1
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Li L, Gong S. The discovery of a novel IκB kinase β inhibitor based on pharmacophore modeling, virtual screening and biological evaluation. Future Med Chem 2024; 16:531-544. [PMID: 38385164 DOI: 10.4155/fmc-2023-0261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/10/2023] [Indexed: 02/23/2024] Open
Abstract
Background: IκB kinase β (IKKβ) plays a pivotal role in the NF-κB signaling pathway and is considered a promising therapeutic target for various diseases. Materials & methods: The authors developed and validated a 3D pharmacophore model of IKKβ inhibitors via the HypoGen algorithm in Discovery Studio 2019, then performed virtual screening, molecular docking and kinase assays to identify hit compounds from the ChemDiv database. The compound with the highest inhibitory activity was further evaluated in adjuvant-induced arthritis rat models. Results: Among the four hit compounds, Hit 4 had the highest IKKβ inhibitory activity (IC50 = 30.4 ± 3.8), and it could significantly ameliorate joint inflammation and damage in vivo. Conclusion: The identified compound, Hit 4, can be optimized as a therapeutic agent for inflammatory diseases.
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Affiliation(s)
- Luyao Li
- Xi'an Jiaotong University, Xi'an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Shouping Gong
- Xi'an Jiaotong University, Xi'an, China
- Department of Neurosurgery, Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Xi'an Medical University, Xi'an, China
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2
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Rullah K, Shamsudin NF, Koeberle A, Tham CL, Fasihi Mohd Aluwi MF, Leong SW, Jantan I, Lam KW. Flavonoid diversity and roles in the lipopolysaccharide-mediated inflammatory response of monocytes and macrophages. Future Med Chem 2024; 16:75-99. [PMID: 38205612 DOI: 10.4155/fmc-2023-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024] Open
Abstract
Targeting lipopolysaccharide (LPS)/toll-like receptor 4 signaling in mononuclear phagocytes has been explored for the treatment of inflammation and inflammation-related disorders. However, only a few key targets have been translated into clinical applications. Flavonoids, a class of ubiquitous plant secondary metabolites, possess a privileged scaffold which serves as a valuable template for designing pharmacologically active compounds directed against diseases with inflammatory components. This perspective provides a general overview of the diversity of flavonoids and their multifaceted mechanisms that interfere with LPS-induced signaling in monocytes and macrophages. Focus is placed on flavonoids targeting MD-2, IκB kinases, c-Jun N-terminal kinases, extracellular signal-regulated kinase, p38 MAPK and PI3K/Akt or modulating LPS-related gene expression.
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Affiliation(s)
- Kamal Rullah
- Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, 25200 Kuantan, Pahang, Malaysia
| | - Nur Farisya Shamsudin
- Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, 25200 Kuantan, Pahang, Malaysia
| | - Andreas Koeberle
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Chau Ling Tham
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang, Malaysia
| | - Sze-Wei Leong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ibrahim Jantan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Kok Wai Lam
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300 Kuala Lumpur, Malaysia
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3
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Shen X, Chen H, Zhang H, Luo L, Wen T, Liu L, Hu Q, Wang L. A natural sesquiterpene lactone isolinderalactone attenuates lipopolysaccharide-induced inflammatory response and acute lung injury through inhibition of NF-κB pathway and activation Nrf2 pathway in macrophages. Int Immunopharmacol 2023; 124:110965. [PMID: 37741124 DOI: 10.1016/j.intimp.2023.110965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/25/2023]
Abstract
Isolinderalactone is the main sesquiterpene lactone isolated from Lindera aggregata, a traditional Chinese medicine widely used to treat pain and inflammation. Although isolinderalactone has been demonstrated to possess anti-cancer effect, its anti-inflammatory activity and underlying mechanism has not been well characterized. Herein, isolinderalactone was able to significantly inhibit the production of NO and PGE2 by reducing the expressions of iNOS and COX2 in LPS-stimulated RAW264.7 macrophages and BMDMs, and decreased the mRNA levels of IL-1β, IL-6, and TNF-α in LPS-induced RAW264.7 cells. In vivo, isolinderalactone effectively alleviated LPS-induced acute lung injury (ALI), which manifested as reduction in pulmonary inflammatory infiltration, myeloperoxidase activity, and production of PGE2, IL-1β, IL-6, TNF-α, and malondialdehyde. Furthermore, isolinderalactone inhibited phosphorylation of IKKα/β, phosphorylation and degradation of IκBα, and nuclear translocation of NF-κB p65, thereby blocking NF-κB pro-inflammatory pathway. Meanwhile, isolinderalactone reduced the intracellular ROS through promoting the activation of Nrf2-HMOX1 antioxidant axis. By using drug affinity responsive target stability assay and molecular docking, isolinderalactone was found to covalently interact with IKKα/β and Keap1, which may contribute to its anti-inflammatory action. Additionally, a thiol donor β-mercaptoethanol significantly abolished isolinderalactone-mediated anti-inflammatory action in vitro, indicating the crucial role of the unsaturated lactone of isolinderalactone on its anti-inflammatory effects. Taken together, isolinderalactone protected against LPS-induced ALI in mice, which may be associated with its inhibition of NF-κB pathway and activation of Nrf2 signaling in macrophages.
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Affiliation(s)
- Xiaofei Shen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hongqing Chen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hai Zhang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liuling Luo
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tian Wen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lu Liu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiongying Hu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Lun Wang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.
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4
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Sharma V, Gupta M. Designing of kinase hinge binders: A medicinal chemistry perspective. Chem Biol Drug Des 2022; 100:968-980. [PMID: 35112799 DOI: 10.1111/cbdd.14024] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/16/2022] [Accepted: 01/29/2022] [Indexed: 01/25/2023]
Abstract
Protein kinases are key regulators of cellular signaling and play a critical role in oncogenesis. Inhibitors of protein kinases are pursued by both industry and academia as a promising target for cancer therapy. Within the protein kinases, the ATP site has produced more than 40 FDA-approved drugs. The ATP site is broadly composed of a hinge region, gatekeeper residues, DFG-loop, ribose pocket, and other hydrophobic regions. The hinge region in the ATP site can be used for designing potent inhibitors. In this review, we discuss some representative studies that will highlight the interactions of heterocyclic compounds with hinge regions of different kinases like BRAF kinase, EGRF kinase, MAP kinase, and Mps1 kinase.
