Nucleosides with a Twist. Can Fixed Forms of Sugar Ring Pucker Influence Biological Activity in Nucleosides and Oligonucleotides?

• Published in: Journal of medicinal chemistry 1996-09, Vol.39 (19), p.3739-3747
• Main Authors: Marquez, Victor E, Siddiqui, Maqbool A, Ezzitouni, Abdallah, Russ, Pamela, Wang, Jianying, Wagner, Richard W, Matteucci, Mark D
• Format: Article
• Language: English
• Subjects: Acyclovir - pharmacology; Antibiotics. Antiinfectious agents. Antiparasitic agents; Antisense Elements (Genetics) - chemistry; Antiviral agents; Antiviral Agents - chemical synthesis; Antiviral Agents - pharmacology; Base Sequence; Biological and medical sciences; Cytopathogenic Effect, Viral; Drug Stability; Herpesvirus 1, Human - drug effects; Herpesvirus 2, Human - drug effects; Humans; Hydrogen Bonding; Medical sciences; Molecular Structure; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes - chemistry; Nucleosides - chemistry; Nucleosides - pharmacology; Oligonucleotides - chemistry; Oligonucleotides - pharmacology; Pharmacology. Drug treatments; Ribonuclease H - metabolism; Structure-Activity Relationship; Thermodynamics; Viral Plaque Assay
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm960306+

The sugar moiety of nucleosides in solution is known to exist in a rapid dynamic equilibrium between extreme Northern and Southern conformations as defined in the pseudorotational cycle. In the present work, we describe how the bicyclo[3.1.0]hexane template fixes the ring pucker of 2‘-deoxy-methanocarba-nucleosides 1−5 and 12 to values corresponding to either one of these two extreme conformations that are typical of nucleosides. The syntheses of the fixed Northern conformers 1−5 were performed by Mitsunobu coupling of the heterocyclic bases with the chiral carbocyclic alcohol 6 [(1R,2S,4R,5S)-1-[(benzyloxy)methyl]-2-(tert-butyloxy)-4-hydroxybicyclo[3.1.0]hexane], while the synthesis of the Southern conformer, (S)-methanocarba-T (12), was reported earlier. Carbocyclic thymidine (carba-T, 13) was used as a reference, flexible carbocyclic nucleoside. Antiviral evaluation of these compounds revealed a very potent antiherpetic activity associated with the Northern thymidine analogue 2, which was more powerful than the reference standard acyclovir against both HSV-1 and HSV-2. (N)-Methanocarba-T (2) was further evaluated as a component of a short oligodeoxynucleotide (ODN) phosphorothioate (5‘-CTTCATTTTTTCTTC-3‘) where all thymidines were replaced by 2. The expected thermodynamic stability resulting from the preorganization of the pseudosugar rings into a Northern conformation, typical of A-DNA, was evident by the increase in T m of the corresponding DNA/RNA heteroduplex. However, the rigid A-tract ODN caused loss of RNase H recruitment. A detailed conformational analysis of (N)-methanocarba-T (2) and (S)-methanocarba-T (12), as representative examples of conformationally rigid pseudorotational antipodes, revealed that in addition to their different forms of ring pucker, (S)-methanocarba-T appears to be a rather stiff molecule with fewer low-energy conformational states available compared to (N)-methanocarba-T. The syn/anti-energy barrier for these nucleoside analogues is 5−6 kcal/mol higher than for common nucleosides.