Mechanism for dissociative hydrolysis of pyrimidine nucleoside d4N:
inversion vs retention
Abstract
Employing the microhydration model that involves two to five explicit
water molecules, two plausible dissociative hydrolysis pathways of
2’,3’-didehydro-2’,3’-dideoxyuridine (d4U), α-path with
configuration-inversion and β-path with configuration-retention, have
been investigated by M06-2X(CPCM)/6-31++G(d,p) method. Using this model,
inclusion of three explicit water molecules (n=3) is shown to be the
smallest system that gives the minimal activation free energy for α-path
and β-path. Our results suggest that the glycoside cleavage is the RDS,
and α-path is more favorable kinetically than β-path. Whereas β-path
with exergonic formation of β-dihydrofuran-like sugar with keto
pyrimidine complex possesses thermodynamic preference over α-path, where
the formation of α-dihydrofuran-like sugar with enol pyrimidine complex
is endergonic. The free energy barriers of RDSs for d4U (24.8 kcal
mol-1) and d4T (27.3 kcal mol-1)
suggest that the glycosidic bond in d4T is more stable than that in d4U.
The relative lower stability of d4U is probably an important factor for
less antiviral activity of d4U. The small free energy barrier
differences of ~1 kcal mol-1 for
β-path over α-path, and the reaction free energy differences of
~ -12 kcal mol-1 for β-path lower than
α-path in d4T and d4U suggest a competitive β-path in pyrimidine d4Ns.
The higher free energy barriers of RDSs in ddU (27.6 kcal
mol-1) and ddT (29.0 kcal mol-1)
indicate that the saturated sugar moiety increases the stability of
glycosidic bond in contrast to the unsaturated counter parts in d4U and
d4T. NBO analysis also shows the kinetic preference of α-path over
β-path. Our results provide an exploration for the less antiviral
activity of d4U and the influence of saturated ribose on the glycosidic
bond stability of pyrimidine d4Ns.