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Yang Y, Xiong Y, Zhu G, Sun M, Zou K, Zhao Y, Zhang Y, Xu Z, Li Y, Zhu W, Jia Q, Li B, Ge G. Discovery of seven-membered ring berberine analogues as highly potent and specific hCES2A inhibitors. Chem Biol Interact 2023; 378:110501. [PMID: 37080375 DOI: 10.1016/j.cbi.2023.110501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/23/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023]
Abstract
Human carboxylesterase 2A (hCES2A) is a key serine hydrolase responsible for the metabolic clearance of large number of compounds bearing the ester- or amide-bond(s). Inhibition of hCES2A can relieve the chemotherapy-induced toxicity and alter the pharmacokinetic bahaviors of some orally administrate esters-containing agents. However, most of the hCES2A inhibitors show poor cell-membrane permeability and poor specificity. Herein, guided by the structure activity relationships (SAR) of fifteen natural alkaloids against hCES2A, fifteen new seven-membered ring berberine analogues were designed and synthesized, and their anti-hCES2A activities were evaluated. Among all tested compounds, compound 28 showed potent anti-hCES2A effect (IC50 = 1.66 μM) and excellent selectivity over hCES1A (IC50 > 100 μM). The SAR analysis revealed that the seven-membered ring of these berberine analogues was a crucial moiety for hCES2A inhibition, while the secondary amine group of the ring-C is important for improving their specificity over other serine hydrolases. Inhibition kinetic analyses and molecular dynamic simulation demonstrated that 28 strongly inhibited hCES2A in a mixed-inhibition manner, with an estimated Ki value of 1.035 μM. Moreover, 28 could inhibit intracellular hCES2A in living HepG2 cells and exhibited suitable metabolic stability. Collectively, the SAR of seven-membered ring berberine analogues as hCES2A inhibitors were studied, while compound 28 acted as a promising candidate for developing highly selective hCES2A inhibitors.
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Affiliation(s)
- Yun Yang
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yuan Xiong
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Guanghao Zhu
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Mengru Sun
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Kun Zou
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yitian Zhao
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yong Zhang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Zhijian Xu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiming Li
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Weiliang Zhu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Jia
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Bo Li
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Guangbo Ge
- School of Pharmacy, Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Zheng X, Pu P, Ding B, Bo W, Qin D, Liang G. Identification of the functional food ingredients with antithrombotic properties via virtual screen and experimental studies. Food Chem 2021; 362:130237. [PMID: 34091163 DOI: 10.1016/j.foodchem.2021.130237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 01/21/2023]
Abstract
Thrombin is a key therapeutic target protein of thrombosis. To date, massive studies have focused on the exploration of antithrombotic compounds. Here we capitalize on molecular docking, molecular simulations and spectroscopic experiments for virtually screening natural products that can inhibit thrombin and elucidating their interaction mechanism. Six compounds are screened from a natural product database by a cross-analysis based on two semi-flexible molecular docking methods. We show that four compounds can effectively inhibit thrombin and Calceolarioside B is the most competitive one based on enzyme inhibition experiments. Moreover, the binding free energies of these compounds with thrombin exhibit a consistent rank trend with their enzyme inhibition assay results. In addition, the Van der Waals is the main force to drive the interaction between the ligands and the receptor, which can be deduced from the fluorescence spectral results. This work provides a new insight into the development of antithrombotic natural compounds.
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Affiliation(s)
- Xin Zheng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Pei Pu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Botian Ding
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Weichen Bo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Dongya Qin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China.
