set of 112 substrates to map out structure-reactivity relationships (SRRs) of the transformation. The coupling exhibits excellent tolerance to a variety of functional groups and N-rich heteroarenes relevant to FBDD and was upscaled in a continuous flow to afford gram-quantities of pharmaceutically relevant sp2-sp3 privileged architectures.
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Affiliation(s)
- Rachel Grainger
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
| | - Tom D Heightman
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
| | - Steven V Ley
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Fabio Lima
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Novartis Pharma AG , Novartis Campus , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge , CB4 0QA , UK . ;
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Cunningham CX, Johnson CN, Barmuta LA, Hollings T, Woehler EJ, Jones ME. Top carnivore decline has cascading effects on scavengers and carrion persistence. Proc Biol Sci 2018; 285:rspb.2018.1582. [PMID: 30487308 DOI: 10.1098/rspb.2018.1582] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/05/2018] [Indexed: 01/24/2023] Open
Abstract
Top carnivores have suffered widespread global declines, with well-documented effects on mesopredators and herbivores. We know less about how carnivores affect ecosystems through scavenging. Tasmania's top carnivore, the Tasmanian devil (Sarcophilus harrisii), has suffered severe disease-induced population declines, providing a natural experiment on the role of scavenging in structuring communities. Using remote cameras and experimentally placed carcasses, we show that mesopredators consume more carrion in areas where devils have declined. Carcass consumption by the two native mesopredators was best predicted by competition for carrion, whereas consumption by the invasive mesopredator, the feral cat (Felis catus), was better predicted by the landscape-level abundance of devils, suggesting a relaxed landscape of fear where devils are suppressed. Reduced discovery of carcasses by devils was balanced by the increased discovery by mesopredators. Nonetheless, carcasses persisted approximately 2.6-fold longer where devils have declined, highlighting their importance for rapid carrion removal. The major beneficiary of increased carrion availability was the forest raven (Corvus tasmanicus). Population trends of ravens increased 2.2-fold from 1998 to 2017, the period of devil decline, but this increase occurred Tasmania-wide, making the cause unclear. This case study provides a little-studied potential mechanism for mesopredator release, with broad relevance to the vast areas of the world that have suffered carnivore declines.
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Affiliation(s)
- Calum X Cunningham
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Christopher N Johnson
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia.,Australian Research Council Centre for Australian Biodiversity and Heritage, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Leon A Barmuta
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Tracey Hollings
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria 3084, Australia.,Centre of Excellence for Biosecurity Risk Analysis, School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Eric J Woehler
- Birdlife Tasmania, GPO Box 68, Hobart, Tasmania, Australia
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
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Abstract
This Miniperspective is the third in a series reviewing fragment-to-lead publications from a given year. Following our reviews for 2015 and 2016, this Miniperspective provides tabulated summaries of relevant articles published in 2017 along with some general observations. In addition, we discuss insights obtained from analysis of the combined data set of 85 examples from all three years of publications.
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Affiliation(s)
- Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ , Amsterdam , The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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Derham TT, Duncan RP, Johnson CN, Jones ME. Hope and caution: rewilding to mitigate the impacts of biological invasions. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0127. [PMID: 30348875 DOI: 10.1098/rstb.2018.0127] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 12/31/2022] Open
Abstract
Rewilding is a novel approach to ecological restoration. Trophic rewilding in particular aims to reinstate ecological functions, especially trophic interactions, through the introduction of animals. We consider the potential for trophic rewilding to address biological invasions. In this broad review, we note some of the important conceptual and ethical foundations of rewilding, including a focus on ecosystem function rather than composition, reliance on animal agency, and an appeal to an ethic of coexistence. Second, we use theory from invasion biology to highlight pathways by which rewilding might prevent or mitigate the impacts of an invasion, including increasing biotic resistance. Third, we use a series of case studies to illustrate how reintroductions can mitigate the impacts of invasions. These include reintroductions and positive management of carnivores and herbivores including European pine martens (Martes martes), Eurasian otters (Lutra lutra), dingoes (Canis dingo), Tasmanian devils (Sarcophilus harrisii) and tule elk (Cervus canadensis nannodes). Fourth, we consider the risk that rewilding may enable a biological invasion or aggravate its impacts. Lastly, we highlight lessons that rewilding science might take from invasion biology.This article is part of the theme issue 'Trophic rewilding: consequences for ecosystems under global change'.
