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Liu HX, Yao WY, Cui G, Zhou J, Yan H, Guo H, Wang YW, Zhang Y. Design, synthesis, and antibacterial activity of pleuromutilin derivatives. Chem Biol Drug Des 2024; 103:e14554. [PMID: 38806405 DOI: 10.1111/cbdd.14554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/25/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
This paper reports the design, synthesis, and antibacterial activity study of pleuromutilin derivatives with 2-methyl-4-nitroaniline and 2-methoxy-4-nitroaniline side chains at the C22 position. The structures of the new compounds were characterized by 1H-NMR, 13C-NMR and HRMS. The inhibitory activity of the compounds against MSSA, pyogeniccoccus, streptococcus, and MRSA strains was determined using the micro broth dilution method. The results showed that the compounds exhibited certain activity against Gram-positive bacteria, among which compounds A8a, A8b, A8c, A8d, and A7 demonstrated superior antibacterial activity against MSSA, MRSA, and pyogeniccoccus compared to tiamulin, although the derivatives showed lower antibacterial activity against streptococcus compared to the control drug. Based on the favorable in vitro activity of A8c, the time-kill kinetics against MRSA were evaluated, revealing that compound A8c could inhibit bacterial proliferation in a concentration-dependent manner.
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Affiliation(s)
- Hui-Xian Liu
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Wen-Yu Yao
- Jinan University College of Pharmacy, Guangzhou, PR China
| | - Ge Cui
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
| | - Jing Zhou
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Hao Yan
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Hui Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Yu-Wei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, PR China
| | - Yue Zhang
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang, PR China
- Hebei Research Center of Pharmaceutical and Chemical Engineering, Shijiazhuang, PR China
- Hebei Province Key Laboratory of Molecular Chemistry for Drug, Shijiazhuang, PR China
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2
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Liu Y, Zhou Q, Huo Y, Sun X, Hu J. Recent advances in developing modified C14 side chain pleuromutilins as novel antibacterial agents. Eur J Med Chem 2024; 269:116313. [PMID: 38503168 DOI: 10.1016/j.ejmech.2024.116313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Owing to the increasing resistance to most existing antimicrobial drugs, research has shifted towards developing novel antimicrobial agents with mechanisms of action distinct from those of current clinical options. Pleuromutilins are antibiotics known for their distinct mechanism of action, inhibiting bacterial protein synthesis by binding to the peptidyl transferase center of the ribosome. Recent studies have revealed that pleuromutilin derivatives can disrupt bacterial cell membranes, thereby enhancing antibacterial efficacy. Both marketed pleuromutilin derivatives and those in clinical trials have been developed by structurally modifying the pleuromutilin C14 side chain to improve their antimicrobial activity. Therefore, this review aims to review advancement in the chemical structural characteristics, antibacterial activities, and structure-activity relationship studies of pleuromutilins, specifically focusing on modifications made to the C14 side chain in recent years. These findings provide a valuable reference for future research and development of pleuromutilins.
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Affiliation(s)
- Yue Liu
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Qinjiang Zhou
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Yiwen Huo
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Xiujuan Sun
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Jinxing Hu
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China.
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3
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Lin C, Feng Y, Xie X, Zhang H, Wu J, Zhu Y, Yu J, Feng J, Su W, Lai S, Zhang A. Antimicrobial resistance characteristics and phylogenetic relationships of pleuromutilin-resistant Enterococcus isolates from different environmental samples along a laying hen production chain. J Environ Sci (China) 2024; 137:195-205. [PMID: 37980008 DOI: 10.1016/j.jes.2023.01.012] [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: 10/17/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 11/20/2023]
Abstract
Antimicrobial resistance in the laying hen production industry has become a serious public health problem. The antimicrobial resistance and phylogenetic relationships of the common conditional pathogen Enterococcus along the laying hen production chain have not been systematically clarified. 105 Enterococcus isolates were obtained from 115 environmental samples (air, dust, feces, flies, sewage, and soil) collected along the laying hen production chain (breeding chicken, chick, young chicken, and commercial laying hen). These Enterococcus isolates exhibited resistance to some clinically relevant antibiotics, such as tetracycline (92.4%), streptomycin (92.4%), and erythromycin (91.4%), and all strains had multidrug resistance phenotypes. Whole genome sequencing characterized 29 acquired antibiotic resistance genes (ARGs) that conferred resistance to 11 classes of antibiotics in 51 pleuromutilin-resistant Enterococcus isolates, and lsa(E), which mediates resistance to pleuromutilins, always co-occurred with lnu(B). Alignments with the Mobile Genetic Elements database identified four transposons (Tn554, Tn558, Tn6261, and Tn6674) with several ARGs (erm(A), ant(9)-la, fex(A), and optrA) that mediated resistance to many clinically important antibiotics. Moreover, we identified two new transposons that carried ARGs in the Tn554 family designated as Tn7508 and Tn7492. A complementary approach based on conventional multi-locus sequence typing and whole genome single nucleotide polymorphism analysis showed that phylogenetically related pleuromutilin-resistant Enterococcus isolates were widely distributed in various environments on different production farms. Our results indicate that environmental contamination by antimicrobial-resistant Enterococcus requires greater attention, and they highlight the risk of pleuromutilin-resistant Enterococcus and ARGs disseminating along the laying hen production chain, thereby warranting effective disinfection.
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Affiliation(s)
- Cong Lin
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuxuan Feng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xianjun Xie
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haoyu Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jie Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yixiao Zhu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jing Yu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jingyi Feng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wen Su
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shanming Lai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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4
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Liu Q, Zhang H, Yi Y, Wang P, Pu W, Wang S, Shang R. Synthesis and evaluation of novel pleuromutilin derivatives targeting the 50S ribosomal subunit for antibacterial ability. Eur J Med Chem 2023; 262:115882. [PMID: 37879170 DOI: 10.1016/j.ejmech.2023.115882] [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: 08/30/2023] [Revised: 09/23/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Multidrug-resistant bacteria, particularly methicillin-resistant Staphylococcus aureus, have become a major global public health concern. Therefore, developing new antibiotics that do not possess cross-resistance for the currently available antibiotics is critical. Herein, we synthesized a novel class of pleuromutilin derivatives containing substituted triazine with improved antibacterial activity. Among these derivatives, 6d, which contains 4-dimethylamino-1,3,5-triazine in the side chain of pleuromutilin, exhibited highly promising antimicrobial activity and mitigated antibiotic resistance. The high antibacterial potency of 6d was further supported by docking model analysis and green fluorescent protein inhibition assay. Additionally, cytotoxicity and acute oral toxicity evaluation and in vivo mouse systemic infection experiments revealed that 6d possessed tolerable toxicity and promising therapeutic efficacy.
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Affiliation(s)
- Qinqin Liu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China.
| | - Hongjuan Zhang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - YunPeng Yi
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, 202 Gongyebeilu, Jinan, 250023, Shandong, China
| | - Panpan Wang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Shengyi Wang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China.
