Doxorubicin-Conjugated Innovative 16-mer DNA Aptamer-Based Annexin A1 Targeted Anti-Cancer Drug Delivery

• Published in: Molecular therapy. Nucleic acids 2020-09, Vol.21, p.1074-1086
• Main Authors: Bavi, Rohit, Hang, Zhang, Banerjee, Parikshit, Aquib, Md, Jadhao, Mahendra, Rane, Niraj, Bavi, Sneha, Bhosale, Raghunath, Kodam, Kisan, Jeon, Byong-Hun, Gu, Yueqing
• Format: Article
• Language: English
• Subjects: annexin A1; aptamer-drug conjugate; binding energy calculations; DNA1 aptamer; doxorubicin; molecular dynamics simulation; virtual screening
• ISSN: 2162-2531; 2162-2531
• DOI: 10.1016/j.omtn.2020.07.038

Aptamers are small, functional single-stranded DNA or RNA oligonucleotides that bind to their targets with high affinity and specificity. Experimentally, aptamers are selected by the systematic evolution of ligands by exponential enrichment (SELEX) method. Here, we have used rational drug designing and bioinformatics methods to design the aptamers, which involves three different steps. First, finding a probable aptamer-binding site, and second, designing the recognition and structural parts of the aptamers by generating a virtual library of sequences, selection of specific sequence via molecular docking, molecular dynamics (MD) simulation, binding energy calculations, and finally evaluating the experimental affinity. Following this strategy, a 16-mer DNA aptamer was designed for Annexin A1 (ANXA1). In a direct binding assay, DNA1 aptamer bound to the ANXA1 with dissociation constants value of 83 nM. Flow cytometry and fluorescence microscopy results also showed that DNA1 aptamer binds specifically to A549, HepG2, U-87 MG cancer cells that overexpress ANXA1 protein, but not to MCF7 and L-02, which are ANXA1 negative cells. We further developed a novel system by conjugating DNA1 aptamer with doxorubicin and its efficacy was studied by cellular uptake and cell viability assay. Also, anti-tumor analysis showed that conjugation of doxorubicin with aptamer significantly enhances targeted therapy against tumors while minimizing overall adverse effects on mice health. [Display omitted] DNA aptamer was designed for ANXA1 by using rational drug designing and bioinformatics approach, involving (1) finding a probable aptamer-binding site and (2) designing the recognition and structural parts of the aptamers by generating a virtual library of sequences, selection of specific sequence via molecular docking, MD simulation, and binding energy calculations. The affinity and specificity of DNA1 aptamer was confirmed by testing it against ANXA1-expressing cancer cell lines. Further, a novel system was developed by conjugating aptamer with doxorubicin, and its efficacy was studied by cellular uptake and cell viability assay. This system significantly enhanced the targeted therapy against tumors while minimizing overall adverse effects on mice health.