1
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Park SY, Qiu J, Wei S, Peterson FC, Beltrán J, Medina-Cucurella AV, Vaidya AS, Xing Z, Volkman BF, Nusinow DA, Whitehead TA, Wheeldon I, Cutler SR. An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity. Nat Chem Biol 2024; 20:103-110. [PMID: 37872402 PMCID: PMC10746540 DOI: 10.1038/s41589-023-01447-7] [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: 10/27/2022] [Accepted: 09/13/2023] [Indexed: 10/25/2023]
Abstract
Plants sense abscisic acid (ABA) using chemical-induced dimerization (CID) modules, including the receptor PYR1 and HAB1, a phosphatase inhibited by ligand-activated PYR1. This system is unique because of the relative ease with which ligand recognition can be reprogrammed. To expand the PYR1 system, we designed an orthogonal '*' module, which harbors a dimer interface salt bridge; X-ray crystallographic, biochemical and in vivo analyses confirm its orthogonality. We used this module to create PYR1*MANDI/HAB1* and PYR1*AZIN/HAB1*, which possess nanomolar sensitivities to their activating ligands mandipropamid and azinphos-ethyl. Experiments in Arabidopsis thaliana and Saccharomyces cerevisiae demonstrate the sensitive detection of banned organophosphate contaminants using living biosensors and the construction of multi-input/output genetic circuits. Our new modules enable ligand-programmable multi-channel CID systems for plant and eukaryotic synthetic biology that can empower new plant-based and microbe-based sensing modalities.
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Affiliation(s)
- Sang-Youl Park
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Jingde Qiu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Shuang Wei
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jesús Beltrán
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | | | - Aditya S Vaidya
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Zenan Xing
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Ian Wheeldon
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA.
- Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA.
| | - Sean R Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
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2
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Burns AR, Baker RJ, Kitner M, Knox J, Cooke B, Volpatti JR, Vaidya AS, Puumala E, Palmeira BM, Redman EM, Snider J, Marwah S, Chung SW, MacDonald MH, Tiefenbach J, Hu C, Xiao Q, Finney CAM, Krause HM, MacParland SA, Stagljar I, Gilleard JS, Cowen LE, Meyer SLF, Cutler SR, Dowling JJ, Lautens M, Zasada I, Roy PJ. Selective control of parasitic nematodes using bioactivated nematicides. Nature 2023:10.1038/s41586-023-06105-5. [PMID: 37225985 DOI: 10.1038/s41586-023-06105-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
Parasitic nematodes are a major threat to global food security, particularly as the world amasses 10 billion people amid limited arable land1-4. Most traditional nematicides have been banned owing to poor nematode selectivity, leaving farmers with inadequate means of pest control4-12. Here we use the model nematode Caenorhabditis elegans to identify a family of selective imidazothiazole nematicides, called selectivins, that undergo cytochrome-p450-mediated bioactivation in nematodes. At low parts-per-million concentrations, selectivins perform comparably well with commercial nematicides to control root infection by Meloidogyne incognita, a highly destructive plant-parasitic nematode. Tests against numerous phylogenetically diverse non-target systems demonstrate that selectivins are more nematode-selective than most marketed nematicides. Selectivins are first-in-class bioactivated nematode controls that provide efficacy and nematode selectivity.