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Affiliation(s)
- Vikas Sharma
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, Oregon, USA.,GreenLight Biosciences, Woburn, MA, United States
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5
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Kim T, Kim K, Park I, Hong S, Park H. Two-Track Virtual Screening Approach to Identify the Dual Inhibitors of Wild Type and C481S Mutant of Bruton's Tyrosine Kinase. J Chem Inf Model 2022; 62:4500-4511. [PMID: 36001093 DOI: 10.1021/acs.jcim.2c00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bruton's tyrosine kinase (BTK) is responsible for the pathogenesis of various autoimmune diseases and chronic lymphocytic leukemia. However, the discovery of efficient medicines has seen limited success due to the constitutively active mutants that acquired the drug resistance. To disclose the dual inhibitors against the wild-type BTK and the problematic drug-resistant C481S mutant, a large chemical library was virtually screened with extensive molecular docking simulations using two target proteins. As a consequence of imposing the configurational restraint to make a hydrogen bond in the hinge region of BTK as well as modifying the ligand dehydration term in the scoring function, a total of 20 dual inhibitors were discovered with the range of the associated IC50 values from 2.5 to 15 μM. All these dual inhibitors revealed the inhibitory activity against the C481S mutant to a comparable extent to that measured for the wild type. Among the new inhibitors, N-(3,5-dimethoxyphenyl)-6,7-dimethoxyquinazolin-4-amine (1) appeared to be most suitable as a starting point of the lead optimization due to the highest biochemical potency against the C481S mutant as well as the lowest molecular weight. To increase the potential of a drug candidate, 1 was modified into 6,7-dimethoxy-N-(pyridin-3-yl)quinazolin-4-amine (12) via chemical synthesis so as to possess better physicochemical properties without loss of the biochemical potency. 12 is suggested as a new effective molecular core from which numerous druggable dual inhibitors of the wild-type BTK and the C481S mutant would be derivatized.
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Affiliation(s)
- Taeho Kim
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
| | - Kewon Kim
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 Korea
| | - Inyoung Park
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141 Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
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6
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IKK β mediates homeostatic function in inflammation via competitively phosphorylating AMPK and I κB α. Acta Pharm Sin B 2022; 12:651-664. [PMID: 35256937 PMCID: PMC8897026 DOI: 10.1016/j.apsb.2021.09.012] [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: 06/02/2021] [Revised: 08/09/2021] [Accepted: 09/03/2021] [Indexed: 12/30/2022] Open
Abstract
Inhibitor of nuclear factor kappa-B kinase subunit beta (IKKβ) is one of important kinases in inflammation to phosphorylate inhibitor of nuclear factor kappa-B (IκBα) and then activate nuclear factor kappa-B (NF-κB). Inhibition of IKKβ has been a therapeutic strategy for inflammatory and autoimmune diseases. Here we report that IKKβ is constitutively activated in healthy donors and healthy IkkβC46A (cysteine 46 mutated to alanine) knock-in mice although they possess intensive IKKβ–IκBα–NF-κB signaling activation. These indicate that IKKβ activation probably plays homeostatic role instead of causing inflammation. Compared to IkkβWT littermates, lipopolysaccharides (LPS) could induce high mortality rate in IkkβC46A mice which is correlated to breaking the homeostasis by intensively activating p-IκBα–NF-κB signaling and inhibiting phosphorylation of 5ʹ adenosine monophosphate-activated protein kinase (p-AMPK) expression. We then demonstrated that IKKβ kinase domain (KD) phosphorylates AMPKα1 via interacting with residues Thr183, Ser184, and Thr388, while IKKβ helix–loop–helix motifs is essential to phosphorylate IκBα according to the previous reports. Kinase assay further demonstrated that IKKβ simultaneously catalyzes phosphorylation of AMPK and IκBα to mediate homeostasis. Accordingly, activation of AMPK rather than inhibition of IKKβ could substantially rescue LPS-induced mortality in IkkβC46A mice by rebuilding the homeostasis. We conclude that IKKβ activates AMPK to restrict inflammation and IKKβ mediates homeostatic function in inflammation via competitively phosphorylating AMPK and IκBα.
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7
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Guo Z, Zhou C, Zhou L, Wang Z, Zhu X, Mu X. Overexpression of DAPK1-mediated inhibition of IKKβ/CSN5/PD-L1 axis enhances natural killer cell killing ability and inhibits tumor immune evasion in gastric cancer. Cell Immunol 2021; 372:104469. [DOI: 10.1016/j.cellimm.2021.104469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022]
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8
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Li Y, Pei J, Lai L. Structure-based de novo drug design using 3D deep generative models. Chem Sci 2021; 12:13664-13675. [PMID: 34760151 PMCID: PMC8549794 DOI: 10.1039/d1sc04444c] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Deep generative models are attracting much attention in the field of de novo molecule design. Compared to traditional methods, deep generative models can be trained in a fully data-driven way with little requirement for expert knowledge. Although many models have been developed to generate 1D and 2D molecular structures, 3D molecule generation is less explored, and the direct design of drug-like molecules inside target binding sites remains challenging. In this work, we introduce DeepLigBuilder, a novel deep learning-based method for de novo drug design that generates 3D molecular structures in the binding sites of target proteins. We first developed Ligand Neural Network (L-Net), a novel graph generative model for the end-to-end design of chemically and conformationally valid 3D molecules with high drug-likeness. Then, we combined L-Net with Monte Carlo tree search to perform structure-based de novo drug design tasks. In the case study of inhibitor design for the main protease of SARS-CoV-2, DeepLigBuilder suggested a list of drug-like compounds with novel chemical structures, high predicted affinity, and similar binding features to those of known inhibitors. The current version of L-Net was trained on drug-like compounds from ChEMBL, which could be easily extended to other molecular datasets with desired properties based on users' demands and applied in functional molecule generation. Merging deep generative models with atomic-level interaction evaluation, DeepLigBuilder provides a state-of-the-art model for structure-based de novo drug design and lead optimization. DeepLigBuilder, a novel deep generative model for structure-based de novo drug design, directly generates 3D structures of drug-like compounds in the target binding site.![]()
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Affiliation(s)
- Yibo Li
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China
| | - Luhua Lai
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China .,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University Beijing 100871 China .,BNLMS, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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9
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Multiple Target Drug Design Using LigBuilder 3. Methods Mol Biol 2021. [PMID: 33759133 DOI: 10.1007/978-1-0716-1209-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Designing drugs that directly interact with multiple targets is a promising approach for treating complicated diseases. In order to successfully bind to multiple targets of different families and achieve the desired ligand efficiency, multi-target-directed ligands (MTDLs) require a higher level of diversity and complexity. De novo design strategies for creating more diverse chemical entities with desired properties may present an improved approach for developing MTDLs. In this chapter, we describe a computational protocol for developing MTDLs using the first reported multi-target de novo program, LigBuilder 3, which combines a binding site prediction module with de novo drug design and optimization modules. As an illustration of each detailed procedure, we design dual-functional compounds of two well-characterized virus enzymes, HIV protease and reverse transcriptase (PR and RT, respectively), using fragments extracted from known inhibitors. LigBuilder 3 is accessible at http://www.pkumdl.cn/ligbuilder3/ .
