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Chen X, Xie B, Cao L, Zhu F, Chen B, Lv H, Fan X, Han L, Bie L, Cao X, Shen X, Cao F. Direct binding of microRNA-21 pre-element with Regorafenib: An alternative mechanism for anti-colorectal cancer chemotherapy? J Mol Graph Model 2017; 73:48-53. [PMID: 28236743 DOI: 10.1016/j.jmgm.2017.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/05/2017] [Accepted: 02/08/2017] [Indexed: 02/07/2023]
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 Kd increase 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.
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Affiliation(s)
- Xiaobing Chen
- Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China.
| | - Bojian Xie
- Department of Surgical Oncology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China
| | - Liang Cao
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450014, China
| | - Feng Zhu
- Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China
| | - Beibei Chen
- Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Huifang Lv
- Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Xingxing Fan
- Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Lili Han
- Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Liangyu Bie
- Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Xinguang Cao
- Department of Internal Oncology, Hennan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Xiaokun Shen
- Department of Surgical Oncology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China.
| | - Feilin Cao
- Department of Surgical Oncology, Taizhou Hospital, Wenzhou Medical University, Taizhou 317000, China.
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