1
|
Kaiser J, Gertzen CGW, Bernauer T, Nitsche V, Höfner G, Niessen KV, Seeger T, Paintner FF, Wanner KT, Steinritz D, Worek F, Gohlke H. Identification of ligands binding to MB327-PAM-1, a binding pocket relevant for resensitization of nAChRs. Toxicol Lett 2024; 398:91-104. [PMID: 38768836 DOI: 10.1016/j.toxlet.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/13/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Desensitization of nicotinic acetylcholine receptors (nAChRs) can be induced by overstimulation with acetylcholine (ACh) caused by an insufficient degradation of ACh after poisoning with organophosphorus compounds (OPCs). Currently, there is no generally applicable treatment for OPC poisoning that directly targets the desensitized nAChR. The bispyridinium compound MB327, an allosteric modulator of nAChR, has been shown to act as a resensitizer of nAChRs, indicating that drugs binding directly to nAChRs can have beneficial effects after OPC poisoning. However, MB327 also acts as an inhibitor of nAChRs at higher concentrations and can thus not be used for OPC poisoning treatment. Consequently, novel, more potent resensitizers are required. To successfully design novel ligands, the knowledge of the binding site is of utmost importance. Recently, we performed in silico studies to identify a new potential binding site of MB327, MB327-PAM-1, for which a more affine ligand, UNC0646, has been described. In this work, we performed ligand-based screening approaches to identify novel analogs of UNC0646 to help further understand the structure-affinity relationship of this compound class. Furthermore, we used structure-based screenings and identified compounds representing four new chemotypes binding to MB327-PAM-1. One of these compounds, cycloguanil, is the active metabolite of the antimalaria drug proguanil and shows a higher affinity towards MB327-PAM-1 than MB327. Furthermore, cycloguanil can reestablish the muscle force in soman-inhibited rat muscles. These results can act as a starting point to develop more potent resensitizers of nAChR and to close the gap in the treatment after OPC poisoning.
Collapse
Affiliation(s)
- Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tamara Bernauer
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Valentin Nitsche
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Georg Höfner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karin V Niessen
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Thomas Seeger
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Franz F Paintner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus T Wanner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany.
| |
Collapse
|
2
|
Higgins WT, Vibhute S, Bennett C, Lindert S. Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods. J Chem Inf Model 2024; 64:435-448. [PMID: 38175956 DOI: 10.1021/acs.jcim.3c01358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
We used a structure-based drug discovery approach to identify novel inhibitors of human dihydroorotate dehydrogenase (DHODH), which is a therapeutic target for treating cancer and autoimmune and inflammatory diseases. In the case of acute myeloid leukemia, no previously discovered DHODH inhibitors have yet succeeded in this clinical application. Thus, there remains a strong need for new inhibitors that could be used as alternatives to the current standard-of-care. Our goal was to identify novel inhibitors of DHODH. We implemented prefiltering steps to omit PAINS and Lipinski violators at the earliest stages of this project. This enriched compounds in the data set that had a higher potential of favorable oral druggability. Guided by Glide SP docking scores, we found 20 structurally unique compounds from the ChemBridge EXPRESS-pick library that inhibited DHODH with IC50, DHODH values between 91 nM and 2.7 μM. Ten of these compounds reduced MOLM-13 cell viability with IC50, MOLM-13 values between 2.3 and 50.6 μM. Compound 16 (IC50, DHODH = 91 nM) inhibited DHODH more potently than the known DHODH inhibitor, teriflunomide (IC50, DHODH = 130 nM), during biochemical characterizations and presented a promising scaffold for future hit-to-lead optimization efforts. Compound 17 (IC50, MOLM-13 = 2.3 μM) was most successful at reducing survival in MOLM-13 cell lines compared with our other hits. The discovered compounds represent excellent starting points for the development and optimization of novel DHODH inhibitors.
Collapse
Affiliation(s)
- William T Higgins
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Medicinal Chemistry Shared Resource, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, United States
| | - Chad Bennett
- Medicinal Chemistry Shared Resource, Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, United States
- Drug Development Institute, Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
3
|
Yang T, Shi X, Li S, Zhao Z, Wang J, Yu P, Li H, Wang R, Chen Z. Targeting DHODH reveals therapeutic opportunities in ATRA-resistant acute promyelocytic leukemia. Biomed Pharmacother 2023; 166:115314. [PMID: 37579695 DOI: 10.1016/j.biopha.2023.115314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/30/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023] Open
Abstract
Although all-trans retinoic acid (ATRA)-induced differentiation has transformed acute promyelocytic leukemia (APL) from the most fatal to the most curable hematological disease, resistance to ATRA in high-risk APL patients remains a clinical challenge. In this paper, we discovered that dihydroorotate dehydrogenase (DHODH) inhibition overcame ATRA resistance. 416, a potent DHODH inhibitor previously obtained in our group, inhibited the occurrence of APL in cells and model mice. Excitingly, 416 effectively overcame ATRA resistance in vitro and in vivo by inducing apoptosis and differentiation. Further mechanistic studies showed that PML/RARα lost the regulation of Bcl-2 and c-Myc in NB4-R1 cells, which probably contributed to ATRA resistance. Notably, 416 maintained its Bcl-2 and c-Myc down-regulation effect in NB4-R1 cells and overcome ATRA resistance by inhibiting DHODH. In conclusion, our study highlights the potential of 416 for APL therapy and overcoming ATRA resistance, supporting the further development of DHODH inhibitors for clinical use in refractory and relapsed APL.
Collapse
Affiliation(s)
- Tingyuan Yang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Xiayu Shi
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Junyi Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Panpan Yu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China; Lingang Laboratory, Shanghai 200031, China.
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China.
| | - Zhuo Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China.
| |
Collapse
|
4
|
Xu Z, Lu S, Liu X, Tang L, Liu Z, Cui J, Wang W, Lu W, Huang J. Drug repurposing of ilepcimide that ameliorates experimental autoimmune encephalomyelitis via restricting inflammatory response and oxidative stress. Toxicol Appl Pharmacol 2023; 458:116328. [PMID: 36455640 DOI: 10.1016/j.taap.2022.116328] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system (CNS) that remains incurable. Herein, we demonstrated that ilepcimide (Antiepilepsirine), an antiepileptic drug used for decades, protects mice from experimental autoimmune encephalomyelitis (EAE), a mouse model of MS. Our studies found that ilepcimide treatment effectively ameliorates demyelination, blood-brain barrier leakage and infiltration of CD4+ and CD8+ T cells in EAE mice. On the one hand, ilepcimide can inhibit dihydroorotate dehydrogenase (DHODH), an important therapeutic target for MS. Computer molecular docking, thermal shift and fluorescence quenching assay demonstrated the directly interaction between ilepcimide and DHODH. Accordingly, ilepcimide observably repressed T cell proliferation in mixed lymphocyte reaction (MLR) assay and concanavalin A (Con-A) model in a DHODH-dependent manner. On the other hand, ilepcimide exhibited neuroprotective effect possibly through activating NRF2 antioxidant pathway in mouse neural crest-derived Neuro2a cells. Collectively, our findings have revealed the therapeutic potential of ilepcimide in EAE mouse model via restricting inflammatory response and oxidative stress, offering a potential opportunity for repurposing existing drug ilepcimide for MS therapy.
