1
|
Sanachai K, Mahalapbutr P, Hengphasatporn K, Shigeta Y, Seetaha S, Tabtimmai L, Langer T, Wolschann P, Kittikool T, Yotphan S, Choowongkomon K, Rungrotmongkol T. Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases. ACS OMEGA 2022; 7:33548-33559. [PMID: 36157769 PMCID: PMC9494641 DOI: 10.1021/acsomega.2c04535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Janus kinases (JAKs) are nonreceptor protein tyrosine kinases that play a role in a broad range of cell signaling. JAK2 and JAK3 have been involved in the pathogenesis of common lymphoid-derived diseases and leukemia cancer. Thus, inhibition of both JAK2 and JAK3 can be a potent strategy to reduce the risk of these diseases. In the present study, the pharmacophore models built based on the commercial drug tofacitinib and the JAK2/3 proteins derived from molecular dynamics (MD) trajectories were employed to search for a dual potent JAK2/3 inhibitor by a pharmacophore-based virtual screening of 54 synthesized pyrazolone derivatives from an in-house data set. Twelve selected compounds from the virtual screening procedure were then tested for their inhibitory potency against both JAKs in the kinase assay. The in vitro kinase inhibition experiment indicated that compounds 3h, TK4g, and TK4b can inhibit both JAKs in the low nanomolar range. Among them, the compound TK4g showed the highest protein kinase inhibition with the half-maximal inhibitory concentration (IC50) value of 12.61 nM for JAK2 and 15.80 nM for JAK3. From the MD simulations study, it could be found that the sulfonamide group of TK4g can form hydrogen bonds in the hinge region at residues E930 and L932 of JAK2 and E903 and L905 of JAK3, while van der Waals interaction also plays a dominant role in ligand binding. Altogether, TK4g, found by virtual screening and biological tests, could serve as a novel therapeutical lead candidate.
Collapse
Affiliation(s)
- Kamonpan Sanachai
- Center
of Excellence in Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Panupong Mahalapbutr
- Department
of Biochemistry, Faculty of Medicine, Khon
Kaen University, Khon Kaen40002, Thailand
| | - Kowit Hengphasatporn
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba305-8577, Ibaraki, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of
Tsukuba, 1-1-1 Tennodai, Tsukuba305-8577, Ibaraki, Japan
| | - Supaphorn Seetaha
- Department
of Biochemistry, Faculty of Science, Kasetsart
University, Bangkok10900, Thailand
| | - Lueacha Tabtimmai
- Department
of Biotechnology, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok10800, Thailand
| | - Thierry Langer
- Department
of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, ViennaA-1090, Austria
| | - Peter Wolschann
- Institute
of Theoretical Chemistry, University of
Vienna, Vienna1090, Austria
| | - Tanakorn Kittikool
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama VI Road, Bangkok10400, Thailand
| | - Sirilata Yotphan
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Mahidol University, Rama VI Road, Bangkok10400, Thailand
| | - Kiattawee Choowongkomon
- Department
of Biochemistry, Faculty of Science, Kasetsart
University, Bangkok10900, Thailand
| | - Thanyada Rungrotmongkol
- Center
of Excellence in Structural and Computational Biology Research Unit,
Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok10330, Thailand
| |
Collapse
|
2
|
Paricharak S, Méndez-Lucio O, Chavan Ravindranath A, Bender A, IJzerman AP, van Westen GJP. Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Brief Bioinform 2018; 19:277-285. [PMID: 27789427 PMCID: PMC6018726 DOI: 10.1093/bib/bbw105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/26/2016] [Indexed: 12/25/2022] Open
Abstract
High-throughput screening (HTS) campaigns are routinely performed in pharmaceutical companies to explore activity profiles of chemical libraries for the identification of promising candidates for further investigation. With the aim of improving hit rates in these campaigns, data-driven approaches have been used to design relevant compound screening collections, enable effective hit triage and perform activity modeling for compound prioritization. Remarkable progress has been made in the activity modeling area since the recent introduction of large-scale bioactivity-based compound similarity metrics. This is evidenced by increased hit rates in iterative screening strategies and novel insights into compound mode of action obtained through activity modeling. Here, we provide an overview of the developments in data-driven approaches, elaborate on novel activity modeling techniques and screening paradigms explored and outline their significance in HTS.