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10
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Rational Computational Design of Fourth-Generation EGFR Inhibitors to Combat Drug-Resistant Non-Small Cell Lung Cancer. Int J Mol Sci 2020; 21:ijms21239323. [PMID: 33297461 PMCID: PMC7730458 DOI: 10.3390/ijms21239323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Although the inhibitors of singly mutated epidermal growth factor receptor (EGFR) kinase are effective for the treatment of non-small cell lung cancer (NSCLC), their clinical efficacy has been limited due to the emergence of various double and triple EGFR mutants with drug resistance. It has thus become urgent to identify potent and selective inhibitors of triple mutant EGFRs resistant to first-, second-, and third-generation EGFR inhibitors. Herein, we report the discovery of potent and highly selective inhibitors of EGFR exon 19 p.E746_A750del/EGFR exon 20 p.T790M/EGFR exon 20 p.C797S (d746-750/T790M/C797S) mutant, which were derived via two-track virtual screening and de novo design. This two-track approach was performed so as to maximize and minimize the inhibitory activity against the triple mutant and the wild type, respectively. Extensive chemical modifications of the initial hit compounds led to the identification of several low-nanomolar inhibitors of the d746-750/T790M/C797S mutant. Among them, two compounds exhibited more than 104-fold selectivity in the inhibition of EGFRd746-750/T790M/C797S over the wild type. The formations of a hydrogen bond with the mutated residue Ser797 and the van der Waals contact with the mutated residue Met790 were found to be a common feature in the interactions between EGFRd746-750/T790M/C797S and the fourth-generation inhibitors. Such an exceptionally high selectivity could also be attributed to the formation of the hydrophobic contact with a Gly loop residue or the hydrogen bond with Asp855 in the activation loop. The discovery of the potent and selective EGFRd746-750/T790M/C797S inhibitors were actually made possible by virtue of the modified protein-ligand binding free energy function involving a new hydration free energy term with enhanced accuracy. The fourth-generation EGFR inhibitors found in this work are anticipated to serve as a new starting point for the discovery of anti-NSCLC medicines to overcome the problematic drug resistance.
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Han HJ, Park C, Hwang J, N.R. T, Kim SO, Han J, Woo M, B S, Ryoo IJ, Lee KH, Cha-Molstad H, Kwon YT, Kim BY, Soung NK. CPPF, A Novel Microtubule Targeting Anticancer Agent, Inhibits the Growth of a Wide Variety of Cancers. Int J Mol Sci 2020; 21:ijms21134800. [PMID: 32645923 PMCID: PMC7370279 DOI: 10.3390/ijms21134800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 12/24/2022] Open
Abstract
In the past, several microtubule targeting agents (MTAs) have been developed into successful anticancer drugs. However, the usage of these drugs has been limited by the acquisition of drug resistance in many cancers. Therefore, there is a constant demand for the development of new therapeutic drugs. Here we report the discovery of 5-5 (3-cchlorophenyl)-N-(3-pyridinyl)-2-furamide (CPPF), a novel microtubule targeting anticancer agent. Using both 2D and 3D culture systems, we showed that CPPF was able to suppress the proliferation of diverse cancer cell lines. In addition, CPPF was able to inhibit the growth of multidrug-resistant cell lines that are resistant to other MTAs, such as paclitaxel and colchicine. Our results showed that CPPF inhibited growth by depolymerizing microtubules leading to mitotic arrest and apoptosis. We also confirmed CPPF anticancer effects in vivo using both a mouse xenograft and a two-step skin cancer mouse model. Using established zebrafish models, we showed that CPPF has low toxicity in vivo. Overall, our study proves that CPPF has the potential to become a successful anticancer chemotherapeutic drug.
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Affiliation(s)
- Ho Jin Han
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
- Department of Biomolecular Science, University of Science and Technology, Daejeon 34113, Korea
| | - Chanmi Park
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - Joonsung Hwang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - Thimmegowda N.R.
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - Sun-Ok Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - Junyeol Han
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
- Department of Biomolecular Science, University of Science and Technology, Daejeon 34113, Korea
| | - Minsik Woo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong, Cheongju 28160, Korea
| | - Shwetha B
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - In-Ja Ryoo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - Kyung Ho Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - Hyunjoo Cha-Molstad
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (Y.T.K.); (B.Y.K.); (N.-K.S.); Tel.: +82-2-740-8547 (Y.T.K.); +82-43-240-6163 (B.Y.K.); +82-43-240-6165 (N.-K.S.); Fax: +82-2-3673-2167 (Y.T.K.); +82-43-240-6259 (B.Y.K.); +82-43-240-6259 (N.-K.S.)
| | - Bo Yeon Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
- Department of Biomolecular Science, University of Science and Technology, Daejeon 34113, Korea
- Correspondence: (Y.T.K.); (B.Y.K.); (N.-K.S.); Tel.: +82-2-740-8547 (Y.T.K.); +82-43-240-6163 (B.Y.K.); +82-43-240-6165 (N.-K.S.); Fax: +82-2-3673-2167 (Y.T.K.); +82-43-240-6259 (B.Y.K.); +82-43-240-6259 (N.-K.S.)
| | - Nak-Kyun Soung
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongju 28116, Korea; (H.J.H.); (C.P.); (J.H.); (T.N.R.); (S.-O.K.); (J.H.); (M.W.); (S.B.); (I.-J.R.); (K.H.L.); (H.C.-M.)
- Correspondence: (Y.T.K.); (B.Y.K.); (N.-K.S.); Tel.: +82-2-740-8547 (Y.T.K.); +82-43-240-6163 (B.Y.K.); +82-43-240-6165 (N.-K.S.); Fax: +82-2-3673-2167 (Y.T.K.); +82-43-240-6259 (B.Y.K.); +82-43-240-6259 (N.-K.S.)
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12
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Xiong MQ, Chen T, Wang YX, Zhu XL, Yang GF. Design and synthesis of potent inhibitors of bc 1 complex based on natural product neopeltolide. Bioorg Med Chem Lett 2020; 30:127324. [PMID: 32631529 DOI: 10.1016/j.bmcl.2020.127324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Neopeltolide, a natural product isolated from deep-water sponge specimen of the family neopeltidae, has been proven to be a novel inhibitor of cytochrome bc1. In this study, a series of neopeltolide derivatives was designed by replacing the 14-membered macrolactone with indole ring and confirmed by 1H NMR, 13C NMR, and HRMS. Based on the binding mode of 12h with bc1 complex, the IC50 values of compounds 16a-f (ranging from 0.70 to 1.46 μM) were improved significantly than the ester derivatives 12a-u by replacing the ester with amide linker. Subsequently, the molecular docking results indicated that compound 16e could form a π-π interaction with Phe274 and two H-bonds with Glu271 and His161 and the latter H-bond was found to account for its high activity. The present work accelerates the discovery of novel bc1 complex inhibitors to deal with the resistance that the existing bc1 complex inhibitors are facing and provides a valuable idea for the design of new fungicides.