Collapse
Affiliation(s)
- Zhaomin Xu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Sisi Lu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xi Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Lu Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zehui Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jiayan Cui
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wanyan Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
| | - Jin Huang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| |
Collapse
|
5
|
Inhibitors of Nucleotide Biosynthesis as Candidates for a Wide Spectrum of Antiviral Chemotherapy. Microorganisms 2022; 10:microorganisms10081631. [PMID: 36014049 PMCID: PMC9413629 DOI: 10.3390/microorganisms10081631] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Emerging and re-emerging viruses have been a challenge in public health in recent decades. Host-targeted antivirals (HTA) directed at cellular molecules or pathways involved in virus multiplication represent an interesting strategy to combat viruses presently lacking effective chemotherapy. HTA could provide a wide range of agents with inhibitory activity against current and future viruses that share similar host requirements and reduce the possible selection of antiviral-resistant variants. Nucleotide metabolism is one of the more exploited host metabolic pathways as a potential antiviral target for several human viruses. This review focuses on the antiviral properties of the inhibitors of pyrimidine and purine nucleotide biosynthesis, with an emphasis on the rate-limiting enzymes dihydroorotate dehydrogenase (DHODH) and inosine monophosphate dehydrogenase (IMPDH) for which there are old and new drugs active against a broad spectrum of pathogenic viruses.
Collapse
|
6
|
Zhang L, Zhang J, Wang J, Ren C, Tang P, Ouyang L, Wang Y. Recent advances of human dihydroorotate dehydrogenase inhibitors for cancer therapy: Current development and future perspectives. Eur J Med Chem 2022; 232:114176. [DOI: 10.1016/j.ejmech.2022.114176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022]
|
7
|
Chen JA, Ma H, Liu Z, Tian J, Lu S, Fang W, Ze S, Lu W, Xie Q, Huang J, Wang Y. Discovery of Orally Available Retinoic Acid Receptor-Related Orphan Receptor γ-t/Dihydroorotate Dehydrogenase Dual Inhibitors for the Treatment of Refractory Inflammatory Bowel Disease. J Med Chem 2021; 65:592-615. [PMID: 34957834 DOI: 10.1021/acs.jmedchem.1c01746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inflammatory bowel disease (IBD) is a multifactorial autoimmune disease, representing a major clinical challenge. Herein, a strategy of dual-targeting approach employing retinoic acid receptor-related orphan receptor γ-t (RORγt) and dihydroorotate dehydrogenase (DHODH) was proposed for the treatment of IBD. Dual RORγt/DHODH inhibitors are expected not only to reduce RORγt-driven Th17 cell differentiation but also to mitigate the expansion and activation of T cells, which may enhance anti-inflammatory effects. Starting from 2-aminobenzothiazole hit 1, a series of 2-aminotetrahydrobenzothiazoles were discovered as potent dual RORγt/DHODH inhibitors. Compound 14d stands out with IC50 values of 0.110 μM for RORγt and of 0.297 μM for DHODH. With acceptable mouse pharmacokinetic profiles, 14d exhibited remarkable in vivo anti-inflammatory activity and dose-dependently alleviated the severity of dextran sulfate sodium (DSS)-induced acute colitis in mice. Taken together, the present study provides a novel framework for the development of therapeutic agents for the treatment of IBD.
Collapse
Affiliation(s)
- Ji-An Chen
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Hui Ma
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zehui Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jinlong Tian
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Sisi Lu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Wenqing Fang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Shuyin Ze
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Qiong Xie
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,Fudan Zhangjiang Institute, 666 Zhangheng Road, Shanghai 201203, China
| | - Jin Huang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yonghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| |
Collapse
|
8
|
Li C, Yang X, Luo Y, Liu H, Zhong X, Zhou X, Zeng T, Tao L, Zhou Y, Gou K, Yang X, Liu X, Chen Q, Zhao Y, Luo Y. Design, Synthesis, and Biological Evaluation of a Novel Series of Teriflunomide Derivatives as Potent Human Dihydroorotate Dehydrogenase Inhibitors for Malignancy Treatment. J Med Chem 2021; 64:18175-18192. [PMID: 34905371 DOI: 10.1021/acs.jmedchem.1c01711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human dihydroorotate dehydrogenase (hDHODH), as the fourth and rate-limiting enzyme of the de novo pyrimidine synthesis pathway, is regarded as an attractive target for malignancy therapy. In the present study, a novel series of teriflunomide derivatives were designed, synthesized, and evaluated as hDHODH inhibitors. 13t was the optimal compound with promising enzymatic activity (IC50 = 16.0 nM), potent antiproliferative activity against human lymphoma Raji cells (IC50 = 7.7 nM), and excellent aqueous solubility (20.1 mg/mL). Mechanistically, 13t directly inhibited hDHODH and induced cell cycle S-phase arrest in Raji cells. The acute toxicity assay indicated a favorable safety profile of 13t. Notably, 13t displayed significant tumor growth inhibition activity with a tumor growth inhibition (TGI) rate of 81.4% at 30 mg/kg in a Raji xenograft model. Together, 13t is a promising inhibitor of hDHODH and a preclinical candidate for antitumor therapy, especially for lymphoma.
Collapse
Affiliation(s)
- Chungen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Xiaowei Yang
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yuan Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Huan Liu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xi Zhong
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xia Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Ting Zeng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lei Tao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yue Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Kun Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Xinyu Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Xiaocong Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Qiang Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yinglan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.,Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| |
Collapse
|
9
|
Ng YL, Salim CK, Chu JJH. Drug repurposing for COVID-19: Approaches, challenges and promising candidates. Pharmacol Ther 2021; 228:107930. [PMID: 34174275 PMCID: PMC8220862 DOI: 10.1016/j.pharmthera.2021.107930] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023]
Abstract
Traditional drug development and discovery has not kept pace with threats from emerging and re-emerging diseases such as Ebola virus, MERS-CoV and more recently, SARS-CoV-2. Among other reasons, the exorbitant costs, high attrition rate and extensive periods of time from research to market approval are the primary contributing factors to the lag in recent traditional drug developmental activities. Due to these reasons, drug developers are starting to consider drug repurposing (or repositioning) as a viable alternative to the more traditional drug development process. Drug repurposing aims to find alternative uses of an approved or investigational drug outside of its original indication. The key advantages of this approach are that there is less developmental risk, and it is less time-consuming since the safety and pharmacological profile of the repurposed drug is already established. To that end, various approaches to drug repurposing are employed. Computational approaches make use of machine learning and algorithms to model disease and drug interaction, while experimental approaches involve a more traditional wet-lab experiments. This review would discuss in detail various ongoing drug repurposing strategies and approaches to combat the current COVID-19 pandemic, along with the advantages and the potential challenges.
