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Combarel D, Dousset L, Bouchet S, Ferrer F, Tetu P, Lebbe C, Ciccolini J, Meyer N, Paci A. Tyrosine kinase inhibitors in cancers: Treatment optimization - Part I. Crit Rev Oncol Hematol 2024; 199:104384. [PMID: 38762217 DOI: 10.1016/j.critrevonc.2024.104384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
A multitude of TKI has been developed and approved targeting various oncogenetic alterations. While these have provided improvements in efficacy compared with conventional chemotherapies, resistance to targeted therapies occurs. Mutations in the kinase domain result in the inability of TKI to inactivate the protein kinase. Also, gene amplification, increased protein expression and downstream activation or bypassing of signalling pathways are commonly reported mechanisms of resistance. Improved understanding of mechanisms involved in TKI resistance has resulted in the development of new generations of targeted agents. In a race against time, the search for new, more potent and efficient drugs, and/or combinations of drugs, remains necessary as new resistance mechanisms to the latest generation of TKI emerge. This review examines the various generations of TKI approved to date and their common mechanisms of resistance, focusing on TKI targeting BCR-ABL, epidermal growth factor receptor, anaplastic lymphoma kinase and BRAF/MEK tyrosine kinases.
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Affiliation(s)
- David Combarel
- Service de Pharmacologie, Département de Biologie et Pathologie médicales, Gustave Roussy, Villejuif 94805, France; Service de Pharmacocinétique, Faculté de Pharmacie, Université Paris Saclay, Châtenay-Malabry 92 296, France
| | - Léa Dousset
- Dermatology Department, Bordeaux University Hospital, Bordeaux, France
| | - Stéphane Bouchet
- Département de Pharmacologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Florent Ferrer
- Department of Pharmacology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France; SMARTc Unit, CRCM Inserm U1068, Aix Marseille Univ and APHM, Marseille, France
| | - Pauline Tetu
- Department of Dermatology, APHP Dermatology, Paris 7 Diderot University, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Céleste Lebbe
- Department of Dermatology, APHP Dermatology, Paris 7 Diderot University, INSERM U976, Hôpital Saint-Louis, Paris, France
| | - Joseph Ciccolini
- SMARTc Unit, CRCM Inserm U1068, Aix Marseille Univ and APHM, Marseille, France
| | - Nicolas Meyer
- Université Paul Sabatier-Toulouse III, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1037-CRCT, Toulouse, France
| | - Angelo Paci
- Service de Pharmacologie, Département de Biologie et Pathologie médicales, Gustave Roussy, Villejuif 94805, France; Service de Pharmacocinétique, Faculté de Pharmacie, Université Paris Saclay, Châtenay-Malabry 92 296, France.
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Xu Y, Zhang N, Hu Y, Chen F, Hu L, Liao C, Jiang G. A preliminary understanding of the relationship between synthetic phenolic antioxidants and early pregnancy loss: Uncovering the potential molecular mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171972. [PMID: 38554970 DOI: 10.1016/j.scitotenv.2024.171972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Mounting evidence suggests that environmental pollutants may affect reproductive health, potentially leading to adverse outcomes like pregnancy loss. However, it remains unclear whether exposure to synthetic phenolic antioxidants (SPAs) correlates with early pregnancy loss (EPL). This study explores SPA exposure's link to EPL and its potential molecular mechanisms. From 2021 to 2022, 265 early pregnant women (136 serum and 129 villus samples) with and without EPL were enrolled. We quantified 17 SPAs in serum and chorionic villus, with AO1010, AO3114, BHT, AO2246, and BHT-Q frequently being detected, suggesting their ability to cross the placental barrier. AO1135 showed a positive relationship with EPL in sera, indicating a significant monotonic dose-response relationship (p-trend <0.001). BHT-Q exhibited a similar relationship with EPL in villi. Inhibitory effects of BHT-Q on estradiol (E2) were observed. Molecular docking revealed SPA-protein interactions involved in E2 synthesis. SPA-induced EPL might occur with specific serum levels of AO1135 and certain villus levels of AO1010, BHT-Q, and AO2246. BHT-Q emerges as a potential biomarker for assessing EPL risk. This study provides insights into understanding of the exposure to SPAs and potential adverse outcomes in pregnant women.
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Affiliation(s)
- Yaqian Xu
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Na Zhang
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Yu Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fu Chen
- Department of Environmental Science and Engineering, School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ligang Hu
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyang Liao
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guibin Jiang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Wang T, Tong J, Zhang X, Wang Z, Xu L, Pan P, Hou T. Structure-based virtual screening of novel USP5 inhibitors targeting the zinc finger ubiquitin-binding domain. Comput Biol Med 2024; 174:108397. [PMID: 38603896 DOI: 10.1016/j.compbiomed.2024.108397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
Abstract
The equilibrium of cellular protein levels is pivotal for maintaining normal physiological functions. USP5 belongs to the deubiquitination enzyme (DUBs) family, controlling protein degradation and preserving cellular protein homeostasis. Aberrant expression of USP5 is implicated in a variety of diseases, including cancer, neurodegenerative diseases, and inflammatory diseases. In this paper, a multi-level virtual screening (VS) approach was employed to target the zinc finger ubiquitin-binding domain (ZnF-UBD) of USP5, leading to the identification of a highly promising candidate compound 0456-0049. Molecular dynamics (MD) simulations were then employed to assess the stability of complex binding and predict hotspot residues in interactions. The results indicated that the candidate stably binds to the ZnF-UBD of USP5 through crucial interactions with residues ARG221, TRP209, GLY220, ASN207, TYR261, TYR259, and MET266. Binding free energy calculations, along with umbrella sampling (US) simulations, underscored a superior binding affinity of the candidate relative to known inhibitors. Moreover, US simulations revealed conformational changes of USP5 during ligand dissociation. These insights provide a valuable foundation for the development of novel inhibitors targeting USP5.
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Affiliation(s)
- Tianhao Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China; College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China
| | - Jianbo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China.
| | - Xing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China; College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China
| | - Zhe Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, 310058, Zhejiang, PR China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, PR China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China.
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, PR China.
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Zhang X, Tong J, Wang T, Wang T, Xu L, Wang Z, Hou T, Pan P. Dissecting the role of ALK double mutations in drug resistance to lorlatinib with in-depth theoretical modeling and analysis. Comput Biol Med 2024; 169:107815. [PMID: 38128254 DOI: 10.1016/j.compbiomed.2023.107815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/03/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is implicated in the genesis of multiple malignant tumors. Lorlatinib stands out as the most advanced and effective inhibitor currently used in the clinic for the treatment of ALK-positive non-small cell lung cancer. However, resistance to lorlatinib has inevitably manifested over time, with double/triple mutations of G1202, L1196, L1198, C1156 and I1171 frequently observed in clinical practice, and tumors regrow within a short time after treatment with lorlatinib. Therefore, elucidating the mechanism of resistance to lorlatinib is paramount in paving the way for innovative therapeutic strategies and the development of next-generation drugs. In this study, we leveraged multiple computational methodologies to delve into the resistance mechanisms of three specific double mutations of ALKG1202R/L1196M, ALKG1202R/L1198F and ALKI1171N/L1198F to lorlatinib. We analyzed these mechanisms through qualitative (PCA, DCCM) and quantitative (MM/GBSA, US) kinetic analyses. The qualitative analysis shows that these mutations exert minimal perturbations on the conformational dynamics of the structural domains of ALK. The energetic and structural assessments show that the van der Waals interactions, formed by the conserved residue Leu1256 within the ATP-binding site and the residues Glu1197 and Met1199 in the hinge domain with lorlatinib, play integral roles in the occurrence of drug resistance. Furthermore, the US simulation results elucidate that the pathways through which lorlatinib dissociates vary across mutant systems, and the distinct environments during the dissociation process culminate in diverse resistance mechanisms. Collectively, these insights provide important clues for the design of novel inhibitors to combat resistance.
