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Chen L, Tang Y, Lang JJ, Lin Y, Yu Z, Li X, Zheng X, Mi P, Lv Y, Lin YW. Design, synthesis and evaluation of C-5 substituted pyrrolopyridine derivatives as potent Janus Kinase 1 inhibitors with excellent selectivity. Eur J Med Chem 2024; 267:116210. [PMID: 38359535 DOI: 10.1016/j.ejmech.2024.116210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
The development of highly selective Janus Kinase 1 (JAK1) inhibitors is crucial for improving efficacy and minimizing adverse effects in the clinical treatment of autoimmune diseases. In a prior study, we designed a series of C-5 4-pyrazol substituted pyrrolopyridine derivatives that demonstrated significant potency against JAK1, with a 10 ∼ 20-fold selectivity over Janus Kinase 2 (JAK2). Building on this foundation, we adopted orthogonal strategy by modifying the C-5 position with 3-pyrazol/4-pyrazol/3-pyrrol groups and tail with substituted benzyl groups on the pyrrolopyridine head to enhance both potency and selectivity. In this endeavor, we have identified several compounds that exhibit excellent potency and selectivity for JAK1. Notably, compounds 12b and 12e, which combined 4-pyrazol group at C-5 site and meta-substituted benzyl tails, displayed IC50 value with 2.4/2.2 nM and high 352-/253-fold selectivity for JAK1 over JAK2 in enzyme assays. Additionally, both compounds showed good JAK1-selective in Ba/F3-TEL-JAK1/2 cell-based assays. These findings mark a substantial improvement, as these compounds are 10-fold more potent and over 10-fold more selective than the best compound identified in our previous study. The noteworthy potency and selectivity properties of compounds 12b and 12e suggest their potential utility in furthering the development of drugs for autoimmune diseases.
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Affiliation(s)
- Limei Chen
- Department of Pharmacy, Hengyang Medicinal School, University of South China, Hengyang, Hunan, 421001, China
| | - Yahua Tang
- The Affiliated Nanhua Hospital, Department of Pharmacy, Institute of Clinical Pharmacy, Hengyang Medical School, University of South China, Hunan, 421001, China
| | - Jia-Jia Lang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, Hunan, 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, Hunan, 421001, China
| | - Yuqing Lin
- Department of Pharmacy, Hengyang Medicinal School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhixin Yu
- Department of Pharmacy, Hengyang Medicinal School, University of South China, Hengyang, Hunan, 421001, China
| | - Xinhao Li
- Department of Pharmacy, Hengyang Medicinal School, University of South China, Hengyang, Hunan, 421001, China
| | - Xing Zheng
- Department of Pharmacy, Hengyang Medicinal School, University of South China, Hengyang, Hunan, 421001, China; Department of Pharmacy, Hunan Vocational College of Science and Technology, Changsha, Hunan, 410004, China
| | - Pengbing Mi
- Department of Pharmacy, Hengyang Medicinal School, University of South China, Hengyang, Hunan, 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, Hunan, 421001, China.
| | - You Lv
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi, 710021, China; Xi'an Amazinggene Co., Ltd, Xi'an, Shaanxi, 710026, China.
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, Hunan, 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang, Hunan, 421001, China.
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Maji L, Sengupta S, Purawarga Matada GS, Teli G, Biswas G, Das PK, Panduranga Mudgal M. Medicinal chemistry perspective of JAK inhibitors: synthesis, biological profile, selectivity, and structure activity relationship. Mol Divers 2024:10.1007/s11030-023-10794-5. [PMID: 38236444 DOI: 10.1007/s11030-023-10794-5] [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: 10/26/2023] [Accepted: 12/07/2023] [Indexed: 01/19/2024]
Abstract
JAK-STAT signalling pathway was discovered more than quarter century ago. The JAK-STAT pathway protein is considered as one of the crucial hubs for cytokine secretion which mediates activation of different inflammatory, cellular responses and hence involved in different etiological factors. The various etiological factors involved are haematopoiesis, immune fitness, tissue repair, inflammation, apoptosis, and adipogenesis. The presence of the active mutation V617K plays a significant role in the progression of the JAK-STAT pathway-related disease. Consequently, targeting the JAK-STAT pathway could be a promising therapeutic approach for addressing a range of causative factors. In this current review, we provided a comprehensive discussion for the in-detail study of anatomy and physiology of the JAK-STAT pathway which contributes structural domain rearrangement, activation, and negative regulation associated with the downstream signaling pathway, relationship between different cytokines and diseases. This review also discussed the recent development of clinical trial entities. Additionally, this review also provides updates on FDA-approved drugs. In the current investigation, we have classified recently developed small molecule inhibitors of JAK-STAT pathway according to different chemical classes and we emphasized their synthetic routes, biological evaluation, selectivity, and structure-activity relationship.
