1
|
Hou W, Xu XL, Huang LJ, Zhang ZY, Zhou ZN, Wang JY, Ouyang X, Xin SY, Zhang ZY, Xiong Y, Huang H, Lan JX. Bioactivities and Action Mechanisms of Ellipticine Derivatives Reported Prior to 2023. Chem Biodivers 2024; 21:e202400210. [PMID: 38433548 DOI: 10.1002/cbdv.202400210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/03/2024] [Accepted: 03/03/2024] [Indexed: 03/05/2024]
Abstract
Currently, natural products are one of the priceless options for finding novel chemical pharmaceutical entities. Ellipticine is a naturally occurring alkaloid isolated from the leaves of Ochrosia elliptica Labill. Ellipticine and its derivatives are characterized by multiple biological activities. The purpose of this review was to provide a critical and systematic assessment of ellipticine and its derivatives as bioactive molecules over the last 60 years. Publications focused mainly on the total synthesis of alkaloids of this type without any evaluation of bioactivity have been excluded. We have reviewed papers dealing with the synthesis, bioactivity evaluation and mechanism of action of ellipticine and its derivatives. It was found that ellipticine and its derivatives showed cytotoxicity, antimicrobial ability, and anti-inflammatory activity, among which cytotoxicity toward cancer cell lines was the most investigated aspect. The inhibition of DNA topoisomerase II was the most relevant mechanism for cytotoxicity. The PI3K/AKT pathway, p53 pathway, and MAPK pathway were also closely related to the antiproliferative ability of these compounds. In addition, the structure-activity relationship was deduced, and future prospects were outlined. We are confident that these findings will lay a scientific foundation for ellipticine-based drug development, especially for anticancer agents.
Collapse
Affiliation(s)
- Wen Hou
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Xin-Liang Xu
- Department of Pharmacy, Xingguo People's Hospital, Xingguo Hospital Affiliated to Gannan Medical University, Ganzhou, 342400, P. R. China
| | - Le-Jun Huang
- College of Rehabilitation, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Zhen-Yu Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Zhi-Nuo Zhou
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Jin-Yang Wang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Xi Ouyang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Su-Ya Xin
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Zi-Yun Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Yi Xiong
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Hao Huang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, P. R. China
| | - Jin-Xia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou, 341000, P. R. China
| |
Collapse
|
2
|
Hou W, Huang L, Huang H, Liu S, Dai W, Tang J, Chen X, Lu X, Zheng Q, Zhou Z, Zhang Z, Lan J. Bioactivities and Mechanisms of Action of Sinomenine and Its Derivatives: A Comprehensive Review. Molecules 2024; 29:540. [PMID: 38276618 PMCID: PMC10818773 DOI: 10.3390/molecules29020540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Sinomenine, an isoquinoline alkaloid extracted from the roots and stems of Sinomenium acutum, has been extensively studied for its derivatives as bioactive agents. This review concentrates on the research advancements in the biological activities and action mechanisms of sinomenine-related compounds until November 2023. The findings indicate a broad spectrum of pharmacological effects, including antitumor, anti-inflammation, neuroprotection, and immunosuppressive properties. These compounds are notably effective against breast, lung, liver, and prostate cancers, exhibiting IC50 values of approximately 121.4 nM against PC-3 and DU-145 cells, primarily through the PI3K/Akt/mTOR, NF-κB, MAPK, and JAK/STAT signaling pathways. Additionally, they manifest anti-inflammatory and analgesic effects predominantly via the NF-κB, MAPK, and Nrf2 signaling pathways. Utilized in treating rheumatic arthritis, these alkaloids also play a significant role in cardiovascular and cerebrovascular protection, as well as organ protection through the NF-κB, Nrf2, MAPK, and PI3K/Akt/mTOR signaling pathways. This review concludes with perspectives and insights on this topic, highlighting the potential of sinomenine-related compounds in clinical applications and the development of medications derived from natural products.
Collapse
Affiliation(s)
- Wen Hou
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Lejun Huang
- College of Rehabilitation, Gannan Medical University, Ganzhou 341000, China;
| | - Hao Huang
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Shenglan Liu
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Wei Dai
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Jianhong Tang
- Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou 341000, China;
| | - Xiangzhao Chen
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Xiaolu Lu
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Qisheng Zheng
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Zhinuo Zhou
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Ziyun Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.L.); (W.D.); (X.C.); (X.L.); (Q.Z.); (Z.Z.); (Z.Z.)
| | - Jinxia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou 341000, China
| |
Collapse
|
3
|
Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
Collapse
Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
4
|
Li X, Liao M, Wang B, Zan X, Huo Y, Liu Y, Bao Z, Xu P, Liu W. A drug repurposing method based on inhibition effect on gene regulatory network. Comput Struct Biotechnol J 2023; 21:4446-4455. [PMID: 37731599 PMCID: PMC10507583 DOI: 10.1016/j.csbj.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
Numerous computational drug repurposing methods have emerged as efficient alternatives to costly and time-consuming traditional drug discovery approaches. Some of these methods are based on the assumption that the candidate drug should have a reversal effect on disease-associated genes. However, such methods are not applicable in the case that there is limited overlap between disease-related genes and drug-perturbed genes. In this study, we proposed a novel Drug Repurposing method based on the Inhibition Effect on gene regulatory network (DRIE) to identify potential drugs for cancer treatment. DRIE integrated gene expression profile and gene regulatory network to calculate inhibition score by using the shortest path in the disease-specific network. The results on eleven datasets indicated the superior performance of DRIE when compared to other state-of-the-art methods. Case studies showed that our method effectively discovered novel drug-disease associations. Our findings demonstrated that the top-ranked drug candidates had been already validated by CTD database. Additionally, it clearly identified potential agents for three cancers (colorectal, breast, and lung cancer), which was beneficial when annotating drug-disease relationships in the CTD. This study proposed a novel framework for drug repurposing, which would be helpful for drug discovery and development.
Collapse
Affiliation(s)
- Xianbin Li
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
- School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Minzhen Liao
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
| | - Bing Wang
- School of Medicine, Southeast University, Nanjing, China
| | - Xiangzhen Zan
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
| | - Yanhao Huo
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
| | - Yue Liu
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
| | - Zhenshen Bao
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
- School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Peng Xu
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
- School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, China
| | - Wenbin Liu
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, China
| |
Collapse
|
5
|
Hou W, Dai W, Huang H, Liu SL, Liu J, Huang LJ, Huang XH, Zeng JL, Gan ZW, Zhang ZY, Lan JX. Pharmacological activity and mechanism of pyrazines. Eur J Med Chem 2023; 258:115544. [PMID: 37300915 DOI: 10.1016/j.ejmech.2023.115544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/25/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Heterocycles are common in the structure of drugs used clinically to deal with diseases. Such drugs usually contain nitrogen, oxygen and sulfur, which possess electron-accepting capacity and can form hydrogen bonds. These properties often bring enhanced target binding ability to these compounds when compared to alkanes. Pyrazine is a nitrogen-containing six-membered heterocyclic ring and many of its derivatives are identified as bioactive molecules. We review here the most active pyrazine compounds in terms of their structure, activity in vitro and in vivo (mainly antitumor activity) and the reported mechanisms of action. References have been downloaded through Web of Science, PubMed, Science Direct, Google Scholar and SciFinder Scholar. Publications reporting only the chemistry of pyrazine derivatives are beyond the scope of this review and have not been included. We found that compounds in which a pyrazine ring was fused into other heterocycles especially pyrrole or imidazole were the highly studied pyrazine derivatives, whose antineoplastic activity had been widely investigated. To the best of our knowledge, this is the first review of pyrazine derivatives and their bioactivity, especially their antitumor activity. This review should be useful for those engaged in development of medications based on heterocyclic compounds especially those based on pyrazine.