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Affiliation(s)
- Andrew R Burns
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Rachel J Baker
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Megan Kitner
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Jessica Knox
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brittany Cooke
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan R Volpatti
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Aditya S Vaidya
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Emily Puumala
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bruna M Palmeira
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Elizabeth M Redman
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jamie Snider
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Sagar Marwah
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Sai W Chung
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Margaret H MacDonald
- USDA-ARS Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, USA
| | - Jens Tiefenbach
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Chun Hu
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Qi Xiao
- Department of Biological Sciences, Host Parasite Interactions Program, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Constance A M Finney
- Department of Biological Sciences, Host Parasite Interactions Program, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Henry M Krause
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sonya A MacParland
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Igor Stagljar
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Susan L F Meyer
- USDA-ARS Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, USA
| | - Sean R Cutler
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - James J Dowling
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mark Lautens
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Inga Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Peter J Roy
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
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3
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Harrington S, Knox JJ, Burns AR, Choo KL, Au A, Kitner M, Haeberli C, Pyche J, D'Amata C, Kim YH, Volpatti JR, Guiliani M, Snider J, Wong V, Palmeira BM, Redman EM, Vaidya AS, Gilleard JS, Stagljar I, Cutler SR, Kulke D, Dowling JJ, Yip CM, Keiser J, Zasada I, Lautens M, Roy PJ. Egg-laying and locomotory screens with C. elegans yield a nematode-selective small molecule stimulator of neurotransmitter release. Commun Biol 2022; 5:865. [PMID: 36002479 PMCID: PMC9402605 DOI: 10.1038/s42003-022-03819-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/08/2022] [Indexed: 12/05/2022] Open
Abstract
Nematode parasites of humans, livestock and crops dramatically impact human health and welfare. Alarmingly, parasitic nematodes of animals have rapidly evolved resistance to anthelmintic drugs, and traditional nematicides that protect crops are facing increasing restrictions because of poor phylogenetic selectivity. Here, we exploit multiple motor outputs of the model nematode C. elegans towards nematicide discovery. This work yielded multiple compounds that selectively kill and/or immobilize diverse nematode parasites. We focus on one compound that induces violent convulsions and paralysis that we call nementin. We find that nementin stimulates neuronal dense core vesicle release, which in turn enhances cholinergic signaling. Consequently, nementin synergistically enhances the potency of widely-used non-selective acetylcholinesterase (AChE) inhibitors, but in a nematode-selective manner. Nementin therefore has the potential to reduce the environmental impact of toxic AChE inhibitors that are used to control nematode infections and infestations. A C. elegans-based screening approach identifies nementin as a nematode-selective nematicide that can be used synergistically with acetylcholinesterase inhibitors
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Affiliation(s)
- Sean Harrington
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Jessica J Knox
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Andrew R Burns
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ken-Loon Choo
- The Department of Chemistry, University of Toronto, Toronto, Canada
| | - Aaron Au
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Megan Kitner
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Cecile Haeberli
- Department of Medical Parasitology and Infection Biology, Swiss-Tropical and Public Health Institute, (Swiss TPH), Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Jacob Pyche
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Cassandra D'Amata
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Yong-Hyun Kim
- The Department of Chemistry, University of Toronto, Toronto, Canada
| | - Jonathan R Volpatti
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Maximillano Guiliani
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Jamie Snider
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Victoria Wong
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Bruna M Palmeira
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Elizabeth M Redman
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Aditya S Vaidya
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.,Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions (HPI) Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Igor Stagljar
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Biochemistry, University of Toronto, Toronto, Canada.,Mediterranean Institute for Life Sciences, Split, Croatia.,School of Medicine, University of Split, Split, Croatia
| | - Sean R Cutler
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.,Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Daniel Kulke
- Research Parasiticides, Bayer Animal Health GmbH, Monheim, Germany.,Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.,Global Innovation, Boehringer Ingelheim Vetmedica GmbH, Ingelheim am Rhein, Germany
| | - James J Dowling
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Christopher M Yip
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss-Tropical and Public Health Institute, (Swiss TPH), Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Inga Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Mark Lautens
- The Department of Chemistry, University of Toronto, Toronto, Canada
| | - Peter J Roy
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada. .,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Canada.
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4
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Abstract
Agricultural productivity in rain-fed crops has been threatened in recent decades due to increased instances of drought and diminishing freshwater resources. This has led to the development of novel chemical and genetic approaches for improving plant water use efficiency. Agrochemical water-banking with the aid of synthetic mimics of phytohormone abscisic acid (ABA) is one such approach, whereby plant transpiration can be chemically tuned to ensure water availability during critical stages of growth. Here, we describe the use of infrared thermography, a noninvasive quantitative technique to evaluate antitranspirant efficacy of existing ABA receptor agonists in crops such as wheat and tomato.
