1
|
Zheng X, Ji N, Campbell V, Slavin A, Zhu X, Chen D, Rong H, Enerson B, Mayo M, Sharma K, Browne CM, Klaus CR, Li H, Massa G, McDonald AA, Shi Y, Sintchak M, Skouras S, Walther DM, Yuan K, Zhang Y, Kelleher J, Liu G, Luo X, Mainolfi N, Weiss MM. Discovery of KT-474─a Potent, Selective, and Orally Bioavailable IRAK4 Degrader for the Treatment of Autoimmune Diseases. J Med Chem 2024. [PMID: 39151120 DOI: 10.1021/acs.jmedchem.4c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
Interleukin-1 receptor associated kinase 4 (IRAK4) is an essential mediator of the IL-1R and TLR signaling pathways, both of which have been implicated in multiple autoimmune conditions. Hence, blocking the activity of IRAK4 represents an attractive approach for the treatment of autoimmune diseases. The activity of this serine/threonine kinase is dependent on its kinase and scaffolding activities; thus, degradation represents a potentially superior approach to inhibition. Herein, we detail the exploration of structure-activity relationships that ultimately led to the identification of KT-474, a potent, selective, and orally bioavailable heterobifunctional IRAK4 degrader. This represents the first heterobifunctional degrader evaluated in a nononcology indication and dosed to healthy human volunteers. This molecule successfully completed phase I studies in healthy adult volunteers and patients with atopic dermatitis or hidradenitis suppurativa. Phase II clinical trials in both of these indications have been initiated.
Collapse
Affiliation(s)
- Xiaozhang Zheng
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Nan Ji
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Veronica Campbell
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Anthony Slavin
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Xiao Zhu
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Dapeng Chen
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Haojing Rong
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Brad Enerson
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Michele Mayo
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Kirti Sharma
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Chris M Browne
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Christine R Klaus
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Haoran Li
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Ginny Massa
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Alice A McDonald
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Yatao Shi
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Mike Sintchak
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Stephanie Skouras
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Dirk M Walther
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Karen Yuan
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Yi Zhang
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Joe Kelleher
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Guang Liu
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Xinbo Luo
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Nello Mainolfi
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| | - Matthew M Weiss
- Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States
| |
Collapse
|
2
|
Zhao Y, Wan Q, He X. Construction of IRAK4 inhibitor activity prediction model based on machine learning. Mol Divers 2024:10.1007/s11030-024-10926-5. [PMID: 38970641 DOI: 10.1007/s11030-024-10926-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
Interleukin-1 receptor-associated kinase 4 (IRAK4) is a crucial serine/threonine protein kinase that belongs to the IRAK family and plays a pivotal role in Toll-like receptor (TLR) and Interleukin-1 receptor (IL-1R) signaling pathways. Due to IRAK4's significant role in immunity, inflammation, and malignancies, it has become an intriguing target for discovering and developing potent small-molecule inhibitors. Consequently, there is a pressing need for rapid and accurate prediction of IRAK4 inhibitor activity. Leveraging a comprehensive dataset encompassing activity data for 1628 IRAK4 inhibitors, we constructed a prediction model using the LightGBM algorithm and molecular fingerprints. This model achieved an R2 of 0.829, an MAE of 0.317, and an RMSE of 0.460 in independent testing. To further validate the model's generalization ability, we tested it on 90 IRAK4 inhibitors collected in 2023. Subsequently, we applied the model to predict the activity of 13,268 compounds with docking scores less than - 9.503 kcal/mol. These compounds were initially screened from a pool of 1.6 million molecules in the chemdiv database through high-throughput molecular docking. Among these, 259 compounds with predicted pIC50 values greater than or equal to 8.00 were identified. We then performed ADMET predictions on these selected compounds. Finally, through a rigorous screening process, we identified 34 compounds that adhere to the four complementary drug-likeness rules, making them promising candidates for further investigation. Additionally, molecular dynamics simulations confirmed the stable binding of the screened compounds to the IRAK4 protein. Overall, this work presents a machine learning model for accurate prediction of IRAK4 inhibitor activity and offers new insights for subsequent structure-guided design of novel IRAK4 inhibitors.
Collapse
Affiliation(s)
- Yihuan Zhao
- Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi, 563006, People's Republic of China.
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China.
- The Key Laboratory of Clinical Pharmacy of Zunyi City, Zunyi Medical University, Zunyi, 563006, China.
| | - Qianwen Wan
- Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi, 563006, People's Republic of China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China
- The Key Laboratory of Clinical Pharmacy of Zunyi City, Zunyi Medical University, Zunyi, 563006, China
| | - Xiaoyu He
- Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi, 563006, People's Republic of China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China
- The Key Laboratory of Clinical Pharmacy of Zunyi City, Zunyi Medical University, Zunyi, 563006, China
| |
Collapse
|
3
|
Chen L, Luo R, Ma L, Xu Y, Cao J, Jiang Z, Chen S, Huang X, Zhang M, Zheng L, Zhang Y, Yin L, Yu J, Zheng X, Zheng L, Huang P, Liang G. Discovery of LC-MI-3: A Potent and Orally Bioavailable Degrader of Interleukin-1 Receptor-Associated Kinase 4 for the Treatment of Inflammatory Diseases. J Med Chem 2024; 67:8060-8076. [PMID: 38722184 DOI: 10.1021/acs.jmedchem.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Interleukin-1 receptor-associated kinase 4 (IRAK4) is a promising therapeutic target in inflammation-related diseases. However, the inhibition of IRAK4 kinase activity may lead to moderate anti-inflammatory efficacy owing to the dual role of IRAK4 as an active kinase and a scaffolding protein. Herein, we report the design, synthesis, and biological evaluation of an efficient and selective IRAK4 proteolysis-targeting chimeric molecule that eliminates IRAK4 scaffolding functions. The most potent compound, LC-MI-3, effectively degraded cellular IRAK4, with a half-maximal degradation concentration of 47.3 nM. LC-MI-3 effectively inhibited the activation of downstream nuclear factor-κB signaling and exerted more potent pharmacological effects than traditional kinase inhibitors. Furthermore, LC-MI-3 exerted significant therapeutic effects in lipopolysaccharide- and Escherichia coli-induced acute and chronic inflammatory skin models compared with kinase inhibitors in vivo. Therefore, LC-MI-3 is a candidate IRAK4 degrader in alternative targeting strategies and advanced drug development.
Collapse
Affiliation(s)
- Lingfeng Chen
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Ruixiang Luo
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Lin Ma
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Ying Xu
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Jiaqi Cao
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Zheng Jiang
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Shiyan Chen
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Xiaohao Huang
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Mingwan Zhang
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou 310000, Zhejiang, China
| | - Lei Zheng
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Yawen Zhang
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Lina Yin
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Jie Yu
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Xiaochun Zheng
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital(Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Lulu Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou 310000, Zhejiang, China
| | - Ping Huang
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
- Center for Clinical Pharmacy, Cancer Center, Department of Pharmacy, Zhejiang Provincial People's Hospital(Affiliated People's Hospital), Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Guang Liang
- School of Pharmacy, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| |
Collapse
|
4
|
Pfaffenbach M, Bolduc PN, Xin Z, Gao F, Evans R, Fang T, Chodaparambil JV, Henry KL, Li P, Mathieu S, Metrick C, Vera Rebollar JA, Gu RF, Mccarl CA, Silbereis J, Peterson EA. Discovery of BIO-8169─A Highly Potent, Selective, and Brain-Penetrant IRAK4 Inhibitor for the Treatment of Neuroinflammation. J Med Chem 2024; 67:8383-8395. [PMID: 38695469 DOI: 10.1021/acs.jmedchem.4c00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Interleukin receptor associated kinase 4 (IRAK4) plays an important role in innate immune signaling through Toll-like and interleukin-1 receptors and represents an attractive target for the treatment of inflammatory diseases and cancer. We previously reported the development of a potent, selective, and brain-penetrant imidazopyrimidine series of IRAK4 inhibitors. However, lead molecule BIO-7488 (1) suffered from low solubility which led to variable PK, compound accumulation, and poor in vivo tolerability. Herein, we describe the discovery of a series of pyridone analogs with improved solubility which are highly potent, selective and demonstrate desirable PK profiles including good oral bioavailability and excellent brain penetration. BIO-8169 (2) reduced the in vivo production of pro-inflammatory cytokines, was well tolerated in safety studies in rodents and dog at margins well above the predicted efficacious exposure and showed promising results in a mouse model for multiple sclerosis.
Collapse
Affiliation(s)
- Magnus Pfaffenbach
- Department of Medicinal Chemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Philippe N Bolduc
- Department of Medicinal Chemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Zhili Xin
- Department of Medicinal Chemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Fang Gao
- Department of Medicinal Chemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ryan Evans
- Department of Medicinal Chemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Terry Fang
- Department of Acute Neurology, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jayanth V Chodaparambil
- Physical Biochemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kate L Henry
- Department of Acute Neurology, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Pei Li
- Drug Metabolism and Pharmacokinetics, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Steven Mathieu
- Pharmaceutical Operations & Technology, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire Metrick
- Physical Biochemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jorge A Vera Rebollar
- Department of Multiple Sclerosis and Immunology, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rong-Fang Gu
- Chemical Biology and Proteomics, Biogen Inc., Cambridge, Massachusetts 02142, United States
| | - Christie-Ann Mccarl
- Department of Multiple Sclerosis and Immunology, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - John Silbereis
- Department of Multiple Sclerosis and Immunology, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Emily A Peterson
- Department of Medicinal Chemistry, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
5
|
Evans R, Bolduc PN, Pfaffenbach M, Gao F, May-Dracka T, Fang T, Hopkins BT, Chodaparambil JV, Henry KL, Li P, Metrick C, Nelson A, Trapa P, Thomas A, Burkly L, Peterson EA. The Discovery of 7-Isopropoxy-2-(1-methyl-2-oxabicyclo[2.1.1]hexan-4-yl)- N-(6-methylpyrazolo[1,5- a]pyrimidin-3-yl)imidazo[1,2- a]pyrimidine-6-carboxamide (BIO-7488), a Potent, Selective, and CNS-Penetrant IRAK4 Inhibitor for the Treatment of Ischemic Stroke. J Med Chem 2024. [PMID: 38467640 DOI: 10.1021/acs.jmedchem.3c02226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Interleukin receptor-associated kinase 4 (IRAK4) is a key node of signaling within the innate immune system that regulates the production of inflammatory cytokines and chemokines. The presence of damage-associated molecular patterns (DAMPs) after tissue damage such as stroke or traumatic brain injury (TBI) initiates signaling through the IRAK4 pathway that can lead to a feed-forward inflammatory loop that can ultimately hinder patient recovery. Herein, we describe the first potent, selective, and CNS-penetrant IRAK4 inhibitors for the treatment of neuroinflammation. Lead compounds from the series were evaluated in CNS PK/PD models of inflammation, as well as a mouse model of ischemic stroke. The SAR optimization detailed within culminates in the discovery of BIO-7488, a highly selective and potent IRAK4 inhibitor that is CNS penetrant and has excellent ADME properties.