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5
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Xia J, Li Y, He C, Yong C, Wang L, Fu H, He XL, Wang ZY, Liu DF, Zhang YY. Synthesis and Biological Activities of Oxazolidinone Pleuromutilin Derivatives as a Potent Anti-MRSA Agent. ACS Infect Dis 2023; 9:1711-1729. [PMID: 37610012 DOI: 10.1021/acsinfecdis.3c00162] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
A series of pleuromutilin derivatives containing an oxazolidinone skeleton were synthesized and evaluated in vitro and in vivo as antibacterial agents. Most of the synthesized derivatives exhibited potent antibacterial activities against three strains of Staphylococcus aureus (including MRSA ATCC 33591, MRSA ATCC 43300, and MSSA ATCC 29213) and two strains of Staphylococcus epidermidis (including MRSE ATCC 51625 and MSSE ATCC 12228). Compound 28 was the most active antibacterial agent in vitro (MIC = 0.008-0.125 μg·mL-1) and exhibited a significant bactericidal effect, low cytotoxicity, and weak inhibition (IC50 = 20.66 μmol·L-1) for CYP3A4, as well as exhibited less possibility to cause bacterial resistance. Furthermore, in vivo activities indicated that the compound was effective in reducing MRSA load in a murine thigh infection model. Moreover, it clearly facilitated the healing of MRSA skin infection and inhibited the secretion of the TNF-α, IL-6, and MCP-1 inflammatory factors in serum. These results suggest that oxazolidinone pleuromutilin is a promising therapeutic candidate for drug-resistant bacterial infections.
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Affiliation(s)
- Jing Xia
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
| | - Yun Li
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
| | - Cailu He
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
| | - Can Yong
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
| | - Li Wang
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
| | - Huan Fu
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
| | - Xiao-Long He
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Zhou-Yu Wang
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Dong-Fang Liu
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Chengdu 610041, China
| | - Yuan-Yuan Zhang
- Department of Chemistry, School of Science, Xihua University, Chengdu 610039, China
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Chengdu 610041, China
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6
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Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmüller H, Nováček J, Wilson DN. Structural conservation of antibiotic interaction with ribosomes. Nat Struct Mol Biol 2023; 30:1380-1392. [PMID: 37550453 PMCID: PMC10497419 DOI: 10.1038/s41594-023-01047-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.
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Affiliation(s)
- Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Bertrand Beckert
- Dubochet Center for Imaging at EPFL-UNIL, Batiment Cubotron, Lausanne, Switzerland
| | | | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jiří Nováček
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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7
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Yi Y, Yang S, Liu Y, Yin B, Zhao Z, Li G, Huang Z, Chen L, Liu F, Shang R, Lin S. Antibiotic resistance and drug modification: Synthesis, characterization and bioactivity of newly modified potent pleuromutilin derivatives with a substituted piperazine moiety. Bioorg Chem 2023; 132:106353. [PMID: 36669358 DOI: 10.1016/j.bioorg.2023.106353] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/27/2022] [Accepted: 01/08/2023] [Indexed: 01/13/2023]
Abstract
Antibiotic-resistant bacteria pose a major global public health concern, owing to the lack of effective antibacterial drugs. Consequently, the discovery and development of innovative antibacterial drug classes with unique mechanisms of action are urgently needed. In this study, we designed, synthesised, and tested a series of novel pleuromutilin derivatives with piperazine linker substituted by amino acids moieties to determine their antibacterial properties. Most synthesized compounds exhibited potent activities against Staphylococcus aureus (S. aureus), methicillin-resistant S. aureus (MRSA), and methicillin-resistant Staphylococcus epidermidis. Compound 6l, the most potent antibacterial agent created in this study, displayed a rapid bactericidal activity against MRSA, Klebsiella pneumoniae and S. aureus cfr N12. Moreover, pharmacokinetics study of compound 6l exhibited good PK performance with a low in vivo clearance (CL = 1965 mL/h/kg) and a suitable half-life (T1/2 = 11.614 ± 5.123 h). Molecular docking experiments revealed the binding model of compound 6l to the unmethylated A2503 of peptidyl transferase centre of 23S rRNA. Interaction pattern of 6l with cfr-mediated ribosomes revealed by molecular dynamics. Moreover in vivo mouse systemic infection experiments with compound 6l revealed its effectiveness against MRSA and S. aureus cfr N12 with the ED50 of 11.08 mg/kg and 14.63 mg/kg body weight, respectively.
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Affiliation(s)
- Yunpeng Yi
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China
| | - Shifa Yang
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China
| | - Yueyue Liu
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China
| | - Bin Yin
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China
| | - Zengcheng Zhao
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China
| | - Guiming Li
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China
| | - Zhongli Huang
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China
| | - Lei Chen
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250014, Shandong, China
| | - Fei Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250023, Shandong, China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China.
| | - Shuqian Lin
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan 250023, Shandong, China.
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8
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Xia J, Xin L, Li J, Tian L, Wu K, Zhang S, Yan W, Li H, Zhao Q, Liang C. Discovery of Quaternized Pyridine-Thiazole-Pleuromutilin Derivatives with Broad-Spectrum Antibacterial and Potent Anti-MRSA Activity. J Med Chem 2023; 66:5061-5078. [PMID: 37051724 DOI: 10.1021/acs.jmedchem.2c02135] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The quaternization of compounds has emerged as a promising molecular design strategy for the development of antibiotics. Herein, we report the design, synthesis, antibacterial activities, and structure-activity relationships of a series of novel pleuromutilin derivatives containing a quaternary amine C-14 side chain. Most of these derivatives exhibited broad-spectrum antibacterial activity against the tested bacteria. 10b was the most effective antibacterial agent that displayed excellent antibacterial activity against five clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, remarkable antimycoplasma activity, rapid bactericidal effects, and a strong ability to damage bacterial biofilms. Further mechanistic studies indicated that 10b destroyed bacterial cell membranes to exert its antibacterial effects. Moreover, 10b exhibited high survival protection and potent in vivo antibacterial efficacy (ED50 = 4.94 mg/kg) in a mouse model of systemic MRSA infection. These findings suggest that 10b is a promising candidate for the treatment of multi-drug-resistant infectious diseases, especially MRSA infections.
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Affiliation(s)
- Juan Xia
- Laboratory of Hematologic Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, P. R. China
| | - Liang Xin
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Jingyi Li
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Lei Tian
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Kangxiong Wu
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Shaojun Zhang
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Wenjing Yan
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Han Li
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Qianqian Zhao
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
| | - Chengyuan Liang
- School of Biology and Medicine, Shaanxi University of Science & Technology, Xi’an 710021, P. R. China
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9
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Goethe O, DiBello M, Herzon SB. Total synthesis of structurally diverse pleuromutilin antibiotics. Nat Chem 2022; 14:1270-1277. [PMID: 36163267 PMCID: PMC9633427 DOI: 10.1038/s41557-022-01027-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/21/2022] [Indexed: 11/08/2022]
Abstract
The emergence of drug-resistant bacterial pathogens has placed renewed emphasis on the total chemical synthesis of novel antibacterials. Tetracyclines, macrolides, streptogramins and lincosamides are now accessible through flexible and general synthetic routes. Pleuromutilins (antibiotics based on the fungal metabolite pleuromutilin) have remained resistant to this approach, in large part due to the difficulties encountered in the de novo construction of the decahydro-3a,9-propanocyclopenta[8]annulene skeleton. Here we present a platform for the total synthesis of pleuromutilins that provides access to diverse derivatives bearing alterations at previously inaccessible skeletal and peripheral positions. The synthesis is enabled by the serendipitous discovery of a vinylogous Wolff rearrangement, which serves to establish the C9 quaternary centre in the targets, and the development of a highly diastereoselective butynylation of an α-quaternary aldehyde, which forms the C14 secondary alcohol. The versatility of the route is demonstrated through the synthesis of seventeen structurally distinct derivatives, with many possessing potent antibacterial activity.
