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DeRatt LG, Pietsch EC, Cisar JS, Jacoby E, Kazmi F, Matico R, Shaffer P, Tanner A, Wang W, Attar R, Edwards JP, Kuduk SD. Discovery of Alternative Binding Poses through Fragment-Based Identification of DHODH Inhibitors. ACS Med Chem Lett 2024; 15:381-387. [PMID: 38505861 PMCID: PMC10945543 DOI: 10.1021/acsmedchemlett.3c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 03/21/2024] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a mitochondrial enzyme that affects many aspects essential to cell proliferation and survival. Recently, DHODH has been identified as a potential target for acute myeloid leukemia therapy. Herein, we describe the identification of potent DHODH inhibitors through a scaffold hopping approach emanating from a fragment screen followed by structure-based drug design to further improve the overall profile and reveal an unexpected novel binding mode. Additionally, these compounds had low P-gp efflux ratios, allowing for applications where exposure to the brain would be required.
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Affiliation(s)
- Lindsey G. DeRatt
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - E. Christine Pietsch
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Justin S. Cisar
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Edgar Jacoby
- Janssen
Pharmaceutical Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Faraz Kazmi
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Rosalie Matico
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Paul Shaffer
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Alexandra Tanner
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Weixue Wang
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Ricardo Attar
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - James P. Edwards
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
| | - Scott D. Kuduk
- Janssen
Pharmaceutical Research and Development, 1400 McKean Rd., Spring
House, Pennsylvania 19477, United States
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2
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Cisar JS, Pietsch C, DeRatt LG, Jacoby E, Kazmi F, Keohane C, Legenski K, Matico R, Shaffer P, Simonnet Y, Tanner A, Wang CY, Wang W, Attar R, Edwards JP, Kuduk SD. N-Heterocyclic 3-Pyridyl Carboxamide Inhibitors of DHODH for the Treatment of Acute Myelogenous Leukemia. J Med Chem 2022; 65:11241-11256. [PMID: 35925768 DOI: 10.1021/acs.jmedchem.2c00788] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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
Acute myelogenous leukemia (AML), a disease of the blood and bone marrow, is characterized by the inability of myeloblasts to differentiate into mature cell types. Dihydroorotate dehydrogenase (DHODH) is an enzyme well-known in the pyrimidine biosynthesis pathway; however, small molecule DHODH inhibitors were recently shown to induce differentiation in multiple AML subtypes. Using virtual screening and structure-based drug design approaches, a new series of N-heterocyclic 3-pyridyl carboxamide DHODH inhibitors were discovered. Two lead compounds, 19 and 29, have potent biochemical and cellular DHODH activity, favorable physicochemical properties, and efficacy in a preclinical model of AML.
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Affiliation(s)
- Justin S Cisar
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Christine Pietsch
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Lindsey G DeRatt
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Edgar Jacoby
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Faraz Kazmi
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Colleen Keohane
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Katie Legenski
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Rosalie Matico
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Paul Shaffer
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Yvan Simonnet
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Alexandra Tanner
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Chao-Yuan Wang
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Weixue Wang
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - Ricardo Attar
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
| | - James P Edwards
- Janssen Research and Development, San Diego, California 92121, United States
| | - Scott D Kuduk
- Janssen Research and Development, 1400 McKean Rd, Spring House, Pennsylvania 19477, United States
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Reardon HT, Herbst RA, Henry CL, Herbst DM, Ngo N, Cisar JS, Weber OD, Niphakis MJ, O’Neill GP. Quantification of In Vivo Target Engagement Using Microfluidic Activity-Based Protein Profiling. SLAS Technol 2019; 24:489-498. [DOI: 10.1177/2472630319852303] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Accurate measurement of drug–target interactions in vivo is critical for both preclinical development and translation to clinical studies, yet many assays rely on indirect measures such as biomarkers associated with target activity. Activity-based protein profiling (ABPP) is a direct method of quantifying enzyme activity using active site-targeted small-molecule covalent probes that selectively label active but not inhibitor-bound enzymes. Probe-labeled enzymes in complex proteomes are separated by polyacrylamide gel electrophoresis and quantified by fluorescence imaging. To accelerate workflows and avoid imaging artifacts that make conventional gels challenging to quantify, we adapted protocols for a commercial LabChip GXII microfluidic instrument to permit electrophoretic separation of probe-labeled proteins in tissue lysates and plasma, and quantification of fluorescence (probe/protein labeling ratio of 1:1). Electrophoretic separation on chips occurred in 40 s per sample, and instrument software automatically identified and quantified peaks, resulting in an overall time savings of 3–5 h per 96-well sample plate. Calculated percent inhibition was not significantly different between the two formats. Chip performance was consistent between chips and sample replicates. Conventional gel imaging was more sensitive but required five times higher sample volume than microfluidic chips. Microfluidic chips produced results comparable to those of gels but with much lower sample consumption, facilitating assay miniaturization for scarce biological samples. The time savings afforded by microfluidic electrophoresis and automatic quantification has allowed us to incorporate microfluidic ABPP early in the drug discovery workflow, enabling routine assessments of tissue distribution and engagement of targets and off-targets in vivo.