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Affiliation(s)
- Lalmohan Maji
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Sindhuja Sengupta
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | | | - Ghanshyam Teli
- School of Pharmacy, Sangam University, Atoon, Bhilwara, 311001, Rajasthan, India
| | - Gourab Biswas
- Department of Pharmaceutical Technology, Brainware University, Kolkata, West Bengal, India
| | - Pronoy Kanti Das
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
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Park E, Park S, Lee SJ, Jeong D, Jin H, Moon H, Cha B, Kim D, Ma S, Seo W, Han SH, Lee YS, Kang S. Identification and Biological Evaluation of a Potent and Selective JAK1 Inhibitor for the Treatment of Pulmonary Fibrosis. J Med Chem 2023; 66:16342-16363. [PMID: 38031930 DOI: 10.1021/acs.jmedchem.3c01712] [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: 12/01/2023]
Abstract
Janus kinase 1 (JAK1) plays a pivotal role in regulating inflammation and fibrosis via the JAK/STAT signaling pathway, making it a promising target for associated diseases. In this study, we explored the modification of an N-methyl 1H-pyrrolo[2,3-b]pyridine-5-carboxylate core, leading to the identification of 4-(((2S,4S)-1-(4-trifluoromethyl)-2-methylpiperidin-4-yl)amino)-N-methyl-1H-pyrrolo[2,3-b]pyridine-5-carboxamide (36b) as a highly potent and selective JAK1 inhibitor. Compound 36b exhibited an impressive IC50 value of 0.044 nM for JAK1 and demonstrated remarkable selectivity of 382-fold, 210-fold, and 1325-fold specificity over JAK2, JAK3, and TYK2, respectively. The kinase panel assays further confirmed its specificity, and cell-based experiments established its efficacy in inhibiting JAK1-STAT phosphorylation in human L-132 or SK-MES-1 cells. Pharmacokinetic studies revealed that compound 36b boasts an oral bioavailability exceeding 36%. In a bleomycin-induced fibrosis mouse model, compound 36b significantly reduced STAT3 phosphorylation, resulting in improvement in body weight and reduced collagen deposition, all achieved without significant side effects.
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Affiliation(s)
- Eunsun Park
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seolhee Park
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun Joo Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Dayeon Jeong
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hee Jin
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Heegyum Moon
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Boksik Cha
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Dayea Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Seonghee Ma
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Wonhyo Seo
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seung-Hee Han
- Central Research Laboratory, KOREA PHARMA Co. Ltd., Jeyakgongdan 3-gil, Hyangnam-eup, Hwaseong-si, Gyeonggi-do 16630, Republic of Korea
| | - Yun-Sil Lee
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Soosung Kang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
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Wang Z, Sun L, Xu Y, Liang P, Xu K, Huang J. Discovery of novel JAK1 inhibitors through combining machine learning, structure-based pharmacophore modeling and bio-evaluation. J Transl Med 2023; 21:579. [PMID: 37641144 PMCID: PMC10464202 DOI: 10.1186/s12967-023-04443-6] [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: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Janus kinase 1 (JAK1) plays a critical role in most cytokine-mediated inflammatory, autoimmune responses and various cancers via the JAK/STAT signaling pathway. Inhibition of JAK1 is therefore an attractive therapeutic strategy for several diseases. Recently, high-performance machine learning techniques have been increasingly applied in virtual screening to develop new kinase inhibitors. Our study aimed to develop a novel layered virtual screening method based on machine learning (ML) and pharmacophore models to identify the potential JAK1 inhibitors. METHODS Firstly, we constructed a high-quality dataset comprising 3834 JAK1 inhibitors and 12,230 decoys, followed by establishing a series of classification models based on a combination of three molecular descriptors and six ML algorithms. To further screen potential compounds, we constructed several pharmacophore models based on Hiphop and receptor-ligand algorithms. We then used molecular docking to filter the recognized compounds. Finally, the binding stability and enzyme inhibition activity of the identified compounds were assessed by molecular dynamics (MD) simulations and in vitro enzyme activity tests. RESULTS The best performance ML model DNN-ECFP4 and two pharmacophore models Hiphop3 and 6TPF 08 were utilized to screen the ZINC database. A total of 13 potentially active compounds were screened and the MD results demonstrated that all of the above molecules could bind with JAK1 stably in dynamic conditions. Among the shortlisted compounds, the four purchasable compounds demonstrated significant kinase inhibition activity, with Z-10 being the most active (IC50 = 194.9 nM). CONCLUSION The current study provides an efficient and accurate integrated model. The hit compounds were promising candidates for the further development of novel JAK1 inhibitors.
