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He M, Li J, Han H, Borges CA, Neiman G, Røise JJ, Hadaczek P, Mendonsa R, Holm VR, Wilson RC, Bankiewicz K, Zhang Y, Sadlowski CM, Healy K, Riley LW, Murthy N. A traceless linker for aliphatic amines that rapidly and quantitatively fragments after reduction. Chem Sci 2020; 11:8973-8980. [PMID: 34123152 PMCID: PMC8163433 DOI: 10.1039/d0sc00929f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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] [Indexed: 12/13/2022] Open
Abstract
Reduction sensitive linkers (RSLs) have the potential to transform the field of drug delivery due to their ease of use and selective cleavage in intracellular environments. However, despite their compelling attributes, developing reduction sensitive self-immolative linkers for aliphatic amines has been challenging due to their poor leaving group ability and high pKa values. Here a traceless self-immolative linker composed of a dithiol-ethyl carbonate connected to a benzyl carbamate (DEC) is presented, which can modify aliphatic amines and release them rapidly and quantitatively after disulfide reduction. DEC was able to reversibly modify the lysine residues on CRISPR–Cas9 with either PEG, the cell penetrating peptide Arg10, or donor DNA, and generated Cas9 conjugates with significantly improved biological properties. In particular, Cas9–DEC–PEG was able to diffuse through brain tissue significantly better than unmodified Cas9, making it a more suitable candidate for genome editing in animals. Furthermore, conjugation of Arg10 to Cas9 with DEC was able to generate a self-delivering Cas9 RNP that could edit cells without transfection reagents. Finally, conjugation of donor DNA to Cas9 with DEC increased the homology directed DNA repair (HDR) rate of the Cas9 RNP by 50% in HEK 293T cell line. We anticipate that DEC will have numerous applications in biotechnology, given the ubiquitous presence of aliphatic amines on small molecule and protein therapeutics. Reduction sensitive linkers (RSLs) have the potential to transform the field of drug delivery due to their ease of use and selective cleavage in intracellular environments.![]()
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Affiliation(s)
- Maomao He
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Jie Li
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Hesong Han
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Clarissa Araujo Borges
- Department of Public Health, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Gabriel Neiman
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Joachim Justad Røise
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA .,Department of Chemistry, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Piotr Hadaczek
- Department of Neurological Surgery, The Ohio State University Columbus OH 43210 USA
| | - Rima Mendonsa
- Innovative Genomics Institute, University of California Berkeley CA 94704 USA
| | - Victoria R Holm
- Innovative Genomics Institute, University of California Berkeley CA 94704 USA
| | - Ross C Wilson
- Innovative Genomics Institute, University of California Berkeley CA 94704 USA
| | - Krystof Bankiewicz
- Department of Neurological Surgery, The Ohio State University Columbus OH 43210 USA
| | - Yumiao Zhang
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA .,School of Chemical Engineering and Technology, Tianjin University 300350 China
| | - Corinne M Sadlowski
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Kevin Healy
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Lee W Riley
- Department of Public Health, University of California Berkeley University Avenue Berkeley CA 94720 USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley University Avenue Berkeley CA 94720 USA .,Innovative Genomics Institute, University of California Berkeley CA 94704 USA
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Abstract
Improvements in in vitro ADME tools and pharmacokinetic prediction models have helped to shift attrition rates in early clinical trials from poor exposure to drug safety concerns, such as drug-induced liver injury (DILI). Assessing a new chemical entity's potential for liver toxicity is an important consideration for the likely success of new drug candidates. Reactive intermediates produced during drug metabolism have been implicated as a cause of DILI, and their formation has been correlated to the addition of a black box warning on a drug label. In this work, we will present contemporary examples of the bioactivation of atypical structures usually regarded as benign and often used by medicinal chemists when attempting to avoid bioactivation. Medicinal chemistry strategies used to derisk bioactivation will be discussed, and an emphasis will be placed on the necessity of a multidisciplinary approach.