Collapse
Affiliation(s)
- Yan Ling Ng
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, 117545, Singapore,Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Cyrill Kafi Salim
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, 117545, Singapore,Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, 117545, Singapore,Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597, Singapore,Collaborative and Translation Unit for HFMD, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore,Corresponding author at: Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| |
Collapse
|
10
|
Combination of consensus and ensemble docking strategies for the discovery of human dihydroorotate dehydrogenase inhibitors. Sci Rep 2021; 11:11417. [PMID: 34075175 PMCID: PMC8169699 DOI: 10.1038/s41598-021-91069-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
The inconsistencies in the performance of the virtual screening (VS) process, depending on the used software and structural conformation of the protein, is a challenging issue in the drug design and discovery field. Varying performance, especially in terms of early recognition of the potential hit compounds, negatively affects the whole process and leads to unnecessary waste of the time and resources. Appropriate application of the ensemble docking and consensus-scoring approaches can significantly increase reliability of the VS results. Dihydroorotate dehydrogenase (DHODH) is a key enzyme in the pyrimidine biosynthesis pathway. It is considered as a valuable therapeutic target in cancer, autoimmune and viral diseases. Based on the conducted benchmark study and analysis of the effect of different combinations of the applied methods and approaches, here we suggested a structure-based virtual screening (SBVS) workflow that can be used to increase the reliability of VS.
Collapse
|
11
|
Berber B, Doluca O. A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin-dopamine receptors. Brief Bioinform 2021; 22:1023-1037. [PMID: 33406218 PMCID: PMC7929379 DOI: 10.1093/bib/bbaa379] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/26/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a key enzyme required for de novo pyrimidine synthesis and it is suggested as a target for COVID19 treatment due to high pyrimidine demand by the virus replication in the infected host cells as well as its proven effect of blocking of cytokine release by the immune cells to prevent inflammation leading to acute respiratory distress. There are a number of clinical trials underway for COVID19 treatment using DHODH inhibitors; however, there are only a small number of known DHODH antagonists available for testing. Here, we have applied a methodology to identify DHODH antagonist candidates, and compared them using in silico target prediction tools. A large set of 7900 FDA-approved and clinical stage drugs obtained from DrugBank were docked against 20 different structures DHODH available in PDB. Drugs were eliminated according to their predicted affinities by Autodock Vina. About 28 FDA-approved and 79 clinical trial ongoing drugs remained. The mode of interaction of these molecules was analyzed by repeating docking using Autodock 4 and DS Visualiser. Finally, the target region predictions of 28 FDA-approved drugs were determined through PASS and SwissTargetPrediction tools. Interestingly, the analysis of in silico target predictions revealed that serotonin-dopamine receptor antagonists could also be potential DHODH inhibitors. Our candidates shared a common attribute, a possible interaction with serotonin-dopamine receptors as well as other oxidoreductases, like DHODH. Moreover, the Bruton Tyrosine Kinase-inhibitor acalabrutunib and serotonin-dopamine receptor inhibitor drugs on our list have been found in the literature that have shown to be effective against Sars-CoV-2, while the path of activity is yet to be identified. Identifying an effective drug that can suppress both inflammation and virus proliferation will play a crucial role in the treatment of COVID. Therefore, we suggest experimental investigation of the 28 FDA-approved drugs on DHODH activity and Sars-CoV-2 virus proliferation. Those who are found experimentally effective can play an important role in COVID19 treatment. Moreover, we suggest investigating COVID19 case conditions in patients using schizophrenia and depression drugs.
Collapse
Affiliation(s)
- Burak Berber
- Eskisehir Technical University, Department of Biology
| | | |
Collapse
|
12
|
Zeng F, Li S, Yang G, Luo Y, Qi T, Liang Y, Yang T, Zhang L, Wang R, Zhu L, Li H, Xu X. Design, synthesis, molecular modeling, and biological evaluation of acrylamide derivatives as potent inhibitors of human dihydroorotate dehydrogenase for the treatment of rheumatoid arthritis. Acta Pharm Sin B 2020; 11:S2211-3835(20)30759-0. [PMID: 33078092 PMCID: PMC7558257 DOI: 10.1016/j.apsb.2020.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 01/15/2023] Open
Abstract
Human dihydroorotate dehydrogenase (DHODH) is a viable target for the development of therapeutics to treat cancer and immunological diseases, such as rheumatoid arthritis (RA), psoriasis and multiple sclerosis (MS). Herein, a series of acrylamide-based novel DHODH inhibitors as potential RA treatment agents were designed and synthesized. 2-Acrylamidobenzoic acid analog 11 was identified as the lead compound for structure-activity relationship (SAR) studies. The replacement of the phenyl group with naphthyl moieties improved inhibitory activity significantly to double-digit nanomolar range. Further structure optimization revealed that an acrylamide with small hydrophobic groups (Me, Cl or Br) at the 2-position was preferred. Moreover, adding a fluoro atom at the 5-position of the benzoic acid enhanced the potency. The optimization efforts led to potent compounds 42 and 53‒55 with IC50 values of 41, 44, 32, and 42 nmol/L, respectively. The most potent compound 54 also displayed favorable pharmacokinetic (PK) profiles and encouraging in vivo anti-arthritic effects in a dose-dependent manner.