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Affiliation(s)
- Zixiao Wang
- Department of Pharmacy, Honghui Hospital, Xi' an Jiaotong University, Xi' an, 710054, China.
| | - Lili Sun
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yu Xu
- State Key Laboratory of Natural Medicines,Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery,China Pharmaceutical University, Nanjing, 210009, China
| | - Peida Liang
- Department of Pharmacy, Honghui Hospital, Xi' an Jiaotong University, Xi' an, 710054, China
| | - Kaiyan Xu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Jing Huang
- Department of Pharmacy, Honghui Hospital, Xi' an Jiaotong University, Xi' an, 710054, China.
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5
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Lang JJ, Lv Y, Kobe B, Chen H, Tan Y, Chen L, Wang X, Mi P, Zheng X, Lin YW. Discovery of C-5 Pyrazole-Substituted Pyrrolopyridine Derivatives as Potent and Selective Inhibitors for Janus Kinase 1. J Med Chem 2023; 66:6725-6742. [PMID: 37163463 DOI: 10.1021/acs.jmedchem.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Developing selective inhibitors for Janus kinase 1 (JAK1) is a significant focus for improving the efficacy and alleviating the adverse effects in treating immune-inflammatory diseases. Herein, we report the discovery of a series of C-5 pyrazole-modified pyrrolopyrimidine derivatives as JAK1-selective inhibitors. The potential hydrogen bond between the pyrazole group and E966 in JAK1 is the key point that enhances JAK1 selectivity. These compounds exhibit 10- to 20-fold JAK1 selectivity over JAK2 in enzyme assays. Compound 12b also exhibits excellent JAK1 selectivity in Ba/F3-TEL-JAK cellular assays. Metabolism studies and the results of the hair growth model in mice indicate that compound 12b may be a viable lead compound for the development of highly JAK1-selective inhibitors for immune and inflammatory diseases.
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Affiliation(s)
- Jia-Jia Lang
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hengyang Medical College, School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - You Lv
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, China
- Xi'an Amazinggene Co., Ltd, Xi'an, Shaanxi 710026, China
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hongfei Chen
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yan Tan
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Limei Chen
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xuechuan Wang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, China
| | - Pengbing Mi
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Xing Zheng
- Department of Pharmacy, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Department of Pharmacy, Hunan Vocational College of Science and Technology, Changsha 410004, China
| | - Ying-Wu Lin
- Hengyang Medical College, School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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6
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Zhou S, Mao W, Su Y, Zheng X, Qian W, Shen M, Shan N, Li Y, Wang D, Wu S, Sun T, Mu L. Identification of TUL01101: A Novel Potent and Selective JAK1 Inhibitor for the Treatment of Rheumatoid Arthritis. J Med Chem 2022; 65:16716-16740. [PMID: 36512734 DOI: 10.1021/acs.jmedchem.2c01550] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Janus kinase 1 (JAK1) is a potential target for the treatment of rheumatoid arthritis (RA). In this study, the introduction of a spiro ring with a difluoro-substituted cyclopropionamide resulted in the identification of TUL01101 (compound 36) based on a triazolo[1,5-a]pyridine core of filgotinib. It showed excellent potency on JAK1 with an IC50 value of 3 nM and exhibited more than 12-fold selectivity for JAK2 and TYK2. Whole blood assay also demonstrated the high activity and selectivity (37-fold for JAK2). At the same time, TUL01101 also demonstrated excellent metabolic stability and pharmacokinetics (PK) profiles were assayed in three species (mouse, rat, and dog). Moreover, it has been validated for effective activity in the treatment of RA both in collagen-induced arthritis (CIA) and adjuvant-induced arthritis (AIA) models, with low dose and low toxicity. Now, TUL01101 has progressed into phase I clinical trials.