Collapse
Affiliation(s)
- Wen Hou
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Wei Dai
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Hao Huang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Sheng-Lan Liu
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Jun Liu
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Le-Jun Huang
- College of Rehabilitation, Gannan Medical University, Ganzhou, 341000, PR China
| | - Xian-Hua Huang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Jun-Lin Zeng
- HuanKui Academy, Nanchang University, Nanchang, 330006, PR China
| | - Zhi-Wei Gan
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Zhen-Yu Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Jin-Xia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou, 341000, PR China.
| |
Collapse
|
6
|
Kusakabe Y, Moriya SS, Sugiyama T, Miyata Y. Isolation and identification of the new baicalin target protein to develop flavonoid structure-based therapeutic agents. Bioorg Med Chem 2023; 90:117362. [PMID: 37320992 DOI: 10.1016/j.bmc.2023.117362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
Proteins are vital constituents of all living organisms. As many therapeutic agents alter the activity of functional proteins, identifying functional target proteins of small bioactive molecules isessential for the rational design of stronger medicines. Flavonoids with antioxidant, anti-allergy, and anti-inflammatory effects are expected to have preventive effects for several diseases closely related to oxidation and inflammation, including heart disease, cancer, neurodegenerative disorders, and eye diseases. Therefore, identifying the proteins involved in the pharmacological actions of flavonoids, and designing a flavonoid structure-based medicine that strongly and specifically inhibits flavonoid target proteins, could aid the development of more effective medicines for treating heart disease, cancer, neurodegenerative disorders, and ocular diseases with few side effects. To isolate the flavonoid target protein, we conducted a novel affinity chromatography in a column wherein baicalin, a representative flavonoid, was attached to Affi-Gel 102. Through affinity chromatography and nano LC-MS/MS, we identified GAPDH as a flavonoid target protein. Then, we performed fluorescence quenching and an enzyme inhibition assay to experimentally confirmbaicalin's binding affinity for, and inhibition of, GAPDH. We also conducted in silico docking simulations to visualize the binding modes of baicalin and the newly identified flavonoid target protein, GAPDH. From the results of this study, it was considered that one of the reasons why baicalin exhibits the effects on cancer and neurodegenerative diseases is that it inhibits the activity of GAPDH. In summary, we showed that Affi-Gel102 could quickly and accurately isolate the target protein for bioactive small molecules, without the need for isotopic labeling or a fluorescent probe. By using the method presented here, it was possible to easily isolate the target protein of a medicine containing a carboxylic acid.
Collapse
Affiliation(s)
- Yoshio Kusakabe
- Faculty of Pharma-Sciences, Teikyo University, Tokyo, Japan.
| | | | - Toru Sugiyama
- Faculty of Pharma-Sciences, Teikyo University, Tokyo, Japan
| | - Yoshiki Miyata
- Faculty of Pharma-Sciences, Teikyo University, Tokyo, Japan
| |
Collapse
|
7
|
Challenges and Perspectives in Target Identification and Mechanism Illustration for Chinese Medicine. Chin J Integr Med 2023:10.1007/s11655-023-3629-9. [PMID: 36809500 DOI: 10.1007/s11655-023-3629-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 02/23/2023]
Abstract
Chinese medicine (CM) is an important resource for human life understanding and discovery of drugs. However, due to the unclear pharmacological mechanism caused by unclear target, research and international promotion of many active components have made little progress in the past decades of years. CM is mainly composed of multi-ingredients with multi-targets. The identification of targets of multiple active components and the weight analysis of multiple targets in a specific pathological environment, that is, the determination of the most important target is the main obstacle to the mechanism clarification and thus hinders its internationalization. In this review, the main approach to target identification and network pharmacology were summarized. And BIBm (Bayesian inference modeling), a powerful method for drug target identification and key pathway determination was introduced. We aim to provide a new scientific basis and ideas for the development and international promotion of new drugs based on CM.
Collapse
|
8
|
Ma D, Wang G, Zhu J, Mu W, Dou D, Liu F. Green Leaf Volatile Trans-2-Hexenal Inhibits the Growth of Fusarium graminearum by Inducing Membrane Damage, ROS Accumulation, and Cell Dysfunction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5646-5657. [PMID: 35481379 DOI: 10.1021/acs.jafc.2c00942] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fusarium graminearum, the main agent of Fusarium head blight (FHB), can cause serious yield loss and secrete mycotoxins to contaminate grain. Here, the biological activity of trans-2-hexenal (T2H) against F. graminearum was determined and its mode of action (MOA) was investigated. Furthermore, surface plasmon resonance with liquid chromatography-tandem mass spectrometry (SPR-LC-MS/MS), bioinformatic analysis, and gene knockout technique were combined to identify the binding proteins of T2H in F. graminearum cells. T2H exhibited satisfactory inhibitory activity against F. graminearum in vitro. Good lipophilicity greatly enhanced the affinity of T2H to F. graminearum mycelia and further caused membrane damage. The FgTRR (thioredoxin reductase) gene negatively regulates the sensitivity of F. graminearum to T2H by reducing the generation of reactive oxygen species (ROS) induced by T2H. Two mutant strains with FgSLX1 (structure-specific endonuclease subunit) and FgCOPB (coatomer subunit β) genes knockout showed decreased sensitivity to T2H, suggesting that these two genes may be involved in the antimicrobial activity of T2H. Taken together, T2H can inhibit F. graminearum growth by multiple MOAs and can be used as a biofumigant to control the occurrence of FHB in the field.
Collapse
Affiliation(s)
- Dicheng Ma
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Guoxian Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Jiamei Zhu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Wei Mu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Daolong Dou
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Feng Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| |
Collapse
|
9
|
Shin I, Li H, Lee CH. A Thiol-Activated Fluorogenic Probe for Detection of a Target Protein. Chem Commun (Camb) 2022; 58:6336-6339. [DOI: 10.1039/d2cc02029g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel fluorogenic probe for facile and efficient detection of a target protein that binds to a bioactive small molecule was developed. The probe was composed of a thiol-activated fluorogenic...
Collapse
|
10
|
Hino M, Kondo T, Kunii Y, Matsumoto J, Wada A, Niwa SI, Setou M, Yabe H. Tubulin/microtubules as novel clozapine targets. Neuropsychopharmacol Rep 2021; 42:32-41. [PMID: 34964309 PMCID: PMC8919115 DOI: 10.1002/npr2.12221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/16/2021] [Accepted: 11/21/2021] [Indexed: 01/06/2023] Open
Abstract
Aim Clozapine is currently the only effective drug for treatment‐resistant schizophrenia; nonetheless, its pharmacological mechanism remains unclear, and its administration is limited because of severe adverse effects. By comparing the binding proteins of clozapine and its derivative olanzapine, which is safer but less effective than clozapine, we attempted to clarify the mechanism of action specific to clozapine. Methods First, using the polyproline rod conjugates attached with clozapine or olanzapine, clozapine‐binding proteins in extracts from the cerebra of 7‐week‐old ICR mice were isolated and separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) and analyzed by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) to identify proteins. Second, the effect of clozapine on tubulin polymerization was determined turbidimetrically. Finally, the cellular effects of clozapine were observed in HeLa cells by immunofluorescence microscopy. Results Alpha and β tubulins were the most abundant clozapine‐binding proteins. We also found that clozapine directly binds with α and β tubulin heterodimers to inhibit their polymerization to form microtubules and disturbs the microtubule network, causing mitotic arrest in HeLa cells. Conclusion These results suggest that α and β tubulin heterodimers are targeted by the clozapine and the microtubules are involved in the etiology of schizophrenia. Clozapine‐binding proteins were investigated in mouse brain by using the polyproline rod method. The most abundant clozapine‐binding proteins were α and β tubulins. This figure shows immunofluorescence staining of HeLa cells treated without or with indicated doses of clozapine for 3 hours with anti‐tubulin antibody, indicating that clozapine disrupts the microtubule network in the cell. Scale bar, 20 μm.![]()
Collapse
Affiliation(s)
- Mizuki Hino
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan.,Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Miyagi, Japan
| | - Takeshi Kondo
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Yasuto Kunii
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan.,Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Miyagi, Japan
| | - Junya Matsumoto
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan
| | - Akira Wada
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan
| | - Shin-Ichi Niwa
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan.,Department of Psychiatry, Aizu Medical Center, School of Medicine, Fukushima Medical University, Aizuwakamatsu, Fukushima, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan.,Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Fukushima, Japan
| |
Collapse
|
11
|
Muroi M, Osada H. Proteomics-based target identification of natural products affecting cancer metabolism. J Antibiot (Tokyo) 2021; 74:639-650. [PMID: 34282314 DOI: 10.1038/s41429-021-00437-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
The Warburg effect, a widely known characteristic of cancer cells, refers to the utilization of glycolysis under aerobic conditions for extended periods of time. Recent studies have revealed that cancer cells are capable of reprogramming their metabolic pathways to meet vigorous metabolic demands. New anticancer drugs that target the complicated metabolic systems of cancer cells are being developed. Identifying the potential targets of novel compounds that affect cancer metabolism may enable the discovery of new therapeutic targets for cancer treatment, and hasten the development of anticancer drugs. Historically, various drug screening techniques such as the analysis of a compound's antiproliferative effect on cancer cells and proteomic methods, that enable target identification have been used to obtain many useful drugs from natural products. Here, we review proteomics-based target identification methods applicable to natural products that affect cancer metabolism.
