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Wu Y, Zhang L, Sun Z, Qiu X, Chen Y, Su K, Yang L, Du Z, Dong Y, Yang F, Li X, Zhang X. Preferred Conformation-Guided Discovery of Potent and Orally Active HIF Prolyl Hydroxylase 2 Inhibitors for the Treatment of Anemia. J Med Chem 2023. [PMID: 37367818 DOI: 10.1021/acs.jmedchem.3c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
In this work, we discovered a novel series of prolyl hydroxylase 2 (PHD2) inhibitors with improved metabolic properties based on a preferred conformation-guided drug design strategy. Piperidinyl-containing linkers with preferred metabolic stability were designed to match the dihedral angle of the desired docking conformation in the PHD2 binding site with the lowest energy conformation. Based on the piperidinyl-containing linkers, a series of PHD2 inhibitors with high PHD2 affinity and favorable druggability were obtained. Remarkably, compound 22, with an IC50 of 22.53 nM toward PHD2, significantly stabilized hypoxia-inducible factor α (HIF-α) and upregulated the expression of erythropoietin (EPO). Furthermore, oral administration of 22 dose-dependently stimulated erythropoiesis in vivo. Preliminary preclinical studies showed that 22 has good pharmacokinetic properties and an excellent safety profile, even at 10 times the efficacious dose (200 mg/kg). Taken together, these results indicate that 22 is a promising candidate for anemia treatment.
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Affiliation(s)
- Yue Wu
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Linjian Zhang
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Zhuoli Sun
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Xusheng Qiu
- Department of Orthopedics, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yafen Chen
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Kaijun Su
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Le Yang
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Zhongqiu Du
- Department of Orthopedics, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Ying Dong
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Fulai Yang
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Xiang Li
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines, and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
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2
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Lobo V, Rocha A, Castro TG, Carvalho MA. Synthesis of Novel 2,9-Disubstituted-6-morpholino Purine Derivatives Assisted by Virtual Screening and Modelling of Class I PI3K Isoforms. Polymers (Basel) 2023; 15:polym15071703. [PMID: 37050317 PMCID: PMC10096987 DOI: 10.3390/polym15071703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The phosphatidylinositol-3 kinase (PI3K) pathway is one of the most frequently activated pathogenic signalling cascades in a wide variety of cancers. In the last 15 years, there has been an increase in the search for selective inhibitors of the four class I isoforms of PI3K, as they demonstrate better specificity and reduced toxicity in comparison to existing inhibitors. A ligand-based and target-based rational drug design strategy was employed to build a virtual library of 105 new compounds. Through this strategy, the four isoforms were compared regarding their activity pocket availability, amino acid sequences, and prone interactions. Additionally, a known active scaffold was used as a molecular base to design new derivatives. The virtual screening of the resultant library toward the four isoforms points to the obtention of 19 selective inhibitors for the PI3Kα and PI3Kγ targets. Three selective ligands, one for α-isoform and two for γ-isoform, present a ∆ (∆Gbinding) equal or greater than 1.5 Kcal/mol and were identified as the most promising candidates. A principal component analysis was used to establish correlations between the affinity data and some of the physicochemical and structural properties of the ligands. The binding modes and interactions established by the selective ligands in the active centre of the α and γ isoforms of PI3K were also investigated. After modelling studies, a synthetic approach to generate selective ligands was developed and applied in synthesising a set of derivatives that were obtained in good to excellent yield.
