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Ma T, Gao S, Zhao LX, Ye F, Fu Y. 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors: From Molecular Design to Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17125-17137. [PMID: 39047218 DOI: 10.1021/acs.jafc.4c01171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Weed resistance is a critical issue in crop production. Among the known herbicides, 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors are crucial for addressing weed resistance. HPPD inhibitors constitute a pivotal aspect of contemporary crop protection strategies. The advantages of these herbicides are their broad weed spectrum, flexible application, and excellent compatibility with other herbicides. They also exhibit satisfactory crop selectivity and low toxicity and are environmentally friendly. An increasing number of new HPPD inhibitors have been designed by combining computer-aided drug design with conventional design approaches. Herein, the molecular design and structural features of innovative HPPD inhibitors are reviewed to guide the development of new HPPD inhibitors possessing an enhanced biological efficacy.
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Affiliation(s)
- Tengfei Ma
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Agricultural Functional Molecule Design and Utilization of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
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2
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Sui X, Dang HT, Porey A, Trevino R, Das A, Fremin SO, Hughes WB, Thompson WT, Dhakal SK, Arman HD, Larionov OV. Acridine photocatalysis enables tricomponent direct decarboxylative amine construction. Chem Sci 2024; 15:9582-9590. [PMID: 38939159 PMCID: PMC11206229 DOI: 10.1039/d4sc02356k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/20/2024] [Indexed: 06/29/2024] Open
Abstract
Amines are centrally important motifs in medicinal chemistry and biochemistry, and indispensable intermediates and linchpins in organic synthesis. Despite their cross-disciplinary prominence, synthetic access to amine continues to rely on two-electron approaches based on reductions and additions of organometallic reagents, limiting their accessible chemical space and necessitating stepwise preassembly of synthetic precursors. We report herein a homogeneous photocatalytic tricomponent decarboxylative radical-mediated amine construction that enables modular access to α-branched secondary amines directly from the broad and structurally diverse chemical space of carboxylic acids in a tricomponent reaction with aldehydes and aromatic amines. Our studies reveal the key role of acridine photocatalysis acting in concert with copper and Brønsted acid catalytic processes in facilitating the previously inaccessible homogeneous photocatalytic reaction and provide a streamlined segue to a wide range of amines and nonproteinogenic α-amino acids.
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Affiliation(s)
- Xianwei Sui
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Hang T Dang
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Arka Porey
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Ramon Trevino
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Arko Das
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Seth O Fremin
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - William B Hughes
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - William T Thompson
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Shree Krishna Dhakal
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Hadi D Arman
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Oleg V Larionov
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
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3
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Kuralt V, Frlan R. Navigating the Chemical Space of ENR Inhibitors: A Comprehensive Analysis. Antibiotics (Basel) 2024; 13:252. [PMID: 38534687 DOI: 10.3390/antibiotics13030252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial resistance is a global health threat that requires innovative strategies against drug-resistant bacteria. Our study focuses on enoyl-acyl carrier protein reductases (ENRs), in particular FabI, FabK, FabV, and InhA, as potential antimicrobial agents. Despite their promising potential, the lack of clinical approvals for inhibitors such as triclosan and isoniazid underscores the challenges in achieving preclinical success. In our study, we curated and analyzed a dataset of 1412 small molecules recognized as ENR inhibitors, investigating different structural variants. Using advanced cheminformatic tools, we mapped the physicochemical landscape and identified specific structural features as key determinants of bioactivity. Furthermore, we investigated whether the compounds conform to Lipinski rules, PAINS, and Brenk filters, which are crucial for the advancement of compounds in development pipelines. Furthermore, we investigated structural diversity using four different representations: Chemotype diversity, molecular similarity, t-SNE visualization, molecular complexity, and cluster analysis. By using advanced bioinformatics tools such as matched molecular pairs (MMP) analysis, machine learning, and SHAP analysis, we were able to improve our understanding of the activity cliques and the precise effects of the functional groups. In summary, this chemoinformatic investigation has unraveled the FAB inhibitors and provided insights into rational antimicrobial design, seamlessly integrating computation into the discovery of new antimicrobial agents.
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Affiliation(s)
- Vid Kuralt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Rok Frlan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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Zhang T, Sun S, Wang R, Li T, Gan B, Zhang Y. BioisoIdentifier: an online free tool to investigate local structural replacements from PDB. J Cheminform 2024; 16:7. [PMID: 38218937 PMCID: PMC10788035 DOI: 10.1186/s13321-024-00801-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024] Open
Abstract
Within the realm of contemporary medicinal chemistry, bioisosteres are empirically used to enhance potency and selectivity, improve adsorption, distribution, metabolism, excretion and toxicity profiles of drug candidates. It is believed that bioisosteric know-how may help bypass granted patents or generate novel intellectual property for commercialization. Beside the synthetic expertise, the drug discovery process also depends on efficient in silico tools. We hereby present BioisoIdentifier (BII), a web server aiming to uncover bioisosteric information for specific fragment. Using the Protein Data Bank as source, and specific substructures that the user attempt to surrogate as input, BII tries to find suitable fragments that fit well within the local protein active site. BII is a powerful computational tool that offers the ligand design ideas for bioisosteric replacing. For the validation of BII, catechol is conceived as model fragment attempted to be replaced, and many ideas are successfully offered. These outputs are hierarchically grouped according to structural similarity, and clustered based on unsupervised machine learning algorithms. In summary, we constructed a user-friendly interface to enable the viewing of top-ranking molecules for further experimental exploration. This makes BII a highly valuable tool for drug discovery. The BII web server is freely available to researchers and can be accessed at http://www.aifordrugs.cn/index/ . Scientific Contribution: By designing a more optimal computational process for mining bioisosteric replacements from the publicly accessible PDB database, then deployed on a web server for throughly free access for researchers. Additionally, machine learning methods are applied to cluster the bioisosteric replacements searched by the platform, making a scientific contribution to facilitate chemists' selection of appropriate bioisosteric replacements. The number of bioisosteric replacements obtained using BII is significantly larger than the currently available platforms, which expanding the search space for effective local structural replacements.
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Affiliation(s)
- Tinghao Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Shaohua Sun
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Runzhou Wang
- School of Management, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Ting Li
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Bicheng Gan
- College of Petroleum Engineering, Northeast Petroleum University, Daqing, 163318, Heilongjiang, China
| | - Yuezhou Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China.
- Ningbo Institute of Northwestern Polytechnical University, Frontiers Science Center for Flexible Electronics (FSCFE), Key Laboratory of Flexible Electronics of Zhejiang Province, Ningbo Institute of Northwestern Polytechnical University, 218 Qingyi Road, Ningbo, 315103, China.
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Xu L, Quan X, Li Z, Maienfisch P. Synthesis and Biological Activity of Silicon-Containing Ethylsulfonylpyridine Insecticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18250-18259. [PMID: 37672484 DOI: 10.1021/acs.jafc.3c04058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Ethylsulfonylpyridines are a novel chemical class of insecticides with excellent broad-spectrum activity and an unprecedented mode of action. With the objective of discovering novel ethylsulfonylpyridines with a broader spectrum, wider range of uses, and/or improved properties, we have started a research program aimed at introducing silicon motifs and studying their biological effects. We designed a series of Oxazosulfyl analogues where the hydrogen atom at the 5-position of the pyridyl moiety is replaced by a trialkylsilyl group and prepared these compounds applying denovo synthetic methodology. Our novel ethylsulfonylpyridines exhibit excellent insecticidal activities. The best compound, A18, resulting from our research exhibited an LC50 value of 0.30 mg/L against Plutella xylostella and reached the activity level of the commercial standard Oxazosulfyl. Our findings confirmed our working hypothesis that at the 5-position of the pyridyl moiety larger groups with different hydrophobic, electronic, and steric properties are tolerated.
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Affiliation(s)
- Liu Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaocao Quan
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- CreInSol Consulting & Biocontrols, CH-4118 Rodersdorf, Switzerland
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6
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Liu P, Jiang Y, Jiao L, Luo Y, Wang X, Yang T. Strategies for the Discovery of Oxazolidinone Antibacterial Agents: Development and Future Perspectives. J Med Chem 2023; 66:13860-13873. [PMID: 37807849 DOI: 10.1021/acs.jmedchem.3c01040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Oxazolidinones represent a significant class of synthetic bacterial protein synthesis inhibitors that are primarily effective against Gram-positive bacteria. The commercial success of linezolid, the first FDA-approved oxazolidinone antibiotic, has motivated researchers to develop more potent oxazolidinones by employing various drug development strategies to fight against antimicrobial resistance, some of which have shown promising results. Thus, this Perspective aims to discuss the strategies employed in constructing oxazolidinone-based antibacterial agents and summarize recent advances in discovering oxazolidinone antibiotics to provide valuable insights for potentially developing next-generation oxazolidinone antibacterial agents or other pharmaceuticals.
