Lamivudine as a Nucleoside Template To Engineer DNA-Like Double-Stranded Helices in Crystals

Lamivudine
(β-l-2′,3′-dideoxy-3′-thiacytidine,
3TC) is a nucleoside-based anti-HIV/HBV drug that has provided insights
into the nucleic acid double-stranded helix assembly. Two crystal
structures thereof assembled with nucleobase pairing and helical stacking
as mimicries of DNA have recently demonstrated that nucleosides bring
themselves the chemical information to assemble DNA duplexes even
if the covalent backbone is absent. Here, we report the third structural
example in which nucleosides are base-paired and helically base-stacked.
A DNA-like double stranded helix was prepared by cocrystallizing lamivudine
with fumaric acid. We have named it lamivudine duplex III. When the
maleic acid present in the first example of lamivudine duplex is substituted
for its trans-stereoisomer, the formation of a DNA-mimic
is still observed. Lamivudine duplex III exhibits both base pairing
motifs present in the antecedent duplexes. In this structure, there
are four protonated lamivudine molecules paired in-plane with four
neutral ones. These base pairs are held together through three hydrogen
bonds as occurs in lamivudine duplex I. But, contrary to duplex I
with pairing between neutral and cationic drug units only, duplex
III has one neutral 3TC3TC pair in its asymmetric unit. These
molecules are kept in contact through only two peripheral N–H···O
hydrogen bonds as in two of the three neutral lamivudine pairs of
the second example of lamivudine duplex. In both structures, each
neutral pair is face-to-face stacked on top of one another and face-to-tail
stacked on bottom of another one. Another remarkable feature of duplex
III is in its fiber periphery. There are hydrogen bonds between the
5′-OH moieties of neighbor pairs pointing in the direction
of the missing phosphodiester linkages that would covalently bond
two adjacent monomers in the strand. Furthermore, the geometry of
these interactions reveals the antiparallel orientation of each strand
relative to one another. 13C CP/MAS NMR and powder X-ray
diffraction analyses have also revealed loss of long-range order upon
grounding lamivudine duplex III crystals. Such phenomenon can be related
to its low melting temperature. In addition, solid state 15N NMR spectra have reinforced the protonation pattern of lamivudine
duplex III. At last, this study adds knowledge on lamivudine versatility
to assemble a DNA-mimic in crystals even without the covalent phosphodiester
linkages, and duplex formation with rational counterion replacement
means base-paired and helically base-stacked structures of nucleosides
can be successfully engineered.