1
|
Rufer AC. Drug discovery for enzymes. Drug Discov Today 2021; 26:875-886. [PMID: 33454380 DOI: 10.1016/j.drudis.2021.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Enzymes are essential, physiological catalysts involved in all processes of life, including metabolism, cellular signaling and motility, as well as cell growth and division. They are attractive drug targets because of the presence of defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Understanding the reaction mechanisms of enzymes and the molecular mode of action of enzyme inhibitors is indispensable for the discovery and development of potent, efficacious, and safe novel drugs. The combination of classical concepts of enzymology with new experimental and data analysis methods opens new routes for drug discovery.
Collapse
Affiliation(s)
- Arne Christian Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 065/208A, 4070 Basel, Switzerland.
| |
Collapse
|
2
|
Yang J, Hou L, Liu KM, He WB, Cai Y, Yang FQ, Hu YJ. ChemGenerator: a web server for generating potential ligands for specific targets. Brief Bioinform 2020; 22:6055961. [PMID: 33381797 DOI: 10.1093/bib/bbaa407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/23/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
In drug discovery, one of the most important tasks is to find novel and biologically active molecules. Given that only a tip of iceberg of drugs was founded in nearly one-century's experimental exploration, it shows great significance to use in silico methods to expand chemical database and profile drug-target linkages. In this study, a web server named ChemGenerator was proposed to generate novel activates for specific targets based on users' input. The ChemGenerator relies on an autoencoder-based algorithm of Recurrent Neural Networks with Long Short-Term Memory by training of 7 million of molecular Simplified Molecular-Input Line-Entry System as the basic model, and further develops target guided generation by transfer learning. As results, ChemGenerator gains lower loss (<0.01) than existing reference model (0.2~0.4) and shows good performance in the case of Epidermal Growth Factor Receptor. Meanwhile, ChemGenerator is now freely accessible to the public by http://smiles.tcmobile.org. In proportion to endless molecular enumeration and time-consuming expensive experiments, this work demonstrates an efficient alternative way for the first virtual screening in drug discovery.
Collapse
Affiliation(s)
- Jing Yang
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, China
| | - Ling Hou
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, China
| | - Kun-Meng Liu
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, China
| | - Wen-Bin He
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Shanxi University of Chinese Medicine, Jinzhong, Shanxi, China
| | - Yong Cai
- Beijing Normal University, Zhuhai, China
| | - Feng-Qing Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, China
| | - Yuan-Jia Hu
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, China
| |
Collapse
|
3
|
Wang H, Liu Z, Guan L, Li J, Chen S, Yu W, Lai M. LYW-6, a novel cryptotanshinone derived STAT3 targeting inhibitor, suppresses colorectal cancer growth and metastasis. Pharmacol Res 2020; 153:104661. [PMID: 31982491 DOI: 10.1016/j.phrs.2020.104661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/15/2019] [Accepted: 01/22/2020] [Indexed: 01/02/2023]
Abstract
The constitutive activation of signal transducer and activator of transcription 3(STAT3) is associated with aggressive development and metastasis in colorectal cancer (CRC), but STAT3-targeting drugs remain elusive in clinic. Here, structure-based strategy was used to remodel the natural compound cryptotanshinone into a more effective STAT3 inhibitor LYW-6. Using the Biolayer Interferometry assay, we observed that LYW-6 exhibited specific interactions with STAT3(KD = 6.6 ± 0.7 μM). Western blot analysis and electrophoretic mobility shift assays (EMSA) showed that LYW-6 inhibited the phosphorylation of STAT3 tyrosine 705 (Tyr-705) and had slight effects on STAT1 and STAT5 phosphorylation. Western blot analysis on the upstream kinases of STAT3 confirmed that the inhibitory mechanism on p-STAT3 was independent of upstream kinases. Further investigation demonstrated that LYW-6 downregulated the expression of downstream oncogenes to inhibit cell viability, cell cycle development, and potently increased cell apoptosis in human CRC cells. The invasion and metastasis linked signaling was also blocked by LYW-6 treatment. LYW-6 was found to reduce the metastasis foci in lung on tail-lung metastasis models. In addition, it was observed that LYW-6 markedly diminished STAT3 phosphorylation in tumor tissue and significantly inhibited tumor growth on xenograft models. Tumor development on chemically-induced colorectal cancer model also significantly inhibited by LYW-6 treatment. These findings provided adequate evidence that STAT3 inhibitor LYW-6 might be a potential candidate agent for CRC treatment.