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Yu X, Wei LH, Zhang JK, Chen TR, Jin Q, Wang YN, Zhang SJ, Dou TY, Cao YF, Guo WZ, Ge GB, Yang L. Anthraquinones from Cassiae semen as thrombin inhibitors: in vitro and in silico studies. PHYTOCHEMISTRY 2019; 165:112025. [PMID: 31207449 DOI: 10.1016/j.phytochem.2019.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Thrombin inhibitor therapy is one of the most effective therapeutic strategies for the prevention and treatment of cardiovascular and thrombotic diseases. Although several marketed direct thrombin inhibitors (DTIs) have been widely used in clinic, the potentially serious complications of these DTIs prompted the researchers to find more DTIs with improved safety profiles. Herein, we report that natural anthraquinones in Cassiae semen (the seed of Cassia obtusifolia L. or C. tora L.), including obtusifolin, obtusin, aurantio-obtusin and chryso-obtusin, display strong to moderate inhibition on human thrombin, with the IC50 values ranging from 9.08 μM to 27.88 μM. Further investigation on the inhibition kinetics demonstrates that these anthraquinones are mixed inhibitors against thrombin-mediated Z-GGRAMC acetate hydrolysis, while obtusifolin and aurantio-obtusin show strong thrombin inhibition capacity, with the Ki values of 9.63 μM and 10.30 μM, respectively. Docking simulations demonstrate that both obtusifolin and aurantio-obtusin can simultaneously bind on the catalytic cavity and the two anion binding exosites (ABE1 and ABE2), while the hydroxyl group at the C-7 site and the methoxyl group at the C-8 site can create key interactions with the amino acids surrounding the catalytic cavity via hydrogen bonding. All these findings suggest that obtusifolin and aurantio-obtusin are strong thrombin inhibitors possessing a unique anthraquinone skeleton, and could be used as lead compounds for the development of new thrombin inhibitors with improved properties.
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Affiliation(s)
- Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University; Henan Key Laboratory of Digestive Organ Transplantation; Zhengzhou Key Laboratory of Hepatobiliary & Pancreatic Diseases and Organ Transplantation; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities; Zhengzhou, 450001, China
| | - Ling-Hua Wei
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University; Henan Key Laboratory of Digestive Organ Transplantation; Zhengzhou Key Laboratory of Hepatobiliary & Pancreatic Diseases and Organ Transplantation; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities; Zhengzhou, 450001, China
| | - Jia-Kai Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University; Henan Key Laboratory of Digestive Organ Transplantation; Zhengzhou Key Laboratory of Hepatobiliary & Pancreatic Diseases and Organ Transplantation; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities; Zhengzhou, 450001, China
| | - Tian-Ran Chen
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University; Henan Key Laboratory of Digestive Organ Transplantation; Zhengzhou Key Laboratory of Hepatobiliary & Pancreatic Diseases and Organ Transplantation; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities; Zhengzhou, 450001, China
| | - Qiang Jin
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yi-Nan Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shui-Jun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University; Henan Key Laboratory of Digestive Organ Transplantation; Zhengzhou Key Laboratory of Hepatobiliary & Pancreatic Diseases and Organ Transplantation; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities; Zhengzhou, 450001, China
| | - Tong-Yi Dou
- School of Life Science and Medicine, Dalian University of Technology, Panjin, 124221, China
| | - Yun-Feng Cao
- Dalian Runsheng Kangtai Medical Laboratory Co.Ltd, Dalian, China
| | - Wen-Zhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University; Henan Key Laboratory of Digestive Organ Transplantation; Zhengzhou Key Laboratory of Hepatobiliary & Pancreatic Diseases and Organ Transplantation; Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities; Zhengzhou, 450001, China.
| | - Guang-Bo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Ling Yang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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Wei LH, Chen TR, Fang HB, Jin Q, Zhang SJ, Hou J, Yu Y, Dou TY, Cao YF, Guo WZ, Ge GB. Natural constituents of St. John's Wort inhibit the proteolytic activity of human thrombin. Int J Biol Macromol 2019; 134:622-630. [DOI: 10.1016/j.ijbiomac.2019.04.181] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 11/16/2022]
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Abstract
Matriptase-2 (MT2) is a membrane-anchored proteolytic enzyme. It acts as the proteolytic key regulator in human iron homeostasis. A high expression level can lead to iron overload diseases, whereas mutations in the gene encoding MT2, TMPRSS6, may result in various forms of iron deficiency anemia. Recently, MT2 has been reported as a positive prognostic factor in breast and prostate cancers. However, the exact functions of MT2 in various pathophysiological conditions are still not fully understood. In this review, we describe the synthetic tools designed and synthesized to regulate or monitor MT2 proteolytic activity and present the latest knowledge about the role of MT2 in iron homeostasis and cancer.
