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Zhang S, Tang Q, Zhang X, Chen X. Proximitomics by Reactive Species. ACS CENTRAL SCIENCE 2024; 10:1135-1147. [PMID: 38947200 PMCID: PMC11212136 DOI: 10.1021/acscentsci.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.
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Affiliation(s)
- Shaoran Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Qi Tang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
| | - Xu Zhang
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
| | - Xing Chen
- College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s
Republic of China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, People’s Republic of China
- Beijing
National Laboratory for Molecular Sciences, Peking University, Beijing 100871, People’s
Republic of China
- Synthetic
and Functional Biomolecules Center, Peking
University, Beijing 100871, People’s
Republic of China
- Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry
of Education, Peking University, Beijing 100871, People’s Republic of China
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2
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Clay WK, Buck AK, He Y, Hernández Sánchez DN, Ward NA, Lear JM, Nguyen KQ, Clark BH, Sapia RJ, Lalisse RF, Sriraman A, Cadieux CL, McElroy CA, Callam CS, Hadad CM. Treatment of Organophosphorus Poisoning with 6-Alkoxypyridin-3-ol Quinone Methide Precursors: Resurrection of Methylphosphonate-Aged Acetylcholinesterase. Chem Res Toxicol 2024; 37:643-657. [PMID: 38556765 DOI: 10.1021/acs.chemrestox.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Organophosphorus (OP) nerve agents inhibit acetylcholinesterase (AChE), creating a cholinergic crisis in which death can occur. The phosphylated serine residue spontaneously dealkylates to the OP-aged form, which current therapeutics cannot reverse. Soman's aging half-life is 4.2 min, so immediate recovery (resurrection) of OP-aged AChE is needed. In 2018, we showed pyridin-3-ol-based quinone methide precursors (QMPs) can resurrect OP-aged electric eel AChE in vitro, achieving 2% resurrection after 24 h of incubation (pH 7, 4 mM). We prepared 50 unique 6-alkoxypyridin-3-ol QMPs with 10 alkoxy groups and five amine leaving groups to improve AChE resurrection. These compounds are predicted in silico to cross the blood-brain barrier and treat AChE in the central nervous system. This library resurrected 7.9% activity of OP-aged recombinant human AChE after 24 h at 250 μM, a 4-fold increase from our 2018 report. The best QMP (1b), with a 6-methoxypyridin-3-ol core and a diethylamine leaving group, recovered 20.8% (1 mM), 34% (4 mM), and 42.5% (predicted maximum) of methylphosphonate-aged AChE activity over 24 h. Seven QMPs recovered activity from AChE aged with Soman and a VX degradation product (EA-2192). We hypothesize that QMPs form the quinone methide (QM) to realkylate the phosphylated serine residue as the first step of resurrection. We calculated thermodynamic energetics for QM formation, but there was no trend with the experimental biochemical data. Molecular docking studies revealed that QMP binding to OP-aged AChE is not the determining factor for the observed biochemical trends; thus, QM formation may be enzyme-mediated.