Collapse
Affiliation(s)
- Ryan Evans
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Philippe N Bolduc
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Magnus Pfaffenbach
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Fang Gao
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Tricia May-Dracka
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Terry Fang
- Department of Acute Neurology, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian T Hopkins
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jayanth V Chodaparambil
- Physical Biochemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kate L Henry
- Department of Acute Neurology, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Pei Li
- Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire Metrick
- Physical Biochemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ashley Nelson
- Department of Acute Neurology, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Patrick Trapa
- Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ankur Thomas
- Department of Acute Neurology, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Linda Burkly
- Department of Acute Neurology, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Emily A Peterson
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
6
|
Joseph J, Mathew J, Alexander J. Scaffold Proteins in Autoimmune Disorders. Curr Rheumatol Rev 2024; 20:14-26. [PMID: 37670692 DOI: 10.2174/1573397119666230904151024] [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: 04/03/2023] [Revised: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Cells transmit information to the external environment and within themselves through signaling molecules that modulate cellular activities. Aberrant cell signaling disturbs cellular homeostasis causing a number of different diseases, including autoimmunity. Scaffold proteins, as the name suggests, serve as the anchor for binding and stabilizing signaling proteins at a particular locale, allowing both intra and intercellular signal amplification and effective signal transmission. Scaffold proteins play a critical role in the functioning of tight junctions present at the intersection of two cells. In addition, they also participate in cleavage formation during cytokinesis, and in the organization of neural synapses, and modulate receptor management outcomes. In autoimmune settings such as lupus, scaffold proteins can lower the cell activation threshold resulting in uncontrolled signaling and hyperactivity. Scaffold proteins, through their binding domains, mediate protein- protein interaction and play numerous roles in cellular communication and homeostasis. This review presents an overview of scaffold proteins, their influence on the different signaling pathways, and their role in the pathogenesis of autoimmune and auto inflammatory diseases. Since these proteins participate in many roles and interact with several other signaling pathways, it is necessary to gain a thorough understanding of these proteins and their nuances to facilitate effective target identification and therapeutic design for the treatment of autoimmune disorders.
Collapse
Affiliation(s)
- Josna Joseph
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - John Mathew
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - Jessy Alexander
- Department of Medicine, Jacobs School of Medicine & Biomedical Sciences, University of Buffalo, New York, USA
| |
Collapse
|
7
|
Behairy MY, Eid RA, Otifi HM, Mohammed HM, Alshehri MA, Asiri A, Aldehri M, Zaki MSA, Darwish KM, Elhady SS, El-Shaer NH, Eldeen MA. Unraveling Extremely Damaging IRAK4 Variants and Their Potential Implications for IRAK4 Inhibitor Efficacy. J Pers Med 2023; 13:1648. [PMID: 38138875 PMCID: PMC10744719 DOI: 10.3390/jpm13121648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Interleukin-1-receptor-associated kinase 4 (IRAK4) possesses a crucial function in the toll-like receptor (TLR) signaling pathway, and the dysfunction of this molecule could lead to various infectious and immune-related diseases in addition to cancers. IRAK4 genetic variants have been linked to various types of diseases. Therefore, we conducted a comprehensive analysis to recognize the missense variants with the most damaging impacts on IRAK4 with the employment of diverse bioinformatics tools to study single-nucleotide polymorphisms' effects on function, stability, secondary structures, and 3D structure. The residues' location on the protein domain and their conservation status were investigated as well. Moreover, docking tools along with structural biology were engaged in analyzing the SNPs' effects on one of the developed IRAK4 inhibitors. By analyzing IRAK4 gene SNPs, the analysis distinguished ten variants as the most detrimental missense variants. All variants were situated in highly conserved positions on an important protein domain. L318S and L318F mutations were linked to changes in IRAK4 secondary structures. Eight SNPs were revealed to have a decreasing effect on the stability of IRAK4 via both I-Mutant 2.0 and Mu-Pro tools, while Mu-Pro tool identified a decreasing effect for the G198E SNP. In addition, detrimental effects on the 3D structure of IRAK4 were also discovered for the selected variants. Molecular modeling studies highlighted the detrimental impact of these identified SNP mutant residues on the druggability of the IRAK4 ATP-binding site towards the known target inhibitor, HG-12-6, as compared to the native protein. The loss of important ligand residue-wise contacts, altered protein global flexibility, increased steric clashes, and even electronic penalties at the ligand-binding site interfaces were all suggested to be associated with SNP models for hampering the HG-12-6 affinity towards IRAK4 target protein. This given model lays the foundation for the better prediction of various disorders relevant to IRAK4 malfunction and sheds light on the impact of deleterious IRAK4 variants on IRAK4 inhibitor efficacy.
Collapse
Affiliation(s)
- Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt;
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Hassan M. Otifi
- Department of Pathology, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (R.A.E.); (H.M.O.)
| | - Heitham M. Mohammed
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohammed A. Alshehri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Ashwag Asiri
- Department of Child Health, College of Medicine, King Khalid University, Abha P.O. Box 62529, Saudi Arabia; (M.A.A.)
| | - Majed Aldehri
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Mohamed Samir A. Zaki
- Department of Anatomy, College of Medicine, King Khalid University, Abha P.O. Box 61421, Saudi Arabia; (H.M.M.); (M.A.); (M.S.A.Z.)
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Nahla H. El-Shaer
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
| | - Muhammad Alaa Eldeen
- Department of Zoology, Faculty of Science, Zagazig University, Zagazig 44511, Egypt;
| |
Collapse
|
8
|
Bhole RP, Kute PR, Chikhale RV, Bonde CG, Pant A, Gurav SS. Unlocking the potential of PROTACs: A comprehensive review of protein degradation strategies in disease therapy. Bioorg Chem 2023; 139:106720. [PMID: 37480814 DOI: 10.1016/j.bioorg.2023.106720] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023]
Abstract
The technology known asPROTACs (PROteolysisTArgeting Chimeras) is a method of protein degradation. Utilising bifunctional small molecules, the ubiquitin-proteosome system (UPS) is used to induce the ubiquitination and degradation of target proteins. In addition to being novel chemical knockdown agents for biological studies that are catalytic, reversible, and rapid, PROTACs used in the treatment for disorders like cancer, immunological disorders, viral diseases, and neurological disorders. The protein degradation field has advanced quickly over the last two years, with a significant rise in research articles on the subject as well as a quick rise in smallmolecule degraders that are currently in or will soon enter the clinical stage. Other new degrading technologies, in addition to PROTAC and molecular glue technology, are also emerging rapidly. In this review article, we mainly focuses on various PROTAC molecules designed with special emphasis on targeted cellular pathways for different diseases i.e., cancer, Viral diseases Immune disorders, Neurodegenerative diseases, etc. We discussed about new technologies based on PROTACs such as Antibody PROTAC, Aptamers, Dual target, Folate caged, TF PROTAC, etc. Also, we listed out the PROTACs which are in clinical trials.
Collapse
Affiliation(s)
- Ritesh P Bhole
- Department of Pharmaceutical Chemistry, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India.
| | - Payal R Kute
- Department of Pharmaceutical Chemistry, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | | | - C G Bonde
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management, SVKM's NMIMS, Shirpur Campus 425 405, India.
| | - Amit Pant
- School of Medicine Creighton University, Omaha, Neraska, USA.
| | - Shailendra S Gurav
- Department of Pharmacognosy, Goa College of Pharmacy, Panaji, Goa University, Goa 403001, India.
| |
Collapse
|
9
|
Yadav H, Shirumalla RK. Emerging trends in IRAK-4 kinase research. Mol Biol Rep 2023; 50:7825-7837. [PMID: 37490192 DOI: 10.1007/s11033-023-08438-w] [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: 05/27/2022] [Accepted: 04/06/2023] [Indexed: 07/26/2023]
Abstract
The IRAK-4 kinase lies at a critical signaling node that drives cancer cell survival through multiple mechanisms, activation, and translocation of NF-κB mediated inflammatory responses and innate immune signaling through regulation of interferon-α/β receptor (IFNα/β). Inhibition, of IRAK-4, has consequently drawn a lot of attention in recent years to address indications ranging from oncology to autoimmune disorders to neurodegeneration, etc. However, the key stumbling block in targeting IRAK-4 is that despite the inhibition of the kinase activity using an inhibitor the target remains effective, reducing the potential of an inhibitor. This is due to the "scaffolding effect" because of which although regulation of downstream processes by IRAK-4 has been primarily linked with kinase function; however, still, various reports have suggested that IRAK-4 has a non-kinase function in a variety of cell types. This is attributed to the myddosome complex formed by IRAK-4 with myd88, IRAK-2, and IRAK-1 which by itself can cause the activation of downstream effector TRAF6 despite inhibition of the kinase domain of IRAK-4. With this challenge, several groups initiated the development of targeting protein degraders of IRAK-4 using Proteolysis-Targeting Chimeras (PROTACs) technology to completely remove the IRAK-4 from the cellular milieu. In this review, we will capture all these developments and the evolving science around this target.
Collapse
Affiliation(s)
- Himanshu Yadav
- SGT College of Pharmacy, SGT University, Budhera, Gurugram, Haryana, 122505, India
| | - Raj Kumar Shirumalla
- SGT College of Pharmacy, SGT University, Budhera, Gurugram, Haryana, 122505, India.
| |
Collapse
|
10
|
Gosu V, Sasidharan S, Saudagar P, Radhakrishnan K, Lee HK, Shin D. Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors. Comput Biol Med 2023; 160:106978. [DOI: https:/doi.org/10.1016/j.compbiomed.2023.106978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
|
11
|
Li SR, Tan YM, Zhang L, Zhou CH. Comprehensive Insights into Medicinal Research on Imidazole-Based Supramolecular Complexes. Pharmaceutics 2023; 15:pharmaceutics15051348. [PMID: 37242590 DOI: 10.3390/pharmaceutics15051348] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The electron-rich five-membered aromatic aza-heterocyclic imidazole, which contains two nitrogen atoms, is an important functional fragment widely present in a large number of biomolecules and medicinal drugs; its unique structure is beneficial to easily bind with various inorganic or organic ions and molecules through noncovalent interactions to form a variety of supramolecular complexes with broad medicinal potential, which is being paid an increasing amount of attention regarding more and more contributions to imidazole-based supramolecular complexes for possible medicinal application. This work gives systematical and comprehensive insights into medicinal research on imidazole-based supramolecular complexes, including anticancer, antibacterial, antifungal, antiparasitic, antidiabetic, antihypertensive, and anti-inflammatory aspects as well as ion receptors, imaging agents, and pathologic probes. The new trend of the foreseeable research in the near future toward imidazole-based supramolecular medicinal chemistry is also prospected. It is hoped that this work provides beneficial help for the rational design of imidazole-based drug molecules and supramolecular medicinal agents and more effective diagnostic agents and pathological probes.