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Affiliation(s)
- Olivia Goethe
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Mikaela DiBello
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
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10
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Hu Y, Chen F, Zhou K, Zhang Z, Li F, Zhang J, Tang Y, Jin Z. In Vitro and In Vivo Antibacterial Activity, Toxicity and Resistance Analysis of Pleuromutilin Derivative Z33 against Methicillin-Resistant Staphylococcus aureus. Molecules 2022; 27:molecules27154939. [PMID: 35956888 PMCID: PMC9370166 DOI: 10.3390/molecules27154939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 12/10/2022] Open
Abstract
The novel pleuromutilin derivative, which showed excellent in vitro antibacterial activity against MRSA, 22-(2-(2-(4-((4-(4-nitrophenyl)piperazin-1-yl)methyl)-1H-1,2,3-triazol-1-yl)acetamido)phenyl)thioacety-l-yl-22-deoxypleuromutilin (Z33), was synthesized and characterized in our previous work. In this study, the preliminary pharmacodynamics and safety of Z33 were further evaluated. In in vitro antibacterial activity assays, Z33 was found to be a potent bactericidal antibiotic against MRSA that induced dose-dependent growth inhibition and long-term post-antibiotic effect (PAE). The drug-resistance test demonstrated that Z33 possessed a narrow mutant selection window and lower propensities to select resistance than that of tiamulin. Cytochrome P450 (CYP450) inhibition assay determined that the inhibitory effect of Z33 was similar to that of tiamulin against the activity of CYP3A4, and was lower than that of tiamulin on the activity of CYP2E1. Toxicity determination showed that both Z33 and tiamulin displayed low cytotoxicity of RAW264.7 cells. Furthermore, Z33 was found to be a high-security compound with a 50% lethal dose (LD50) above 5000 mg/kg in the acute oral toxicity test in mice. In an in vivo antibacterial activity test, Z33 displayed better therapeutic effectiveness than tiamulin in the neutropenic mouse thigh infection model. In summary, Z33 was worthy of further development as a highly effective and safe antibiotic agent against MRSA infection.
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Affiliation(s)
- Yuhan Hu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
| | - Fang Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
| | - Kexin Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
| | - Zhe Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
| | - Fei Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
| | - Jianfeng Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
| | - Youzhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Y.T.); (Z.J.); Fax: +86-20-85280665 (Y.T.)
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (F.C.); (K.Z.); (Z.Z.); (F.L.); (J.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Y.T.); (Z.J.); Fax: +86-20-85280665 (Y.T.)
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11
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Zhou Y, Yi Y, Wang J, Yang Z, Liu Q, Pu W, Shang R. Discovery of novel pleuromutilin derivatives as potent antibacterial agents. Eur J Med Chem 2022; 237:114403. [PMID: 35472849 DOI: 10.1016/j.ejmech.2022.114403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 11/22/2022]
Abstract
Novel pleuromutilin derivatives with 3,4-dihydropyrimidin and pyrimidine moieties were designed, synthesized, and evaluated for their antibacterial activities. Most of the synthesized derivatives, especially the compounds bearing the pyrimidine moieties, exhibited potent antibacterial activities against methicillin-resistant Staphylococcus aureus BNCC 337371 (MRSA-337371), Staphylococcus aureus ATCC 25923 (S. aureus-25923) and methicillin-resistant Staphylococcus epidermidis ATCC 51625 (MRSE-51625). Compounds 5a, 5g and 5h exerted the excellent antibacterial activities and selected to evaluate their bacterial killing kinetics. Compound 5h displayed the highest antibacterial activities with bacteriostatic activities against MRSA and further evaluated its efficacy in mouse systemic infection. The results showed that compound 5h exhibited potent in vivo antibacterial effects to significantly improve the survival rate of mice (ED50 = 16.14 mg/kg), reduce the bacterial load and alleviate the pathological changes in the lungs of the affected mice. Furthermore, molecular docking studies revealed that the selected compounds successfully localized in the pocket of 50S ribosomal subunit and the formed hydrogen bonds were the main interaction.
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Affiliation(s)
- Yuhang Zhou
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China.
| | - Yunpeng Yi
- Shandong Provincial Animal and Poultry Green Health Products Creation Engineering Laboratory, Institute of Poultry Science, Shandong Academy of Agricultural Science, 202 Gongyebeilu Jinan, 250023, Shandong, China.
| | - Jiangkun Wang
- School of Basic Medical Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Zheng Yang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Qinqin Liu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, 730050, China.
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12
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Wang X, Wang R, Zhang ZS, Zhang GY, Jin Z, Shen R, Du D, Tang YZ. Semisynthetic pleuromutilin antimicrobials with therapeutic potential against methicillin-resistant Staphylococcus aureus by targeting 50S ribosomal subunit. Eur J Med Chem 2022; 237:114341. [PMID: 35430480 DOI: 10.1016/j.ejmech.2022.114341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/17/2022] [Accepted: 03/31/2022] [Indexed: 11/04/2022]
Abstract
A series of pleuromutilin analogs with a substituted 1,2,4-triazole were designed, synthesized and assessed for their in vitro and in vivo antibacterial activity. Initially, the MIC of the synthesized derivatives against five strains of Staphylococcus aureus (MRSA ATCC 43300, S. aureus ATCC 29213, clinical isolation of S. aureus AD3, S. aureus 144 and S. aureus SA17) were tested by the broth dilution method. Compounds 30a, 31b and 32a were the most active antibacterial agents in vitro against MRSA (MIC = 0.0625 μg/mL). The results of the time-kill curves showed that compounds 30a and 32a could reduce the amount of MRSA in vitro quickly (-7.70 log10 CFU/mL and -7.10 log10 CFU/mL reduction). In the experiment to further evaluate the in vivo antibacterial activity of compound 30a against MRSA, compound 30a (-1.71 log10 CFU/g) was effective in reducing MRSA load in thigh infected mice. Compound 30a (survival rate was 50%) displayed superior in vivo efficacy to that of tiamulin (survival rate was 30%) in the mouse systemic model. The results of further pharmacokinetic studies on compound 30a showed that the half-life (t1/2), clearance rate (Cl) and the area under the plasma concentration time curve (AUC0→∞) of compound 30a were 0.37 h, 5.43 L/h/kg and 1.84 μg h/mL, respectively. After affinity measurement by surface plasmon resonance (SPR), compound 30a exhibited high affinity with the 50S ribosome, with KD value of 1.95 × 10-6 M. Furthermore, the results of molecular docking studies revealed that compound 30a was successfully localized inside the binding pocket of 50S ribosomal subunit (ΔGb = -9.40 kcal/mol). Meanwhile, most of these compounds had no significant inhibitory effect on RAW 264.7 cells and 16HBE cells at the concentration of 8 μg/mL. The obtained outcomes showed that compound 30a could be utilized as an encouraging perspective in the development of a new therapeutic candidate for bacterial infection.
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Affiliation(s)
- Xiao Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rui Wang
- Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhao-Sheng Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Guang-Yu Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rong Shen
- Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Dan Du
- Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China.
| | - You-Zhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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13
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Abstract
Synthesis of a potent inhibitor of bacterial protein synthesis, pleuromutilin, is described. Assembly of the critical cyclooctane fragment relies on an oxidative ring-expansion, and complete stereochemical relay in the synthetic sequence is enabled by the judicious choice of tactics. The requisite connectivity pattern of the perhydroindanone motif is rapidly established in a sequence of cycloaddition and radical cyclization events. Application of this strategy allows for preparation of the target natural product in 16 steps from commercially available material.
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Affiliation(s)
- Nicholas J Foy
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Sergey V Pronin
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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14
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Chen HY, Lei JY, Li SL, Guo LQ, Lin JF, Wu GH, Lu J, Ye ZW. Progress in biological activities and biosynthesis of edible fungi terpenoids. Crit Rev Food Sci Nutr 2022; 63:7288-7310. [PMID: 35238261 DOI: 10.1080/10408398.2022.2045559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The edible fungi have both edible and medicinal functions, in which terpenoids are one of the most important active ingredients. Terpenoids possess a wide range of biological activities and show great potential in the pharmaceutical and healthcare industries. In this review, the diverse biological activities of edible fungi terpenoids were summarized with emphasis on the mechanism of anti-cancer and anti-inflammation. Subsequently, this review focuses on advances in knowledge and understanding of the biosynthesis of terpenoids in edible fungi, especially in the generation of sesquiterpenes, diterpenes, and triterpenes. This paper is aim to provide an overview of biological functions and biosynthesis developed for utilizing the terpenoids in edible fungi.