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Affiliation(s)
- William K Clay
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anne K Buck
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yiran He
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dalyanne N Hernández Sánchez
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nathan A Ward
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeremy M Lear
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kenny Q Nguyen
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin H Clark
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ryan J Sapia
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Remy F Lalisse
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aishwarya Sriraman
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
- U.S. Army Medical Research Institute of Chemical Defense, 8350 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - C Linn Cadieux
- U.S. Army Medical Research Institute of Chemical Defense, 8350 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Craig A McElroy
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher S Callam
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
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3
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Wang R, Gan YF, Li YY, Chen XQ, Guo YY. Recent Advances in Quinone Methide Chemistry for Protein-Proximity Capturing. SYNTHESIS-STUTTGART 2023. [DOI: 10.1055/s-0042-1751402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
AbstractHere we summarize the most recent findings in the chemical-, photo-, or enzyme-triggered generation of nitrogen and oxygen anions leading to the formation of quinone methide intermediates (QMIs). This short review is divided into two categories: generation of nitrogen and oxygen anions. Based on quinone methide intermediates (QMIs), proximate capture of a wide range of proteins has been widely determined and studied. Generally, the triggers include, photoirradiation using 365/254 nm UV light, small molecules (ROS/TBAF/s-tetrazine), metal catalysis (iridium catalysis), and enzymes (NQO1/β-galactosidase). New directions including far-red light, heat, force, microwave, and more practical approaches are explored and illustrated.1 Introduction2 Generation of the Nitrogen Anion3 Generation of the Oxygen Anion4 Conclusion
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Affiliation(s)
- Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
- Shenzhen Huazhong University of Science and Technology Research Institute
| | - You F. Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
| | - Yuan Y. Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
| | - Xiao Q. Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
| | - Yu Y. Guo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
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4
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Liu J, Cheng R, Van Eps N, Wang N, Morizumi T, Ou WL, Klauser PC, Rozovsky S, Ernst OP, Wang L. Genetically Encoded Quinone Methides Enabling Rapid, Site-Specific, and Photocontrolled Protein Modification with Amine Reagents. J Am Chem Soc 2020; 142:17057-17068. [PMID: 32915556 DOI: 10.1021/jacs.0c06820] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific modification of proteins with functional molecules provides powerful tools for researching and engineering proteins. Here we report a new chemical conjugation method which photocages highly reactive but chemically selective moieties, enabling the use of protein-inert amines for selective protein modification. New amino acids FnbY and FmnbY, bearing photocaged quinone methides (QMs), were genetically incorporated into proteins. Upon light activation, they generated highly reactive QM, which rapidly reacted with amine derivatives. This method features a rare combination of desired properties including fast kinetics, small and stable linkage, compatibility with low temperature, photocontrollability, and widely available reagents. Moreover, labeling via FnbY occurs on the β-carbon, affording the shortest linkage to protein backbone which is essential for advanced studies involving orientation and distance. We installed various functionalities onto proteins and attached a spin label as close as possible to the protein backbone, achieving high resolution in double electron-electron paramagnetic resonance distance measurements.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Rujin Cheng
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Paul C Klauser
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
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5
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Liu J, Li S, Aslam NA, Zheng F, Yang B, Cheng R, Wang N, Rozovsky S, Wang PG, Wang Q, Wang L. Genetically Encoding Photocaged Quinone Methide to Multitarget Protein Residues Covalently in Vivo. J Am Chem Soc 2019; 141:9458-9462. [PMID: 31184146 DOI: 10.1021/jacs.9b01738] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetically introducing covalent bonds into proteins in vivo with residue specificity is affording innovative ways for protein research and engineering, yet latent bioreactive unnatural amino acids (Uaas) genetically encoded to date react with one to few natural residues only, limiting the variety of proteins and the scope of applications amenable to this technology. Here we report the genetic encoding of (2 R)-2-amino-3-fluoro-3-(4-((2-nitrobenzyl)oxy) phenyl) propanoic acid (FnbY) in Escherichia coli and mammalian cells. Upon photoactivation, FnbY generated a reactive quinone methide (QM), which selectively reacted with nine natural amino acid residues placed in proximity in proteins directly in live cells. In addition to Cys, Lys, His, and Tyr, photoactivated FnbY also reacted with Trp, Met, Arg, Asn, and Gln, which are inaccessible with existing latent bioreactive Uaas. FnbY thus dramatically expanded the number of residues for covalent targeting in vivo. QM has longer half-life than the intermediates of conventional photo-cross-linking Uaas, and FnbY exhibited cross-linking efficiency higher than p-azido-phenylalanine. The photoactivatable and multitargeting reactivity of FnbY with selectivity toward nucleophilic residues will be valuable for addressing diverse proteins and broadening the scope of applications through exploiting covalent bonding in vivo for chemical biology, biotherapeutics, and protein engineering.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Shanshan Li