Collapse
Affiliation(s)
- Shu-Rui Li
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yi-Min Tan
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ling Zhang
- School of Chemical Technology, Shijiazhuang University, Shijiazhuang 050035, China
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| |
Collapse
|
12
|
Gosu V, Sasidharan S, Saudagar P, Radhakrishnan K, Lee HK, Shin D. Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors. Comput Biol Med 2023; 160:106978. [PMID: 37172355 DOI: 10.1016/j.compbiomed.2023.106978] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/14/2023]
Abstract
Interleukin-1 receptor-associated kinase 4 (IRAK4) is a vital protein involved in Toll-like and interleukin-1 receptor signal transduction. Several studies have reported regarding the crystal structure, dynamic properties, and interactions with inhibitors of the phosphorylated form of IRAK4. However, no dynamic properties of inhibitor-bound unphosphorylated IRAK4 have been previously studied. Herein, we report the intrinsic dynamics of unphosphorylated IRAK4 (uIRAK4) bound to type I and type II inhibitors. The corresponding apo and inhibitor-bound forms of uIRAK4 were subjected to three independent simulations of 500 ns (total 1.5 μs) each, and their trajectories were analyzed. The results indicated that all three systems were relatively stable, except for the type II inhibitor-bound form of uIRAK4, which exhibited less compact folding and higher solvent surface area. The intra-hydrogen bonds corroborated the structural deformation of the type-II inhibitor-bound complex, which could be attributed to the long molecular structure of the type-II inhibitor. Moreover, the type II inhibitor bound to uIRAK4 showed higher binding free energy with uIRAK4 than the type I inhibitor. The free energy landscape analysis showed a reorientation of Phe330 side chain from the DFG motif at different metastable states for all the systems. The intra-residual distance between residues Lys213, Glu233, Tyr262, and Phe330 suggests a functional interplay when the inhibitors are bound to uIRAK4, thereby hinting at their crucial role in the inhibition mechanism. Ultimately, the intrinsic dynamics study observed between type I/II inhibitor-bound forms of uIRAK4 may assist in better understanding the enzyme and designing therapeutic compounds.
Collapse
Affiliation(s)
- Vijayakumar Gosu
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, 506004, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, 506004, India
| | - Kamalakannan Radhakrishnan
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea; Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| |
Collapse
|
13
|
Kelm JM, Pandey DS, Malin E, Kansou H, Arora S, Kumar R, Gavande NS. PROTAC'ing oncoproteins: targeted protein degradation for cancer therapy. Mol Cancer 2023; 22:62. [PMID: 36991452 PMCID: PMC10061819 DOI: 10.1186/s12943-022-01707-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 03/31/2023] Open
Abstract
Molecularly targeted cancer therapies substantially improve patient outcomes, although the durability of their effectiveness can be limited. Resistance to these therapies is often related to adaptive changes in the target oncoprotein which reduce binding affinity. The arsenal of targeted cancer therapies, moreover, lacks coverage of several notorious oncoproteins with challenging features for inhibitor development. Degraders are a relatively new therapeutic modality which deplete the target protein by hijacking the cellular protein destruction machinery. Degraders offer several advantages for cancer therapy including resiliency to acquired mutations in the target protein, enhanced selectivity, lower dosing requirements, and the potential to abrogate oncogenic transcription factors and scaffolding proteins. Herein, we review the development of proteolysis targeting chimeras (PROTACs) for selected cancer therapy targets and their reported biological activities. The medicinal chemistry of PROTAC design has been a challenging area of active research, but the recent advances in the field will usher in an era of rational degrader design.
Collapse
Affiliation(s)
- Jeremy M Kelm
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Deepti S Pandey
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Evan Malin
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Hussein Kansou
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Navnath S Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA.
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
| |
Collapse
|
14
|
Wang C, Zhang Y, Deng J, Liang B, Xing D. Developments of PROTACs technology in immune-related diseases. Eur J Med Chem 2023; 249:115127. [PMID: 36724631 DOI: 10.1016/j.ejmech.2023.115127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023]
Abstract
Traditional chemotherapy and immunotherapy are primary disease-treatment strategies. However, they face numerous challenges, including limited therapeutic benefits, off-target effects, serious adverse effects, drug resistance, long half-life time, poor oral bioavailability, and drugging undruggable proteins. Proteolytic targeted chimeras (PROTACs) were suggested to solve these problems. PROTACs are heterogeneous functional molecules linked by a chemical linker and contain a binding ligand for the protein of interest and a recruiting ligand for the E3 ligand. The binding of a PROTAC to a target protein brings the E3 ligand enzyme into proximity, initiating polyubiquitination of the target protein, followed by protease-mediated degradation. To date, PROTACs against dozens of immunological targets have been successfully developed, many of which have been clinically validated drug targets, and several have entered clinical trials for immune-related diseases. This article reviews the role of PROTACs-mediated degradation of critical proteins in immune disorders and cancer immunotherapy. Chemical structures, cellular and in vivo activities, and pharmacodynamics of these PROTACs are summarized. Lastly, we also discuss the prospects and potential limitations that PROTACs face.
Collapse
Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Junwen Deng
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China
| | - Bing Liang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; Cancer Institute, Qingdao University, Qingdao, 266071, Shandong, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
15
|
Liu Z, Hu M, Yang Y, Du C, Zhou H, Liu C, Chen Y, Fan L, Ma H, Gong Y, Xie Y. An overview of PROTACs: a promising drug discovery paradigm. MOLECULAR BIOMEDICINE 2022; 3:46. [PMID: 36536188 PMCID: PMC9763089 DOI: 10.1186/s43556-022-00112-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Proteolysis targeting chimeras (PROTACs) technology has emerged as a novel therapeutic paradigm in recent years. PROTACs are heterobifunctional molecules that degrade target proteins by hijacking the ubiquitin-proteasome system. Currently, about 20-25% of all protein targets are being studied, and most works focus on their enzymatic functions. Unlike small molecules, PROTACs inhibit the whole biological function of the target protein by binding to the target protein and inducing subsequent proteasomal degradation. PROTACs compensate for limitations that transcription factors, nuclear proteins, and other scaffolding proteins are difficult to handle with traditional small-molecule inhibitors. Currently, PROTACs have successfully degraded diverse proteins, such as BTK, BRD4, AR, ER, STAT3, IRAK4, tau, etc. And ARV-110 and ARV-471 exhibited excellent efficacy in clinical II trials. However, what targets are appropriate for PROTAC technology to achieve better benefits than small-molecule inhibitors are not fully understood. And how to rationally design an efficient PROTACs and optimize it to be orally effective poses big challenges for researchers. In this review, we summarize the features of PROTAC technology, analyze the detail of general principles for designing efficient PROTACs, and discuss the typical application of PROTACs targeting different protein categories. In addition, we also introduce the progress of relevant clinical trial results of representative PROTACs and assess the challenges and limitations that PROTACs may face. Collectively, our studies provide references for further application of PROTACs.
Collapse
Affiliation(s)
- Zi Liu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Mingxing Hu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yu Yang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Chenghao Du
- grid.42505.360000 0001 2156 6853Department of Biological Sciences, USC Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, 90089 USA
| | - Haoxuan Zhou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Chengyali Liu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yuanwei Chen
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Lei Fan
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Hongqun Ma
- Hinova Pharmaceuticals Inc., Chengdu, 610041 China
| | - Youling Gong
- grid.13291.380000 0001 0807 1581Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Yongmei Xie
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| |
Collapse
|
16
|
Wang C, Zhang Y, Zhang T, Shi L, Geng Z, Xing D. Proteolysis-targeting chimaeras (PROTACs) as pharmacological tools and therapeutic agents: advances and future challenges. J Enzyme Inhib Med Chem 2022; 37:1667-1693. [PMID: 35702041 PMCID: PMC9225776 DOI: 10.1080/14756366.2022.2076675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Proteolysis-targeting chimaeras (PROTACs) have been developed to be an emerging technology for targeted protein degradation and attracted the favour of academic institutions, large pharmaceutical enterprises, and biotechnology companies. The mechanism is based on the inhibition of protein function by hijacking a ubiquitin E3 ligase for protein degradation. The heterobifunctional PROTACs contain a ligand for recruiting an E3 ligase, a linker, and another ligand to bind with the protein targeted for degradation. To date, PROTACs targeting ∼70 proteins, many of which are clinically validated drug targets, have been successfully developed with several in clinical trials for diseases therapy. In this review, the recent advances in PROTACs against clinically validated drug targets are summarised and the chemical structure, cellular and in vivo activity, pharmacokinetics, and pharmacodynamics of these PROTACs are highlighted. In addition, the potential advantages, challenges, and prospects of PROTACs technology in disease treatment are discussed.
Collapse
Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China.,School of Pharmacy, Qingdao University, Qingdao, China
| | - Tingting Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Lingyu Shi
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Zhongmin Geng
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China.,School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
17
|
Bhujbal SP, He W, Hah JM. Design of Novel IRAK4 Inhibitors Using Molecular Docking, Dynamics Simulation and 3D-QSAR Studies. Molecules 2022; 27:6307. [PMID: 36234844 PMCID: PMC9570937 DOI: 10.3390/molecules27196307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 02/05/2023] Open
Abstract
Treatment of several autoimmune diseases and types of cancer has been an intense area of research over the past two decades. Many signaling pathways that regulate innate and/or adaptive immunity, as well as those that induce overexpression or mutation of protein kinases, have been targeted for drug discovery. One of the serine/threonine kinases, Interleukin-1 Receptor Associated Kinase 4 (IRAK4) regulates signaling through various Toll-like receptors (TLRs) and interleukin-1 receptor (IL1R). It controls diverse cellular processes including inflammation, apoptosis, and cellular differentiation. MyD88 gain-of-function mutations or overexpression of IRAK4 has been implicated in various types of malignancies such as Waldenström macroglobulinemia, B cell lymphoma, colorectal cancer, pancreatic ductal adenocarcinoma, breast cancer, etc. Moreover, over activation of IRAK4 is also associated with several autoimmune diseases. The significant role of IRAK4 makes it an interesting target for the discovery and development of potent small molecule inhibitors. A few potent IRAK4 inhibitors such as PF-06650833, RA9 and BAY1834845 have recently entered phase I/II clinical trial studies. Nevertheless, there is still a need of selective inhibitors for the treatment of cancer and various autoimmune diseases. A great need for the same intrigued us to perform molecular modeling studies on 4,6-diaminonicotinamide derivatives as IRAK4 inhibitors. We performed molecular docking and dynamics simulation of 50 ns for one of the most active compounds of the dataset. We also carried out MM-PBSA binding free energy calculation to identify the active site residues, interactions of which are contributing to the total binding energy. The final 50 ns conformation of the most active compound was selected to perform dataset alignment in a 3D-QSAR study. Generated RF-CoMFA (q2 = 0.751, ONC = 4, r2 = 0.911) model revealed reasonable statistical results. Overall results of molecular dynamics simulation, MM-PBSA binding free energy calculation and RF-CoMFA model revealed important active site residues of IRAK4 and necessary structural properties of ligand to design more potent IRAK4 inhibitors. We designed few IRAK4 inhibitors based on these results, which possessed higher activity (predicted pIC50) than the most active compounds of the dataset selected for this study. Moreover, ADMET properties of these inhibitors revealed promising results and need to be validated using experimental studies.
