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

Rohit Bavi; Zhang Hang; Parikshit Banerjee; Md Aquib; Mahendra Jadhao; Niraj Rane; Sneha Bavi; Raghunath Bhosale; Kisan Kodam; Byong-Hun Jeon; Yueqing Gu

doi:10.1016/j.omtn.2020.07.038

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

Mol Ther Nucleic Acids. 2020 Sep 4:21:1074-1086. doi: 10.1016/j.omtn.2020.07.038. Epub 2020 Jul 31.

Authors

Rohit Bavi¹, Zhang Hang², Parikshit Banerjee³, Md Aquib⁴, Mahendra Jadhao⁵, Niraj Rane⁶, Sneha Bavi⁷, Raghunath Bhosale⁸, Kisan Kodam⁹, Byong-Hun Jeon¹⁰, Yueqing Gu¹¹

Affiliations

¹ State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Xiang, Nanjing, Gulou District 210009, China; School of Chemical Sciences, Punyashlok Ahilyadevi Holkar Solapur University, Solapur 413255, Maharashtra, India.
² State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Xiang, Nanjing, Gulou District 210009, China.
³ School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
⁴ Department of Pharmaceutics, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, China.
⁵ Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
⁶ Biochemistry Division, Department of Chemistry, Savitribai Phule Pune University, Pune 411007, Maharashtra, India; Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
⁷ Axiom Market Research and Consulting, Pune 411014, Maharashtra, India.
⁸ School of Chemical Sciences, Punyashlok Ahilyadevi Holkar Solapur University, Solapur 413255, Maharashtra, India.
⁹ Biochemistry Division, Department of Chemistry, Savitribai Phule Pune University, Pune 411007, Maharashtra, India.
¹⁰ Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea. Electronic address: bhjeon@hanyang.ac.kr.
¹¹ State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Xiang, Nanjing, Gulou District 210009, China. Electronic address: guengineering@cpu.edu.cn.

Abstract

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.

Keywords: DNA1 aptamer; annexin A1; aptamer-drug conjugate; binding energy calculations; doxorubicin; molecular dynamics simulation; virtual screening.