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Affiliation(s)
- Pingxian Liu
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunhan Jiang
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Jiao
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaodong Wang
- Department of Breast Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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7
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Omara M, Hagras M, Elsebaie MM, Abutaleb NS, Nour El-Din HT, Mekhail MO, Attia AS, Seleem MN, Sarg MT, Mayhoub AS. Exploring novel aryl/heteroaryl-isosteres of phenylthiazole against multidrug-resistant bacteria. RSC Adv 2023; 13:19695-19709. [PMID: 37425632 PMCID: PMC10323310 DOI: 10.1039/d3ra02778c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Antimicrobial resistance has become a concern as a worldwide threat. A novel scaffold of phenylthiazoles was recently evaluated against multidrug-resistant Staphylococci to control the emergence and spread of antimicrobial resistance, showing good results. Several structural modifications are needed based on the structure-activity relationships (SARs) of this new antibiotic class. Previous studies revealed the existence of two key structural features essential for the antibacterial activity, the guanidine head and lipophilic tail. In this study, a new series of twenty-three phenylthiazole derivatives were synthesized utilizing the Suzuki coupling reaction to explore the lipophilic part. The in vitro antibacterial activity was evaluated against a range of clinical isolates. The three most promising compounds, 7d, 15d and 17d, with potent MIC values against MRSA USA300 were selected for further antimicrobial evaluation. The tested compounds exhibited potent results against the tested MSSA, MRSA, and VRSA strains (concentration: 0.5 to 4 μg mL-1). Compound 15d inhibited MRSA USA400 at a concentration of 0.5 μg mL-1 (one-fold more potent than vancomycin) and showed low MIC values against ten clinical isolates, including linezolid-resistant strain MRSA NRS119 and three vancomycin-resistant isolates VRSA 9/10/12. Moreover, compound 15d retained its potent antibacterial activity using the in vivo model by the burden reduction of MRSA USA300 in skin-infected mice. The tested compounds also showed good toxicity profiles and were found to be highly tolerable to Caco-2 cells at concentrations of up to 16 μg mL-1, with 100% of the cells remaining viable.
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Affiliation(s)
- Mariam Omara
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Girls), Al-Azhar University Cairo Egypt
| | - Mohamed Hagras
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Boys), Al-Azhar University Cairo 11884 Egypt
| | - Mohamed M Elsebaie
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Boys), Al-Azhar University Cairo 11884 Egypt
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University Blacksburg Virginia 24061 USA
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University Zagazig 44519 Egypt
| | - Hanzada T Nour El-Din
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Maria O Mekhail
- PharmD-Clinical Pharmacy Undergraduate Program, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Ahmed S Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
- Department of Microbiology and Immunology, School of Pharmacy, Newgiza University Giza Egypt
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University Blacksburg Virginia 24061 USA
- Center for One Health Research, Virginia Polytechnic Institute and State University Blacksburg Virginia 24061 USA
| | - Marwa T Sarg
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Girls), Al-Azhar University Cairo Egypt
| | - Abdelrahman S Mayhoub
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy (Boys), Al-Azhar University Cairo 11884 Egypt
- Nanoscience Program, University of Science and Technology, Zewail City of Science and Technology Giza Egypt
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Yan YC, Zhang H, Hu K, Zhou SM, Chen Q, Qu RY, Yang GF. A mini-review on synthesis and antiviral activity of natural product oxetanocin A derivatives. Bioorg Med Chem 2022; 72:116968. [PMID: 36054994 DOI: 10.1016/j.bmc.2022.116968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Abstract
Oxetanocin A (Oxt-A), a novel oxetanosyl N-glycoside nucleoside, was isolated from Bacillus megaterium in 1986. It carries an oxetane ring on the sugar moiety of the nucleoside scaffold, which contributes to differences in its structure from those of common tetrahydrofuranyl-based nucleosides. In view of the unique 3D-spatial framework, the complete synthesis of Oxt-A has been achieved by multiple research groups. The pharmacological properties of this natural product have also been broadly investigated by pharmacists and chemists since its discovery. Notably, the potential antiviral effect of Oxt-A has captured attention of researchers in the field of antiviral agent development. Furthermore, epidemic outbreaks caused by viruses have been stimulating the preparation and modification of various Oxt-A analogs over the past few decades. However, none of the studies have overviewed the antiviral efficacies of this naturally occurring scaffold yet. Thus, the present review summarizes the synthesis, structural modification, and antiviral activities of Oxt-A and its derivatives. We believe that these comprehensive descriptions will provide a novel perspective for the discovery of antivirus drugs with well-improved performance and pave newer paths for combating sudden public health issues triggered by viruses in the future.
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Affiliation(s)
- Yao-Chao Yan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Hu Zhang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Kai Hu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Shao-Meng Zhou
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Qiong Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
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Madushanka A, Verma N, Freindorf M, Kraka E. Papaya Leaf Extracts as Potential Dengue Treatment: An In-Silico Study. Int J Mol Sci 2022; 23:ijms232012310. [PMID: 36293162 PMCID: PMC9610845 DOI: 10.3390/ijms232012310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) cause serious public health problems, with nearly 390 million people affected and 20,000 deaths per year in tropical and subtropical countries. Despite numerous attempts, no antiviral drug or vaccine is currently available to combat the manifestation. The challenge of discovering an efficient vaccine is enhanced by the surplus presence of efficient vectors and drug resistance from the virus. For centuries, papaya (Carica papaya) extracts have been traditionally used to treat DF, DHF, and DSS. In the present study, we systematically investigated seven compounds isolated from papaya leaf extract with regard to their potential as inhibitors for non-structural (NS) proteins, NS3 and NS5, which play a crucial role in viral RNA replication. The computational tools applied stretched across classical molecular docking, molecular dynamics (MD) simulations and SwissADME used to calculate binding affinities; binding free energies; Absorption, Distribution, Metabolism, and Excretion (ADME); and drug-likeness properties, thus, identifying Kaempferol, Chlorogenic acid, and Quercetin as potential candidates, with Kaempferol and Quercetin scoring best. Therefore, for the Kaempferol and Quercetin complexes, hybrid quantum mechanical/molecular mechanical (QM/MM) geometry and frequency calculations were performed, followed by the local mode analysis developed in our group to quantify Kaempferol-NS and Quercetin-NS hydrogen bonding. Given the non-toxic nature and the wide availability of the Kaempferol and Quercetin papaya extract in almost all of the susceptible regions, and our results showing high NS3 and NS5 binding affinities and energies, strong hydrogen bonding with both NS3 and NS5, and excellent ADME properties, we suggest Kaempferol and Quercetin as a strong NS3 and NS5 inhibitor to be further investigated in vitro.
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Design, Synthesis and Evaluation of Novel 1,4-Disubstituted Piperazine-2,5-dione Derivatives as Antioxidants against H2O2-Induced Oxidative Injury via the IL-6/Nrf2 Loop Pathway. Antioxidants (Basel) 2022; 11:antiox11102014. [PMID: 36290737 PMCID: PMC9598289 DOI: 10.3390/antiox11102014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 11/17/2022] Open
Abstract
Excessive reactive oxygen species (ROS) production leads to oxidative stress in cells, impairing the function of mitochondria and finally inducing cell apoptosis. Considering the essential role of oxidative stress in the pathogenesis of various neurodegenerative diseases and psychiatric disorders, the discovery of novel antioxidants has attracted increasing attention. Herein, a series of novel 1,4-disubstituted piperazine-2,5-dione derivatives were designed, synthesized and evaluated for their antioxidative activity. The results of the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay indicated that none of the tested compounds showed significant toxicity to SH-SY5Y cells at concentrations up to 80 μM. Cell counting via flow cytometry revealed that most of the tested compounds could effectively protect SH-SY5Y cells from H2O2-induced oxidative damage at 20 μM. Among these compounds, compound 9r exhibited the best antioxidative activity. Further mechanistic investigation indicated that 9r decreased ROS production and stabilized the mitochondrial membrane potential to restrain cell apoptosis, and promoted cell survival via an IL-6/Nrf2 positive-feedback loop. These results suggested the potential of compound 9r as a novel antioxidative candidate for the treatment of diseases caused by oxidative stress.
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Zhou C, Wang X, Quan X, Cheng J, Li Z, Maienfisch P. Silicon-Containing Complex II Acaricides─Design, Synthesis, and Pharmacological Optimization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11063-11074. [PMID: 35575634 DOI: 10.1021/acs.jafc.2c00804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bioisosteric replacement has been proven to be a powerful strategy in life science research. In this review, general aspects of carbon-silicon bioisosteric substitution and its applications in pharmaceutical and crop protection research are described. Carbon and their silicon analogues possess similar intrinsic properties. Replacing carbon with silicon in pharmaceuticals and pesticides has shown to result in positive effects on efficacy and selectivity, physicochemical properties, and bioavailability and also to eliminate or improve human or environmental safety properties as well as to provide novelty and new intellectual property in many cases. Furthermore, the application of carbon-silicon substitution in the search for new complex II acaricides is highlighted. This research led to the discovery of sila-cyflumetofen 23a and other silicon-containing analogues of cyflumetofen that match or exceed the acaricidal activity of cyflumetofen. The molecular design strategy, synthetic aspects, biological activity, computational modeling work, and structure-activity relationships will be discussed.