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Díez-Buitrago B, Briz N, Liz-Marzán LM, Pavlov V. Biosensing strategies based on enzymatic reactions and nanoparticles. Analyst 2018; 143:1727-1734. [DOI: 10.1039/c7an02067h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Application of new nanomaterials to detection of enzymatic activities allows the development of new sensitive and selective bioanalytical assays based on enzymes for recognition and signal amplification.
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Affiliation(s)
| | - Nerea Briz
- Tecnalia
- 20009 Donostia-San Sebastián
- Spain
| | - Luis M. Liz-Marzán
- CIC BiomaGUNE
- 20014 Donostia-San Sebastián
- Spain
- Ikerbasque
- Basque Foundation for Science
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Ogawa F, Takeda M, Miyanaga K, Tani K, Yamazawa R, Ito K, Tarui A, Sato K, Omote M. Development of a fluorogenic small substrate for dipeptidyl peptidase-4. Beilstein J Org Chem 2017; 13:2690-2697. [PMID: 29564006 PMCID: PMC5753067 DOI: 10.3762/bjoc.13.267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 11/23/2022] Open
Abstract
A series of aniline and m-phenylenediamine derivatives with electron-withdrawing 3,3,3-trifluoropropenyl substituents were synthesized as small and chemically stable fluorescent organic compounds. Their fluorescence performances were evaluated by converting 2,4-disubstituted aniline 1 to the non-fluorescent dipeptide analogue H-Gly-Pro-1 for the use as a fluorogenic substrate for dipeptidyl peptidase-4 (DPP-4). The progress of the enzymatic hydrolysis of H-Gly-Pro-1 with DPP-4 was monitored by fluorometric determination of 1 released into the reaction medium. The results suggest that 1 could be used as fluorophore in OFF–ON-type fluorogenic probes.
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Affiliation(s)
- Futa Ogawa
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Masanori Takeda
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kanae Miyanaga
- Division of Natural Sciences, Osaka Kyoiku University, Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Keita Tani
- Division of Natural Sciences, Osaka Kyoiku University, Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Ryuji Yamazawa
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kiyoshi Ito
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Atsushi Tarui
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Kazuyuki Sato
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Masaaki Omote
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
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Cellier M, James AL, Orenga S, Perry JD, Rasul AK, Stanforth SP. Detection of l-alanylaminopeptidase activity in microorganisms using chromogenic self-immolative enzyme substrates. Bioorg Med Chem Lett 2017; 27:2102-2106. [PMID: 28389152 DOI: 10.1016/j.bmcl.2017.03.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 11/19/2022]
Abstract
Three potential chromogenic enzymatic probes, each possessing a self-immolative spacer unit, were synthesised for the purpose of detecting l-alanylaminopeptidase activity in microorganisms. An Alizarin-based probe was the most effective, allowing several species to generate strongly coloured colonies in the presence of metal ions.
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Affiliation(s)
- Marie Cellier
- Research & Development Microbiology, bioMérieux SA, 3 route de Port Michaud, 38 390 La-Balme-les-Grottes, France
| | - Arthur L James
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Sylvain Orenga
- Research & Development Microbiology, bioMérieux SA, 3 route de Port Michaud, 38 390 La-Balme-les-Grottes, France
| | - John D Perry
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Ari K Rasul
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Stephen P Stanforth
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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