Collapse
Affiliation(s)
- Huan Wang
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, China
| | - Zhe Liu
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, China
| | - Lingnan Guan
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, China
| | - Jiankang Li
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, China
| | - Siyi Chen
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, China.
| | - Maode Lai
- School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, China; Department of Pathology, School of Medicine, Zhejiang University, China.
| |
Collapse
|
4
|
Affiliation(s)
- Ulrich Kauhl
- Institute of Organic Chemistry, University of Mainz, Duesbergweg 10−14, D-55128 Mainz, Germany
| | - Lars Andernach
- Institute of Organic Chemistry, University of Mainz, Duesbergweg 10−14, D-55128 Mainz, Germany
| | - Till Opatz
- Institute of Organic Chemistry, University of Mainz, Duesbergweg 10−14, D-55128 Mainz, Germany
| |
Collapse
|
5
|
Facile Chemical Access to Biologically Active Norcantharidin Derivatives from Biomass. Molecules 2017; 22:molecules22122210. [PMID: 29231880 PMCID: PMC6149738 DOI: 10.3390/molecules22122210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/30/2017] [Accepted: 12/07/2017] [Indexed: 01/21/2023] Open
Abstract
Reductive amination of 2,5-diformylfuran (DFF) was used to implement the transition from bio-derived 5-hydroxymethylfurfural (HMF) to pharmaceuticals. The synthesized bis(aminomethyl)furans were utilized as building blocks for the construction of new derivatives with structural cores of naturally occurring biologically active compounds. Using the one-pot procedure, which included the Diels–Alder reaction followed by hydrogenation of the double bond, bio-derived analogues of the anticancer drug norcantharidin were obtained. The cyclization process was diastereoselective, and resulted in the formation of tricyclic products with the endo configuration. Analysis of cytotoxycity for the resulting tricyclic amine-containing compounds showed an increase of anticancer activity as compared with the unsubstituted norcantharimide.
Collapse
|
6
|
Hirota-Takahata Y, Ishimoto Y, Kurosawa E, Iwadate Y, Onozawa Y, Tanaka I, Tanaka M, Kobayashi H. F-36316 A and B, novel vasoactive compounds, isolated from Incrucipulum sp. SANK 10414. J Antibiot (Tokyo) 2017; 70:981-986. [PMID: 28792011 DOI: 10.1038/ja.2017.84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 11/09/2022]
Abstract
In the course of our screening program for vasoactive compounds using co-culture assay of endothelial cells and fibroblast cells, potent activity was detected in the cultured broth of Incrucipulum sp. SANK 10414. Two active compounds, F-36316 A and B, and a non-active homolog, F-36316 C, were isolated from the broth. The structures of F-36316 A, B and C were elucidated by physicochemical data and spectral analyses, and found to be new 3-acylated tetronic acid homologs. F-36316 A and B induced morphological changes of endothelial cells different from vascular endothelial growth factor (VEGF) or vestaines in the assay with EC50 values of 1.8 and 11.7 μM, respectively. Furthermore, F-36316 A and B suppressed VEGF-induced vascular permeability induction in mice.
Collapse
Affiliation(s)
| | - Yoko Ishimoto
- Frontier Research Laboratories, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Emi Kurosawa
- Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, Tokyo, Japan
| | - Yuko Iwadate
- Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, Tokyo, Japan
| | - Yoshiko Onozawa
- Frontier Research Laboratories, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Isshin Tanaka
- Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, Tokyo, Japan
| | - Masahiro Tanaka
- Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, Tokyo, Japan
| | - Hideki Kobayashi
- Frontier Research Laboratories, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| |
Collapse
|
7
|
Zaghouani M, Nay B. 3-Acylated tetramic and tetronic acids as natural metal binders: myth or reality? Nat Prod Rep 2016; 33:540-8. [PMID: 26879987 DOI: 10.1039/c5np00144g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 20153-Acylated tetramic and tetronic acids are characterized by a low pKa and are likely to be deprotonated under physiological conditions. In addition, their structure makes them excellent chelators of metallic cations. We will discuss the significance of these chemical properties with regard to the biological properties and mechanisms of action of these compounds, highlighting the importance of considering them as salts or chelates for biological purposes, rather than acids.
Collapse
Affiliation(s)
- Mehdi Zaghouani
- Muséum National d'Histoire Naturelle, CNRS, UMR 7245 Molécules de Communication et Adaptation des Micro-organismes, 57 rue Cuvier (CP 54), 75005 Paris, France.
| | | |
Collapse
|
8
|
Hirai G, Asanuma M, Tsuchiya A, Sodeoka M. Development of Dual-specificity Protein Phosphatases Inhibitors based on Focused Library Approach: Modification of a Core Structure and Unique Inhibition Mechanism. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Go Hirai
- Synthetic Organic Chemistry Laboratory, RIKEN; RIKEN CSRS
| | | | | | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN; RIKEN CSRS
| |
Collapse
|