Biologically Active Oligodeoxyribonucleotides. 5. 5‘-End-Substituted d(TGGGAG) Possesses Anti-Human Immunodeficiency Virus Type 1 Activity by Forming a G-Quadruplex Structure

Abstract

A series of hexadeoxyribonucleotides (6-mers), d(TGGGAG), substituted with a variety of aromatic groups at the 5'-end were synthesized and tested for anti-human immunodeficiency virus type 1 (HIV-1) activity. While unmodified d(TGGGAG) (31) had no anti-HIV-1 activity, compound 23 with a 3,4-di(benzyloxy)benzyl (DBB) group at the 5'-end potently inhibited the HIV-1IIIB-induced cytopathicity of MT-4 cells in vitro (IC50 = 0.37 microM) without cytotoxicity up to 40 microM. A thermal denaturation study on the 5'-end-substituted 6-mers by means of the circular dichroism (CD) spectra demonstrated that the aromatic substituent attached at the 5'-end of the 6-mer strongly enhanced the formation of a parallel helical structure consisting of four strands (quadruplex). On the contrary, compound 36, in which one of the guanosines of 23 was replaced by a thymidine, did not form a quadruplex, thus exhibiting no anti-HIV-1 activity. Moreover, both compound 15, with a tert-butyldiphenylsilyl group solely at its 3'-end, and compound 21, with a relatively small substituent, a benzyl group, at the 5'-end, formed quadruplexes but had no anti-HIV-1 activity. These findings led us to the conclusion that both the quadruplex structure and the aromatic substituent with adequate size at the 5'-end are crucial for the interaction of the 5'-end-substituted 6-mers with the V3 loop as well as the CD4 binding site on viral gp120, resulting in anti-HIV-1 activity.

DNA Duplexes with Hydrophobic Modifications Inhibit Fusion between HIV-1 and Cell Membranes

“…These aptamers fold into defined three-dimensional (3D) structures and interact with HIV-1-associated proteins, such as HIV-1 reverse transcriptases (6,7), RNase H (8), Tat proteins (9), integrase (10)(11)(12)(13), and surface glycoproteins (14,15). A subcategory of aptamers possess an additional intermolecular assembly feature such as the quadruplex d(TGGGAG) 4 described by Hotoda et al, which was assembled by four 6-mer G-rich sequences in parallel with the 5=-end attaching to aromatic substituents of adequate size, such as tert-butyldiphenylsilyl (TBDPS) and 4=4-dimethoxytriphenyl (DMT) (16)(17)(18)(19)(20)(21)(22)(23)(24). These quadruplexes are aptamer-like since they interact with the V3 loop or the CD4 binding site on viral gp120, preventing viral adhesion and fusion with target cells (17,25,26).…”

“…Although there was no sequential specificity for the targeting interaction, the whole complex still needs to assemble into a rigid, defined framework possessing negative charges and hydrophobic groups. Specifically, the 5= hydrophobic group might contribute to the hydrophobic interactions (18). Based on the quadruplex model, we previously constructed several DNA quadruplex inhibitors containing TBDPS aromatic groups derived from the nucleobase at the 5=-end with similar HIV-1 fusion inhibitory activity.…”

Newly Designed Six-Membered Azasugar Nucleotide-Containing Phosphorothioate Oligonucleotides as Potent Human Immunodeficiency Virus Type 1 Inhibitors

“…We introduced the 6-AZN to the G quartet PAS ON, synthesizing DBM 2200. DBM 2201 contains a dimethoxytrityl group on the 5Ј-end of the modified G-quadruplex in its PAO linkage, which was synthesized as described in previous reports (13,16,53). However, neither of these exhibited any significant anti-HIV-1 activity (Table 1).…”

“…The mechanisms suggested have included adsorption blocking (9,16,47,50,51,53) and inhibition of HIV-1-specific enzymes, such as reverse transcriptase (29)(30)(31) or integrase (21-23, 36, 42). However, most studies of the antiviral mechanisms of PAS ONs, as well as recent studies with small interfering RNA (siRNA) against HIV-1 (3,5,7,35,38,39,49), have been conducted by transfection or viral vector-mediated delivery (4,17,27,33,34), rather than simple treatment of the infected culture.…”

Potential uses of G-quadruplex-forming aptamers

“…GGGTGGGGTGGGTGGGT GGGCGGGCGGGCGGGC GIGTGGGTGGGTGGGT Do et al 2011 HIV-1 gp120 V3 loop TTGGGTT Wyatt et al 1994 HIV-1 gp120 V3 loop/CD4 binding site TGGGAG Hotoda et al 1998;Olieviero et al 2010 charged binding side at the ligands. This is largely due to the fact that the negative charge density of G-quadruplexes is twice as high as that of linear DNA (Gatto et al 2009), although other forces, such as Van der Waals, π-π stacking and hydrophobic interactions are also important.…”