Collapse
Affiliation(s)
- Shardul Paricharak
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, RA Leiden, The Netherlands
| | - Oscar Méndez-Lucio
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, Mexico
| | - Aakash Chavan Ravindranath
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, RA Leiden, The Netherlands
| | - Gerard J P van Westen
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, RA Leiden, The Netherlands
| |
Collapse
|
3
|
Xiang J, Zhang Z, Mu Y, Xu X, Guo S, Liu Y, Russo DP, Zhu H, Yan B, Bai X. Discovery of Novel Tricyclic Thiazepine Derivatives as Anti-Drug-Resistant Cancer Agents by Combining Diversity-Oriented Synthesis and Converging Screening Approach. ACS COMBINATORIAL SCIENCE 2016; 18:230-5. [PMID: 27082930 DOI: 10.1021/acscombsci.6b00010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An efficient discovery strategy by combining diversity-oriented synthesis and converging cellular screening is described. By a three-round screening process, we identified novel tricyclic pyrido[2,3-b][1,4]benzothiazepines showing potent inhibitory activity against paclitaxel-resistant cell line H460TaxR (EC50 < 1.0 μM), which exhibits much less toxicity toward normal cells (EC50 > 100 μM against normal human fibroblasts). The most active hits also exhibited drug-like properties suitable for further preclinical research. This redeployment of antidepressing compounds for anticancer applications provides promising future prospects for treating drug-resistant tumors with fewer side effects.
Collapse
Affiliation(s)
- Jinbao Xiang
- The
Center for Combinatorial Chemistry and Drug Discovery, The School
of Pharmaceutical Sciences, and The College of Chemistry, Jilin University, Changchun, Jilin 130021, P. R. China
| | - Zhuoqi Zhang
- The
Center for Combinatorial Chemistry and Drug Discovery, The School
of Pharmaceutical Sciences, and The College of Chemistry, Jilin University, Changchun, Jilin 130021, P. R. China
| | - Yan Mu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Xianxiu Xu
- The
Center for Combinatorial Chemistry and Drug Discovery, The School
of Pharmaceutical Sciences, and The College of Chemistry, Jilin University, Changchun, Jilin 130021, P. R. China
| | - Sigen Guo
- The
Center for Combinatorial Chemistry and Drug Discovery, The School
of Pharmaceutical Sciences, and The College of Chemistry, Jilin University, Changchun, Jilin 130021, P. R. China
| | - Yongjin Liu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Daniel P. Russo
- The Rutgers Center for Computational and Integrative Biology, Camden, New Jersey 08102, United States
| | - Hao Zhu
- The Rutgers Center for Computational and Integrative Biology, Camden, New Jersey 08102, United States
- Department
of Chemistry, Rutgers University, Camden, New Jersey 08102, United States
| | - Bing Yan
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Xu Bai
- The
Center for Combinatorial Chemistry and Drug Discovery, The School
of Pharmaceutical Sciences, and The College of Chemistry, Jilin University, Changchun, Jilin 130021, P. R. China
| |
Collapse
|
4
|
Bajusz D, Ferenczy GG, Keserű GM. Discovery of Subtype Selective Janus Kinase (JAK) Inhibitors by Structure-Based Virtual Screening. J Chem Inf Model 2015; 56:234-47. [DOI: 10.1021/acs.jcim.5b00634] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research
Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., Budapest 1117, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research
Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., Budapest 1117, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research
Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., Budapest 1117, Hungary
| |
Collapse
|
5
|
Cox BD, Prosser AR, Sun Y, Li Z, Lee S, Huang MB, Bond VC, Snyder JP, Krystal M, Wilson LJ, Liotta DC. Pyrazolo-Piperidines Exhibit Dual Inhibition of CCR5/CXCR4 HIV Entry and Reverse Transcriptase. ACS Med Chem Lett 2015; 6:753-7. [PMID: 26191361 DOI: 10.1021/acsmedchemlett.5b00036] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/06/2015] [Indexed: 01/19/2023] Open
Abstract
We report novel anti-HIV-1 agents with combined dual host-pathogen pharmacology. Lead compound 3, composed of a pyrazole-piperidine core, exhibits three concurrent mechanisms of action: (1) non-nucleoside reverse transcriptase inhibition, (2) CCR5-mediated M-tropic viral entry inhibition, and (3) CXCR4-based T-tropic viral entry inhibition that maintains native chemokine ligand binding. This discovery identifies important tool compounds for studying viral infectivity and prototype agents that block HIV-1 entry through dual chemokine receptor ligation.