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Affiliation(s)
- Cong Zhou
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xin Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xiaocao Quan
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- CreInSol MCB, CH-4118 Rodersdorf, Switzerland
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Jackson V, Jordan L, Burgin RN, McGaw OJS, Muir CW, Ceban V. Application of Molecular-Modeling, Scaffold-Hopping, and Bioisosteric Approaches to the Discovery of New Heterocyclic Picolinamides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11031-11041. [PMID: 35852973 DOI: 10.1021/acs.jafc.2c03755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Macrocyclic natural products and their derivatives are a valuable source for biologically active crop protection products and have had significant impact on the development of conventional agrochemicals. However, they can be challenging starting points for lead-generation efforts because of their size, structural complexity, and developability. Using molecular modeling and electrostatic analysis, alternative bicyclic isosteres were identified as replacements for the antifungal nine-membered macrocycle UK-2A. By application of a structure-based conformational approach, a series of heterocyclic replacements were derivatized to deliver promising fungicidal activity and scaffold bioisosteres were further diversified to investigate structure-activity relationships.
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Affiliation(s)
- Victoria Jackson
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Linda Jordan
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Ryan N Burgin
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Oliver J S McGaw
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Calum W Muir
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Victor Ceban
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
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13
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Chen M, Li Z, Shao X, Maienfisch P. Scaffold-Hopping Approach To Identify New Chemotypes of Dimpropyridaz. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11109-11122. [PMID: 35412307 DOI: 10.1021/acs.jafc.2c00636] [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
Dimpropyridaz is a pyrazole carboxamide insecticide with a novel mode of action, currently under worldwide development by BASF, providing excellent activity against sucking pests. A series of dimpropyridaz analogues were designed to investigate the impact of bioisosteric heterocyclic replacements on the biological activity and molecular properties. Focus was given to prepare analogues where the 4-pyridazinyl moiety was replaced by 5-pyrimidinyl, 2-pyrimidinyl, 3-pyridazinyl, and 2-pyrazinyl groups. Five different synthetic routes were developed for the preparation of these analogues, delivering the target compounds in moderate to good yields. We explained some aspects of the observed structure-activity relationship by a density functional theory (DFT) calculation and DFT-derived Multiwfn and VMD program models. These findings provide first insights into the important role of the 4-pyridazinyl heterocyclic moiety in the pyrazole carboxamide insecticide chemical class and the mechanism of action of dimpropyridaz.
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Affiliation(s)
- Meijun Chen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- CreInSol Consulting & Biocontrols, CH-4118 Rodersdorf, Switzerland
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14
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Chen M, Li Z, Shao X, Maienfisch P. Bioisosteric-Replacement-Driven Lead Optimization of Tyclopyrazoflor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11123-11137. [PMID: 35561416 DOI: 10.1021/acs.jafc.2c00654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A heterocyclic replacement strategy has been applied attempting to further optimize the biological properties of the new insecticide tyclopyrazoflor, a pyridinyl-pyrazole compound with excellent activity against sap-feeding insects recently discovered by Corteva. Our research program on this novel chemical class of insecticide was targeted to evaluate the importance of both the pyridyl and pyrazole moieties on the biological activity, properties, and structure-activity. Synthetic methodologies have been developed delivering our designed target compounds in moderate to good yields. In our attempt to rationalize the biological activity differences of tyclopyrazoflor analogues, a potential surface analysis based on a density functional theory (DFT) calculation and DFT-derived Multiwfn and VMD program model was performed. Furthermore, the SwissBioisostere online database was applied as a great source for inspiration for bioisosteric replacements.
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Affiliation(s)
- Meijun Chen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Peter Maienfisch
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- CreInSol Consulting & Biocontrols, CH-4118 Rodersdorf, Switzerland
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15
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Jiménez-Arellanes MA, Peña-Rico MÁ, Castro-Cerritos KV, Sifuentes-Vázquez LD, Reyes-González MA, Ramírez-Marroquín OA. Mechanosynthesis of phosphonocinnamic esters through solvent-free Horner-Wadsworth-Emmons reaction. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2053976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- María Adelina Jiménez-Arellanes
- Unidad de Investigación Médica en Farmacología, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Miguel Ángel Peña-Rico
- Centro de Investigaciones Científicas, Instituto de Química Aplicada, Universidad del Papaloapan, Tuxtepec, Mexico
| | | | | | - Miguel Angel Reyes-González
- Investigador de Cátedras CONACyT-ITNL, Centro de Investigación e Innovación Tecnológica-TecNM/ITNL, Apodaca, N.L., México
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16
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Prasher P, Sharma M. Medicinal chemistry of pyrophosphate mimics: A mini review. Drug Dev Res 2021; 83:3-15. [PMID: 34506652 DOI: 10.1002/ddr.21877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/21/2022]
Abstract
The pyrophosphate mimicking groups offer rational modification of the pyrophosphate-bearing natural substrates of the overexpressed enzymes that cause the onset of disease progression. Mainly, the modified substrate interacts differently with the enzyme active site eventually causing its deactivation, or provides the therapeutically active products at the completion of the catalytic cycle that contribute toward the inhibition of the target enzyme. Many of the pyrophosphate mimic-containing molecules serve as competitive or allosteric inhibitors of the target enzyme to achieve the desirable properties for the mitigation of the target enzyme's pathophysiology. This review presents an epigrammatic overview of the pyrophosphate mimics in medicinal chemistry.
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Affiliation(s)
- Parteek Prasher
- UGC Sponsored Centre for Advanced Studies, Department of Chemistry, Guru Nanak Dev University, Amritsar, India.,Department of Chemistry, University of Petroleum & Energy Studies, Dehradun, India
| | - Mousmee Sharma
- UGC Sponsored Centre for Advanced Studies, Department of Chemistry, Guru Nanak Dev University, Amritsar, India.,Department of Chemistry, Uttaranchal University, Dehradun, India
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17
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Alves L, Santos DA, Cendron R, Rocho FR, Matos TKB, Leitão A, Montanari CA. Nitrile-based peptoids as cysteine protease inhibitors. Bioorg Med Chem 2021; 41:116211. [PMID: 33991733 DOI: 10.1016/j.bmc.2021.116211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
Peptidomimetics of the class of dipeptidyl nitrile analog peptoids were synthesized as inhibitors of mammalian cysteine proteases of the papain superfamily. The dipeptidyl nitrile side chains were attached to the peptide backbone's nitrogen atom, not to the α-carbons. Synthesized nitrile-based peptoid analogs that lack the hydrogen amide at P2-P3 are responsible for many of the secondary structure elements in peptides and proteins, making them resistant to proteolysis. The designed peptoids would lose a hydrogen bond with cruzain Asp161 decreasing the affinity toward the enzyme. A structure-activity relationship and matched molecular pair-based analysis between the dipeptidyl nitrile Neq0409 and its peptoid 4a yielded the following cruzain affinities: pKiNeq0409 = 6.5 and pKi4a = 5.2. respectively. A retrosynthetic matched molecular pair cliff (RMMP-cliff) analysis with a ΔpKiNeq0409-4a of 1.3 log is found for this transformation. These novel peptoids were then optimized, leading to compound 4i, with high cruzain inhibition (pKi = 6.8). Cross-class cathepsin activity was observed for some of these novel compounds against cathepsins K, L and S, while other compounds presented a selective inhibition of cathepsin K (4b, 4c, 4k) over ten times higher than the other enzymes. The putative mode of binding was determined by using covalent docking, which also aided to describe the structure-activity relationship (SAR). Interestingly, none of the peptoids inhibited CatB to any appreciable extent. These results provide guidance to identify novel bioactive nitrile-based peptoids.
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Affiliation(s)
- Luana Alves
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Deborah A Santos
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil.
| | - Rodrigo Cendron
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Fernanda R Rocho
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Thiago K B Matos
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil.
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group (NEQUIMED), Institute of Chemistry of São Carlos, University of São Paulo, São Carlos/SP, Brazil
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18
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Patel KR, Brahmbhatt JG, Pandya PA, Bhadresha K, Daraji DG, Patel HD, Rawal RM, Baran SK, Jayanthi S. Design, Synthesis and Biological Evaluation of Novel 5‐Phenyl‐5‐(thiophen‐2‐yl)‐4
H
‐1,2,4‐triazole‐3‐thiols as an Anticancer Agent. ChemistrySelect 2021. [DOI: 10.1002/slct.202100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Krupa R. Patel
- Department of Chemistry School of Sciences Gujarat University Ahmedabad 380009 Gujarat India
| | - Jpan G. Brahmbhatt
- Department of Life Science School of Sciences Gujarat University Ahmedabad 380009 Gujarat India
| | - Pranav A. Pandya
- Department of Chemistry School of Sciences Gujarat University Ahmedabad 380009 Gujarat India
| | - Kinjal Bhadresha
- Department of Life Science School of Sciences Gujarat University Ahmedabad 380009 Gujarat India
| | - Drashti G. Daraji
- Department of Chemistry School of Sciences Gujarat University Ahmedabad 380009 Gujarat India
| | - Hitesh D. Patel
- Department of Chemistry School of Sciences Gujarat University Ahmedabad 380009 Gujarat India
| | - Rakesh M. Rawal
- Department of Life Science School of Sciences Gujarat University Ahmedabad 380009 Gujarat India
| | - Sujit K. Baran
- Department of Chemistry The M. S. University of Baroda Vadodara 390002 Gujarat India
| | - Sivaraman Jayanthi
- Computational Drug Design Lab School of Bio Sciences and Technology Vellore Institute of Technology Vellore 632014 Tamil Nadu India
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19
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Chen LZ, Shu HY, Wu J, Yu YL, Ma D, Huang X, Liu MM, Liu XH, Shi JB. Discovery and development of novel pyrimidine and pyrazolo/thieno-fused pyrimidine derivatives as potent and orally active inducible nitric oxide synthase dimerization inhibitor with efficacy for arthritis. Eur J Med Chem 2021; 213:113174. [PMID: 33515864 DOI: 10.1016/j.ejmech.2021.113174] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/24/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022]
Abstract
In order to discover and develop drug-like anti-inflammatory agents against arthritis, based on "Hit" we found earlier and to overcome drawbacks of toxicity, twelve series of total 89 novel pyrimidine, pyrazolo[4,3-d]pyrimidine and thieno[3,2-d]pyrimidine derivatives were designed, synthesized and screened for their anti-inflammatory activity against NO and toxicity for normal liver cells (LO2). Relationships of balance toxicity and activity have been summarized through multi-steps, and title compounds 22o, 22l were found to show lower toxicity (against LO2: IC50 = 2934, 2301 μM, respectively) and potent effect against NO release (IR = 98.3, 97.67%, at 10 μM, respectively). Furthermore, compound 22o showed potent iNOS inhibitory activity with value of IC50 is 0.96 μM and could interfere stability and formation of the active dimeric iNOS. It's anti-inflammatory activity in vivo was assessed by AIA rat model. Furthermore, the results of metabolic stability, CYP, PK study in vivo, acute toxicity study and subacute toxicity assessment indicated this compound had good drug-like properties for treatment.