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Affiliation(s)
- Xing Zhang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jianbo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China.
| | - Tianhao Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tianyue Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Gao H, Zhang JY, Zhao LJ, Guo YY. Synthesis and clinical application of small-molecule inhibitors and PROTACs of anaplastic lymphoma kinase. Bioorg Chem 2023; 140:106807. [PMID: 37651895 DOI: 10.1016/j.bioorg.2023.106807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/13/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Pharmacological interventions that specifically target protein products of oncogenes in tumors have surfaced as a propitious therapeutic approach. Among infrequent genetic alterations, rearrangements of the anaplastic lymphoma kinase (ALK) gene, typically involving a chromosome 2 inversion that culminates in a fusion with the echinoderm microtubule-associated protein like 4 (EML4), lead to anomalous expression and activation of ALK. The inhibition of autophosphorylation and subsequent blockade of signal transduction by ALK tyrosine kinase inhibitors (TKIs) has been observed to elicit anti-tumor effects. Currently, four generations of ALK-positive targeted drugs have been investigated, providing a promising outlook for patients. The aim of this review is to furnish a comprehensive survey of the synthesis and clinical application of prototypical small-molecule ALK inhibitors in both preclinical and clinical phases, offering guidance for further development of ALK inhibitors for cancer therapy.
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Affiliation(s)
- Hua Gao
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jing-Yi Zhang
- The Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States; College of Chemistry and Chemical Engineering, Zhengzhou Normal University 450044, China.
| | - Li-Jie Zhao
- The Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, United States.
| | - Yuan-Yuan Guo
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou 450052, China.
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Yu Y, Wang Z, Wang L, Wang Q, Tang R, Xiang S, Deng Q, Hou T, Sun H. Deciphering the Shared and Specific Drug Resistance Mechanisms of Anaplastic Lymphoma Kinase via Binding Free Energy Computation. RESEARCH (WASHINGTON, D.C.) 2023; 6:0170. [PMID: 37342628 PMCID: PMC10278961 DOI: 10.34133/research.0170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Anaplastic lymphoma kinase (ALK), a tyrosine receptor kinase, has been proven to be associated with the occurrence of numerous malignancies. Although there have been already at least 3 generations of ALK inhibitors approved by FDA or in clinical trials, the occurrence of various mutations seriously attenuates the effectiveness of the drugs. Unfortunately, most of the drug resistance mechanisms still remain obscure. Therefore, it is necessary to reveal the bottom reasons of the drug resistance mechanisms caused by the mutations. In this work, on the basis of verifying the accuracy of 2 main kinds of binding free energy calculation methodologies [end-point method of Molecular Mechanics with Poisson-Boltzmann/Generalized Born and Surface Area (MM/PB(GB)SA) and alchemical method of Thermodynamic Integration (TI)], we performed a systematic analysis on the ALK systems to explore the underlying shared and specific drug resistance mechanisms, covering the one-drug-multiple-mutation and multiple-drug-one-mutation cases. Through conventional molecular dynamics (cMD) simulation in conjunction with MM/PB(GB)SA and umbrella sampling (US) in conjunction with contact network analysis (CNA), the resistance mechanisms of the in-pocket, out-pocket, and multiple-site mutations were revealed. Especially for the out-pocket mutation, a possible transfer chain of the mutation effect was revealed, and the reason why different drugs exhibited various sensitivities to the same mutation was also uncovered. The proposed mechanisms may be prevalent in various drug resistance cases.
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Affiliation(s)
- Yang Yu
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine ofZhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qinghua Wang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Rongfan Tang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Sutong Xiang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qirui Deng
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine ofZhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Huiyong Sun
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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Qiu YF, Song LH, Jiang GL, Zhang Z, Liu XY, Wang G. Hallmarks of Anaplastic Lymphoma Kinase Inhibitors with Its Quick Emergence of Drug Resistance. PHARMACEUTICAL FRONTS 2022. [DOI: 10.1055/s-0042-1758542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is one of the most popular targets for anticancer therapies. In the past decade, the use of anaplastic lymphoma tyrosine kinase inhibitors (ALK-TKIs), including crizotinib and ceritinib, has been a reliable and standard options for patients with lung cancer, particularly for patients with nonsmall cell lung carcinoma. ALK-targeted therapies initially benefit the patients, yet, resistance eventually occurs. Therefore, resistance mechanisms of ALK-TKIs and the solutions have become a formidable challenge in the development of ALK inhibitors. In this review, based on the knowledge of reported ALK inhibitors, we illustrated the crystal structures of ALK, summarized the resistance mechanisms of ALK-targeted drugs, and proposed potential therapeutic strategies to prevent or overcome the resistance.
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Affiliation(s)
- Yong-Fu Qiu
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry, Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Lian-Hua Song
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Gang-Long Jiang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry, Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Zhen Zhang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry, Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, People's Republic of China
| | - Xu-Yan Liu
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry, Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
| | - Guan Wang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry, Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai, People's Republic of China
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Pratap Reddy Gajulapalli V, Lee J, Sohn I. Ligand-Based Pharmacophore Modelling in Search of Novel Anaplastic Lymphoma Kinase Inhibitors. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Cui Y, Tan Z, Liu S, Cao Z, Shao B, Guo M, Jiang N, Zhai X. Fragment-based discovery of novel phenyltriazolyl derivatives as allosteric type-I 1/2 ALK inhibitors with promising antitumor effects. Bioorg Med Chem Lett 2022; 75:128990. [PMID: 36113668 DOI: 10.1016/j.bmcl.2022.128990] [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: 07/21/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/02/2022]
Abstract
Based on the high-throughput screening hit BY-1, a series of phenyltriazolyl derivatives were developed. Satisfyingly, most compounds were detected moderate to excellent antitumor effects against Karpas299 and H2228 cells. Among them, 12k bearing 4‑hydroxypiperidinyl group exhibited the optimal activities against tested cells with IC50 values of 51 nM and 175 nM, as well as promising inhibitory effects on ALKWT (3.7 nM) and ALKL1196M (6.8 nM). Unlike the conventional type-I ALK inhibitors, molecular models identified 12k as an allosteric type-I1/2 inhibitor by forming key interactions in both the ATP binding region and the hydrophobic back pocket of ALK. Intriguingly, 12k could dose-dependently induce apoptosis on H2228 cell and inhibit colony formation and tumor cell migration. Taken together, the rationalization of 12k may shed new light on the identification of novel allosteric type-I1/2 ALK inhibitors.
