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. 2019 Feb 27;141(8):3723-3732.
doi: 10.1021/jacs.9b00669. Epub 2019 Feb 12.

Open-Air Alkylation Reactions in Photoredox-Catalyzed DNA-Encoded Library Synthesis

Affiliations

Open-Air Alkylation Reactions in Photoredox-Catalyzed DNA-Encoded Library Synthesis

James P Phelan et al. J Am Chem Soc. .

Abstract

DNA-encoded library (DEL) technology is a powerful tool commonly used by the pharmaceutical industry for the identification of compounds with affinity to biomolecular targets. Success in this endeavor lies in sampling diverse chemical libraries. However, current DELs tend to be deficient in C(sp3) carbon counts. We report unique solutions to the challenge of increasing both the chemical diversity of these libraries and their C(sp3) carbon counts by merging Ni/photoredox dual catalytic C(sp2)-C(sp3) cross-coupling as well as photoredox-catalyzed radical/polar crossover alkylation protocols with DELs. The successful integration of multiple classes of radical sources enables the rapid incorporation of a diverse set of alkyl fragments.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1.
Figure 1.
Workflow in generating and utilizing DELs.
Figure 2.
Figure 2.
Mechanistic view of Ni/photoredox dual catalytic C(sp2)–C(sp3) cross-coupling.
Figure 3.
Figure 3.
Major DNA-containing side products from the cross-coupling.
Figure 4.
Figure 4.
Radical/polar crossover defluorinative alkylation of trifluoromethyl alkenes.