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States.,Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | - Nayyar A Aslam
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Feng Zheng
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Bing Yang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Rujin Cheng
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Peng G Wang
- Department of Chemistry and Center for Therapeutics and Diagnostics , Georgia State University , Atlanta , Georgia 30302 , United States
| | - Qian Wang
- Hangzhou Research Institute of Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Hangzhou 310018 , China
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute , University of California San Francisco , 555 Mission Bay Boulevard South , San Francisco , California 94158 , United States
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6
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Liu Z, Hao W, Gao W, Zhu G, Li X, Tong L, Tang B. Silver-catalyzed three-component reaction: synthesis of N2-substituted 1,2,3-triazoles via direct benzylic amination. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9455-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Franjesevic AJ, Sillart SB, Beck JM, Vyas S, Callam CS, Hadad CM. Resurrection and Reactivation of Acetylcholinesterase and Butyrylcholinesterase. Chemistry 2019; 25:5337-5371. [PMID: 30444932 PMCID: PMC6508893 DOI: 10.1002/chem.201805075] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/15/2018] [Indexed: 01/10/2023]
Abstract
Organophosphorus (OP) nerve agents and pesticides present significant threats to civilian and military populations. OP compounds include the nefarious G and V chemical nerve agents, but more commonly, civilians are exposed to less toxic OP pesticides, resulting in the same negative toxicological effects and thousands of deaths on an annual basis. After decades of research, no new therapeutics have been realized since the mid-1900s. Upon phosphylation of the catalytic serine residue, a process known as inhibition, there is an accumulation of acetylcholine (ACh) in the brain synapses and neuromuscular junctions, leading to a cholinergic crisis and eventually death. Oxime nucleophiles can reactivate select OP-inhibited acetylcholinesterase (AChE). Yet, the fields of reactivation of AChE and butyrylcholinesterase encounter additional challenges as broad-spectrum reactivation of either enzyme is difficult. Additional problems include the ability to cross the blood brain barrier (BBB) and to provide therapy in the central nervous system. Yet another complication arises in a competitive reaction, known as aging, whereby OP-inhibited AChE is converted to an inactive form, which until very recently, had been impossible to reverse to an active, functional form. Evaluations of uncharged oximes and other neutral nucleophiles have been made. Non-oxime reactivators, such as aromatic general bases and Mannich bases, have been developed. The issue of aging, which generates an anionic phosphylated serine residue, has been historically recalcitrant to recovery by any therapeutic approach-that is, until earlier this year. Mannich bases not only serve as reactivators of OP-inhibited AChE, but this class of compounds can also recover activity from the aged form of AChE, a process referred to as resurrection. This review covers the modern efforts to address all of these issues and notes the complexities of therapeutic development along these different lines of research.
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Affiliation(s)
- Andrew J Franjesevic
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH, 43210, USA
| | - Sydney B Sillart
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH, 43210, USA
| | - Jeremy M Beck
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH, 43210, USA
| | - Shubham Vyas
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH, 43210, USA
- Current Address: Department of Chemistry, Colorado School of Mines, 1500 Illinois St., Golden, CO, 80401, USA
| | - Christopher S Callam
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH, 43210, USA
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH, 43210, USA
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8
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Zhuang Q, Franjesevic AJ, Corrigan TS, Coldren WH, Dicken R, Sillart S, DeYong A, Yoshino N, Smith J, Fabry S, Fitzpatrick K, Blanton TG, Joseph J, Yoder RJ, McElroy CA, Ekici ÖD, Callam CS, Hadad CM. Demonstration of In Vitro Resurrection of Aged Acetylcholinesterase after Exposure to Organophosphorus Chemical Nerve Agents. J Med Chem 2018; 61:7034-7042. [PMID: 29870665 DOI: 10.1021/acs.jmedchem.7b01620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