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Affiliation(s)
- Youbao Cui
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zehui Tan
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shuyu Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhi Cao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bin Shao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengrao Guo
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Nan Jiang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Wang R, Zheng Q. Multiple Molecular Dynamics Simulations and Free-Energy Predictions Uncover the Susceptibility of Variants of HIV-1 Protease against Inhibitors Darunavir and KNI-1657. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:14407-14418. [PMID: 34851643 DOI: 10.1021/acs.langmuir.1c02348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
HIV-1 protease (PR) is considered to be the main targets of anti-AIDS drug design because of its role in the proteolytic processing of viral polyproteins. However, the emergence of drug-resistant HIV has become a major problem in the therapy of HIV-1-infected patients. Focused on the complexes of wild type (WT) PR and two mutant PRs (V32I/L33F/I54M/V82I and V32I/L33F/I54M/I84 V) with inhibitors Darunavir (DRV) and KNI-1657 (KNI), respectively, we have conducted research on the conformational dynamics and the resistance mechanism caused by residue mutations through multiple molecular dynamics (MD) simulations combined with an energy (MM-PBSA and solvated interaction energy (SIE)) prediction. The results indicate that mutated residues of PR alter the distance between flap regions and catalytic sites, the volume of the inner catalytic site, and the curling degree of the flap tips, thereby affecting DRV and KNI inhibitor binding to PR. These mutated residues reduced the binding affinity of the two mutant PRs to DRV, resulting in drug resistance, whereas the two mutant PRs increase the binding affinity with KNI, indicating they enhance the sensitivity to KNI. Compared with the WT PR, the changes in van der Waals interaction and electrostatic interaction in the two variant PRs play a vital part in the binding of PR with DRV and KNI. These results may supply valuable guidance for the design of anti-AIDS drugs targeting PR.
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Lin X, Fang Y, Hao Z, Wu H, Zhao M, Wang S, Liu Y. Bacteria-Triggered Multifunctional Hydrogel for Localized Chemodynamic and Low-Temperature Photothermal Sterilization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2103303. [PMID: 34643054 DOI: 10.1002/smll.202103303] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Pathogenic infections seriously threaten public health and have been considered as one of the most critical challenges in clinical therapy. Construction of a safe and efficient photothermal antibacterial platform is a promising strategy for treatment of bacterial infections. Considering that high temperature does harm to the normal tissues and cells, herein, a bacteria-triggered multifunctional hydrogel is constructed for low-temperature photothermal sterilization with high efficiency by integrating localized chemodynamic therapy (L-CDT). The hydrogel is constructed by incorporating copper sulfide nanoparticles (CuSNPs ) with photothermal profile into the network of hyaluronic acid (HA) and Fe3+ -EDTA complexes, named as CHFH (CuSNPs -HA-Fe3+ -EDTA hydrogel). Bacteria can be accumulated on the surface of CHFH, which secretes hyaluronidase to decompose the HA and release Fe3+ . The Fe3+ is reduced into Fe2+ in microenvironment of bacteria to trigger Fenton reaction. The generated hydroxyl radicals result in sterilization based on L-CDT within short range. By integrating with photothermal property of CuSNPs , low-temperature photothermal therapy (LT-PTT) for sterilization is realized, which improves the antibacterial efficiency while minimizes damage to normal tissues. The CHFH is further used to prepare Band aid which effectively promotes the Staphylococcus aureus-infected wound healing process in vivo, confirming the great potential for clinical application.
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Affiliation(s)
- Xiaodong Lin
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Yuan Fang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Zhe Hao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Haotian Wu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Minyang Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Yaqing Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China
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12
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Discovery of a small molecule inhibitor of cullin neddylation that triggers ER stress to induce autophagy. Acta Pharm Sin B 2021; 11:3567-3584. [PMID: 34900537 PMCID: PMC8642603 DOI: 10.1016/j.apsb.2021.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/17/2021] [Accepted: 07/01/2021] [Indexed: 12/30/2022] Open
Abstract
Protein neddylation is catalyzed by a three-enzyme cascade, namely an E1 NEDD8-activating enzyme (NAE), one of two E2 NEDD8 conjugation enzymes and one of several E3 NEDD8 ligases. The physiological substrates of neddylation are the family members of cullin, the scaffold component of cullin RING ligases (CRLs). Currently, a potent E1 inhibitor, MLN4924, also known as pevonedistat, is in several clinical trials for anti-cancer therapy. Here we report the discovery, through virtual screening and structural modifications, of a small molecule compound HA-1141 that directly binds to NAE in both in vitro and in vivo assays and effectively inhibits neddylation of cullins 1–5. Surprisingly, unlike MLN4924, HA-1141 also triggers non-canonical endoplasmic reticulum (ER) stress and PKR-mediated terminal integrated stress response (ISR) to activate ATF4 at an early stage, and to inhibit protein synthesis and mTORC1 activity at a later stage, eventually leading to autophagy induction. Biologically, HA-1141 suppresses growth and survival of cultured lung cancer cells and tumor growth in in vivo xenograft lung cancer models at a well-tolerated dose. Taken together, our study has identified a small molecule compound with the dual activities of blocking neddylation and triggering ER stress, leading to growth suppression of cancer cells.
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Brenner AK, Gunnes MW. Therapeutic Targeting of the Anaplastic Lymphoma Kinase (ALK) in Neuroblastoma-A Comprehensive Update. Pharmaceutics 2021; 13:pharmaceutics13091427. [PMID: 34575503 PMCID: PMC8470592 DOI: 10.3390/pharmaceutics13091427] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 01/27/2023] Open
Abstract
Neuroblastoma (NBL) is an embryonic malignancy of the sympathetic nervous system and mostly affects children under the age of five. NBL is highly heterogeneous and ranges from spontaneously regressing to highly aggressive disease. One of the risk factors for poor prognosis are aberrations in the receptor tyrosine kinase anaplastic lymphoma kinase (ALK), which is involved in the normal development and function of the nervous system. ALK mutations lead to constitutive activation of ALK and its downstream signalling pathways, thus driving tumorigenesis. A wide range of steric ALK inhibitors has been synthesized, and several of these inhibitors are already in clinical use. Major challenges are acquired drug resistance to steric inhibitors and pathway evasion strategies of cancer cells upon targeted therapy. This review will give a comprehensive overview on ALK inhibitors in clinical use in high-risk NBL and on the potential and limitations of novel inhibitors. Because combinatory treatment regimens are probably less likely to induce drug resistance, a special focus will be on the combination of ALK inhibitors with drugs that either target downstream signalling pathways or that affect the survival and proliferation of cancer cells in general.