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Affiliation(s)
- Mao-Qian Xiong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China
| | - Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China
| | - Yu-Xia Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, PR China.
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13
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Park H, Jung HY, Mah S, Kim K, Hong S. Kinase and GPCR polypharmacological approach for the identification of efficient anticancer medicines. Org Biomol Chem 2020; 18:8402-8413. [PMID: 33112339 DOI: 10.1039/d0ob01917h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Discovery of an anticancer medicine using a single target protein has often been unsuccessful due to the complexity of pathogenic mechanisms as well as the presence of redundant signaling pathways. In this work, we attempted to find promising anticancer drug candidates by simultaneously targeting casein kinase 1 delta (CK1δ) and muscarinic acetylcholine receptor M3 (M3R). Through the structure-based virtual screening and de novo design with the modified potential function for protein-ligand binding, a series of benzo[4,5]imidazo[1,2-a][1,3,5]triazine-2-amine (BITA) derivatives were identified as CK1δ inhibitors and also as M3R antagonists. The biochemical potencies of these bifunctional molecules reached the nanomolar and low-micromolar levels with respect to CK1δ and M3R, respectively. A common interaction feature in the calculated CK1δ-inhibitor and M3R-antagonist complexes is that the BITA moiety is well-stabilized in the orthosteric site of M3R and the hinge region of CK1δ through the establishment of the three hydrogen bonds and the hydrophobic contacts in the vicinity. The computational and experimental results found in this work exemplify the efficiency of kinase and GPCR polypharmacology in developing anticancer medicines.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Republic of Korea.
| | - Hoi-Yun Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Shinmee Mah
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kewon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Sungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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14
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Elkamhawy A, Kim NY, Hassan AHE, Park JE, Paik S, Yang JE, Oh KS, Lee BH, Lee MY, Shin KJ, Pae AN, Lee KT, Roh EJ. Thiazolidine-2,4-dione-based irreversible allosteric IKK-β kinase inhibitors: Optimization into in vivo active anti-inflammatory agents. Eur J Med Chem 2019; 188:111955. [PMID: 31893550 DOI: 10.1016/j.ejmech.2019.111955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
Selective kinase inhibitors development is a cumbersome task because of ATP binding sites similarities across kinases. On contrast, irreversible allosteric covalent inhibition offers opportunity to develop novel selective kinase inhibitors. Previously, we reported thiazolidine-2,4-dione lead compounds eliciting in vitro irreversible allosteric inhibition of IKK-β. Herein, we address optimization into in vivo active anti-inflammatory agents. We successfully developed potent IKK-β inhibitors with the most potent compound eliciting IC50 = 0.20 μM. Cellular assay of a set of active compounds using bacterial endotoxin lipopolysaccharide (LPS)-stimulated macrophages elucidated significant in vitro anti-inflammatory activity. In vitro evaluation of microsomal and plasma stabilities showed that the promising compound 7a is more stable than compound 7p. Finally, in vivo evaluation of 7a, which has been conducted in a model of LPS-induced septic shock in mice, showed its ability to protect mice against septic shock induced mortality. Accordingly, this study presents compound 7a as a novel potential irreversible allosteric covalent inhibitor of IKK-β with verified in vitro and in vivo anti-inflammatory activity.
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Affiliation(s)
- Ahmed Elkamhawy
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Nam Youn Kim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Jung-Eun Park
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Sora Paik
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Department of Fundamental Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jeong-Eun Yang
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Kwang-Seok Oh
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 34114, Republic of Korea
| | - Byung Ho Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 34114, Republic of Korea
| | - Mi Young Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 34114, Republic of Korea
| | - Kye Jung Shin
- Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Ae Nim Pae
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kyung-Tae Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Eun Joo Roh
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea.
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15
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Crosstalk between the Akt/mTORC1 and NF-κB signaling pathways promotes hypoxia-induced pulmonary hypertension by increasing DPP4 expression in PASMCs. Acta Pharmacol Sin 2019; 40:1322-1333. [PMID: 31316183 DOI: 10.1038/s41401-019-0272-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Abnormal wound healing by pulmonary artery smooth muscle cells (PASMCs) promotes vascular remodeling in hypoxia-induced pulmonary hypertension (HPH). Increasing evidence shows that both the mammalian target of rapamycin complex 1 (mTORC1) and nuclear factor-kappa B (NF-κB) are involved in the development of HPH. In this study, we explored the crosstalk between mTORC1 and NF-κB in PASMCs cultured under hypoxic condition and in a rat model of hypoxia-induced pulmonary hypertension (HPH). We showed that hypoxia promoted wound healing of PASMCs, which was dose-dependently blocked by the mTORC1 inhibitor rapamycin (5-20 nM). In PASMCs, hypoxia activated mTORC1, which in turn promoted the phosphorylation of NF-κB. Molecular docking revealed that mTOR interacted with IκB kinases (IKKs) and that was validated by immunoprecipitation. In vitro kinase assays and mass spectrometry demonstrated that mTOR phosphorylated IKKα and IKKβ separately. Inhibition of mTORC1 decreased the level of phosphorylated IKKα/β, thus reducing the phosphorylation and transcriptional activity of NF-κB. Bioinformatics study revealed that dipeptidyl peptidase-4 (DPP4) was a target gene of NF-κB; DPP4 inhibitor, sitagliptin (10-500 μM) effectively inhibited the abnormal wound healing of PASMCs under hypoxic condition. In the rat model of HPH, we showed that NF-κB activation (at 3 weeks) was preceded by mTOR signaling activation (after 1 or 2 weeks) in lungs, and administration of sitagliptin (1-5 mg/kg every day, ig) produced preventive effects against the development of HPH. In conclusion, hypoxia activates the crosstalk between mTORC1 and NF-κB, and increased DPP4 expression in PASMCs that leads to vascular remodeling. Sitagliptin, a DPP4 inhibitor, exerts preventive effect against HPH.