Collapse
Affiliation(s)
- Makoto Muroi
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama, Japan.
| |
Collapse
|
12
|
Schepers AG, Shan J, Cox AG, Huang A, Evans H, Walesky C, Fleming HE, Goessling W, Bhatia SN. Identification of NQO2 As a Protein Target in Small Molecule Modulation of Hepatocellular Function. ACS Chem Biol 2021; 16:1770-1778. [PMID: 34427427 DOI: 10.1021/acschembio.1c00503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The utility of in vitro human disease models is mainly dependent on the availability and functional maturity of tissue-specific cell types. We have previously screened for and identified small molecules that can enhance hepatocyte function in vitro. Here, we characterize the functional effects of one of the hits, FH1, on primary human hepatocytes in vitro, and also in vivo on primary hepatocytes in a zebrafish model. Furthermore, we conducted an analogue screen to establish the structure-activity relationship of FH1. We performed affinity-purification proteomics that identified NQO2 to be a potential binding target for this small molecule, revealing a possible link between inflammatory signaling and hepatocellular function in zebrafish and human hepatocyte model systems.
Collapse
Affiliation(s)
- Arnout G. Schepers
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Jing Shan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrew G. Cox
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ada Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Helen Evans
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chad Walesky
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Heather E. Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wolfram Goessling
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, United States
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard−MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
13
|
Thiouracil SecA inhibitors: bypassing the effects of efflux pumps and attenuating virulence factor secretion in MRSA and Bacillus anthracis. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02750-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
14
|
da Cunha BR, Zoio P, Fonseca LP, Calado CRC. Technologies for High-Throughput Identification of Antibiotic Mechanism of Action. Antibiotics (Basel) 2021; 10:565. [PMID: 34065815 PMCID: PMC8151116 DOI: 10.3390/antibiotics10050565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
There are two main strategies for antibiotic discovery: target-based and phenotypic screening. The latter has been much more successful in delivering first-in-class antibiotics, despite the major bottleneck of delayed Mechanism-of-Action (MOA) identification. Although finding new antimicrobial compounds is a very challenging task, identifying their MOA has proven equally challenging. MOA identification is important because it is a great facilitator of lead optimization and improves the chances of commercialization. Moreover, the ability to rapidly detect MOA could enable a shift from an activity-based discovery paradigm towards a mechanism-based approach. This would allow to probe the grey chemical matter, an underexplored source of structural novelty. In this study we review techniques with throughput suitable to screen large libraries and sufficient sensitivity to distinguish MOA. In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. Ultimately, new and reinvigorated phenotypic assays bring renewed hope in the discovery of a new generation of antibiotics.
Collapse
Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Paulo Zoio
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Luís P. Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Cecília R. C. Calado
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| |
Collapse
|
15
|
Tkachenko AG, Kashevarova NM, Sidorov RY, Nesterova LY, Akhova AV, Tsyganov IV, Vaganov VY, Shipilovskikh SA, Rubtsov AE, Malkov AV. A synthetic diterpene analogue inhibits mycobacterial persistence and biofilm formation by targeting (p)ppGpp synthetases. Cell Chem Biol 2021; 28:1420-1432.e9. [PMID: 33621482 DOI: 10.1016/j.chembiol.2021.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/14/2020] [Accepted: 01/25/2021] [Indexed: 01/23/2023]
Abstract
Bacterial persistence coupled with biofilm formation is directly associated with failure of antibiotic treatment of tuberculosis. We have now identified 4-(4,7-DiMethyl-1,2,3,4-tetrahydroNaphthalene-1-yl)Pentanoic acid (DMNP), a synthetic diterpene analogue, as a lead compound that was capable of suppressing persistence and eradicating biofilms in Mycobacterium smegmatis. By using two reciprocal experimental approaches - ΔrelMsm and ΔrelZ gene knockout mutations versus relMsm and relZ overexpression technique - we showed that both RelMsm and RelZ (p)ppGpp synthetases are plausible candidates for serving as targets for DMNP. In vitro, DMNP inhibited (p)ppGpp-synthesizing activity of purified RelMsm in a concentration-dependent manner. These findings, supplemented by molecular docking simulation, suggest that DMNP targets the structural sites shared by RelMsm, RelZ, and presumably by a few others as yet unidentified (p)ppGpp producers, thereby inhibiting persister cell formation and eradicating biofilms. Therefore, DMNP may serve as a promising lead for development of antimycobacterial drugs.
Collapse
Affiliation(s)
- Alexander G Tkachenko
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia.
| | - Natalya M Kashevarova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia
| | - Roman Yu Sidorov
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | - Larisa Yu Nesterova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | - Anna V Akhova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | - Ivan V Tsyganov
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | | | | | | | - Andrei V Malkov
- Department of Chemistry, Loughborough University Address: University Road, Loughborough, Leicestershire LE11 3TU, UK.
| |
Collapse
|
16
|
Ribeiro da Cunha B, Fonseca LP, Calado CRC. Simultaneous elucidation of antibiotic mechanism of action and potency with high-throughput Fourier-transform infrared (FTIR) spectroscopy and machine learning. Appl Microbiol Biotechnol 2021; 105:1269-1286. [PMID: 33443637 DOI: 10.1007/s00253-021-11102-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022]
Abstract
The low rate of discovery and rapid spread of resistant pathogens have made antibiotic discovery a worldwide priority. In cell-based screening, the mechanism of action (MOA) is identified after antimicrobial activity. This increases rediscovery, impairs low potency candidate detection, and does not guide lead optimization. In this study, high-throughput Fourier-transform infrared (FTIR) spectroscopy was used to discriminate the MOA of 14 antibiotics at pathway, class, and individual antibiotic level. For that, the optimal combinations and parametrizations of spectral preprocessing were selected with cross-validated partial least squares discriminant analysis, to which various machine learning algorithms were applied. This coherently resulted in very good accuracies, independently of the algorithms, and at all levels of MOA. Particularly, an ensemble of subspace discriminants predicted the known pathway (98.6%), antibiotic classes (100%), and individual antibiotics (97.8%) with exceptional accuracy, and similar results were obtained for simulated novel MOA. Even at very low concentrations (1 μg/mL) and growth inhibition (15%), over 70% pathway and class accuracy was achieved, suggesting FTIR spectroscopy can probe the grey chemical matter. Prediction of inhibitory effect was also examined, for which a squared exponential Gaussian process regression yielded a root mean square error of 0.33 and a R2 of 0.92, indicating that metabolic alterations leading to growth inhibition are intrinsically reflected on FTIR spectra beyond cell density. KEY POINTS: • Antibiotic MOA and potency estimated with high-throughput FTIR spectroscopy • Sub-inhibitory MOA identification suggests ability to explore grey chemical matter • Data analysis optimization improved MOA identification at antibiotic level by 38.
Collapse
Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001, Lisbon, Portugal. .,Departamento de Engenharia Química, ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa (IPL), R. Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal.
| | - Luís P Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Cecília R C Calado
- Departamento de Engenharia Química, ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa (IPL), R. Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal
| |
Collapse
|
17
|
Van den Kerkhof M, Sterckx YGJ, Leprohon P, Maes L, Caljon G. Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites. Microorganisms 2020; 8:E950. [PMID: 32599761 PMCID: PMC7356981 DOI: 10.3390/microorganisms8060950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different 'omics' approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed.