After the inhibition of acetylcholinesterase (AChE) by organophosphorus (OP) nerve agents, a dealkylation reaction of the phosphylated serine, referred to as aging, can occur. When aged, known reactivators of OP-inhibited AChE are no longer effective. Realkylation of aged AChE may provide a route to reversing aging. We designed and synthesized a library of quinone methide precursors (QMPs) as proposed realkylators of aged AChE. Our lead compound (C8) from an in vitro screen successfully resurrected 32.7 and 20.4% of the activity of methylphosphonate-aged and isopropyl phosphate-aged electric-eel AChE, respectively, after 4 days. C8 displays properties of both resurrection (recovery from the aged to the native state) and reactivation (recovery from the inhibited to the native state). Resurrection of methylphosphonate-aged AChE by C8 was significantly pH-dependent, recovering 21% of activity at 4 mM and pH 9 after only 1 day. C8 is also effective against isopropyl phosphate-aged human AChE.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Travis G Blanton
- Department of Chemistry and Biochemistry , The Ohio State University-Marion , Marion , Ohio 43302 , United States
| | | | - Ryan J Yoder
- Department of Chemistry and Biochemistry , The Ohio State University-Marion , Marion , Ohio 43302 , United States
| | | | - Özlem Doğan Ekici
- Department of Chemistry and Biochemistry , The Ohio State University-Newark , Newark , Ohio 43055 , United States
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9
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Yoder RJ, Zhuang Q, Beck JM, Franjesevic A, Blanton TG, Sillart S, Secor T, Guerra L, Brown JD, Reid C, McElroy CA, Doğan Ekici Ö, Callam CS, Hadad CM. Study of para-Quinone Methide Precursors toward the Realkylation of Aged Acetylcholinesterase. ACS Med Chem Lett 2017. [PMID: 28626522 DOI: 10.1021/acsmedchemlett.7b00037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Acetylcholinesterase (AChE) is an essential enzyme that can be targeted by organophosphorus (OP) compounds, including nerve agents. Following exposure to OPs, AChE becomes phosphylated (inhibited) and undergoes a subsequent aging process where the OP-AChE adduct is dealkylated. The aged AChE is unable to hydrolyze acetylcholine, resulting in accumulation of the neurotransmitter in the central nervous system (CNS) and elsewhere. Current therapeutics are only capable of reactivating inhibited AChE. There are no known therapeutic agents to reverse the aging process or treat aged AChE. Quinone methides (QMs) have been shown to alkylate phosphates under physiological conditions. In this study, a small library of novel quinone methide precursors (QMPs) has been synthesized and examined as potential alkylating agents against model nucleophiles, including a model phosphonate. Computational studies have been performed to evaluate the affinity of QMPs for the aged AChE active site, and preliminary testing with electric eel AChE has been performed.
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Affiliation(s)
- Ryan J. Yoder
- Department
of Chemistry and Biochemistry, The Ohio State University, Marion
Campus, 1465 Mt. Vernon Avenue, Marion, Ohio 43302, United States
| | - Qinggeng Zhuang
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jeremy M. Beck
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Andrew Franjesevic
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Travis G. Blanton
- Department
of Chemistry and Biochemistry, The Ohio State University, Marion
Campus, 1465 Mt. Vernon Avenue, Marion, Ohio 43302, United States
| | - Sydney Sillart
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Tyler Secor
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Leah Guerra
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jason D. Brown
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Carolyn Reid
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Craig A. McElroy
- College
of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Özlem Doğan Ekici
- Department
of Chemistry and Biochemistry, The Ohio State University, Newark
Campus, 1179 University Drive, Newark, Ohio 43055, United States
| | - Christopher S. Callam
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Christopher M. Hadad
- Department
of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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10
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Willcockson MG, Toteva MM, Stella VJ. Hydrolysis of the Quinone Methide of Butylated Hydroxytoluene in Aqueous Solutions. J Pharm Sci 2013; 102:3579-85. [DOI: 10.1002/jps.23657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 11/09/2022]
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11
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Zhou Q, Xu T, Mangrum JB. Selective N1-Alkylation of 2′-Deoxyguanosine with a Quinolinyl Quinone Methide. Chem Res Toxicol 2007; 20:1069-74. [PMID: 17630703 DOI: 10.1021/tx700162d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleobase modification by quinone methides (QMs) has been extensively studied in the past decade, and multiple QM adducts were observed. For 2'-deoxyguanosine (dG), the N (2)-dG alkylation adduct was favored under aqueous buffered conditions over other N1-dG, N7-dG, and N7-guanine adducts. We report in this communication that the N1-dG adduct was selectively formed with a quinolinyl QM in 30% aqueous DMF and 10 mM phosphate buffer (pH 7.0) as a favored dG alkylation product. The quinolinyl QM was formed through the fluoride-induced desilylation and elimination of acetate, and the structure of the N1-dG adduct was fully established by one- and two-dimensional NMR analyses. In addition, the concentration of salt played a significant role in N1-dG adduct formation. Further HPLC analysis indicated that the addition of salt decreased the rate of QM formation from the acetate intermediate, although an in-depth mechanistic study is needed.
