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Valdés-Albuernes JL, Díaz-Pico E, Alfaro S, Caballero J. Advanced modeling of salt-inducible kinase (SIK) inhibitors incorporating protein flexibility through molecular dynamics and cross-docking. Sci Rep 2025; 15:18868. [PMID: 40442221 PMCID: PMC12122877 DOI: 10.1038/s41598-025-03699-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2025] [Accepted: 05/21/2025] [Indexed: 06/02/2025] Open
Abstract
Salt-inducible kinases (SIK1, SIK2, and SIK3) regulate metabolism and immune responses, making them promising targets for inflammatory and autoimmune diseases. Understanding inhibitor selectivity among isoforms is crucial for therapeutic development. In this study, 44 compounds were investigated as SIK inhibitors using molecular modeling. A flexible treatment of the kinases via molecular dynamics (MD) simulations captured binding site conformational changes, followed by molecular docking to generate protein kinase (PK)-ligand complex models. Ligand orientations were validated against crystallographic data using LigRMSD and interaction fingerprints (IFPs). A genetic algorithm was applied to select conformations that maximize correlation between docking energies and biological activities, yielding R² values of 0.821, 0.646, and 0.620 for SIK1, SIK2, and SIK3, respectively. Our results highlight the importance of protein flexibility in achieving accurate correlations between docking energies and experimental pIC50 values, enhancing inhibitor selectivity predictions.
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Affiliation(s)
- Jorge Luis Valdés-Albuernes
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Erbio Díaz-Pico
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Sergio Alfaro
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca, Chile.
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Guo C, Li Q, Xiao J, Ma F, Xia X, Shi M. Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2023; 41:8654-8670. [PMID: 36281703 DOI: 10.1080/07391102.2022.2135601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC50 of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chuan Guo
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Qinxuan Li
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Jiujia Xiao
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Feng Ma
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xun Xia
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
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Shi M, Zheng X, Zhou Y, Yin Y, Lu Z, Zou Z, Hu Y, Liang Y, Chen T, Yang Y, Jing M, Lei D, Yang P, Li X. Selectivity Mechanism of Pyrrolopyridone Analogues Targeting Bromodomain 2 of Bromodomain-Containing Protein 4 from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:33658-33674. [PMID: 37744850 PMCID: PMC10515184 DOI: 10.1021/acsomega.3c03935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Bromodomain and extra-terminal domain (BET) proteins play an important role in epigenetic regulation and are linked to several diseases; therefore, they are interesting targets. BET has two bromodomains: bromodomain 1 (BD1) and BD2. Selective targeting of BD1 or BD2 may produce different activities and greater effects than pan-BD inhibitors. However, the selective mechanism of the specific core must be studied at the atomic level. This study determined the effectiveness of pyrrolopyridone analogues to selectively inhibit BD2 using a pan-BD inhibitor (ABBV-075) and a selective-BD2 inhibitor (ABBV-744). Molecular dynamics simulations and calculations of binding free energies were used to systematically study the selectivity of BD2 inhibition by the pyrrolopyridone analogues. Overall, the pyrrolopyridone analogue inhibitors targeting BD2 interacted mainly with the following amino acid pairs between bromodomain-containing protein 4 (BRD4)-BD1 and BRD4-BD2 complexes: I146/V439, N140/N433, D144/H437, P82/P375, V87/V380, D88/D381, and Y139/Y432. The pyrrolopyridone analogues targeting BRD4-BD2 were divided into five regions based on selectivity mechanism. These results suggest that the R3 and R5 regions of pyrrolopyridone analogues can be modified to improve the selectivity between BRD4-BD1 and BRD4-BD2. The selectivity of BD2 inhibition by pyrrolopyridone analogues can be used to design novel BD2 inhibitors based on a pyrrolopyridone core.