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Affiliation(s)
- Liu Zeng Chen
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China
| | - Hai Yang Shu
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China
| | - Jing Wu
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China
| | - Yun Long Yu
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China
| | - Duo Ma
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China
| | - Xin Huang
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China
| | - Ming Ming Liu
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China
| | - Xin Hua Liu
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China.
| | - Jing Bo Shi
- School of Pharmacy, Anhui Medical University, Hefei, 230032, PR China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, PR China.
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20
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Arevalo R, López R, Falvello LR, Riera L, Perez J. Building C(sp 3 ) Molecular Complexity on 2,2'-Bipyridine and 1,10-Phenanthroline in Rhenium Tricarbonyl Complexes. Chemistry 2021; 27:379-389. [PMID: 33001533 DOI: 10.1002/chem.202003814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/12/2020] [Indexed: 12/21/2022]
Abstract
The reactions of [Re(N-N)(CO)3 (PMe3 )]OTf (N-N=2,2'-bipyridine, bipy; 1,10-phenanthroline, phen) compounds with tBuLi and with LiHBEt3 have been explored. Addition to the N-N chelate took place with different site-selectivity depending on both chelate and nucleophile. Thus, with tBuLi, an unprecedented addition to C5 of bipy, a regiochemistry not accessible for free bipy, was obtained, whereas coordinated phen underwent tBuLi addition to C2 and C4. Remarkably, when LiHBEt3 reacted with [Re(bipy)(CO)3 (PMe3 )]OTf, hydride addition to the 4 and 6 positions of bipy triggered an intermolecular cyclodimerization of two dearomatized pyridyl rings. In contrast, hydride addition to the phen analog resulted in partial reduction of one pyridine ring. The resulting neutral ReI products showed a varied reactivity with HOTf and with MeOTf to yield cationic complexes. These strategies rendered access to ReI complexes containing bipy- and phen-derived chelates with several C(sp3 ) centers.
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Affiliation(s)
- Rebeca Arevalo
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, Julián Clavería, 8, 33006, Oviedo, Spain.,Current address: Department of Chemistry and Chemical Biology, University of California, Merced, 5200 N. Lake Road, 95343, Merced, CA, USA
| | - Ramón López
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería, 8, 33006, Oviedo, Spain
| | - Larry R Falvello
- Departamento de Química Inorgánica, Instituto de Ciencia de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC, 50009, Zaragoza, Spain
| | - Lucía Riera
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, Julián Clavería, 8, 33006, Oviedo, Spain.,Centro de Investigación en Nanomateriales y Nanotecnología-CINN, CSIC- Universidad de Oviedo-Principado de Asturias, Avda. de la Vega 4-6, 33940, El Entrego, Spain
| | - Julio Perez
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, Julián Clavería, 8, 33006, Oviedo, Spain.,Centro de Investigación en Nanomateriales y Nanotecnología-CINN, CSIC- Universidad de Oviedo-Principado de Asturias, Avda. de la Vega 4-6, 33940, El Entrego, Spain
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21
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22
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Mostinski Y, Heynen GJJE, López-Alberca MP, Paul J, Miksche S, Radetzki S, Schaller D, Shanina E, Seyffarth C, Kolomeets Y, Ziebart N, de Schryver J, Oestreich S, Neuenschwander M, Roske Y, Heinemann U, Rademacher C, Volkamer A, von Kries JP, Birchmeier W, Nazaré M. From Pyrazolones to Azaindoles: Evolution of Active-Site SHP2 Inhibitors Based on Scaffold Hopping and Bioisosteric Replacement. J Med Chem 2020; 63:14780-14804. [PMID: 33210922 DOI: 10.1021/acs.jmedchem.0c01265] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The tyrosine phosphatase SHP2 controls the activity of pivotal signaling pathways, including MAPK, JAK-STAT, and PI3K-Akt. Aberrant SHP2 activity leads to uncontrolled cell proliferation, tumorigenesis, and metastasis. SHP2 signaling was recently linked to drug resistance against cancer medications such as MEK and BRAF inhibitors. In this work, we present the development of a novel class of azaindole SHP2 inhibitors. We applied scaffold hopping and bioisosteric replacement concepts to eliminate unwanted structural motifs and to improve the inhibitor characteristics of the previously reported pyrazolone SHP2 inhibitors. The most potent azaindole 45 inhibits SHP2 with an IC50 = 0.031 μM in an enzymatic assay and with an IC50 = 2.6 μM in human pancreas cells (HPAF-II). Evaluation in a series of cellular assays for metastasis and drug resistance demonstrated efficient SHP2 blockade. Finally, 45 inhibited proliferation of two cancer cell lines that are resistant to cancer drugs and diminished ERK signaling.
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Affiliation(s)
- Yelena Mostinski
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Guus J J E Heynen
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Maria Pascual López-Alberca
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Jerome Paul
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sandra Miksche
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Silke Radetzki
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - David Schaller
- Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Elena Shanina
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg, 1, 14476 Potsdam, Germany
| | - Carola Seyffarth
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Yuliya Kolomeets
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Nandor Ziebart
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Judith de Schryver
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sylvia Oestreich
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christoph Rademacher
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg, 1, 14476 Potsdam, Germany
| | - Andrea Volkamer
- Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Walter Birchmeier
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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23
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Jiang B, Guo B, Cui J, Dong Y, Cui L, Zhang L, Yang Q, Yang X. New lead discovery of insect growth regulators based on the scaffold hopping strategy. Bioorg Med Chem Lett 2020; 30:127500. [PMID: 32822762 DOI: 10.1016/j.bmcl.2020.127500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/27/2020] [Accepted: 08/15/2020] [Indexed: 11/18/2022]
Abstract
Insect growth regulators (IGRs), which can interrupt or inhibit pest life cycles, are low-toxicity pesticides widely used in integrated pest management (IPM). Ecdysone analogues and chitinase inhibitors are familiar IGRs that have attracted considerable attention because of their unique modes of action and low toxicity to non-target organisms. To find new and highly effective candidate IGRs with novel mechanisms, D-08 (N-(4-(tert-butyl)phenyl)-2-phenyl-2,4,5,6,7,8-hexahydrocyclohepta[c]pyrazole-5-carboxamide) was chosen as a lead compound, and a series of novel heptacyclic pyrazolamide derivatives were designed and synthesized using the scaffold hopping strategy. The bioassay showed that III-27 (N-(2-methylphenethyl)-1-phenyl-1,4,5,6,7,8-hexahydrocyclohepta[c]pyrazole-5-carboxamide) had excellent activity against Plutella xylostella. Protein verification and molecular docking indicated that III-27 could act on both the ecdysone receptor (EcR) and Ostrinia furnacalis chitinase (Of ChtI) and is a promising new lead IGRs. The interaction mechanism of III-27 with EcR and Of ChtI was then studied by molecular docking. These results provide important guidance for the study of new dual-target IGRs.
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Affiliation(s)
- Biaobiao Jiang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Bingbo Guo
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Jialin Cui
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yawen Dong
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Li Cui
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Li Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China.
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinling Yang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China.
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24
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Douguet D, Payan F. sensaas: Shape-based Alignment by Registration of Colored Point-based Surfaces. Mol Inform 2020; 39:e2000081. [PMID: 32573978 PMCID: PMC7507133 DOI: 10.1002/minf.202000081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
Abstract
sensaas is a tool developed for aligning and comparing molecular shapes and sub-shapes. Alignment is obtained by registration of 3D point-based representations of the van der Waals surface. The method uses local properties of the shape to identify the correspondence relationships between two point clouds containing up to several thousand colored (labeled) points. Our rigid-body superimposition method follows a two-stage approach. An initial alignment is obtained by matching pose-invariant local 3D descriptors, called FPFH, of the input point clouds. This stage provides a global superimposition of the molecular surfaces, without any knowledge of their initial pose in 3D space. This alignment is then refined by optimizing the matching of colored points. In our study, each point is colored according to its closest atom, which itself belongs to a user defined physico-chemical class. Finally, sensaas provides an alignment and evaluates the molecular similarity by using Tversky coefficients. To assess the efficiency of this approach, we tested its ability to reproduce the superimposition of X-ray structures of the benchmarking AstraZeneca (AZ) data set and, compared its results with those generated by the two shape-alignment approaches shaep and shafts. We also illustrated submatching properties of our method with respect to few substructures and bioisosteric fragments. The code is available upon request from the authors (demo version at https://chemoinfo.ipmc.cnrs.fr/SENSAAS).