Collapse
Key Words
- AML, acute myeloid leukemia
- Acrylamide derivatives
- BPO, benzoyl peroxide
- CIA, collagen-induced arthritis
- DCE, 1,2-dichloroethane
- DCM, dichloromethane
- DHODH
- DHODH inhibitors
- DHODH, dihydroorotate dehydrogenase
- DMAP, 4-dimethylaminopyridine
- DMARDs, disease-modifying antirheumatic drugs
- DMF, N,N-dimethylformamide
- DMSO, dimethyl sulfoxide
- De novo pyrimidine biosynthesis
- EA, ethyl acetate
- FMN, flavin mononucleotide
- HPLC, high performance liquid chromatography
- HRMS, high-resolution mass spectrometry
- IBD, inflammatory bowel disease
- LAH, lithium aluminium hydride
- LCMS, liquid chromatography mass spectrometry
- MS, multiple sclerosis
- MeOH, methanol
- NBS, N-bromosuccinimide
- NCS, N-chlorosuccinimide
- NSAIDs, non-steroidal anti-inflammatory drugs
- PDA, photodiode array detector
- PE, petroleum ether
- PK, pharmacokinetic
- PhMe, toluene
- RA, rheumatoid arthritis
- Rheumatoid arthritis
- SEL, systemic lupus erythematosus
- TEA, triethylamine
- TFA, trifluoroacetic acid
- THF, tetrahydrofuran
- TsCl, tosyl chloride
Collapse
Affiliation(s)
- Fanxun Zeng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Guantian Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Yating Luo
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Tiantian Qi
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Yingfan Liang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Tingyuan Yang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Letian Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| | - Xiaoyong Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China
| |
Collapse
|
13
|
Xu Y, Jiang H. Potential treatment of COVID-19 by inhibitors of human dihydroorotate dehydrogenase. Protein Cell 2020; 11:699-702. [PMID: 32761523 PMCID: PMC7406694 DOI: 10.1007/s13238-020-00769-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yechun Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
14
|
Xiong R, Zhang L, Li S, Sun Y, Ding M, Wang Y, Zhao Y, Wu Y, Shang W, Jiang X, Shan J, Shen Z, Tong Y, Xu L, Chen Y, Liu Y, Zou G, Lavillete D, Zhao Z, Wang R, Zhu L, Xiao G, Lan K, Li H, Xu K. Novel and potent inhibitors targeting DHODH are broad-spectrum antivirals against RNA viruses including newly-emerged coronavirus SARS-CoV-2. Protein Cell 2020; 11:723-739. [PMID: 32754890 DOI: 10.1101/2020.03.11.983056] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 05/18/2023] Open
Abstract
Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of the novel coronavirus SARS-CoV-2. Herein, we identified two potent inhibitors of human DHODH, S312 and S416, with favorable drug-likeness and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus, Zika virus, Ebola virus, and particularly against SARS-CoV-2. Notably, S416 is reported to be the most potent inhibitor so far with an EC50 of 17 nmol/L and an SI value of 10,505.88 in infected cells. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knock-out cells. This work demonstrates that both S312/S416 and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-regulation may have clinical potentials to cure SARS-CoV-2 or other RNA viruses circulating worldwide, no matter such viruses are mutated or not.
Collapse
Affiliation(s)
- Rui Xiong
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuan Sun
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Minyi Ding
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yong Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongliang Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiaming Jiang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiwei Shan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Zihao Shen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yi Tong
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Liuxin Xu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gang Zou
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dimitri Lavillete
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Ke Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| |
Collapse
|
15
|
Xiong R, Zhang L, Li S, Sun Y, Ding M, Wang Y, Zhao Y, Wu Y, Shang W, Jiang X, Shan J, Shen Z, Tong Y, Xu L, Chen Y, Liu Y, Zou G, Lavillete D, Zhao Z, Wang R, Zhu L, Xiao G, Lan K, Li H, Xu K. Novel and potent inhibitors targeting DHODH are broad-spectrum antivirals against RNA viruses including newly-emerged coronavirus SARS-CoV-2. Protein Cell 2020; 11:723-739. [PMID: 32754890 PMCID: PMC7402641 DOI: 10.1007/s13238-020-00768-w] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 12/28/2022] Open
Abstract
Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of the novel coronavirus SARS-CoV-2. Herein, we identified two potent inhibitors of human DHODH, S312 and S416, with favorable drug-likeness and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus, Zika virus, Ebola virus, and particularly against SARS-CoV-2. Notably, S416 is reported to be the most potent inhibitor so far with an EC50 of 17 nmol/L and an SI value of 10,505.88 in infected cells. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knock-out cells. This work demonstrates that both S312/S416 and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-regulation may have clinical potentials to cure SARS-CoV-2 or other RNA viruses circulating worldwide, no matter such viruses are mutated or not.
Collapse
Affiliation(s)
- Rui Xiong
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuan Sun
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Minyi Ding
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yong Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongliang Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiaming Jiang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiwei Shan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Zihao Shen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yi Tong
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Liuxin Xu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gang Zou
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dimitri Lavillete
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Ke Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| |
Collapse
|
16
|
Liu Z, Hu Q, Wang W, Lu S, Wu D, Ze S, He J, Huang Y, Chen W, Xu Y, Lu W, Huang J. Natural product piperine alleviates experimental allergic encephalomyelitis in mice by targeting dihydroorotate dehydrogenase. Biochem Pharmacol 2020; 177:114000. [PMID: 32353424 DOI: 10.1016/j.bcp.2020.114000] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023]
Abstract
Multiple sclerosis (MS) is the most popular chronic and debilitating inflammatory disease of the central nervous system (CNS) that remains incurable. Dihydroorotate dehydrogenase (DHODH) is critical to the activity of T lymphocytes and represents a potential therapeutic target for MS. Here we identify piperine, a bioactive constituent of black pepper, as a potent inhibitor of DHODH with an IC50 value of 0.88 μM. Isothermal titration calorimetry and thermofluor assay demonstrate the directly interaction between piperine and DHODH. The co-complex crystal structure of DHODH and piperine at 1.98 Å resolution further reveal that Tyr356 residue of DHODH is crucial for piperine binding. Importantly, we show that piperine can inhibit T cell overactivation in a DHODH-dependent manner in concanavalin A-triggered T-cell assay and mixed lymphocyte reaction assay. Finally, piperine exhibits strong preventive and therapeutic effect in the MOG-induced experimental allergic encephalomyelitis (EAE), a useful model for studying potential treatments for MS, by restricting inflammatory cells infiltration into the CNS and preventing myelin destruction and blood-brain barrier (BBB) disruption. Taken together, these findings highlight DHODH as a therapeutic target for autoimmune disease of the nervous system, and demonstrate a novel role for piperine in the treatment of MS.
Collapse
Affiliation(s)
- Zehui Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qian Hu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wanyan Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Sisi Lu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Dang Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Shuyin Ze
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiacheng He
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ying Huang
- Guangdong Institute for Drug Control, Guangdong, China
| | - Wuyan Chen
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| |
Collapse
|
17
|
Popova G, Ladds MJGW, Johansson L, Saleh A, Larsson J, Sandberg L, Sahlberg SH, Qian W, Gullberg H, Garg N, Gustavsson AL, Haraldsson M, Lane D, Yngve U, Lain S. Optimization of Tetrahydroindazoles as Inhibitors of Human Dihydroorotate Dehydrogenase and Evaluation of Their Activity and In Vitro Metabolic Stability. J Med Chem 2020; 63:3915-3934. [PMID: 32212728 DOI: 10.1021/acs.jmedchem.9b01658] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human dihydroorotate dehydrogenase (DHODH), an enzyme in the de novo pyrimidine synthesis pathway, is a target for the treatment of rheumatoid arthritis and multiple sclerosis and is re-emerging as an attractive target for cancer therapy. Here we describe the optimization of recently identified tetrahydroindazoles (HZ) as DHODH inhibitors. Several of the HZ analogues synthesized in this study are highly potent inhibitors of DHODH in an enzymatic assay, while also inhibiting cancer cell growth and viability and activating p53-dependent transcription factor activity in a reporter cell assay. Furthermore, we demonstrate the specificity of the compounds toward the de novo pyrimidine synthesis pathway through supplementation with an excess of uridine. We also show that induction of the DNA damage marker γ-H2AX after DHODH inhibition is preventable by cotreatment with the pan-caspase inhibitor Z-VAD-FMK. Additional solubility and in vitro metabolic stability profiling revealed compound 51 as a favorable candidate for preclinical efficacy studies.
