An Ensemble Docking Approach for Analyzing and Designing Aptamer Heterodimers Targeting VEGF₁₆₅

Vascular endothelial growth factor 165 (VEGF₁₆₅) is a prominent isoform of the VEGF-A protein that plays a crucial role in various angiogenesis-related diseases. It is homodimeric, and each of its monomers is composed of two domains connected by a flexible linker. DNA aptamers, which have emerged as potent therapeutic molecules for many proteins with high specificity and affinity, can also work for VEGF₁₆₅. A DNA aptamer heterodimer composed of monomers of V7t1 and del5-1 connected by a flexible linker (V7t1:del5-1) exhibits a greater binding affinity with VEGF₁₆₅ compared to either of the two monomers alone. Although the structure of the complex formed between the aptamer heterodimer and VEGF₁₆₅ is unknown due to the highly flexible linkers, gaining structural information will still be valuable for future developments. Toward this end of accessing structural information, we adopt an ensemble docking approach here. We first obtain an ensemble of structures for both VEGF₁₆₅ and the aptamer heterodimer by considering both small- and large-scale motions. We then proceed through an extraction process based on ensemble docking, molecular dynamics simulations, and binding free energy calculations to predict the structures of the VEGF₁₆₅/V7t1:del5-1 complex. Through the same procedures, we reach a new aptamer heterodimer that bears a locked nucleic acid-modified counterpart of V7t1, namely RNV66:del5-1, which also binds well with VEGF₁₆₅. We apply the same protocol to the monomeric units V7t1, RNV66, and del5-1 to target VEGF₁₆₅. We observe that V7t1:del5-1 and RNV66:del5-1 show higher binding affinities with VEGF₁₆₅ than any of the monomers, consistent with experiments that support the notion that aptamer heterodimers are more effective anti-VEGF₁₆₅ aptamers than monomeric aptamers. Among the five different aptamers studied here, the newly designed RNV66:del5-1 shows the highest binding affinity with VEGF₁₆₅. We expect that our ensemble docking approach can help in de novo designs of homo/heterodimeric anti-angiogenic drugs to target the homodimeric VEGF₁₆₅.