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References

    1. Denton KE; Wang S; Gignac MC; Milosevich N; Hof F; Dykhuizen EC; Krusemark CJ; Robustness of In Vitro Selection Assays of DNA-Encoded Peptidomimetic Ligands to CBX7 and CBX8. SLAS Discovery 2018, 23, 417–428; - PMC - PubMed
    2. Favalli N; Biendl S; Hartmann M; Piazzi J; Sladojevich F; Gräslund S; Brown PJ; Näreoja K; Schüler H; Scheuermann J; Franzini R; Neri D A DNA-Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition. ChemMedChem 2018, 13, 1303–1307; - PMC - PubMed
    3. Usanov DL; Chan AI; Maianti JP; Liu DR; Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules. Nature Chemistry 2018, 10, 704–714; - PMC - PubMed
    4. Ahn S; Kahsai AW; Pani B; Wang Q-T; Zhao S; Wall AL; Strachan RT; Staus DP; Wingler LM; Sun LD; Sinnaeve J; Choi M; Cho T; Xu TT; Hansen GM; Burnett MB; Lamerdin JE; Bassoni DL; Gavino BJ; Husemoen G; Olsen EK; Franch T; Costanzi S; Chen X; Lefkowitz RJ Allosteric “beta-blocker” isolated from a DNA-encoded small molecule library. Proc. Natl. Acad. Sci. U. S. A 2017, 114, 1708–1713; - PMC - PubMed
    5. Mendes KR; Malone ML; Ndungu JM; Suponitsky-Kroyter I; Cavett VJ; McEnaney PJ; Mac-Connell AB; Doran TM; Ronacher K; Stanley K ∥; Utset O; Walzl G ∥; Paegel BM; Kodadek T; High-throughput Identification of DNA-Encoded IgG Ligands that Distinguish Active and Latent Mycobacterium tuberculosis Infections. ACS Chem. Biol 2017, 12, 234–243; - PMC - PubMed
    6. Zambaldo C; Daguer J-P; Saarbach J; Barluenga S; Winssinger N; Screening for covalent inhibitors using DNA-display of small molecule libraries functionalized with cysteine reactive moie-ties. Med. Chem. Commun 2016, 7, 1340–1351;
    7. Skopic MK; Bugain O; Jung K; Onstein S; Brandherm S; Kalliokoski T; Brunschweiger A Design and synthesis of DNA-encoded libraries based on a benzodiazepine and a pyra-zolopyrimidine scaffold. Med. Chem. Commun 2016, 7, 1957–1965;
    8. Daguer J-P; Zambaldo C; Abegg D; Barluenga S; Tallant C; Müller S; Adibekian A; Winssinger N; Identification of Covalent Bromodomain Binders through DNA Display of Small Molecules. Angew. Chem., Int. Ed 2015. 54, 6057–6061; - PubMed
    9. Franzini RM; Ekblad T; Zhong N; Wichert M; Decurtins W; Nauer A; Zimmermann M; Samain F; Scheuermann J; Brown PJ; Hall J; Gräslund S; Schüler H; Dario Neri D; Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA Encoded Chemical Library. Angew. Chem., Int. Ed 2015. 54, 3927–3931. - PubMed
    1. Richter H; Satz AL; Bedoucha M; Buettelmann B; Petersen AC; Harmeier A; Hermosilla R; Hochstrasser R; Burger D; Gsell B; Gasser R; Huber S; Hug MN; Kocer B; Kuhn B; Ritter M; Rudolph MG; Weibel F; Molina-David J; Kim J-J; Santos JV; Stihle M; Georges GJ; Bonfil RD; Fridman R; Uhles S; Moll S; Faul C; Fornoni A; Prunotto M; DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome. ACS Chem Bio 2018, ASAP doi:10.1021/acschembio.8b00866; - DOI - PMC - PubMed
    2. Satz AL What Do You Get from DNA-Encoded Libraries? ACS Med. Chem. Lett 2018, 9, 408–410; - PMC - PubMed
    3. Harris PA; Berger SB; Jeong JU; Nagilla R; Bandyopadhyay D; Campobasso N; Capriotti CA; Cox JA; Dare L; Dong X; Eidam PM; Finger JN; Hoffman SJ; Kang J; Kasparcova V; King BW; Lehr R; Lan Y; Leister LK; Lich JD; MacDonald TT; Miller NA; Ouellette MT; Pao CS; Rahman A; Reilly MA; Rendina AR; Rivera EJ; Schaeffer MC; Sehon CA; Singhaus RR; Sun HH; Swift BA; Totoritis RD; Vossenkämper A; Ward P; Wisnoski DD; Zhang D; Marquis RW; Gough PJ; Bertin J Discovery of a First-in-Class Receptor Interacting Protein 1 (RIP1) Kinase Specific Clinical Candidate (GSK2982772) for the Treatment of Inflammatory Diseases. J. Med. Chem 2017, 60, 1247–1261; - PubMed