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3
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Al-Mustafa A, Al-Zereini W, Ashram M, Al-Sha’er MA. Evaluation of antibacterial, antioxidant, cytotoxic, and acetylcholinesterase inhibition activities of novel [1,4] benzoxazepines fused to heterocyclic systems with a molecular modeling study. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02999-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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4
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Rai BK, Sresht V, Yang Q, Unwalla R, Tu M, Mathiowetz AM, Bakken GA. TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics. J Chem Inf Model 2022; 62:785-800. [PMID: 35119861 DOI: 10.1021/acs.jcim.1c01346] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast and accurate assessment of small-molecule dihedral energetics is crucial for molecular design and optimization in medicinal chemistry. Yet, accurate prediction of torsion energy profiles remains challenging as the current molecular mechanics (MM) methods are limited by insufficient coverage of drug-like chemical space and accurate quantum mechanical (QM) methods are too expensive. To address this limitation, we introduce TorsionNet, a deep neural network (DNN) model specifically developed to predict small-molecule torsion energy profiles with QM-level accuracy. We applied active learning to identify nearly 50k fragments (with elements H, C, N, O, F, S, and Cl) that maximized the coverage of our corporate compound library and leveraged massively parallel cloud computing resources for density functional theory (DFT) torsion scans of these fragments, generating a training data set of 1.2 million DFT energies. After training TorsionNet on this data set, we obtain a model that can rapidly predict the torsion energy profile of typical drug-like fragments with DFT-level accuracy. Importantly, our method also provides an uncertainty estimate for the predicted profiles without any additional calculations. In this report, we show that TorsionNet can accurately identify the preferred dihedral geometries observed in crystal structures. Our TorsionNet-based analysis of a diverse set of protein-ligand complexes with measured binding affinity shows a strong association between high ligand strain and low potency. We also present practical applications of TorsionNet that demonstrate how consideration of DNN-based strain energy leads to substantial improvement in existing lead discovery and design workflows. TorsionNet500, a benchmark data set comprising 500 chemically diverse fragments with DFT torsion profiles (12k MM- and DFT-optimized geometries and energies), has been created and is made publicly available.
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Affiliation(s)
- Brajesh K Rai
- Simulation and Modeling Sciences, Pfizer Worldwide Research Development and Medical, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Vishnu Sresht
- Simulation and Modeling Sciences, Pfizer Worldwide Research Development and Medical, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Qingyi Yang
- Medicine Design, Pfizer Worldwide Research Development and Medical, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Ray Unwalla
- Medicine Design, Pfizer Worldwide Research Development and Medical, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Meihua Tu
- Medicine Design, Pfizer Worldwide Research Development and Medical, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Alan M Mathiowetz
- Medicine Design, Pfizer Worldwide Research Development and Medical, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Gregory A Bakken
- Digital, Pfizer, Eastern Point Road, Groton, Connecticut 06340, United States
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5
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Ouvry G. Recent applications of seven-membered rings in drug design. Bioorg Med Chem 2022; 57:116650. [PMID: 35123178 DOI: 10.1016/j.bmc.2022.116650] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/28/2023]
Abstract
This short review aims at highlighting recent design strategies hinged on using seven-membered rings. Analyses of the different selected examples coupled with torsion profiles derived from the CCDC suggest some of these strategies could have broad applications.
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Affiliation(s)
- Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
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6
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Mata G, Miles DH, Drew SL, Fournier J, Lawson KV, Mailyan AK, Sharif EU, Yan X, Beatty JW, Banuelos J, Chen J, Ginn E, Chen A, Gerrick KY, Pham AT, Wong K, Soni D, Dhanota P, Shaqfeh SG, Meleza C, Narasappa N, Singh H, Zhao X, Jin L, Schindler U, Walters MJ, Young SW, Walker NP, Leleti MR, Powers JP, Jeffrey JL. Design, Synthesis, and Structure-Activity Relationship Optimization of Pyrazolopyrimidine Amide Inhibitors of Phosphoinositide 3-Kinase γ (PI3Kγ). J Med Chem 2021; 65:1418-1444. [PMID: 34672584 DOI: 10.1021/acs.jmedchem.1c01153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphoinositide-3-kinase γ (PI3Kγ) is highly expressed in immune cells and promotes the production and migration of inflammatory mediators. The inhibition of PI3Kγ has been shown to repolarize the tumor immune microenvironment to a more inflammatory phenotype, thereby controlling immune suppression in cancer. Herein, we report the structure-based optimization of an early lead series of pyrazolopyrimidine isoindolinones, which culminated in the discovery of highly potent and isoform-selective PI3Kγ inhibitors with favorable drug-like properties. X-ray cocrystal structure analysis, molecular docking studies, and detailed structure-activity relationship investigations resulted in the identification of the optimal amide and isoindolinone substituents to achieve a desirable combination of potency, selectivity, and metabolic stability. Preliminary in vitro studies indicate that inhibition of PI3Kγ with compound 56 results in a significant immune response by increasing pro-inflammatory cytokine gene expression in M1 macrophages.
