1
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Zhu J, Meng H, Li X, Jia L, Xu L, Cai Y, Chen Y, Jin J, Yu L. Optimization of virtual screening against phosphoinositide 3-kinase delta: Integration of common feature pharmacophore and multicomplex-based molecular docking. Comput Biol Chem 2024; 109:108011. [PMID: 38198965 DOI: 10.1016/j.compbiolchem.2023.108011] [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: 11/23/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
Extensive research has accumulated which suggests that phosphatidylinositol 3-kinase delta (PI3Kδ) is closely related to the occurrence and development of various human diseases, making PI3Kδ a highly promising drug target. However, PI3Kδ exhibits high homology with other members of the PI3K family, which poses significant challenges to the development of PI3Kδ inhibitors. Therefore, in the present study, a hybrid virtual screening (VS) approach based on a ligand-based pharmacophore model and multicomplex-based molecular docking was developed to find novel PI3Kδ inhibitors. 13 crystal structures of the human PI3Kδ-inhibitor complex were collected to establish models. The inhibitors were extracted from the crystal structures to generate the common feature pharmacophore. The crystallographic protein structures were used to construct a naïve Bayesian classification model that integrates molecular docking based on multiple PI3Kδ conformations. Subsequently, three VS protocols involving sequential or parallel molecular docking and pharmacophore approaches were employed. External predictions demonstrated that the protocol combining molecular docking and pharmacophore resulted in a significant improvement in the enrichment of active PI3Kδ inhibitors. Finally, the optimal VS method was utilized for virtual screening against a large chemical database, and some potential hit compounds were identified. We hope that the developed VS strategy will provide valuable guidance for the discovery of novel PI3Kδ inhibitors.
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Affiliation(s)
- Jingyu Zhu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Huiqin Meng
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xintong Li
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lei Jia
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Yanfei Cai
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yun Chen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Jin
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Li Yu
- School of Inspection and Testing Certification, Changzhou Vocational Institute of Engineering, Changzhou, Jiangsu 213164, China.
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2
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Mazzucato R, Roberti M, Capelli AM, Rancati F, Biagetti M, Fiorelli C, Bruno P, Ronchi P, Bertolini S, Corsi M, Pala D. Application of an "inhalation by design" approach to the identification and in-vitro evaluation of novel purine based PI3Kδ inhibitors. Eur J Med Chem 2023; 254:115331. [PMID: 37094451 DOI: 10.1016/j.ejmech.2023.115331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/26/2023]
Abstract
PI3Kδ is a lipid kinase which plays a key role in airway inflammatory conditions. Accordingly, the inhibition of PI3Kδ can be considered a valuable strategy for the treatment of chronic respiratory diseases such as Asthma and Chronic obstructive pulmonary disease (COPD). In this work, we describe our efforts to identify new PI3Kδ inhibitors following an "inhalation by design" strategy. Starting from the identification of a purine scaffold, we carried out a preliminary SAR expansion which led to the identification of a new hit characterized by a high enzymatic potency and moderate PI3Kδ selectivity. A subsequent optimization led to novel purine based derivatives with favorable in vitro ADME profiles, which might represent promising starting points for future development of new inhaled drug candidates.
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Affiliation(s)
- Roberta Mazzucato
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy.
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Anna Maria Capelli
- Corporate Drug Development, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Fabio Rancati
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Matteo Biagetti
- Pipeline Innovation Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Claudio Fiorelli
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Paolo Bruno
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Paolo Ronchi
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Serena Bertolini
- Experimental Pharmacology and Translational Science, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy
| | - Mauro Corsi
- In Vitro Biology Department, Aptuit, an Evotec Company, Via A. Fleming 4, 37135, Verona, Italy
| | - Daniele Pala
- Chemistry Research and Drug Design Department, Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche, Largo Belloli 11/a, 43122, Parma, Italy.
