An inverse substrate orientation for the regioselective acylation of 3′,5′-diaminonucleosides catalyzed by Candida antarctica lipase B?

Iván Lavandera, Susana Fernández, Julia Magdalena, Miguel Ferrero, Romas J. Kazlauskas, Vicente Gotor

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52 Scopus citations


Candida antarctica lipaseB (CAL-B) catalyzes the regioselective acylation of natural thymidine with oxime esters and also the regioselective acylation of an analogue, 3′,5′-diamino-3′,5′-dideoxythymidine with nonactivated esters. In both cases, acylation favors the less hindered 5′-position over the 3′-position by upto 80-fold. Computer modeling of phosphonate transition-state analogues for the acylation of thymidine suggests that CAL-B favors acylation of the 5′-position because this orientation allows the thymine ring to bind in a hydrophobic pocket and forms stronger key hydrogen bonds than acylation of the 3′-position. On the other hand, computer modeling of phosphonamidate analogues of the transition states for acylation of either the 3′- or 5′-amino groups in 3′,5′-diamino-3′,5′-dideoxythymidine shows similar orientations and hydrogen bonds and, thus, does not explain the high regioselectivity. However, computer modeling of inverse structures, in which the acyl chain binds in the nucleophile pocket and vice versa, does rationalize the observed regioselectivity. The inverse structures fit the 5′-, but not the 3′-intermediate thymine ring, into the hydrophobic pocket, and form a weak new hydrogen bond between the 0-2 carbonyl atom of the thymine and the nucleophile amine only for the 5′-intermediate. A water molecule might transfer a proton from the ammonium group to the active-site histidine. As a test of this inverse orientation, we compared the acylation of thymidine and 3′,5′-diamino-3′,5′-dideoxythymidine with butyryl acyl donors and with isosteric methoxyacetyl acyl donors. Both acyl donors reacted at equal rates with thymidine, but the methoxyacetyl acyl donor reacted four times faster than the butyryl acyl donor with 3′,5′-diamino-3′, 5′-dideoxythymidine. This faster rate is consistent with an inverse orientation for 3′,5′-diamino-3′,5′-dideoxythymidine, in which the ether oxygen atom of the methoxyacetyl group can form a similar hydrogen bond to the nucleophilic amine. This combination of modeling and experiments suggests that such lipase-catalyzed reactions of apparently close substrate analogues like alcohols and amines might follow different pathways.

Original languageEnglish (US)
Pages (from-to)1381-1390
Number of pages10
Issue number8
StatePublished - Aug 2005


  • Aminolysis
  • Biotransformations
  • Enzyme catalysis
  • Molecular modeling
  • Nucleosides


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