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16
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Elkamhawy A, Youn Kim N, Hassan AHE, Park JE, Yang JE, Elsherbeny MH, Paik S, Oh KS, Lee BH, Lee MY, Shin KJ, Pae AN, Lee KT, Roh EJ. Optimization study towards more potent thiazolidine-2,4-dione IKK-β modulator: Synthesis, biological evaluation and in silico docking simulation. Bioorg Chem 2019; 92:103261. [PMID: 31542718 DOI: 10.1016/j.bioorg.2019.103261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/28/2022]
Abstract
Inhibition of IKK-β (inhibitor of nuclear factor kappa-B kinase subunit beta) has been broadly documentedas a promising approach for treatment of acute and chronic inflammatory diseases, cancer, and autoimmune diseases. Recently, we have identified a novel class of thiazolidine-2,4-diones as structurally novel modulators for IKK-β. Herein, we report a hit optimization study via analog synthesis strategy aiming to acquire more potent derivative(s), probe the structure activity relationship (SAR), and get reasonable explanations for the elicited IKK-β inhibitory activities though an in silico docking simulation study. Accordingly, a new series of eighteen thiazolidine-2,4-dione derivatives was rationally designed, synthesized, identified with different spectroscopic techniques and biologically evaluated as noteworthy IKK-β potential modulators. Successfully, new IKK-β potent modulators were obtained, including the most potent analog up-to-date 7m with IC50 value of 260 nM. A detailed structure activity relationship (SAR) was discussed and a mechanistic study for 7m was carried out indicating its irreversible inhibition mode with IKK-β (Kinact value = 0.01 (min-1). Furthermore, the conducted in silico simulation study provided new insights for the binding modes of this novel class of modulators with IKK-β.
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Affiliation(s)
- Ahmed Elkamhawy
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Nam Youn Kim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Jung-Eun Park
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Jeong-Eun Yang
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Mohamed H Elsherbeny
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Sora Paik
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kwang-Seok Oh
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon 34114, Republic of Korea
| | - Byung Ho Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon 34114, Republic of Korea
| | - Mi Young Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon 34114, Republic of Korea
| | - Kye Jung Shin
- Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Ae Nim Pae
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kyung-Tae Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Eun Joo Roh
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea.
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17
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Slater O, Kontoyianni M. The compromise of virtual screening and its impact on drug discovery. Expert Opin Drug Discov 2019; 14:619-637. [PMID: 31025886 DOI: 10.1080/17460441.2019.1604677] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: Docking and structure-based virtual screening (VS) have been standard approaches in structure-based design for over two decades. However, our understanding of the limitations, potential, and strength of these techniques has enhanced, raising expectations. Areas covered: Based on a survey of reports in the past five years, we assess whether VS: (1) predicts binding poses in agreement with crystallographic data (when available); (2) is a superior screening tool, as often claimed; (3) is successful in identifying chemical scaffolds that can be starting points for subsequent lead optimization cycles. Data shows that knowledge of the target and its chemotypes in postprocessing lead to viable hits in early drug discovery endeavors. Expert opinion: VS is capable of accurate placements in the pocket for the most part, but does not consistently score screening collections accurately. What matters is capitalization on available resources to get closer to a viable lead or optimizable series. Integration of approaches, subjective hit selection guided by knowledge of the receptor or endogenous ligand, libraries driven by experimental guides, validation studies to identify the best docking/scoring that reproduces experimental findings, constraints regarding receptor-ligand interactions, thoroughly designed methodologies, and predefined cutoff scoring criteria strengthen VS's position in pharmaceutical research.
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Affiliation(s)
- Olivia Slater
- a Department of Pharmaceutical Sciences , Southern Illinois University Edwardsville , Edwardsville , IL , USA
| | - Maria Kontoyianni
- a Department of Pharmaceutical Sciences , Southern Illinois University Edwardsville , Edwardsville , IL , USA
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18
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Žuvela P, Liu JJ, Yi M, Pomastowski PP, Sagandykova G, Belka M, David J, Bączek T, Szafrański K, Żołnowska B, Sławiński J, Supuran CT, Wong MW, Buszewski B. Target-based drug discovery through inversion of quantitative structure-drug-property relationships and molecular simulation: CA IX-sulphonamide complexes. J Enzyme Inhib Med Chem 2018; 33:1430-1443. [PMID: 30220229 PMCID: PMC6151961 DOI: 10.1080/14756366.2018.1511551] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In this work, a target-based drug screening method is proposed exploiting the synergy effect of ligand-based and structure-based computer-assisted drug design. The new method provides great flexibility in drug design and drug candidates with considerably lower risk in an efficient manner. As a model system, 45 sulphonamides (33 training, 12 testing ligands) in complex with carbonic anhydrase IX were used for development of quantitative structure-activity-lipophilicity (property)-relationships (QSPRs). For each ligand, nearly 5,000 molecular descriptors were calculated, while lipophilicity (logkw) and inhibitory activity (logKi) were used as drug properties. Genetic algorithm-partial least squares (GA-PLS) provided a QSPR model with high prediction capability employing only seven molecular descriptors. As a proof-of-concept, optimal drug structure was obtained by inverting the model with respect to reference drug properties. 3509 ligands were ranked accordingly. Top 10 ligands were further validated through molecular docking. Large-scale MD simulations were performed to test the stability of structures of selected ligands obtained through docking complemented with biophysical experiments.
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Affiliation(s)
- Petar Žuvela
- a Department of Chemistry , National University of Singapore , Singapore.,b Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - J Jay Liu
- c Department of Chemical Engineering , Pukyong National University , Busan , Korea
| | - Myunggi Yi
- d Department of Biomedical Engineering , Pukyong National University , Busan , Korea
| | - Paweł P Pomastowski
- b Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Gulyaim Sagandykova
- e Interdisciplinary Centre for Modern Technologies, Nicolaus Copernicus University , Toruń , Poland
| | - Mariusz Belka
- f Department of Pharmaceutical Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Jonathan David
- a Department of Chemistry , National University of Singapore , Singapore
| | - Tomasz Bączek
- f Department of Pharmaceutical Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Krzysztof Szafrański
- g Department of Organic Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Beata Żołnowska
- g Department of Organic Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Jarosław Sławiński
- g Department of Organic Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Claudiu T Supuran
- h Dipartimento di Chimica, Universita degli Studi di Firenze , Polo Scientifico, Laboratorio di Chimica Bioinorganica , Sesto Fiorentino (Florence) , Italy.,i NEUROFARBA Department, Sezione di Scienze Farmaceutiche , Università degli Studi di Firenze , Sesto Fiorentino (Florence) , Italy
| | - Ming Wah Wong
- a Department of Chemistry , National University of Singapore , Singapore
| | - Bogusław Buszewski
- b Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland.,e Interdisciplinary Centre for Modern Technologies, Nicolaus Copernicus University , Toruń , Poland
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19
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Ku B, Yun HY, Lee KW, Shin HC, Lee SR, Kim CH, Park H, Yi KY, Lee CH, Kim SJ. Identification of N-(5-(phenoxymethyl)-1,3,4-thiadiazol-2-yl)acetamide derivatives as novel protein tyrosine phosphatase epsilon inhibitors exhibiting anti-osteoclastic activity. Bioorg Med Chem 2018; 26:5204-5211. [PMID: 30249496 DOI: 10.1016/j.bmc.2018.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 01/06/2023]
Abstract
Cytosolic protein tyrosine phosphatase epsilon (cyt-PTPε) plays a central role in controlling differentiation and function of osteoclasts, whose overactivation causes osteoporosis. Based on our previous study reporting a number of cyt-PTPε inhibitory chemical compounds, we carried out a further and extended analysis of our compounds to examine their effects on cyt-PTPε-mediated dephosphorylation and on osteoclast organization and differentiation. Among five compounds showing target selectivity to cyt-PTPε over three other phosphatases in vitro, two compounds exhibited an inhibitory effect against the dephosphorylation of cellular Src protein, the cyt-PTPε substrate. Moreover, these two compounds caused destabilization of the podosome structure that is necessary for the bone-resorbing activity of osteoclasts, and also attenuated cellular differentiation of monocytes into osteoclasts, without affecting cell viability. Therefore, these findings not only verified anti-osteoclastic effects of our cyt-PTPε inhibitory compounds, but also showed that cyt-PTPε expressed in osteoclasts could be a putative therapeutic target worth considering.
