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Liu X, Zhang H, Cao J, Zhuo Y, Jin J, Gao Q, Yuan X, Yang L, Li D, Wang Y. Isobavachalcone Activates Antitumor Immunity on Orthotopic Pancreatic Cancer Model: A Screening and Validation. Front Pharmacol 2022; 13:919035. [PMID: 36091768 PMCID: PMC9452641 DOI: 10.3389/fphar.2022.919035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Pancreatic cancer is accompanied by poor prognosis and accounts for a significant number of deaths every year. Since Psoralea corylifolia L. (PCL) possesses a broad spectrum of bioactivities, it is commonly used in traditional Chinese medicine. The study explored potential antitumor agents of PCL and underlying mechanisms in vitro and vivo. Based on network pharmacology, bioinformatics, and molecular docking, we considered isobavachalcone (IBC) as a valuable compound. The activity and potential mechanisms of IBC were investigated by RT-qPCR, immunohistochemistry, immunofluorescence, and flow cytometry. It was confirmed that IBC could inhibit Panc 02 cell proliferation and induce apoptosis via increasing the production of reactive oxygen species. IBC could attenuate the weight of solid tumors, increase CD8+ T cells, and reduce M2 macrophages in the tumor tissue and spleen. Another promising finding was that IBC alleviated the proportion of myeloid-derived suppressor cells (MDSCs) in the tumor tissue but had no change in the spleen. The study of pharmacological effects of IBC was carried out and suggested IBC restrained M2-like polarization of RAW 264.7 cells by inhibiting the expression of ARG1 and MRC1 and suppressed the expression of ARG1 and TGF-β in bone marrow-derived MDSC. In summary, this research screened IBC as an antineoplastic agent, which could attenuate the growth of pancreatic cancer via activating the immune activity and inducing cell apoptosis. It might be a reference for the antitumor ability of IBC and the treatment of the tumor microenvironment in pancreatic cancer.
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Affiliation(s)
- Xuanming Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hongbo Zhang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin Nankai Hospital, Tianjin, China
| | - Jianlin Cao
- Department of Gynaecology and Obstetrics, Shanxi Provincial People’s Hospital, Shanxi, China
| | - Yuzhen Zhuo
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin Nankai Hospital, Tianjin, China
| | - Jiahui Jin
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qiaoying Gao
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin Nankai Hospital, Tianjin, China
| | - Xiangfei Yuan
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin Nankai Hospital, Tianjin, China
| | - Lei Yang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin Nankai Hospital, Tianjin, China
- *Correspondence: Lei Yang, @126.com; Dihua Li, ; Yan Wang,
| | - Dihua Li
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Tianjin Nankai Hospital, Tianjin, China
- *Correspondence: Lei Yang, @126.com; Dihua Li, ; Yan Wang,
| | - Yan Wang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin, China
- *Correspondence: Lei Yang, @126.com; Dihua Li, ; Yan Wang,
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2
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He D, Li X, Wang S, Wang C, Liu X, Zhang Y, Cui Y, Yu S. Mechanism of drug resistance of BVDV induced by F224S mutation in RdRp: A case study of VP32947. Comput Biol Chem 2022; 99:107715. [PMID: 35751995 DOI: 10.1016/j.compbiolchem.2022.107715] [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: 12/21/2021] [Revised: 06/04/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022]
Abstract
Bovine viral diarrhea virus (BVDV) is an enveloped virus with an RNA genome, causing serious economic losses to the areas dominated by livestock industry. Currently, although several compounds with biological activities of inhibiting virus replication have been reported, amino acid mutations (especially F224S mutation) frequently occurring in the RNA-dependent RNA polymerase (RdRp) have greatly reduce their value of further research. In this study, we introduced an effective and rapid in silico strategy to explore the differences in the binding modes of VP32947 between the wild/mutant-type RdRp at the molecular level, and further explained the main reasons for the variations in the inhibitory activities of VP32947 against the two types of enzymes. Firstly, the binding site of VP32947 in the finger domain was determined based on the previously reported experimental data, and the initial conformation of VP32947 in the wild RdRp was constructed using molecular docking. Then, the mutant research system was obtained directly by artificial mutation strategy. Afterwards, the built research systems were subjected to microsecond-timescale molecular dynamic simulation, and the conformational and energic profile analyses were performed according to the simulation trajectories. It was found that after 1 μs simulation, VP32947 in the mutant system was transferred to the left side of Loop α, and its interactions with the residues in the loop region were weakened. However, VP32947 in the wild system remained at the right side of Loop α, and could have a good fit with the sub-pocket formed by F224, I261, P262, N264, S532, which was conducive to maintaining its stable binding conformation in the wild RdRp. The illustration of the difference in the binding mechanisms of VP32947 in the wild/mutant RdRp would provide a theoretical basis for the rational design of innovative inhibitors based on the enzyme.
