Entropic Fragment‐Based Approach to Aptamer Design

Abstract

Aptamers are short RNA ⁄ DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology. They are recognized as having potential therapeutic and diagnostic clinical applications. The success of the systematic evolution of ligands by exponential enrichment process requires that the RNA ⁄ DNA pools used in the process have a sufficient level of sequence diversity and structural complexity. While the systematic evolution of ligands by exponential enrichment technology is well developed, it remains a challenge in the efficient identification of correct aptamers. In this article, we propose a novel information-driven approach to a theoretical design of aptamer templates based solely on the knowledge regarding the biomolecular target structures. We have investigated both theoretically and experimentally the applicability of the proposed approach by considering two specific targets: the serum protein thrombin and the cell membrane phospholipid phosphatidylserine. Both of these case studies support our method and indicate a promising advancement in theoretical aptamer design. In unfavorable cases where the designed sequences show weak binding affinity, these template sequences can be still modified to enhance their affinities without going through the systematic evolution of ligands by exponential enrichment process.Key words: bioinformatics, mechanism-based drug design, molecular recognition, structure-based drug design Received 18 October 2010, revised 24 February 2011 and accepted for publication 1 April 2011 Aptamers, short RNA ⁄ DNA sequences, are selected through an experimental technique known as systematic evolution of ligands by exponential enrichment (SELEX) to bind to specific biomolecular targets including small molecules, proteins, nucleic acids, phospholipids as well as complex structures such as cells, tissues, bacteria, and other organisms. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology with recognized therapeutic and diagnostic clinical applications (1-5). SELEX consists of a number of rounds of in vitro selection in which the RNA ⁄ DNA pool is incubated with the binding target. The non-binding or loosely binding sequences are discarded, while the binding sequences are expanded using the polymerase chain reaction method to provide a pool of sequences for the next round of testing. In practice, multiple rounds of selection and expansion are required before unique tightly binding sequences can be identified. Additionally, isolated aptamers will often need to be reengineered to reduce their sequence length and impart additional favorable biological properties. These issues pose a challenge for the efficient identification of correct aptamers.Over the past several years, various research groups have attempted...

Aptamers as Both Drugs and Drug-Carriers

“…Their structures and related physical properties like geometry and charge residues are expected to dictate in the target interaction raised creation of stable or semistable complex structures in the vicinity of the binding regions. In binding with targets aptamers show high affinity and specificity [11]. Unlike small interfering RNAs (siRNAs), antisense oligonucleotides, and so forth, that inhibit protein translation by Watson-Crick base-pairing to their respective messenger RNAs, aptamers bind to targets in proteins and occasionally to other targets, for example, lipids [11].…”

“…In binding with targets aptamers show high affinity and specificity [11]. Unlike small interfering RNAs (siRNAs), antisense oligonucleotides, and so forth, that inhibit protein translation by Watson-Crick base-pairing to their respective messenger RNAs, aptamers bind to targets in proteins and occasionally to other targets, for example, lipids [11]. In this section, I shall discuss various techniques that have so far been used to design aptamers targeting various binding sites.…”

“…To gain clarity one can read a few case studies performed using various biophysical techniques as mentioned here. The understanding of chemotherapy drugs' bioavailability at the biological structures responsible for causing cancer [4–6], the development of the aptamer designing formalisms for ensuring target molecule specific binding of agents [7–11], and addressing the ion channels' stability inside lipid membranes through electrical charge based interaction energetic coupling [12] are among a few best ones found so far. The computational scientists like computational chemists use computer aided drug design to make drug library.…”

“…The number of the members in a group thus increases and the candidates appear with different quantitative binding potencies towards specific targets [2, 14]. Among various chemicals colchicine [2, 14], taxol [15–18], aptamers [7–11], and so forth are especially mentionable that are used for modifications and thus to create drug banks. The primary targets of these molecules are different or we can consider these molecules to be target specific.…”

“…They are now tried as medicines or possible candidates for treating age-related macular degeneration [22–24], cancer [11, 25–28], acute coronary syndrome [29, 30], thrombotic thrombocytopenic purpura [31], coronary artery bypass grafting [32], diabetic nephropathy [27, 33], hemophilia, anemia [34, 35], and so forth. It has already covered a wide range of interests.…”