Collapse
Affiliation(s)
- Swapnil P. Bhujbal
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 426-791, Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Korea
| | - Weijie He
- Second Affiliated Hospital of Shantou University Medical College, Shantou University, Shantou 515000, China
| | - Jung-Mi Hah
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan 426-791, Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Korea
| |
Collapse
|
18
|
Recent Advances in PROTACs for Drug Targeted Protein Research. Int J Mol Sci 2022; 23:ijms231810328. [PMID: 36142231 PMCID: PMC9499226 DOI: 10.3390/ijms231810328] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 01/30/2023] Open
Abstract
Proteolysis-targeting chimera (PROTAC) is a heterobifunctional molecule. Typically, PROTAC consists of two terminals which are the ligand of the protein of interest (POI) and the specific ligand of E3 ubiquitin ligase, respectively, via a suitable linker. PROTAC degradation of the target protein is performed through the ubiquitin–proteasome system (UPS). The general process is that PROTAC binds to the target protein and E3 ligase to form a ternary complex and label the target protein with ubiquitination. The ubiquitinated protein is recognized and degraded by the proteasome in the cell. At present, PROTAC, as a new type of drug, has been developed to degrade a variety of cancer target proteins and other disease target proteins, and has shown good curative effects on a variety of diseases. For example, PROTACs targeting AR, BR, BTK, Tau, IRAK4, and other proteins have shown unprecedented clinical efficacy in cancers, neurodegenerative diseases, inflammations, and other fields. Recently, PROTAC has entered a phase of rapid development, opening a new field for biomedical research and development. This paper reviews the various fields of targeted protein degradation by PROTAC in recent years and summarizes and prospects the hot targets and indications of PROTAC.
Collapse
|
19
|
He M, Cao C, Ni Z, Liu Y, Song P, Hao S, He Y, Sun X, Rao Y. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021). Signal Transduct Target Ther 2022; 7:181. [PMID: 35680848 PMCID: PMC9178337 DOI: 10.1038/s41392-022-00999-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) technology is a new protein-degradation strategy that has emerged in recent years. It uses bifunctional small molecules to induce the ubiquitination and degradation of target proteins through the ubiquitin-proteasome system. PROTACs can not only be used as potential clinical treatments for diseases such as cancer, immune disorders, viral infections, and neurodegenerative diseases, but also provide unique chemical knockdown tools for biological research in a catalytic, reversible, and rapid manner. In 2019, our group published a review article "PROTACs: great opportunities for academia and industry" in the journal, summarizing the representative compounds of PROTACs reported before the end of 2019. In the past 2 years, the entire field of protein degradation has experienced rapid development, including not only a large increase in the number of research papers on protein-degradation technology but also a rapid increase in the number of small-molecule degraders that have entered the clinical and will enter the clinical stage. In addition to PROTAC and molecular glue technology, other new degradation technologies are also developing rapidly. In this article, we mainly summarize and review the representative PROTACs of related targets published in 2020-2021 to present to researchers the exciting developments in the field of protein degradation. The problems that need to be solved in this field will also be briefly introduced.
Collapse
Affiliation(s)
- Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
- Tsinghua-Peking Center for Life Sciences, 100084, Beijing, P. R. China
| | - Zhihao Ni
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yongbo Liu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Peilu Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Shuang Hao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.
- School of Pharmaceutical Sciences, Zhengzhou University, 450001, Zhengzhou, China.
| |
Collapse
|
20
|
Wang C, Zhang Y, Shi L, Yang S, Chang J, Zhong Y, Li Q, Xing D. Recent advances in IAP-based PROTACs (SNIPERs) as potential therapeutic agents. J Enzyme Inhib Med Chem 2022; 37:1437-1453. [PMID: 35589670 PMCID: PMC9122363 DOI: 10.1080/14756366.2022.2074414] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Proteolytic targeting chimaeras (PROTACs) have been developed as an effective technology for targeted protein degradation. PROTACs are heterobifunctional molecules that can trigger the polyubiquitination of proteins of interest (POIs) by recruiting the ubiquitin-proteasome system, thereby inhibiting the intracellular level of POIs. To date, a variety of small-molecule PROTACs (CRBN, VHL, IAP, and MDM2-based PROTACs) have been developed. IAP-based PROTACs, also known as specific and nongenetic IAP-dependent protein erasers (SNIPERs), are used to degrade the target proteins closely related to diseases. Their structures consist of three parts, including target protein ligand, E3 ligase ligand, and the linker between them. So far, many SNIPERs have been extensively studied worldwide and have performed well in multiple diseases, especially cancer. In this review, we will present the most relevant advances in the field of SNIPERs and provide our perspective on the opportunities and challenges for SNIPERs to become therapeutic agents.
Collapse
Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Lingyu Shi
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Shanbo Yang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Jing Chang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Yingjie Zhong
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Qian Li
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Cancer Institute, Qingdao University, Qingdao, China.,School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
21
|
Li L, Liu S, Tan J, Wei L, Wu D, Gao S, Weng Y, Chen J. Recent advance in treatment of atherosclerosis: Key targets and plaque-positioned delivery strategies. J Tissue Eng 2022; 13:20417314221088509. [PMID: 35356091 PMCID: PMC8958685 DOI: 10.1177/20417314221088509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Atherosclerosis, a chronic inflammatory disease of vascular wall, is a progressive pathophysiological process with lipids oxidation/depositing initiation and innate/adaptive immune responses. The coordination of multi systems covering oxidative stress, dysfunctional endothelium, diseased lipid uptake, cell apoptosis, thrombotic and pro-inflammatory responding as well as switched SMCs contributes to plaque growth. In this circumstance, inevitably, targeting these processes is considered to be effective for treating atherosclerosis. Arriving, retention and working of payload candidates mediated by targets in lesion direct ultimate therapeutic outcomes. Accumulating a series of scientific studies and clinical practice in the past decades, lesion homing delivery strategies including stent/balloon/nanoparticle-based transportation worked as the potent promotor to ensure a therapeutic effect. The objective of this review is to achieve a very brief summary about the effective therapeutic methods cooperating specifical targets and positioning-delivery strategies in atherosclerosis for better outcomes.
Collapse
Affiliation(s)
- Li Li
- Key Laboratory of Advanced Technology of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, PR China
| | - Sainan Liu
- Key Laboratory of Advanced Technology of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, PR China
| | - Jianying Tan
- Key Laboratory of Advanced Technology of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, PR China
| | - Lai Wei
- Key Laboratory of Advanced Technology of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, PR China
| | - Dimeng Wu
- Chengdu Daxan Innovative Medical Tech. Co., Ltd., Chengdu, PR China
| | - Shuai Gao
- Chengdu Daxan Innovative Medical Tech. Co., Ltd., Chengdu, PR China
| | - Yajun Weng
- Key Laboratory of Advanced Technology of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, PR China
| | - Junying Chen
- Key Laboratory of Advanced Technology of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, PR China
| |
Collapse
|
22
|
Wang C, Zhang Y, Wang J, Xing D. VHL-based PROTACs as potential therapeutic agents: Recent progress and perspectives. Eur J Med Chem 2022; 227:113906. [PMID: 34656901 DOI: 10.1016/j.ejmech.2021.113906] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023]
Abstract
Proteolysis targeting chimeras (PROTACs), which hijack proteins of interest (POIs) and recruit E3 ligases for target degradation via the ubiquitin-proteasome pathway, are a novel drug discovery paradigm that has been widely used as biological tools and medicinal molecules with the potential of clinical application value. To date, a wide variety of small molecule PROTACs have been developed. Importantly, VHL-based PROTACs have emerged to be a promising approach for proteins, including those non-druggable ones, such as transcriptional factors and scaffold proteins. VHL-based PRTOACs have been developed for the treatment of diseases that are difficult to be dealt with by conventional methods, such as radiotherapy, chemotherapy, and small molecule inhibitors. In this review, the recent advances of VHL-based PRTOACs were summarized, and the chances and challenges associated with this area were also highlighted.
Collapse
Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; School of Pharmacy, Qingdao University, Qingdao, 266021, Shandong, China.
| | - Jie Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
23
|
Wang C, Zhang Y, Wu Y, Xing D. Developments of CRBN-based PROTACs as potential therapeutic agents. Eur J Med Chem 2021; 225:113749. [PMID: 34411892 DOI: 10.1016/j.ejmech.2021.113749] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022]
Abstract
Protease-targeted chimeras (PROTACs) are a new technology that is receiving much attention in the treatment of diseases. The mechanism is to inhibit protein function by hijacking the ubiquitin E3 ligase for protein degradation. Heterogeneous bifunctional PROTACs contain a ligand for recruiting E3 ligase, a linker, and another ligand to bind to the target protein for degradation. A variety of small-molecule PROTACs (CRBN, VHL, IAPs, MDM2, DCAF15, DCAF16, and RNF114-based PROTACs) have been identified so far. In particular, CRBN-based PROTACs (e.g., ARV-110 and ARV-471) have received more attention for their promising therapeutic intervention. To date, CRBN-based PRTOACs have been extensively explored worldwide and have excelled not only in cancer diseases but also in cardiovascular diseases, immune diseases, neurodegenerative diseases, and viral infections. In this review, we will provide a comprehensive update on the latest research progress in CRBN-based PRTOACs area. Following the criteria, such as disease area and drug target class, we will present the degradants in alphabetical order by target. We also provide our own perspective on the future prospects and potential challenges facing PROTACs.