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Affiliation(s)
- Dian He
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Xuedong Li
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Songsong Wang
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Chengzhao Wang
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Xingang Liu
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Yang Zhang
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China.
| | - Yan Cui
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Sijiu Yu
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
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Zhang F, Chen X, Chen J, Xu Y, Li S, Guo Y, Pu X. Probing Allosteric Regulation Mechanism of W7.35 on Agonist-Induced Activity for μOR by Mutation Simulation. J Chem Inf Model 2021; 62:5120-5135. [PMID: 34779608 DOI: 10.1021/acs.jcim.1c00650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The residue located at 15 positions before the most conserved residue in TM7 (7.35 of Ballesteros-Weinstein number) plays important roles in ligand binding and the receptor activity for class A GPCRs. Nevertheless, its regulation mechanism has not been clearly clarified in experiments, and some controversies also exist for its impact on μ-opioid receptors (μOR) bound by agonists. Thus, we chose the μ-opioid receptor (μOR) of class A GPCRs as a representative and utilized a microsecond accelerated molecular dynamics simulation (aMD) coupled with a protein structure network (PSN) to explore the effect of W3187.35 on its functional activity induced by the agonist endomorphin2 mainly by a comparison of the wild system and its W7.35A mutant. When endomorphin2 binds to the wild-type μOR, TM6 in μOR moves outward to form an open intracellular conformation that is beneficial to accommodating the β-arrestin transducer, rather than the G-protein transducer due to the clash with the α5 helix of G-protein, thus acting as a β-arrestin biased agonist. However, the W318A mutation induces the intracellular part of μOR to form a closed state, which disfavors coupling with either G-protein or β-arrestin. The allosteric pathway analysis further reveals that the binding of endomorphin2 to the wild-type μOR transmits more activation signals to the β-arrestin binding site while the W318A mutation induces more structural signals to transmit to common binding residues of the G protein and β-arrestin. More interestingly, the residue at the 7.35 position regulates the shortest allosteric pathway in indirect ways by influencing the interactions between other ligand-binding residues and endomorphin2. W2936.48 and F2896.44 are important for regulating the different activities of μOR induced either by the agonist or by the mutation. Y3367.53, F3438.50, and D3408.47 play crucial roles in activating the β-arrestin biased signal induced by the agonist endomorphin2, while L1583.43 and V2866.41 devote important contributions to the change in the activity of endomorphin2 from the β-arrestin biased agonist to the antagonist upon the W318A mutation.
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Affiliation(s)
- Fuhui Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xin Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yanjiani Xu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shiqi Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, China
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Zhu J, Jiang Y, Jia L, Xu L, Cai Y, Chen Y, Zhu N, Li H, Jin J. A multi-conformational virtual screening approach based on machine learning targeting PI3Kγ. Mol Divers 2021; 25:1271-1282. [PMID: 34160714 DOI: 10.1007/s11030-021-10243-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022]
Abstract
Nowadays, more and more attention has been attracted to develop selective PI3Kγ inhibitors, but the unique structural features of PI3Kγ protein make it a very big challenge. In the present study, a virtual screening strategy based on machine learning with multiple PI3Kγ protein structures was developed to screen novel PI3Kγ inhibitors. First, six mainstream docking programs were chosen to evaluate their scoring power and screening power; CDOCKER and Glide show satisfactory reliability and accuracy against the PI3Kγ system. Next, virtual screening integrating multiple PI3Kγ protein structures was demonstrated to significantly improve the screening enrichment rate comparing to that with an individual protein structure. Last, a multi-conformational Naïve Bayesian Classification model with the optimal docking programs was constructed, and it performed a true capability in the screening of PI3Kγ inhibitors. Taken together, the current study could provide some guidance for the docking-based virtual screening to discover novel PI3Kγ inhibitors.