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Affiliation(s)
- Aditya S Vaidya
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA. .,Botany and Plant Sciences, University of California, Riverside, CA, USA.
| | - Sean R Cutler
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.,Botany and Plant Sciences, University of California, Riverside, CA, USA
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5
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Vaidya AS, Park SY, Xing Z, Cutler SR. Synthesis and characterization of abscisic acid receptor modulators. Methods Enzymol 2022; 671:435-470. [DOI: 10.1016/bs.mie.2022.03.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Abstract
Plant stress tolerance relies on intricate signaling networks that are not fully understood. Several plant hormones are involved in the adaptation to different environmental conditions. Abscisic acid (ABA) has an essential role in stress tolerance, especially in the adaptation to drought. During the last years, chemical genomics has gained attention as an alternative approach to decipher complex traits. Additionally, chemical-based strategies have been very useful to untangle genetic redundancy, which is hard to address by other approaches such as classical genetics. Here, we describe the use of an ABA-inducible luciferase (LUC) reporter line for the high-throughput identification of chemical activators of the ABA signaling pathway. In this assay, seven-day-old pMAPKKK18-LUC+ seedlings are grown on 96-well plates and treated with test compounds. Next, the activity of the LUC reporter is quantified semiautomatically by image analysis. Candidate compounds able to activate the reporter are thus identified and subjected to a secondary screen by analyzing their effect on ABA-related phenotypes (e.g., inhibition of seed germination). This assay is fast, high-throughput, nondestructive, semiquantitative and can be applied to any other luciferase reporter lines, making it ideal for forward chemical genetic screenings.
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Affiliation(s)
- Irene García-Maquilón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain
| | - Aditya S Vaidya
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain.
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7
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Vaidya AS, Helander JDM, Peterson FC, Elzinga D, Dejonghe W, Kaundal A, Park SY, Xing Z, Mega R, Takeuchi J, Khanderahoo B, Bishay S, Volkman BF, Todoroki Y, Okamoto M, Cutler SR. Dynamic control of plant water use using designed ABA receptor agonists. Science 2020; 366:366/6464/eaaw8848. [PMID: 31649167 DOI: 10.1126/science.aaw8848] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/11/2019] [Indexed: 12/25/2022]
Abstract
Drought causes crop losses worldwide, and its impact is expected to increase as the world warms. This has motivated the development of small-molecule tools for mitigating the effects of drought on agriculture. We show here that current leads are limited by poor bioactivity in wheat, a widely grown staple crop, and in tomato. To address this limitation, we combined virtual screening, x-ray crystallography, and structure-guided design to develop opabactin (OP), an abscisic acid (ABA) mimic with up to an approximately sevenfold increase in receptor affinity relative to ABA and up to 10-fold greater activity in vivo. Studies in Arabidopsis thaliana reveal a role of the type III receptor PYRABACTIN RESISTANCE-LIKE 2 for the antitranspirant efficacy of OP. Thus, virtual screening and structure-guided optimization yielded newly discovered agonists for manipulating crop abiotic stress tolerance and water use.
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Affiliation(s)
- Aditya S Vaidya
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Jonathan D M Helander
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Dezi Elzinga
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Wim Dejonghe
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Amita Kaundal
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Plants, Soils and Climate, Utah State University, Logan, UT 84322, USA
| | - Sang-Youl Park
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Zenan Xing
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Ryousuke Mega
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Jun Takeuchi
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Bardia Khanderahoo
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Steven Bishay
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yasushi Todoroki
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine, Utsunomiya, Tochigi 321-8505, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Sean R Cutler
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA. .,Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
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8