Collapse
Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Yudong Wu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
24
|
Khanfar MA. Structure-Based Pharmacophore Screening Coupled with QSAR Analysis Identified Potent Natural-Product-Derived IRAK-4 Inhibitors. Mol Inform 2021; 40:e2100025. [PMID: 34427398 DOI: 10.1002/minf.202100025] [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: 01/24/2021] [Accepted: 08/13/2021] [Indexed: 11/10/2022]
Abstract
Interleukin-1 Receptor-Associated Kinase 4 (IRAK-4) has crucial functions in inflammation, innate immunity, and malignancy. Structure-based pharmacophore modeling integrated with validated QSAR analysis was implemented to discover structurally novel IRAK-4 inhibitors from natural products database. The QSAR model combined molecular descriptors with structure-based pharmacophore capable of explaining bioactivity variation of structurally diverse IRAK-4 inhibitors. Manually built pharmacophore model, validated with receiver operating characteristic curve, and selected using the statistically optimum QSAR equation, was applied as a 3D-search query to mine AnalytiCon Discovery database of natural products. Experimental in vitro testing of highest-ranked hits identified uvaretin, saucerneol, and salvianolic acid B as active IRAK-4 inhibitors with IC50 values in low micromolar range.
Collapse
Affiliation(s)
- Mohammad A Khanfar
- College of Pharmacy, Alfaisal University, Al Takhassusi Rd, P.O. Box 50927, Riyadh 1, 1533, Saudi Arabia.,Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, P.O Box 13140, Amman, 11942, Jordan
| |
Collapse
|
25
|
Winkler A, Sun W, De S, Jiao A, Sharif MN, Symanowicz PT, Athale S, Shin JH, Wang J, Jacobson BA, Ramsey SJ, Dower K, Andreyeva T, Liu H, Hegen M, Homer BL, Brodfuehrer J, Tilley M, Gilbert SA, Danto SI, Beebe JJ, Barnes BJ, Pascual V, Lin LL, Kilty I, Fleming M, Rao VR. The Interleukin-1 Receptor-Associated Kinase 4 Inhibitor PF-06650833 Blocks Inflammation in Preclinical Models of Rheumatic Disease and in Humans Enrolled in a Randomized Clinical Trial. Arthritis Rheumatol 2021; 73:2206-2218. [PMID: 34423919 PMCID: PMC8671219 DOI: 10.1002/art.41953] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the role of PF-06650833, a highly potent and selective small-molecule inhibitor of interleukin-1-associated kinase 4 (IRAK4), in autoimmune pathophysiology in vitro, in vivo, and in the clinical setting. METHODS Rheumatoid arthritis (RA) inflammatory pathophysiology was modeled in vitro through 1) stimulation of primary human macrophages with anti-citrullinated protein antibody immune complexes (ICs), 2) RA fibroblast-like synoviocyte (FLS) cultures stimulated with Toll-like receptor (TLR) ligands, as well as 3) additional human primary cell cocultures exposed to inflammatory stimuli. Systemic lupus erythematosus (SLE) pathophysiology was simulated in human neutrophils, dendritic cells, B cells, and peripheral blood mononuclear cells stimulated with TLR ligands and SLE patient ICs. PF-06650833 was evaluated in vivo in the rat collagen-induced arthritis (CIA) model and the mouse pristane-induced and MRL/lpr models of lupus. Finally, RNA sequencing data generated with whole blood samples from a phase I multiple-ascending-dose clinical trial of PF-06650833 were used to test in vivo human pharmacology. RESULTS In vitro, PF-06650833 inhibited human primary cell inflammatory responses to physiologically relevant stimuli generated with RA and SLE patient plasma. In vivo, PF-06650833 reduced circulating autoantibody levels in the pristane-induced and MRL/lpr murine models of lupus and protected against CIA in rats. In a phase I clinical trial (NCT02485769), PF-06650833 demonstrated in vivo pharmacologic action pertinent to SLE by reducing whole blood interferon gene signature expression in healthy volunteers. CONCLUSION These data demonstrate that inhibition of IRAK4 kinase activity can reduce levels of inflammation markers in humans and provide confidence in the rationale for clinical development of IRAK4 inhibitors for rheumatologic indications.
Collapse
Affiliation(s)
| | | | - Saurav De
- The Feinstein Institute, Manhasset, New York
| | | | | | | | - Shruti Athale
- Baylor Institute for Immunology Research, Dallas, Texas
| | | | - Ju Wang
- Pfizer, Cambridge, Massachusetts
| | | | | | | | | | - Heng Liu
- Pfizer, Cambridge, Massachusetts
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Wang C, Zhang Y, Xing D, Zhang R. PROTACs technology for targeting non-oncoproteins: Advances and perspectives. Bioorg Chem 2021; 114:105109. [PMID: 34175722 DOI: 10.1016/j.bioorg.2021.105109] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) have been developed to be an effective technology for targeted protein degradation. Each PROTAC contains three key components: a protein-of-interest (POI) ligand, an E3 ligase ligand, and a linker. These bifunctional molecules can hijack the intracellular inherent ubiquitin-proteasome system to degrade different POIs. With several advantages over other therapeutic strategies, PROTACs have set off a new upsurge of drug discovery in recent years. PRTOACs have been extensively explored worldwide and have excelled not only in cancer diseases but also in cardiovascular diseases, fatty liver disease, immune diseases, neurodegenerative diseases, and viral infections. In this review, we aim to summarize the rapid progress from 2010 to 2021 in PROTACs targeting various non-oncoproteins and elucidate the advantages of PROTACs technology. Finally, the potential challenges of this dynamic field are also discussed.
Collapse
Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Cancer Institute, Qingdao 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao 266071, Shandong, China.
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Cancer Institute, Qingdao 266071, Shandong, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Renshuai Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Cancer Institute, Qingdao 266071, Shandong, China.
| |
Collapse
|
27
|
Xie Z, Yang X, Duan Y, Han J, Liao C. Small-Molecule Kinase Inhibitors for the Treatment of Nononcologic Diseases. J Med Chem 2021; 64:1283-1345. [PMID: 33481605 DOI: 10.1021/acs.jmedchem.0c01511] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Great successes have been achieved in developing small-molecule kinase inhibitors as anticancer therapeutic agents. However, kinase deregulation plays essential roles not only in cancer but also in almost all major disease areas. Accumulating evidence has revealed that kinases are promising drug targets for different diseases, including cancer, autoimmune diseases, inflammatory diseases, cardiovascular diseases, central nervous system disorders, viral infections, and malaria. Indeed, the first small-molecule kinase inhibitor for treatment of a nononcologic disease was approved in 2011 by the U.S. FDA. To date, 10 such inhibitors have been approved, and more are in clinical trials for applications other than cancer. This Perspective discusses a number of kinases and their small-molecule inhibitors for the treatment of diseases in nononcologic therapeutic fields. The opportunities and challenges in developing such inhibitors are also highlighted.
Collapse
Affiliation(s)
- Zhouling Xie
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiaoxiao Yang
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jihong Han
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chenzhong Liao
- Department of Pharmaceutical Sciences and Engineering, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| |
Collapse
|
28
|
Abstract
INTRODUCTION PROTACs represent a novel class of heterobifunctional molecules that simultaneously bind to a target protein and to an E3 ligase complex, resulting in the transfer of ubiquitin and initiating a process ultimately causing the proteasomal degradation of the target protein. This mechanism of action imbues PROTACs with the ability to modulate target biology in unique ways compared to inhibitors, and the development of PROTACs as therapeutic agents is expected to result in new medicines to treat multiple diseases. AREAS COVERED This review includes published PCT (WO) patent applications covering January 2013 through June 2020. Only English-language patent applications with exemplified PROTACs reported to degrade a target protein(s) were deemed in scope, and the definition of 'PROTAC' was restricted to a bifunctional molecule which contains a discrete binding element for a specific degradation target(s), as well as a separate discrete E3 ligase-binding moiety. EXPERT OPINION Delivering on the enormous potential of PROTACs will require the development of PROTAC medicines that are differentiated from traditional small-molecule inhibitors. The modular composition of PROTACs affords both opportunities and challenges in securing robust intellectual property, and we envision that requirements for novelty are likely to evolve as this area matures.
Collapse
|
29
|
Zhai W, Lu Y, Zhu Y, Zhou M, Ye C, Shi ZZ, Qian W, Hu T, Chen L. Discovery and optimization of a potent and selective indazolamine series of IRAK4 inhibitors. Bioorg Med Chem Lett 2020; 31:127686. [PMID: 33242574 DOI: 10.1016/j.bmcl.2020.127686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 10/22/2022]
Abstract
IRAK4 is a key mediator of innate immunity. There is a high interest in identifying novel IRAK4 inhibitors for the treatment of inflammatory autoimmune diseases. We describe here a highly potent and selective IRAK4 inhibitor (HS271) that exhibited superior enzymatic and cellular activities, as well as excellent pharmacokinetic properties. HS271 displayed robust in vivo anti-inflammatory efficacy as evaluated in rat models of LPS induced TNFα production and collagen-induced arthritis.
Collapse
Affiliation(s)
- Wenqiang Zhai
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| | - Yongping Lu
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| | - Yabo Zhu
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| | - Mengguang Zhou
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| | - Cheng Ye
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| | - Zheng-Zheng Shi
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| | - Wenjian Qian
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China.
| | - Taishan Hu
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| | - Lei Chen
- Zhejiang Hisun Pharmaceutical Co. Ltd., China, 46 Waisha Rd., Taizhou 318099, China
| |
Collapse
|
30
|
Affiliation(s)
- Jie Li
- School of Medicine Huaqiao University Quanzhou 362021 P. R. China
| | - Jieqing Liu
- School of Medicine Huaqiao University Quanzhou 362021 P. R. China
| |
Collapse
|
31
|
Chen L, Zheng L, Chen P, Liang G. Myeloid Differentiation Primary Response Protein 88 (MyD88): The Central Hub of TLR/IL-1R Signaling. J Med Chem 2020; 63:13316-13329. [DOI: 10.1021/acs.jmedchem.0c00884] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lingfeng Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Lulu Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310000, China
| | - Pengqin Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| |
Collapse
|
32
|
Melgar K, Walker MM, Jones LM, Bolanos LC, Hueneman K, Wunderlich M, Jiang JK, Wilson KM, Zhang X, Sutter P, Wang A, Xu X, Choi K, Tawa G, Lorimer D, Abendroth J, O'Brien E, Hoyt SB, Berman E, Famulare CA, Mulloy JC, Levine RL, Perentesis JP, Thomas CJ, Starczynowski DT. Overcoming adaptive therapy resistance in AML by targeting immune response pathways. Sci Transl Med 2020; 11:11/508/eaaw8828. [PMID: 31484791 DOI: 10.1126/scitranslmed.aaw8828] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022]
Abstract
Targeted inhibitors to oncogenic kinases demonstrate encouraging clinical responses early in the treatment course; however, most patients will relapse because of target-dependent mechanisms that mitigate enzyme-inhibitor binding or through target-independent mechanisms, such as alternate activation of survival and proliferation pathways, known as adaptive resistance. Here, we describe mechanisms of adaptive resistance in FMS-like receptor tyrosine kinase (FLT3)-mutant acute myeloid leukemia (AML) by examining integrative in-cell kinase and gene regulatory network responses after oncogenic signaling blockade by FLT3 inhibitors (FLT3i). We identified activation of innate immune stress response pathways after treatment of FLT3-mutant AML cells with FLT3i and showed that innate immune pathway activation via the interleukin-1 receptor-associated kinase 1 and 4 (IRAK1/4) complex contributes to adaptive resistance in FLT3-mutant AML cells. To overcome this adaptive resistance mechanism, we developed a small molecule that simultaneously inhibits FLT3 and IRAK1/4 kinases. The multikinase FLT3-IRAK1/4 inhibitor eliminated adaptively resistant FLT3-mutant AML cells in vitro and in vivo and displayed superior efficacy as compared to current targeted FLT3 therapies. These findings uncover a polypharmacologic strategy for overcoming adaptive resistance to therapy in AML by targeting immune stress response pathways.