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Affiliation(s)
- Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Yingmin Jiang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Lei Jia
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Yanfei Cai
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Yun Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Nannan Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Huazhong Li
- School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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5
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Shao Q, Liu T, Wang W, Duan Q, Liu T, Xu L, Huang G, Chen Z. The Chinese herbal prescription JZ-1 induces autophagy to protect against herpes simplex Virus-2 in human vaginal epithelial cells by inhibiting the PI3K/Akt/mTOR pathway. JOURNAL OF ETHNOPHARMACOLOGY 2020; 254:112611. [PMID: 32088246 PMCID: PMC7126429 DOI: 10.1016/j.jep.2020.112611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 05/09/2023]
Abstract
ETHNOPHAMACOLOGICAL RELEVANCE The Chinese herbal prescription JieZe-1 (JZ-1) is based on the modification of Yihuang Tang, which was first described in Fu Qingzhu Nvke by the famous Qing Dynasty doctor Shan Fu as a treatment for leukorrheal diseases. As an in-hospital preparation, JZ-1 has been used in Tongji Hospital for many years to treat various infectious diseases of the lower female genital tract, including cervicitis, vaginitis, genital herpes and condyloma acuminatum. Our previous studies have shown that JZ-1 has curative effects on Candida albicans, Trichomonas vaginalis and Ureaplasma urealyticum infections. AIM OF THE STUDY Genital herpes is among the most common sexually transmitted diseases (STDs) worldwide and is mainly caused by herpes simplex virus type-2 (HSV-2). Current therapies can relieve symptoms in patients but do not cure or prevent the spread of the virus. This study was designed to investigate the effect of JZ-1 on HSV-2 infection and its mechanism, which is based on autophagy induction, to provide new ideas and a basis for the study of antiviral drugs. MATERIALS AND METHODS Evaluation of the antiviral activity of JZ-1 was conducted by MTT assay and western blotting. Then, Western blot and immunofluorescence analyses, observations through transmission electron microscopy and experiments with the recombinant lentivirus vector mRFP-GFP-LC3B were used to monitor autophagic flux in VK2/E6E7 cells. To explore the mechanism by which JZ-1 regulates autophagy, western blotting and real-time quantitative PCR (qRT-PCR) were used to determine the expression of phosphoinositide 3-kinase (PI3K)/Akt/mTOR pathway proteins and to detect changes in critical molecules in the pathway after the application of a PI3K inhibitor. Additionally, the mRNA expression levels of inflammatory cytokines, namely, IL-6, IFN-α, IFN-β and TNF-α, were measured with qRT-PCR. RESULTS HSV-2 infection inhibited autophagy in the VK2/E6E7 cells. Further study revealed that the activation of the PI3K/Akt/mTOR pathway induced by HSV-2 infection may result in the blocked autophagic flux and inhibited autophagosome and autolysosome formation. JZ-1 exhibited significant antiviral activity in the VK2/E6E7 cells, which showed increased cell vitality and reduced viral protein expression, namely, earliest virus-specific infected cell polypeptides 5 (ICP5) and glycoprotein D (gD). We found that JZ-1 treatment inhibited the upregulation of the PI3K/Akt/mTOR pathway proteins and promoted autophagy to combat HSV-2 infection, while PI3K inhibitor pretreatment prevented the enhanced autophagy induced by JZ-1. Moreover, JZ-1 attenuated the increase in inflammatory cytokines that had been induced HSV-2 infection. CONCLUSION Our results showed that JZ-1 protects against HSV-2 infection, and this beneficial effect may be mediated by inducing autophagy via inhibition of the PI3K/Akt/mTOR signaling axis.
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Affiliation(s)
- Qingqing Shao
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Tong Liu
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Wenjia Wang
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Qianni Duan
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Tianli Liu
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Lijun Xu
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Guangying Huang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zhuo Chen
- Institute of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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6
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Shen L, Yuan Y, Guo Y, Li M, Li C, Pu X. Probing the Druggablility on the Interface of the Protein-Protein Interaction and Its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer. Front Pharmacol 2019; 10:1310. [PMID: 31787895 PMCID: PMC6855241 DOI: 10.3389/fphar.2019.01310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/15/2019] [Indexed: 12/19/2022] Open
Abstract
Modulating protein–protein interactions (PPIs) with small drug-like molecules targeting it exhibits great promise in modern drug discovery. G protein-coupled receptors (GPCRs) are the largest family of targeted proteins and could form dimers in living biological cells through PPIs. However, compared to drug development of the orthosteric site, there has been lack of investigations on the druggability of the PPI interface for GPCRs and its functional implication on experiments. Thus, in order to address these issues, we constructed a novel computational strategy, which involved in molecular dynamics simulation, virtual screening and protein structure network (PSN), to study one representative GPCR homodimer (CXCR4). One druggable pocket was identified in the PPI interface and one small molecule targeting it was screened, which could strengthen PPI mainly through hydrophobic interaction between the benzene rings of the PPI molecule and TM4 of the receptor. The PSN results further reveals that the PPI molecule could increase the number of the allosteric regulation pathways between the druggable pocket of the dimer interface to the orthostatic site for the subunit A but only play minor role for the other subunit B, leading to the asymmetric change in the volume of the binding pockets for the two subunits (increase for the subunit A and minor change for the subunit B). Consequently, the screening performance of the subunit A to the antagonists is enhanced while the subunit B is unchanged nearly, implying that the PPI molecule may be beneficial to enhance the drug efficacies of the antagonists. In addition, one main regulation pathway with the highest frequency was identified for the subunit A, which consists of Trp1955.34–Tyr190ECL2–Val1965.35–Gln2005.39–Asp2626.58–Cys28N-term, revealing their importance in the allosteric regulation from the PPI molecule. The observations from the work could provide valuable information for the development of the PPI drug-like molecule for GPCRs.