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14
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Li Z, Liu F, Wu S, Ding S, Chen Y, Liu J. Research progress on the drug resistance of ALK kinase inhibitors. Curr Med Chem 2021; 29:2456-2475. [PMID: 34365942 DOI: 10.2174/0929867328666210806120347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The fusion and rearrangement of the ALK gene of anaplastic lymphoma kinase is an important cause of a variety of cancers, including non-small cell lung cancer (NSCLC) and anaplastic large cell lymphoma (ALCL). Since crizotinib first came out, many ALK inhibitors have come out one after another, but the fatal flaw in each generation of ALK inhibitors is the body's resistance to drugs. Therefore, how to solve the problem of drug resistance has become an important bottleneck in the application and development of ALK inhibitors. This article briefly introduces the drug resistance of ALK inhibitors and the modified forms of ALK inhibitors, which provide a theoretical basis for solving the drug resistance of ALK inhibitors and the development of a new generation of ALK kinase inhibitors. METHOD We use relevant databases to query relevant literature, and then screen and select based on the relevance and cutting edge of the content. We then summarize and analyze appropriate articles, integrate and classify relevant studies, and finally write articles based on topics. RESULT This article starts with the problem of ALK resistance, first introduces the composition of ALK kinase, and then introduces the problem of resistance of ALK kinase inhibitors. Later, the structural modification to overcome ALK resistance was introduced, and finally, the method to overcome ALK resistance was introduced. CONCLUSION This article summarizes the resistance pathways of ALK kinase inhibitors, and integrates the efforts made to overcome the structural modification of ALK resistance problems, and hopes to provide some inspiration for the development of the next generation of ALK kinase inhibitors.
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Affiliation(s)
- Zhen Li
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Fang Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Shuang Wu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Shi Ding
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ye Chen
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
| | - Ju Liu
- College of Pharmacy of Liaoning University, Shenyang, Liaoning 10036. China
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15
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Chen K, Yuan S, Wang D, Qi D, Chen F, Qiu X. Curcumin-loaded high internal phase emulsions stabilized with lysine modified lignin: a biological agent with high photothermal protection and antibacterial properties. Food Funct 2021; 12:7469-7479. [PMID: 34196335 DOI: 10.1039/d1fo00128k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial infections and multidrug resistance can seriously endanger the health and lives of humans, therefore the development of novel and efficient antibacterial strategies and drugs is urgently needed. Herein, a series of highly biocompatible lysine modified enzymatic hydrolysis lignins (EHL-Lys-x) were synthesized using the Mannich reaction. The sterilizing efficiency of EHL-Lys-2.0 against S. aureus and E. coli at 20 mg mL-1 is 93% and 50%, respectively, which is 26% higher than pure EHL. Quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM) analysis showed that the adsorption and adhesive force between EHL-Lys-x and bacteria increase with the increased amount of grafting of Lys on EHL owing to the increase of the electrostatic interaction between the EHL-Lys-x and bacteria, which results in an improvement in the antimicrobial activity of EHL-Lys-x. Subsequently, EHL-Lys-x combined with alkyl polyglucoside (APG) was used to stabilize the high internal phase emulsion containing curcumin (HIPEs-cur). The dispersed phase fraction of HIPE-cur is 87 vol%, which is the highest internal phase reported to date in the medical research area. The highest residual levels of curcumin in HIPEs are 60-fold, 3-fold and 5-fold compared to that in bulk oil after treatment with UV radiation, thermal emittance and after storage, respectively. The minimum inhibitory concentrations of HIPEs-cur against S. aureus and E. coli were found to be 1.56 and 6.25 mg mL-1, respectively, which are far higher than that of pure EHL-Lys-x. This strategy not only increases the chemical stability and bioavailability of curcumin, but also provides a novel method for the application of lignin in biomedical science.
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Affiliation(s)
- Kai Chen
- College or Textile Science and Engineering (International institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, China
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16
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Iżykowska K, Rassek K, Korsak D, Przybylski GK. Novel targeted therapies of T cell lymphomas. J Hematol Oncol 2020; 13:176. [PMID: 33384022 PMCID: PMC7775630 DOI: 10.1186/s13045-020-01006-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/22/2020] [Indexed: 02/06/2023] Open
Abstract
T cell lymphomas (TCL) comprise a heterogeneous group of non-Hodgkin lymphomas (NHL) that often present at an advanced stage at the time of diagnosis and that most commonly have an aggressive clinical course. Treatment in the front-line setting is most often cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) or CHOP-like regimens, which are effective in B cell lymphomas, but in TCL are associated with a high failure rate and frequent relapses. Furthermore, in contrast to B cell NHL, in which substantial clinical progress has been made with the introduction of monoclonal antibodies, no comparable advances have been seen in TCL. To change this situation and improve the prognosis in TCL, new gene-targeted therapies must be developed. This is now possible due to enormous progress that has been made in the last years in the understanding of the biology and molecular pathogenesis of TCL, which enables the implementation of the research findings in clinical practice. In this review, we present new therapies and current clinical and preclinical trials on targeted treatments for TCL using histone deacetylase inhibitors (HDACi), antibodies, chimeric antigen receptor T cells (CARTs), phosphatidylinositol 3-kinase inhibitors (PI3Ki), anaplastic lymphoma kinase inhibitors (ALKi), and antibiotics, used alone or in combinations. The recent clinical success of ALKi and conjugated anti-CD30 antibody (brentuximab-vedotin) suggests that novel therapies for TCL can significantly improve outcomes when properly targeted.
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Affiliation(s)
- Katarzyna Iżykowska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Karolina Rassek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Dorota Korsak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Grzegorz K Przybylski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland.
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17
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Zhu J, Wu Y, Xu L, Jin J. Theoretical Studies on the Selectivity Mechanisms of Glycogen Synthase Kinase 3β (GSK3β) with Pyrazine ATP-competitive Inhibitors by 3DQSAR, Molecular Docking, Molecular Dynamics Simulation and Free Energy Calculations. Curr Comput Aided Drug Des 2020; 16:17-30. [PMID: 31284868 PMCID: PMC6967214 DOI: 10.2174/1573409915666190708102459] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/16/2019] [Accepted: 06/09/2019] [Indexed: 01/11/2023]
Abstract
Background Glycogen synthase kinase-3 (GSK3) is associated with various key biological processes and has been considered as an important therapeutic target for the treatment of many diseases. Great efforts have been made on the development of GSK3 inhibitors, especially ATP-competitive GSK3β inhibitor, but it is still a great challenge to develop selective GSK3β inhibitors because of the high sequence homology with other kinases. Objective In order to reveal the selectivity mechanisms of GSK3β inhibition at the molecular level, a series of ATP-competitive GSK3β inhibitor was analyzed by a systematic computational method, combining 3D-QSAR, molecular docking, molecular dynamic simulations and free energy calculations. Methods Firstly, 3D-QSAR with CoMFA was built to explore the general structure activity relationships. Secondly, CDOCKER and Flexible docking were employed to predicted the reasonable docking poses of all studied inhibitors. And then, both GSK3β and CDK2 complexes were selected to conduct molecular dynamics simulations. Finally, the free energy calculations were employed to find the key selective-residues. Results CoMFA model suggested the steric, hydrophobic fields play key roles in the bioactivities of inhibitors, and the binding mechanisms were well analyzed through molecular docking. The binding free energies predicted are in good agreement with the experimental bioactivities and the free energy calculations showed that the binding of GSK3β/inhibitors was mainly contributed from hydrogen bonding and hydrophobic interaction. Conclusion Some key residues for selective binding were highlighted, which may afford important guidance for the rational design of novel ATP-competitive GSK3β inhibitors.