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Affiliation(s)
- Guillaume Mata
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Dillon H Miles
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Samuel L Drew
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jeremy Fournier
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Kenneth V Lawson
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Artur K Mailyan
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Ehesan U Sharif
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Xuelei Yan
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Joel W Beatty
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jesus Banuelos
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jie Chen
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Elaine Ginn
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Ada Chen
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Kimberline Y Gerrick
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Amber T Pham
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Kent Wong
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Divyank Soni
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Puja Dhanota
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Stefan G Shaqfeh
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Cesar Meleza
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Nell Narasappa
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Hema Singh
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Xiaoning Zhao
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Lixia Jin
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Ulrike Schindler
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Matthew J Walters
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Stephen W Young
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Nigel P Walker
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Manmohan Reddy Leleti
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jay P Powers
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
| | - Jenna L Jeffrey
- Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States
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7
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Che J, Dai X, Gao J, Sheng H, Zhan W, Lu Y, Li D, Gao Z, Jin Z, Chen B, Luo P, Yang B, Hu Y, He Q, Weng Q, Dong X. Discovery of N-((3 S,4 S)-4-(3,4-Difluorophenyl)piperidin-3-yl)-2-fluoro-4-(1-methyl-1 H-pyrazol-5-yl)benzamide (Hu7691), a Potent and Selective Akt Inhibitor That Enables Decrease of Cutaneous Toxicity. J Med Chem 2021; 64:12163-12180. [PMID: 34375113 DOI: 10.1021/acs.jmedchem.1c00815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rash is one of the primary dose-limiting toxicities of Akt (protein kinase B) inhibitors in clinical trials. Here, we demonstrate the inhibition of Akt2 isozyme may be a driver for keratinocyte apoptosis, which promotes us to search for new selective Akt inhibitors with an improved cutaneous safety property. According to our previous research, compound 2 is selected for further optimization for overcoming the disadvantages of compound 1, including high Akt2 inhibition and high toxicity against HaCaT keratinocytes. The dihedral angle-based design and molecular dynamics simulation lead to the identification of Hu7691 (B5) that achieves a 24-fold selectivity between Akt1 and Akt2. Hu7691 exhibits low activity in inducing HaCaT apoptosis, promising kinase selectivity, and excellent anticancer cell proliferation potencies. Based on the superior results of safety property, pharmacokinetic profile, and in vivo efficacy, the National Medical Products Administration (NMPA) approved the investigational new drug (IND) application of Hu7691.
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Affiliation(s)
- Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Xiaoyang Dai
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Jian Gao
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Haichao Sheng
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Wenhu Zhan
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yang Lu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Dan Li
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Zizheng Gao
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Zegao Jin
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Binhui Chen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Peihua Luo
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Bo Yang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yongzhou Hu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Qiaojun He
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou 310058, P. R. China
| | - Qinjie Weng
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, P. R. China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou 310058, P. R. China
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8
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Structural Insights into the Interactions of Digoxin and Na +/K +-ATPase and Other Targets for the Inhibition of Cancer Cell Proliferation. Molecules 2021; 26:molecules26123672. [PMID: 34208576 PMCID: PMC8234910 DOI: 10.3390/molecules26123672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Digoxin is a cardiac glycoside long used to treat congestive heart failure and found recently to show antitumor potential. The hydroxy groups connected at the C-12, C-14, and C-3′a positions; the C-17 unsaturated lactone unit; the conformation of the steroid core; and the C-3 saccharide moiety have been demonstrated as being important for digoxin’s cytotoxicity and interactions with Na+/K+-ATPase. The docking profiles for digoxin and several derivatives and Na+/K+-ATPase were investigated; an additional small Asn130 side pocket was revealed, which could be useful in the design of novel digoxin-like antitumor agents. In addition, the docking scores for digoxin and its derivatives were found to correlate with their cytotoxicity, indicating a potential use of these values in the prediction of the cancer cell cytotoxicity of other cardiac glycosides. Moreover, in these docking studies, digoxin was found to bind to FIH-1 and NF-κB but not HDAC, IAP, and PI3K, suggesting that this cardiac glycoside directly targets FIH-1, Na+/K+-ATPase, and NF-κB to mediate its antitumor potential. Differentially, digoxigenin, the aglycon of digoxin, binds to HDAC and PI3K, but not FIH-1, IAP, Na+/K+-ATPase, and NF-κB, indicating that this compound may target tumor autophagy and metabolism to mediate its antitumor propensity.