Collapse
Affiliation(s)
- Magali Van den Kerkhof
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| |
Collapse
|
18
|
Metabolic Fingerprinting with Fourier-Transform Infrared (FTIR) Spectroscopy: Towards a High-Throughput Screening Assay for Antibiotic Discovery and Mechanism-of-Action Elucidation. Metabolites 2020; 10:metabo10040145. [PMID: 32283661 PMCID: PMC7240953 DOI: 10.3390/metabo10040145] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 01/02/2023] Open
Abstract
The discovery of antibiotics has been slowing to a halt. Phenotypic screening is once again at the forefront of antibiotic discovery, yet Mechanism-Of-Action (MOA) identification is still a major bottleneck. As such, methods capable of MOA elucidation coupled with the high-throughput screening of whole cells are required now more than ever, for which Fourier-Transform Infrared (FTIR) spectroscopy is a promising metabolic fingerprinting technique. A high-throughput whole-cell FTIR spectroscopy-based bioassay was developed to reveal the metabolic fingerprint induced by 15 antibiotics on the Escherichia coli metabolism. Cells were briefly exposed to four times the minimum inhibitory concentration and spectra were quickly acquired in the high-throughput mode. After preprocessing optimization, a partial least squares discriminant analysis and principal component analysis were conducted. The metabolic fingerprints obtained with FTIR spectroscopy were sufficiently specific to allow a clear distinction between different antibiotics, across three independent cultures, with either analysis algorithm. These fingerprints were coherent with the known MOA of all the antibiotics tested, which include examples that target the protein, DNA, RNA, and cell wall biosynthesis. Because FTIR spectroscopy acquires a holistic fingerprint of the effect of antibiotics on the cellular metabolism, it holds great potential to be used for high-throughput screening in antibiotic discovery and possibly towards a better understanding of the MOA of current antibiotics.
Collapse
|
19
|
Takada N, Sutoh S, Toyota M, Yamazaki Y, Kitano-Yamashita N, Ushida C, Yamashita K. Methiin as a nematode attractant inAllium sativum. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Damage to garlic (Allium sativum L.) caused by nematodes (Ditylenchus destructor Thorne) is becoming a serious agricultural hazard, leading to a great loss in garlic production. Once the garlic bulbs are invaded, the pathogenic nematode drastically increases in number along with the rotting of bulbs. It was therefore conceived that nematode attractants are present in the bulbs. Based on this hypothesis, chemical investigations were performed to explore a nematode attractant in A. sativum bulbs, which resulted in the identification of methiin (S-methyl-l-cysteine S-oxide) as an attractant. Bioassay and quantification experiments of methiin in extracts of A. sativum bulb led to the conclusion that methiin possesses sufficient potential to attract D. destructor into A. sativum bulbs. Moreover, an activity comparing study of methiin with its analogs showed that the sulfoxide functionality is essential for attractant activity. Moreover, methiin was revealed to attract Caenorhabditis elegans. Further investigation of methiin will help to elucidate the neuronal system of D. destructor.
Collapse
Affiliation(s)
- Noboru Takada
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Sayaka Sutoh
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Masuru Toyota
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Yoshihisa Yamazaki
- Aomori Prefectural Industrial Technology Research Center, Kuroishi 036-0522, Japan
| | - Nozomi Kitano-Yamashita
- Vegetable Research Institute, Aomori Prefectural Industrial Technology Research Center, Inuotose, Rokunohe-ho, 033-0071, Japan
| | - Chisato Ushida
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Kazuo Yamashita
- Vegetable Research Institute, Aomori Prefectural Industrial Technology Research Center, Inuotose, Rokunohe-ho, 033-0071, Japan
| |
Collapse
|
20
|
Zhang L, Huang Y, Ling J, Xiang Y, Zhuo W. Screening of key genes and prediction of therapeutic agents in Arsenic-induced lung carcinoma. Cancer Biomark 2020; 25:351-360. [PMID: 31322542 DOI: 10.3233/cbm-182333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Evidence indicates that inorganic arsenic (iAs) can directly damage cells and result in malignant transformation with unclear complicated mechanisms. In the present study, we aimed to explore the possible molecules, pathways and therapeutic agents by using bioinformatics methods. METHODS Microarray-based data were retrieved and analyzed to screen the differentially expressed genes (DEGs) between iAs-treated lung cells and controls. Then, the functions of DEGs were annotated and the hub genes were filtrated. The key genes were selected from the hub genes through validation in The Cancer Genome Atlas (TCGA) cohorts. Possible drugs were predicted by using CMAP tool. RESULTS Two datasets (GSE33520 and GSE36684) were retrieved, and 61 up-regulated and 228 down-regulated DEGs were screened out, which were enriched in various pathways, particularly metabolism-related pathways. Among the DEGs, four hub genes including MTIF2, ACOX1, CAV1, and MRPL17, which might affect lung cancer prognosis, were selected as the key genes. Interestingly, Quinostatin was predicted to be a potential agent reversing iAs-induced lung cell malignant transformation. CONCLUSION The present study sheds novel insights into the mechanisms of iAs-induced lung cell malignant transformation and identified several potential small agents for iAs toxicity prevention and therapy.
Collapse
Affiliation(s)
- Liang Zhang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China.,Department of Oncology, Chongqing Institute of Traditional Chinese Medicine, Chongqing, China
| | - Yu Huang
- Department of Invasive Technology, Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Junjun Ling
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China.,Department of Oncology, Chongqing Institute of Traditional Chinese Medicine, Chongqing, China
| | - Ying Xiang
- Department of Epidemiology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, China
| | - Wenlei Zhuo
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China.,Cancer Immunology Nutrition Group, Cancer Nutrition Professional Committee, China Anti-Cancer Association, China
| |
Collapse
|
21
|
Ahmed NS, Wober J. Synthesis of novel flexible tamoxifen analogues to overcome CYP2D6 polymorphism and their biological evaluation on MCF-7 cell line. Drug Dev Res 2020; 81:444-455. [PMID: 31916635 DOI: 10.1002/ddr.21637] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/01/2019] [Accepted: 12/21/2019] [Indexed: 11/08/2022]
Abstract
Tamoxifen (TAM) is currently the endocrine treatment of choice for all stages of breast cancer; it has proven success in ER positive and ER negative patients. TAM is activated by endogenous CYP450 enzymes to the more biologically active metabolites 4-hydroxytamoxifen and endoxifen mainly via CYP2D6 and CYP3A4/5. CYP2D6 has been investigated for polymorphism; there is a large interindividual variation in the enzyme activity, this drastically effects clinical outcomes of tamoxifen treatment. Here in we report the design and synthesis of 10 novel compounds bearing a modified tamoxifen skeleton, ring C is substituted with different ester groups to bypass the CYP2D6 enzyme metabolism and employ esterase enzymes for activation. All compounds endorse flexibility on ring A. Compounds (II-X) showed MCF-7% growth inhibition >50% at a screening dose of 10 μM. These results were validated by yeast estrogen screen (YES) and E-Screen assay combined with XTT assay. Compound II (E/Z 4-[1-4-(3-Dimethylamino-propoxy)-phenyl)-3-(4-methoxy-phenyl)-2-methyl-propenyl]-phenol) showed nanomolar antiestrogenic activity (IC50 = 510 nM in YES assay) and was five times more potent in inhibiting the growth of MCF-7 BUS (IC50 = 96 nM) compared to TAM (IC50 = 503 nM). Esterified analogues VI, VII were three times more active than TAM on MCF-7 BUS (IC50 = 167 nM). Novel analogues are prodrugs that can ensure equal clinical outcomes to all breast cancer patients.