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Affiliation(s)
| | | | | | | | - Nhi Ngo
- Abide Therapeutics, San Diego, CA, USA
| | - Justin S. Cisar
- Abide Therapeutics, San Diego, CA, USA
- Janssen Research & Development, Spring House, PA
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Clapper JR, Henry CL, Niphakis MJ, Knize AM, Coppola AR, Simon GM, Ngo N, Herbst RA, Herbst DM, Reed AW, Cisar JS, Weber OD, Viader A, Alexander JP, Cunningham ML, Jones TK, Fraser IP, Grice CA, Ezekowitz RAB, O’Neill GP, Blankman JL. Monoacylglycerol Lipase Inhibition in Human and Rodent Systems Supports Clinical Evaluation of Endocannabinoid Modulators. J Pharmacol Exp Ther 2018; 367:494-508. [DOI: 10.1124/jpet.118.252296] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/05/2018] [Indexed: 12/15/2022] Open
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Cisar JS, Weber OD, Clapper JR, Blankman JL, Henry CL, Simon GM, Alexander JP, Jones TK, Ezekowitz RAB, O’Neill GP, Grice CA. Identification of ABX-1431, a Selective Inhibitor of Monoacylglycerol Lipase and Clinical Candidate for Treatment of Neurological Disorders. J Med Chem 2018; 61:9062-9084. [DOI: 10.1021/acs.jmedchem.8b00951] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Justin S. Cisar
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Olivia D. Weber
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Jason R. Clapper
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Jacqueline L. Blankman
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Cassandra L. Henry
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Gabriel M. Simon
- Vividion Therapeutics, 3565 General Atomics Court, Suite 100, San Diego, California 92121, United States
| | - Jessica P. Alexander
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Todd K. Jones
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - R. Alan B. Ezekowitz
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Gary P. O’Neill
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
| | - Cheryl A. Grice
- Abide Therapeutics, 10835 Road to the Cure, Suite 250, San Diego, California 92121, United States
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Keow JY, Pond ED, Cisar JS, Cravatt BF, Crawford BD. Activity-based labeling of matrix metalloproteinases in living vertebrate embryos. PLoS One 2012; 7:e43434. [PMID: 22952682 PMCID: PMC3429480 DOI: 10.1371/journal.pone.0043434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [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: 09/17/2011] [Accepted: 07/23/2012] [Indexed: 12/25/2022] Open
Abstract
Extracellular matrix (ECM) remodeling is a physiologically and developmentally essential process mediated by a family of zinc-dependent extracellular proteases called matrix metalloproteinases (MMPs). In addition to complex transcriptional control, MMPs are subject to extensive post-translational regulation. Because of this, classical biochemical, molecular and histological techniques that detect the expression of specific gene products provide useful but limited data regarding the biologically relevant activity of MMPs. Using benzophenone-bearing hydroxamate-based probes that interact with the catalytic zinc ion in MMPs, active proteases can be covalently ‘tagged’ by UV cross-linking. This approach has been successfully used to tag MMP-2 in vitro in tissue culture supernatants, and we show here that this probe tags proteins with mobilities consistent with known MMPs and detectable gelatinolytic activity in homogenates of zebrafish embryos. Furthermore, because of the transparency of the zebrafish embryo, UV-photocroslinking can be accomplished in vivo, and rhodamated benzophenone probe is detected in striking spatial patterns consistent with known distributions of active matrix remodeling in embryos. Finally, in metamorphosing Xenopus tadpoles, this probe can be used to biotinylate active MMP-2 by injecting it and cross-linking it in vivo, allowing the protein to be subsequently extracted and biochemically identified.