Collapse
Affiliation(s)
- Gergana Popova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Stockholm, Sweden
| | - Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23, SE-171 21 Solna, Stockholm, Sweden
| | - Lars Johansson
- Chemical Biology Consortium Sweden, SciLifeLab, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden
| | - Aljona Saleh
- SciLifeLab, Drug Discovery and Development Platform, ADME of Therapeutics Facility, Department of Pharmacy, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
| | - Johanna Larsson
- SciLifeLab, Drug Discovery and Development Platform, Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Lars Sandberg
- SciLifeLab, Drug Discovery and Development Platform, Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden.,SciLifeLab, Drug Discovery and Development Platform, Department of Organic Chemistry, Stockholm University, Box 1030, SE-171 21 Solna, Stockholm, Sweden
| | - Sara Häggblad Sahlberg
- SciLifeLab, Drug Discovery and Development Platform, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21 Solna, Stockholm, Sweden
| | - Weixing Qian
- Chemical Biology Consortium Sweden, Laboratories for Chemical Biology Umeå, Umeå University, SE-901 87 Umeå, Sweden
| | - Hjalmar Gullberg
- SciLifeLab, Drug Discovery and Development Platform, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21 Solna, Stockholm, Sweden
| | - Neeraj Garg
- SciLifeLab, Drug Discovery and Development Platform, Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, SciLifeLab, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, SciLifeLab, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden
| | - David Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Stockholm, Sweden
| | - Ulrika Yngve
- SciLifeLab, Drug Discovery and Development Platform, Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
| | - Sonia Lain
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23, SE-171 21 Solna, Stockholm, Sweden
| |
Collapse
|
18
|
Diastereoselective [3 + 3] cycloaddition reaction of 2-arylideneindan-1,3-diones with β-naphthols: Efficient assemble of immunosuppressive pentacyclic chromanes. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2019.151579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
19
|
Mariadasse R, Choubey SK, Jeyakanthan J. Insights into Exogenous Tryptophan-Mediated Allosteric Communication and Helical Transition of TRP Protein for Transcription Regulation. J Chem Inf Model 2019; 60:175-191. [DOI: 10.1021/acs.jcim.9b00755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Mariadasse
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Sanjay Kumar Choubey
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| |
Collapse
|
20
|
Hayek S, Pietrancosta N, Hovhannisyan AA, Alves de Sousa R, Bekaddour N, Ermellino L, Tramontano E, Arnould S, Sardet C, Dairou J, Diaz O, Lotteau V, Nisole S, Melikyan G, Herbeuval JP, Vidalain PO. Cerpegin-derived furo[3,4-c]pyridine-3,4(1H,5H)-diones enhance cellular response to interferons by de novo pyrimidine biosynthesis inhibition. Eur J Med Chem 2019; 186:111855. [PMID: 31740051 DOI: 10.1016/j.ejmech.2019.111855] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022]
Abstract
There is an increasing interest in the field of cancer therapy for small compounds targeting pyrimidine biosynthesis, and in particular dihydroorotate dehydrogenase (DHODH), the fourth enzyme of this metabolic pathway. Three available DHODH structures, featuring three different known inhibitors, were used as templates to screen in silico an original chemical library from Erevan University. This process led to the identification of P1788, a compound chemically related to the alkaloid cerpegin, as a new class of pyrimidine biosynthesis inhibitors. In line with previous reports, we investigated the effect of P1788 on the cellular innate immune response. Here we show that pyrimidine depletion by P1788 amplifies cellular response to both type-I and type II interferons, but also induces DNA damage as assessed by γH2AX staining. Moreover, the addition of inhibitors of the DNA damage response led to the suppression of the P1788 stimulatory effects on the interferon pathway. This demonstrates that components of the DNA damage response are bridging the inhibition of pyrimidine biosynthesis by P1788 to the interferon signaling pathway. Altogether, these results provide new insights on the mode of action of novel pyrimidine biosynthesis inhibitors and their development for cancer therapies.
Collapse
Affiliation(s)
- Simon Hayek
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Nicolas Pietrancosta
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | | | - Rodolphe Alves de Sousa
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Nassima Bekaddour
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Laura Ermellino
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France; Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Stéphanie Arnould
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Claude Sardet
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Julien Dairou
- Chimie Bio-inorganique des Dérivés Soufrés et Pharmacochimie (CBDSP), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Olivier Diaz
- Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier, CNRS UMR9004, Université de Montpellier, Montpellier, France
| | - Gagik Melikyan
- Department of Organic Chemistry, Yerevan State University, Yerevan, Armenia.
| | - Jean-Philippe Herbeuval
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France
| | - Pierre-Olivier Vidalain
- Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, CNRS UMR8601, Paris, France.
| |
Collapse
|
21
|
TMSBr-Promoted Cascade Cyclization of ortho-Propynol Phenyl Azides for the Synthesis of 4-Bromo Quinolines and Its Applications. Molecules 2019; 24:molecules24213999. [PMID: 31694215 PMCID: PMC6864654 DOI: 10.3390/molecules24213999] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Difficult-to-access 4-bromo quinolines are constructed directly from easily prepared ortho-propynol phenyl azides using TMSBr as acid-promoter. The cascade transformation performs smoothly to generate desired products in moderate to excellent yields with good functional groups compatibility. Notably, TMSBr not only acted as an acid-promoter to initiate the reaction, and also as a nucleophile. In addition, 4-bromo quinolines as key intermediates could further undergo the coupling reactions or nucleophilic reactions to provide a variety of functionalized compounds with molecular diversity at C4 position of quinolines.