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Affiliation(s)
- Shuhao Zhou
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
| | - Weiwei Mao
- WuXi AppTec (Shanghai) Co., Ltd., 288 FuTe Zhong Road, Shanghai 200131, P. R. China
| | - Yuan Su
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
| | - Xuejian Zheng
- WuXi AppTec (Shanghai) Co., Ltd., 288 FuTe Zhong Road, Shanghai 200131, P. R. China
| | - Wenyuan Qian
- WuXi AppTec (Shanghai) Co., Ltd., 288 FuTe Zhong Road, Shanghai 200131, P. R. China
| | - Meiyue Shen
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
| | - Ningli Shan
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
| | - Yaoshuang Li
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
| | - Degang Wang
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
| | - Shouting Wu
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
| | - Tiemin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Liwei Mu
- Zhuhai United Laboratories Co., Ltd., NO.12 Jialian Road, Tanzhou Township, Zhongshan, Guangdong 528467, P. R. China
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Tang YX, Liu M, Liu L, Zhen BR, Wang TT, Li N, Lv N, Zhu Z, Sun G, Wang X, Chen S. Lipophilic Constituents in Salvia miltiorrhiza Inhibit Activation of the Hepatic Stellate Cells by Suppressing the JAK1/STAT3 Signaling Pathway: A Network Pharmacology Study and Experimental Validation. Front Pharmacol 2022; 13:770344. [PMID: 35517817 PMCID: PMC9065469 DOI: 10.3389/fphar.2022.770344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Liver fibrosis is currently a global health challenge with no approved therapy, with the activation of hepatic stellate cells being a principal factor. Lipophilic constituents in Salvia miltiorrhiza (LS) have been reported to improve liver function and reduce the indicators of liver fibrosis for patients with chronic hepatitis B induced hepatic fibrosis. However, the pharmacological mechanisms of LS on liver fibrosis have not been clarified. In this study, 71 active compounds, 342 potential target proteins and 22 signaling pathways of LS were identified through a network pharmacology strategy. Through text mining and data analysis, the JAK1/STAT3 signaling pathway was representatively selected for further experimental validation. We firstly confirmed the protective effect of LS on liver fibrosis in vivo by animal experiments. Hepatic stellate cells, which proliferated and displayed a fibroblast-like morphology similar to activated primary stellate cells, were applied to evaluate its underlying mechanisms. The results showed that LS could inhibit the cell viability, promote the cell apoptosis, decrease the expression of liver fibrosis markers, and downregulate the JAK1/STAT3 signaling pathway. These results demonstrated that LS could exert anti-liver-fibrosis effects by inhibiting the activation of HSCs and regulating the JAK1/STAT3 signaling pathway, which is expected to benefit its clinical application.