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Affiliation(s)
- Jonathan Y. Keow
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Eric D. Pond
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Justin S. Cisar
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Benjamin F. Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Bryan D. Crawford
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
- * E-mail:
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Abstract
Phenotypic screening offers a powerful approach to identify small molecules that perturb complex biological processes in cells and organisms. The tendency of small molecules, however, to interact with multiple protein targets, often with moderate to weak affinities, along with the lack of straightforward technologies to characterize these interactions in living systems, has hindered efforts to understand the mechanistic basis for pharmacological activity. Here we address this challenge by creating a fully functionalized small-molecule library whose membership is endowed with: (1) one or more diversity elements to promote interactions with different protein targets in cells, (2) a photoreactive group for UV light-induced covalent cross-linking to interacting proteins, and (3) an alkyne handle for reporter tag conjugation to visualize and identify cross-linked proteins. A library member was found to inhibit cancer cell proliferation selectively under nutrient-limiting (low glucose) conditions. Quantitative chemoproteomics identified MT-ND1, an integral membrane subunit of the ∼1 MDa NADH:ubiquinone oxidoreductase (complex 1) involved in oxidative phosphorylation, as a specific target of the active probe. We further demonstrated that the active probe inhibits complex 1 activity in vitro (IC(50) = 720 nM), an effect that is known to induce cell death in low-glucose conditions. Based on this proof of principle study, we anticipate that the generation and integration of fully functionalized compound libraries into phenotypic screening programs should facilitate the discovery of bioactive probes that are amenable to accelerated target identification and mechanistic characterization using advanced chemoproteomic technologies.
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Affiliation(s)
- Justin S Cisar
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Long JZ, Cisar JS, Milliken D, Niessen S, Wang C, Trauger SA, Siuzdak G, Cravatt BF. Metabolomics annotates ABHD3 as a physiologic regulator of medium-chain phospholipids. Nat Chem Biol 2011; 7:763-5. [PMID: 21926997 PMCID: PMC3201731 DOI: 10.1038/nchembio.659] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [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: 05/06/2011] [Accepted: 07/08/2011] [Indexed: 01/08/2023]
Abstract
All organisms, including humans, possess a huge number of uncharacterized enzymes. Here, we describe a general cell-based screen for enzyme substrate discovery by untargeted metabolomics and its application to identify α/β-hydrolase domain-containing 3 (ABHD3) as a lipase that selectively cleaves medium-chain and oxidatively-truncated phospholipids. Abhd3−/− mice possess elevated myristoyl (C14)-phospholipids, including the bioactive lipid C14-lysophosphatidylcholine, confirming the physiological relevance of our substrate assignments.