Collapse
|
22
|
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
23
|
Wu D, Wang W, Chen W, Lian F, Lang L, Huang Y, Xu Y, Zhang N, Chen Y, Liu M, Nussinov R, Cheng F, Lu W, Huang J. Pharmacological inhibition of dihydroorotate dehydrogenase induces apoptosis and differentiation in acute myeloid leukemia cells. Haematologica 2018; 103:1472-1483. [PMID: 29880605 PMCID: PMC6119157 DOI: 10.3324/haematol.2018.188185] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/30/2018] [Indexed: 01/24/2023] Open
Abstract
Acute myeloid leukemia is a disorder characterized by abnormal differentiation of myeloid cells and a clonal proliferation derived from primitive hematopoietic stem cells. Interventions that overcome myeloid differentiation have been shown to be a promising therapeutic strategy for acute myeloid leukemia. In this study, we demonstrate that CRISPR/Cas9-mediated knockout of dihydroorotate dehydrogenase leads to apoptosis and normal differentiation of acute myeloid leukemia cells, indicating that dihydroorotate dehydrogenase is a potential differentiation regulator and a therapeutic target in acute myeloid leukemia. By screening a library of natural products, we identified a novel dihydroorotate dehydrogenase inhibitor, isobavachalcone, derived from the traditional Chinese medicine Psoralea corylifolia Using enzymatic analysis, thermal shift assay, pull down, nuclear magnetic resonance, and isothermal titration calorimetry experiments, we demonstrate that isobavachalcone inhibits human dihydroorotate dehydrogenase directly, and triggers apoptosis and differentiation of acute myeloid leukemia cells. Oral administration of isobavachalcone suppresses subcutaneous HL60 xenograft tumor growth without obvious toxicity. Importantly, our results suggest that a combination of isobavachalcone and adriamycin prolonged survival in an intravenous HL60 leukemia model. In summary, this study demonstrates that isobavachalcone triggers apoptosis and differentiation of acute myeloid leukemia cells via pharmacological inhibition of human dihydroorotate dehydrogenase, offering a potential therapeutic strategy for acute myeloid leukemia.
Collapse
MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Apoptosis/genetics
- Biomarkers, Tumor
- Cell Differentiation/drug effects
- Cell Differentiation/genetics
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Chalcones/chemistry
- Chalcones/pharmacology
- Dihydroorotate Dehydrogenase
- Disease Models, Animal
- Drug Synergism
- Enzyme Activation/drug effects
- Enzyme Inhibitors/pharmacology
- Gene Expression
- Gene Knockdown Techniques
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Mice
- Models, Molecular
- Molecular Structure
- Neoplastic Stem Cells/metabolism
- Oxidoreductases Acting on CH-CH Group Donors/antagonists & inhibitors
- Oxidoreductases Acting on CH-CH Group Donors/genetics
- Oxidoreductases Acting on CH-CH Group Donors/metabolism
- Prognosis
- RNA Interference
- Structure-Activity Relationship
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Dang Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, China
| | - Wanyan Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, China
| | - Wuyan Chen
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), China
| | - Fulin Lian
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), China
| | - Li Lang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, China
| | - Ying Huang
- Guangdong Institute for Drug Control, Guangzhou, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), China
| | - Naixia Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), China
| | - Yinbin Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, China
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, MD, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Israel
| | - Feixiong Cheng
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, USA
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, OH, USA
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, China
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, China
| |
Collapse
|
24
|
Lang L, Hu Q, Wang J, Liu Z, Huang J, Lu W, Huang Y. Coptisine, a natural alkaloid from Coptidis Rhizoma
, inhibits plasmodium falciparum dihydroorotate dehydrogenase. Chem Biol Drug Des 2018; 92:1324-1332. [DOI: 10.1111/cbdd.13197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/22/2018] [Accepted: 03/17/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Li Lang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Qian Hu
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Jingyuan Wang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Zehui Liu
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology; Institute of Biomedical Sciences and School of Life Sciences; East China Normal University; Shanghai China
| | - Ying Huang
- Guangdong Institute for Drug Control; Guangzhou Guangdong China
| |
Collapse
|
25
|
Kumar S, Bhardwaj TR, Prasad DN, Singh RK. Drug targets for resistant malaria: Historic to future perspectives. Biomed Pharmacother 2018; 104:8-27. [PMID: 29758416 DOI: 10.1016/j.biopha.2018.05.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/22/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023] Open
Abstract
New antimalarial targets are the prime need for the discovery of potent drug candidates. In order to fulfill this objective, antimalarial drug researches are focusing on promising targets in order to develop new drug candidates. Basic metabolism and biochemical process in the malaria parasite, i.e. Plasmodium falciparum can play an indispensable role in the identification of these targets. But, the emergence of resistance to antimalarial drugs is an escalating comprehensive problem with the progress of antimalarial drug development. The development of resistance has highlighted the need for the search of novel antimalarial molecules. The pharmaceutical industries are committed to new drug development due to the global recognition of this life threatening resistance to the currently available antimalarial therapy. The recent developments in the understanding of parasite biology are exhilarating this resistance issue which is further being ignited by malaria genome project. With this background of information, this review was aimed to highlights and provides useful information on various present and promising treatment approaches for resistant malaria, new progresses, pursued by some innovative targets that have been explored till date. This review also discusses modern and futuristic multiple approaches to antimalarial drug discovery and development with pictorial presentations highlighting the various targets, that could be exploited for generating promising new drugs in the future for drug resistant malaria.
Collapse
Affiliation(s)
- Sahil Kumar
- School of Pharmacy and Emerging Sciences, Baddi University of Emerging Sciences & Technology, Baddi, Dist. Solan, 173205, Himachal Pradesh, India
| | - T R Bhardwaj
- School of Pharmacy and Emerging Sciences, Baddi University of Emerging Sciences & Technology, Baddi, Dist. Solan, 173205, Himachal Pradesh, India
| | - D N Prasad
- Department of Pharmaceutical Chemistry, Shivalik College of Pharmacy, Nangal, Dist. Rupnagar, 140126, Punjab, India
| | - Rajesh K Singh
- Department of Pharmaceutical Chemistry, Shivalik College of Pharmacy, Nangal, Dist. Rupnagar, 140126, Punjab, India.
| |
Collapse
|
26
|
Song XR, Li R, Ding H, Chen X, Yang T, Bai J, Xiao Q, Liang YM. An efficient approach to 4-chloro quinolines via TMSCl-mediated cascade cyclization of ortho-propynol phenyl azides. Org Chem Front 2018. [DOI: 10.1039/c8qo00162f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel and efficient strategy for the synthesis of 4-chloro quinolines via the TMSCl-mediated cascade cyclization of easily prepared ortho-propynol phenyl azides is developed.