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Affiliation(s)
- Liting Shen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, China
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Pedini F, De Luca G, Felicetti F, Puglisi R, Boe A, Arasi MB, Fratini F, Mattia G, Spada M, Caporali S, Biffoni M, Giuliani A, Carè A, Felli N. Joint action of miR-126 and MAPK/PI3K inhibitors against metastatic melanoma. Mol Oncol 2019; 13:1836-1854. [PMID: 31115969 PMCID: PMC6717748 DOI: 10.1002/1878-0261.12506] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/17/2019] [Accepted: 05/20/2019] [Indexed: 02/03/2023] Open
Abstract
Emerging data support the rationale of combined therapies in advanced melanoma. Specifically, the combined use of drugs with different mechanisms of action can reduce the probability of selecting resistant clones. To identify agents active against melanoma cells, we screened a library of 349 anti‐cancer compounds, currently in clinical use or trials, and selected PIK‐75, an inhibitor of the phosphatidylinositol 3‐kinase/protein kinase B (PI3K/AKT) pathway, as the ‘top active’ drug. PIK‐75 was then used alone or in combination with vemurafenib, the first BRAF inhibitor approved for patients with melanoma harboring BRAF mutations. We identified a combined dose of PIK‐75 and vemurafenib that inhibited both the PI3K/AKT and mitogen‐activated protein kinase pathways, thereby overcoming any compensatory activation. In view of the important tumor suppressor function induced by restoring expression of microRNA (miR)‐126 in metastatic melanoma cells, we examined whether miR‐126 has a synergistic role when included in a triple combination alongside PIK‐75 and vemurafenib. We found that enforced expression of miR‐126 (which alone can reduce tumorigenicity) significantly increased PIK‐75 activity when used as either a single agent or in combination with vemurafenib. Interestingly, PIK‐75 proved to be effective against early passage cell lines derived from patients’ biopsies and on melanoma cell lines resistant to either vemurafenib or dabrafenib, thus suggesting that it potentially has the capability to overcome drug resistance. Finally, the synergistic role played by miR‐126 in combination with vemurafenib and/or PIK‐75 was demonstrated in vivo in mouse xenograft models, in which tumor growth inhibition was associated with increased apoptosis. These results not only show the efficacy of PIK‐75 and vemurafenib co‐treatment but also indicate that restoration of miR‐126 expression in advanced melanoma can enhance their antitumor activity, which may possibly allow dose reduction to decrease adverse events without reducing the therapeutic benefits.
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Affiliation(s)
- Francesca Pedini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Gabriele De Luca
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Federica Felicetti
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Rossella Puglisi
- Center for Gender Medicine, Oncology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Boe
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Beatrice Arasi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Gianfranco Mattia
- Center for Gender Medicine, Oncology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Spada
- Center of Animal Research and Welfare, Istituto Superiore di Sanità, Rome, Italy
| | - Simona Caporali
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata-IRCCS, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Carè
- Center for Gender Medicine, Oncology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Nadia Felli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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Miller MS, Thompson PE, Gabelli SB. Structural Determinants of Isoform Selectivity in PI3K Inhibitors. Biomolecules 2019; 9:biom9030082. [PMID: 30813656 PMCID: PMC6468644 DOI: 10.3390/biom9030082] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) are important therapeutic targets for the treatment of cancer, thrombosis, and inflammatory and immune diseases. The four highly homologous Class I isoforms, PI3K, PI3K, PI3K and PI3K have unique, non-redundant physiological roles and as such, isoform selectivity has been a key consideration driving inhibitor design and development. In this review, we discuss the structural biology of PI3Ks and how our growing knowledge of structure has influenced the medicinal chemistry of PI3K inhibitors. We present an analysis of the available structure-selectivity-activity relationship data to highlight key insights into how the various regions of the PI3K binding site influence isoform selectivity. The picture that emerges is one that is far from simple and emphasizes the complex nature of protein-inhibitor binding, involving protein flexibility, energetics, water networks and interactions with non-conserved residues.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia.
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Departments of Medicine, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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9
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Tesch R, Becker C, Müller MP, Beck ME, Quambusch L, Getlik M, Lategahn J, Uhlenbrock N, Costa FN, Polêto MD, Pinheiro PDSM, Rodrigues DA, Sant'Anna CMR, Ferreira FF, Verli H, Fraga CAM, Rauh D. Eine ungewöhnliche intramolekulare Halogenbindung führt zu konformationeller Selektion. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Roberta Tesch
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Christian Becker
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Matthias Philipp Müller
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Michael Edmund Beck
- Bayer AG; division Crop Science; Alfred-Nobel-Straße 50 40789 Monheim am Rhein Deutschland
| | - Lena Quambusch
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Matthäus Getlik
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Jonas Lategahn
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Niklas Uhlenbrock
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | | | - Marcelo D. Polêto
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brasilien
| | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Daniel Alencar Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Carlos Mauricio R. Sant'Anna
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
- Departamento de Química; Instituto de Ciências Exatas Universidade Federal Rural do Rio de Janeiro; Seropédica Brasilien
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; São Paulo Brasilien
| | - Hugo Verli
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brasilien
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Daniel Rauh
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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10
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Tesch R, Becker C, Müller MP, Beck ME, Quambusch L, Getlik M, Lategahn J, Uhlenbrock N, Costa FN, Polêto MD, Pinheiro PDSM, Rodrigues DA, Sant'Anna CMR, Ferreira FF, Verli H, Fraga CAM, Rauh D. An Unusual Intramolecular Halogen Bond Guides Conformational Selection. Angew Chem Int Ed Engl 2018; 57:9970-9975. [DOI: 10.1002/anie.201804917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/01/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Roberta Tesch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Christian Becker