Collapse
Affiliation(s)
- Bryan D. Cox
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anthony R. Prosser
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yongnian Sun
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Zhufang Li
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Sangil Lee
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Ming B. Huang
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia 30310, United States
| | - Vincent C. Bond
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia 30310, United States
| | - James P. Snyder
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Mark Krystal
- Bristol-Myers Squibb, Wallingford, Connecticut 06492, United States
| | - Lawrence J. Wilson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Dennis C. Liotta
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
6
|
Menet CJ, Rompaey LV, Geney R. Advances in the discovery of selective JAK inhibitors. PROGRESS IN MEDICINAL CHEMISTRY 2013; 52:153-223. [PMID: 23384668 DOI: 10.1016/b978-0-444-62652-3.00004-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this review, we describe the current knowledge of the biology of the JAKs. The JAK family comprises the four nonreceptor tyrosine kinases JAK1, JAK2, JAK3, and Tyk2, all key players in the signal transduction from cytokine receptors to transcription factor activation. We also review the progresses made towards the optimization of JAK inhibitors and the importance of their selectivity profile. Indeed, the full array of many medicinal chemistry enabling tools (HTS, X-ray crystallography, scaffold morphing, etc.) has been deployed to successfully design molecules that discriminate among JAK family and other kinases. While the first JAK inhibitor was launched in 2011, this review also summarizes the status of several other small-molecule JAK inhibitors currently in development to treat arthritis, psoriasis, organ rejection, and multiple cancer types.
Collapse
|
7
|
Abstract
Computer-aided drug design plays a vital role in drug discovery and development and has become an indispensable tool in the pharmaceutical industry. Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds. This article reviews software and other resources related to computer-aided drug design approaches, putting particular emphasis on structure-based drug design, ligand-based drug design, chemical databases and chemoinformatics tools.
Collapse
|
8
|
Matter H, Sotriffer C. Applications and Success Stories in Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
9
|
Oh K, Joo KM, Jung YS, Lee J, Kang H, Lee HY, Lee DS. A receptor-independent, cell-based JAK activation assay for screening for JAK3-specific inhibitors. J Immunol Methods 2010; 354:45-52. [PMID: 20138049 DOI: 10.1016/j.jim.2010.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 01/22/2010] [Accepted: 01/26/2010] [Indexed: 10/19/2022]
Abstract
New immunosuppressive compounds with less systemic toxicity that could replace calcineurin inhibitors are urgently needed. For identification of specific inhibitors of JAK3, a potential new drug target, from large chemical libraries we developed a cell-based screening system. TEL-JAK fusion proteins composed of an oligomerization domain of TEL and kinase and/or pseudokinase domains of JAKs provided constitutive activation of JAKs without receiving a signal from the cytokine receptors. These fusion proteins also induced STAT5b phosphorylation in the absence of cytokine receptors. Both the kinase and pseudokinase domains of JAKs were required for full activation of the JAKs, and four copies of STAT5 response elements provided the greatest luciferase activity. The sensitivity and specificity of the system was evaluated using specific JAK3, JAK2, or MEK inhibitors. Thus, we generated a receptor-independent, cell-based selective screening system for specific JAK3 inhibitors, which is easily convertible to a high-throughput screening platform.
Collapse
Affiliation(s)
- Keunhee Oh
- Laboratory of Immunology, Department of Anatomy, Seoul National University College of Medicine, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
10
|
Liew CY, Ma XH, Yap CW. Consensus model for identification of novel PI3K inhibitors in large chemical library. J Comput Aided Mol Des 2010; 24:131-41. [PMID: 20148286 DOI: 10.1007/s10822-010-9321-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 02/02/2010] [Indexed: 01/28/2023]
Abstract
Phosphoinositide 3-kinases (PI3Ks) inhibitors have treatment potential for cancer, diabetes, cardiovascular disease, chronic inflammation and asthma. A consensus model consisting of three base classifiers (AODE, kNN, and SVM) trained with 1,283 positive compounds (PI3K inhibitors), 16 negative compounds (PI3K non-inhibitors) and 64,078 generated putative negatives was developed for predicting compounds with PI3K inhibitory activity of IC(50) < or = 10 microM. The consensus model has an estimated false positive rate of 0.75%. Nine novel potential inhibitors were identified using the consensus model and several of these contain structural features that are consistent with those found to be important for PI3K inhibitory activities. An advantage of the current model is that it does not require knowledge of 3D structural information of the various PI3K isoforms, which is not readily available for all isoforms.
Collapse
Affiliation(s)
- Chin Yee Liew
- Pharmaceutical Data Exploration Laboratory, Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | | | | |
Collapse
|
11
|
Chapter 12 Advances in the Discovery of Small Molecule JAK3 Inhibitors. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2009. [DOI: 10.1016/s0065-7743(09)04412-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|