Collapse
Affiliation(s)
- Nermin S Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Jannette Wober
- Institute of Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
22
|
Narita S, Kobayashi N, Mori K, Sakurai K. Clickable gold nanoparticles for streamlining capture, enrichment and release of alkyne-labelled proteins. Bioorg Med Chem Lett 2019; 29:126768. [PMID: 31690474 DOI: 10.1016/j.bmcl.2019.126768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 01/08/2023]
Abstract
Alkyne-labelled proteins are generated as key intermediates in the chemical probe-based approaches to proteomics analysis. Their efficient and selective detection and isolation is an important problem. We designed and synthesized azide-functionalized gold nanoparticles as new clickable capture reagents to streamline click chemistry-mediated capture, enrichment and release of the alkyne-labelled proteins in one-pot to expedite the post-labelling analysis. Because hydrophobic surface functionalities are known to render gold nanoparticles poorly water-dispersible, hydrophilic PEG linkers with two different lengths were explored to confer colloidal stability to the clickable capture reagents. We demonstrated the ability of the capture reagents to conjugate the alkyne containing proteins at a nanomolar concentration via click chemistry, which can be immediately followed by their enrichment and elution. Furthermore, a bifunctional clickable capture reagent bearing sulforhodamine and azide groups was shown to conveniently attach a fluorophore to the alkyne-labelled protein upon click capture, which facilitated their rapid detection in the gel analysis.
Collapse
Affiliation(s)
- Sho Narita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Naohiro Kobayashi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Kanna Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan
| | - Kaori Sakurai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Life Science, 2-24-16, Naka-cho, Koganei-shi, Tokyo 184-8588, Japan.
| |
Collapse
|
23
|
Design and Synthesis of Anti-Cancer Chimera Molecules Based on Marine Natural Products. Mar Drugs 2019; 17:md17090500. [PMID: 31461968 PMCID: PMC6780274 DOI: 10.3390/md17090500] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/07/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022] Open
Abstract
In this paper, the chemical conjugation of marine natural products with other bioactive molecules for developing an advanced anti-cancer agent is described. Structural complexity and the extraordinary biological features of marine natural products have led to tremendous research in isolation, structural elucidation, synthesis, and pharmacological evaluation. In addition, this basic scientific achievement has made it possible to hybridize two or more biologically important skeletons into a single compound. The hybridization strategy has been used to identify further opportunities to overcome certain limitations, such as structural complexity, scarcity problems, poor solubility, severe toxicity, and weak potency of marine natural products for advanced development in drug discovery. Further, well-designed marine chimera molecules can function as a platform for target discovery or degradation. In this review, the design, synthesis, and biological evaluation of recent marine chimera molecules are presented.
Collapse
|
24
|
The power of combining phenotypic and target-focused drug discovery. Drug Discov Today 2019; 24:526-532. [DOI: 10.1016/j.drudis.2018.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/10/2018] [Accepted: 10/16/2018] [Indexed: 01/09/2023]
|
25
|
Matilla MA, Krell T. The effect of bacterial chemotaxis on host infection and pathogenicity. FEMS Microbiol Rev 2018; 42:4563582. [PMID: 29069367 DOI: 10.1093/femsre/fux052] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/19/2017] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis enables microorganisms to move according to chemical gradients. Although this process requires substantial cellular energy, it also affords key physiological benefits, including enhanced access to growth substrates. Another important implication of chemotaxis is that it also plays an important role in infection and disease, as chemotaxis signalling pathways are broadly distributed across a variety of pathogenic bacteria. Furthermore, current research indicates that chemotaxis is essential for the initial stages of infection in different human, animal and plant pathogens. This review focuses on recent findings that have identified specific bacterial chemoreceptors and corresponding chemoeffectors associated with pathogenicity. Pathogenicity-related chemoeffectors are either host and niche-specific signals or intermediates of the host general metabolism. Plant pathogens were found to contain an elevated number of chemotaxis signalling genes and functional studies demonstrate that these genes are critical for their ability to enter the host. The expanding body of knowledge of the mechanisms underlying chemotaxis in pathogens provides a foundation for the development of new therapeutic strategies capable of blocking infection and preventing disease by interfering with chemotactic signalling pathways.
Collapse
Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| |
Collapse
|
26
|
|
27
|
Target Identification Using Cell Permeable and Cleavable Chloroalkane Derivatized Small Molecules. Methods Mol Biol 2018; 1647:91-108. [PMID: 28808997 DOI: 10.1007/978-1-4939-7201-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
An important aspect for gaining functional insight into the activity of small molecules revealed through phenotypic screening is the identification of their interacting proteins. Yet, isolating and validating these interacting proteins remains difficult. Here, we present a new approach utilizing a chloroalkane (CA) moiety capture handle, which can be chemically attached to small molecules to isolate their respective protein targets. Derivatization of small molecules with the CA moiety has been shown to not significantly impact their cell permeability or potency, allowing for phenotypic validation of the derivatized small molecule prior to capture. The retention of cell permeability also allows for treatment of live cells with the derivatized small molecule and the CA moiety enables rapid covalent capture onto HaloTag coated magnetic beads. Additionally, several options are available for the elution of interacting proteins, including chemical cleavage of the CA moiety, competitive elution using excess unmodified small molecule, or sodium dodecyl sulfate (SDS) elution. These features taken together yield a highly robust and efficient process for target identification, including capture of weak or low abundance interactors.
Collapse
|
28
|
Wang DY, Cao Y, Zheng LY, Chen LD, Chen XF, Hong ZY, Zhu ZY, Li X, Chai YF. Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA-Programmed Affinity Labeling. Chemistry 2017; 23:10906-10914. [DOI: 10.1002/chem.201702033] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Dong-Yao Wang
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Yan Cao
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Le-Yi Zheng
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Lang-Dong Chen
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Xiao-Fei Chen
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Zhan-Ying Hong
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Zhen-Yu Zhu
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| | - Xiaoyu Li
- Department of Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong SAR China
| | - Yi-Feng Chai
- School of Pharmacy; Second Military Medical University; No. 325 Guohe Road Shanghai 200433 P.R. China
| |
Collapse
|
29
|
Elliott DC, Beutler JA, Parker KA. Importance of a 4-Alkyl Substituent for Activity in the Englerin Series. ACS Med Chem Lett 2017; 8:746-750. [PMID: 28740610 DOI: 10.1021/acsmedchemlett.7b00161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/05/2017] [Indexed: 11/30/2022] Open
Abstract
The ring closing metathesis/transannular etherification approach to the englerin nucleus was adapted to provide two key intermediates for analogue synthesis: the 4-desmethyl Δ5,6 tricycle and the 4-oxo Δ5,6 tricycle. The former was elaborated to 4-desmethyl englerin A and the latter served as a common precursor for englerin A, 4-ethyl englerin A, and 4-isopropyl englerin A. 4-Desmethyl englerin A was less active than the natural product by an order of magnitude, but the 4-ethyl and 4-isopropyl analogues were comparable in activity to englerin A. These results are consistent with the premise that the 4-alkyl group enforces the binding conformation of the cinnamoyl ester substituent. Furthermore, they suggest that 4-alkyl englerin structures may prove to be useful tool compounds.
Collapse
Affiliation(s)
- Daniel C. Elliott
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - John A. Beutler
- Molecular
Targets Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Kathlyn A. Parker
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| |
Collapse
|
30
|
Zhuang C, Zhang W, Sheng C, Zhang W, Xing C, Miao Z. Chalcone: A Privileged Structure in Medicinal Chemistry. Chem Rev 2017; 117:7762-7810. [PMID: 28488435 PMCID: PMC6131713 DOI: 10.1021/acs.chemrev.7b00020] [Citation(s) in RCA: 757] [Impact Index Per Article: 108.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Privileged structures have been widely used as an effective template in medicinal chemistry for drug discovery. Chalcone is a common simple scaffold found in many naturally occurring compounds. Many chalcone derivatives have also been prepared due to their convenient synthesis. These natural products and synthetic compounds have shown numerous interesting biological activities with clinical potentials against various diseases. This review aims to highlight the recent evidence of chalcone as a privileged scaffold in medicinal chemistry. Multiple aspects of chalcone will be summarized herein, including the isolation of novel chalcone derivatives, the development of new synthetic methodologies, the evaluation of their biological properties, and the exploration of the mechanisms of action as well as target identification. This review is expected to be a comprehensive, authoritative, and critical review of the chalcone template to the chemistry community.
Collapse
Affiliation(s)
- Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Wen Zhang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Wannian Zhang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
| | - Chengguo Xing
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive,
Gainesville, Florida 32610, United States
| | - Zhenyuan Miao
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| |
Collapse
|
31
|
Chiba K, Asanuma M, Ishikawa M, Hashimoto Y, Dodo K, Sodeoka M, Yamaguchi T. Specific fluorescence labeling of target proteins by using a ligand–4-azidophthalimide conjugate. Chem Commun (Camb) 2017; 53:8751-8754. [DOI: 10.1039/c7cc03252h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two distinct model studies demonstrate that the ligand–4-azidophthalimide conjugate strategy is useful for specific fluorescence labeling of target proteins.