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Affiliation(s)
- Hai-Ying Chen
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Jin-Yu Lei
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Shu-Li Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Li-Qiong Guo
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Jun-Fang Lin
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Guang-Hong Wu
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jun Lu
- Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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15
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Fan Y, Fu Y, Zhou Y, Liu Y, Hao B, Shang R. Acute, subacute oral toxicity and Ames test of Py-mulin: an antibacterial drug candidate. BMC Pharmacol Toxicol 2022; 23:2. [PMID: 34983673 PMCID: PMC8725322 DOI: 10.1186/s40360-021-00543-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/17/2021] [Indexed: 11/12/2022] Open
Abstract
Background Py-mulin is a new pleuromutilin derivative with potent antibacterial activities in vitro and in vivo, suggesting this compound may lead to a promising antibacterial drug after further development. The present study is aimed to evaluate the acute and subacute oral toxicity, and the genotoxicity with the standard Ames test according to standard protocols. Methods Acute oral toxicity of Py-mulin was determined using Kunming mice. The 28-day repeated dose oral toxicity study in SD rats was performed according to OECD guideline No. 407. The bacterial reverse mutation (Ames test) was carried out using four Salmonella typhimurium (S. typhimurium) strains TA97, TA98, TA100 and TA1535 with and without S9 metabolic activation. Results The LD50 values in acute oral toxicity were 2973 mg/kg (female mice) and 3891 mg/kg (male mice) calculated by the Bliss method. In subacute toxicity study, 50 mg/kg Py-mulin did not induce any abnormality in body weight, food consumption, clinical sign, hematology, clinical chemistry, organ weight, and histopathology in all of the treatment groups. However, high doses of Py-mulin (100 and 300 mg/kg) displayed slightly hepatotoxicity to female rats. Furthermore, Py-mulin did not significantly increase the number of revertant colonies of four standard S. typhimurium strains with the doses of 0.16–1000 μg/plate in the Ames study. Conclusions Based on our findings, our study provides some information for the safety profile of Py-mulin.
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Affiliation(s)
- Yuan Fan
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou, 730050, People's Republic of China
| | - Yunxing Fu
- Zhengzhou Key Laboratory of Immunopharmacology of effective components of Chinese Veterinary Medicine, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, 450046, Zhengzhou, People's Republic of China
| | - Yuhang Zhou
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou, 730050, People's Republic of China
| | - Yu Liu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou, 730050, People's Republic of China
| | - Baocheng Hao
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou, 730050, People's Republic of China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences, No. 335, Qilihe District, Lanzhou, 730050, People's Republic of China.
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16
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [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] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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17
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Bartholomäus A, Kolte B, Mustafayeva A, Goebel I, Fuchs S, Benndorf D, Engelmann S, Ignatova Z. smORFer: a modular algorithm to detect small ORFs in prokaryotes. Nucleic Acids Res 2021; 49:e89. [PMID: 34125903 PMCID: PMC8421149 DOI: 10.1093/nar/gkab477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/29/2021] [Accepted: 05/18/2021] [Indexed: 11/15/2022] Open
Abstract
Emerging evidence places small proteins (≤50 amino acids) more centrally in physiological processes. Yet, their functional identification and the systematic genome annotation of their cognate small open-reading frames (smORFs) remains challenging both experimentally and computationally. Ribosome profiling or Ribo-Seq (that is a deep sequencing of ribosome-protected fragments) enables detecting of actively translated open-reading frames (ORFs) and empirical annotation of coding sequences (CDSs) using the in-register translation pattern that is characteristic for genuinely translating ribosomes. Multiple identifiers of ORFs that use the 3-nt periodicity in Ribo-Seq data sets have been successful in eukaryotic smORF annotation. They have difficulties evaluating prokaryotic genomes due to the unique architecture (e.g. polycistronic messages, overlapping ORFs, leaderless translation, non-canonical initiation etc.). Here, we present a new algorithm, smORFer, which performs with high accuracy in prokaryotic organisms in detecting putative smORFs. The unique feature of smORFer is that it uses an integrated approach and considers structural features of the genetic sequence along with in-frame translation and uses Fourier transform to convert these parameters into a measurable score to faithfully select smORFs. The algorithm is executed in a modular way, and dependent on the data available for a particular organism, different modules can be selected for smORF search.
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Affiliation(s)
- Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany.,Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Baban Kolte
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Ayten Mustafayeva
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Ingrid Goebel
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | | | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, 39106 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Susanne Engelmann
- Helmholtz Center for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany.,Inst. Microbiology, TU Braunschweig, Braunschweig, Germany
| | - Zoya Ignatova
- Inst. Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
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18
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Fu Y, Leng C, Fan Y, Ma X, Li X, Wang X, Guo Z, Wang X, Shang R. In Vitro and In Vivo Activity of 14- O-[(4,6-Diamino-pyrimidine-2-yl) thioacetyl] Mutilin against Methicillin-Resistant Staphylococcus aureus. Molecules 2021; 26:3277. [PMID: 34071703 PMCID: PMC8199141 DOI: 10.3390/molecules26113277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a major human pathogen that requires new antibiotics with unique mechanism. A new pleuromutilin derivative, 14-O-[(4,6-Diamino-pyrimidine-2-yl) thioacetyl] mutilin (DPTM), has been synthesized and proved as a potent antibacterial agent using in vitro and in vivo assays. In the present study, DPTM was further in vitro evaluated against methicillin-resistant Staphylococcus aureus (MRSA) isolated from dairy farms and outperformed tiamulin fumarate, a pleuromutilin drug used for veterinary. Moreover, a murine skin wound model caused by MRSA infection was established, and the healing effect of DPTM was investigated. The results showed that DPTM could promote the healing of MRSA skin infection, reduce the bacterial burden of infected skin MRSA and decrease the secretion of IL-6 and TNF-α inflammatory cytokines in plasma. These results provided the basis for further in-depth drug targeted studies of DPTM as a novel antibacterial agent.
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Affiliation(s)
- Yunxing Fu
- Zhengzhou Key Laboratory of Immunopharmacology of Effective Components of Chinese Veterinary Medicine, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China; (Y.F.); (X.M.); (X.L.); (X.W.); (Z.G.)
- Henan Provincial Research Center for the Inheritance and Innovation of Chinese Veterinary Medicine Classic Prescriptions, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Chunqing Leng
- Department of Animal Production, Jinhua Polytechnic, Jinhua 321000, China;
| | - Yuan Fan
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China;
| | - Xia Ma
- Zhengzhou Key Laboratory of Immunopharmacology of Effective Components of Chinese Veterinary Medicine, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China; (Y.F.); (X.M.); (X.L.); (X.W.); (Z.G.)
- Henan Provincial Research Center for the Inheritance and Innovation of Chinese Veterinary Medicine Classic Prescriptions, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Xianghui Li
- Zhengzhou Key Laboratory of Immunopharmacology of Effective Components of Chinese Veterinary Medicine, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China; (Y.F.); (X.M.); (X.L.); (X.W.); (Z.G.)
- Henan Provincial Research Center for the Inheritance and Innovation of Chinese Veterinary Medicine Classic Prescriptions, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Xuefei Wang
- Zhengzhou Key Laboratory of Immunopharmacology of Effective Components of Chinese Veterinary Medicine, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China; (Y.F.); (X.M.); (X.L.); (X.W.); (Z.G.)
