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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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de la Campa R, Manzano R, Calleja P, Ellis SR, Dixon DJ. Enantioselective Silver-Catalyzed Cascade Synthesis of Fused Lactone and Lactam Oxazolines. Org Lett 2018; 20:6033-6036. [DOI: 10.1021/acs.orglett.8b02383] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raquel de la Campa
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Rubén Manzano
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Paul Calleja
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Sam R. Ellis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Darren J. Dixon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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Nobuta T, Kawabata T. Catalyst-controlled site-selective asymmetric epoxidation of nerylamine and geranylamine derivatives. Chem Commun (Camb) 2017; 53:9320-9323. [PMID: 28771263 DOI: 10.1039/c7cc04809b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Novel catalysts for site- and enantioselective epoxidation of nerylamine and geranylamine derivatives have been developed. Although mCPBA oxidation took place selectively at the more electron-rich double bond to give the 6,7-epoxides, these catalysts provide the 2,3-epoxides in moderate to high enantioselectivity via the oxidation of the relatively electron-deficient double bond.
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Affiliation(s)
- Tomoya Nobuta
- Research Foundation Itsuu Laboratory, C1232, Kanagawa Science Park R&D Building, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
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Hussain H, Al-Harrasi A, Green IR, Ahmed I, Abbas G, Rehman NU. meta-Chloroperbenzoic acid (mCPBA): a versatile reagent in organic synthesis. RSC Adv 2014. [DOI: 10.1039/c3ra45702h] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review aims to collect and discuss the synthetic applications of meta-chloroperbenzoic acid (mCPBA) over the past few decades.
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Affiliation(s)
- Hidayat Hussain
- UoN Chair of Oman's Medicinal Plants and Marine Natural Products
- University of Nizwa
- Nizwa, Sultanate of Oman
- Department of Chemistry
- University of Paderborn
| | - Ahmed Al-Harrasi
- UoN Chair of Oman's Medicinal Plants and Marine Natural Products
- University of Nizwa
- Nizwa, Sultanate of Oman
| | - Ivan R. Green
- Department of Chemistry and Polymer Science
- University of Stellenbosch
- , South Africa
| | - Ishtiaq Ahmed
- Karlsruhe Institute of Technology (KIT)
- DFG Centre for Functional Nanostructures
- 76131 Karlsruhe, Germany
| | - Ghulam Abbas
- UoN Chair of Oman's Medicinal Plants and Marine Natural Products
- University of Nizwa
- Nizwa, Sultanate of Oman
| | - Najeeb Ur Rehman
- UoN Chair of Oman's Medicinal Plants and Marine Natural Products
- University of Nizwa
- Nizwa, Sultanate of Oman
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5
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Recent synthetic approaches to oseltamivir phosphate (Tamiflu™) for the treatment of influenza. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.07.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Berkowitz DB, Karukurichi KR, de la Salud-Bea R, Nelson DL, McCune CD. Use of Fluorinated Functionality in Enzyme Inhibitor Development: Mechanistic and Analytical Advantages. J Fluor Chem 2008; 129:731-742. [PMID: 19727327 PMCID: PMC2598403 DOI: 10.1016/j.jfluchem.2008.05.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
On the one hand, owing to its electronegativity, relatively small size, and notable leaving group ability from anionic intermediates, fluorine offers unique opportunities for mechanism-based enzyme inhibitor design. On the other, the "bio-orthogonal" and NMR-active 19-fluorine nucleus allows the bioorganic chemist to follow the mechanistic fate of fluorinated substrate analogues or inhibitors as they are enzymatically processed. This article takes an overview of the field, highlighting key developments along these lines. It begins by highlighting new screening methodologies for drug discovery that involve appropriate tagging of either substrate or the target protein itself with (19)F-markers, that then report back on turnover and binding, respectively, via an the NMR screen. Taking this one step further, substrate-tagging with fluorine can be done is such a manner as to provide stereochemical information on enzyme mechanism. For example, substitution of one of the terminal hydrogens in phosphoenolpyruvate, provides insight into the, otherwise latent, facial selectivity of C-C bond formation in KDO synthase. Perhaps, most importantly, from the point of view of this discussion, appropriately tailored fluorinated functionality can be used to form to stabilized "transition state analogue" complexes with a target enzymes. Thus, 5-fluorinated pyrimidines, alpha-fluorinated ketones, and 2-fluoro-2-deoxysugars each lead to covalent adduction of catalytic active site residues in thymidylate synthase, serine protease and glycosidase enzymes, respectively. In all such cases, (19)F NMR allows the bioorganic chemist to spectrally follow "transition state analogue" formation. Finally, the use of specific fluorinated functionality to engineer "suicide substrates" is highlighted in a discussion of the development of the alpha-(2'Z-fluoro)vinyl trigger for amino acid decarboxylase inactivation. Here (19)F NMR allows the bioorganic chemist to glean useful partition ratio data directly out of the NMR tube.
