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Ibrahim HS, Abdelsalam M, Zeyn Y, Zessin M, Mustafa AHM, Fischer MA, Zeyen P, Sun P, Bülbül EF, Vecchio A, Erdmann F, Schmidt M, Robaa D, Barinka C, Romier C, Schutkowski M, Krämer OH, Sippl W. Synthesis, Molecular Docking and Biological Characterization of Pyrazine Linked 2-Aminobenzamides as New Class I Selective Histone Deacetylase (HDAC) Inhibitors with Anti-Leukemic Activity. Int J Mol Sci 2021; 23:ijms23010369. [PMID: 35008795 PMCID: PMC8745332 DOI: 10.3390/ijms23010369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022] Open
Abstract
Class I histone deacetylases (HDACs) are key regulators of cell proliferation and they are frequently dysregulated in cancer cells. We report here the synthesis of a novel series of class-I selective HDAC inhibitors (HDACi) containing a 2-aminobenzamide moiety as a zinc-binding group connected with a central (piperazin-1-yl)pyrazine or (piperazin-1-yl)pyrimidine moiety. Some of the compounds were additionally substituted with an aromatic capping group. Compounds were tested in vitro against human HDAC1, 2, 3, and 8 enzymes and compared to reference class I HDACi (Entinostat (MS-275), Mocetinostat, CI994 and RGFP-966). The most promising compounds were found to be highly selective against HDAC1, 2 and 3 over the remaining HDAC subtypes from other classes. Molecular docking studies and MD simulations were performed to rationalize the in vitro data and to deduce a complete structure activity relationship (SAR) analysis of this novel series of class-I HDACi. The most potent compounds, including 19f, which blocks HDAC1, HDAC2, and HDAC3, as well as the selective HDAC1/HDAC2 inhibitors 21a and 29b, were selected for further cellular testing against human acute myeloid leukemia (AML) and erythroleukemic cancer (HEL) cells, taking into consideration their low toxicity against human embryonic HEK293 cells. We found that 19f is superior to the clinically tested class-I HDACi Entinostat (MS-275). Thus, 19f is a new and specific HDACi with the potential to eliminate blood cancer cells of various origins.
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Affiliation(s)
- Hany S. Ibrahim
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo 11829, Egypt
| | - Mohamed Abdelsalam
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Yanira Zeyn
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
| | - Matthes Zessin
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Al-Hassan M. Mustafa
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
- Department of Zoology, Faculty of Science, Aswan University, Aswan 81528, Egypt
| | - Marten A. Fischer
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
| | - Patrik Zeyen
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Ping Sun
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Emre F. Bülbül
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Anita Vecchio
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Frank Erdmann
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Matthias Schmidt
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 25250 Vestec, Czech Republic;
| | - Christophe Romier
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS, INSERM, Université de Strasbourg, CEDEX, 67404 Illkirch, France;
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Oliver H. Krämer
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; (Y.Z.); (A.-H.M.M.); (M.A.F.)
- Correspondence: (O.H.K.); (W.S.)
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle (Saale), Germany; (H.S.I.); (M.A.); (M.Z.); (P.Z.); (P.S.); (E.F.B.); (A.V.); (F.E.); (M.S.); (D.R.)
- Correspondence: (O.H.K.); (W.S.)
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Ming J, Liu W, Wu H, Li Y, Yang E, Wang Z, Xiao H, Quan R, Hu X. The active ingredients and mechanisms of Longchai Jiangxue Formula in treating PV, based on UPLC/Q-TOF-MS/MS, systematic pharmacology, and molecular biology validation. Biomed Pharmacother 2021; 140:111767. [PMID: 34058439 DOI: 10.1016/j.biopha.2021.111767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Polycythemia vera (PV) is a refractory hematological disease that lack of effective therapy. Chinese traditional medicine Longchai Jiangxue formula (LCJX) has showed the powerful effects on PV. However, the active ingredients and mechanisms of this formula have not been elucidated. We explored the active ingredients and mechanisms of LCJX for treating PV. METHODS The chemical constituents of LCJX were qualitatively analyzed by UPLC/Q-TOF-MS/MS. On this basis, the TCMSP, ETCM, PubChem BioAssay and ChEMBL databases were searched to predict the potential targets of chemical components of LCJX. Then Genecards, GEO, DisGeNET, and OMIM databases were used to retrieve data of targets related to PV. Drug-disease-target network and protein-protein-interaction (PPI) network were built. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed. Finally, Molecular docking, CCK-8 assay, Annexin V-FITC/PI staining and western blot were processed so as to screen the active components related to PV and elucidate its mechanisms. RESULTS A total of 84 compounds were identified from LCJX by UPLC/Q-TOF-MS/MS. After removed duplicate items, there were 143 targets linked to both disease and drugs. Crucial genes, such as MTOR, HIF1A, JAK2, VEGFA, STAT3, AKT1, TERT, MAPK1, were shown in PPI network. GO enrichment indicated that oxidative stress process, tyrosine kinase activity and phosphatase binding function, and cell membrane structure were in reference to LCJX against PV. KEGG enrichment showed that JAK-STAT signaling pathway and PI3K-Akt signaling pathway, were put in an important position of the treatment. Furthermore, Molecular docking, CCK-8 assay, Annexin V-FITC/PI staining and western blot technique proved the therapeutic effect of Saikosaponin A, main ingredient of LCJX. CONCLUSION This study, combined with UPLC/Q-TOF-MS/MS, network pharmacology and molecular biology, provides a reference for the identification of effective components, screening of quality markers and analysis of its action mechanism of LCJX.
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Affiliation(s)
- Jing Ming
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China; Postdoctoral Research Programme of China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Weiyi Liu
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China.
| | - Hongwei Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China.
| | - Yujin Li
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China; Graduate School, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Erpeng Yang
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China; Graduate School, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Ziqing Wang
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China; Graduate School, Beijing University of Chinese Medicine, Beijing 100029, China.
| | - Haiyan Xiao
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China.
| | - Richeng Quan
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China.
| | - Xiaomei Hu
- Department of Hematology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China.
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