Collapse
Affiliation(s)
- Katelyn Melgar
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan M Walker
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Lyndsey C Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kathleen Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jian-Kang Jiang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Patrick Sutter
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Wang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xin Xu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Gregory Tawa
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Eric O'Brien
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Scott B Hoyt
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellin Berman
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher A Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ross L Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John P Perentesis
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA. .,Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20829, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA. .,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| |
Collapse
|
33
|
Litak J, Grochowski C, Litak J, Osuchowska I, Gosik K, Radzikowska E, Kamieniak P, Rolinski J. TLR-4 Signaling vs. Immune Checkpoints, miRNAs Molecules, Cancer Stem Cells, and Wingless-Signaling Interplay in Glioblastoma Multiforme-Future Perspectives. Int J Mol Sci 2020; 21:ijms21093114. [PMID: 32354122 PMCID: PMC7247696 DOI: 10.3390/ijms21093114] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
Toll-like-receptor (TLR) family members were detected in the central nervous system (CNS). TLR occurrence was noticed and widely described in glioblastomamultiforme (GBM) cells. After ligand attachment, TLR-4 reorients domains and dimerizes, activates an intracellular cascade, and promotes further cytoplasmatic signaling. There is evidence pointing at a strong relation between TLR-4 signaling and micro ribonucleic acid (miRNA) expression. The TLR-4/miRNA interplay changes typical signaling and encourages them to be a target for modern immunotherapy. TLR-4 agonists initiate signaling and promote programmed death ligand-1 (PD-1L) expression. Most of those molecules are intensively expressed in the GBM microenvironment, resulting in the autocrine induction of regional immunosuppression. Another potential target for immunotreatment is connected with limited TLR-4 signaling that promotes Wnt/DKK-3/claudine-5 signaling, resulting in a limitation of GBM invasiveness. Interestingly, TLR-4 expression results in bordering proliferative trends in cancer stem cells (CSC) and GBM. All of these potential targets could bring new hope for patients suffering from this incurable disease. Clinical trials concerning TLR-4 signaling inhibition/promotion in many cancers are recruiting patients. There is still a lot to do in the field of GBM immunotherapy.
Collapse
Affiliation(s)
- Jakub Litak
- Department of Neurosurgery and Pediatric Neurosurgery, Medical University of Lublin, 20-954 Lublin, Poland
- Department of Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Cezary Grochowski
- Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
- Laboratory of Virtual Man, Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
- Correspondence:
| | - Joanna Litak
- St. John‘s Cancer Center in Lublin, 20-090 Lublin, Poland
| | - Ida Osuchowska
- Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Krzysztof Gosik
- Department of Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | | | - Piotr Kamieniak
- Department of Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Jacek Rolinski
- Department of Immunology, Medical University of Lublin, 20-093 Lublin, Poland
| |
Collapse
|
34
|
Wiese MD, Manning-Bennett AT, Abuhelwa AY. Investigational IRAK-4 inhibitors for the treatment of rheumatoid arthritis. Expert Opin Investig Drugs 2020; 29:475-482. [PMID: 32255710 DOI: 10.1080/13543784.2020.1752660] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Rheumatoid arthritis (RA) is a chronic inflammatory auto-immune disease that can lead to permanent disability and deformity. Despite current treatment modalities, many patients are still unable to reach remission. Interleukin-1 receptor-associated kinase 4 (IRAK-4) inhibitors are novel agents designed to suppress immune signaling pathways involved in inflammation and joint destruction in RA. Four IRAK-4 inhibitors have entered clinical trials. AREAS COVERED This review summarizes the current stage of development of IRAK-4 inhibitors in clinical trials, detailing their chemistry, pharmacokinetics, and therapeutic potential in the treatment of RA. PubMed, Embase and restricted Google searches were conducted using the term 'IRAK-4', and publicly accessible clinical trial databases were reviewed. EXPERT OPINION IRAK-4 inhibitors are an exciting therapeutic option in RA management because unlike other targeted disease-modifying agents, they target the innate immune system. The role of IRAK-4 as a key component of Toll/Interleukin-1 receptor signaling and its potential for a low rate of infectious complications is particularly exciting and this may facilitate their use in combination treatment. A key aspect of upcoming clinical trials will be the identification of biomarkers predictive of treatment efficacy, which will help to define if and how they will be used in the clinic.
Collapse
Affiliation(s)
- Michael D Wiese
- Clinical and Health Sciences, University of South Australia , Adelaide, Australia.,Health and Biomedical Innovation Group, University of South Australia , Adelaide, Australia
| | - Arkady T Manning-Bennett
- Clinical and Health Sciences, University of South Australia , Adelaide, Australia.,Health and Biomedical Innovation Group, University of South Australia , Adelaide, Australia
| | - Ahmad Y Abuhelwa
- Clinical and Health Sciences, University of South Australia , Adelaide, Australia.,Australian Centre for Precision Medicine, Cancer Research Institute, University of South Australia , Adelaide, Australia
| |
Collapse
|
35
|
Rajapaksa NS, Gobbi A, Drobnick J, Do S, Kolesnikov A, Liang J, Chen Y, Sujatha-Bhaskar S, Huang Z, Brightbill H, Francis R, Yu C, Choo EF, DeMent K, Ran Y, An L, Emson C, Maher J, Wai J, McKenzie BS, Lupardus PJ, Zarrin AA, Kiefer JR, Bryan MC. Discovery of Potent Benzolactam IRAK4 Inhibitors with Robust in Vivo Activity. ACS Med Chem Lett 2020; 11:327-333. [PMID: 32184965 DOI: 10.1021/acsmedchemlett.9b00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022] Open
Abstract
IRAK4 kinase activity transduces signaling from multiple IL-1Rs and TLRs to regulate cytokines and chemokines implicated in inflammatory diseases. As such, there is high interest in identifying selective IRAK4 inhibitors for the treatment of these disorders. We previously reported the discovery of potent and selective dihydrobenzofuran inhibitors of IRAK4. Subsequent studies, however, showed inconsistent inhibition in disease-relevant pharmacodynamic models. Herein, we describe application of a human whole blood assay to the discovery of a series of benzolactam IRAK4 inhibitors. We identified potent molecule 19 that achieves robust in vivo inhibition of cytokines relevant to human disease.
Collapse
Affiliation(s)
- Naomi S. Rajapaksa
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Alberto Gobbi
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Joy Drobnick
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Steven Do
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Aleksandr Kolesnikov
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Jun Liang
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Yongsheng Chen
- WuXi Apptech, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, P. R. China
| | | | - Zhiyu Huang
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Hans Brightbill
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Ross Francis
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Christine Yu
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Edna F. Choo
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Kevin DeMent
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Yingqing Ran
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Le An
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Claire Emson
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Jonathan Maher
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - John Wai
- WuXi Apptech, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, P. R. China
| | - Brent S. McKenzie
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Patrick J. Lupardus
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Ali A. Zarrin
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - James R. Kiefer
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| | - Marian C. Bryan
- Genentech, Inc., One DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
36
|
Scarneo SA, Hughes PF, Yang KW, Carlson DA, Gurbani D, Westover KD, Haystead TAJ. A highly selective inhibitor of interleukin-1 receptor-associated kinases 1/4 (IRAK-1/4) delineates the distinct signaling roles of IRAK-1/4 and the TAK1 kinase. J Biol Chem 2020; 295:1565-1574. [PMID: 31914413 PMCID: PMC7008364 DOI: 10.1074/jbc.ra119.011857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Interleukin-1 receptor-associated kinase-1 (IRAK-1) and IRAK-4, as well as transforming growth factor β-activated kinase 1 (TAK1), are protein kinases essential for transducing inflammatory signals from interleukin receptors. IRAK family proteins and TAK1 have high sequence identity within the ATP-binding pocket, limiting the development of highly selective IRAK-1/4 or TAK1 inhibitors. Beyond kinase activity, IRAKs and TAK1 act as molecular scaffolds along with other signaling proteins, complicating the interpretation of experiments involving knockin or knockout approaches. In contrast, pharmacological manipulation offers the promise of targeting catalysis-mediated signaling without grossly disrupting the cellular architecture. Recently, we reported the discovery of takinib, a potent and highly selective TAK1 inhibitor that has only marginal activity against IRAK-4. On the basis of the TAK1-takinib complex structure and the structure of IRAK-1/4, here we defined critical contact sites of the takinib scaffold within the nucleotide-binding sites of each respective kinase. Kinase activity testing of takinib analogs against IRAK-4 identified a highly potent IRAK-4 inhibitor (HS-243). In a kinome-wide screen of 468 protein kinases, HS-243 had exquisite selectivity toward both IRAK-1 (IC50 = 24 nm) and IRAK-4 (IC50 = 20 nm), with only minimal TAK1-inhibiting activity (IC50 = 0.5 μm). Using HS-243 and takinib, we evaluated the consequences of cytokine/chemokine responses after selective inhibition of IRAK-1/4 or TAK1 in response to lipopolysaccharide challenge in human rheumatoid arthritis fibroblast-like synoviocytes. Our results indicate that HS-243 specifically inhibits intracellular IRAKs without TAK1 inhibition and that these kinases have distinct, nonredundant signaling roles.