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Affiliation(s)
- Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuanqing Wu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, Jiangsu 214122, China
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18
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Chen J, Wang W, Sun H, Pang L, Yin B. Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics. J Comput Aided Mol Des 2020; 34:1289-1305. [DOI: 10.1007/s10822-020-00355-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022]
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19
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Wang J, Cao D, Tang C, Xu L, He Q, Yang B, Chen X, Sun H, Hou T. DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges. Brief Bioinform 2020; 22:6278692. [PMID: 34020543 DOI: 10.1093/bib/bbaa183] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/06/2020] [Accepted: 07/15/2020] [Indexed: 01/18/2023] Open
Abstract
Atomic charges play a very important role in drug-target recognition. However, computation of atomic charges with high-level quantum mechanics (QM) calculations is very time-consuming. A number of machine learning (ML)-based atomic charge prediction methods have been proposed to speed up the calculation of high-accuracy atomic charges in recent years. However, most of them used a set of predefined molecular properties, such as molecular fingerprints, for model construction, which is knowledge-dependent and may lead to biased predictions due to the representation preference of different molecular properties used for training. To solve the problem, we present a new architecture based on graph convolutional network (GCN) and develop a high-accuracy atomic charge prediction model named DeepAtomicCharge. The new GCN architecture is designed with only the atomic properties and the connection information between the atoms in molecules and can dynamically learn and convert molecules into appropriate atomic features without any prior knowledge of the molecules. Using the designed GCN architecture, substantial improvement is achieved for the prediction accuracy of atomic charges. The average root-mean-square error (RMSE) of DeepAtomicCharge is 0.0121 e, which is obviously more accurate than that (0.0180 e) reported by the previous benchmark study on the same two external test sets. Moreover, the new GCN architecture needs much lower storage space compared with other methods, and the predicted DDEC atomic charges can be efficiently used in large-scale structure-based drug design, thus opening a new avenue for high-performance atomic charge prediction and application.
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Affiliation(s)
- Jike Wang
- School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410004, Hunan, P. R. China
| | - Cunchen Tang
- School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China.,National Engineering Research Center for Multimedia Software, School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China.,Artificial Intelligence Institute, School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, Jiangsu, P. R. China
| | - Qiaojun He
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Bo Yang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Xi Chen
- School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China.,National Engineering Research Center for Multimedia Software, School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China.,Artificial Intelligence Institute, School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P.R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
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20
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Wang E, Liu H, Wang J, Weng G, Sun H, Wang Z, Kang Y, Hou T. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities. J Chem Inf Model 2020; 60:5353-5365. [DOI: 10.1021/acs.jcim.0c00024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Gaoqi Weng
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Yu Kang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
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21
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Design, synthesis and biological evaluation of 2-arylaminopyrimidine derivatives bearing 1,3,8-triazaspiro[4,5]decan-4-one or piperidine-3-carboxamide moiety as novel Type-I1/2 ALK inhibitors. Bioorg Chem 2020; 94:103456. [DOI: 10.1016/j.bioorg.2019.103456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/05/2019] [Accepted: 11/19/2019] [Indexed: 11/19/2022]
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22
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Wang RG, Zhang HX, Zheng QC. Revealing the binding and drug resistance mechanism of amprenavir, indinavir, ritonavir, and nelfinavir complexed with HIV-1 protease due to double mutations G48T/L89M by molecular dynamics simulations and free energy analyses. Phys Chem Chem Phys 2020; 22:4464-4480. [DOI: 10.1039/c9cp06657h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MD simulations, MM-PBSA, and SIE analyses were used to investigate the drug resistance mechanisms of two mutations G48T and L89M in HIV-1 protease toward four inhibitors.
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Affiliation(s)
- Rui-Ge Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
- P. R. China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Jilin University
- Changchun 130023
- P. R. China
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23
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Liu S, Jiang Y, Yan R, Li Z, Wan S, Zhang T, Wu X, Hou J, Zhu Z, Tian Y, Zhang J. Design, synthesis and biological evaluations of 2-amino-4-(1-piperidine) pyridine derivatives as novel anti crizotinib-resistant ALK/ROS1 dual inhibitors. Eur J Med Chem 2019; 179:358-375. [PMID: 31260890 DOI: 10.1016/j.ejmech.2019.06.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/29/2019] [Accepted: 06/15/2019] [Indexed: 12/11/2022]
Abstract
ALK and ROS1 kinases have become promising therapeutic targets since Crizotinib was used to treat non-small-cell lung cancer clinically. Aiming to explore new potent inhibitors, a series of 2-amino-4-(1-piperidine) pyridine derivatives that stabilized a novel DFG-shifted conformation in the kinase domain of ALK were designed and synthesized on the base of lead compound A. Biological evaluation highlighted that most of these new compounds could also potently inhibit ROS1 kinase, leading to the promising inhibitors against both ROS1 and ALK. Among them, the representative compound 2e stood out potent anti-proliferative activity against ALK-addicted H3122 and ROS1-addicted HCC78 cell lines (IC50 = 6.27 μM and 10.71 μM, respectively), which were comparable to that of Crizotinib. Moreover, 2e showed impressive enzyme activity against clinically Crizotinib-resistant ALKL1196M with an IC50 value of 41.3 nM, which was about 2-fold more potent than that of Crizotinib. 2e also showed potent inhibitory activity in about 6-fold superior to Crizotinib (IC50: 104.7 nM vs. 643.5 nM) in Ba/F3 cell line harboring ROS1G2032R. Furthermore, molecular modeling disclosed that all the representative inhibitors could dock into the active site of ALK and ROS1, which gave a probable explanation of anti Crizotinib-resistant mutants. These results indicated that our work has established a path forward for the generation of anti Crizotinib-resistant ALK/ROS1 dual inhibitors.
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Affiliation(s)
- Siming Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ying Jiang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ruohong Yan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhonghuang Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Tingting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Xiaoyun Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Ju Hou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Zhengguang Zhu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China
| | - Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, PR China.