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9
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Rathinaswamy MK, Gaieb Z, Fleming KD, Borsari C, Harris NJ, Moeller BE, Wymann MP, Amaro RE, Burke JE. Disease-related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors. eLife 2021; 10:e64691. [PMID: 33661099 PMCID: PMC7955810 DOI: 10.7554/elife.64691] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Class I Phosphoinositide 3-kinases (PI3Ks) are master regulators of cellular functions, with the class IB PI3K catalytic subunit (p110γ) playing key roles in immune signalling. p110γ is a key factor in inflammatory diseases and has been identified as a therapeutic target for cancers due to its immunomodulatory role. Using a combined biochemical/biophysical approach, we have revealed insight into regulation of kinase activity, specifically defining how immunodeficiency and oncogenic mutations of R1021 in the C-terminus can inactivate or activate enzyme activity. Screening of inhibitors using HDX-MS revealed that activation loop-binding inhibitors induce allosteric conformational changes that mimic those in the R1021C mutant. Structural analysis of advanced PI3K inhibitors in clinical development revealed novel binding pockets that can be exploited for further therapeutic development. Overall, this work provides unique insights into regulatory mechanisms that control PI3Kγ kinase activity and shows a framework for the design of PI3K isoform and mutant selective inhibitors.
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Affiliation(s)
- Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of VictoriaVictoriaCanada
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California San DiegoSan DiegoUnited States
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of VictoriaVictoriaCanada
| | - Chiara Borsari
- University of Basel, Department of BiomedicineBaselSwitzerland
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of VictoriaVictoriaCanada
| | - Brandon E Moeller
- Department of Biochemistry and Microbiology, University of VictoriaVictoriaCanada
| | | | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San DiegoSan DiegoUnited States
| | - John E Burke
- Department of Biochemistry and Microbiology, University of VictoriaVictoriaCanada
- Department of Biochemistry and Molecular Biology, The University of British ColumbiaVancouverCanada
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10
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Research advances on selective phosphatidylinositol 3 kinase δ (PI3Kδ) inhibitors. Bioorg Med Chem Lett 2020; 30:127457. [PMID: 32755681 DOI: 10.1016/j.bmcl.2020.127457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022]
Abstract
PI3Kδ in B cells mediates antigen receptor signaling and promote neutrophil chemotaxis. The activation of PI3Kδ can cause mast cell maturation and degranulation, myeloid cell dysfunction, and cytokine release. As a key signal molecule, PI3Kδ interacts with the lipid binding domain of a variety of cellular proteins as a secondary messenger, ultimately affecting a series of significant cellular pathways in disease pathology. Therefore, many research organizations and pharmaceutical companies have studied it to develop effectively selective PI3Kδ inhibitors as therapeutics. This review summarizes research advances in varying chemical classes of selective PI3Kδ inhibitors and the structure-activity relationship, and it mainly focuses on the propeller- versus flat-type class of inhibitors.
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11
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Doiron JE, Le CA, Bacsa J, Breton GW, Martin KL, Aller SG, Turlington M. Structural Consequences of the 1,2,3‐Triazole as an Amide Bioisostere in Analogues of the Cystic Fibrosis Drugs VX‐809 and VX‐770. ChemMedChem 2020; 15:1720-1730. [DOI: 10.1002/cmdc.202000220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/07/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Jake E. Doiron
- Department of Chemistry and Biochemistry Berry College Mount Berry GA 30149 USA
| | - Christina A. Le
- Department of Pharmacology and Toxicology University of Alabama at Birmingham Birmingham AL 35205 USA
| | - John Bacsa
- X-ray Crystallography Center Emory University Atlanta GA 30322 USA
| | - Gary W. Breton
- Department of Chemistry and Biochemistry Berry College Mount Berry GA 30149 USA
| | - Kenneth L. Martin
- Department of Chemistry and Biochemistry Berry College Mount Berry GA 30149 USA
| | - Stephen G. Aller
- Department of Pharmacology and Toxicology University of Alabama at Birmingham Birmingham AL 35205 USA
| | - Mark Turlington
- Department of Chemistry and Biochemistry Berry College Mount Berry GA 30149 USA
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12
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Rai BK, Sresht V, Yang Q, Unwalla R, Tu M, Mathiowetz AM, Bakken GA. Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein–Ligand Complexes using ab Initio Calculations. J Chem Inf Model 2019; 59:4195-4208. [DOI: 10.1021/acs.jcim.9b00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | | | | | | | | | | | - Gregory A. Bakken
- Simulation and Modeling Sciences, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
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13
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Jarvis A, Ouvry G. Essential ingredients for rational drug design. Bioorg Med Chem Lett 2019; 29:126674. [PMID: 31521476 DOI: 10.1016/j.bmcl.2019.126674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 01/09/2023]
Abstract
This short review focuses on three aspects of rational drug design that we consider of utmost importance: the conformation of small molecules in solid form, the conformation of small molecules in solution and lesser studied interactions in protein-ligand complexes. Using examples from recent literature, we will illustrate these different aspects and how they have contributed to the discovery of potent modulators.