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Matthias Philipp Müller
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Michael Edmund Beck
- Bayer AG; division Crop Science; Alfred-Nobel-Strasse 50 40789 Monheim am Rhein Germany
| | - Lena Quambusch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Matthäus Getlik
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jonas Lategahn
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Niklas Uhlenbrock
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | | | - Marcelo D. Polêto
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brazil
| | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Daniel Alencar Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Carlos Mauricio R. Sant'Anna
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
- Departamento de Química; Instituto de Ciências Exatas Universidade Federal Rural do Rio de Janeiro; Seropédica Brazil
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; São Paulo Brazil
| | - Hugo Verli
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brazil
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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11
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Liang T, Yuan Y, Wang R, Guo Y, Li M, Pu X, Li C. Structural Features and Ligand Selectivity for 10 Intermediates in the Activation Process of β 2-Adrenergic Receptor. ACS OMEGA 2017; 2:8557-8567. [PMID: 30023586 PMCID: PMC6045391 DOI: 10.1021/acsomega.7b01031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/14/2017] [Indexed: 06/08/2023]
Abstract
It has already been suggested by researchers that there should be multiple intermediate states in the activation process for G-protein-coupled receptors (GPCRs). However, the intermediate states are very short-lived and hardly captured by the experiments, leading to very limited understanding of their structural features and drug efficacies. In this work, a novel joint strategy of targeted molecular dynamics simulation, conventional molecular dynamics simulation, and virtual screening is developed to address the problems. The results from 10 intermediate conformations obtained from the work reveal that the ligand pocket is very unstable and fluctuates between the inactive state and the active one in the case of ligand-free, in particular for ECL2 as a gate-keeper of the ligand-binding. The ligand-binding site could be stable in the active state with a small volume and a completely closed ECL2, only when the G-protein-binding region is fully activated. In addition, the activations of the ligand-binding pocket and G-protein-binding site are relatively independent and exhibit a loose allosteric coupling, which contributes to the existence of multiple intermediate conformations. Interestingly, the screening performance of the agonists does not increase on increasing the overall activity of the intermediate state, but is dependent on the activated extent of the ligand pocket. The receptor is prone to bind the agonist when closing ECL2 and reducing the ligand-binding pocket volume, whereas it is more favorable for binding the antagonist when opening ECL2 and increasing the pocket volume. These observations added to previous studies could help us better understand the activation mechanism of GPCRs and provide valuable information for drug design.
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Affiliation(s)
- Tao Liang
- College
of Chemistry and College of Computer Science, Sichuan University, No. 29 Jiuyanqiao Wangjiang Road, Chengdu 610064, People’s Republic
of China
| | - Yuan Yuan
- College
of Management, Southwest University for
Nationalities, No. 16 South Section 4, Yihuan Road, Chengdu 610041, People’s Republic
of China
| | - Ran Wang
- College
of Chemistry and College of Computer Science, Sichuan University, No. 29 Jiuyanqiao Wangjiang Road, Chengdu 610064, People’s Republic
of China
| | - Yanzhi Guo
- College
of Chemistry and College of Computer Science, Sichuan University, No. 29 Jiuyanqiao Wangjiang Road, Chengdu 610064, People’s Republic
of China
| | - Menglong Li
- College
of Chemistry and College of Computer Science, Sichuan University, No. 29 Jiuyanqiao Wangjiang Road, Chengdu 610064, People’s Republic
of China
| | - Xuemei Pu
- College
of Chemistry and College of Computer Science, Sichuan University, No. 29 Jiuyanqiao Wangjiang Road, Chengdu 610064, People’s Republic
of China
| | - Chuan Li
- College
of Chemistry and College of Computer Science, Sichuan University, No. 29 Jiuyanqiao Wangjiang Road, Chengdu 610064, People’s Republic
of China
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12
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Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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13
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Han J, Chen Y, Yang C, Liu T, Wang M, Xu H, Zhang L, Zheng C, Song Y, Zhu J. Structure-based optimization leads to the discovery of NSC765844, a highly potent, less toxic and orally efficacious dual PI3K/mTOR inhibitor. Eur J Med Chem 2016; 122:684-701. [DOI: 10.1016/j.ejmech.2016.06.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/01/2023]
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14
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Definition of the binding mode of phosphoinositide 3-kinase α-selective inhibitor A-66S through molecular dynamics simulation. J Mol Model 2014; 20:2166. [PMID: 24633771 DOI: 10.1007/s00894-014-2166-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/06/2014] [Indexed: 12/28/2022]
Abstract
Activation of the phosphatidylinositol 3-kinase α (PI3Kα) is commonly observed in human cancer and is critical for tumor progression, which has made PI3Kα an attractive target for anticancer drug discovery. To systematically investigate the binding mode of A-66S, a new selective PI3Kα inhibitor for PI3Kα, molecular docking, molecular dynamics simulation and ensuing energetic analysis were performed. The binding free energy between PI3Kα and A-66S is -11.27 kcal•mol⁻¹ using MMPBSA method, while -14.67 kcal•mol⁻¹ using MMGBSA method, which is beneficial for the binding, and the van der Waals/hydrophobic and electrostatic interactions are critical for the binding. The conserved hydrophobic adenine region of PI3Kα made up of Met772, Pro778, Ile800, Tyr836, Ile848, Val850, Val851, Met922, Phe930 and Ile932 accommodates the flat 2-tert-butyl-4'-methyl-4,5'-bithiazol moiety of A-66S, and the NH of Val851 forms a hydrogen with the nitrogen atom embedded in the aminothiazole ring of A-66S. The (S)-pyrrolidine carboxamide urea moiety especially extends toward the region of the binding site wall (Ser854-Gln859) defined by the C-terminal lobe, and has three hydrogen-bond arms with the backbone of Ser854 and the side chain of Gln859. Notably the interaction between the non-conserved residue Gln859 and A-66S is responsible for the selectivity profile of A-66S. The binding mode of A-66S for PI3Kα presented in this study should aid in the design of a new highly selective PI3Kα inhibitor.