Collapse
Affiliation(s)
- Xian-Rong Song
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Ren Li
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Haixin Ding
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Xi Chen
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Tao Yang
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Jiang Bai
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Qiang Xiao
- Institute of Organic Chemistry
- Jiangxi Science & Technology Normal University
- Key Laboratory of Organic Chemistry
- Nanchang 330013
- China
| | - Yong-Min Liang
- State Key Laboratory of Applied Organic Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| |
Collapse
|
27
|
Pavadai E, El Mazouni F, Wittlin S, de Kock C, Phillips MA, Chibale K. Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening. J Chem Inf Model 2016; 56:548-62. [PMID: 26915022 DOI: 10.1021/acs.jcim.5b00680] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH), a key enzyme in the de novo pyrimidine biosynthesis pathway, which the Plasmodium falciparum relies on exclusively for survival, has emerged as a promising target for antimalarial drugs. In an effort to discover new and potent PfDHODH inhibitors, 3D-QSAR pharmacophore models were developed based on the structures of known PfDHODH inhibitors and the validated Hypo1 model was used as a 3D search query for virtual screening of the National Cancer Institute database. The virtual hit compounds were further filtered based on molecular docking and Molecular Mechanics/Generalized Born Surface Area binding energy calculations. The combination of the pharmacophore and structure-based virtual screening resulted in the identification of nine new compounds that showed >25% inhibition of PfDHODH at a concentration of 10 μM, three of which exhibited IC50 values in the range of 0.38-20 μM. The most active compound, NSC336047, displayed species-selectivity for PfDHODH over human DHODH and inhibited parasite growth with an IC50 of 26 μM. In addition to this, 13 compounds inhibited parasite growth with IC50 values of ≤ 50 μM, 4 of which showed IC50 values in the range of 5-12 μM. These compounds could be further explored in the identification and development of more potent PfDHODH and parasite growth inhibitors.
Collapse
Affiliation(s)
| | - Farah El Mazouni
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute , Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel , 4002 Basel, Switzerland
| | - Carmen de Kock
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town , Observatory 7925, South Africa
| | - Margaret A Phillips
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
| | | |
Collapse
|
28
|
Yao R, Rong G, Yan B, Qiu L, Xu X. Dual-Functionalization of Alkynes via Copper-Catalyzed Carbene/Alkyne Metathesis: A Direct Access to the 4-Carboxyl Quinolines. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02648] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ruwei Yao
- Key
Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry,
Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Guangwei Rong
- Key
Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry,
Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Bin Yan
- Jinghua Anti-Cancer
Pharmaceutical Engineering Center, Nantong 226407, China
| | - Lihua Qiu
- Key
Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry,
Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xinfang Xu
- Key
Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry,
Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
- Jinghua Anti-Cancer
Pharmaceutical Engineering Center, Nantong 226407, China
| |
Collapse
|
29
|
Methods for Testing Immunological Factors. DRUG DISCOVERY AND EVALUATION: PHARMACOLOGICAL ASSAYS 2016. [PMCID: PMC7122208 DOI: 10.1007/978-3-319-05392-9_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hypersensitivity reactions can be elicited by various factors: either immunologically induced, i.e., allergic reactions to natural or synthetic compounds mediated by IgE, or non-immunologically induced, i.e., activation of mediator release from cells through direct contact, without the induction of, or the mediation through immune responses. Mediators responsible for hypersensitivity reactions are released from mast cells. An important preformed mediator of allergic reactions found in these cells is histamine. Specific allergens or the calcium ionophore 48/80 induce release of histamine from mast cells. The histamine concentration can be determined with the o-phthalaldehyde reaction.
Collapse
|
30
|
Wang J, Diao Y, Zhu J, Li S, Zhao Z, Li H, Zhu L. Biological evaluation of quinoline derivatives as inhibitors of human dihydroorotate dehydrogenase. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00024j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Compound A9 was identified as an inhibitor against hDHODH and its interactions were verified by TSA, SPR and X-ray crystallography.
Collapse
Affiliation(s)
- Jiawei Wang
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yanyan Diao
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Junsheng Zhu
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| |
Collapse
|
31
|
Song W, Li S, Tong Y, Wang J, Quan L, Chen Z, Zhao Z, Xu Y, Zhu L, Qian X, Li H. Structure-based design of potent human dihydroorotate dehydrogenase inhibitors as anticancer agents. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00179c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of hydrazino-thiazole derivatives were synthesized, of which compound 22 was the most potent inhibitor of hDHODH (IC50 = 1.8 nM). Furthermore, 22 exhibited better antiproliferative activity than brequinar in cancer cell lines.
Collapse
|
32
|
Rational Design of Benzylidenehydrazinyl-Substituted Thiazole Derivatives as Potent Inhibitors of Human Dihydroorotate Dehydrogenase with in Vivo Anti-arthritic Activity. Sci Rep 2015; 5:14836. [PMID: 26443076 PMCID: PMC4595849 DOI: 10.1038/srep14836] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/09/2015] [Indexed: 12/14/2022] Open
Abstract
Human dihydroorotate dehydrogenase (hDHODH) is an attractive therapeutic target for the treatment of rheumatoid arthritis, transplant rejection and other autoimmune diseases. Based on the X-ray structure of hDHODH in complex with lead compound 7, a series of benzylidenehydrazinyl-substituted thiazole derivatives as potent inhibitors of hDHODH were designed and synthesized, of which 19 and 30 were the most potent with IC50 values in the double-digit nanomolar range. Moreover, compound 19 displayed significant anti-arthritic effects and favorable pharmacokinetic profiles in vivo. Further X-ray structure and SAR analyses revealed that the potencies of the designed inhibitors were partly attributable to additional water-mediated hydrogen bond networks formed by an unexpected buried water between hDHODH and the 2-(2-methylenehydrazinyl)thiazole scaffold. This work not only elucidates promising scaffolds targeting hDHODH for the treatment of rheumatoid arthritis, but also demonstrates that the water-mediated hydrogen bond interaction is an important factor in molecular design and optimization.
Collapse
|
33
|
Vicente EF, Sahu ID, Costa-Filho AJ, Cilli EM, Lorigan GA. Conformational changes of the HsDHODH N-terminal Microdomain via DEER Spectroscopy. J Phys Chem B 2015; 119:8693-7. [PMID: 26086954 DOI: 10.1021/acs.jpcb.5b01706] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The human enzyme dihydroorotate dehydrogenase (HsDHODH) has been studied for being a target for development of new antineoplasic and antiproliferative drugs. The synthetic peptide N-t(DH) represents the N-terminal microdomain of this enzyme, responsible for anchoring it to the inner mitochondrial membrane. Also, it is known to harbor quinones that are essential for enzyme catalysis. Here we report structural features of the peptide/membrane interactions obtained by using CD and DEER spectroscopic techniques, both in micelles and in lipid vesicles. The data revealed different peptide conformational states in micelles and liposomes, which could suggest that this microdomain acts in specific regions or areas of the mitochondria, which can be related with the control of the quinone access to the HsDHODH active site. This is the first study to report on conformational changes of the HsDHODH N-terminal microdomain through a combination of CD and DEER spectroscopic techniques.
