A promising approach for preventing viral infection is blocking host-cell receptors from binding with viral surface proteins. A critical step in the entry pathway for Human Immunodeficiency Virus (HIV) is the interaction of the envelope glycoprotein, gp120, with host CD4 receptors. Inhibition of this binding has been shown to be an efficacious target for antiviral agents. A powerful method for developing novel binding agents (aptamers) is the selective amplification and evolution of nucleic acids.
Nucleic acid aptamers demonstrate little to no immunogenicity or toxicity and are easily produced using automated nucleic acid synthesizers. However, there are two main barriers to the drug-applicability of in vitro selected nucleic acids. They are often too large for facile absorption and distribution to pathologic targets, and they are unstable to biological and chemical degradation. With only a four nucleotide alphabet, shear size and number of interactions must substitute for good chemical complementarity with the target. In addition, the necessity for fixed primer binding sites for PCR amplification adds at least 24 extra nucleotides with no gain in functionality. These large sizes engender polymer instability and poor drug-like properties.
The long-term goal of our lab is the development of therapeutically effective nucleic acid-based aptamers. We plan to achieve this by expanding the chemical alphabet of in vitro-selected nucleic acids while maintaining the effectiveness of polymerase-based amplification. We will employ a modified library that specifically encodes for, and is encoded by, unmodified deoxyribonucleic acids. The modified and natural sequences will substitute for each other, with selection occurring on the modified library, and amplification occurring on their unmodified complements. Communication between the two systems will occur through base-pairing. The modified library may contain chemical functionality nearly equivalent to that of peptides. The unmodified library will include the 5'- and 3'-primer binding sites necessary for PCR amplification. The system is designed to be bidirectional, so that in each step the modified library may be translated to natural sequence space, amplified, then retranslated back.