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15
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Structure, function and inhibition of the phosphoinositide 3-kinase p110α enzyme. Biochem Soc Trans 2014; 42:120-4. [DOI: 10.1042/bst20130255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The PI3K (phosphoinositide 3-kinase) p110α isoform is activated by oncogenic mutations in many cancers. This has stimulated intense interest in identifying inhibitors of the PI3K pathway as well as p110α-selective inhibitors, and understanding the mechanisms underlying activation by the oncogenic mutations. In the present article, we review recent progress in the structure and function of the p110α enzyme and two of its most common oncogenic mutations, the development of isoform-selective inhibitors, and p110α pharmacology.
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16
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Zhu J, Pan P, Li Y, Wang M, Li D, Cao B, Mao X, Hou T. Theoretical studies on beta and delta isoform-specific binding mechanisms of phosphoinositide 3-kinase inhibitors. MOLECULAR BIOSYSTEMS 2013; 10:454-66. [PMID: 24336903 DOI: 10.1039/c3mb70314b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) is known to be closely related to tumorigenesis and cell proliferation, and controls a variety of cellular processes, including proliferation, growth, apoptosis, migration, metabolism, etc. The PI3K family comprises eight catalytic isoforms, which are subdivided into three classes. Recently, the discovery of inhibitors that block a single isoform of PI3K has continued to attract special attention because they may have higher selectivity for certain tumors and less toxicity for healthy cells. The PI3Kβ and PI3Kδ share fewer studies than α/γ, and therefore, in this work, the combination of molecular dynamics simulations and free energy calculations was employed to explore the binding of three isoform-specific PI3K inhibitors (COM8, IC87114, and GDC-0941) to PI3Kβ or PI3Kδ. The isoform specificities of the studied inhibitors derived from the predicted binding free energies are in good agreement with the experimental data. In addition, the key residues critical for PI3Kβ or PI3Kδ selectivity were highlighted by decomposing the binding free energies into the contributions from individual residues. It was observed that although PI3Kβ and PI3Kδ share the conserved ATP-binding pockets, individual residues do behave differently, particularly the residues critical for PI3Kβ or PI3Kδ selectivity. It can be concluded that the inhibitor specificity between PI3Kβ and PI3Kδ is determined by the additive contributions from multiple residues, not just a single one. This study provides valuable information for understanding the isoform-specific binding mechanisms of PI3K inhibitors, and should be useful for the rational design of novel and selective PI3K inhibitors.
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Affiliation(s)
- Jingyu Zhu
- Cyrus Tang Hematology Center, Soochow University, Suzhou, Jiangsu 215123, China.
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17
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Wang F, Chen Y. Pharmacophore models generation by catalyst and phase consensus-based virtual screening protocol against PI3Kα inhibitors. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.751592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Morales GA, Garlich JR, Su J, Peng X, Newblom J, Weber K, Durden DL. Synthesis and cancer stem cell-based activity of substituted 5-morpholino-7H-thieno[3,2-b]pyran-7-ones designed as next generation PI3K inhibitors. J Med Chem 2013; 56:1922-39. [PMID: 23410005 DOI: 10.1021/jm301522m] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Dysregulation of the phosphatidylinositol-3-kinase (PI3K) pathway in a wide range of tumors has made PI3K a consensus target to inhibit as illustrated by more than 15 inhibitors now in clinical trials. Our previous work, built on the early pioneering multikinase inhibitor LY294002, resulted in the only PI3K vascular-targeted PI3K inhibitor prodrug, SF1126, which has now completed Phase I clinical trials. This inhibitor has properties that impart more in vivo activity than should be warranted by its enzymatic potency, which in general is much lower than other clinical stage PI3K inhibitors. We embarked on the exploration of scaffolds that retained such properties while simultaneously exhibiting an increased potency toward PI3K. This work resulted in the discovery of the 5-morpholino-7H-thieno[3,2-b]pyran-7-one system as the foundation of a new compound class of potential PI3K inhibitors having improved potency toward PI3K. The synthesis and cancer stem cell-based activity of these compounds are reported herein.