- Henan Provincial Research Center for the Inheritance and Innovation of Chinese Veterinary Medicine Classic Prescriptions, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Zhenghuan Guo
- Zhengzhou Key Laboratory of Immunopharmacology of Effective Components of Chinese Veterinary Medicine, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China; (Y.F.); (X.M.); (X.L.); (X.W.); (Z.G.)
- Henan Provincial Research Center for the Inheritance and Innovation of Chinese Veterinary Medicine Classic Prescriptions, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Xiujun Wang
- Zhengzhou Key Laboratory of Immunopharmacology of Effective Components of Chinese Veterinary Medicine, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China; (Y.F.); (X.M.); (X.L.); (X.W.); (Z.G.)
- Henan Provincial Research Center for the Inheritance and Innovation of Chinese Veterinary Medicine Classic Prescriptions, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Ruofeng Shang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China;
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19
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de Mattos-Shipley KMJ, Foster GD, Bailey AM. Cprp-An Unusual, Repetitive Protein Which Impacts Pleuromutilin Biosynthesis in the Basidiomycete Clitopilus passeckerianus. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:655323. [PMID: 37744150 PMCID: PMC10512284 DOI: 10.3389/ffunb.2021.655323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/04/2021] [Indexed: 09/26/2023]
Abstract
Interrogation of an EST database for Clitopilus passeckerianus identified a putative homolog to the unusual stress response gene from yeast; ddr48, as being upregulated under pleuromutilin production conditions. Silencing of this gene, named cprp, produced a population of transformants which demonstrated significantly reduced pleuromutilin production. Attempts to complement a Saccharomyces cerevisiae ddr48 mutant strain (strain Y16748) with cprp were hampered by the lack of a clearly identifiable mutant phenotype, but interestingly, overexpression of either ddr48 or cprp in S. cerevisiae Y16748 led to a conspicuous and comparable reduction in growth rate. This observation, combined with the known role of DDR48 proteins from a range of fungal species in nutrient starvation and stress responses, raises the possibility that this family of proteins plays a role in triggering oligotrophic growth. Localization studies via the production of a Cprp:GFP fusion protein in C. passeckerianus showed clear localization adjacent to the hyphal septa and, to a lesser extent, cell walls, which is consistent with the identification of DDR48 as a cell wall-associated protein in various yeast species. To our knowledge this is the first study demonstrating that a DDR48-like protein plays a role in the regulation of a secondary metabolite, and represents the first DDR48-like protein from a basidiomycete. Potential homologs can be identified across much of the Dikarya, suggesting that this unusual protein may play a central role in regulating both primary and secondary metabolism in fungi.
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Affiliation(s)
| | | | - Andy M. Bailey
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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20
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Mukherjee S, Kundu I, Askari M, Barai RS, Venkatesh KV, Idicula-Thomas S. Exploring the druggable proteome of Candida species through comprehensive computational analysis. Genomics 2021; 113:728-739. [PMID: 33484798 DOI: 10.1016/j.ygeno.2020.12.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
Candida albicans and non-albicans Candida spp. are major cause of systemic mycoses. Antifungal drugs such as azoles and polyenes are not efficient to successfully eradicate Candida infection owing to their fungistatic nature or low bioavailability. Here, we have adopted a comprehensive computational workflow for identification, prioritization and validation of targets from proteomes of Candida albicans and Candida tropicalis. The protocol involves identification of essential drug-target candidates using subtractive genomics, protein-protein interaction network properties and systems biology based methods. The essentiality of the novel metabolic and non-metabolic targets was established by performing in silico gene knockouts, under aerobic as well as anaerobic conditions, and in vitro drug inhibition assays respectively. Deletion of twelve genes that are involved in amino acid, secondary metabolite, and carbon metabolism showed zero growth in metabolic model under simulated conditions. The algorithm, used in this study, can be downloaded from http://pbit.bicnirrh.res.in/offline.php and executed locally.
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Affiliation(s)
- Shuvechha Mukherjee
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Indra Kundu
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - Mehdi Askari
- Department of Bioinformatics, Guru Nanak Khalsa College, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Ram Shankar Barai
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India.
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai 400012, Maharashtra, India.
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21
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Shen T, Penewit K, Waalkes A, Xu L, Salipante SJ, Nath A, Werth BJ. Identification of a novel tedizolid resistance mutation in rpoB of MRSA after in vitro serial passage. J Antimicrob Chemother 2021; 76:292-296. [PMID: 33057715 DOI: 10.1093/jac/dkaa422] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/13/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Tedizolid is an oxazolidinone antimicrobial with activity against Gram-positive bacteria, including MRSA. Tedizolid resistance is uncommon and tedizolid's capacity to select for cross-resistance to other antimicrobials is incompletely understood. The objective of this study was to further explore the phenotypic and genetic basis of tedizolid resistance in MRSA. METHODS We selected for tedizolid resistance in an MRSA laboratory strain, N315, by serial passage until an isolate with an MIC ≥1 log2 dilution above the breakpoint for resistance (≥2 mg/L) was recovered. This isolate was subjected to WGS and susceptibility to a panel of related and unrelated antimicrobials was tested in order to determine cross-resistance. Homology modelling was performed to evaluate the potential impact of the mutation on target protein function. RESULTS After 10 days of serial passage we recovered a phenotypically stable mutant with a tedizolid MIC of 4 mg/L. WGS revealed only one single nucleotide variant (A1345G) in rpoB, corresponding to amino acid substitution D449N. MICs of linezolid, chloramphenicol, retapamulin and quinupristin/dalfopristin increased by ≥2 log2 dilutions, suggesting the emergence of the so-called 'PhLOPSa' resistance phenotype. Susceptibility to other drugs, including rifampicin, was largely unchanged. Homology models revealed that the mutated residue of RNA polymerase would be unlikely to directly affect oxazolidinone action. CONCLUSIONS To the best of our knowledge, this is the first time that an rpoB mutation has been implicated in resistance to PhLOPSa antimicrobials. The mechanism of resistance remains unclear, but is likely indirect, involving σ-factor binding or other alterations in transcriptional regulation.
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Affiliation(s)
- Tianwei Shen
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Adam Waalkes
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Brian J Werth
- Department of Pharmacy, School of Pharmacy, University of Washington, Seattle, WA, USA
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22
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Gressler M, Löhr NA, Schäfer T, Lawrinowitz S, Seibold PS, Hoffmeister D. Mind the mushroom: natural product biosynthetic genes and enzymes of Basidiomycota. Nat Prod Rep 2021; 38:702-722. [PMID: 33404035 DOI: 10.1039/d0np00077a] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to September 2020 Mushroom-forming fungi of the division Basidiomycota have traditionally been recognised as prolific producers of structurally diverse and often bioactive secondary metabolites, using the methods of chemistry for research. Over the past decade, -omics technologies were applied on these fungi, and sophisticated heterologous gene expression platforms emerged, which have boosted research into the genetic and biochemical basis of the biosyntheses. This review provides an overview on experimentally confirmed natural product biosyntheses of basidiomycete polyketides, amino acid-derived products, terpenoids, and volatiles. We also present challenges and solutions particular to natural product research with these fungi. 222 references are cited.