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Affiliation(s)
- Tristan T Derham
- School of Natural Sciences and Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Christopher N Johnson
- School of Natural Sciences and Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
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Johnson CN, Prior LD, Archibald S, Poulos HM, Barton AM, Williamson GJ, Bowman DMJS. Can trophic rewilding reduce the impact of fire in a more flammable world? Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0443. [PMID: 30348870 PMCID: PMC6231065 DOI: 10.1098/rstb.2017.0443] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/02/2022] Open
Abstract
Large vertebrates affect fire regimes in several ways: by consuming plant matter that would otherwise accumulate as fuel; by controlling and varying the density of vegetation; and by engineering the soil and litter layer. These processes can regulate the frequency, intensity and extent of fire. The evidence for these effects is strongest in environments with intermediate rainfall, warm temperatures and graminoid-dominated ground vegetation. Probably, extinction of Quaternary megafauna triggered increased biomass burning in many such environments. Recent and continuing declines of large vertebrates are likely to be significant contributors to changes in fire regimes and vegetation that are currently being experienced in many parts of the world. To date, rewilding projects that aim to restore large herbivores have paid little attention to the value of large animals in moderating fire regimes. Rewilding potentially offers a powerful tool for managing the risks of wildfire and its impacts on natural and human values. This article is part of the theme issue ‘Trophic rewilding: consequences for ecosystems under global change’.
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Affiliation(s)
- Christopher N Johnson
- School of Natural Sciences and Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Lynda D Prior
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Sally Archibald
- Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Private Bag, Johannesburg, South Africa
| | - Helen M Poulos
- College of the Environment, Wesleyan University, 284 High St., Middletown, CT 06459, USA
| | - Andrew M Barton
- Department of Biology, University of Maine at Farmington, 173 High Street, Preble Hall, Farmington, ME 04938, USA
| | - Grant J Williamson
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - David M J S Bowman
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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Radwański PB, Johnson CN, Györke S, Veeraraghavan R. Cardiac Arrhythmias as Manifestations of Nanopathies: An Emerging View. Front Physiol 2018; 9:1228. [PMID: 30233404 PMCID: PMC6131669 DOI: 10.3389/fphys.2018.01228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/14/2018] [Indexed: 12/21/2022] Open
Abstract
A nanodomain is a collection of proteins localized within a specialized, nanoscale structural environment, which can serve as the functional unit of macroscopic physiologic processes. We are beginning to recognize the key roles of cardiomyocyte nanodomains in essential processes of cardiac physiology such as electrical impulse propagation and excitation–contraction coupling (ECC). There is growing appreciation of nanodomain dysfunction, i.e., nanopathy, as a mechanistic driver of life-threatening arrhythmias in a variety of pathologies. Here, we offer an overview of current research on the role of nanodomains in cardiac physiology with particular emphasis on: (1) sodium channel-rich nanodomains within the intercalated disk that participate in cell-to-cell electrical coupling and (2) dyadic nanodomains located along transverse tubules that participate in ECC. The beat to beat function of cardiomyocytes involves three phases: the action potential, the calcium transient, and mechanical contraction/relaxation. In all these phases, cell-wide function results from the aggregation of the stochastic function of individual proteins. While it has long been known that proteins that exist in close proximity influence each other’s function, it is increasingly appreciated that there exist nanoscale structures that act as functional units of cardiac biophysical phenomena. Termed nanodomains, these structures are collections of proteins, localized within specialized nanoscale structural environments. The nano-environments enable the generation of localized electrical and/or chemical gradients, thereby conferring unique functional properties to these units. Thus, the function of a nanodomain is determined by its protein constituents as well as their local structural environment, adding an additional layer of complexity to cardiac biology and biophysics. However, with the emergence of experimental techniques that allow direct investigation of structure and function at the nanoscale, our understanding of cardiac physiology and pathophysiology at these scales is rapidly advancing. Here, we will discuss the structure and functions of multiple cardiomyocyte nanodomains, and novel strategies that target them for the treatment of cardiac arrhythmias.
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Affiliation(s)
- Przemysław B Radwański
- Bob and Corinne Frick Center for Heart Failure and Arrhythmia, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, United States.,Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Christopher N Johnson
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Vanderbilt Center for Arrhythmia Research and Therapeutics, Nashville, TN, United States
| | - Sándor Györke
- Bob and Corinne Frick Center for Heart Failure and Arrhythmia, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Rengasayee Veeraraghavan
- Bob and Corinne Frick Center for Heart Failure and Arrhythmia, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States.,Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, United States.,Department of Biomedical Engineering, The Ohio State University, Columbus, OH, United States
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