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Affiliation(s)
- Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea; Department of Bioscience, University of Science and Technology KRIBB School, Daejeon 34113, Republic of Korea
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea; Department of Bioscience, University of Science and Technology KRIBB School, Daejeon 34113, Republic of Korea
| | - Kyung Won Lee
- Center for Information-Based Drug Research, Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Chang Hyen Kim
- Department of Oral and Maxillofacial Surgery, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Kyu Yang Yi
- Center for Information-Based Drug Research, Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Chang Hoon Lee
- Center for Information-Based Drug Research, Bio and Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea; Department of Bioscience, University of Science and Technology KRIBB School, Daejeon 34113, Republic of Korea.
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20
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Elkamhawy A, Kim NY, Hassan AHE, Park JE, Yang JE, Oh KS, Lee BH, Lee MY, Shin KJ, Lee KT, Hur W, Roh EJ. Design, synthesis and biological evaluation of novel thiazolidinedione derivatives as irreversible allosteric IKK-β modulators. Eur J Med Chem 2018; 157:691-704. [PMID: 30130718 DOI: 10.1016/j.ejmech.2018.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 12/18/2022]
Abstract
The kinase known as IKK-β activates NF-κB signaling pathway leading to expression of several genes contributing to inflammation, immune response, and cell proliferation. Modulation of IKK-β kinase activity could be useful for treatment and management of such diseases. Starting from a discovered weakly active hit compound, twenty four thiazolidinedione-scaffold based chemical entities belonging to five series have been designed, synthesized and evaluated as potential IKK-β modulators. Among them, compounds 6q, 6r and 6u showed low micromolar IC50 values while compounds 6v, 6w, and 6x elicited submicromolar IC50 values equal to 0.4, 0.7 and 0.9 μM respectively. These submicromolar IC50 values are 243, 139 and 105 folds the value of the reported IC50 of the starting hit compound. Kinetic study of compounds 6v and 6w confirmed this class of modulators as irreversible inhibitors. LPS-treated RAW 264.7 macrophages proved the anti-inflammatory activity of compounds 6q and 6v. Assay of hERG inhibition demonstrated a safe profile of compound 6q suggesting it as a lead for further development of IKK-β modulators.
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Affiliation(s)
- Ahmed Elkamhawy
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Nam Youn Kim
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Jung-Eun Park
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Jeong-Eun Yang
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Kwang-Seok Oh
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 34114, Republic of Korea
| | - Byung Ho Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 34114, Republic of Korea
| | - Mi Young Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 34114, Republic of Korea
| | - Kye Jung Shin
- Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Kyung-Tae Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Wooyoung Hur
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Eun Joo Roh
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea.
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21
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Pippione AC, Sainas S, Federico A, Lupino E, Piccinini M, Kubbutat M, Contreras JM, Morice C, Barge A, Ducime A, Boschi D, Al-Karadaghi S, Lolli ML. N-Acetyl-3-aminopyrazoles block the non-canonical NF-kB cascade by selectively inhibiting NIK. MEDCHEMCOMM 2018; 9:963-968. [PMID: 30108985 PMCID: PMC6071728 DOI: 10.1039/c8md00068a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/07/2018] [Indexed: 01/13/2023]
Abstract
NF-κB-inducing kinase (NIK), an oncogenic drug target that is associated with various cancers, is a central signalling component of the non-canonical pathway. A blind screening process, which established that amino pyrazole related scaffolds have an effect on IKKbeta, led to a hit-to-lead optimization process that identified the aminopyrazole 3a as a low μM selective NIK inhibitor. Compound 3a effectively inhibited the NIK-dependent activation of the NF-κB pathway in tumour cells, confirming its selective inhibitory profile.
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Affiliation(s)
- Agnese C Pippione
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy .
| | - Stefano Sainas
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy .
| | - Antonella Federico
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy .
| | - Elisa Lupino
- Department of Oncology , University of Torino , via Michelangelo 27/B , 10126 Torino , Italy
| | - Marco Piccinini
- Department of Oncology , University of Torino , via Michelangelo 27/B , 10126 Torino , Italy
| | | | - Jean-Marie Contreras
- Prestwick Chemical , 220 Boulevard Gonthier d'Andernach , 67400 Illkirch , France
| | - Christophe Morice
- Prestwick Chemical , 220 Boulevard Gonthier d'Andernach , 67400 Illkirch , France
| | - Alessandro Barge
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy .
| | - Alex Ducime
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy .
| | - Donatella Boschi
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy .
| | | | - Marco L Lolli
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy .
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22
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Pippione AC, Federico A, Ducime A, Sainas S, Boschi D, Barge A, Lupino E, Piccinini M, Kubbutat M, Contreras JM, Morice C, Al-Karadaghi S, Lolli ML. 4-Hydroxy- N-[3,5-bis(trifluoromethyl)phenyl]-1,2,5-thiadiazole-3-carboxamide: a novel inhibitor of the canonical NF-κB cascade. MEDCHEMCOMM 2017; 8:1850-1855. [PMID: 30108896 DOI: 10.1039/c7md00278e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/22/2017] [Indexed: 12/21/2022]
Abstract
The NF-κB signaling pathway is a validated oncological target. Here, we applied scaffold hopping to IMD-0354, a presumed IKKβ inhibitor, and identified 4-hydroxy-N-[3,5-bis(trifluoromethyl)phenyl]-1,2,5-thiadiazole-3-carboxamide (4) as a nM-inhibitor of the NF-κB pathway. However, both 4 and IMD-0354, being potent inhibitors of the canonical NF-κB pathway, were found to be inactive in human IKKβ enzyme assays.