Collapse
Affiliation(s)
- Kosuke Chiba
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Miwako Asanuma
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Minoru Ishikawa
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Yuichi Hashimoto
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory
- RIKEN
- Wako
- Japan
- AMED-CREST
| | - Takao Yamaguchi
- Institute of Molecular and Cellular Biosciences
- The University of Tokyo
- Tokyo 113-0032
- Japan
| |
Collapse
|
32
|
Fan XX, Li F, Lv YN, Zhang Y, Kou JP, Yu BY. An integrated shotgun proteomics and bioinformatics approach for analysis of brain proteins from MCAO model using serial affinity chromatograph with four active ingredients from Shengmai preparations as ligands. Neurochem Int 2017; 103:45-56. [PMID: 28049027 DOI: 10.1016/j.neuint.2016.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 11/28/2022]
Abstract
Identification and validation of disease-relevant target proteins for natural products is an essential component of modern pharmaceutical research. In the present study, an integrated shotgun proteomics and bioinformatics approach was established to profile the interaction of active small molecules derived from ShengMai preparations (SMXZF) with hundreds of endogenously expressed proteins from middle cerebral artery occlusion (MCAO) model. Affinity-based proteomic strategies for isolation and identification of targets for the bioactive components is a classic, but still powerful approach. The proteins bound by SMXZF of the brain tissue proteins from MCAO model via serial affinity chromatograph were analyzed by nano liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) and all MS/MS spectra were then automatically searched by the SEQUEST program. A total of 154 proteins had been identified, with the molecular weight ranging from 21,369.6 to 332,393.21 and the pI from 4.32 to 10.88. Bioinformatic analysis was also implemented to better understand the identified proteins. In the gene ontology (GO) annotation, all the identified proteins were classified into 39, 18 and 12 groups according to biological process, cellular component and molecular function, respectively. KEGG pathways analysis of the identified proteins was conducted with 46 corresponding pathways found. In addition, the gene network was also constructed to analyze the relationship of these genes each other. Further validation of some targets were performed in MCAO model by Western blotting. The results indeed supported the notion that proteins MAPK/ERK1/2, CaMKII and VIM were involved in the disease development of MCAO and played an essential role in the protective effect of SMXZF. This study highlights the effectiveness and reliability of this integrated shotgun proteomics and bioinformatics approach, which is a promising paradigm for target identification and elucidating the mechanism of natural products in future research.
Collapse
Affiliation(s)
- Xiao-Xue Fan
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, PR China
| | - Fang Li
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, PR China
| | - Yan-Ni Lv
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, PR China
| | - Yu Zhang
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, PR China
| | - Jun-Ping Kou
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, PR China.
| | - Bo-Yang Yu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Complex Prescription of TCM, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, PR China.
| |
Collapse
|
33
|
Kim D, Hwang HY, Kim JY, Lee JY, Yoo JS, Marko-Varga G, Kwon HJ. FK506, an Immunosuppressive Drug, Induces Autophagy by Binding to the V-ATPase Catalytic Subunit A in Neuronal Cells. J Proteome Res 2016; 16:55-64. [PMID: 28056508 DOI: 10.1021/acs.jproteome.6b00638] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The drug FK506 (tacrolimus, fujimycin) exerts its immunosuppressive effects by regulating the nuclear factor of the activated T-cell (NFAT) family of transcription factors. However, FK506 also exhibits neuroprotective effects, but its direct target proteins that mediate these effects have not been determined. To identify the target proteins responsible for FK506's neuroprotective effects, the drug affinity responsive target stability (DARTS) method was performed using label-free FK506, and LC-MS/MS analysis of the FK506-treated proteome was also performed. Using DARTS and LC-MS/MS analyses in combination with reference studies, V-ATPase catalytic subunit A (ATP6V1A) was identified as a new target protein of FK506. The biological relevance of ATP6V1A in mediating the neuroprotective effects of FK506 was validated by analyzing FK506 activity with respect to autophagy via acridine orange staining and transcription factor EB (TFEB) translocation assay. These analyses demonstrated that the binding of FK506 with ATP6V1A induces autophagy by activating the translocation of TFEB from the cytosol into the nucleus. Because autophagy has been identified as a mechanism for treating neurodegenerative diseases and because we have demonstrated that FK506 induces autophagy, this study demonstrates that FK506 is a possible new therapy for treating neurodegenerative diseases.
Collapse
Affiliation(s)
- Dongyoung Kim
- Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University , Seoul 120-749, Korea
| | - Hui-Yun Hwang
- Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University , Seoul 120-749, Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute , Ochang, Chungbuk 28119, Korea
| | - Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute , Ochang, Chungbuk 28119, Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute , Ochang, Chungbuk 28119, Korea
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University , BMC D13, SE-221 84 Lund, Sweden
| | - Ho Jeong Kwon
- Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University , Seoul 120-749, Korea.,Department of Internal Medicine, College of Medicine, Yonsei University , Seoul 120-752, Korea
| |
Collapse
|
34
|
Tuo X, Chen J, Zhao S, Xie P. Chemical proteomic analysis of the potential toxicological mechanisms of microcystin-RR in zebrafish (Danio rerio) liver. ENVIRONMENTAL TOXICOLOGY 2016; 31:1206-1216. [PMID: 25854999 DOI: 10.1002/tox.22128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/27/2015] [Accepted: 02/02/2015] [Indexed: 06/04/2023]
Abstract
Microcystins (MCs) are common toxins produced by freshwater cyanobacteria, and they represent a potential health risk to aquatic organisms and animals, including humans. Specific inhibition of protein phosphatases 1 and 2A is considered the typical mechanism of MCs toxicity, but the exact mechanism has not been fully elucidated. To further our understanding of the toxicological mechanisms induced by MCs, this study is the first to use a chemical proteomic approach to screen proteins that exhibit special interactions with MC-arginine-arginine (MC-RR) from zebrafish (Danio rerio) liver. Seventeen proteins were identified via affinity blocking test. Integration of the results of previous studies and this study revealed that these proteins play a crucial role in various toxic phenomena of liver induced by MCs, such as the disruption of cytoskeleton assembly, oxidative stress, and metabolic disorder. Moreover, in addition to inhibition of protein phosphate activity, the overall toxicity of MCs was simultaneously modulated by the distribution of MCs in cells and their interactions with other target proteins. These results provide new insight into the mechanisms of hepatotoxicity induced by MCs. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1206-1216, 2016.
Collapse
Affiliation(s)
- Xun Tuo
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan, 430072, People's Republic of China
- Basic Chemistry Experimental Center, Nanchang University, Nanchang, Jiangxi, 330031, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jun Chen
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan, 430072, People's Republic of China
| | - Sujuan Zhao
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan, 430072, People's Republic of China
| |
Collapse
|
35
|
Friedman Ohana R, Levin S, Wood MG, Zimmerman K, Dart ML, Schwinn MK, Kirkland TA, Hurst R, Uyeda HT, Encell LP, Wood KV. Improved Deconvolution of Protein Targets for Bioactive Compounds Using a Palladium Cleavable Chloroalkane Capture Tag. ACS Chem Biol 2016; 11:2608-17. [PMID: 27414062 DOI: 10.1021/acschembio.6b00408] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The benefits provided by phenotypic screening of compound libraries are often countered by difficulties in identifying the underlying cellular targets. We recently described a new approach utilizing a chloroalkane capture tag, which can be chemically attached to bioactive compounds to facilitate the isolation of their respective targets for subsequent identification by mass spectrometry. The tag minimally affects compound potency and membrane permeability, enabling target engagement inside cells. Effective enrichment of these targets is achieved through selectivity in both their rapid capture onto immobilized HaloTag and their subsequent release by competitive elution. Here, we describe a significant improvement to this method where selective elution was achieved through palladium-catalyzed cleavage of an allyl-carbamate linkage incorporated into the chloroalkane capture tag. Selective tag cleavage provided robust release of captured targets exhibiting different modes of binding to the bioactive compound, including prolonged residence time and covalent interactions. Using the kinase inhibitors ibrutinib and BIRB796 as model compounds, we demonstrated the capability of this new method to identify both expected targets and "off-targets" exhibiting a range of binding affinities, cellular abundances, and binding characteristics.