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Affiliation(s)
- Markus Gressler
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Nikolai A Löhr
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Tim Schäfer
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Stefanie Lawrinowitz
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Paula Sophie Seibold
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
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23
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Meydan S, Klepacki D, Mankin AS, Vázquez-Laslop N. Identification of Translation Start Sites in Bacterial Genomes. Methods Mol Biol 2021; 2252:27-55. [PMID: 33765270 DOI: 10.1007/978-1-0716-1150-0_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The knowledge of translation start sites is crucial for annotation of genes in bacterial genomes. However, systematic mapping of start codons in bacterial genes has mainly relied on predictions based on protein conservation and mRNA sequence features which, although useful, are not always accurate. We recently found that the pleuromutilin antibiotic retapamulin (RET) is a specific inhibitor of translation initiation that traps ribosomes specifically at start codons, and we used it in combination with ribosome profiling to map start codons in the Escherichia coli genome. This genome-wide strategy, that was named Ribo-RET, not only verifies the position of start codons in already annotated genes but also enables identification of previously unannotated open reading frames and reveals the presence of internal start sites within genes. Here, we provide a detailed Ribo-RET protocol for E. coli. Ribo-RET can be adapted for mapping the start codons of the protein-coding sequences in a variety of bacterial species.
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Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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24
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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25
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Alberti F, Kaleem S, Weaver JA. Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research. Biol Open 2020; 9:bio056010. [PMID: 33268478 PMCID: PMC7725599 DOI: 10.1242/bio.056010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Basidiomycota are a large and diverse phylum of fungi. They can make bioactive metabolites that are used or have inspired the synthesis of antibiotics and agrochemicals. Terpenoids are the most abundant class of natural products encountered in this taxon. Other natural product classes have been described, including polyketides, peptides, and indole alkaloids. The discovery and study of natural products made by basidiomycete fungi has so far been hampered by several factors, which include their slow growth and complex genome architecture. Recent developments of tools for genome and metabolome studies are allowing researchers to more easily tackle the secondary metabolome of basidiomycete fungi. Inexpensive long-read whole-genome sequencing enables the assembly of high-quality genomes, improving the scaffold upon which natural product gene clusters can be predicted. CRISPR/Cas9-based engineering of basidiomycete fungi has been described and will have an important role in linking natural products to their genetic determinants. Platforms for the heterologous expression of basidiomycete genes and gene clusters have been developed, enabling natural product biosynthesis studies. Molecular network analyses and publicly available natural product databases facilitate data dereplication and natural product characterisation. These technological advances combined are prompting a revived interest in natural product discovery from basidiomycete fungi.This article has an associated Future Leader to Watch interview with the first author of the paper.
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Affiliation(s)
- Fabrizio Alberti
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Saraa Kaleem
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jack A Weaver
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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26
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Fan Y, Liu Y, Wang H, Shi T, Cheng F, Hao B, Yi Y, Shang R. Novel pleuromutilin derivatives with substituted 6-methylpyrimidine: Design, synthesis and antibacterial evaluation. Eur J Med Chem 2020; 207:112735. [PMID: 32827940 DOI: 10.1016/j.ejmech.2020.112735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 10/23/2022]
Abstract
A series of novel pleuromutilin derivatives with substituted 6-methylpyrimidine moieties was designed, synthesized, and evaluated for their antibacterial activities. Most of the tested compounds exhibited potent antibacterial activities against Staphylococcus aureus ATCC 25923 (S. aureus-25923), methicillin-resistant Staphylococcus epidermidis ATCC 51625 (MRSE-51625), methicillin-resistant Staphylococcus aureus BNCC 337371 (MRSA-337371), Streptococcus dysgalactiae (S. dysgalactiae) and Streptococcus agalactiae (S. agalactiae). Compounds 5c and 5g were the most active and displayed bacteriostatic activities against MRSA. In vivo mouse systemic infection experiment showed that 5c significantly improved the survival rate of mice (ED50 = 18.02 mg/kg), reduced the bacterial load and alleviated the pathological changes in the lungs of the affected mice.
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Affiliation(s)
- Yuan Fan
- Key Laboratory of New Animal Drug Project, Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, No. 335, Qilihe District, Lanzhou, 730050, China.
| | - Yu Liu
- Key Laboratory of New Animal Drug Project, Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, No. 335, Qilihe District, Lanzhou, 730050, China
| | - Hao Wang
- Key Laboratory of New Animal Drug Project, Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, No. 335, Qilihe District, Lanzhou, 730050, China
| | - Tao Shi
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Feng Cheng
- Key Laboratory of New Animal Drug Project, Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, No. 335, Qilihe District, Lanzhou, 730050, China
| | - Baocheng Hao
- Key Laboratory of New Animal Drug Project, Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, No. 335, Qilihe District, Lanzhou, 730050, China
| | - Yunpeng Yi
- Key Laboratory of New Animal Drug Project, Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, No. 335, Qilihe District, Lanzhou, 730050, China.
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, No. 335, Qilihe District, Lanzhou, 730050, China.
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27
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Kurkcuoglu O, Gunes MU, Haliloglu T. Local and Global Motions Underlying Antibiotic Binding in Bacterial Ribosome. J Chem Inf Model 2020; 60:6447-6461. [PMID: 33231066 DOI: 10.1021/acs.jcim.0c00967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial ribosome is one of the most important targets in the treatment of infectious diseases. As antibiotic resistance in bacteria poses a growing threat, a significant amount of effort is concentrated on exploring new drug-binding sites where testable predictions are of significance. Here, we study the dynamics of a ribosomal complex and 67 small and large subunits of the ribosomal crystal structures (64 antibiotic-bound, 3 antibiotic-free) from Deinococcus radiodurans, Escherichia coli, Haloarcula marismortui, and Thermus thermophilus by the Gaussian network model. Interestingly, a network of nucleotides coupled in high-frequency fluctuations reveals known antibiotic-binding sites. These sites are seen to locate at the interface of dynamic domains that have an intrinsic dynamic capacity to interfere with functional globular motions. The nucleotides and the residues fluctuating in the fast and slow modes of motion thus have promise for plausible antibiotic-binding and allosteric sites that can alter antibiotic binding and resistance. Overall, the present analysis brings a new dynamic perspective to the long-discussed link between small-molecule binding and large conformational changes of the supramolecule.
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Affiliation(s)
- Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul 34469, Turkey
| | - M Unal Gunes
- Polymer Research Center, Bogazici University, Istanbul 34342, Turkey
| | - Turkan Haliloglu
- Polymer Research Center, Bogazici University, Istanbul 34342, Turkey
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28
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Fu Y, Yi Y, Fan Y, Shang R. Cytochrome P450 inhibition potential and initial genotoxic evaluation of 14-O-[(4,6-diaminopyrimidine-2-yl)thioacetyl] mutilin. Sci Rep 2020; 10:13474. [PMID: 32778735 PMCID: PMC7417534 DOI: 10.1038/s41598-020-70400-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 06/03/2020] [Indexed: 01/05/2023] Open
Abstract
14-O-[(4,6-Diaminopyrimidine-2-yl)thioacetyl] mutilin (DPTM) is a promising drug candidate with excellent antibacterial activity against Gram-positive bacteria. The present study was designed to characterize its Cytochrome P450 (CYP) enzymes inhibition activities and the genotoxicity with the standard Ames test. We determined the inhibitory effects of DPTM on CYP1A2, CYP2D1/6, CYP2E1, CYP2C11/9 and CYP3A/4 in rat liver microsomes (RLMs) and in human liver microsomes (HLMs). The mRNA expressions of the above CYP isoforms and their transcriptional regulators were also evaluated using the Hep G2 cell model. The results showed DPTM exhibited a moderate inhibitory potential against CYP3A/4 (IC50 values of 10 ± 2 and 8 ± 2 μM, respectively) and weak against the other CYP enzymes based on their IC50 values. Compared to the control, CYP isoforms and their transcriptional regulators mRNA expressions significantly increased when the Hep G2 cells were treated with DPTM for a certain period of time. In the Ames test, Salmonella strains TA97, TA98, TA100, TA102 and TA1535 were treated with or without the metabolic activation (S9). Analysis showed the average number of revertant colonies per plate was less in double in the groups treated with DPTM than that in the negative control plate and showed no dose-related increase.