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Affiliation(s)
- Mingsong Shi
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
- Innovation
Center of Nursing Research, Nursing Key Laboratory of Sichuan Province,
West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xueting Zheng
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Zhou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuan Yin
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhou Lu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhiyan Zou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Hu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuanyuan Liang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Tingting Chen
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuhan Yang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Meng Jing
- Department
of Pathology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Dan Lei
- School
of Life Science and Engineering, Southwest
University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Pei Yang
- Department
of Hepatobiliary Surgery, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Xiaoan Li
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
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Zhou Y, Li X, Luo P, Chen H, Zhou Y, Zheng X, Yin Y, Wei H, Liu H, Xia W, Shi M, Li X. Identification of abemaciclib derivatives targeting cyclin-dependent kinase 4 and 6 using molecular dynamics, binding free energy calculation, synthesis, and pharmacological evaluation. Front Pharmacol 2023; 14:1154654. [PMID: 37234717 PMCID: PMC10206264 DOI: 10.3389/fphar.2023.1154654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
CDK4/6 plays a crucial role in various cancers and is an effective anticancer drug target. However, the gap between clinical requirements and approved CDK4/6 drugs is unresolved. Thus, there is an urgent need to develop selective and oral CDK4/6 inhibitors, particularly for monotherapy. Here, we studied the interaction between abemaciclib and human CDK6 using molecular dynamics simulations, binding free energy calculations, and energy decomposition. V101 and H100 formed stable hydrogen bonds with the amine-pyrimidine group, and K43 interacted with the imidazole ring via an unstable hydrogen bond. Meanwhile, I19, V27, A41, and L152 interacted with abemaciclib through π-alkyl interactions. Based on the binding model, abemaciclib was divided into four regions. With one region modification, 43 compounds were designed and evaluated using molecular docking. From each region, three favorable groups were selected and combined with each other to obtain 81 compounds. Among them, C2231-A, which was obtained by removing the methylene group from C2231, showed better inhibition than C2231. Kinase profiling revealed that C2231-A showed inhibitory activity similar to that of abemaciclib; additionally, C2231-A inhibited the growth of MDA-MB-231 cells to a greater extent than did abemaciclib. Based on molecular dynamics simulation, C2231-A was identified as a promising candidate compound with considerable inhibitory effects on human breast cancer cell lines.
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Affiliation(s)
- Yanting Zhou
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xiandeng Li
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Peifang Luo
- Department of Cardiovascular Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Huiting Chen
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Yan Zhou
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Xueting Zheng
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Yuan Yin
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Haoche Wei
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongji Liu
- Department of Ophthalmology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Wen Xia
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Mingsong Shi
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Xiaoan Li
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
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Shi M, Zhou Y, Wei H, Zhang X, Du M, Zhou Y, Yin Y, Li X, Tang X, Sun L, Xu D, Li X. Interactions between curcumin and human salt-induced kinase 3 elucidated from computational tools and experimental methods. Front Pharmacol 2023; 14:1116098. [PMID: 37124223 PMCID: PMC10133576 DOI: 10.3389/fphar.2023.1116098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Natural products are widely used for treating mitochondrial dysfunction-related diseases and cancers. Curcumin, a well-known natural product, can be potentially used to treat cancer. Human salt-induced kinase 3 (SIK3) is one of the target proteins for curcumin. However, the interactions between curcumin and human SIK3 have not yet been investigated in detail. In this study, we studied the binding models for the interactions between curcumin and human SIK3 using computational tools such as homology modeling, molecular docking, molecular dynamics simulations, and binding free energy calculations. The open activity loop conformation of SIK3 with the ketoenol form of curcumin was the optimal binding model. The I72, V80, A93, Y144, A145, and L195 residues played a key role for curcumin binding with human SIK3. The interactions between curcumin and human SIK3 were also investigated using the kinase assay. Moreover, curcumin exhibited an IC50 (half-maximal inhibitory concentration) value of 131 nM, and it showed significant antiproliferative activities of 9.62 ± 0.33 µM and 72.37 ± 0.37 µM against the MCF-7 and MDA-MB-23 cell lines, respectively. This study provides detailed information on the binding of curcumin with human SIK3 and may facilitate the design of novel salt-inducible kinases inhibitors.
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Affiliation(s)
- Mingsong Shi
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Yan Zhou
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Haoche Wei
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xinyu Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Meng Du
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, China
| | - Yanting Zhou
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yuan Yin
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
| | - Xinghui Li
- West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xinyi Tang
- West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Liang Sun
- Shenzhen Shuli Tech Co., Ltd, Shenzhen, Guangdong, China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Dingguo Xu, ; Xiaoan Li,
| | - Xiaoan Li
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, Sichuan, China
- *Correspondence: Dingguo Xu, ; Xiaoan Li,
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