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Sk MF, Samanta S, Poddar S, Kar P. Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey. J Comput Aided Mol Des 2024; 38:8. [PMID: 38324213 DOI: 10.1007/s10822-023-00548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/24/2023] [Indexed: 02/08/2024]
Abstract
The Janus kinases (JAK) are crucial targets in drug development for several diseases. However, accounting for the impact of possible structural rearrangements on the binding of different kinase inhibitors is complicated by the extensive conformational variability of their catalytic kinase domain (KD). The dynamic KD contains mainly four prominent mobile structural motifs: the phosphate-binding loop (P-loop), the αC-helix within the N-lobe, the Asp-Phe-Gly (DFG) motif, and the activation loop (A-loop) within the C-lobe. These distinct structural orientations imply a complex signal transmission path for regulating the A-loop's flexibility and conformational preference for optimal JAK function. Nevertheless, the precise dynamical features of the JAK induced by different types of inhibitors still remain elusive. We performed comparative, microsecond-long, Gaussian accelerated molecular dynamics simulations in triplicate of three phosphorylated JAK2 systems: the KD alone, type-I ATP-competitive inhibitor (CI) bound KD in the catalytically active DFG-in conformation, and the type-II inhibitor (AI) bound KD in the catalytically inactive DFG-out conformation. Our results indicate significant conformational variations observed in the A-loop and αC helix motions upon inhibitor binding. Our studies also reveal that the DFG-out inactive conformation is characterized by the closed A-loop rearrangement, open catalytic cleft of N and C-lobe, the outward movement of the αC helix, and open P-loop states. Moreover, the outward positioning of the αC helix impacts the hallmark salt bridge formation between Lys882 and Glu898 in an inactive conformation. Finally, we compared their ligand binding poses and free energy by the MM/PBSA approach. The free energy calculations suggested that the AI's binding affinity is higher than CI against JAK2 due to an increased favorable contribution from the total non-polar interactions and the involvement of the αC helix. Overall, our study provides the structural and energetic insights crucial for developing more promising type I/II JAK2 inhibitors for treating JAK-related diseases.
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Affiliation(s)
- Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, NIH Resource for Macromolecular Modeling and Visualization, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India
| | - Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, MP, 453552, India.
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Akinboade MW, Egbemhenghe AU, Abdulkareem TO, Ibrahim IA, Omotara BS, Aderemi OE, Egejuru WA, Ajala CF, Meejay Kanu I, Oluwafemi OO, Aderemi CO, Ddamulira C, Afuape AR, Adekola AT, Ojeyemi T, Otuomagie OI. Identification of promising small-molecule inhibitors targeting STK17B for cancer therapeutics: molecular docking and molecular dynamics investigations. J Biomol Struct Dyn 2023:1-8. [PMID: 38147404 DOI: 10.1080/07391102.2023.2296605] [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: 06/10/2023] [Accepted: 10/02/2023] [Indexed: 12/28/2023]
Abstract
Cancer is a complex disease characterized by the uncontrolled growth of abnormal cells, leading to the formation of tumours. STK17B, a member of the DAPK family, has been implicated in various cancers and is considered a potential therapeutic target. However, no drug in the market has been approved for the treatment of STK17 B-associated cancer disease. This research aimed to identify direct inhibitors of STK17B using computational techniques. Ligand-based virtual screening and molecular docking were performed, resulting in the selection of three lead compounds (CID_135698391, CID_135453100, CID_136599608) with superior binding affinities compared to the reference compound dovitinib. While molecular docking simulation revealed specific interactions between the lead compounds and key amino acid residues at the binding pocket of STK17B, molecular dynamics simulations demonstrated that CID_135453100 and CID_136599608 exhibit stable conformations and comparable flexibility to dovitinib. However, CID_135698391 did not perform well using this metric as it displayed poor stability. Overall, small-molecule compounds CID_135453100 and CID_136599608 showed promising binding interactions and stability, suggesting their potential as direct inhibitors of STK17B. These findings could contribute to the exploration of novel therapeutic options targeting STK17B in cancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | - Bamidele Samson Omotara
- Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT, USA
| | - Olajide Enoch Aderemi
- Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT, USA
| | | | | | - Ihunanya Meejay Kanu
- Department of Epidemiology and Biotatistics, Jackson State University, Jackson, MS, USA
| | | | | | | | | | | | - Toluwalase Ojeyemi
- Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA
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Decoding the Conformational Selective Mechanism of FGFR Isoforms: A Comparative Molecular Dynamics Simulation. Molecules 2023; 28:molecules28062709. [PMID: 36985681 PMCID: PMC10052029 DOI: 10.3390/molecules28062709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Fibroblast growth factor receptors (FGFRs) play critical roles in the regulation of cell growth, differentiation, and proliferation. Specifically, FGFR2 gene amplification has been implicated in gastric and breast cancer. Pan-FGFR inhibitors often cause large toxic side effects, and the highly conserved ATP-binding pocket in the FGFR1/2/3 isoforms poses an immense challenge in designing selective FGFR2 inhibitors. Recently, an indazole-based inhibitor has been discovered that can selectively target FGFR2. However, the detailed mechanism involved in selective inhibition remains to be clarified. To this end, we performed extensive molecular dynamics simulations of the apo and inhibitor-bound systems along with multiple analyses, including Markov state models, principal component analysis, a cross-correlation matrix, binding free energy calculation, and community network analysis. Our results indicated that inhibitor binding induced the phosphate-binding loop (P-loop) of FGFR2 to switch from the open to the closed conformation. This effect enhanced extensive hydrophobic FGFR2-inhibitor contacts, contributing to inhibitor selectivity. Moreover, the key conformational intermediate states, dynamics, and driving forces of this transformation were uncovered. Overall, these findings not only provided a structural basis for understanding the closed P-loop conformation for therapeutic potential but also shed light on the design of selective inhibitors for treating specific types of cancer.