Collapse
Affiliation(s)
- Scott A Scarneo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Kelly W Yang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - David A Carlson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, Dallas, Texas 75390
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, Dallas, Texas 75390
| | - Timothy A J Haystead
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710.
| |
Collapse
|
37
|
Kargbo RB. PROTAC Degradation of IRAK4 for the Treatment of Cancer. ACS Med Chem Lett 2019; 10:1370-1371. [PMID: 31620217 PMCID: PMC6792152 DOI: 10.1021/acsmedchemlett.9b00423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Robert B. Kargbo
- Usona Institute, 277 Granada Drive, San Luis
Obispo, California 93401-7337, United States
| |
Collapse
|
38
|
Li H, Chen T, Sun H, Wu X, Jiang X, Ren C. Functional characterisation of Holothuria leucospilota Fas-associated death domain in the innate immune-related signalling pathways. Innate Immun 2019; 26:138-145. [PMID: 31550955 PMCID: PMC7016406 DOI: 10.1177/1753425919877680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this study, the functions of Holothuria leucospilota Fas-associated death domain (HLFADD) in the innate immune-related signalling pathways were investigated. The results showed that over-expression of HLFADD in HEK293T cells could activate the transcription factors NF-κB and activator protein-1 (AP-1), and induce the secretion of downstream pro-inflammatory cytokines IL-6, IL-8 and IL-18, suggesting the involvement of the sea cucumber FADD in activating the NF-κB and c-Jun NH2-terminal kinase-dependent pathways. On the other hand, HLFADD could down-regulate the activations of NF-κB and AP-1 that induced by over-expression of H. leucospilota myeloid differentiation factor 88 (HLMyD88), which is supposed to be mediated through its interaction with HLMyD88 to keep the MyD88-dependent TLR signalling at a proper magnitude. The interaction of HLFADD and HLMyD88 were further supported by a co-immunoprecipitation assay. Moreover, HLFADD could activate transcription factor IFN regulatory factor-3 and induced the secretion of downstream IFN-α and IFN-β, indicating that the sea cucumber FADD may also activate the antiviral IFN signalling pathway. In summary, our study may give new insights on the functions of sea cucumber FADD in the innate immune-related signalling pathways.
Collapse
Affiliation(s)
- Haipeng Li
- School of Environmental Science and Engineering, Guangzhou University, PR China
| | - Ting Chen
- CAS Key laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China
| | - Hongyan Sun
- College of Marine Sciences, South China Agricultural University, PR China
| | - Xiaofen Wu
- CAS Key laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China
| | - Xiao Jiang
- CAS Key laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China
| | - Chunhua Ren
- CAS Key laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, PR China.,Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China
| |
Collapse
|
39
|
Kargbo RB. PROTAC Degradation of IRAK4 for the Treatment of Neurodegenerative and Cardiovascular Diseases. ACS Med Chem Lett 2019; 10:1251-1252. [PMID: 31531192 PMCID: PMC6746078 DOI: 10.1021/acsmedchemlett.9b00385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Indexed: 01/25/2023] Open
Affiliation(s)
- Robert B. Kargbo
- Usona Institute, 277 Granada Drive, San Luis
Obispo, California 93401-7337, United States
| |
Collapse
|
40
|
Nunes J, McGonagle GA, Eden J, Kiritharan G, Touzet M, Lewell X, Emery J, Eidam H, Harling JD, Anderson NA. Targeting IRAK4 for Degradation with PROTACs. ACS Med Chem Lett 2019; 10:1081-1085. [PMID: 31312412 DOI: 10.1021/acsmedchemlett.9b00219] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Interleukin-1 Receptor-Associated Kinase 4 (IRAK4) is a key mediator of innate immunity. IRAK4 overactivation is linked with several autoimmune diseases. To date, many IRAK4 inhibitors have been developed to block the protein's kinase activity with the most advanced reaching Phase II clinical trials. Nevertheless, several reports suggest kinase activity is not disease-relevant in certain cell types, so removing scaffolding signaling in addition to IRAK4 kinase activity may offer a better therapeutic outcome. Herein, we describe the design and synthesis of an IRAK4 Proteolysis Targeted Chimera (PROTAC). We show that IRAK4 degradation induced by compound 9 leads to the inhibition of multiple cytokines in PBMCs. However, in IL-1β stimulated human dermal fibroblasts, inhibition of IL-6 and TNF-α release was not observed despite IRAK4 degradation. Nonetheless, the possibility of targeting both IRAK4 kinase and scaffolding function could potentially lead to new therapeutic opportunities to treat autoimmune, inflammatory, and oncological diseases.
Collapse
Affiliation(s)
- Joao Nunes
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| | - Grant A. McGonagle
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| | - Jessica Eden
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| | - Girieshanie Kiritharan
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| | - Megane Touzet
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| | - Xiao Lewell
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| | - John Emery
- GlaxoSmithKline, King of Prussia, Pennsylvania 19406, United States
| | - Hilary Eidam
- GlaxoSmithKline, King of Prussia, Pennsylvania 19406, United States
| | - John D. Harling
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| | - Niall A. Anderson
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K
| |
Collapse
|
41
|
Bryan MC, Drobnick J, Gobbi A, Kolesnikov A, Chen Y, Rajapaksa N, Ndubaku C, Feng J, Chang W, Francis R, Yu C, Choo EF, DeMent K, Ran Y, An L, Emson C, Huang Z, Sujatha-Bhaskar S, Brightbill H, DiPasquale A, Maher J, Wai J, McKenzie BS, Lupardus PJ, Zarrin AA, Kiefer JR. Development of Potent and Selective Pyrazolopyrimidine IRAK4 Inhibitors. J Med Chem 2019; 62:6223-6240. [PMID: 31082230 DOI: 10.1021/acs.jmedchem.9b00439] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A series of pyrazolopyrimidine inhibitors of IRAK4 were developed from a high-throughput screen (HTS). Modification of an HTS hit led to a series of bicyclic heterocycles with improved potency and kinase selectivity but lacking sufficient solubility to progress in vivo. Structure-based drug design, informed by cocrystal structures with the protein and small-molecule crystal structures, yielded a series of dihydrobenzofurans. This semisaturated bicycle provided superior druglike properties while maintaining excellent potency and selectivity. Improved physicochemical properties allowed for progression into in vivo experiments, where lead molecules exhibited low clearance and showed target-based inhibition of IRAK4 signaling in an inflammation-mediated PK/PD mouse model.
Collapse
Affiliation(s)
- Marian C Bryan
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Joy Drobnick
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Alberto Gobbi
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Aleksandr Kolesnikov
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Yongsheng Chen
- WuXi Apptec , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone , Shanghai 200131 , P. R. China
| | - Naomi Rajapaksa
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Chudi Ndubaku
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Jianwen Feng
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Willy Chang
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Ross Francis
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Christine Yu
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Edna F Choo
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Kevin DeMent
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Yingqing Ran
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Le An
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Claire Emson
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Zhiyu Huang
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | | | - Hans Brightbill
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Antonio DiPasquale
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Jonathan Maher
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - John Wai
- WuXi Apptec , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone , Shanghai 200131 , P. R. China
| | - Brent S McKenzie
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Patrick J Lupardus
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - Ali A Zarrin
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| | - James R Kiefer
- Genentech, Inc. , One DNA Way , South San Francisco , California 94080 , United States
| |
Collapse
|
42
|
McElroy WT. Interleukin-1 receptor-associated kinase 4 (IRAK4) inhibitors: an updated patent review (2016-2018). Expert Opin Ther Pat 2019; 29:243-259. [PMID: 30916602 DOI: 10.1080/13543776.2019.1597850] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Interleukin-1 receptor-associated kinase 4 (IRAK4) is the most upstream kinase in Toll/Interleukin-1 receptor (TIR) signaling. Human and rodent genetics support the role of IRAK4 in immune function and the involvement of IRAK4-dependent signaling in certain cancers is hypothesized. The accumulating evidence has motivated the discovery of IRAK4 inhibitors that could be used therapeutically. AREAS COVERED This review summarizes patents published in 2016-2018 claiming IRAK4 inhibitors. Representative analogues from each patent are presented with a focus on compounds that have been profiled in cellular and in vivo assays. EXPERT OPINION The last three years have seen an increased number of IRAK4 inhibitors with which to assess the therapeutic potential of the target. At least 5 companies are believed to have advanced to the clinic. Pfizer is in phase II for rheumatoid arthritis (RA). The outcomes of these studies should inform on the therapeutic potential in autoimmune disease and cancer.
Collapse
Affiliation(s)
- William T McElroy
- a Merck Sharp & Dohme Corp , a subsidiary of Merck & Co., Inc , Kenilworth , NJ , USA
| |
Collapse
|
43
|
Khanfar MA, Alqtaishat S. Discovery of potent IRAK-4 inhibitors as potential anti-inflammatory and anticancer agents using structure-based exploration of IRAK-4 pharmacophoric space coupled with QSAR analyses. Comput Biol Chem 2019; 79:147-154. [PMID: 30818109 DOI: 10.1016/j.compbiolchem.2019.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022]
Abstract
Interleukin-1 Receptor-Associated Kinase 4 (IRAK-4) has an important role in immunity, inflammation, and malignancy. The significant role of IRAK-4 makes it an interesting target for the discovery and development of potent small molecule inhibitors. In the current study, multiple linear regression -based QSAR analyses coupled with structure-based pharmacophoric exploration was applied to reveal the structural and physiochemical properties required for IRAK-4 inhibition. Manually built pharmacophoric models were initially validated with receiver operating characteristic curve, and best-ranked models were subsequently integrated in QSAR analysis along with other physiochemical descriptors. The pharmacophore model, selected using the statistically optimum QSAR equation, was implied as a 3D-search filter to mine the National Cancer Institute database for novel IRAK-4 inhibitors. Whereas the associated QSAR model prioritized the bioactivities of captured hits for in vitro evaluation. Experimental validation identified several potent IRAK-4 inhibitors of novel structural scaffolds. The most potent captured hit exhibited an IC50 value of 157 nM.