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Affiliation(s)
- Dominique Douguet
- Université Côte d'AzurInserm, CNRS, IPMC660 route des lucioles06560ValbonneFrance
| | - Frédéric Payan
- Université Côte d'AzurCNRS, I3S, Les Algorithmes - Euclide B2000 route des lucioles06900Sophia AntipolisFrance
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25
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Discovery of novel NF-кB inhibitor based on scaffold hopping: 1,4,5,6,7,8-hexahydropyrido[4,3-d]pyrimidine. Eur J Med Chem 2020; 198:112366. [PMID: 32371335 DOI: 10.1016/j.ejmech.2020.112366] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/19/2020] [Accepted: 04/19/2020] [Indexed: 12/24/2022]
Abstract
NF-κB is a key signaling pathway molecule linking hepatoma and chronic inflammation. Inhibition of NF-κB activation can alleviate inflammation, and promote hepatoma cell apoptosis. In this study, a series of fluoro-substituted 1,4,5,6,7,8-hexahydropyrido[4,3-d]pyrimidines (PPMs, 31-57) were synthesized from 3,5-bis(arylidene)-4-piperidones (BAPs, 4-30) based on scaffold hopping. We successfully discovered the most potent 43 substituted by electron-withdrawing substitutes (3-F and 4-CF3) exhibited less toxicity and higher anti-inflammatory activity. Preliminary mechanistic studies revealed that 43 induced dose-dependent cell apoptosis at cell and protein level, while inhibited NF-κB activation by suppressing LPS-induced phosphorylation levels of p65, IκBα and Akt, and by indirectly suppressing MAPK signaling, and by inhibiting the nuclear translocation of NF-κB induced by TNF-α or LPS. Docking analysis verified simulated 43 could reasonably bind to the active site of Bcl-2, p65 and p38 proteins. This compound, as a novel NF-κB inhibitor, also demonstrated both anti-inflammatory and anti-hepatoma activities, warranting its further development as a potential multifunctional agent for the clinical treatment of liver cancers and inflammatory diseases.
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26
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Hellyer SD, Aggarwal S, Chen ANY, Leach K, Lapinsky DJ, Gregory KJ. Development of Clickable Photoaffinity Ligands for Metabotropic Glutamate Receptor 2 Based on Two Positive Allosteric Modulator Chemotypes. ACS Chem Neurosci 2020; 11:1597-1609. [PMID: 32396330 DOI: 10.1021/acschemneuro.0c00009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The metabotropic glutamate receptor 2 (mGlu2) is a transmembrane-spanning class C G protein-coupled receptor that is an attractive therapeutic target for multiple psychiatric and neurological disorders. A key challenge has been deciphering the contribution of mGlu2 relative to other closely related mGlu receptors in mediating different physiological responses, which could be achieved through the utilization of subtype selective pharmacological tools. In this respect, allosteric modulators that recognize ligand-binding sites distinct from the endogenous neurotransmitter glutamate offer the promise of higher receptor-subtype selectivity. We hypothesized that mGlu2-selective positive allosteric modulators could be derivatized to generate bifunctional pharmacological tools. Here we developed clickable photoaffinity probes for mGlu2 based on two different positive allosteric modulator scaffolds that retained similar pharmacological activity to parent compounds. We demonstrate successful probe-dependent incorporation of a commercially available clickable fluorophore using bioorthogonal conjugation. Importantly, we also show the limitations of using these probes to assess in situ fluorescence of mGlu2 in intact cells where significant nonspecific membrane binding is evident.
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Affiliation(s)
- Shane D. Hellyer
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - Shaili Aggarwal
- Division of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Amy N. Y. Chen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
| | - David J. Lapinsky
- Division of Pharmaceutical Sciences, School of Pharmacy, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Karen J. Gregory
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia
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Xue L, Deng D, Zheng S, Tang M, Yang Z, Pei H, Chen Y, Yang T, Liu K, Ye H, Chen L. Design, synthesis and discovery of 2(1H)-quinolone derivatives for the treatment of pulmonary fibrosis through inhibition of TGF-β/smad dependent and independent pathway. Eur J Med Chem 2020; 197:112259. [PMID: 32334267 DOI: 10.1016/j.ejmech.2020.112259] [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: 01/21/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 02/05/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, life-threatening and interstitial lung disease with the median survival of only 3-5 years. However, due to the unclear etiology and problems in accurate diagnosis, up to now only two drugs were approved by FDA for the treatment of IPF and their outcome responses are limited. Numerous studies have shown that TGF-β is the most important cytokine in the development of pulmonary fibrosis and plays a role through its downstream signaling molecule TGF-binding receptor Smads protein. In this paper, compounds bearing 2(1H)-quinolone scaffold were designed and their anti-fibrosis effects were evaluated. Of these compounds, 20f was identified as the most active one and could inhibit TGF-β-induced collagen deposition of NRK-49F cells and mouse fibroblasts migration with comparable activity and lower cytotoxicity than nintedanib in vitro. Further mechanism studies indicated that 20f reduced the expression of fibrogenic phenotypic protein α-SMA and collagen Ⅰ by inhibiting the TGF-β/Smad dependent pathways and ERK1/2 and p38 pathways. Moreover, compared with the nintedanib, 20f (100 mg/kg/day, p.o) more effectively alleviated collagen deposition in lung tissue and delayed the destruction of lung tissue structure both in bleomycin-induced prevention and treatment mice pulmonary fibrosis models. The immunohistochemical experiments further showed that 20f could block the expression level of phosphorylated Smad3 in the lung tissue cells, which resulted in its anti-fibrosis effects in vivo. In addition, 20f demonstrated good bioavailability (F = 41.55% vs 12%, compare with nintedanib) and an appropriate elimination half-life (T1/2 = 3.5 h), suggesting that 20f may be a potential drug candidate for the treatment of pulmonary fibrosis.
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Affiliation(s)
- Linlin Xue
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Dexin Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Shoujun Zheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Minghai Tang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Zhuang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Heying Pei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Yong Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Kongjun Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China
| | - Haoyu Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China.
| | - Lijuan Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, PR China.
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28
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Kawano T, Sugawara A, Ohashi T, Ogawa S, Matsumoto N, Nakanishi-Matsui M, Tamura S. Synthesis and Biological Evaluation of New Curcumin Analogs Inhibiting Osteoclastogenesis. HETEROCYCLES 2020. [DOI: 10.3987/com-20-14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Negami T, Araki M, Okuno Y, Terada T. Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs. Sci Rep 2019; 9:16586. [PMID: 31719645 PMCID: PMC6851376 DOI: 10.1038/s41598-019-53120-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/28/2019] [Indexed: 11/11/2022] Open
Abstract
The human ether-a-go-go-related gene (hERG) encodes a voltage-gated potassium channel that plays an essential role in the repolarization of action potentials in cardiac muscle. However, various drugs can block the ion current by binding to the hERG channel, resulting in potentially lethal cardiac arrhythmia. Accordingly, in silico studies are necessary to clarify the mechanisms of how these drugs bind to the hERG channel. Here, we used the experimental structure of the hERG channel, determined by cryo-electron microscopy, to perform docking simulations to predict the complex structures that occur between the hERG channel and structurally diverse drugs. The absolute binding free energies for the models were calculated using the MP-CAFEE method; calculated values were well correlated with experimental ones. By applying the regression equation obtained here, the affinity of a drug for the hERG channel can be accurately predicted from the calculated value of the absolute binding free energy.
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Affiliation(s)
- Tatsuki Negami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yasushi Okuno
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Tohru Terada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Interfaculty Initiative in Information Studies, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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30
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Dos Santos MB, Bertholin Anselmo D, de Oliveira JG, Jardim-Perassi BV, Alves Monteiro D, Silva G, Gomes E, Lucia Fachin A, Marins M, de Campos Zuccari DAP, Octavio Regasini L. Antiproliferative activity and p53 upregulation effects of chalcones on human breast cancer cells. J Enzyme Inhib Med Chem 2019; 34:1093-1099. [PMID: 31117836 PMCID: PMC6534249 DOI: 10.1080/14756366.2019.1615485] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chalcones are valuable structures for drug discovery due to their broad bioactivity spectrum. In this study, we evaluated 20 synthetic chalcones against estrogen-receptor-positive breast cancer cells (MCF-7 line) and triple-negative breast cancer (TNBC) cells (MDA-MB-231 line). Antiproliferative screening by MTT assay resulted in two most active compounds: 2-fluoro-4’-aminochalcone (11) and 3-pyridyl-4’-aminochalcone (17). Their IC50 values ranged from 13.2 to 34.7 µM against both cell lines. Selected chalcones are weak basic compounds and maintained their antiproliferative activity under acidosis conditions (pH 6.7), indicating their resistance to ion-trapping effect. The mode of breast cancer cells death was investigated and chalcones 11 and 17 were able to induce apoptosis rather than necrosis in both lines. Antiproliferative target investigations with MCF-7 cells suggested 11 and 17 upregulated p53 protein expression and did not affect Sp1 protein expression. Future studies on chalcones 11 and 17 can define their in vivo therapeutic potential.