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Affiliation(s)
- Agnese C Pippione
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy
| | - Antonella Federico
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy
| | - Alex Ducime
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy
| | - Stefano Sainas
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy
| | - Donatella Boschi
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy
| | - Alessandro Barge
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy
| | - Elisa Lupino
- Department of Oncology , University of Torino , via Michelangelo 27/B , 10126 Torino , Italy
| | - Marco Piccinini
- Department of Oncology , University of Torino , via Michelangelo 27/B , 10126 Torino , Italy
| | | | - Jean-Marie Contreras
- Prestwick Chemical , 220 Boulevard Gonthier d'Andernach , 67400 Illkirch , France
| | - Christophe Morice
- Prestwick Chemical , 220 Boulevard Gonthier d'Andernach , 67400 Illkirch , France
| | - Salam Al-Karadaghi
- SARomics Biostructures and Department of Biochemistry & Structural Biology , Lund University , Lund , Sweden
| | - Marco L Lolli
- Department of Science and Drug Technology , University of Torino , via Pietro Giuria 9 , 10125 Torino , Italy
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23
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Park H, Jung HY, Mah S, Hong S. Discovery of EGF Receptor Inhibitors That Are Selective for the d746-
750/T790M/C797S Mutant through Structure-Based de Novo Design. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology; Sejong University; Seoul 143-747 Korea
| | - Hoi-Yun Jung
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalization; Institute for Basic Science (IBS); Daejeon 34141 Korea
| | - Shinmee Mah
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalization; Institute for Basic Science (IBS); Daejeon 34141 Korea
| | - Sungwoo Hong
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalization; Institute for Basic Science (IBS); Daejeon 34141 Korea
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24
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Park H, Jung HY, Mah S, Hong S. Discovery of EGF Receptor Inhibitors That Are Selective for the d746-
750/T790M/C797S Mutant through Structure-Based de Novo Design. Angew Chem Int Ed Engl 2017; 56:7634-7638. [DOI: 10.1002/anie.201703389] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/09/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology; Sejong University; Seoul 143-747 Korea
| | - Hoi-Yun Jung
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalization; Institute for Basic Science (IBS); Daejeon 34141 Korea
| | - Shinmee Mah
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalization; Institute for Basic Science (IBS); Daejeon 34141 Korea
| | - Sungwoo Hong
- Department of Chemistry; Korea Advanced Institute of Science and Technology; Daejeon 34141 Korea
- Center for Catalytic Hydrocarbon Functionalization; Institute for Basic Science (IBS); Daejeon 34141 Korea
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25
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Sakchaisri K, Kim SO, Hwang J, Soung NK, Lee KH, Choi TW, Lee Y, Park CM, Thimmegowda NR, Lee PY, Shwetha B, Srinivasrao G, Pham TTH, Jang JH, Yum HW, Surh YJ, Lee KS, Park H, Kim SJ, Kwon YT, Ahn JS, Kim BY. Anticancer activity of a novel small molecule tubulin inhibitor STK899704. PLoS One 2017; 12:e0173311. [PMID: 28296906 PMCID: PMC5351965 DOI: 10.1371/journal.pone.0173311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/17/2017] [Indexed: 12/15/2022] Open
Abstract
We have identified the small molecule STK899704 as a structurally novel tubulin inhibitor. STK899704 suppressed the proliferation of cancer cell lines from various origins with IC50 values ranging from 0.2 to 1.0 μM. STK899704 prevented the polymerization of purified tubulin in vitro and also depolymerized microtubule in cultured cells leading to mitotic arrest, associated with increased Cdc25C phosphorylation and the accumulation of both cyclin B1 and polo-like kinase 1 (Plk1), and apoptosis. Unlike many anticancer drugs such as Taxol and doxorubicin, STK899704 effectively displayed antiproliferative activity against multidrug-resistant cancer cell lines. The proposed binding mode of STK899704 is at the interface between αβ-tubulin heterodimer overlapping with the colchicine-binding site. Our in vivo carcinogenesis model further showed that STK 899704 is potent in both the prevention and regression of tumors, remarkably reducing the number and volume of skin tumor by STK899704 treatment. Moreover, it was significant to note that the efficacy of STK899704 was surprisingly comparable to 5-fluorouracil, a widely used anticancer therapeutic. Thus, our results demonstrate the potential of STK899704 to be developed as an anticancer chemotherapeutic and an alternative candidate for existing therapies.
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Affiliation(s)
- Krisada Sakchaisri
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
- Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Sun-Ok Kim
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Joonsung Hwang
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Nak Kyun Soung
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Kyung Ho Lee
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Tae Woong Choi
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Yongjun Lee
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Chan-Mi Park
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Naraganahalli R. Thimmegowda
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Phil Young Lee
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Bettaswamigowda Shwetha
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Ganipisetti Srinivasrao
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Thi Thu Huong Pham
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
- The Key Laboratory of Enzyme & Protein Technology (KLEPT), VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Jae-Hyuk Jang
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Hye-Won Yum
- College of Pharmacy, Seoul National University, Seoul, Korea
| | - Young-Joon Surh
- College of Pharmacy, Seoul National University, Seoul, Korea
| | - Kyung S. Lee
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Seoul, Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Yong Tae Kwon
- Department of Biomedical Sciences and Protein Metabolism Medical Research Center, College of Medicine, Seoul National University, Seoul, Korea
| | - Jong Seog Ahn
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
| | - Bo Yeon Kim
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Cheongwon, Korea
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26
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Kim D, Park JY, Kim JH. Docking-based In SilicoScreening for Identification of Micromolar Inhibitors of Tropomyosin-related Kinase A from Natural Origin. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Daehyun Kim
- Department of Chemistry; Chung-Ang University; Seoul 06974 Korea
| | - Jung Youl Park
- Industry-Academic Cooperation Foundation; Hanbat National University; Daejeon 34158 Korea
| | - Ji-Hyun Kim
- National CRI-Center for Chemical Dynamics in Living Cells; Chung-Ang University; Seoul 06974 Korea
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27
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Patel AR, Hardianto A, Ranganathan S, Liu F. Divergent response of homologous ATP sites to stereospecific ligand fluorination for selectivity enhancement. Org Biomol Chem 2017; 15:1570-1574. [PMID: 28119986 DOI: 10.1039/c7ob00129k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Acquiring a divergent response from homologous protein domains is essential for selective ligand-protein interactions. Stereospecific fluorination of (-)-balanol, an ATP mimic, uncovers a new source of selectivity from integrated chemical and conformational perturbation that differentiates homologous sites by the level of congruency in their response to local and remote fluorine effects.
