Molecular design guided by a local map of sequence space: DNA aptamers that inhibit cathepsin E

It has been strongly demanded by a number of people to elevate activities of molecules of a particular function. Currently, there is no general guide available for this purpose. Here we present a novel approach for this; a local sequence space map-directed method for exploring molecules of a higher activity. This approach exploits the knowledge of a local sequence space so far established and obtains the shape of sequence space (map) by intra- and extrapolating the known landscape, which was drawn through the principal coordinates analysis. In this method, we successfully obtained 16 DNA aptamers of cathepsin E (CE) inhibitory activity that have comparable or higher activities than the ancestral ones on which the designed molecules were based. Some of them had a 30% higher activity than the previously reported top one (SFR-6-3). This high efficiency in obtaining functional molecules (16 out of 21 newly designed ones) is by no means usual because most of molecules generated at random are known to have no function, showing the effectiveness of the map-based approach. The selected molecules were confirmed to have the i-motif structure, consistent to the fact that they have a C-rich sequence and their CE-inhibitory activities were measured at an acidic pH, both of which are favorable for the i-motif. This structure of CE-inhibitory aptamers was inferred to contribute to the structural stability but not to the function itself directly.