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Affiliation(s)
- Mariana Bastos Dos Santos
- a Department of Chemistry and Environmental Chemistry, Institute of Biosciences, Humanities and Exact Sciences (IBILCE) , São Paulo State University (UNESP) , São Paulo , Brazil
| | - Daiane Bertholin Anselmo
- a Department of Chemistry and Environmental Chemistry, Institute of Biosciences, Humanities and Exact Sciences (IBILCE) , São Paulo State University (UNESP) , São Paulo , Brazil
| | | | - Bruna V Jardim-Perassi
- b Department of Molecular Biology , Medicine College of São José do Rio Preto (FAMERP) , São Paulo , Brazil
| | - Diego Alves Monteiro
- c Department of Biology, Institute of Biosciences, Humanities and Exact Sciences (IBILCE) , São Paulo State University (UNESP) , São Paulo , Brazil
| | - Gabriel Silva
- d Biotechnology Unit , University of Ribeirão Preto (UNAERP) , São Paulo , Brazil
| | - Eleni Gomes
- c Department of Biology, Institute of Biosciences, Humanities and Exact Sciences (IBILCE) , São Paulo State University (UNESP) , São Paulo , Brazil
| | - Ana Lucia Fachin
- d Biotechnology Unit , University of Ribeirão Preto (UNAERP) , São Paulo , Brazil
| | - Mozart Marins
- d Biotechnology Unit , University of Ribeirão Preto (UNAERP) , São Paulo , Brazil
| | | | - Luis Octavio Regasini
- a Department of Chemistry and Environmental Chemistry, Institute of Biosciences, Humanities and Exact Sciences (IBILCE) , São Paulo State University (UNESP) , São Paulo , Brazil
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31
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Wang X, Ji C, Zhang H, Shan Y, Ren Y, Hu Y, Shi L, Guo L, Zhu W, Xia Y, Liu B, Rong Z, Wu B, Ming Z, Ren X, Song J, Yang J, Zhang Y. Identification of a small-molecule compound that inhibits homodimerization of oncogenic NAC1 protein and sensitizes cancer cells to anticancer agents. J Biol Chem 2019; 294:10006-10017. [PMID: 31101655 DOI: 10.1074/jbc.ra119.007664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/09/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleus accumbens-associated protein-1 (NAC1) is a transcriptional repressor encoded by the NACC1 gene, which is amplified and overexpressed in various human cancers and plays critical roles in tumor development, progression, and drug resistance. NAC1 has therefore been explored as a potential therapeutic target for managing malignant tumors. However, effective approaches for effective targeting of this nuclear protein remain elusive. In this study, we identified a core unit consisting of Met7 and Leu90 in NAC1's N-terminal domain (amino acids 1-130), which is critical for its homodimerization and stability. Furthermore, using a combination of computational analysis of the NAC1 dimerization interface and high-throughput screening (HTS) for small molecules that inhibit NAC1 homodimerization, we identified a compound (NIC3) that selectively binds to the conserved Leu-90 of NAC1 and prevents its homodimerization, leading to proteasomal NAC1 degradation. Moreover, we demonstrate that NIC3-mediated down-regulation of NAC1 protein sensitizes drug-resistant tumor cells to conventional chemotherapy and enhances the antimetastatic effect of the antiangiogenic agent bevacizumab both in vitro and in vivo These results suggest that small-molecule inhibitors of NAC1 homodimerization may effectively sensitize cancer cells to some anticancer agents and that NAC1 homodimerization could be further explored as a potential therapeutic target in the development of antineoplastic agents.
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Affiliation(s)
- XiaoHui Wang
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - Cheng Ji
- Department of Respiratory Medicine, First Affiliated Hospital, Soochow University, 215000 Suzhou, Jiangsu, China
| | - HongHan Zhang
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - Yu Shan
- Institute of Botany, Jiangsu Province and Chinese Academy of Science, 210014 Nanjing, Jiangsu, China
| | - YiJie Ren
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - YanWei Hu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - LiangRong Shi
- Radiological Intervention Center, Department of Radiology, Xiangya Hospital, Central South University, 410013 Changsha, Hunan, China
| | - LingChuan Guo
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - WeiDong Zhu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - YuJuan Xia
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - BeiJia Liu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - ZiYun Rong
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - BiLian Wu
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - ZhiJun Ming
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China
| | - XingCong Ren
- Department of Cancer Biology and Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40506
| | - JianXun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas 77843, and
| | - JinMing Yang
- Department of Cancer Biology and Toxicology, Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky 40506
| | - Yi Zhang
- From the Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, 215123 Suzhou, Jiangsu, China,
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Structural modification of indomethacin toward selective inhibition of COX-2 with a significant increase in van der Waals contributions. Bioorg Med Chem 2019; 27:1789-1794. [DOI: 10.1016/j.bmc.2019.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 11/24/2022]
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33
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Shi JB, Chen LZ, Wang BS, Huang X, Jiao MM, Liu MM, Tang WJ, Liu XH. Novel Pyrazolo[4,3-d]pyrimidine as Potent and Orally Active Inducible Nitric Oxide Synthase (iNOS) Dimerization Inhibitor with Efficacy in Rheumatoid Arthritis Mouse Model. J Med Chem 2019; 62:4013-4031. [DOI: 10.1021/acs.jmedchem.9b00039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jing Bo Shi
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
| | - Liu Zeng Chen
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
| | - Bao Shi Wang
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
| | - Xin Huang
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
| | - Ming Ming Jiao
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
| | - Ming Ming Liu
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
| | - Wen Jian Tang
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
| | - Xin Hua Liu
- School of Pharmacy, Anhui Medical University, Hefei 230032, P. R. China
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Abstract
INTRODUCTION The success of binding site comparisons in drug discovery is based on the recognized fact that many different proteins have similar binding sites. Indeed, binding site comparisons have found many uses in drug development and have the potential to dramatically cut the cost and shorten the time necessary for the development of new drugs. Areas covered: The authors review recent methods for comparing protein binding sites and their use in drug repurposing and polypharmacology. They examine emerging fields including the use of binding site comparisons in precision medicine, the prediction of structured water molecules, the search for targets of natural compounds, and their application in the development of protein-based drugs by loop modeling and for comparison of RNA binding sites. Expert opinion: Binding site comparisons have produced many interesting results in drug development, but relatively little work has been done on protein-protein interaction sites, which are particularly relevant in view of the success of biological drugs. Growth of protein loop modeling for modulating biological drugs is anticipated. The fusion of currently distinct methods for the comparison of RNA and protein binding sites into a single comprehensive approach could allow the search for new selective ribosomal antibiotics and initiate pharmaceutical research into other nucleoproteins.
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Affiliation(s)
- Janez Konc
- a Theory Department , National Institute of Chemistry , Ljubljana , Slovenia.,b Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia.,c Faculty of Mathematics , Natural Sciences and Information Technologies, University of Primorska , Koper , Slovenia.,d Faculty of Chemistry and Chemical Technology , University of Maribor , Maribor , Slovenia
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35
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Xing H, Houston SD, Chen X, Ghassabian S, Fahrenhorst-Jones T, Kuo A, Murray CEP, Conn KA, Jaeschke KN, Jin DY, Pasay C, Bernhardt PV, Burns JM, Tsanaktsidis J, Savage GP, Boyle GM, De Voss JJ, McCarthy J, Walter GH, Burne THJ, Smith MT, Tie JK, Williams CM. Cyclooctatetraene: A Bioactive Cubane Paradigm Complement. Chemistry 2019; 25:2729-2734. [PMID: 30681236 PMCID: PMC6436534 DOI: 10.1002/chem.201806277] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/14/2022]
Abstract
Cubane was recently validated as a phenyl ring (bio)isostere, but highly strained caged carbocyclic systems lack π character, which is often critical for mediating key biological interactions. This electronic property restriction associated with cubane has been addressed herein with cyclooctatetraene (COT), using known pharmaceutical and agrochemical compounds as templates. COT either outperformed or matched cubane in multiple cases suggesting that versatile complementarity exists between the two systems for enhanced bioactive molecule discovery.