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Li X, Li B, Li J, Yang M, Bai Y, Chen K, Chen Z, Mao N. Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase. Front Mol Biosci 2022; 9:1104942. [PMID: 36601586 PMCID: PMC9806222 DOI: 10.3389/fmolb.2022.1104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Calcium (Ca2+) signaling plays an important role in the regulation of many cellular functions. Ca2+-binding protein calmodulin (CaM) serves as a primary effector of calcium function. Ca2+/CaM binds to the death-associated protein kinase 1 (DAPK1) to regulate intracellular signaling pathways. However, the mechanism underlying the influence of Ca2+ on the conformational dynamics of the DAPK1-CaM interactions is still unclear. Here, we performed large-scale molecular dynamics (MD) simulations of the DAPK1-CaM complex in the Ca2+-bound and-unbound states to reveal the importance of Ca2+. MD simulations revealed that removal of Ca2+ increased the anti-correlated inter-domain motions between DAPK1 and CaM, which weakened the DAPK1-CaM interactions. Binding free energy calculations validated the decreased DAPK1-CaM interactions in the Ca2+-unbound state. Structural analysis further revealed that Ca2+ removal caused the significant conformational changes at the DAPK1-CaM interface, especially the helices α1, α2, α4, α6, and α7 from the CaM and the basic loop and the phosphate-binding loop from the DAPK1. These results may be useful to understand the biological role of Ca2+ in physiological processes.
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Affiliation(s)
- Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Bo Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jun Li
- Department of Orthopedics, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Mingyuan Yang
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yushu Bai
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Kai Chen
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yushu Bai, ; Kai Chen, ; Ziqiang Chen, ; Ningfang Mao,
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Liu C, Zhang Y, Zhang Y, Liu Z, Mao F, Chai Z. Mechanistic Insights into the Mechanism of Inhibitor Selectivity toward the Dark Kinase STK17B against Its High Homology STK17A. Molecules 2022; 27:molecules27144655. [PMID: 35889528 PMCID: PMC9317881 DOI: 10.3390/molecules27144655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 12/10/2022] Open
Abstract
As a member of the death-associated protein kinase (DAPK) family, STK17B plays an important role in the regulation of cellular apoptosis and has been considered as a promising drug target for hepatocellular carcinoma. However, the highly conserved ATP-binding site of protein kinases represents a challenge to design selective inhibitors for a specific DAPK isoform. In this study, molecular docking, multiple large-scale molecular dynamics (MD) simulations, and binding free energy calculations were performed to decipher the molecular mechanism of the binding selectivity of PKIS43 toward STK17B against its high homology STK17A. MD simulations revealed that STK17A underwent a significant conformational arrangement of the activation loop compared to STK17B. The binding free energy predictions suggested that the driving force to control the binding selectivity of PKIS43 was derived from the difference in the protein–ligand electrostatic interactions. Furthermore, the per-residue free energy decomposition unveiled that the energy contribution from Arg41 at the phosphate-binding loop of STK17B was the determinant factor responsible for the binding specificity of PKIS43. This study may provide useful information for the rational design of novel and potent selective inhibitors toward STK17B.
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Affiliation(s)
- Chang Liu
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China; (C.L.); (Z.L.)
| | - Yichi Zhang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai 200092, China;
| | - Yuqing Zhang
- MD Cancer Center, Yue Yang Hospital of Integrative Traditional Chinese and Western Medicine, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China;
| | - Zonghan Liu
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China; (C.L.); (Z.L.)
| | - Feifei Mao
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, China
- Correspondence: (F.M.); (Z.C.)
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China; (C.L.); (Z.L.)
- Department of Hepatic Surgery, Shanghai Geriatric Center, Shanghai 201104, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China
- Correspondence: (F.M.); (Z.C.)
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