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Affiliation(s)
- Guillermo A Morales
- BIO5 Institute (Oro Valley), The University of Arizona, 1580 East Hanley Boulevard, Oro Valley, Arizona 85737, United States.
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19
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Sabbah DA, Vennerstrom JL, Zhong HA. Binding Selectivity Studies of Phosphoinositide 3-Kinases Using Free Energy Calculations. J Chem Inf Model 2012; 52:3213-24. [DOI: 10.1021/ci3003057] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Dima A. Sabbah
- College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska
Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Jonathan L. Vennerstrom
- College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska
Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Haizhen A. Zhong
- DSC 362, Department of Chemistry, The University of Nebraska, 6001 Dodge Street, Omaha,
Nebraska 68182, United States
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20
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Discovery of pyrazolo[1,5-a]pyridines as p110α-selective PI3 kinase inhibitors. Bioorg Med Chem 2012; 20:69-85. [DOI: 10.1016/j.bmc.2011.11.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/09/2011] [Accepted: 11/16/2011] [Indexed: 11/20/2022]
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21
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Yang Y, Shen Y, Li S, Jin N, Liu H, Yao X. Molecular dynamics and free energy studies on Aurora kinase A and its mutant bound with MLN8054: insight into molecular mechanism of subtype selectivity. MOLECULAR BIOSYSTEMS 2012; 8:3049-60. [DOI: 10.1039/c2mb25217a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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22
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Wang J, Wang F, Xiao Z, Sheng G, Li Y, Wang Y. Molecular simulation of a series of benzothiazole PI3Kα inhibitors: probing the relationship between structural features, anti-tumor potency and selectivity. J Mol Model 2011; 18:2943-58. [PMID: 22139479 DOI: 10.1007/s00894-011-1299-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 11/02/2011] [Indexed: 11/25/2022]
Abstract
The phosphatidylinositol 3-kinase α (PI3Kα) was genetically validated as a promising therapeutic target for developing novel anticancer drugs. In order to explore the structure-activity correlation of benzothiazole series as inhibitors of PI3Kα, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) were performed on 61 promising molecules to build 3D-QSAR models based on both the ligand- and receptor-based methods. The best CoMFA and CoMSIA models had a cross-validated coefficient r(cv)(2) of 0.618 and 0.621, predicted correlation coefficient r(pred) (2) of 0.812 and 0.83, respectively, proving their high correlative and predictive abilities on both the training and test sets. In addition, docking analysis and molecular dynamics simulation (MD) were also applied to elucidate the probable binding modes of these inhibitors at the ATP binding pocket. Based on the contour maps and MD results, some key structural factors responsible for the activity of this series of compounds were revealed as follows: (1) Ring-A has a strong preference for bulky hydrophobic or aromatic groups; (2) Electron-withdrawing groups at the para position of ring-B and hydrophilic substituents in ring-B region may benefit the potency; (3) A polar substituent like -NHSO(2)- between ring-A and ring-B can enhance the activity of the drug by providing hydrogen bonding interaction with the protein target. The satisfactory results obtained from this work strongly suggest that the developed 3D-QSAR models and the obtained PI3Kα inhibitor binding structures are reasonable for the prediction of the activity of new inhibitors and be helpful in future PI3Kα inhibitor design.
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Affiliation(s)
- Jinan Wang
- Center of Bioinformatics, Northwest A & F University, Yangling, Shaanxi 712100, China
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23
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Li Y, Zhang J, He D, Liang Q, Wang Y. Characterization of molecular recognition of phosphoinositide-3-kinase α inhibitor through molecular dynamics simulation. J Mol Model 2011; 18:1907-16. [PMID: 21870199 DOI: 10.1007/s00894-011-1211-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 08/04/2011] [Indexed: 11/26/2022]
Abstract
Phosphatidylinositol 3-kinase α (PI3Kα) is a promising target for anticancer drug discovery due to its overactivation in tumor cells. To systematically investigate the interactions between PI3Kα and PIK75 which is the most selective PI3Kα inhibitor reported to date, molecular docking, molecular dynamics simulation, and ensuing energetic analysis were utilized. The binding free energy between PI3Kα and PIK75 is -10.04 kcal•mol(-1) using MMPBSA method, while -13.88 kcal•mol(-1) using MMGBSA method, which is beneficial for the binding. The van der Waals/hydrophobic and electrostatic interactions play critical roles for the binding. The binding mode of PIK75 for PI3Kα is predicted. The conserved hydrophobic adenine region of PI3Kα made up of Ile800, Ile848, Val850, Val851, Met922, Phe930, and Ile932 accommodates the flat 6-bromine imidazo[1,2-a]pyridine ring of PIK75. The 2-methyl-5-nitrophenyl group of PIK75 extends to the P-loop region, and has four hydrogen-bond arms with the backbone and side chain of Ser773 and Ser774. And the distinct conformation of the P-loop induced by PIK75 is speculated to be responsible for the selectivity profile of PIK75. The predicted binding mode of PIK75 for PI3Kα presented in this study may help design high affinity and selective compounds to target PI3Kα.