    4. Belyanskaya SL; Ding Y; Callahan JF; Lazaar AL; Israel DI Discovering Drugs with DNA-Encoded Library Technology: From Concept to Clinic with an Inhibitor of Soluble Epoxide Hydrolase. ChemBioChem 2017, 18, 837–842. - PubMed
    5. Cuozzo JW; Centrella PA; Gikunju D; Habeshian S; Hupp CD; Keefe AD; Sigel EA; Soutter HH; Thomson HA; Zhang Y; Clark MA; Discovery of a Potent BTK Inhibitor with a Novel Binding Mode by Using Parallel Selections with a DNA Encoded Chemical Library. ChemBioChem 2017, 18, 864–871; - PubMed
    6. Soutter HH; Centrella P; Clark MA; Cuozzo JW; Dumelin CE; Guie M-A; Habeshian S; Keefe AD; Kennedy KM; Sigel EA; Troast DM; Zhang Y; Ferguson AD; Davies G; Stead ER; Breed J; Madhavapeddi P; Read JA; Discovery of cofactor-specific, bactericidal Mycobacterium tuberculosis InhA inhibitors using DNA-encoded library technology. Proc. Natl. Acad. Sci. U. S. A 2016, 113, 7880–7889; - PMC - PubMed
    7. Mullard A; DNA tags help the hunt for drugs. Nature 2016, 367–369; - PubMed
    8. Deng H; Zhou J; Sundersingh FS; F. S; Summerfield J; Somers D; Messer JA; Satz AL; Ancellin N; Arico-Muendel CC; Bedard KL; Beljean A; S. L; Bingham R; Smith SE; Eric Boursier E; Carter P; Centrella PA; Clark MA; Chung C.-w.; Davie CP; Delorey JL; Ding Y; Franklin GJ; Grady LC; Herry K; Hobbs C; Kollmann CS; Morgan BA; Kaushansky LJ; Zhou Q Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library. ACS Med. Chem. Lett, 2015, 6, 919–924; - PMC - PubMed
    9. Ding Y; O’Keefe H; DeLorey JL; Israel DI; Messer JA; Chiu CH; Skinner SR; Matico RE; Murray-Thompson MF; Li F; Clark MA; Cuozzo JW; Arico-Muendel C; Morgan BA; ACS Med. Chem. Lett 2015, 6, 888–893; - PMC - PubMed
    10. Disch JS; Evindar G; Chiu CH; Blum CA; Dai H; Jin L; Schuman E; Lind KE; Belyanskaya SL; Deng J; Coppo F; Aquilani L; Graybill TL; Cuozzo JW; Lavu S; Mao C; Vlasuk GP; Perni RB; Discovery of Thieno[3,2-d]pyrimidine-6-carboxamides as Potent Inhibitors of SIRT1, SIRT2, and SIRT3. J. Med. Chem 2013, 56, 3666–3679; - PubMed
    11. Gilmartin AG; Faitg TH; Richter M; Groy A; Seefeld MA; Darcy MG; Peng X; Federowicz K; Yang J; Zhang S-Y; Minthorn E; Jaworski J-P Schaber M; Martens S; McNulty DE; Sinnamon RH; Zhang H; Kirkpatrick RB; Nevins N; Cui G; Pietrak B; Diaz E; Jones A; Brandt M; Schwartz B; Heerding DA; Kumar R; Allosteric Wip1 phosphatase inhibition through flap-subdomain interaction. Nat. Chem. Bio 2014, 10, 181–187. - PubMed
    1. Brenner S; Lerner RA Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. U. S. A 1992, 89, 5381–5383. - PMC - PubMed
    1. Zhu Z; Shaginian A; Grady LC; O’Keeffe T; Shi XE; Davie CP; Simpson GL; Messer JA; Evindar G; Bream RN; Thansandote PP; Prentice NR; Mason AM; Pal S Design and application of DNA-encoded macrocyclic peptide library. ACS Chem. Biol 2018, 13, 53–59; - PubMed
    2. Skopic MK; Bugain O; Jung K; Onstein S; Brandherm S; Kalliokoski T; Brunschweiger A Design and synthesis of DNA-encoded libraries based on a benzodiazepine and a pyrazolopyrimidine scaffold. Med. Chem. Commun 2016, 7, 1957–1965.
    1. Goodnow RA Jr.; Dumelin CE; Keefe AD DNA-encoded chemistry: enabling the deeper sampling of chemical space. Nat. Rev. Drug Discovery 2017, 16, 131–147; - PubMed
    2. Clark MA; Acharya RA; Arico-Muendel CC; Belyanskaya SL; Benjamin DR; Carlson NR; Centrella PA; Chiu CH; Creaser SP; Cuozzo JW; Davie CP; Ding Y; Franklin GJ; Franzen KD; Gefter ML; Hale SP; Hansen NJV; Israel DI; Jiang J; Kavarana MJ; Kelley MS; Kollmann CS; Li F; Lind K; Mataruse S; Medeiros PF; Messer JA; Myers P; O’Keefe H; Oliff MC; Rise CE; Satz AL; Skinner SR; Svendsen JL; Tang L; van Vloten K; Wagner RW; Yao G; Zhao B; Morgan BA Design, synthesis and selection of DNA-encoded small molecule libraries. Nat. Chem. Biol 2009, 5, 647–654. - PubMed

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