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Lu X, Olsen SK, Capili AD, Cisar JS, Lima CD, Tan DS. Designed semisynthetic protein inhibitors of Ub/Ubl E1 activating enzymes. J Am Chem Soc 2010; 132:1748-9. [PMID: 20099854 DOI: 10.1021/ja9088549] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Semisynthetic, mechanism-based protein inhibitors of ubiquitin (Ub) and ubiquitin-like modifier (Ubl) activating enzymes (E1s) have been developed to target E1-catalyzed adenylation and thioesterification of the Ub/Ubl C-terminus during the processes of protein SUMOylation and ubiquitination. The inhibitors were generated by intein-mediated expressed protein ligation using a truncated Ub/Ubl protein (SUMO residues 1-94; Ub residues 1-71) with a C-terminal thioester and synthetic tripeptides having a C-terminal adenosine analogue and an N-terminal cysteine residue. SUMO-AMSN (4a) and Ub-AMSN (4b) contain a sulfamide group as a nonhydrolyzable mimic of the phosphate group in the cognate Ub/Ubl-AMP adenylate intermediate in the first half-reaction, and these constructs selectively inhibit SUMO E1 and Ub E1, respectively, in a dose-dependent manner. SUMO-AVSN (5a) and Ub-AVSN (5b) contain an electrophilic vinyl sulfonamide designed to trap the incoming E1 cysteine nucleophile (Uba2 Cys173 in SUMO E1; Uba1 Cys593 in Ub E1) in the second half-reaction, and these constructs selectively, covalently, and stably cross-link to SUMO E1 and Ub E1, respectively, in a cysteine nucleophile-dependent manner. These inhibitors are powerful tools to probe outstanding mechanistic questions in E1 function and can also be used to study the biological functions of E1 enzymes.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, USA
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10
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Abstract
A variety of natural products modulate critical biological processes in the microorganisms that produce them. Thus, inhibition of the corresponding natural product biosynthesis pathways represents a promising avenue to develop novel antibiotics. In this tutorial review, we describe several recent examples of designed small molecule inhibitors of microbial natural product biosynthesis and their use in evaluating this emerging antibiotic strategy.
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Affiliation(s)
- Justin S Cisar
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 422, New York, NY 10065, USA
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11
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Cisar JS, Ferreras JA, Soni RK, Quadri LEN, Tan DS. Exploiting ligand conformation in selective inhibition of non-ribosomal peptide synthetase amino acid adenylation with designed macrocyclic small molecules. J Am Chem Soc 2007; 129:7752-3. [PMID: 17542590 PMCID: PMC2565600 DOI: 10.1021/ja0721521] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin S. Cisar
- Tri-Institutional Training Program in Chemical Biology, Tri-Institutional Research Program and Molecular Pharmacology & Chemistry Program, 1275 York Avenue, Box 422, New York, New York 10021
- Memorial Sloan–Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10021,
| | - Julian A. Ferreras
- Department of Microbiology & Immunology and Molecular Biology Program, Weill Medical College of Cornell University, 1300 York Avenue, Box 62, New York, New York 10021,
| | - Rajesh K. Soni
- Department of Microbiology & Immunology and Molecular Biology Program, Weill Medical College of Cornell University, 1300 York Avenue, Box 62, New York, New York 10021,
| | - Luis E. N. Quadri
- Tri-Institutional Training Program in Chemical Biology, Tri-Institutional Research Program and Molecular Pharmacology & Chemistry Program, 1275 York Avenue, Box 422, New York, New York 10021
- Department of Microbiology & Immunology and Molecular Biology Program, Weill Medical College of Cornell University, 1300 York Avenue, Box 62, New York, New York 10021,
| | - Derek S. Tan
- Tri-Institutional Training Program in Chemical Biology, Tri-Institutional Research Program and Molecular Pharmacology & Chemistry Program, 1275 York Avenue, Box 422, New York, New York 10021
- Memorial Sloan–Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10021,
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12
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Abstract
Conjugated polymers capable of responding to external stimuli by changes in optical, electrical, or electrochemical properties can be used for the construction of direct sensing devices. Polydiacetylene-based systems are attractive for sensing applications due to their colorimetric response to changes in the local environment. Here we present the design, preparation, and characterization of self-assembling functional bolaamphiphilic polydiacetylenes (BPDAs) inspired by nature's strategy for membrane stabilization. We show that by placing polar headgroups on both ends of the diacetylene lipids in a transmembranic fashion and by altering the chemical nature of the polar surface residues, the conjugated polymers can be engineered to display a range of radiation-, thermal-, and pH-induced colorimetric responses. We observed dramatic nanoscopic morphological transformations accompanying charge-induced chromatic transitions, suggesting that both side-chain disordering and main-chain rearrangement play important roles in altering the effective conjugation lengths of the poly(ene-yne). These results establish the foundation for further development of BPDA-based colorimetric sensors.
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Affiliation(s)
- Jie Song
- Materials Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA.
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