Collapse
Affiliation(s)
| | - Sergiy Levin
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Monika G. Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Kris Zimmerman
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Melanie L. Dart
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Thomas A. Kirkland
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Robin Hurst
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - H. Tetsuo Uyeda
- Promega Biosciences LLC, San Luis Obispo, California 93401, United States
| | - Lance P. Encell
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
| |
Collapse
|
36
|
Hati S, Tripathy S, Dutta PK, Agarwal R, Srinivasan R, Singh A, Singh S, Sen S. Spiro[pyrrolidine-3, 3´-oxindole] as potent anti-breast cancer compounds: Their design, synthesis, biological evaluation and cellular target identification. Sci Rep 2016; 6:32213. [PMID: 27573798 PMCID: PMC5004205 DOI: 10.1038/srep32213] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/03/2016] [Indexed: 11/09/2022] Open
Abstract
The spiro[pyrrolidine-3, 3´-oxindole] moiety is present as a core in number of alkaloids with substantial biological activities. Here in we report design and synthesis of a library of compounds bearing spiro[pyrrolidine-3, 3´-oxindole] motifs that demonstrated exceptional inhibitory activity against the proliferation of MCF-7 breast cancer cells. The synthesis involved a one pot Pictet Spengler-Oxidative ring contraction of tryptamine to the desired scaffolds and occurred in 1:1 THF and water with catalytic trifluoroacetic acid and stoichiometric N-bromosuccinimide as an oxidant. Phenotypic profiling indicated that these molecules induce apoptotic cell death in MCF-7 cells. Target deconvolution with most potent compound 5l from the library, using chemical proteomics indicated histone deacetylase 2 (HDAC2) and prohibitin 2 as the potential cellular binding partners. Molecular docking of 5l with HDAC2 provided insights pertinent to putative binding interactions.
Collapse
Affiliation(s)
- Santanu Hati
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Chithera, Gautam Buddha Nagar, 201314, Uttar Pradesh, India
| | - Sayantan Tripathy
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Chithera, Gautam Buddha Nagar, 201314, Uttar Pradesh, India
| | - Pratip Kumar Dutta
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Chithera, Gautam Buddha Nagar, 201314, Uttar Pradesh, India
| | - Rahul Agarwal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Chithera, Gautam Buddha Nagar, 201314, Uttar Pradesh, India
| | - Ramprasad Srinivasan
- Shantani Proteome Analytics Pvt. Ltd. 100 NCL Innovation Park, Dr. HomiBhabha Road, Pune - 411 008, India
| | - Ashutosh Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Chithera, Gautam Buddha Nagar, 201314, Uttar Pradesh, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Chithera, Gautam Buddha Nagar, 201314, Uttar Pradesh, India
| | - Subhabrata Sen
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Chithera, Gautam Buddha Nagar, 201314, Uttar Pradesh, India
| |
Collapse
|
37
|
A Hybrid Chalcone Combining the Trimethoxyphenyl and Isatinyl Groups Targets Multiple Oncogenic Proteins and Pathways in Hepatocellular Carcinoma Cells. PLoS One 2016; 11:e0161025. [PMID: 27525972 PMCID: PMC4985065 DOI: 10.1371/journal.pone.0161025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/28/2016] [Indexed: 12/20/2022] Open
Abstract
Small molecule inhibitors that can simultaneously inhibit multiple oncogenic proteins in essential pathways are promising therapeutic chemicals for hepatocellular carcinoma (HCC). To combine the anticancer effects of combretastatins, chalcones and isatins, we synthesized a novel hybrid molecule 3’,4’,5’-trimethoxy-5-chloro-isatinylchalcone (3MCIC). 3MCIC inhibited proliferation of cultured HepG2 cells, causing rounding-up of the cells and massive vacuole accumulation in the cytoplasm. Paxillin and focal adhesion plaques were downregulated by 3MCIC. Surprisingly, unlike the microtubule (MT)-targeting agent CA-4 that inhibits tubulin polymerization, 3MCIC stabilized tubulin polymers both in living cells and in cell lysates. 3MCIC treatment reduced cyclin B1, CDK1, p-CDK1/2, and Rb, but increased p53 and p21. Moreover, 3MCIC caused GSK3β degradation by promoting GSK3β-Ser9 phosphorylation. Nevertheless, 3MCIC inhibited the Wnt/β-catenin pathway by downregulating β-catenin, c-Myc, cyclin D1 and E2F1. 3MCIC treatment not only activated the caspase-3-dependent apoptotic pathway, but also caused massive autophagy evidenced by rapid and drastic changes of LC3 and p62. 3MCIC also promoted cleavage and maturation of the lysosomal protease cathepsin D. Using ligand-affinity chromatography (LAC), target proteins captured onto the Sephacryl S1000-C12-3MCIC resins were isolated and analyzed by mass spectrometry (MS). Some of the LAC-MS identified targets, i.e., septin-2, vimentin, pan-cytokeratin, nucleolin, EF1α1/2, EBP1 (PA2G4), cyclin B1 and GSK3β, were further detected by Western blotting. Moreover, both septin-2 and HIF-1α decreased drastically in 3MCIC-treated HepG2 cells. Our data suggest that 3MCIC is a promising anticancer lead compound with novel targeting mechanisms, and also demonstrate the efficiency of LAC-MS based target identification in anticancer drug development.
Collapse
|
38
|
Lee H, Lee JW. Target identification for biologically active small molecules using chemical biology approaches. Arch Pharm Res 2016; 39:1193-201. [DOI: 10.1007/s12272-016-0791-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
|
39
|
Park H, Koo JY, Srikanth YVV, Oh S, Lee J, Park J, Park SB. Nonspecific protein labeling of photoaffinity linkers correlates with their molecular shapes in living cells. Chem Commun (Camb) 2016; 52:5828-31. [DOI: 10.1039/c6cc01426g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular shape of photoaffinity linkers significantly influences their nonspecific protein labeling of the cellular proteome.
Collapse
Affiliation(s)
- Hankum Park
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul
- Korea
| | - Ja Young Koo
- Department of Chemistry
- Seoul National University
- Seoul
- Korea
| | | | - Sangmi Oh
- Department of Chemistry
- Seoul National University
- Seoul
- Korea
| | - Jiyoon Lee
- Mass Spectrometer Laboratory
- National Instrument Center for Environmental Management
- Seoul National University
- Seoul
- Korea
| | - Jongmin Park
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul
- Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul
- Korea
- Department of Chemistry
| |
Collapse
|
40
|
Kanoh N. Photo-cross-linked small-molecule affinity matrix as a tool for target identification of bioactive small molecules. Nat Prod Rep 2016; 33:709-18. [DOI: 10.1039/c5np00117j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review describes the status of the photo-cross-linked small-molecule affinity matrix while providing a useful tutorial for academic and industrial chemical biologists who are involved or interested in drug target identification.
Collapse
Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
| |
Collapse
|
41
|
Farha MA, Brown ED. Strategies for target identification of antimicrobial natural products. Nat Prod Rep 2016; 33:668-80. [DOI: 10.1039/c5np00127g] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite a pervasive decline in natural product research at many pharmaceutical companies over the last two decades, natural products have undeniably been a prolific and unsurpassed source for new lead antibacterial compounds.