Collapse
Affiliation(s)
- Mohammad A Khanfar
- Heinrich Heine University Düsseldorf, Institute of Pharmaceutical and Medicinal Chemistry, Universitaetsstr. 1, 40225 Düsseldorf, Germany; College of Pharmacy, Alfaisal University, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia.
| | - Saja Alqtaishat
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, P.O Box 13140, Amman 11942, Jordan
| |
Collapse
|
44
|
Zhao L, Jiang X, Chen T, Sun H, Ren C. Molecular characterization and functional analysis of MyD88 from the tropical sea cucumber, Holothuria leucospilota. FISH & SHELLFISH IMMUNOLOGY 2018; 83:1-7. [PMID: 30194053 DOI: 10.1016/j.fsi.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/01/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
In this study, a myeloid differentiation factor 88 (MyD88) named as HLMyD88 was identified from the sea cucumber Holothuria leucospilota. The full-length cDNA of HLMyD88 is 4797 bp in size, containing a 227 bp 5'-untranslated region (UTR), a 3721 bp 3'-UTR and an 849 bp open reading frame (ORF) encoding a protein of 282 amino acids with a deduced molecular weight of 32.25 kDa HLMyD88 contains an N-terminal death domain and a C-terminal Toll/interluekin-1 receptor (TIR) domain with three highly conserved sequence motifs named as Box 1, Box 2 and Box 3. The results of luciferase reporter assay showed that over-expressed HLMyD88 in HEK293T cells could activate the transcription factors nuclear factor-κB (NF-κB) and activator protein 1 (AP-1). Additionally, the secretion of proinflammatory cytokines IL-1β and TNF-α in the HEK293T cells was increased by over-expressed HLMyD88, indicating the potential role of HLMyD88 in the innate immunity of sea cucumber. Moreover, we further confirmed that over-expressed HLMyD88 could also induce apoptosis.
Collapse
Affiliation(s)
- Lin Zhao
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
| | - Hongyan Sun
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, PR China.
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China.
| |
Collapse
|
45
|
Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches. Molecules 2018; 23:molecules23123136. [PMID: 30501110 PMCID: PMC6321621 DOI: 10.3390/molecules23123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/28/2018] [Accepted: 11/28/2018] [Indexed: 01/13/2023] Open
Abstract
Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositioning of a known kinase inhibitor in the ATP binding sites of kinases that exhibited a TWN similar to interleukin-1 receptor-associated kinase 4 (IRAK4) allowed us to identify a hit molecule. Another hit molecule was obtained from a commercial chemical library using pharmacophore-based virtual screening and molecular docking approaches. Pharmacophoric features of the hit molecules were hybridized to design a novel compound that inhibited IRAK4 at low nanomolar levels in the in vitro assay.
Collapse
|
46
|
Wright SW, Li B, Peng Z, Wei L, McInturff E, Place D, Damon DB, Singer RA. Improvements to Enable the Large Scale Synthesis of 1-{[(2S,3S,4S)-3-Ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833). Org Process Res Dev 2018. [DOI: 10.1021/acs.oprd.8b00386] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen W. Wright
- Medicine Design, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Bryan Li
- Chemical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Zhihui Peng
- Chemical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lulin Wei
- Chemical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Emma McInturff
- Chemical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - David Place
- Chemical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - David B. Damon
- Chemical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Robert A. Singer
- Chemical Research and Development, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| |
Collapse
|
47
|
Shamilov R, Aneskievich BJ. TNIP1 in Autoimmune Diseases: Regulation of Toll-like Receptor Signaling. J Immunol Res 2018; 2018:3491269. [PMID: 30402506 PMCID: PMC6192141 DOI: 10.1155/2018/3491269] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/17/2018] [Indexed: 02/08/2023] Open
Abstract
TNIP1 protein is increasingly being recognized as a key repressor of inflammatory signaling and a potential factor in multiple autoimmune diseases. In addition to earlier foundational reports of TNIP1 SNPs in human autoimmune diseases and TNIP1 protein-protein interaction with receptor regulating proteins, more recent studies have identified new potential interaction partners and signaling pathways likely modulated by TNIP1. Subdomains within the TNIP1 protein as well as how they interact with ubiquitin have not only been mapped but inflammatory cell- and tissue-specific consequences subsequent to their defective function are being recognized and related to human disease states such as lupus, scleroderma, and psoriasis. In this review, we emphasize receptor signaling complexes and regulation of cytoplasmic signaling steps downstream of TLR given their association with some of the same autoimmune diseases where TNIP1 has been implicated. TNIP1 dysfunction or deficiency may predispose healthy cells to the inflammatory response to otherwise innocuous TLR ligand exposure. The recognition of the anti-inflammatory roles of TNIP1 and improved integrated understanding of its physical and functional association with other signaling pathway proteins may position TNIP1 as a candidate target for the design and/or testing of next-generation anti-inflammatory therapeutics.
Collapse
Affiliation(s)
- Rambon Shamilov
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA
- Stem Cell Institute, University of Connecticut, Storrs, CT 06269-3092, USA
| |
Collapse
|
48
|
Balka KR, De Nardo D. Understanding early TLR signaling through the Myddosome. J Leukoc Biol 2018; 105:339-351. [PMID: 30256449 DOI: 10.1002/jlb.mr0318-096r] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/27/2018] [Accepted: 09/06/2018] [Indexed: 12/27/2022] Open
Abstract
TLRs are expressed on the plasma and endosomal membranes of innate immune cells acting as sensors of foreign and inherent danger signals that threaten the host. Upon activation, TLRs facilitate the assembly of large intracellular oligomeric signaling complexes, termed Myddosomes, which initiate key signal transduction pathways to elicit critical inflammatory immune responses. The formation of the Myddosome is integral for TLR signaling; however, the molecular mechanisms controlling its formation, disassembly, and the subsequent proximal signaling events remain to be clearly defined. In this review, we present a brief overview of TLR signal transduction pathways, summarize the current understanding of the Myddosome and the proteins that comprise its structure, including MyD88 and members of the IL-1 receptor-associated kinase (IRAK) family. Finally, we will discuss recent advances and open questions regarding early TLR signaling in the context of the Myddosome complex.
Collapse
Affiliation(s)
- Katherine R Balka
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Dominic De Nardo
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
49
|
Singer JW, Fleischman A, Al-Fayoumi S, Mascarenhas JO, Yu Q, Agarwal A. Inhibition of interleukin-1 receptor-associated kinase 1 (IRAK1) as a therapeutic strategy. Oncotarget 2018; 9:33416-33439. [PMID: 30279971 PMCID: PMC6161786 DOI: 10.18632/oncotarget.26058] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 08/15/2018] [Indexed: 02/06/2023] Open
Abstract
Interleukin-1 receptor-associated kinases (IRAK1, IRAK2, IRAK3 [IRAK-M], and IRAK4) are serine-threonine kinases involved in toll-like receptor and interleukin-1 signaling pathways, through which they regulate innate immunity and inflammation. Evidence exists that IRAKs play key roles in the pathophysiologies of cancers, and metabolic and inflammatory diseases, and that IRAK inhibition has potential therapeutic benefits. Molecules capable of selectively interfering with IRAK function and expression have been reported, paving the way for the clinical evaluation of IRAK inhibition. Herein, we focus on IRAK1, review its structure and physiological roles, and summarize emerging data for IRAK1 inhibitors in preclinical and clinical studies.
Collapse
Affiliation(s)
| | - Angela Fleischman
- Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | | | - John O Mascarenhas
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qiang Yu
- Genome Institute of Singapore, Singapore, SG, Singapore
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
50
|
De S, Karim F, Kiessu E, Cushing L, Lin LL, Ghandil P, Hoarau C, Casanova JL, Puel A, Rao VR. Mechanism of dysfunction of human variants of the IRAK4 kinase and a role for its kinase activity in interleukin-1 receptor signaling. J Biol Chem 2018; 293:15208-15220. [PMID: 30115681 DOI: 10.1074/jbc.ra118.003831] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/08/2018] [Indexed: 01/13/2023] Open
Abstract
Interleukin-1 receptor (IL1R)-associated kinase 4 (IRAK4) is a central regulator of innate immune signaling, controlling IL1R and Toll-like receptor (TLR)-mediated responses and containing both scaffolding and kinase activities. Humans deficient in IRAK4 activity have autosomal recessive primary immune deficiency (PID). Here, we characterized the molecular mechanism of dysfunction of two IRAK4 PID variants, G298D and the compound variant R12C (R12C/R391H/T458I). Using these variants and the kinase-inactive D329A variant to delineate the contributions of IRAK4's scaffolding and kinase activities to IL1R signaling, we found that the G298D variant is kinase-inactive and expressed at extremely low levels, acting functionally as a null mutation. The R12C compound variant possessed WT kinase activity, but could not interact with myeloid differentiation primary response 88 (MyD88) and IRAK1, causing impairment of IL-1-induced signaling and cytokine production. Quantitation of IL-1 signaling in IRAK4-deficient cells complemented with either WT or the R12C or D329A variant indicated that the loss of MyD88 interaction had a greater impact on IL-1-induced signaling and cytokine expression than the loss of IRAK4 kinase activity. Importantly, kinase-inactive IRAK4 exhibited a greater association with MyD88 and a weaker association with IRAK1 in IRAK4-deficient cells expressing kinase-inactive IRAK4 and in primary cells treated with a selective IRAK4 inhibitor. Loss of IRAK4 kinase activity only partially inhibited IL-1-induced cytokine and NF-κB signaling. Therefore, the IRAK4-MyD88 scaffolding function is essential for IL-1 signaling, but IRAK4 kinase activity can control IL-1 signal strength by modulating the association of IRAK4, MyD88, and IRAK1.
Collapse
Affiliation(s)
- Saurav De
- From the Inflammation and Immunology Research Unit, Pfizer Inc., Cambridge, Massachusetts 02139
| | - Fawziya Karim
- From the Inflammation and Immunology Research Unit, Pfizer Inc., Cambridge, Massachusetts 02139
| | - Ezechielle Kiessu
- From the Inflammation and Immunology Research Unit, Pfizer Inc., Cambridge, Massachusetts 02139
| | - Leah Cushing
- From the Inflammation and Immunology Research Unit, Pfizer Inc., Cambridge, Massachusetts 02139
| | - Lih-Ling Lin
- From the Inflammation and Immunology Research Unit, Pfizer Inc., Cambridge, Massachusetts 02139
| | - Pegah Ghandil
- the Diabetes Research Center and.,Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Cyrille Hoarau
- the Transversal Unit of Allergology and Clinical Immunology, Regional University Hospital Center of Tours, 37044 Tours cedex 9, France, and
| | - Jean-Laurent Casanova
- the Imagine Institute, Paris Descartes University, 75015 Paris, France.,the St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York 10065.,the Pediatric Hematology-Immunology Unit, Assistance Publique-Hôpitaux de Paris (AP-HP), Necker Hospital for Sick Children, 75015 Paris, France.,the Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, 75015 Paris, France.,the Howard Hughes Medical Institute, New York, New York 10065
| | - Anne Puel
- the Imagine Institute, Paris Descartes University, 75015 Paris, France.,the St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York 10065.,the Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, 75015 Paris, France
| | - Vikram R Rao
- From the Inflammation and Immunology Research Unit, Pfizer Inc., Cambridge, Massachusetts 02139,
| |
Collapse
|