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24
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Kong X, Pan P, Sun H, Xia H, Wang X, Li Y, Hou T. Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK). J Med Chem 2019; 62:10927-10954. [PMID: 31419130 DOI: 10.1021/acs.jmedchem.9b00446] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As a receptor tyrosine kinase of insulin receptor (IR) subfamily, anaplastic lymphoma kinase (ALK) has been validated to play important roles in various cancers, especially anaplastic large cell lymphoma (ALCL), nonsmall cell lung cancer (NSCLC), and neuroblastomas. Currently, five small-molecule inhibitors of ALK, including Crizotinib, Ceritinib, Alectinib, Brigatinib, and Lorlatinib, have been approved by the U.S. Food and Drug Administration (FDA) against ALK-positive NSCLCs. Novel type-I1/2 and type-II ALK inhibitors with improved kinase selectivity and enhanced capability to combat drug resistance have also been reported. Moreover, the "proteolysis targeting chimera" (PROTAC) technique has been successfully applied in developing ALK degraders, which opened a new avenue for targeted ALK therapies. This review provides an overview of the physiological and biological functions of ALK, the discovery and development of drugs targeting ALK by focusing on their chemotypes, activity, selectivity, and resistance as well as potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaotian Kong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China.,Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Peichen Pan
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Hongguang Xia
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital , Zhejiang University , Hangzhou 310058 , China
| | - Xuwen Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM) , Soochow University , Suzhou , Jiangsu 215123 , China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences , Zhejiang University , Hangzhou , Zhejiang 310058 , China
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25
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Molecular Modeling of ALK L1198F and/or G1202R Mutations to Determine Differential Crizotinib Sensitivity. Sci Rep 2019; 9:11390. [PMID: 31388026 PMCID: PMC6684801 DOI: 10.1038/s41598-019-46825-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/17/2019] [Indexed: 01/29/2023] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that has been recognized as a therapeutic target for EML4-ALK fusion-positive nonsmall cell lung cancer (NSCLC) treatment using type I kinase inhibitors such as crizotinib to take over the ATP binding site. According to Shaw’s measurements, ALK carrying G1202R mutation shows reduced response to crizotinib (IC50 = 382 nM vs. IC50 = 20 nM for wild-type), whereas L1198F mutant is more responsive (IC50 = 0.4 nM). Interestingly, the double mutant L1198F/G1202R maintains a similar response (IC50 = 31 nM) to the wild-type. Herein we conducted molecular modeling simulations to elucidate the varied crizotinib sensitivities in three mutants carrying L1198F and/or G1202R. Both L1198 and G1202 are near the ATP pocket. Mutation G1202R causes steric hindrance that blocks crizotinib accessibility, which greatly reduces efficacy, whereas mutation L1198F enlarges the binding pocket entrance and hydrophobically interacts with crizotinib to enhance sensitivity. With respect to the double mutant L1198F/G1202R, F1198 indirectly pulls R1202 away from the binding entrance and consequently alleviates the steric obstacle introduced by R1202. These results demonstrated how the mutated residues tune the crizotinib response and may assist kinase inhibitor development especially for ALK G1202R, analogous to the ROS1 G2302R and MET G1163R mutations that are also resistant to crizotinib treatment in NSCLC.
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Zhu J, Ke K, Xu L, Jin J. Theoretical studies on the selectivity mechanisms of PI3Kδ inhibition with marketed idelalisib and its derivatives by 3D-QSAR, molecular docking, and molecular dynamics simulation. J Mol Model 2019; 25:242. [DOI: 10.1007/s00894-019-4129-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/09/2019] [Indexed: 01/01/2023]
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Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Li K, Zhu J, Xu L, Jin J. Rational Design of Novel Phosphoinositide 3-Kinase Gamma (PI3Kγ) Selective Inhibitors: A Computational Investigation Integrating 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation. Chem Biodivers 2019; 16:e1900105. [PMID: 31111650 DOI: 10.1002/cbdv.201900105] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/20/2019] [Indexed: 11/08/2022]
Abstract
Phosphoinositide 3-kinase gamma (PI3Kγ) draws an increasing attention due to its link with deadly cancer, chronic inflammation and allergy. But the development of PI3Kγ selective inhibitors is still a challenging endeavor because of the high sequence homology with the other PI3K isoforms. In order to acquire valuable information about the interaction mechanism between potent inhibitors and PI3Kγ, a series of PI3Kγ isoform-selective inhibitors were analyzed by a systematic computational method, combining 3D-QSAR, molecular docking, molecular dynamic (MD) simulations, free energy calculations and decomposition. The general structure-activity relationships were revealed and some key residues relating to selectivity and high activity were highlighted. It provides precious guidance for rational virtual screening, modification and design of selective PI3Kγ inhibitors. Finally, ten novel inhibitors were optimized and P10 showed satisfactory predicted bioactivity, demonstrating the feasibility to develop potent PI3Kγ inhibitors through this computational modeling and optimization.
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Affiliation(s)
- Kan Li
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, P. R. China
| | - Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, P. R. China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, P. R. China
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Niu Y, Yao X, Ji H. Importance of protein flexibility in ranking ERK2 Type I 1/2 inhibitor affinities: a computational study. RSC Adv 2019; 9:12441-12454. [PMID: 35515820 PMCID: PMC9063686 DOI: 10.1039/c9ra01657k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022] Open
Abstract
Extracellular-regulated kinase (ERK2) has been regarded as an essential target for various cancers, especially melanoma. Recently, pyrrolidine piperidine derivatives were reported as Type I1/2 inhibitors of ERK2, which occupy both the ATP binding pocket and the allosteric pocket. Due to the dynamic behavior of ERK2 upon the binding of Type I1/2 inhibitors, it is difficult to predict the binding structures and relative binding potencies of these inhibitors with ERK2 accurately. In this work, the binding mechanism of pyrrolidine piperidines was discussed by using different simulation techniques, including molecular docking, ensemble docking based on multiple receptor conformation, molecular dynamics simulations and free energy calculations. Our computational results show that the traditional docking method cannot predict the relative binding ability of the studied inhibitors with high accuracy, but incorporating ERK2 protein flexibility into docking is an effective method to improve the prediction accuracy. It is worth noting that the binding free energies predicted by MM/GBSA or MM/PBSA based on the MD simulations for the docked poses have the highest correlation with the experimental data, which highlights the importance of protein flexibility for accurately predicting the binding ability of Type I1/2 inhibitors of ERK2. In addition, the comprehensive analysis of several representative inhibitors indicates that hydrogen bonds and hydrophobic interactions are of significance for improving the binding affinities of the inhibitors. We hope this work will provide valuable information for further design of novel and efficient Type I1/2 ERK2 inhibitors.
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Affiliation(s)
- Yuzhen Niu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, College of Life Sciences, Shandong University of Technology Zibo 255049 China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University Lanzhou 730000 China
| | - Hongfang Ji
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, College of Life Sciences, Shandong University of Technology Zibo 255049 China
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Shen C, Liu H, Wang X, Lei T, Wang E, Xu L, Yu H, Li D, Yao X. Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I 1/2 NIK Inhibitors. Front Pharmacol 2019; 10:345. [PMID: 31024312 PMCID: PMC6465739 DOI: 10.3389/fphar.2019.00345] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/20/2019] [Indexed: 12/15/2022] Open
Abstract
NF-κB inducing kinase (NIK), which is considered as the central component of the non-canonical NF-κB pathway, has been proved to be an important target for the regulation of the immune system. In the past few years, NIK inhibitors with various scaffolds have been successively reported, among which type I1/2 inhibitors that can not only bind in the ATP-binding pocket at the DFG-in state but also extend into an additional back pocket, make up the largest proportion of the NIK inhibitors, and are worthy of more attention. In this study, an integration protocol that combines molecule docking, MD simulations, ensemble docking, MM/GB(PB)SA binding free energy calculations, and decomposition was employed to understand the binding mechanism of 21 tricyclic type I1/2 NIK inhibitors. It is found that the docking accuracy is largely dependent on the selection of docking protocols as well as the crystal structures. The predictions given by the ensemble docking based on multiple receptor conformations (MRCs) and the MM/GB(PB)SA calculations based on MD simulations showed higher linear correlations with the experimental data than those given by conventional rigid receptor docking (RRD) methods (Glide, GOLD, and Autodock Vina), highlighting the importance of incorporating protein flexibility in predicting protein–ligand interactions. Further analysis based on MM/GBSA demonstrates that the hydrophobic interactions play the most essential role in the ligand binding to NIK, and the polar interactions also make an important contribution to the NIK-ligand recognition. A deeper comparison of several pairs of representative derivatives reveals that the hydrophobic interactions are vitally important in the structural optimization of analogs as well. Besides, the H-bond interactions with some key residues and the large desolvation effect in the back pocket devote to the affinity distinction. It is expected that our study could provide valuable insights into the design of novel and potent type I1/2 NIK inhibitors.