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
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Jones MC, Marsden SP. Total Synthesis of the Immunosuppressants Myriocin and 2-epi-Myriocin. Org Lett 2008; 10:4125-8. [DOI: 10.1021/ol801709c] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew C. Jones
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
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Berkowitz DB, Wu B, Li H. A formal [3,3]-sigmatropic rearrangement route to quaternary alpha-vinyl amino acids: use of allylic N-PMP trifluoroacetimidates. Org Lett 2006; 8:971-4. [PMID: 16494487 PMCID: PMC2504469 DOI: 10.1021/ol060019s] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pd(II)-mediated rearrangement of allylic N-PMP (p-methoxyphenyl) trifluoroacetimidates provides the first formal sigmatropic route to quaternary, alpha-vinylic amino acids, potential suicide substrates for PLP enzymes. The amino acid side chains enter via transition-metal-mediated C-C bond constructions, including (i) Cu(I)-mediated conjugate addition (Ala); (ii) Pd(0)/AsPh3-mediated Stille coupling (allyl-Gly, Phe, DOPA, m-Tyr); and (iii) Pd(0)/Pt-Bu3-mediated Negishi coupling (Leu). In the synthesis of the DOPA decarboxylase inactivator, alpha-vinyl-m-tyrosine, the new N-PMP trifluoroacetimidate rearranges much more efficiently than the corresponding trichloroacetimidate.
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, USA.
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Spetzler JC, Hoeg-Jensen T. A new amino acid derivative with a masked side-chain aldehyde and its use in peptide synthesis and chemoselective ligation. J Pept Sci 2001; 7:537-51. [PMID: 11695649 DOI: 10.1002/psc.349] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A new amino acid derivative with a diol side-chain, L-2-amino-4,5-dihydroxy-pentanoic acid (Adi), has been prepared from L-allylglycine by suitable protection, for use in peptide synthesis, as Fmoc-L-Adi(Trt)2. This building block enables the introduction of a side-chain aldehyde at any position in a given peptide sequence without use of specialized side-chain protection schemes. The aldehyde is revealed by mild oxidation with sodium periodate, circumventing the problematic release of reactive peptidic aldehydes in TFA solution. Peptides with aldehyde side-chains are useful for chemo-selective ligation, reacting selectively with oxyamines to yield oxime links, while all other peptide functions can be left unprotected. The utility of the new building block has been demonstrated by the synthesis of peptide dimers and a cyclo-peptide.
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Berkowitz DB, Chisowa E, McFadden JM. Stereocontrolled Synthesis of Quaternary β,γ-Unsaturated Amino Acids: Chain Extension of D- & L- α-(2-Tributylstannyl)Vinyl Amino Acids. Tetrahedron 2001; 57:6329-6343. [PMID: 29973743 PMCID: PMC6027620 DOI: 10.1016/s0040-4020(01)00499-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A pair of diastereomeric (4S,5S)- and (4S,5R)-4-methoxycarbonyl-5-phenylselenomethyl-2-phenyl oxazolines, derived from L-vinylglycine, serve as precursors to protected, quaternary, L- and D-α-(2-tributylstannyl)vinyl amino acids, respectively, in three steps {(i) alkylative side chain installation, (ii) eliminative ring-opening and (iii) vinyl selenide to vinyl stannane interconversion}. The title compounds may be protodestannylated to the corresponding free, quaternary L- and D-vinyl amino acids. Alternatively, the 2-stannylvinyl α-branch (or the derivative 2-iodovinyl branch) may be exploited to access novel quaternary, L- and D-β,γ-unsaturated amino acids via a range of transition metal-mediated cross coupling reactions.
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
| | - Esmort Chisowa
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
| | - Jill M McFadden
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
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O'Donnel CJ, Burke SD. Selective Mesylation of Vicinal Diols: A Systematic Case Study. J Org Chem 1998. [DOI: 10.1021/jo981532p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher J. O'Donnel
- Department of Chemistry, University of WisconsinMadison, 1101 University Avenue, Madison, Wisconsin 53706-1396
| | - Steven D. Burke
- Department of Chemistry, University of WisconsinMadison, 1101 University Avenue, Madison, Wisconsin 53706-1396
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Berkowitz DB, Jahng WJ, Pedersen ML. α-VINYLLYSINE AND α-VINYLARGININE ARE TIME-DEPENDENT INHIBITORS OF THEIR COGNATE DECARBOXYLASES. Bioorg Med Chem Lett 1996; 6:2151-2156. [PMID: 29123334 DOI: 10.1016/0960-894x(96)00366-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
(±)-α-Vinyllysine and (±)-α-vinylarginine display time-dependent inhibition of L-lysine decarboxylase from B. cadaveris, and L-arginine decarboxylase from E. coli, respectively. A complete Kitz-Wilson analysis has been performed using a modification of the Palcic continuous UV assay for decarboxylase activity.
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Wan-Jin Jahng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Michelle L Pedersen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
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Berkowitz DB, Pedersen ML, Jahng WJ. Synthesis of Higher α-Chlorovinyl and α-Bromovinyl Amino Acids: The Amino Protecting Group Determines the Reaction Course. Tetrahedron Lett 1996; 37:4309-4312. [PMID: 29200438 PMCID: PMC5708561 DOI: 10.1016/0040-4039(96)00832-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
N-Trifluoroacetyl α-vinyl amino esters are smoothly converted to the corresponding α-chlorovinyl or α-bromovinyl amino esters through the agency of phenyselenyl chloride or phenylselenyl bromide, respectively, followed by oxidation and pyrolysis. Exclusively the (E)-extemal halovinyl isomer and the internal halovinyl isomer are observed. The amino protecting group is a critical determinant of the reaction course (alkene addition vs. 5-exo-trig-like cyclization).
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Michelle L Pedersen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Wan-Jin Jahng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
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