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Abdelkarim H, Neelarapu R, Madriaga A, Vaidya AS, Kastrati I, Wang YT, Taha TY, Thatcher GRJ, Frasor J, Petukhov PA. Design, Synthesis, Molecular Modeling, and Biological Evaluation of Novel Amine-based Histone Deacetylase Inhibitors. ChemMedChem 2017; 12:2030-2043. [PMID: 29080240 PMCID: PMC5881582 DOI: 10.1002/cmdc.201700449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/19/2017] [Indexed: 01/08/2023]
Abstract
Histone deacetylases (HDACs) are promising drug targets for a variety of therapeutic applications. Herein we describe the design, synthesis, biological evaluation in cellular models of cancer, and preliminary drug metabolism and pharmacokinetic studies (DMPK) of a series of secondary and tertiary N-substituted 7-aminoheptanohydroxamic acid-based HDAC inhibitors. Introduction of an amino group with one or two surface binding groups (SBGs) yielded a successful strategy to develop novel and potent HDAC inhibitors. The secondary amines were found to be generally more potent than the corresponding tertiary amines. Docking studies suggested that the SBGs of tertiary amines cannot be favorably accommodated at the gorge region of the binding site. The secondary amines with naphthalen-2-ylmethyl, 5-phenylthiophen-2-ylmethyl, and 1H-indol-2-ylmethyl (2 j) substituents exhibited the highest potency against class I HDACs: HDAC1 IC50 39-61 nm, HDAC2 IC50 260-690 nm, HDAC3 IC50 25-68 nm, and HDAC8 IC50 320-620 nm. The cytotoxicity of a representative set of secondary and tertiary N-substituted 7-aminoheptanoic acid hydroxyamide-based inhibitors against HT-29, SH-SY5Y, and MCF-7 cancer cells correlated with their inhibition of HDAC1, 2, and 3 and was found to be similar to or better than that of suberoylanilide hydroxamic acid (SAHA). Compounds in this series increased the acetylation of histones H3 and H4 in a time-dependent manner. DMPK studies indicated that secondary amine 2 j is metabolically stable and has plasma and brain concentrations >23- and >1.6-fold higher than the IC50 value for class I HDACs, respectively. Overall, the secondary and tertiary N-substituted 7-aminoheptanoic acid hydroxyamide-based inhibitors exhibit excellent lead- and drug-like properties and therapeutic capacity for cancer applications.
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Affiliation(s)
- Hazem Abdelkarim
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Raghupathi Neelarapu
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Antonett Madriaga
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Aditya S. Vaidya
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Irida Kastrati
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yue-ting Wang
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Taha Y. Taha
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Gregory R. J. Thatcher
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
| | - Jonna Frasor
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Pavel A. Petukhov
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, USA
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Vaidya AS, Peterson FC, Yarmolinsky D, Merilo E, Verstraeten I, Park SY, Elzinga D, Kaundal A, Helander J, Lozano-Juste J, Otani M, Wu K, Jensen DR, Kollist H, Volkman BF, Cutler SR. A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration. ACS Chem Biol 2017; 12:2842-2848. [PMID: 28949512 DOI: 10.1021/acschembio.7b00650] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing drought and diminishing freshwater supplies have stimulated interest in developing small molecules that can be used to control transpiration. Receptors for the plant hormone abscisic acid (ABA) have emerged as key targets for this application, because ABA controls the apertures of stomata, which in turn regulate transpiration. Here, we describe the rational design of cyanabactin, an ABA receptor agonist that preferentially activates Pyrabactin Resistance 1 (PYR1) with low nanomolar potency. A 1.63 Å X-ray crystallographic structure of cyanabactin in complex with PYR1 illustrates that cyanabactin's arylnitrile mimics ABA's cyclohexenone oxygen and engages the tryptophan lock, a key component required to stabilize activated receptors. Further, its sulfonamide and 4-methylbenzyl substructures mimic ABA's carboxylate and C6 methyl groups, respectively. Isothermal titration calorimetry measurements show that cyanabactin's compact structure provides ready access to high ligand efficiency on a relatively simple scaffold. Cyanabactin treatments reduce Arabidopsis whole-plant stomatal conductance and activate multiple ABA responses, demonstrating that its in vitro potency translates to ABA-like activity in vivo. Genetic analyses show that the effects of cyanabactin, and the previously identified agonist quinabactin, can be abolished by the genetic removal of PYR1 and PYL1, which form subclade A within the dimeric subfamily III receptors. Thus, cyanabactin is a potent and selective agonist with a wide spectrum of ABA-like activities that defines subfamily IIIA receptors as key target sites for manipulating transpiration.