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Affiliation(s)
- Qibing Zhou
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
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12
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Freccero M, Gandolfi R. Modeling Acid and Cationic Catalysis on the Reactivity of Duocarmycins. J Org Chem 2005; 70:7098-106. [PMID: 16122228 DOI: 10.1021/jo050751p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several catalyzed alkylation reactions of 9-methyladenine by a model [CPI, cyclopropa[c]pyrrolo[3,2-e]indol-4(5H)-one (1)] of duocarmycin anticancer drugs have been compared to the uncatalyzed reaction in gas phase and in water solvent bulk, using density functional theory at the B3LYP level with the 6-31+G(d,p) basis set and C-PCM solvation model. The effect on the CPI reactivity induced by water, formic and phosphoric acids (general acid catalysis), H3O+ (specific acid catalysis), sodium, and ammonium cation complexation (cationic catalysis) has been investigated. The calculations indicate that the specific acid catalysis and the catalysis induced by sodium cation complexation are strong in the gas phase, but solvation reduces them dramatically by electrostatic effects. The specific acid catalysis is still operative, but strongly reduced in water solution, where the reaction barrier is reduced by 8.6 kcal mol(-1) in comparison to the uncatalyzed reaction. The general acid catalysis induced by phosphoric acid (-7.3 kcal mol(-1)) and the catalysis induced by Na+ and NH4+ complexation become competitive, with a catalytic effect of -3.6 and -4.1 kcal mol(-1) in water, respectively. With the specific acid catalysis, the high acidity (low pK(a) value) of the conjugated acid of CPI (CPIH+), computed in water solution using both C-PCM (pK(a) = +2.6) and PCM-B3LYP/6-31+G(d,p) (pK(a) = +2.4) solvation models, suggests that the catalytic effects induced by NH4+ complexation could become more important than the specific acid catalysis and the general catalysis by H3PO4 under physiological conditions, due to concentration effects of the catalysts.
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, V.le Taramelli 10, 27100 Pavia Italy.
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13
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Bakke BA, McIntosh MC, Turnbull KD. Improved alkylation and product stability in phosphotriester formation through quinone methide reactions with dialkyl phosphates. J Org Chem 2005; 70:4338-45. [PMID: 15903309 DOI: 10.1021/jo050050s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Investigating reactions of functionalized p-quinone methides continues to advance our design of a reagent being developed for controlled, in situ modification of DNA via phosphodiester alkylation. Previously reported investigations of p-quinone methides derived from catechols allowed for trapping of isolable trialkyl phosphates for characterization and mechanistic information. However, lactone formation with these derivatives required long reaction times, resulting in an unfavorable mixture of trialkyl phosphate and hydrolysis products. To enhance the rate and efficacy of trialkyl phosphate formation and trapping, a phenol derived p-quinone methide has been designed to enforce a conformation favoring lactonization of the dialkyl phosphate alkylated intermediate. The relative rates of phosphodiester alkylation and subsequent trapping of the phosphotriester adduct have been examined by UV and (1)H NMR analysis for p-quinone methide precursor 1 and the corresponding control, 1'. The incorporation of a methyl group at the meta-position of 1 (relative to 1') significantly improves the rate of lactionization to provide a much higher yield of the desired product, lactonized phosphotriester 5. The control reaction with 1' afforded only a minor amount of the corresponding lactonized trialkyl phosphate 5'.