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Affiliation(s)
- Alpesh Ramanlal Patel
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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28
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Shin Y, Lim SM, Yan HH, Jung S, Fang Z, Jung KH, Hong SS, Hong S. Optimization and biological evaluation of aminopyrimidine-based IκB kinase β inhibitors with potent anti-inflammatory effects. Eur J Med Chem 2016; 123:544-556. [PMID: 27517803 DOI: 10.1016/j.ejmech.2016.07.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 11/20/2022]
Abstract
Targeting IκB kinase β (IKKβ) can be a promising strategy in the development of a therapeutic treatment of inflammatory diseases because IKKβ is well-recognized as a key mediator of the NF-κB signaling pathway. In this study, we have successfully developed a structure-activity relationship (SAR) profile of the aminopyrimidine-based IKKβ inhibitors through the structure-based design strategy to improve the physicochemical properties and cellular activity in terms of the anti-inflammatory effects. Representative compounds exhibited desirable activity in nitric oxide (NO) reduction by inhibiting the synthesis of inducible nitric oxide synthase (iNOS), and strongly inhibited the expression of pro-inflammatory cytokines (IL-1α, IL-6, and TNF-α). The inhibitory effects of 8e on the phosphorylation in the NF-κB pathway further supported that the suppression of the NF-κB signaling pathway induced the anti-inflammatory effect in LPS-stimulated Raw 264.7 cells.
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Affiliation(s)
- Yongje Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea; Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 34141, South Korea
| | - Sang Min Lim
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 34141, South Korea; Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea
| | - Hong Hua Yan
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon 400-712, South Korea
| | - Sungwoo Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea; Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 34141, South Korea
| | - Zhenghuan Fang
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon 400-712, South Korea
| | - Kyung Hee Jung
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon 400-712, South Korea
| | - Soon-Sun Hong
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon 400-712, South Korea.
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 34141, South Korea; Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea.
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29
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Park H, Lee HS, Kim SJ. Virtual Screening with Docking Simulations and Biochemical Evaluation of VHY Phosphatase Inhibitors. Chem Pharm Bull (Tokyo) 2016; 63:807-11. [PMID: 26423037 DOI: 10.1248/cpb.c15-00431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although VH1-related member Y (VHY) phosphatase is responsible for the pathogenesis of neuroinflammatory diseases, no small-molecule inhibitor of VHY has been reported so far. Here we first report eight VHY inhibitors identified from molecular docking-based virtual screening and subsequent enzyme inhibition assays. These inhibitors exhibit good biochemical potencies against VHY, with associated IC50 values ranging from 1 to 9 µM. Because all these inhibitors were also screened in silico for having desirable physicochemical properties as a drug candidate, they deserve further investigation by structure-activity relationship studies to develop new medicines for the treatment of neuroinflammatory diseases. The structural features of VHY-inhibitor interactions relevant to the micromolar-level inhibitory activity are addressed in detail.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University
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30
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Shin S, Mah S, Hong S, Park H. Discovery of Low Micromolar Dual Inhibitors for Wild Type and L1196M Mutant of Anaplastic Lymphoma Kinase through Structure-Based Virtual Screening. J Chem Inf Model 2016; 56:802-10. [PMID: 27014917 DOI: 10.1021/acs.jcim.6b00026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although anaplastic lymphoma kinase (ALK) is involved in a variety of malignant human cancers, the emergence of constitutively active mutants with drug resistance has rendered it difficult to identify the new medicines for ALK-dependent cancers. To find the common inhibitors of the wild type ALK and the most abundant drug-resistant mutant (L1196M), we performed molecular docking-based virtual screening of a large chemical library in parallel for the two target proteins. As a consequence of augmenting the accuracy of the docking simulation by implementing a sophisticated hydration free energy term in the scoring function, 12 common inhibitors are discovered with the inhibitory activities ranging from submicromolar to low micromolar levels. The results of the binding free energy decomposition indicate that the biochemical potency of ALK inhibitors can be optimized by reducing the dehydration cost for binding to the receptor protein as well as by strengthening the interactions with amino acid residues in the ATP-binding site. The newly identified ALK inhibitors are found to have a little higher inhibitory activity for the L1196M mutant than for the wild type due to the strengthening of the hydrogen bond interactions in the ATP-binding site. Of the 12 common inhibitors, 2-(5-methyl-benzooxazol-2-ylamino)-quinazolin-4-ol (3) is anticipated to serve as a new molecular scaffold to optimize the biochemical potency because it exhibits low micromolar inhibitory activity with respect to both the wild type and L1196M mutant in spite of the low molecular weight (292.3 amu).
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Affiliation(s)
- Saemina Shin
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University , 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea
| | - Shinmee Mah
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) & Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 305-701, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) & Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 305-701, Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University , 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea
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31
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Park H, Lee S, Hong S. Discovery of Dual Inhibitors for Wild Type and D816V Mutant of c-KIT Kinase through Virtual and Biochemical Screening of Natural Products. JOURNAL OF NATURAL PRODUCTS 2016; 79:293-299. [PMID: 26807861 DOI: 10.1021/acs.jnatprod.5b00851] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although stem cell factor receptor (c-KIT) kinase is responsible for various malignant human cancers, the presence of constitutively active gain-of-function mutants has made it difficult to discover new anticancer agents using c-KIT as the target protein. To identify the common inhibitors of wild-type c-KIT and the most abundant gain-of-function mutant (D816V), the virtual screening of natural products was performed for the two target proteins in parallel with the scoring function improved by implementing a sophisticated solvation free energy term. As a result, four common inhibitors of natural origin are found with biochemical potencies ranging from low micromolar to submicromolar levels. The results of extensive docking simulations show that although the natural-product inhibitors establish weaker hydrophobic interactions with the D816V mutant than with the wild type, they exhibit a little higher inhibitory activity for the former than the latter by strengthening the hydrogen-bond interactions to a sufficient extent. Of the four natural-product inhibitors, (Z)-6-hydroxy-2-(4-methoxybenzylidene)benzofuran-3(2H)-one (3) is anticipated to serve as a new molecular core for the structure-activity relationship studies to optimize the biochemical potencies because it exhibits good inhibitory activity against both the wild type and D816V mutant despite its low molecular weight (268.3 amu).
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University , 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea
| | - Soyoung Lee
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) & Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 305-701, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) & Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 305-701, Korea
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32
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Lim SM, Jeong Y, Lee S, Im H, Tae HS, Kim BG, Park HD, Park J, Hong S. Identification of β-Lapachone Analogs as Novel MALT1 Inhibitors To Treat an Aggressive Subtype of Diffuse Large B-Cell Lymphoma. J Med Chem 2015; 58:8491-502. [DOI: 10.1021/acs.jmedchem.5b01415] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sang Min Lim
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 305-701, Korea
| | - Yujeong Jeong
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 305-701, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Suhyun Lee
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 305-701, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Honggu Im
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 305-701, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Hyun Seop Tae
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 305-701, Korea
| | - Byung Gyu Kim
- Drug Discovery Institute, LG Life Sciences, Daejeon 305-738, Korea
| | - Hee Dong Park
- Drug Discovery Institute, LG Life Sciences, Daejeon 305-738, Korea
| | - Jonghoon Park
- Drug Discovery Institute, LG Life Sciences, Daejeon 305-738, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute of Basic Science (IBS), Daejeon 305-701, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
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