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Affiliation(s)
- Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuwen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Tailong Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lei Xu
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Huidong Yu
- Rongene Pharma Co., Ltd., Shenzhen, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
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Discovery of 3,6-diaryl-1H-pyrazolo[3,4-b]pyridines as potent anaplastic lymphoma kinase (ALK) inhibitors. Bioorg Med Chem Lett 2019; 29:912-916. [PMID: 30777610 DOI: 10.1016/j.bmcl.2019.01.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 11/22/2022]
Abstract
A new series of 3,6-diaryl-1H-pyrazolo[3,4-b]pyridine compounds have been discovered as potent anaplastic lymphoma kinase (ALK) inhibitors. The 4-hydroxyphenyl in the 6-position of 1H-pyrazolo[3,4-b]pyridine were crucial and a fluorine atom substitution could give promising inhibitory activity. The IC50 of compound 9v against ALK was up to 1.58 nM and a binding mechanism was proposed.
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32
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He MY, Li WK, Meiler J, Zheng QC, Zhang HX. Insight on mutation-induced resistance to anaplastic lymphoma kinase inhibitor ceritinib from molecular dynamics simulations. Biopolymers 2019; 110:e23257. [PMID: 30664251 DOI: 10.1002/bip.23257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 11/09/2022]
Abstract
Ceritinib, an advanced anaplastic lymphoma kinase (ALK) next-generation inhibitor, has been proved excellent antitumor activity in the treatment of ALK-associated cancers. However, the accumulation of acquired resistance mutations compromise the therapeutic efficacy of ceritinib. Despite abundant mutagenesis data, the structural determinants for reduced ceritinib binding in mutants remains elusive. Focusing on the G1123S and F1174C mutations, we applied molecular dynamics (MD) simulations to study possible reasons for drug resistance caused by these mutations. The MD simulations predict that the studied mutations allosterically impact the configurations of the ATP-binding pocket. An important hydrophobic cluster is identified that connects P-loop and the αC-helix, which has effects on stabilizing the conformation of ATP-binding pocket. It is suggested, in this study, that the G1123S and F1174C mutations can induce the conformational change of P-loop thereby causing the reduced ceritinib affinity and causing drug resistance.
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Affiliation(s)
- Mu-Yang He
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China
| | - Wei-Kang Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, People's Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China
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Zhu J, Li K, Xu L, Jin J. Insight into the selective mechanism of phosphoinositide 3-kinase γ with benzothiazole and thiazolopiperidine γ-specific inhibitors by in silico approaches. Chem Biol Drug Des 2019; 93:818-831. [PMID: 30582283 DOI: 10.1111/cbdd.13469] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/23/2018] [Accepted: 12/19/2018] [Indexed: 11/29/2022]
Abstract
The phosphoinositide 3-kinase γ (PI3Kγ) has been verified to be a potential drug target for the treatments of various human physical disorders. Although received lots of attention, the development of PI3Kγ-selective inhibitors is still a challenging subject because of its unique protein structural features. Aiming to uncover the interaction mechanism between the selective inhibitors and PI3Kγ, a series of benzothiazole and thiazolopiperidine PI3Kγ isoform-selective inhibitors were studied with an integrated in silico strategy by combining molecular docking, molecular dynamic simulations, binding free energy calculations, and decomposition analysis. Firstly, three molecular docking models, including rigid receptor docking, induced fit docking (IFD), and quantum mechanical-polarized ligand docking, were respectively, built, and the IFD preliminarily predicted the docking poses of all studied inhibitors and roughly analyzed the binding mechanism. Secondly, four binding complexes with representative inhibitors were selected to perform molecular dynamic simulations and free energy calculations. The predicted binding energies were consistent with the experimental bioactivities and different binding patterns between potent and weak inhibitors were uncovered. Finally, through the Molecular Mechanics/Generalized Born Surface Area binding free energy decomposition, residue-inhibitor interactions spectra were obtained and several key residues contributing to favorable binding were highlighted, which provides valuable information for rational PI3Kγ inhibitor design and modification.
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Affiliation(s)
- Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Kan Li
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, China
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Shen C, Wang Z, Yao X, Li Y, Lei T, Wang E, Xu L, Zhu F, Li D, Hou T. Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. Brief Bioinform 2018; 21:282-297. [PMID: 30379986 DOI: 10.1093/bib/bby103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/08/2018] [Accepted: 09/26/2018] [Indexed: 12/16/2022] Open
Abstract
Protein kinases have been regarded as important therapeutic targets for many diseases. Currently, a total of 41 kinase inhibitors have been approved by the Food and Drug Administration, along with a large number of kinase inhibitors being evaluated in clinical and preclinical trials. Among all, allosteric inhibitors, such as type II kinase inhibitors, have attracted extensive attention owing to their potential high selectivity. Nowadays, molecular docking has become a powerful tool to search for novel kinase inhibitors. However, as for type II kinase inhibitors, their allosteric characteristics may exert a deep influence on docking accuracy. In this study, a comprehensive assessment was conducted to evaluate the effectiveness of nine docking algorithms towards type II kinase inhibitors. The calculation results showed that most tested docking programs, especially Glide with XP scoring, LeDock and Surflex-Dock, succeeded in the accurate identification of near-native binding poses, with the success rates ranging from 0.80 to 0.90, and the scoring functions in GOLD and LeDock outperformed the others in the prediction of relative binding affinities. In terms of the P-values, areas under the curve and enrichment factors, Glide with XP scoring, Surflex-Dock, GOLD with Astex Statistical Potential scoring and LeDock had better screening power to discriminate between active compounds and decoys. However, the screening power is sensitive to different initial conformations of the same target. It is expected that our study can provide some guidance for docking-based virtual screening to discover novel type II kinase inhibitors, as well as other allosteric inhibitors.
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Affiliation(s)
- Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health,Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau (SAR), P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu, P. R. China
| | - Tailong Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, P. R. China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, P. R. China
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35
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Niu Y, Zhang Y, Yao X. Resistance mechanism of the oncogenic β3-αC deletion mutation in BRAF kinase to dabrafenib and vemurafenib revealed by molecular dynamics simulations and binding free energy calculations. Chem Biol Drug Des 2018; 93:177-187. [PMID: 30225883 DOI: 10.1111/cbdd.13399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/10/2018] [Accepted: 09/02/2018] [Indexed: 12/15/2022]
Abstract
BRAF kinase is an essential target for anti-cancer drug development. Emergence of the β3-αC loop deletion mutation (ΔNVTAP) in BRAF kinase frequently occurred in human cancers seriously compromises the therapeutic efficacy of some BRAF kinase inhibitors, such as dabrafenib and vemurafenib. However, the mechanism of this resistance is still not well understood. In this study, the influence of the β3-αC deletion mutation on the binding profiles of three BRAF kinase inhibitors (AZ628, dabrafenib, and vemurafenib) with BRAFV600E or BRAFΔNVTAP was explored by conventional molecular dynamics (MD) simulations and binding free energy calculations. The simulation results indicated that the β3-αC deletion mutation enhances the flexibility of the αC helix and alters their conformations, which amplify the conformational entropy change (-TΔS) and weaken the interactions between the inhibitors and BRAF. The further per-residue binding free energy decomposition analysis revealed that the ΔNVTAP mutation changed the contributions of a few key residues to the bindings of dabrafenib or vemurafenib, such as L57, L66, W83, C84, F135, G145, and F147, but did not have obvious impact on the contributions of these residues to AZ628. Our results provide valuable clues to understand the mechanisms of drug resistance conferred by the β3-αC deletion mutation.