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Affiliation(s)
- Ashley Jarvis
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom.
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14
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Cole JC, Wiggin S, Stanzione F. New insights and innovation from a million crystal structures in the Cambridge Structural Database. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:054301. [PMID: 31489338 PMCID: PMC6713555 DOI: 10.1063/1.5116878] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/13/2019] [Indexed: 05/23/2023]
Abstract
The Cambridge Structural Database (CSD) is the world's largest and most comprehensive collection of organic, organometallic, and metal-organic crystal structure information. Analyses using the data have wide impact across the chemical sciences in allowing understanding of structural preferences. In this short review, we illustrate the more common methods by which CSD data influence molecular design. We show how more data could lead to more refined insights into the future using a simple example of trifluoromethylphenyl fragments, highlighting how with sufficient data one can build a reasonable model of geometric change in a chemical fragment with torsional rotation, and show some recent examples where the CSD has been used in conjunction with other methods to provide design ideas and more computationally tractable workflows for derivation of useful insights into structural design.
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Affiliation(s)
- Jason C Cole
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Seth Wiggin
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Francesca Stanzione
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
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15
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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16
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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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17
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Perry MWD, Abdulai R, Mogemark M, Petersen J, Thomas MJ, Valastro B, Westin Eriksson A. Evolution of PI3Kγ and δ Inhibitors for Inflammatory and Autoimmune Diseases. J Med Chem 2018; 62:4783-4814. [DOI: 10.1021/acs.jmedchem.8b01298] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Raolat Abdulai
- Respiratory, Inflammation & Autoimmunity Translational Medicine Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Boston, Massachusetts 02451, United States
- Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
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18
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Garces AE, Stocks MJ. Class 1 PI3K Clinical Candidates and Recent Inhibitor Design Strategies: A Medicinal Chemistry Perspective. J Med Chem 2018; 62:4815-4850. [DOI: 10.1021/acs.jmedchem.8b01492] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Aimie E. Garces
- Centre for Biomolecular Sciences, University Park Nottingham, Nottingham NG7 2RD, U.K
| | - Michael J. Stocks
- Centre for Biomolecular Sciences, University Park Nottingham, Nottingham NG7 2RD, U.K
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19
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Dalziel ME, Deichert JA, Carrera DE, Beaudry D, Han C, Zhang H, Angelaud R. Magnesium Ethoxide Promoted Conversion of Nitriles to Amidines and Its Application in 5,6-Dihydroimidazobenzoxazepine Synthesis. Org Lett 2018; 20:2624-2627. [DOI: 10.1021/acs.orglett.8b00824] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael E. Dalziel
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Julie A. Deichert
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Diane E. Carrera
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Danial Beaudry
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Chong Han
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Haiming Zhang
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Remy Angelaud
- Department of Small Molecule Process Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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20
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Bakulina O, Chizhova M, Dar'in D, Krasavin M. A General Way to Construct Arene-Fused Seven-Membered Nitrogen Heterocycles. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701642] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Olga Bakulina
- Saint Petersburg State University; 199034 Saint Petersburg Russian Federation
| | - Maria Chizhova
- Saint Petersburg State University; 199034 Saint Petersburg Russian Federation
| | - Dmitry Dar'in
- Saint Petersburg State University; 199034 Saint Petersburg Russian Federation
| | - Mikhail Krasavin
- Saint Petersburg State University; 199034 Saint Petersburg Russian Federation
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