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Affiliation(s)
- Hui Xing
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD, Australia
| | - Sevan D Houston
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD, Australia
| | - Xuejie Chen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sussan Ghassabian
- Centre for Integrated Preclinical Drug Development, University of Queensland (UQ), Australia
| | - Tyler Fahrenhorst-Jones
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD, Australia
| | - Andy Kuo
- Centre for Integrated Preclinical Drug Development, University of Queensland (UQ), Australia
| | | | - Kyna-Anne Conn
- Queensland Brain Institute, University of Queensland (UQ), Australia
| | - Kara N Jaeschke
- Queensland Brain Institute, University of Queensland (UQ), Australia
| | - Da-Yun Jin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Cielo Pasay
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, QLD, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD, Australia
| | - Jed M Burns
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD, Australia
| | - John Tsanaktsidis
- CISRO Manufacturing, Ian Wark Laboratory, Melbourne, 3168, Victoria (VIC, Australia
| | - G Paul Savage
- CISRO Manufacturing, Ian Wark Laboratory, Melbourne, 3168, Victoria (VIC, Australia
| | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, QLD, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD, Australia
| | - James McCarthy
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, QLD, Australia
| | - Gimme H Walter
- School of Biological Sciences, University of Queensland (UQ), Australia
| | - Thomas H J Burne
- Queensland Brain Institute, University of Queensland (UQ), Australia
| | - Maree T Smith
- Centre for Integrated Preclinical Drug Development, University of Queensland (UQ), Australia
| | - Jian-Ke Tie
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland (UQ), Brisbane, 4072, Queensland (QLD, Australia
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36
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Baumeister S, Schepmann D, Wünsch B. Synthesis and receptor binding of thiophene bioisosteres of potent GluN2B ligands with a benzo[7]annulene-scaffold. MEDCHEMCOMM 2019; 10:315-325. [PMID: 30881618 DOI: 10.1039/c8md00545a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/04/2019] [Indexed: 11/21/2022]
Abstract
The involvement of NMDA receptors containing the GluN2B subunit in neurodegenerative disorders including Alzheimer's and Parkinson's disease renders this NMDA receptor subtype an interesting pharmacological target. The aim of this study was the bioisosteric replacement of benzene, methoxybenzene and aniline moieties of known potent GluN2B selective NMDA receptor antagonists by a thiophene ring. In a nine-step synthesis starting from commercially available propionic acid 9 the thiophene derivative 7a was obtained as a bioisostere of the potent GluN2B ligands cis-3 and trans-3. [7]Annuleno[b]thiophene 8a without a benzylic OH moiety was prepared in a six-step synthesis starting from carboxylic acid 18. 8a represents a bioisostere of potent GluN2B ligands 4 and 5. [7]Annulenothiophene 8a without a benzylic OH moiety reveals approx. 8-fold higher GluN2B affinity (K i = 26 nM) than the analogous thiophene derivative 7a with a benzylic OH moiety (K i = 204 nM). Both thiophene bioisosteres show a slight preference for GluN2B receptors over both σ receptors. The data indicate that the bioisosteric replacement of benzene or substituted benzene rings by a thiophene ring is well tolerated by the NMDA receptor. Furthermore, the benzylic OH moiety seems not to be essential for high GluN2B affinity.
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Affiliation(s)
- Sören Baumeister
- Institut für Pharmazeutische und Medizinische Chemie der Universität Münster , Corrensstraße 48 , D-48149 Münster , Germany . ; ; Tel: +49 251 83 33311
| | - Dirk Schepmann
- Institut für Pharmazeutische und Medizinische Chemie der Universität Münster , Corrensstraße 48 , D-48149 Münster , Germany . ; ; Tel: +49 251 83 33311
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie der Universität Münster , Corrensstraße 48 , D-48149 Münster , Germany . ; ; Tel: +49 251 83 33311.,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM) , Westfälische Wilhelms-Universität Münster , Germany
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Araki M, Iwata H, Ma B, Fujita A, Terayama K, Sagae Y, Ono F, Tsuda K, Kamiya N, Okuno Y. Improving the Accuracy of Protein-Ligand Binding Mode Prediction Using a Molecular Dynamics-Based Pocket Generation Approach. J Comput Chem 2018; 39:2679-2689. [DOI: 10.1002/jcc.25715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Mitsugu Araki
- Graduate School of Medicine; Kyoto University; 53 Shogoin-Kawaharacho, Sakyo-ku Kyoto 606-8507 Japan
- RIKEN Advanced Institute for Computational Sciences; 7-1-26 Minatojima-Minamimachi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Hiroaki Iwata
- Graduate School of Medicine; Kyoto University; 53 Shogoin-Kawaharacho, Sakyo-ku Kyoto 606-8507 Japan
- Research and Development Group for In Silico Drug Discovery, Pro-Cluster Kobe; Foundation for Biomedical Research and Innovation (FBRI); 6-3-5, Minatojima-Minamimachi Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Biao Ma
- Research and Development Group for In Silico Drug Discovery, Pro-Cluster Kobe; Foundation for Biomedical Research and Innovation (FBRI); 6-3-5, Minatojima-Minamimachi Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Atsuto Fujita
- Research and Development Group for In Silico Drug Discovery, Pro-Cluster Kobe; Foundation for Biomedical Research and Innovation (FBRI); 6-3-5, Minatojima-Minamimachi Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Kei Terayama
- Department of Computational Biology and Medical Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba 277-8561 Japan
| | - Yukari Sagae
- Graduate School of Medicine; Kyoto University; 53 Shogoin-Kawaharacho, Sakyo-ku Kyoto 606-8507 Japan
| | - Fumie Ono
- Graduate School of Medicine; Kyoto University; 53 Shogoin-Kawaharacho, Sakyo-ku Kyoto 606-8507 Japan
| | - Koji Tsuda
- Department of Computational Biology and Medical Sciences; Graduate School of Frontier Sciences, The University of Tokyo; Chiba 277-8561 Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies; University of Hyogo; 7-1-28 Minatojima-Minamimachi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Yasushi Okuno
- Graduate School of Medicine; Kyoto University; 53 Shogoin-Kawaharacho, Sakyo-ku Kyoto 606-8507 Japan
- RIKEN Advanced Institute for Computational Sciences; 7-1-26 Minatojima-Minamimachi, Chuo-ku Kobe Hyogo 650-0047 Japan
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38
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Elias TC, de Oliveira HCB, da Silveira NJF. MB-Isoster: A software for bioisosterism simulation. J Comput Chem 2018; 39:2481-2487. [DOI: 10.1002/jcc.25581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/01/2018] [Accepted: 08/15/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Thiago Castilho Elias
- Labroratory of Molecular Modeling and Computer Simulation - MolMod-CS; Institute of Chemical, Federal University of Alfenas - UNIFAL-MG; Street Gabriel Monteiro da Silva, 700, 37130-000 Brazil
| | - Humberto César Brandão de Oliveira
- Laboratory of Research and Development, Department of Computer Science; Federal University of Alfenas - UNIFAL-MG; Street Gabriel Monteiro da Silva, 700, 37130-000 Brazil
| | - Nelson José Freitas da Silveira
- Labroratory of Molecular Modeling and Computer Simulation - MolMod-CS; Institute of Chemical, Federal University of Alfenas - UNIFAL-MG; Street Gabriel Monteiro da Silva, 700, 37130-000 Brazil
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39
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Protein structure and computational drug discovery. Biochem Soc Trans 2018; 46:1367-1379. [DOI: 10.1042/bst20180202] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022]
Abstract
The first protein structures revealed a complex web of weak interactions stabilising the three-dimensional shape of the molecule. Small molecule ligands were then found to exploit these same weak binding events to modulate protein function or act as substrates in enzymatic reactions. As the understanding of ligand–protein binding grew, it became possible to firstly predict how and where a particular small molecule might interact with a protein, and then to identify putative ligands for a specific protein site. Computer-aided drug discovery, based on the structure of target proteins, is now a well-established technique that has produced several marketed drugs. We present here an overview of the various methodologies being used for structure-based computer-aided drug discovery and comment on possible future developments in the field.
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40
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A secondary RET mutation in the activation loop conferring resistance to vandetanib. Nat Commun 2018; 9:625. [PMID: 29434222 PMCID: PMC5809600 DOI: 10.1038/s41467-018-02994-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/08/2018] [Indexed: 01/09/2023] Open
Abstract
Resistance to vandetanib, a type I RET kinase inhibitor, developed in a patient with metastatic lung adenocarcinoma harboring a CCDC6-RET fusion that initially exhibited a response to treatment. The resistant tumor acquired a secondary mutation resulting in a serine-to-phenylalanine substitution at codon 904 in the activation loop of the RET kinase domain. The S904F mutation confers resistance to vandetanib by increasing the ATP affinity and autophosphorylation activity of RET kinase. A reduced interaction with the drug is also observed in vitro for the S904F mutant by thermal shift assay. A crystal structure of the S904F mutant reveals a small hydrophobic core around F904 likely to enhance basal kinase activity by stabilizing an active conformer. Our findings indicate that missense mutations in the activation loop of the kinase domain are able to increase kinase activity and confer drug resistance through allosteric effects. Mechanisms of acquired resistance to RET tyrosine kinase inhibitors in lung cancers are largely unknown. Here, the authors report in a lung adenocarcinoma patient harboring a CCDC6-RET mutation in the RET kinase (S904F) that results in resistance to the kinase inhibitor vandetanib by increasing the ATP affinity and autophosphorylation activity of RET kinase.