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3
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Liu L, Li X, Bu W, Jin N, Meng Y, Wang Y, Wang D, Xu X, Zhou D, Sun H. Carbon dots enhance extracellular matrix secretion for dentin-pulp complex regeneration through PI3K/Akt/mTOR pathway-mediated activation of autophagy. Mater Today Bio 2022; 16:100344. [PMID: 35833197 PMCID: PMC9272035 DOI: 10.1016/j.mtbio.2022.100344] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 12/11/2022] Open
Abstract
Pulp injury is one of the most common clinical diseases, and severe cases are usually associated with the functional loss of the tooth, while the current clinical treatment modality is only a cavity filling procedure without the regeneration of the dentin-pulp complex, thus leading to a devitalized and brittle tooth. In this study, carbon dots (CDots) with excellent biocompatibility are prepared from ascorbic acid and polyethyleneimine via a hydrothermal method. The as-prepared CDots can enhance extracellular matrix (ECM) secretion of human dental pulp stem cells (DPSCs), giving rise to increased cell adhesion on ECM and a stronger osteogenic/odontogenic differentiation capacity of DPSCs. Further, the mechanism underlying CDots-enhanced ECM secretion is revealed by the transcriptome analysis, Western blot assay and molecular dynamics simulation, identifying that the pharmacological activities of CDots are originated from a reasonable activation of the autophagy, which is mediated by regulating phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin signaling pathway. Based on the abundant CDots-induced ECM and thereby the reinforcement of the cell-ECM adhesion, an intact dental pulp stem cell sheet can be achieved, which in return promote in vivo the efficient regeneration of dentin-pulp complex as well as blood vessels.
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Affiliation(s)
- Lili Liu
- Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Jilin University, Changchun, 130021, PR China
| | - Xianjing Li
- Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Jilin University, Changchun, 130021, PR China
| | - Wenhuan Bu
- School and Hospital of Stomatology, China Medical University, Shenyang, 110122, PR China
| | - Nianqiang Jin
- School and Hospital of Stomatology, China Medical University, Shenyang, 110122, PR China
| | - Yuan Meng
- School and Hospital of Stomatology, China Medical University, Shenyang, 110122, PR China
| | - Yi Wang
- Graduate Program in Applied Physics, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Duan Wang
- Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Jilin University, Changchun, 130021, PR China
| | - Xiaowei Xu
- Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
- Corresponding author. Hospital of Stomatology, Jilin University, Changchun, 130021, PR China.
| | - Ding Zhou
- Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
- Corresponding author.
| | - Hongchen Sun
- Hospital of Stomatology, Jilin University, Changchun, 130021, PR China
- Corresponding author.
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4
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Chen X, Huang Y, Xu W, Cai Y, Yang Y. 4-Aminopyrazolopyrimidine scaffold and its deformation in the design of tyrosine and serine/threonine kinase inhibitors in medicinal chemistry. RSC Med Chem 2022; 13:1008-1028. [DOI: 10.1039/d2md00139j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/08/2022] [Indexed: 11/21/2022] Open
Abstract
Deformation of the 4-aminopyrazolopyrimidine scaffold in designing small-molecule inhibitors.
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Affiliation(s)
- Xiaolu Chen
- Department of Pharmacy, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Yajiao Huang
- Department of Pharmacy, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Wanghan Xu
- Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou 311202, Zhejiang, P. R. China
| | - Yuepiao Cai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yuanrong Yang
- Department of Pharmacy, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
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5
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Li T, Stayrook SE, Tsutsui Y, Zhang J, Wang Y, Li H, Proffitt A, Krimmer SG, Ahmed M, Belliveau O, Walker IX, Mudumbi KC, Suzuki Y, Lax I, Alvarado D, Lemmon MA, Schlessinger J, Klein DE. Structural basis for ligand reception by anaplastic lymphoma kinase. Nature 2021; 600:148-152. [PMID: 34819665 PMCID: PMC8639777 DOI: 10.1038/s41586-021-04141-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/14/2021] [Indexed: 11/09/2022]
Abstract
The proto-oncogene ALK encodes anaplastic lymphoma kinase, a receptor tyrosine kinase that is expressed primarily in the developing nervous system. After development, ALK activity is associated with learning and memory1 and controls energy expenditure, and inhibition of ALK can prevent diet-induced obesity2. Aberrant ALK signalling causes numerous cancers3. In particular, full-length ALK is an important driver in paediatric neuroblastoma4,5, in which it is either mutated6 or activated by ligand7. Here we report crystal structures of the extracellular glycine-rich domain (GRD) of ALK, which regulates receptor activity by binding to activating peptides8,9. Fusing the ALK GRD to its ligand enabled us to capture a dimeric receptor complex that reveals how ALK responds to its regulatory ligands. We show that repetitive glycines in the GRD form rigid helices that separate the major ligand-binding site from a distal polyglycine extension loop (PXL) that mediates ALK dimerization. The PXL of one receptor acts as a sensor for the complex by interacting with a ligand-bound second receptor. ALK activation can be abolished through PXL mutation or with PXL-targeting antibodies. Together, these results explain how ALK uses its atypical architecture for its regulation, and suggest new therapeutic opportunities for ALK-expressing cancers such as paediatric neuroblastoma.
