1
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Saito Y, Cho SM, Danieli LA, Matsunaga A, Kobayashi S. A highly efficient catalytic method for the synthesis of phosphite diesters. Chem Sci 2024; 15:8190-8196. [PMID: 38817565 PMCID: PMC11134407 DOI: 10.1039/d4sc01401d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024] Open
Abstract
In contrast to conventional methods that rely on stoichiometric activation of phosphonylating reagents, we have developed a highly efficient catalytic method for the synthesis of phosphite diesters using a readily available phosphonylation reagent and alcohols with environmentally benign Zn(ii) catalysts. Two alcohols could be introduced consecutively on the P center with release of trifluoroethanol as the sole byproduct, without any additive, under mild conditions. The products could be oxidized smoothly to access phosphate triesters. A range of alcohols, including sterically demanding and highly functionalized alcohols such as carbohydrates and nucleosides, can be applied in this reaction.
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Affiliation(s)
- Yuki Saito
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku Tokyo Japan
| | - Soo Min Cho
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku Tokyo Japan
| | - Luca Alessandro Danieli
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku Tokyo Japan
| | - Akira Matsunaga
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku Tokyo Japan
| | - Shū Kobayashi
- Department of Chemistry, School of Science, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku Tokyo Japan
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2
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Formica M, Ferko B, Marsh T, Davidson TA, Yamazaki K, Dixon DJ. Second Generation Catalytic Enantioselective Nucleophilic Desymmetrization at Phosphorus (V): Improved Generality, Efficiency and Modularity. Angew Chem Int Ed Engl 2024; 63:e202400673. [PMID: 38381534 DOI: 10.1002/anie.202400673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
A broadly improved second generation catalytic two-phase strategy for the enantioselective synthesis of stereogenic at phosphorus (V) compounds is described. This protocol, consisting of a bifunctional iminophosphorane (BIMP) catalyzed nucleophilic desymmetrization of prochiral, bench stable P(V) precursors and subsequent enantiospecific substitution allows for divergent access to a wide range of C-, N-, O- and S- substituted P(V) containing compounds from a handful of enantioenriched intermediates. A new ureidopeptide BIMP catalyst/thiaziolidinone leaving group combination allowed for a far wider substrate scope and increased reaction efficiency and practicality over previously established protocols. The resulting enantioenriched intermediates could then be transformed into an even greater range of distinct classes of P(V) compounds by displacement of the remaining leaving group as well as allowing for even further diversification downstream. Density functional theory (DFT) calculations were performed to pinpoint the origin of enantioselectivity for the BIMP-catalyzed desymmetrization, to rationalize how a superior catalyst/leaving group combination leads to increased generality in our second-generation catalytic system, as well as shed light onto observed stereochemical retention and inversion pathways when performing late-stage enantiospecific SN2@P reactions with Grignard reagents.
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Affiliation(s)
- Michele Formica
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Branislav Ferko
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Thomas Marsh
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Timothy A Davidson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Ken Yamazaki
- Division of Applied Chemistry, Okayama University, Tsushimanaka, Okayama, 700-8530, Japan
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
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3
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Rössler SL, Grob NM, Buchwald SL, Pentelute BL. Abiotic peptides as carriers of information for the encoding of small-molecule library synthesis. Science 2023; 379:939-945. [PMID: 36862767 PMCID: PMC10064805 DOI: 10.1126/science.adf1354] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Encoding small-molecule information in DNA has been leveraged to accelerate the discovery of ligands for therapeutic targets such as proteins. However, oligonucleotide-based encoding is hampered by inherent limitations of information stability and density. In this study, we establish abiotic peptides for next-generation information storage and apply them for the encoding of diverse small-molecule synthesis. The chemical stability of the peptide-based tag allows the use of palladium-mediated reactions to efficiently synthesize peptide-encoded libraries (PELs) with broad chemical diversity and high purity. We demonstrate the successful de novo discovery of small-molecule protein ligands from PELs by affinity selection against carbonic anhydrase IX and the oncogenic protein targets BRD4(1) and MDM2. Collectively, this work establishes abiotic peptides as carriers of information for the encoding of small-molecule synthesis, leveraged herein for the discovery of protein ligands.