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41
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Seddon MP, Cosgrove DA, Gillet VJ. Bioisosteric Replacements Extracted from High-Quality Structures in the Protein Databank. ChemMedChem 2018; 13:607-613. [DOI: 10.1002/cmdc.201700679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/21/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew P. Seddon
- Information School; The University of Sheffield; Regent Court, 211 Portobello Sheffield S1 4DP UK
| | - David A. Cosgrove
- Chemical Innovation Centre, Discovery Sciences, IMED Biotech Unit; AstraZeneca; Alderley Park UK
- Current address: CozChemIx Limited; Macclesfield Cheshire UK
| | - Valerie J. Gillet
- Information School; The University of Sheffield; Regent Court, 211 Portobello Sheffield S1 4DP UK
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42
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Lamberth C. Agrochemical lead optimization by scaffold hopping. PEST MANAGEMENT SCIENCE 2018; 74:282-292. [PMID: 28991418 DOI: 10.1002/ps.4755] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
Scaffold hopping, the exchange of a specific portion of a potential active ingredient with another substructure with the aim of finding isofunctional molecular structures with significantly different molecular backbones, often offers the chance in lead discovery or optimization to mitigate problems related to toxicity, intellectual property, and insufficient potency or stability. Scaffold hopping tools such as isosteric ring replacement including 1,3 nitrogen shift and cyclic imine-amide isosterism, but also ring opening and ring closure approaches, functional group isosterism, reversion of functional groups, chain shortening, chain lengthening, and scaffolds delivered by natural products, have become a permanent fixture of the innovation and optimization process in crop protection research. Their appropriate use will be explained through examples of success stories in the field of agrochemistry. Analogies to, but also differences from, the main categories of scaffold hopping in medicinal drug discovery are discussed. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Clemens Lamberth
- Syngenta Crop Protection AG, Chemical Research, Stein, Switzerland
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BoBER: web interface to the base of bioisosterically exchangeable replacements. J Cheminform 2017; 9:62. [PMID: 29234984 PMCID: PMC5727005 DOI: 10.1186/s13321-017-0251-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioisosterism and scaffold hopping are key concepts in drug design and optimization, and can be defined as replacements of biologically active compound's fragments with other fragments to improve activity, reduce toxicity, change bioavailability or to diversify the scaffold space. Our web server enables fast and user-friendly searches for bioisosteric and scaffold replacements which were obtained by mining the whole Protein Data Bank. The working of the web server is presented on an existing MurF inhibitor as example. BoBER web server enables medicinal chemists to quickly search for and get new and unique ideas about possible bioisosteric or scaffold hopping replacements that could be used to improve hit or lead drug-like compounds.
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44
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Identification of novel PI3K inhibitors through a scaffold hopping strategy. Bioorg Med Chem Lett 2017; 27:4794-4799. [DOI: 10.1016/j.bmcl.2017.09.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 11/17/2022]
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45
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Brand S, Ko EJ, Viayna E, Thompson S, Spinks D, Thomas M, Sandberg L, Francisco AF, Jayawardhana S, Smith VC, Jansen C, De Rycker M, Thomas J, MacLean L, Osuna-Cabello M, Riley J, Scullion P, Stojanovski L, Simeons FRC, Epemolu O, Shishikura Y, Crouch SD, Bakshi TS, Nixon CJ, Reid IH, Hill AP, Underwood TZ, Hindley SJ, Robinson SA, Kelly JM, Fiandor JM, Wyatt PG, Marco M, Miles TJ, Read KD, Gilbert IH. Discovery and Optimization of 5-Amino-1,2,3-triazole-4-carboxamide Series against Trypanosoma cruzi. J Med Chem 2017; 60:7284-7299. [PMID: 28844141 PMCID: PMC5601362 DOI: 10.1021/acs.jmedchem.7b00463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Chagas’
disease, caused by the protozoan parasite Trypanosoma
cruzi, is the most common cause of cardiac-related
deaths in endemic regions of Latin America. There is an urgent need
for new safer treatments because current standard therapeutic options,
benznidazole and nifurtimox, have significant side effects and are
only effective in the acute phase of the infection with limited efficacy
in the chronic phase. Phenotypic high content screening against the
intracellular parasite in infected VERO cells was used to identify
a novel hit series of 5-amino-1,2,3-triazole-4-carboxamides (ATC).
Optimization of the ATC series gave improvements in potency, aqueous
solubility, and metabolic stability, which combined to give significant
improvements in oral exposure. Mitigation of a potential Ames and hERG liability ultimately led to two promising compounds, one of which demonstrated significant suppression of parasite burden in a mouse model of Chagas’ disease.
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Affiliation(s)
- Stephen Brand
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Eun Jung Ko
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Elisabet Viayna
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Stephen Thompson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Daniel Spinks
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Michael Thomas
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Lars Sandberg
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Amanda F Francisco
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT, U.K
| | - Shiromani Jayawardhana
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT, U.K
| | - Victoria C Smith
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Chimed Jansen
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Manu De Rycker
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - John Thomas
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Lorna MacLean
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Maria Osuna-Cabello
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Paul Scullion
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Laste Stojanovski
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Frederick R C Simeons
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Yoko Shishikura
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Sabrinia D Crouch
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Tania S Bakshi
- GlaxoSmithKline , 1250 South Collegeville Road, PO Box 5089, Collegeville, Pennsylvania 19426-0989, United States
| | - Christopher J Nixon
- GlaxoSmithKline , 1250 South Collegeville Road, PO Box 5089, Collegeville, Pennsylvania 19426-0989, United States
| | - Iain H Reid
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alan P Hill
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Tim Z Underwood
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sean J Hindley
- Medicines Research Centre, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sharon A Robinson
- David Jack Centre for R&D, GlaxoSmithKline , Park Road, Ware, Hertfordshire SG12 0DP, United Kingdom
| | - John M Kelly
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine , Keppel Street, London WC1E 7HT, U.K
| | - Jose M Fiandor
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Paul G Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Maria Marco
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Timothy J Miles
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Kevin D Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
| | - Ian H Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Sir James Black Centre, Dundee DD1 5EH, U.K
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46
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Maienfisch P, Edmunds AJ. Thiazole and Isothiazole Ring–Containing Compounds in Crop Protection. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.04.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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47
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Mok NY, Brown N. Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information. J Chem Inf Model 2016; 57:27-35. [PMID: 27990817 PMCID: PMC6152611 DOI: 10.1021/acs.jcim.6b00386] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Establishing
structure–activity relationships (SARs) in
hit identification during early stage drug discovery is important
in accelerating hit confirmation and expansion. We describe the development
of EnCore, a systematic molecular scaffold enumeration
protocol using single atom mutations, to enhance the application of
objective scaffold definitions and to enrich SAR information from
analysis of high-throughput screening output. A list of 43 literature
medicinal chemistry compound series, each containing a minimum of
100 compounds, published in the Journal of Medicinal Chemistry was collated to validate the protocol. Analysis using the top representative
Level 1 scaffolds this list of literature compound series demonstrated
that EnCore could mimic the scaffold exploration
conducted when establishing SAR. When EnCore was
applied to analyze an HTS library containing over 200 000 compounds,
we observed that over 70% of the molecular scaffolds matched extant
scaffolds within the library after enumeration. In particular, over
60% of the singleton scaffolds with only one representative compound
were found to have structurally related compounds after enumeration.
These results illustrate the potential of EnCore to
enrich SAR information. A case study using literature cyclooxygenase-2
inhibitors further demonstrates the advantage of EnCore application in establishing SAR from structurally related scaffolds. EnCore complements literature enumeration methods in enabling
changes to the physicochemical properties of molecular scaffolds and
structural modifications to aliphatic rings and linkers. The enumerated
scaffold clusters generated would constitute a comprehensive collection
of scaffolds for scaffold morphing and hopping.
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Affiliation(s)
- N Yi Mok
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research , London, SM2 5NG, U.K
| | - Nathan Brown
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research , London, SM2 5NG, U.K
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48
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Synthesis and fungicidal activity of some novel thiazole Schiff bases derived from benzo[d][1,3]dioxole. Chem Res Chin Univ 2016. [DOI: 10.1007/s40242-016-5284-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Gawehn E, Hiss JA, Schneider G. Deep Learning in Drug Discovery. Mol Inform 2015; 35:3-14. [PMID: 27491648 DOI: 10.1002/minf.201501008] [Citation(s) in RCA: 309] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/01/2015] [Indexed: 12/18/2022]
Abstract
Artificial neural networks had their first heyday in molecular informatics and drug discovery approximately two decades ago. Currently, we are witnessing renewed interest in adapting advanced neural network architectures for pharmaceutical research by borrowing from the field of "deep learning". Compared with some of the other life sciences, their application in drug discovery is still limited. Here, we provide an overview of this emerging field of molecular informatics, present the basic concepts of prominent deep learning methods and offer motivation to explore these techniques for their usefulness in computer-assisted drug discovery and design. We specifically emphasize deep neural networks, restricted Boltzmann machine networks and convolutional networks.
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Affiliation(s)
- Erik Gawehn
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland, Fax: +41 44 633 13 79, Tel: +41 44 633 74 38
| | - Jan A Hiss
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland, Fax: +41 44 633 13 79, Tel: +41 44 633 74 38
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland, Fax: +41 44 633 13 79, Tel: +41 44 633 74 38.
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50
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Lolli M, Narramore S, Fishwick CW, Pors K. Refining the chemical toolbox to be fit for educational and practical purpose for drug discovery in the 21st Century. Drug Discov Today 2015; 20:1018-26. [DOI: 10.1016/j.drudis.2015.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/08/2015] [Accepted: 04/29/2015] [Indexed: 12/16/2022]
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