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Affiliation(s)
- James P Driscoll
- MyoKardia, Inc., 333 Allerton Avenue, South San Francisco, California 94080, United States
| | - Corinne M Sadlowski
- MyoKardia, Inc., 333 Allerton Avenue, South San Francisco, California 94080, United States
| | - Nina R Shah
- MyoKardia, Inc., 333 Allerton Avenue, South San Francisco, California 94080, United States
| | - Antonio Feula
- MyoKardia, Inc., 333 Allerton Avenue, South San Francisco, California 94080, United States
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deBoer TR, Tarlton NJ, Yamaji R, Adams-Sapper S, Wu TZ, Maity S, Vesgesna GK, Sadlowski CM, DePaola P, Riley LW, Murthy N. Cover Feature: An Enzyme-Mediated Amplification Strategy Enables Detection of β-Lactamase Activity Directly in Unprocessed Clinical Samples for Phenotypic Detection of β-Lactam Resistance (ChemBioChem 20/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800571] [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: 11/08/2022]
Affiliation(s)
- Tara R. deBoer
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Nicole J. Tarlton
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Reina Yamaji
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Sheila Adams-Sapper
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Tiffany Z. Wu
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Santanu Maity
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Giri K. Vesgesna
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Corinne M. Sadlowski
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Peter DePaola
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Lee W. Riley
- Department of Public Health; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
| | - Niren Murthy
- Department of Bioengineering; University of California, Berkeley; University Avenue Berkeley CA 94720 USA
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deBoer TR, Tarlton NJ, Yamaji R, Adams-Sapper S, Wu TZ, Maity S, Vesgesna GK, Sadlowski CM, DePaola P, Riley LW, Murthy N. An Enzyme-Mediated Amplification Strategy Enables Detection of β-Lactamase Activity Directly in Unprocessed Clinical Samples for Phenotypic Detection of β-Lactam Resistance. Chembiochem 2018; 19:2173-2177. [PMID: 30079487 DOI: 10.1002/cbic.201800443] [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] [Received: 08/01/2018] [Indexed: 11/09/2022]
Abstract
Biochemical assays that can identify β-lactamase activity directly from patient samples have the potential to significantly improve the treatment of bacterial infections. However, current β-lactamase probes do not have the sensitivity needed to measure β-lactam resistance directly from patient samples. Here, we report the development of an instrument-free signal amplification technology, DETECT, that connects the activity of two enzymes in series to effectively amplify the activity of β-lactamase 40 000-fold, compared to the standard β-lactamase probe nitrocefin.
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Affiliation(s)
- Tara R deBoer
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Nicole J Tarlton
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Reina Yamaji
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Sheila Adams-Sapper
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Tiffany Z Wu
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Santanu Maity
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Giri K Vesgesna
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Corinne M Sadlowski
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Peter DePaola
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Lee W Riley
- Department of Public Health, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, University Avenue, Berkeley, CA, 94720, USA
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Maity S, Sadlowski CM, George Lin JM, Chen CH, Peng LH, Lee ES, Vegesna GK, Lee C, Kim SH, Mochly-Rosen D, Kumar S, Murthy N. Thiophene bridged aldehydes (TBAs) image ALDH activity in cells via modulation of intramolecular charge transfer. Chem Sci 2017; 8:7143-7151. [PMID: 29081945 PMCID: PMC5635522 DOI: 10.1039/c7sc03017g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/01/2017] [Indexed: 12/15/2022] Open
Abstract
Aldehyde dehydrogenases (ALDHs) catalyze the oxidation of an aldehyde to a carboxylic acid and are implicated in the etiology of numerous diseases. However, despite their importance, imaging ALDH activity in cells is challenging due to a lack of fluorescent imaging probes. In this report, we present a new family of fluorescent probes composed of an oligothiophene flanked by an aldehyde and an electron donor, termed thiophene-bridged aldehydes (TBAs), which can image ALDH activity in cells. The TBAs image ALDH activity via a fluorescence sensing mechanism based on the modulation of intramolecular charge transfer (ICT) and this enables the TBAs and their ALDH-mediated oxidized products, thiophene-bridged carboxylates (TBCs), to have distinguishable fluorescence spectra. Herein, we show that the TBAs can image ALDH activity in cells via fluorescence microscopy, flow cytometry, and in a plate reader. Using TBA we were able to develop a cell-based high throughput assay for ALDH inhibitors, for the first time, and screened a large, 1460-entry electrophile library against A549 cells. We identified α,β-substituted acrylamides as potent electrophile fragments that can inhibit ALDH activity in cells. These inhibitors sensitized drug-resistant glioblastoma cells to the FDA approved anti-cancer drug, temozolomide. The TBAs have the potential to make the analysis of ALDH activity in cells routinely possible given their ability to spectrally distinguish between an aldehyde and a carboxylic acid.
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Affiliation(s)
- Santanu Maity
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Corinne M Sadlowski
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Jung-Ming George Lin
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
- The UC Berkeley-UCSF Graduate Program in Bioengineering , UC Berkeley , Berkeley , California , USA
| | - Che-Hong Chen
- Department of Chemical and Systems Biology , Stanford University , School of Medicine , Stanford , CA 94305-5174 , USA
| | - Li-Hua Peng
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Eun-Soo Lee
- Korea Research Institute of Standards and Science , 267 Gajeong-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Giri K Vegesna
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Charles Lee
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Se-Hwa Kim
- Korea Research Institute of Standards and Science , 267 Gajeong-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology , Stanford University , School of Medicine , Stanford , CA 94305-5174 , USA
| | - Sanjay Kumar
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
- The UC Berkeley-UCSF Graduate Program in Bioengineering , UC Berkeley , Berkeley , California , USA
| | - Niren Murthy
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
- The UC Berkeley-UCSF Graduate Program in Bioengineering , UC Berkeley , Berkeley , California , USA
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Maity S, Das S, Sadlowski CM, Zhang J, Vegesna GK, Murthy N. Thiophene bridged hydrocyanine – a new fluorogenic ROS probe. Chem Commun (Camb) 2017; 53:10184-10187. [DOI: 10.1039/c7cc04847e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this report, we present a new hydrocyanine analog, termed as thiophene-bridged hydrocyanine (TBHC), which has its double bonds replaced with a bisthiophene, is 8.06-fold more stable to auto-oxidation than hydro-Cy5 and significantly better in cell culture.
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