title: Direct binding of microRNA-21 pre-element with Regorafenib: An alternative mechanism for anti-colorectal cancer chemotherapy?
abstract: The Regorafenib is a broad-spectrum kinase inhibitor that has been approved to treat colorectal cancer (CRC). However, evidences have shown that the agent is also implicated in drug interaction with microRNA-21 (miR-21), an oncogenic miRNA which plays a key role in resisting programmed cell death in CRC cells. Here, we supposed that, instead of kinase inhibition, Regorafenib can directly bind to and then stabilize miR-21 pre-element, thus preventing RNase Dicer-meditated cleavage of the pre-element to mature miR-21. In order to verify the notion, an in silico-in vitro integrated investigation of the direct intermolecular interaction between Regorafenib and miR-21 pre-element was performed by using active pocket identification, RNA-ligand docking, molecular dynamics (MD) simulation, binding energetic analysis, and fluorescence-based assay. It was revealed that the Regorafenib can bind at the major groove-like stem region of miR-21 pre-element through three geometrically satisfactory hydrogen bonds (H-bonds) as well as a number of hydrophobic forces and π-π stacking, conferring strong specificity and high stability to the RNA-ligand complex system (Kd=0.73μM). Separate inversion mutation of two base pairs (G6C, C12G) and (A13U, U4A) that are involved in the H-bonding can considerably impair the affinity of Regorafenib to miR-21 pre-element, with Kdincrease to 27 and 96μM, respectively. All these supported that Regorafenib can directly bind to miR-21 pre-element at molecular level and the binding mode can be properly modeled by using the proposed integrated strategy. This study would provide a potential, alternative mechanism for anti-colorectal cancer chemotherapy with Regorafenib.
authors.affiliation: Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China. Electronic address: 2290773710@qq.com.
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Surgical Oncology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China.
authors.forename: Bojian
authors.initials: B
authors.lastname: Xie
authors.affiliation: The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450014, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Cao
authors.affiliation: Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhu
authors.affiliation: Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China.
authors.forename: Beibei
authors.initials: B
authors.lastname: Chen
authors.affiliation: Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China.
authors.forename: Huifang
authors.initials: H
authors.lastname: Lv
authors.affiliation: Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China.
authors.forename: Xingxing
authors.initials: X
authors.lastname: Fan
authors.affiliation: Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Han
authors.affiliation: Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China.
authors.forename: Liangyu
authors.initials: L
authors.lastname: Bie
authors.affiliation: Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China.
authors.forename: Xinguang
authors.initials: X
authors.lastname: Cao
authors.affiliation: Department of Surgical Oncology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China. Electronic address: shenven@hotmail.com.
authors.forename: Xiaokun
authors.initials: X
authors.lastname: Shen
authors.affiliation: Department of Surgical Oncology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China. Electronic address: tzyyrjk@hotmail.com.
authors.forename: Feilin
authors.initials: F
authors.lastname: Cao
mesh_terms: D016880:Anisotropy; D000970:Antineoplastic Agents / Q000737:chemistry / Q000494:pharmacology / Q000627:therapeutic use*; D001483:Base Sequence; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D006801:Humans; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation / Q000235:genetics; D010671:Phenylurea Compounds / Q000737:chemistry / Q000494:pharmacology / Q000627:therapeutic use*; D011725:Pyridines / Q000737:chemistry / Q000494:pharmacology / Q000627:therapeutic use*; D013816:Thermodynamics
chemical_list: D000970:Antineoplastic Agents; D008024:Ligands; C524940:MIRN21 microRNA, human; D035683:MicroRNAs; D010671:Phenylurea Compounds; D011725:Pyridines; C559147:regorafenib
keywords: Colorectal cancer; Molecular docking; Molecular dynamics; Regorafenib; microRNA