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Affiliation(s)
- Tongqing Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Steven E Stayrook
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Yuko Tsutsui
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Jianan Zhang
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Yueyue Wang
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Hengyi Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | | | - Stefan G Krimmer
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Mansoor Ahmed
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Olivia Belliveau
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Ian X Walker
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Krishna C Mudumbi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Yoshihisa Suzuki
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Irit Lax
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | | | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Daryl E Klein
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
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6
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Singh S, Utreja D, Kumar V. Pyrrolo[2,1-f][1,2,4]triazine: a promising fused heterocycle to target kinases in cancer therapy. Med Chem Res 2021; 31:1-25. [PMID: 34803342 PMCID: PMC8590428 DOI: 10.1007/s00044-021-02819-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022]
Abstract
Cancer is the second leading cause of death worldwide responsible for about 10 million deaths per year. To date several approaches have been developed to treat this deadly disease including surgery, chemotherapy, radiation therapy, hormonal therapy, targeted therapy, and synthetic lethality. The targeted therapy refers to targeting only specific proteins or enzymes that are dysregulated in cancer rather than killing all rapidly dividing cells, has gained much attention in the recent past. Kinase inhibition is one of the most successful approaches in targeted therapy. As of 30 March 2021, FDA has approved 65 small molecule protein kinase inhibitors and most of them are for cancer therapy. Interestingly, several kinase inhibitors contain one or more fused heterocycles as part of their structures. Pyrrolo[2,1-f][1,2,4]triazine is one the most interesting fused heterocycle that is an integral part of several kinase inhibitors and nucleoside drugs viz. avapritinib and remdesivir. This review articles focus on the recent advances made in the development of kinase inhibitors containing pyrrolo[2,1-f][1,2,4]triazine scaffold. ![]()
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Affiliation(s)
- Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198 USA
| | - Divya Utreja
- Department of Chemistry, Punjab Agricultural University, Ludhiana, 141004 Punjab India
| | - Vimal Kumar
- Department of Chemistry, Dr B. R. Ambedkar National Institute of Technology (NIT), Jalandhar, 144011 Punjab India
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7
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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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8
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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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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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10
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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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11
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Hoegenauer K, Soldermann N, Zécri F, Strang RS, Graveleau N, Wolf RM, Cooke NG, Smith AB, Hollingworth GJ, Blanz J, Gutmann S, Rummel G, Littlewood-Evans A, Burkhart C. Discovery of CDZ173 (Leniolisib), Representing a Structurally Novel Class of PI3K Delta-Selective Inhibitors. ACS Med Chem Lett 2017; 8:975-980. [PMID: 28947947 DOI: 10.1021/acsmedchemlett.7b00293] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022] Open
Abstract
The predominant expression of phosphoinositide 3-kinase δ (PI3Kδ) in leukocytes and its critical role in B and T cell functions led to the hypothesis that selective inhibitors of this isoform would have potential as therapeutics for the treatment of allergic and inflammatory disease. Targeting specifically PI3Kδ should avoid potential side effects associated with the ubiquitously expressed PI3Kα and β isoforms. We disclose how morphing the heterocyclic core of previously discovered 4,6-diaryl quinazolines to a significantly less lipophilic 5,6,7,8-tetrahydropyrido[4,3-d]pyrimidine, followed by replacement of one of the phenyl groups with a pyrrolidine-3-amine, led to a compound series with an optimal on-target profile and good ADME properties. A final lipophilicity adjustment led to the discovery of CDZ173 (leniolisib), a potent PI3Kδ selective inhibitor with suitable properties and efficacy for clinical development as an anti-inflammatory therapeutic. In vitro, CDZ173 inhibits a large spectrum of immune cell functions, as demonstrated in B and T cells, neutrophils, monocytes, basophils, plasmocytoid dendritic cells, and mast cells. In vivo, CDZ173 inhibits B cell activation in rats and monkeys in a concentration- and time-dependent manner. After prophylactic or therapeutic dosing, CDZ173 potently inhibited antigen-specific antibody production and reduced disease symptoms in a rat collagen-induced arthritis model. Structurally, CDZ173 differs significantly from the first generation of PI3Kδ and PI3Kγδ-selective clinical compounds. Therefore, CDZ173 could differentiate by a more favorable safety profile. CDZ173 is currently in clinical studies in patients suffering from primary Sjögren's syndrome and in APDS/PASLI, a disease caused by gain-of-function mutations of PI3Kδ.
