Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Feb 1;7(2):1257-1261.
doi: 10.1039/c5sc03259h. Epub 2015 Nov 11.

Discovery of new mutually orthogonal bioorthogonal cycloaddition pairs through computational screening

Maruthi Kumar Narayanam  1 , Yong Liang  2 , K N Houk  2   3 , Jennifer M Murphy  1
Affiliations

Discovery of new mutually orthogonal bioorthogonal cycloaddition pairs through computational screening

Maruthi Kumar Narayanam et al. Chem Sci. .

Abstract

Density functional theory (DFT) calculations and experiments in tandem led to discoveries of new reactivities and selectivities involving bioorthogonal sydnone cycloadditions. Dibenzocyclooctyne derivatives (DIBAC and BARAC) were identified to be especially reactive dipolarophiles, which undergo the (3 + 2) cycloadditions with N-phenyl sydnone with the rate constant of up to 1.46 M-1 s-1. Most significantly, the sydnone-dibenzocyclooctyne and norbornene-tetrazine cycloadditions were predicted to be mutually orthogonal. This was validated experimentally and used for highly selective fluorescence labeling of two proteins simultaneously.

PubMed Disclaimer

Figures

Scheme 1
Scheme 1. Reactivity of the (3 + 2) cycloadditions involving N-phenyl sydnone (aonly one regioisomer is depicted).
Fig. 1
Fig. 1. Energetics and transition states for the (3 + 2) cycloaddition of N-phenyl sydnone (1) with BCN 4 and subsequent CO2 release.
Fig. 2
Fig. 2. (a) DFT-computed activation free energies for the (3 + 2) cycloadditions of sydnone 1 with eight strained alkenes and alkynes at the CPCM(water)-M06-2X/6-311+G(d,p)//M06-2X/6-31G(d) level of theory and the predicted rate constants in water at 25 °C. (b) DFT-computed activation free energies and predicted rate constants for the (4 + 2) cycloadditions of tetrazine 9 with norbornene, DIBAC, and BARAC.
Scheme 2
Scheme 2. Mutual orthogonality between sydnone-DIBAC and norbornene-tetrazine cycloadditions (aR = CH2CH2NH2, R′ = NH(CH2)3NHBoc; only one regioisomer is depicted).
Fig. 3
Fig. 3. Modifications of protein surfaces via bioorthogonal cycloadditions. (a) Dibenzoazacyclooctyne (DIBAC) and 5-norbornene-2-acetic acid (Nor) were appended to BSA and OVA (20 mg mL–1 in PBS) respectively, via NHS ester-amine coupling conditions (20 mM labeling reagent). The labeled proteins BSA-DIBAC and OVA-Nor (2 mg mL–1) simultaneously react with sydnone-BODIPY (Syd-630) and tetrazine-BODIPY (Tz-504). (b) Gel analysis of BSA functionalized with DIBAC and OVA functionalized with Nor incubated for 1 h with either Syd-630, Tz-504, both reagents simultaneously, or no reagent (–). (c) Gel analysis of DIBAC-modified BSA and Nor-modified OVA with both Syd-630 and Tz-504 simultaneously for 1–60 min or no reagent (–). The protein loading on the gels was assessed with Coomassie stain.
See this image and copyright information in PMC

References

    1. Sletten E. M., Bertozzi C. R. Angew. Chem., Int. Ed. 2009;48:6974–6998. - PMC - PubMed
    2. Grammel M., Hang H. C. Nat. Chem. Biol. 2013;9:475–484. - PMC - PubMed
    3. McKay C. S., Finn M. Chem. Biol. 2014;21:1075–1101. - PMC - PubMed
    4. Borrmann A., van Hest J. C. Chem. Sci. 2014;5:2123–2134.
    1. Saxon E., Bertozzi C. R. Science. 2000;287:2007–2010. - PubMed
    1. Agard N. J., Prescher J. A., Bertozzi C. R. J. Am. Chem. Soc. 2004;126:15046–15047. - PubMed
    2. Sletten E. M., Bertozzi C. R. Acc. Chem. Res. 2011;44:666–676. - PMC - PubMed
    1. Jewett J. C., Bertozzi C. R. Chem. Soc. Rev. 2010;39:1272–1279. - PMC - PubMed
    2. Patterson D. M., Nazarova L. A., Prescher J. A. ACS Chem. Biol. 2014;9:592–605. - PubMed
    1. Baskin J. M., Prescher J. A., Laughlin S. T., Agard N. J., Chang P. V., Miller I. A., Lo A., Codelli J. A., Bertozzi C. R. Proc. Natl. Acad. Sci. U.S.A. 2007;104:16793–16797. - PMC - PubMed
    2. Codelli J. A., Baskin J. M., Agard N. J., Bertozzi C. R. J. Am. Chem. Soc. 2008;130:11486–11493. - PMC - PubMed
    3. Ning X., Guo J., Wolfert M. A., Boons G. J. Angew. Chem., Int. Ed. 2008;47:2253–2255. - PMC - PubMed
    4. Debets M. F., van Berkel S. S., Schoffelen S., Rutjes F. P. J. T., van Hest J. C. M., van Delft F. L. Chem. Commun. 2010;46:97–99. - PubMed
    5. Jewett J. C., Sletten E. M., Bertozzi C. R. J. Am. Chem. Soc. 2010;132:3688–3690. - PMC - PubMed
    6. Dommerholt J., Schmidt S., Temming R., Hendriks L. J., Rutjes F. P., van Hest J., Lefeber D. J., Friedl P., van Delft F. L. Angew. Chem., Int. Ed. 2010;49:9422–9425. - PMC - PubMed
    7. Plass T., Milles S., Koehler C., Schultz C., Lemke E. A. Angew. Chem., Int. Ed. 2011;50:3878–3881. - PMC - PubMed
    8. Debets M. F., Van Berkel S. S., Dommerholt J., Dirks A. J., Rutjes F. P., van Delft F. L. Acc. Chem. Res. 2011;44:805–815. - PubMed
    9. Lim R. K., Lin Q. Acc. Chem. Res. 2011;44:828–839. - PMC - PubMed
    10. Yu Z., Pan Y., Wang Z., Wang J., Lin Q. Angew. Chem., Int. Ed. 2012;51:10600–10604. - PMC - PubMed
    11. Yu Z., Ohulchanskyy T. Y., An P., Prasad P. N., Lin Q. J. Am. Chem. Soc. 2013;135:16766–16769. - PMC - PubMed
    12. Yu Z., Lin Q. J. Am. Chem. Soc. 2014;136:4153–4156. - PMC - PubMed