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Affiliation(s)
- Simon L Rössler
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nathalie M Grob
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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4
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Mahdavi-Amiri Y, Hu MSJ, Frias N, Movahedi M, Csakai A, Marcaurelle LA, Hili R. Photoredox-catalysed hydroaminoalkylation of on-DNA N-arylamines. Org Biomol Chem 2023; 21:1463-1467. [PMID: 36655521 DOI: 10.1039/d2ob01956f] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An efficient approach to the photoredox-catalysed hydroaminoalkylation between on-DNA secondary N-substituted (hetero)arylamines and vinylarenes has been developed and explored. The methodology was examined with a broad scope of vinylarenes and secondary arylamines to establish a preferred building block profile for the process. Compatible substrates furnished the desired derivitised amine products in modest to excellent conversions and with minimal or no detectable by-products.
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Affiliation(s)
- Yasaman Mahdavi-Amiri
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada.
| | - Molly S J Hu
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada.
| | - Nicole Frias
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada.
| | - Matina Movahedi
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada.
| | - Adam Csakai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Lisa A Marcaurelle
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GSK, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, ON, M3J 1P3, Canada.
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5
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Tota EM, Devaraj NK. Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525207. [PMID: 36747847 PMCID: PMC9900779 DOI: 10.1101/2023.01.23.525207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Bacterial tRNA guanine transglycosylases (TGTs) catalyze the exchange of guanine for the 7-deazaguanine queuine precursor, prequeuosine1 (preQ1). While the native nucleic acid substrate for bacterial TGTs is the anticodon loop of queuine-cognate tRNAs, the minimum recognition sequence for the enzyme is a structured hairpin containing the target G nucleobase in a "UGU" loop motif. Previous work has established an RNA modification system, RNA-TAG, in which E. coli TGT exchanges the target G on an RNA of interest for chemically modified preQ1 substrates linked to a small molecule reporter such as biotin or a fluorophore. While extending the substrate scope of RNA transglycosylases to include DNA would enable numerous applications, it has been previously reported that TGT is incapable of modifying native DNA. Here we demonstrate that TGT can in fact recognize and label specific DNA substrates. Through iterative testing of rationally mutated DNA hairpin sequences, we determined the minimal sequence requirements for transglycosylation of unmodified DNA by E. coli TGT. Controlling steric constraint in the DNA hairpin dramatically affects labeling efficiency, and, when optimized, can lead to near quantitative site-specific modification. We demonstrate the utility of our newly developed DNA-TAG system by rapidly synthesizing probes for fluorescent Northern blotting of spliceosomal U6 RNA and RNA FISH visualization of the long noncoding RNA, MALAT1. The ease and convenience of the DNA-TAG system will provide researchers with a tool for accessing a wide variety of affordable modified DNA substrates.
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6
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Ishizawa S, Tumurkhuu M, Gross EJ, Ohata J. Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids. Chem Sci 2022; 13:1780-1788. [PMID: 35282632 PMCID: PMC8826848 DOI: 10.1039/d1sc05204g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/15/2022] [Indexed: 11/21/2022] Open
Abstract
Site-specific chemical modification of unprotected DNAs through a phosphine-mediated amine–azide coupling reaction in ionic liquid.
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Affiliation(s)
- Seiya Ishizawa
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Munkhtuya Tumurkhuu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Elizabeth J. Gross
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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7
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Ociepa M, Knouse KW, He D, Vantourout JC, Flood DT, Padial NM, Chen JS, Sanchez BB, Sturgell EJ, Zheng B, Qiu S, Schmidt MA, Eastgate MD, Baran PS. Mild and Chemoselective Phosphorylation of Alcohols Using a Ψ-Reagent. Org Lett 2021; 23:9337-9342. [PMID: 34499517 PMCID: PMC8733960 DOI: 10.1021/acs.orglett.1c02736] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An operationally simple, scalable, and chemoselective method for the direct phosphorylation of alcohols using a P(V)-approach based on the Ψ-reagent platform is disclosed. The method features a broad substrate scope of utility in both simple and complex settings and provides access to valuable phosphorylated alcohols that would be otherwise difficult to obtain.