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Affiliation(s)
- Yiping Li
- Department of Pharmacy, College of Medicine, Xi'an Jiaotong University, Xi'an, Peoples Republic of China
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24
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Zheng Z, Amran SI, Thompson PE, Jennings IG. Isoform-selective inhibition of phosphoinositide 3-kinase: identification of a new region of nonconserved amino acids critical for p110α inhibition. Mol Pharmacol 2011; 80:657-64. [PMID: 21778304 DOI: 10.1124/mol.111.072546] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The combination of molecular modeling and X-ray crystallography has failed to yield a consensus model of the mechanism for selective binding of inhibitors to the phosphoinositide 3-kinase (PI3K) p110 α-isoform. Here we have used kinetic analysis to determine that the p110α-selective inhibitor 2-methyl-5-nitro-2-[(6-bromoimidazo[1,2-α]pyridin-3-yl)methylene]-1-methylhydrazide-benzenesulfonic acid (PIK-75) is a competitive inhibitor with respect to a substrate, phosphatidylinositol (PI) in contrast to most other PI3K inhibitors, which bind at or near the ATP site. Using sequence analysis and the existing crystal structures of inhibitor complexes with the p110γ and -δ isoforms, we have identified a new region of nonconserved amino acids (region 2) that was postulated to be involved in PIK-75 p110α selectivity. Analysis of region 2, using in vitro mutation of identified nonconserved amino acids to alanine, showed that Ser773 was a critical amino acid involved in PIK-75 binding, with an 8-fold-increase in the IC(50) compared with wild-type. Kinetic analysis showed that, with respect to PI, the PIK-75 K(i) for the isoform mutant S773D increased 64-fold compared with wild-type enzyme. In addition, a nonconserved amino acid, His855, from the previously identified region 1 of nonconserved amino acids, was found to be involved in PIK-75 binding. These results show that these two regions of nonconserved amino acids that are close to the substrate binding site could be targeted to produce p110α isoform-selective inhibitors.
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Affiliation(s)
- Zhaohua Zheng
- Medicinal Chemistry & Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus),Victoria, Australia
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25
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Sabbah DA, Vennerstrom JL, Zhong H. Docking studies on isoform-specific inhibition of phosphoinositide-3-kinases. J Chem Inf Model 2011; 50:1887-98. [PMID: 20866085 DOI: 10.1021/ci1002679] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphatidylinositol 3-kinase α (PI3Kα) is a promising target for anticancer drug design. Oncogenic mutation H1047R in the catalytic domain is observed in many tumors and may enhance PI3Kα kinase activity by affecting loop confirmations as well as membrane binding. We applied docking methods to 33 PI3K inhibitors against the wild type (wt) PI3Kα, the H1047R mutant of PI3Kα and the γ isoform of PI3K (PI3Kγ). We also investigated the effect of protein flexibility on ligand binding by docking the same set of ligands to conformations of the wt and mutant PI3Kα generated by molecular dynamics simulations. Our data suggests that conformational differences in Gln859, Ser854, Tyr836, and Ser774 between the PI3Kα wt and H1047R mutant may be used to design ligands that are active against both the wt and H1047R mutant isoforms. Gln859, Ser854 and Ser774 may play critical roles in ligand binding to the α isoform H1047R mutant while formation of H-bonds with Ser806 of PI3Kγ may enhance γ-isoform-specific inhibition. In addition to H-bond interactions, structural and size differences in the activation and hydrophobic domains of PI3Kα, PI3Kγ, and the PI3Kα H1047R mutant could be exploited to direct the design of isoform- and/or mutant-specific PI3K inhibitors. Our data provide a reasonable explanation for the activity and selectivity of small molecular PI3K inhibitors and are in good agreement with available experimental and computational data.
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Affiliation(s)
- Dima A Sabbah
- College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA
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26
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Pinson JA, Schmidt-Kittler O, Zhu J, Jennings IG, Kinzler KW, Vogelstein B, Chalmers DK, Thompson PE. Thiazolidinedione-based PI3Kα inhibitors: an analysis of biochemical and virtual screening methods. ChemMedChem 2011; 6:514-22. [PMID: 21360822 PMCID: PMC3187668 DOI: 10.1002/cmdc.201000467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/29/2010] [Indexed: 12/27/2022]
Abstract
A series of synthesized and commercially available compounds were assessed against PI3Kα for in vitro inhibitory activity and the results compared to binding calculated in silico. Using published crystal structures of PI3Kγ and PI3Kδ co-crystallized with inhibitors as a template, docking was able to identify the majority of potent inhibitors from a decoy set of 1000 compounds. On the other hand, PI3Kα in the apo-form, modeled by induced fit docking, or built as a homology model gave only poor results. A PI3Kα homology model derived from a ligand-bound PI3Kδ crystal structure was developed that has a good ability to identify active compounds. The docking results identified binding poses for active compounds that differ from those identified to date and can contribute to our understanding of structure-activity relationships for PI3K inhibitors.
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Affiliation(s)
- Jo-Anne Pinson
- Medicinal Chemistry & Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
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