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Affiliation(s)
- Yunxing Fu
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Qilihe District, No. 335, Lanzhou, 730050, People's Republic of China.,Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, People's Republic of China
| | - Yunpeng Yi
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Qilihe District, No. 335, Lanzhou, 730050, People's Republic of China
| | - Yuan Fan
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Qilihe District, No. 335, Lanzhou, 730050, People's Republic of China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Qilihe District, No. 335, Lanzhou, 730050, People's Republic of China.
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29
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Tiamulin-Resistant Mutants of the Thermophilic Bacterium Thermus thermophilus. Antibiotics (Basel) 2020; 9:antibiotics9060313. [PMID: 32526926 PMCID: PMC7345174 DOI: 10.3390/antibiotics9060313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022] Open
Abstract
Tiamulin is a semisynthetic pleuromutilin antibiotic that binds to the 50S ribosomal subunit A site and whose (((2-diethylamino)ethyl)thio)-acetic acid tail extends into the P site to interfere with peptide bond formation. We have isolated spontaneous tiamulin-resistant mutants of the thermophilic bacterium Thermus thermophilus, containing either single amino acid substitutions in ribosomal protein uL3 or single base substitutions in the peptidyltransferase active site of 23S rRNA. These mutations are consistent with those found in other organisms and are in close proximity to the crystallographically determined tiamulin binding site. We also conducted a cross-resistance analysis of nine other single-base substitutions in or near the peptidyltransferase active site, previously selected for resistance to structurally unrelated antibiotics. While some of the base substitutions in 23S rRNA are positioned to directly affect tiamulin-ribosome contacts, others are some distance from the tiamulin binding site, indicating an indirect mechanism of resistance. Similarly, amino acid substitutions in uL3 are predicted to act indirectly by destabilizing rRNA conformation in the active site. We interpret these observations in light of the available ribosome X-ray crystal structures. These results provide a more comprehensive profile of tiamulin resistance caused by mutations in the bacterial ribosome.
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30
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Abstract
This article describes 20 years of research that investigated a second novel target for ribosomal antibiotics, the biogenesis of the two subunits. Over that period, we have examined the effect of 52 different antibiotics on ribosomal subunit formation in six different microorganisms. Most of the antimicrobials we have studied are specific, preventing the formation of only the subunit to which they bind. A few interesting exceptions have also been observed. Forty-one research publications and a book chapter have resulted from this investigation. This review will describe the methodology we used and the fit of our results to a hypothetical model. The model predicts that inhibition of subunit assembly and translation are equivalent targets for most of the antibiotics we have investigated.
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Affiliation(s)
- W Scott Champney
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
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31
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Zuo X, Fang X, Zhang Z, Jin Z, Xi G, Liu Y, Tang Y. Antibacterial Activity and Pharmacokinetic Profile of a Promising Antibacterial Agent: 22-(2-Amino-phenylsulfanyl)-22-Deoxypleuromutilin. Molecules 2020; 25:E878. [PMID: 32079232 PMCID: PMC7071076 DOI: 10.3390/molecules25040878] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
A new pleuromutilin derivative, 22-(2-amino-phenylsulfanyl)-22-deoxypleuromutilin (amphenmulin), has been synthesized and proved excellent in vitro and in vivo efficacy than that of tiamulin against methicillin-resistant Staphylococcus aureus (MRSA), suggesting this compound may lead to a promising antibacterial agent to treat MRSA infections. In this study, the effectiveness and safety of amphenmulin were further investigated. Amphenmulin showed excellent antibacterial activity against MRSA (minimal inhibitory concentration = 0.0156~8 µg/mL) and performed time-dependent growth inhibition and a concentration-dependent postantibiotic effect (PAE). Acute oral toxicity test in mice showed that amphenmulin was a practical non-toxic drug and possessed high security as a new drug with the 50% lethal dose (LD50) above 5000 mg/kg. The pharmacokinetic properties of amphenmulin were then measured. After intravenous administration, the elimination half-life (T1/2), total body clearance (Clβ), and area under curve to infinite time (AUC0→∞) were 1.92 ± 0.28 h, 0.82 ± 0.09 L/h/kg, and 12.23 ± 1.35 μg·h/mL, respectively. After intraperitoneal administration, the T1/2, Clβ/F and AUC0→∞ were 2.64 ± 0.72 h, 4.08 ± 1.14 L/h/kg, and 2.52 ± 0.81 μg·h/mL, respectively, while for the oral route were 2.91 ± 0.81 h, 6.31 ± 2.26 L/h/kg, 1.67 ± 0.66 μg·h/mL, respectively. Furthermore, we evaluated the antimicrobial activity of amphenmulin in an experimental model of MRSA wound infection. Amphenmulin enhanced wound closure and promoted the healing of wound, which inhibited MRSA bacterial counts in the wound and decreased serum levels of the pro-inflammatory cytokines TNF-α, IL-6, and MCP-1.
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Affiliation(s)
- Xiangyi Zuo
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (X.Z.); (X.F.); (Z.Z.); (Z.J.); (Y.L.)
| | - Xi Fang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (X.Z.); (X.F.); (Z.Z.); (Z.J.); (Y.L.)
| | - Zhaosheng Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (X.Z.); (X.F.); (Z.Z.); (Z.J.); (Y.L.)
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (X.Z.); (X.F.); (Z.Z.); (Z.J.); (Y.L.)
| | - Gaolei Xi
- Technology Center for China Tobacco Henan Industrial Limited Company, No. 8 The Third Street, Economic & Technology Development District, Zhengzhou 450000, China
| | - Yahong Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (X.Z.); (X.F.); (Z.Z.); (Z.J.); (Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Youzhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510642, China; (X.Z.); (X.F.); (Z.Z.); (Z.J.); (Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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32
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Wang Z. Construction of all-carbon quaternary stereocenters by catalytic asymmetric conjugate addition to cyclic enones in natural product synthesis. Org Chem Front 2020. [DOI: 10.1039/d0qo00763c] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review discusses the construction of all-carbon quaternary stereocenters using catalytic asymmetric conjugate addition and its application in natural product synthesis.
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Affiliation(s)
- Zhuo Wang
- Southern University of Science and Technology
- School of Medicine
- Shenzhen
- People's Republic of China
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33
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Yñigez-Gutierrez AE, Bachmann BO. Fixing the Unfixable: The Art of Optimizing Natural Products for Human Medicine. J Med Chem 2019; 62:8412-8428. [PMID: 31026161 DOI: 10.1021/acs.jmedchem.9b00246] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecules isolated from natural sources including bacteria, fungi, and plants are a long-standing source of therapeutics that continue to add to our medicinal arsenal today. Despite their potency and prominence in the clinic, complex natural products often exhibit a number of liabilities that hinder their development as therapeutics, which may be partially responsible for the current trend away from natural product discovery, research, and development. However, advances in synthetic biology and organic synthesis have inspired a new generation of natural product chemists to tackle powerful undeveloped scaffolds. In this Perspective, we will present case studies demonstrating the historical and current focus on making targeted, but significant, changes to natural product scaffolds via biosynthetic gene cluster manipulation, total synthesis, semisynthesis, or a combination of these methods, with a focus on increasing activity, decreasing toxicity, or improving chemical and pharmacological properties.