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Affiliation(s)
- Aditya S. Vaidya
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Francis C. Peterson
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Dmitry Yarmolinsky
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Ebe Merilo
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | | | - Sang-Youl Park
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Dezi Elzinga
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Amita Kaundal
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Jonathan Helander
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | | | - Masato Otani
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Kevin Wu
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Davin R. Jensen
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Hannes Kollist
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Brian F. Volkman
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Sean R. Cutler
- Department
of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, United States
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Helander JDM, Vaidya AS, Cutler SR. Chemical manipulation of plant water use. Bioorg Med Chem 2015; 24:493-500. [PMID: 26612713 DOI: 10.1016/j.bmc.2015.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 12/13/2022]
Abstract
Agricultural productivity is dictated by water availability and consequently drought is the major source of crop losses worldwide. The phytohormone abscisic acid (ABA) is elevated in response to water deficit and modulates drought tolerance by reducing water consumption and inducing other drought-protective responses. The recent identification of ABA receptors, elucidation of their structures and understanding of the core ABA signaling network has created new opportunities for agrochemical development. An unusually large gene family encodes ABA receptors and, until recently, it was unclear if selective or pan-agonists would be necessary for modulating water use. The recent identification of the selective agonist quinabactin has resolved this issue and defined Pyrabactin Resistance 1 (PYR1) and its close relatives as key targets for water use control. This review provides an overview of the structure and function of ABA receptors, progress in the development of synthetic agonists, and the use of orthogonal receptors to enable agrochemical control in transgenic plants.
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Affiliation(s)
- Jonathan D M Helander
- Institute for Integrative Genome Biology, Center for Plant Cell Biology, and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Aditya S Vaidya
- Institute for Integrative Genome Biology, Center for Plant Cell Biology, and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sean R Cutler
- Institute for Integrative Genome Biology, Center for Plant Cell Biology, and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
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Birmole BJ, Kulkarni BK, Vaidya AS, Borwankar SS. Intrathoracic enteric foregut duplication cyst. J Postgrad Med 1994; 40:228-30. [PMID: 9136248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A one month old male child presented with respiratory distress since day 10 of life. There was intercostal retraction and decreased air entry on the right side. Investigations revealed a well defined cystic mass in the posterior mediastinum with vertebral anomalies, the cyst was excised by posterolateral thoracotomy. Histopathology revealed it to be an enteric foregut duplication cyst.
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Affiliation(s)
- B J Birmole
- Dept of Paediatric Surgery, KEM Hospital, Parel, Bombay, Maharashtra
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Birmole BJ, Borwankar SS, Vaidya AS, Kulkarni BK. Crossed renal ectopia. J Postgrad Med 1993; 39:149-51. [PMID: 8051646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A 2 year old male child presented with mass on right side of abdomen. The clinical diagnosis of renal lump was made and rest of the examination did not reveal any abnormality. His intravenous pyelography showed non-functioning left kidney. Cystoscopy and ascending pyelography on left side showed normal ureteric orifices and crossing of the left ureter to opposite side. Ectopic kidney was removed without any damage to the lower pole of the right kidney.
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Affiliation(s)
- B J Birmole
- Dept of Paediatric Surgery, KEM Hospital, Parel, Bombay, Maharashtra
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Supe AN, Vaidya AS, Nair RG, Samsi AB, Chawla KP, Shikare S. Non penetrating traumatic perforation of gall bladder with massive choleperitoneum. Indian J Gastroenterol 1991; 10:25-6. [PMID: 2004799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- A N Supe
- Department of Surgery, Seth G S Medical College, Parel, Bombay
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Abstract
Baclofen, the parachlorophenyl analog of GABA, was found to induce catalepsy and to inhibit the traction response in mice. However, baclofen pretreatment, instead of antagonizing methamphetamine stereotypy and apomorphine-induced cage climbing behavior, was found to potentiate these behaviors, thereby ruling out the possibility of its possessing postsynaptic dopamine (DA) receptor blocking activity. The possible mechanism involved in the induction of catalepsy and in the inhibition of the traction response by baclofen is discussed on the basis that baclofen, by inhibiting the firing of the nigrostriatal and mesolimbic DA neurons, reduces the release of DA and thereby produces a functional lack of DA at postsynaptic DA receptor sites with resultant induction of catalepsy and inhibition of the traction response. Further, the hyper-responsiveness to methamphetamine and apomorphine is explained on the basis that, as the postsynaptic DA receptors are acutely deprived of their transmitter, following baclofen pretreatment, they become supersensitive to the DA agonists.
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