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Affiliation(s)
- Klemens Hoegenauer
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Nicolas Soldermann
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Frédéric Zécri
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Ross S. Strang
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Nadege Graveleau
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Romain M. Wolf
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Nigel G. Cooke
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Alexander B. Smith
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Gregory J. Hollingworth
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Joachim Blanz
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Sascha Gutmann
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Gabriele Rummel
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Amanda Littlewood-Evans
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Christoph Burkhart
- Global
Discovery Chemistry, ‡PK Sciences, §Chemical Biology and Therapeutics, and ∥Autoimmunity,
Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
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12
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Marcoux D, Qin LY, Ruan Z, Shi Q, Ruan Q, Weigelt C, Qiu H, Schieven G, Hynes J, Bhide R, Poss M, Tino J. Identification of highly potent and selective PI3Kδ inhibitors. Bioorg Med Chem Lett 2017; 27:2849-2853. [DOI: 10.1016/j.bmcl.2017.01.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 01/22/2023]
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Liu Q, Shi Q, Marcoux D, Batt DG, Cornelius L, Qin LY, Ruan Z, Neels J, Beaudoin-Bertrand M, Srivastava AS, Li L, Cherney RJ, Gong H, Watterson SH, Weigelt C, Gillooly KM, McIntyre KW, Xie JH, Obermeier MT, Fura A, Sleczka B, Stefanski K, Fancher RM, Padmanabhan S, Rp T, Kundu I, Rajareddy K, Smith R, Hennan JK, Xing D, Fan J, Levesque PC, Ruan Q, Pitt S, Zhang R, Pedicord D, Pan J, Yarde M, Lu H, Lippy J, Goldstine C, Skala S, Rampulla RA, Mathur A, Gupta A, Arunachalam PN, Sack JS, Muckelbauer JK, Cvijic ME, Salter-Cid LM, Bhide RS, Poss MA, Hynes J, Carter PH, Macor JE, Ruepp S, Schieven GL, Tino JA. Identification of a Potent, Selective, and Efficacious Phosphatidylinositol 3-Kinase δ (PI3Kδ) Inhibitor for the Treatment of Immunological Disorders. J Med Chem 2017; 60:5193-5208. [PMID: 28541707 DOI: 10.1021/acs.jmedchem.7b00618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PI3Kδ plays an important role controlling immune cell function and has therefore been identified as a potential target for the treatment of immunological disorders. This article highlights our work toward the identification of a potent, selective, and efficacious PI3Kδ inhibitor. Through careful SAR, the successful replacement of a polar pyrazole group by a simple chloro or trifluoromethyl group led to improved Caco-2 permeability, reduced Caco-2 efflux, reduced hERG PC activity, and increased selectivity profile while maintaining potency in the CD69 hWB assay. The optimization of the aryl substitution then identified a 4'-CN group that improved the human/rodent correlation in microsomal metabolic stability. Our lead molecule is very potent in PK/PD assays and highly efficacious in a mouse collagen-induced arthritis model.
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Affiliation(s)
- Qingjie Liu
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Qing Shi
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - David Marcoux
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Douglas G Batt
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Lyndon Cornelius
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Lan-Ying Qin
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Zheming Ruan
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - James Neels
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Myra Beaudoin-Bertrand
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Anurag S Srivastava
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Ling Li
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Robert J Cherney
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Hua Gong
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Scott H Watterson
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Carolyn Weigelt
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Kathleen M Gillooly
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Kim W McIntyre
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jenny H Xie
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Mary T Obermeier
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Aberra Fura
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Bogdan Sleczka
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Kevin Stefanski
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - R M Fancher
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Shweta Padmanabhan
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb Research Centre , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bengaluru 560099, India
| | - Thatipamula Rp
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb Research Centre , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bengaluru 560099, India
| | - Ipsit Kundu
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb Research Centre , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bengaluru 560099, India
| | | | - Rodney Smith
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - James K Hennan
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Dezhi Xing
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jingsong Fan
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Paul C Levesque
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Qian Ruan
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Sidney Pitt
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Rosemary Zhang
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Donna Pedicord
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jie Pan
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Melissa Yarde
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Hao Lu
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jonathan Lippy
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Christine Goldstine
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Stacey Skala
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Richard A Rampulla
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Arvind Mathur
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Anuradha Gupta
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb Research Centre , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bengaluru 560099, India
| | - Pirama Nayagam Arunachalam
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb Research Centre , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bengaluru 560099, India
| | - John S Sack
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jodi K Muckelbauer
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Mary Ellen Cvijic
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Luisa M Salter-Cid
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Rajeev S Bhide
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb Research Centre , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bengaluru 560099, India
| | - Michael A Poss
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - John Hynes
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Percy H Carter
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | | | - Stefan Ruepp
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Gary L Schieven
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Joseph A Tino
- Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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