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Affiliation(s)
- Brian A Bakke
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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14
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Freccero M, Gandolfi R. Modeling Substituent and Conformational Effects on the Reactivity of Antitumor Agents Containing a Cyclopropylcyclohexadienone Subunit. J Org Chem 2004; 69:6202-13. [PMID: 15357577 DOI: 10.1021/jo049193p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The uncatalyzed alkylation reactions of ammonia by the parent spirocyclopropylcyclohexadienone (6), its 3-amino analogue (7), the cyclic derivative (8), its N-formyl derivative (9), and a closer model (10) of the CPI (1-4) drugs have been investigated in gas phase and in water solvent bulk, using density functional theory at the B3LYP level with several basis sets and the C-PCM solvation model. The effect of several structural key features such as the vinylogous amide conjugation, the acylation of the 2-amino substituent, the ring constraint of the heterocyclic nitrogen atom at C(2) carbon in a ring, and the presence of a condensed pyrrole ring on the reaction activation energy have been investigated. Substrate 7, which is a flexible conformational model of the cyclopropylpyrroloindole moiety (CPI) contained in the duocarmycins, has been used to model the shape-dependent reactivity of these drugs, in gas phase and water solutions. The calculations indicate that shape dependence of reactivity is strongly operative both in gas phase and in polar solvents, since conformational effects are capable of reducing the reaction activation energy by -8.4 and -4.3 kcal mol(-1) in gas phase and in water solution, respectively, that is required to promote "conformational catalysis".
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
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15
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Kumar D, Veldhuyzen WF, Zhou Q, Rokita SE. Conjugation of a Hairpin Pyrrole-Imidazole Polyamide to a Quinone Methide for Control of DNA Cross-Linking. Bioconjug Chem 2004; 15:915-22. [PMID: 15264882 DOI: 10.1021/bc049941h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of quinone methide precursors designed for DNA cross-linking were prepared and conjugated to a pyrrole-imidazole polyamide for selective association to the minor groove. Although reaction was only observed for DNA containing the predicted recognition sequence, yields of strand alkylation were low. Interstrand cross-linking was more efficient than alkylation but still quite modest and equivalent to that generated by a comparable conjugate containing the N-mustard chlorambucil. Varying the length of the linker connecting the polyamide and quinone methide derivative did not greatly affect the yield of DNA cross-linking. Instead, intramolecular trapping of the quinone methide intermediate by nucleophiles of the attached polyamide appears to be the major determinant that limits its reaction with DNA. Self-adducts of the quinone methide conjugate form readily and irreversibly as detected by a combination of chromatography and mass spectroscopy. This result is unlike comparable self-adducts observed for oligonucleotide conjugates that form more slowly and remain reversible. Equivalent intramolecular alkylation of a polyamide by its attached chlorambucil mustard was not observed under similar condition. The presence of DNA, however, did facilitate hydrolysis of this mustard conjugate.
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Affiliation(s)
- Dalip Kumar
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, USA
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16
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Freccero M, Gandolfi R, Sarzi-Amadè M. Selectivity of purine alkylation by a quinone methide. Kinetic or thermodynamic control? J Org Chem 2003; 68:6411-23. [PMID: 12895079 DOI: 10.1021/jo0346252] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The alkylation reaction of 9-methyladenine and 9-methylguanine (as prototype substrates of deoxy-adenosine and -guanosine), by the parent o-quinone methide (o-QM), has been investigated in the gas phase and in aqueous solution, using density functional theory at the B3LYP/6-311+G(d,p) level. The effect of the medium on the reactivity, and on the stability of the resulting adducts, has been investigated by using the C-PCM solvation model to assess which adduct arises from the kinetically favorable path, or from an equilibrating process. The calculations indicate that the most nucleophilic site of the methyl-substituted nucleobases in the gas phase is the guanine oxygen atom (O(6)) (DeltaG()(gas) = 5.6 kcal mol(-)(1)), followed by the adenine N1 (DeltaG)(gas) = 10.3 kcal mol(-)(1)), while other centers exhibit a substantially lower nucleophilicity. The bulk effect of water as a solvent is the dramatic reduction of the nucleophilicity of both 9-methyladenine N1 (DeltaG)(solv) = 14.5 kcal mol(-)(1)) and 9-methylguanine O(6) (DeltaG)(solv) = 17.0 kcal mol(-)(1)). As a result there is a reversal of the nucleophilicity order of the purine bases. While O(6) and N7 nucleophilic centers of 9-methylguanine compete almost on the same footing, the reactivity gap between N1 and N7 of 9-methyladenine in solution is highly reduced. Regarding product stability, calculations predict that only two of the adducts of o-QM with 9-methyladenine, those at NH(2) and N1 positions, are lower in energy than reactants, both in the gas phase and in water. However, the adduct at N1 can easily dissociate in water. The adducts arising from the covalent modification of 9-methylguanine are largely more stable than reactants in the gas phase, but their stability is markedly reduced in water. In particular, the oxygen alkylation adduct becomes slightly unstable in water (DeltaG(solv) = +1.4 kcal mol(-)(1)), and the N7 alkylation product remains only moderately more stable than free reactants (DeltaG(solv) = -2.8 kcal mol(-)(1)). Our data show that site alkylations at the adenine N1 and the guanine O(6) and N7 in water are the result of kinetically controlled processes and that the selective modification of the exo-amino groups of guanine N2 and adenine N6 are generated by thermodynamic equilibrations. The ability of o-QM to form several metastable adducts with purine nucleobases (at guanine N7 and O(2), and adenine N1) in water suggests that the above adducts may act as o-QM carriers.