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Affiliation(s)
- Yuzhen Niu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Yan Zhang
- Guiyang College of Traditional Chinese Medicine, Guiyang, China
| | - Xiaojun Yao
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou, China
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Tu J, Song LT, Liu RR, Zhai HL, Wang J, Zhang XY. Molecular inhibitory mechanism study on the potent inhibitor brigatinib against four crizotinib‐resistant ALK mutations. J Cell Biochem 2018; 120:562-574. [DOI: 10.1002/jcb.27412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/10/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Jing Tu
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Li Ting Song
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Rui Rui Liu
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Juan Wang
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
| | - Xiao Yun Zhang
- College of Chemistry & Chemical Engineering, Lanzhou University Lanzhou China
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He MY, Li WK, Zheng QC, Zhang HX. Conformational Transition of Key Structural Features Involved in Activation of ALK Induced by Two Neuroblastoma Mutations and ATP Binding: Insight from Accelerated Molecular Dynamics Simulations. ACS Chem Neurosci 2018; 9:1783-1792. [PMID: 29638111 DOI: 10.1021/acschemneuro.8b00105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Deregulated kinase activity of anaplastic lymphoma kinase (ALK) has been observed to be implicated in the development of tumor progression. The activation mechanism of ALK is proposed to be similar to other receptor tyrosine kinases (RTKs), but the distinct static X-ray crystal conformation of ALK suggests its unique conformational transition. Herein, we have illustrated the dynamic conformational property of wild-type ALK as well as the kinase activation equilibrium variation induced by two neuroblastoma mutations (R1275Q and Y1278S) and ATP binding by performing enhanced sampling accelerated Molecular Dynamics (aMD) simulations. The results suggest that the wild-type ALK is mostly favored in the inactive state, whereas the mutations and ATP binding promote a clear shift toward the active-like conformation. The R1275Q mutant stabilizes the active conformation by rigidifying the αC-in conformation. The Y1278S mutant promotes activation at the expense of a π-stacking hydrophobic cluster, which plays a critical role in the stabilization of the inactive conformation of native ALK. ATP produces a more compact active site and thereby facilitates the activation of ALK. Taken together, these findings not only elucidate the diverse conformations in different ALKs but can also shed light on new strategies for protein engineering and structural-based drug design for ALK.
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Affiliation(s)
- Mu-Yang He
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Wei-Kang Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Qing-Chuan Zheng
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, People’s Republic of China
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun 130023, People’s Republic of China
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38
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Xie X, Mao C, Liu X, Tan L, Cui Z, Yang X, Zhu S, Li Z, Yuan X, Zheng Y, Yeung KWK, Chu PK, Wu S. Tuning the Bandgap of Photo-Sensitive Polydopamine/Ag 3PO 4/Graphene Oxide Coating for Rapid, Noninvasive Disinfection of Implants. ACS CENTRAL SCIENCE 2018; 4:724-738. [PMID: 29974068 PMCID: PMC6026779 DOI: 10.1021/acscentsci.8b00177] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Indexed: 05/20/2023]
Abstract
Bacterial infection and associated complications are threats to human health especially when biofilms form on biomedical devices and artificial implants. Herein, a hybrid polydopamine (PDA)/Ag3PO4/graphene oxide (GO) coating is designed and constructed to achieve rapid bacteria killing and eliminate biofilms in situ. By varying the amount of GO in the hybrid coating, the bandgap can be tuned from 2.52 to 2.0 eV so that irradiation with 660 nm visible light produces bacteria-killing effects synergistically in concert with reactive oxygen species (ROS). GO regulates the release rate of Ag+ to minimize the cytotoxicity while maintaining high antimicrobial activity, and a smaller particle size enhances the yield of ROS. After irradiation with 660 nm visible light for 15 min, the antimicrobial rates of the PDA/Ag3PO4/GO hybrid coating against Escherichia coli and Staphylococcus aureus are 99.53% and 99.66%, respectively. In addition, this hybrid coating can maintain a repeatable and sustained antibacterial efficacy. The released Ag+ and photocatalytic Ag3PO4 produce synergistic antimicrobial effects in which the ROS increases the permeability of the bacterial membranes to increase the probability of Ag+ to enter the cells to kill them together with ROS synergistically.
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Affiliation(s)
- Xianzhou Xie
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
- Hubei
Collaborative Innovation Center for Advanced Organic Chemical Materials,
Ministry-of-Education Key Laboratory for the Green Preparation and
Application of Functional Materials, Hubei Key Laboratory of Polymer
Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Congyang Mao
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
- Hubei
Collaborative Innovation Center for Advanced Organic Chemical Materials,
Ministry-of-Education Key Laboratory for the Green Preparation and
Application of Functional Materials, Hubei Key Laboratory of Polymer
Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Xiangmei Liu
- Hubei
Collaborative Innovation Center for Advanced Organic Chemical Materials,
Ministry-of-Education Key Laboratory for the Green Preparation and
Application of Functional Materials, Hubei Key Laboratory of Polymer
Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Lei Tan
- Hubei
Collaborative Innovation Center for Advanced Organic Chemical Materials,
Ministry-of-Education Key Laboratory for the Green Preparation and
Application of Functional Materials, Hubei Key Laboratory of Polymer
Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Zhenduo Cui
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Xianjin Yang
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Shengli Zhu
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Zhaoyang Li
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Xubo Yuan
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Yufeng Zheng
- State
Key Laboratory for Turbulence and Complex System and Department of
Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Kelvin Wai Kwok Yeung
- Department
of Orthopaedics & Traumatology, Li KaShing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong 999077, China
| | - Paul K. Chu
- Department
of Physics and Department of Materials Science and Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Shuilin Wu
- School
of Materials Science & Engineering, Tianjin University, Tianjin 300072, China
- Hubei
Collaborative Innovation Center for Advanced Organic Chemical Materials,
Ministry-of-Education Key Laboratory for the Green Preparation and
Application of Functional Materials, Hubei Key Laboratory of Polymer
Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
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39
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Kong X, Sun H, Pan P, Zhu F, Chang S, Xu L, Li Y, Hou T. Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK. Phys Chem Chem Phys 2018; 20:4851-4863. [DOI: 10.1039/c7cp08241j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Anaplastic lymphoma kinase (ALK) has been regarded as a promising target for the therapy of various cancers.
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Affiliation(s)
- Xiaotian Kong
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
- Institute of Functional Nano and Soft Materials (FUNSOM)
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Feng Zhu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
- Institute of Functional Nano and Soft Materials (FUNSOM)
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