Collapse
Affiliation(s)
- Eduardo F Vicente
- †UNESP - Univ Estadual Paulista, Campus de Tupã, 17602-496, Tupã, SP Brazil
| | - Indra D Sahu
- ‡Department of Chemistry and Biochemistry, Miami University, 45056, Oxford, Ohio United States
| | - Antonio J Costa-Filho
- §Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo - USP,14040-901, Ribeirão Preto, SP Brazil
| | - Eduardo M Cilli
- ∥Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP - Univ Estadual Paulista, 14800-900, Araraquara, SP Brazil
| | - Gary A Lorigan
- ‡Department of Chemistry and Biochemistry, Miami University, 45056, Oxford, Ohio United States
| |
Collapse
|
34
|
Yoshino R, Yasuo N, Inaoka DK, Hagiwara Y, Ohno K, Orita M, Inoue M, Shiba T, Harada S, Honma T, Balogun EO, da Rocha JR, Montanari CA, Kita K, Sekijima M. Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method. PLoS One 2015; 10:e0125829. [PMID: 25961853 PMCID: PMC4427443 DOI: 10.1371/journal.pone.0125829] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 03/26/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment molecular orbital (FMO) calculation for orotate, oxonate, and 43 orotate derivatives. METHODOLOGY/PRINCIPAL FINDINGS Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN), whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue. CONCLUSIONS/SIGNIFICANCE FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.
Collapse
Affiliation(s)
- Ryunosuke Yoshino
- Global Scientific Information and Computing Center, Tokyo Institute of Technology, Meguro, Tokyo, 152–8550, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113–8657, Japan
| | - Nobuaki Yasuo
- Department of Computer Science, Tokyo Institute of Technology, Meguro, Tokyo, 152–8550, Japan
| | - Daniel Ken Inaoka
- Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, 113–0033, Japan
| | - Yohsuke Hagiwara
- Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki, 305–8585, Japan
| | - Kazuki Ohno
- Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki, 305–8585, Japan
| | - Masaya Orita
- Global Scientific Information and Computing Center, Tokyo Institute of Technology, Meguro, Tokyo, 152–8550, Japan
- Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki, 305–8585, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, 113–0033, Japan
| | - Tomoo Shiba
- Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo, Kyoto, 606–8585, Japan
| | - Shigeharu Harada
- Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo, Kyoto, 606–8585, Japan
| | - Teruki Honma
- Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, 113–0033, Japan
| | - Emmanuel Oluwadare Balogun
- Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, 113–0033, Japan
- Department of Biochemistry, Ahmadu Bello University, Zaria, 2222, Nigeria
| | | | | | - Kiyoshi Kita
- Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, 113–0033, Japan
| | - Masakazu Sekijima
- Global Scientific Information and Computing Center, Tokyo Institute of Technology, Meguro, Tokyo, 152–8550, Japan
- Department of Computer Science, Tokyo Institute of Technology, Meguro, Tokyo, 152–8550, Japan
| |
Collapse
|
35
|
Xu W, Lucke AJ, Fairlie DP. Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets. J Mol Graph Model 2015; 57:76-88. [PMID: 25682361 DOI: 10.1016/j.jmgm.2015.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 12/17/2022]
Abstract
Accurately predicting relative binding affinities and biological potencies for ligands that interact with proteins remains a significant challenge for computational chemists. Most evaluations of docking and scoring algorithms have focused on enhancing ligand affinity for a protein by optimizing docking poses and enrichment factors during virtual screening. However, there is still relatively limited information on the accuracy of commercially available docking and scoring software programs for correctly predicting binding affinities and biological activities of structurally related inhibitors of different enzyme classes. Presented here is a comparative evaluation of eight molecular docking programs (Autodock Vina, Fitted, FlexX, Fred, Glide, GOLD, LibDock, MolDock) using sixteen docking and scoring functions to predict the rank-order activity of different ligand series for six pharmacologically important protein and enzyme targets (Factor Xa, Cdk2 kinase, Aurora A kinase, COX-2, pla2g2a, β Estrogen receptor). Use of Fitted gave an excellent correlation (Pearson 0.86, Spearman 0.91) between predicted and experimental binding only for Cdk2 kinase inhibitors. FlexX and GOLDScore produced good correlations (Pearson>0.6) for hydrophilic targets such as Factor Xa, Cdk2 kinase and Aurora A kinase. By contrast, pla2g2a and COX-2 emerged as difficult targets for scoring functions to predict ligand activities. Although possessing a high hydrophobicity in its binding site, β Estrogen receptor produced reasonable correlations using LibDock (Pearson 0.75, Spearman 0.68). These findings can assist medicinal chemists to better match scoring functions with ligand-target systems for hit-to-lead optimization using computer-aided drug design approaches.
Collapse
Affiliation(s)
- Weijun Xu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
36
|
Zhu J, Han L, Diao Y, Ren X, Xu M, Xu L, Li S, Li Q, Dong D, Huang J, Liu X, Zhao Z, Wang R, Zhu L, Xu Y, Qian X, Li H. Design, Synthesis, X-ray Crystallographic Analysis, and Biological Evaluation of Thiazole Derivatives as Potent and Selective Inhibitors of Human Dihydroorotate Dehydrogenase. J Med Chem 2015; 58:1123-39. [DOI: 10.1021/jm501127s] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Junsheng Zhu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Le Han
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yanyan Diao
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoli Ren
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Minghao Xu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Liuxin Xu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Shiliang Li
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Qiang Li
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Dong Dong
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jin Huang
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaofeng Liu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhenjiang Zhao
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Rui Wang
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lili Zhu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yufang Xu
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuhong Qian
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Honglin Li
- State Key Laboratory
of Bioreactor Engineering, Shanghai Key Laboratory
of New Drug Design, and ‡Shanghai Key Laboratory of Chemical Biology, School
of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
37
|
Xu M, Zhu J, Diao Y, Zhou H, Ren X, Sun D, Huang J, Han D, Zhao Z, Zhu L, Xu Y, Li H. Novel Selective and Potent Inhibitors of Malaria Parasite Dihydroorotate Dehydrogenase: Discovery and Optimization of Dihydrothiophenone Derivatives. J Med Chem 2013; 56:7911-24. [DOI: 10.1021/jm400938g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | - Hongchang Zhou
- Department
of Microbiology, Medical School of Huzhou Teachers College, Huzhou 313000, China
| | | | | | | | - Dongmei Han
- Instrumental
Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | | | | | | |
Collapse
|
38
|
Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. PLoS One 2013; 8:e75992. [PMID: 24098414 PMCID: PMC3787967 DOI: 10.1371/journal.pone.0075992] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/13/2013] [Indexed: 12/19/2022] Open
Abstract
Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×1010 to 4×1010 to 1×1011 to 2×1011 to 5×1011 mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.
Collapse
Affiliation(s)
- Ryan G. Coleman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Michael Carchia
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Teague Sterling
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - John J. Irwin
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
39
|
Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL. On dihydroorotate dehydrogenases and their inhibitors and uses. J Med Chem 2013; 56:3148-67. [PMID: 23452331 DOI: 10.1021/jm301848w] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.
Collapse
Affiliation(s)
- Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | | | | | | |
Collapse
|