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, Viale Taramelli 10, 27100 Pavia, Italy.
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17
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Freccero M, Di Valentin C, Sarzi-Amadè M. Modeling H-bonding and solvent effects in the alkylation of pyrimidine bases by a prototype quinone methide: a DFT study. J Am Chem Soc 2003; 125:3544-53. [PMID: 12643716 DOI: 10.1021/ja028732+] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleophilicity of NH(2), N3, and O(2) centers of cytosine toward a model quinone methide (o-QM) as alkylating agent has been studied using DFT computational analysis [at the B3LYP/6-311+G(d,p) level]. Specific and bulk effects of water (by C-PCM model) on the alkylation pathways have been evaluated by analyzing both unassisted and water-assisted reaction mechanisms. An ancillary water molecule, H-bonded to the alkylating agent, may interact monofunctionally with the o-QM oxygen atom (passive mechanisms) or may participate bifunctionally in cyclic hydrogen-bonded structures as a proton shuttle (active mechanisms). A comparison of the unassisted with the water-assisted reaction mechanisms has been made on the basis of activation Gibbs free energies (DeltaG(++)). The gas-phase alkylation reaction at N3 does proceed through a passive mechanism that is preferred over both the active (by -6.3 kcal mol(-1)) and the unassisted process. In contrast, in the gas phase, the active assisted processes at NH(2) and O(2) centers are both favored over their unassisted counterparts by -4.0 and -2.2 kcal mol(-1), respectively. The catalytic effect of a water molecule, in gas phase, reduces the gap between the TSs of the O(2) and NH(2) reaction pathways, but the former remains more stable. Water bulk effect significantly modifies the relative importance of the unassisted and water-assisted alkylation mechanisms, favoring the former, in comparison to the gas-phase reactions. In particular, the unassisted alkylation becomes the preferred mechanism for the reaction at both the exocyclic (NH(2)) and the heterocyclic (N3) nitrogen atoms. By contrast, alkylation at the cytosine oxygen atom is a water-catalyzed process, since in water the active water-assisted mechanism is still favored. As far as competition, among all the possible mechanisms, our calculations unambiguously suggest that the most nucleophilic site both in gas phase (naked reagents: N3 >> O(2) >or= NH(2)) and in water solution (solvated reagents: N3 >> NH(2) >> O(2)) is the heterocyclic nitrogen atom (N3) (DeltaG(++)(gas) = +7.1 kcal mol(-1), and DeltaG(++)(solv) = +13.7 kcal mol(-1)). Our investigation explains the high reactivity and selectivity of the cytosine moiety toward o-QM-like structures both in deoxymononucleoside and in a single-stranded DNA, on the basis of strong H-bonding interactions between reactants and solvent bulk effect. It also offers two general reactivity models in water, uncatalyzed and active water-catalyzed mechanisms (for nitrogen and oxygen nucleophiles, respectively), which should provide a general tool for the planning of nucleic acid modification.
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, V.le Taramelli 10, 27100 Pavia Italy.
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