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Affiliation(s)
- Michał Ociepa
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Kyle W. Knouse
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - David He
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Julien C. Vantourout
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Dillon T. Flood
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Natalia M. Padial
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Jason S. Chen
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Brittany B. Sanchez
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Emily J. Sturgell
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
| | - Bin Zheng
- Chemical Process Development, Bristol Myers Squibb, One Squibb Drive, New Brunswick, New Jersey, 08901, United States
| | - Shenjie Qiu
- Chemical Process Development, Bristol Myers Squibb, One Squibb Drive, New Brunswick, New Jersey, 08901, United States
| | - Michael A. Schmidt
- Chemical Process Development, Bristol Myers Squibb, One Squibb Drive, New Brunswick, New Jersey, 08901, United States
| | - Martin D. Eastgate
- Chemical Process Development, Bristol Myers Squibb, One Squibb Drive, New Brunswick, New Jersey, 08901, United States
| | - Phil S. Baran
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, United States
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8
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Knouse KW, Flood DT, Vantourout JC, Schmidt MA, Mcdonald IM, Eastgate MD, Baran PS. Nature Chose Phosphates and Chemists Should Too: How Emerging P(V) Methods Can Augment Existing Strategies. ACS CENTRAL SCIENCE 2021; 7:1473-1485. [PMID: 34584948 PMCID: PMC8461637 DOI: 10.1021/acscentsci.1c00487] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 05/27/2023]
Abstract
Phosphate linkages govern life as we know it. Their unique properties provide the foundation for many natural systems from cell biology and biosynthesis to the backbone of nucleic acids. Phosphates are ideal natural moieties; existing as ionized species in a stable P(V)-oxidation state, they are endowed with high stability but exhibit enzymatically unlockable potential. Despite intense interest in phosphorus catalysis and condensation chemistry, organic chemistry has not fully embraced the potential of P(V) reagents. To be sure, within the world of chemical oligonucleotide synthesis, modern approaches utilize P(III) reagent systems to create phosphate linkages and their analogs. In this Outlook, we present recent studies from our laboratories suggesting that numerous exciting opportunities for P(V) chemistry exist at the nexus of organic synthesis and biochemistry. Applications to the synthesis of stereopure antisense oligonucleotides, cyclic dinucleotides, methylphosphonates, and phosphines are reviewed as well as chemoselective modification to peptides, proteins, and nucleic acids. Finally, an outlook into what may be possible in the future with P(V) chemistry is previewed, suggesting these examples represent just the tip of the iceberg.
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Affiliation(s)
- Kyle W. Knouse
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julien C. Vantourout
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael A. Schmidt
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Ivar M. Mcdonald
- Small
Molecule Drug Discovery, Bristol Myers Squibb, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Martin D. Eastgate
- Chemical
and Synthetic Development, Bristol Myers
Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Phil S. Baran
- Elsie
Biotechnologies, 4955
Directors Place, San Diego, California 92121, United States
- Department
of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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9
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Jbara M, Rodriguez J, Dhanjee HH, Loas A, Buchwald SL, Pentelute BL. Oligonucleotide Bioconjugation with Bifunctional Palladium Reagents. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Muhammad Jbara
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Jacob Rodriguez
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Heemal H. Dhanjee
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Andrei Loas
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Stephen L. Buchwald
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of Chemistry Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge MA 02139 USA
- The Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology 500 Main Street Cambridge MA 02142 USA
- Center for Environmental Health Sciences Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- Broad Institute of MIT and Harvard 415 Main Street Cambridge MA 02142 USA
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10
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Jbara M, Rodriguez J, Dhanjee HH, Loas A, Buchwald SL, Pentelute BL. Oligonucleotide Bioconjugation with Bifunctional Palladium Reagents. Angew Chem Int Ed Engl 2021; 60:12109-12115. [PMID: 33730425 DOI: 10.1002/anie.202103180] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 01/01/2023]
Abstract
Organometallic reagents enable practical strategies for bioconjugation. Innovations in the design of water-soluble ligands and the enhancement of reaction rates have allowed for chemoselective cross-coupling reactions of peptides and proteins to be carried out in water. There are currently no organometallic-based methods for oligonucleotide bioconjugation to other biomolecules. Here we report bifunctional palladium(II)-oxidative addition complexes (OACs) as reagents for high-yielding oligonucleotide bioconjugation reactions. These bifunctional OACs react chemoselectively with amine-modified oligonucleotides to generate the first isolable, bench stable oligonucleotide-palladium(II) OACs. These complexes undergo site-selective C-S arylation with a broad range of native thiol-containing biomolecules at low micromolar concentrations in under one hour. This approach provided oligonucleotide-peptide, oligonucleotide-protein, oligonucleotide-small molecule, and oligonucleotide-oligonucleotide conjugates in >80 % yield and afforded conjugation of multiple copies of oligonucleotides onto a monoclonal antibody.
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Affiliation(s)
- Muhammad Jbara
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Jacob Rodriguez
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Heemal H Dhanjee
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139, USA.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
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