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Affiliation(s)
- Ya-Xin Tang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
- School of Medicine, Shanghai University, Shanghai, China
- GongQing Institute of Science and Technology, Gong Qing, China
| | - Mingming Liu
- Lianyungang Second People’s Hospital, Lianyungang, China
| | - Long Liu
- GongQing Institute of Science and Technology, Gong Qing, China
| | - Bo-Rui Zhen
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Tian-Tian Wang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Na Li
- School of Medicine, Shanghai University, Shanghai, China
| | - Nanning Lv
- Lianyungang Second People’s Hospital, Lianyungang, China
| | - Zhenyu Zhu
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Guoquan Sun
- Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Guoquan Sun, ; Xiaobo Wang, ; Si Chen,
| | - Xiaobo Wang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
- The 967th Hospital of the Chinese People’s Liberation Army Joint Logistics Support Force, Dalian, China
- *Correspondence: Guoquan Sun, ; Xiaobo Wang, ; Si Chen,
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
- *Correspondence: Guoquan Sun, ; Xiaobo Wang, ; Si Chen,
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8
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Wang Y, Gu Y, Lou C, Gong Y, Wu Z, Li W, Tang Y, Liu G. A multitask GNN-based interpretable model for discovery of selective JAK inhibitors. J Cheminform 2022; 14:16. [PMID: 35292114 PMCID: PMC8922399 DOI: 10.1186/s13321-022-00593-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/26/2022] [Indexed: 11/10/2022] Open
Abstract
The Janus kinase (JAK) family plays a pivotal role in most cytokine-mediated inflammatory and autoimmune responses via JAK/STAT signaling, and administration of JAK inhibitors is a promising therapeutic strategy for several diseases including COVID-19. However, to screen and design selective JAK inhibitors is a daunting task due to the extremely high homology among four JAK isoforms. In this study, we aimed to simultaneously predict pIC50 values of compounds for all JAK subtypes by constructing an interpretable GNN multitask regression model. The final model performance was positive, with R2 values of 0.96, 0.79 and 0.78 on the training, validation and test sets, respectively. Meanwhile, we calculated and visualized atom weights, followed by the rank sum tests and local mean comparisons to obtain key atoms and substructures that could be fine-tuned to design selective JAK inhibitors. Several successful case studies have demonstrated that our approach is feasible and our model could learn the interactions between proteins and small molecules well, which could provide practitioners with a novel way to discover and design JAK inhibitors with selectivity.
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Affiliation(s)
- Yimeng Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yaxin Gu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Chaofeng Lou
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuning Gong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
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9
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Keretsu S, Ghosh S, Cho SJ. Computer aided designing of novel pyrrolopyridine derivatives as JAK1 inhibitors. Sci Rep 2021; 11:23051. [PMID: 34845259 PMCID: PMC8630053 DOI: 10.1038/s41598-021-02364-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/10/2021] [Indexed: 02/07/2023] Open
Abstract
Janus kinases (JAKs) are a family of non-receptor kinases that play a key role in cytokine signaling and their aberrant activities are associated with the pathogenesis of various immune diseases. The JAK1 isoform plays an essential role in the types 1 and II interferon signaling and elicits signals from the interleukin-2, interleukin-4, gp130, and class 2 receptor families. It is ubiquitously expressed in humans and its overexpression has been linked with autoimmune diseases such as myeloproliferative neoplasm. Although JAK1 inhibitors such as Tofacitinib have been approved for medical use, the low potency and off-target effects of these inhibitors have limited their use and calls for the development of novel JAK1 inhibitors. In this study, we used computational methods on a series of pyrrolopyridine derivatives to design new JAK1 inhibitors. Molecular docking and molecular dynamics simulation methods were used to study the protein-inhibitor interactions. 3D-quantitative structure–activity relationship models were developed and were used to predict the activity of newly designed compounds. Free energy calculation methods were used to study the binding affinity of the inhibitors with JAK1. Of the designed compounds, seventeen of the compounds showed a higher binding energy value than the most active compound in the dataset and at least six of the compounds showed higher binding energy value than the pan JAK inhibitor Tofacitinib. The findings made in this study could be utilized for the further development of JAK1 inhibitors.
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Affiliation(s)
- Seketoulie Keretsu
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 501-759, Republic of Korea
| | - Suparna Ghosh
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 501-759, Republic of Korea
| | - Seung Joo Cho
- Department of Biomedical Sciences, College of Medicine, Chosun University, 375 Seosuk-dong, Dong-gu, Gwangju, 501-759, Republic of Korea. .,Department of Cellular Molecular Medicine, College of Medicine, Chosun University, Gwangju, 501-759, Republic of Korea.
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