Collapse
Affiliation(s)
- Maya A. Farha
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| | - Eric D. Brown
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| |
Collapse
|
42
|
Friedman Ohana R, Kirkland TA, Woodroofe CC, Levin S, Uyeda HT, Otto P, Hurst R, Robers MB, Zimmerman K, Encell LP, Wood KV. Deciphering the Cellular Targets of Bioactive Compounds Using a Chloroalkane Capture Tag. ACS Chem Biol 2015; 10:2316-24. [PMID: 26162280 DOI: 10.1021/acschembio.5b00351] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenotypic screening of compound libraries is a significant trend in drug discovery, yet success can be hindered by difficulties in identifying the underlying cellular targets. Current approaches rely on tethering bioactive compounds to a capture tag or surface to allow selective enrichment of interacting proteins for subsequent identification by mass spectrometry. Such methods are often constrained by ineffective capture of low affinity and low abundance targets. In addition, these methods are often not compatible with living cells and therefore cannot be used to verify the pharmacological activity of the tethered compounds. We have developed a novel chloroalkane capture tag that minimally affects compound potency in cultured cells, allowing binding interactions with the targets to occur under conditions relevant to the desired cellular phenotype. Subsequent isolation of the interacting targets is achieved through rapid lysis and capture onto immobilized HaloTag protein. Exchanging the chloroalkane tag for a fluorophore, the putative targets identified by mass spectrometry can be verified for direct binding to the compound through resonance energy transfer. Using the interaction between histone deacetylases (HDACs) and the inhibitor, Vorinostat (SAHA), as a model system, we were able to identify and verify all the known HDAC targets of SAHA as well as two previously undescribed targets, ADO and CPPED1. The discovery of ADO as a target may provide mechanistic insight into a reported connection between SAHA and Huntington's disease.
Collapse
Affiliation(s)
| | | | | | - Sergiy Levin
- Promega Biosciences LLC, San Luis Obispo, California, United States
| | - H. Tetsuo Uyeda
- Promega Biosciences LLC, San Luis Obispo, California, United States
| | - Paul Otto
- Promega Corporation, Madison, Wisconsin, United States
| | - Robin Hurst
- Promega Corporation, Madison, Wisconsin, United States
| | | | | | | | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin, United States
| |
Collapse
|
43
|
Yan SK, Liu RH, Jin HZ, Liu XR, Ye J, Shan L, Zhang WD. "Omics" in pharmaceutical research: overview, applications, challenges, and future perspectives. Chin J Nat Med 2015; 13:3-21. [PMID: 25660284 DOI: 10.1016/s1875-5364(15)60002-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 12/18/2022]
Abstract
In the post-genomic era, biological studies are characterized by the rapid development and wide application of a series of "omics" technologies, including genomics, proteomics, metabolomics, transcriptomics, lipidomics, cytomics, metallomics, ionomics, interactomics, and phenomics. These "omics" are often based on global analyses of biological samples using high through-put analytical approaches and bioinformatics and may provide new insights into biological phenomena. In this paper, the development and advances in these omics made in the past decades are reviewed, especially genomics, transcriptomics, proteomics and metabolomics; the applications of omics technologies in pharmaceutical research are then summarized in the fields of drug target discovery, toxicity evaluation, personalized medicine, and traditional Chinese medicine; and finally, the limitations of omics are discussed, along with the future challenges associated with the multi-omics data processing, dynamics omics analysis, and analytical approaches, as well as amenable solutions and future prospects.
Collapse
Affiliation(s)
- Shi-Kai Yan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Run-Hui Liu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Hui-Zi Jin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Ru Liu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Ji Ye
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lei Shan
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Wei-Dong Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; School of Pharmacy, Second Military Medical University, Shanghai 200433, China; Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China.
| |
Collapse
|
44
|
Salvador-Reyes LA, Luesch H. Biological targets and mechanisms of action of natural products from marine cyanobacteria. Nat Prod Rep 2015; 32:478-503. [PMID: 25571978 DOI: 10.1039/c4np00104d] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Marine cyanobacteria are an ancient group of organisms and prolific producers of bioactive secondary metabolites. These compounds are presumably optimized by evolution over billions of years to exert high affinity for their intended biological target in the ecologically relevant organism but likely also possess activity in different biological contexts such as human cells. Screening of marine cyanobacterial extracts for bioactive natural products has largely focused on cancer cell viability; however, diversification of the screening platform led to the characterization of many new bioactive compounds. Targets of compounds have oftentimes been elusive if the compounds were discovered through phenotypic assays. Over the past few years, technology has advanced to determine mechanism of action (MOA) and targets through reverse chemical genetic and proteomic approaches, which has been applied to certain cyanobacterial compounds and will be discussed in this review. Some cyanobacterial molecules are the most-potent-in-class inhibitors and therefore may become valuable tools for chemical biology to probe protein function but also be templates for novel drugs, assuming in vitro potency translates into cellular and in vivo activity. Our review will focus on compounds for which the direct targets have been deciphered or which were found to target a novel pathway, and link them to disease states where target modulation may be beneficial.
Collapse
Affiliation(s)
- Lilibeth A Salvador-Reyes
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, USA.
| | | |
Collapse
|
45
|
Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
|
46
|
Yamaura K, Kuwata K, Tamura T, Kioi Y, Takaoka Y, Kiyonaka S, Hamachi I. Live cell off-target identification of lapatinib using ligand-directed tosyl chemistry. Chem Commun (Camb) 2015; 50:14097-100. [PMID: 25275302 DOI: 10.1039/c4cc05885b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that ligand-directed tosyl (LDT) chemistry is applicable to off-target identification in live cells. Lapatinib (Lap)-based LDT reagents not only labeled a receptor tyrosine kinase, HER2, target protein, but also the protein disulfide isomerase (PDI) that should be an off-target protein for Lap.
Collapse
Affiliation(s)
- Kei Yamaura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | | | | | | | | | | | | |
Collapse
|
47
|
Ursu A, Waldmann H. Hide and seek: Identification and confirmation of small molecule protein targets. Bioorg Med Chem Lett 2015; 25:3079-86. [PMID: 26115575 DOI: 10.1016/j.bmcl.2015.06.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 12/14/2022]
Abstract
Target identification and confirmation for small molecules is often the rate limiting step in drug discovery. A robust method to identify proteins addressed by small molecules is affinity chromatography using chemical probes. These usually consist of the compound of interest equipped with a linker molecule and a proper tag. Recently, methods emerged that allow the identification of protein targets without prior functionalization of the small molecule of interest. The digest offers an update on the newest developments in the area of target identification with special focus on confirmation techniques.
Collapse
Affiliation(s)
- Andrei Ursu
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany.
| |
Collapse
|
48
|
Target deconvolution of bioactive small molecules: the heart of chemical biology and drug discovery. Arch Pharm Res 2015; 38:1627-41. [DOI: 10.1007/s12272-015-0618-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/19/2015] [Indexed: 01/01/2023]
|
49
|
Krell T. Tackling the bottleneck in bacterial signal transduction research: high-throughput identification of signal molecules. Mol Microbiol 2015; 96:685-8. [DOI: 10.1111/mmi.12975] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Tino Krell
- Department of Environmental Protection; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas; C/ Prof. Albareda, 1 Granada 18008 Spain
| |
Collapse
|
50
|
Zhang C, Chen Y, Yin Y, Ji HH, Shim WB, Hou Y, Zhou M, Li XD, Ma Z. A small molecule species specifically inhibits Fusarium myosin I. Environ Microbiol 2015; 17:2735-46. [PMID: 25404531 DOI: 10.1111/1462-2920.12711] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 11/28/2022]
Abstract
Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating disease of cereal crops worldwide. Recently, a novel fungicide JS399-19 has been launched into the marketplace to manage FHB. It is compelling that JS399-19 shows highly inhibitory activity towards some Fusarium species, but not to other fungi, indicating that it is an environmentally compatible fungicide. To explore the mode of action of this species-specific compound, we conducted a whole-genome transcript profiling together with genetic and biochemical assays, and discovered that JS399-19 targets the myosin I of F. graminearum (FgMyo1). FgMyo1 is essential for F. graminearum growth. A point mutation S217L or E420K in FgMyo1 is responsible for F. graminearum resistance to JS399-19. In addition, transformation of F. graminearum with the myosin I gene of Magnaporthe grisea, the causal agent of rice blast, also led to JS399-19 resistance. JS399-19 strongly inhibits the ATPase activity of the wild-type FgMyo1, but not the mutated FgMyo1(S217L/E420K) . These results provide us a new insight into the design of species-specific antifungal compounds. Furthermore, our strategy can be applied to identify novel drug targets in various pathogenic organisms.
Collapse
Affiliation(s)
- Chengqi Zhang
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yun Chen
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yanni Yin
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Huan-Hong Ji
- National Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843-2132, USA
| | - Yiping Hou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiang-Dong Li
- National Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhonghua Ma
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|