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Affiliation(s)
| | - Brian O Bachmann
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
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Wicha WW, Prince WT, Lell C, Heilmayer W, Gelone SP. Pharmacokinetics and tolerability of lefamulin following intravenous and oral dosing. J Antimicrob Chemother 2019; 74:iii19-iii26. [PMID: 30949704 PMCID: PMC6449572 DOI: 10.1093/jac/dkz087] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES To explore the pharmacokinetics (PK) of oral and intravenous (iv) lefamulin after single and multiple doses, and the effect of food on bioavailability. METHODS Lefamulin PK was examined in four studies. In Study 1, PK was assessed in patients with acute bacterial skin and skin structure infections who received repeated iv lefamulin q12h (150 mg). In Study 2, a four-period crossover study, healthy subjects received a single dose of oral lefamulin [immediate-release (IR) tablet, 1 × 600 mg] in a fasted and fed state, oral lefamulin (capsule, 3 × 200 mg) in a fasted state, and iv lefamulin in a fasted state. In Study 3, a three-period crossover study, healthy males received a single oral lefamulin dose (IR) in the following states: fasted, fasted followed by a high-calorie meal 1 h post-dose, and fed. Study 4 had two parts; in part A, healthy males received a single lefamulin dose (IR) in a fasted and fed state; in part B, subjects received repeated doses of lefamulin (IR, q12h) or placebo. Adverse events (AEs) were recorded in each study. RESULTS Single and repeated dosing of iv and oral lefamulin resulted in comparable exposure. Intravenous and oral lefamulin (given fasted or with a meal 1 h post-dose) resulted in bioequivalence. Bioequivalence was not established between oral lefamulin in the fed state and iv or oral administration in the fasted state. All AEs were mild or moderate in severity, no serious AEs were reported, and no participant discontinued because of an AE. CONCLUSIONS The PK of lefamulin supports successful switch from iv to oral therapy; lefamulin was generally well tolerated.
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Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. Mol Cell 2019; 74:481-493.e6. [PMID: 30904393 DOI: 10.1016/j.molcel.2019.02.017] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/25/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022]
Abstract
The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes, but strikingly, it also revealed putative internal start sites in a number of Escherichia coli genes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at internal in-frame and out-of-frame start sites, can be functionally important and contribute to the "alternative" bacterial proteome. The internal start sites may also play regulatory roles in gene expression.
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Huffman BJ, Shenvi RA. Natural Products in the "Marketplace": Interfacing Synthesis and Biology. J Am Chem Soc 2019; 141:3332-3346. [PMID: 30682249 PMCID: PMC6446556 DOI: 10.1021/jacs.8b11297] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Drugs are discovered through the biological screening of collections of compounds, followed by optimization toward functional end points. The properties of screening collections are often balanced between diversity, physicochemical favorability, intrinsic complexity, and synthetic tractability (Huggins, D. J.; et al. ACS Chem. Biol. 2011, 6, 208; DOI: 10.1021/cb100420r ). Whereas natural product (NP) collections excel in the first three attributes, NPs suffer a disadvantage on the last point. Academic total synthesis research has worked to solve this problem by devising syntheses of NP leads, diversifying late-stage intermediates, or derivatizing the NP target. This work has led to the discovery of reaction mechanisms, the invention of new methods, and the development of FDA-approved drugs. Few drugs, however, are themselves NPs; instead, NP analogues predominate. Here we highlight past examples of NP analogue development and successful NP-derived drugs. More recently, chemists have explored how NP analogues alter the retrosynthetic analysis of complex scaffolds, merging structural design and synthetic design. This strategy maintains the intrinsic complexity of the NP but can alter the physicochemical properties of the scaffold, like core instability that renders the NP a poor chemotype. Focused libraries based on these syntheses may exclude the NP but maintain the molecular properties that distinguish NP space from synthetic space (Stratton, C. F.; et al. Bioorg. Med. Chem. Lett. 2015, 25, 4802; DOI: 10.1016/j.bmcl.2015.07.014 ), properties that have statistical advantages in clinical progression (Luker, T.; et al. Bioorg. Med. Chem. Lett. 2011, 21, 5673, DOI: 10.1016/j.bmcl.2011.07.074 ; Ritchie, T. J.; Macdonald, S. J. F. Drug Discovery Today 2009, 14, 1011, DOI: 10.1016/j.drudis.2009.07.014 ). Research that expedites synthetic access to NP motifs can prevent homogeneity of chemical matter available for lead discovery. Easily accessed, focused libraries of NP scaffolds can fill empty but active gaps in screening sets and expand the molecular diversity of synthetic collections.
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Affiliation(s)
- Benjamin J. Huffman
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Fu Y, Liu Y, Yi Y, Liang J, Wu Q, Shang R. A Validated HPLC-MS/MS Assay for 14- O-[(4,6-Diaminopyrimidine-2-yl)thioacetyl] Mutilin in Biological Samples and Its Pharmacokinetic, Distribution and Excretion via Urine and Feces in Rats. Molecules 2019; 24:E790. [PMID: 30813235 PMCID: PMC6413085 DOI: 10.3390/molecules24040790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/09/2019] [Accepted: 02/15/2019] [Indexed: 11/16/2022] Open
Abstract
14-O-[(4,6-Diaminopyrimidine-2-yl)thioacetyl] mutilin (DPTM), a novel pleuromutilin candidate with a substituted pyrimidine moiety, has been confirmed to possess excellent antibacterial activity against Gram-positive bacteria. To illustrate the pharmacokinetic profile after intravenous (i.v.), intramuscular (i.m.) and oral (p.o.) administrations with DPTM, as well as tissue distribution and excretion via urine and feces in vivo, a specific, sensitive and robust HPLC-MS/MS method was first developed to determine DPTM in rat plasma, various tissues, urine and feces. The plasma, tissues, urine and feces samples were treated by protein precipitation with acetonitrile using tiamulin fumarate as an internal standard (IS). This method which was achieved on an HPLC system detector equipped with an ESI interface, was sensitive with 5 ng/mL as the lower limit of detection and exhibited good linearity (R² > 0.9900) in the range of 5⁻4000 ng/mL for plasma, various tissues, urine and feces, as well as intra-day precision, inter-day precision and accuracy. The matrix effects ranged from 94.2 to 109.7% with RSD ≤ 9.4% and the mean extraction recoveries ranged from 95.4 to 109.5% in plasma, tissue homogenates, urine and feces (RSD ≤ 9.9). After i.v., i.m. and p.o. administrations, DPTM was rapidly absorbed and metabolized in rats with the half-life (t1/2) of 1.70⁻1.86, 3.23⁻3.49 and 4.38⁻4.70 for 10, 25 and 75 mg/kg doses, respectively. The tissue distribution showed that DPTM was diffused into all the tested tissues, especially into the intestine and lung. Excretion via urine and feces studies demonstrated that DPTM was mainly excreted by feces after administration.
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Affiliation(s)
- Yunxing Fu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China.
| | - Yu Liu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China.
| | - Yunpeng Yi
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China.
| | - Jianping Liang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China.
| | - Qingfeng Wu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China.
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Abstract
Genetic coding in bacteria largely operates via the "one gene-one protein" paradigm. However, the peculiarities of the mRNA structure, the versatility of the genetic code, and the dynamic nature of translation sometimes allow organisms to deviate from the standard rules of protein encoding. Bacteria can use several unorthodox modes of translation to express more than one protein from a single mRNA cistron. One such alternative path is the use of additional translation initiation sites within the gene. Proteins whose translation is initiated at different start sites within the same reading frame will differ in their N termini but will have identical C-terminal segments. On the other hand, alternative initiation of translation in a register different from the frame dictated by the primary start codon will yield a protein whose sequence is entirely different from the one encoded in the main frame. The use of internal mRNA codons as translation start sites is controlled by the nucleotide sequence and the mRNA folding. The proteins of the alternative proteome generated via the "genes-within-genes" strategy may carry important functions. In this review, we summarize the currently known examples of bacterial genes encoding more than one protein due to the utilization of additional translation start sites and discuss the known or proposed functions of the alternative polypeptides in relation to the main protein product of the gene. We also discuss recent proteome- and genome-wide approaches that will allow the discovery of novel translation initiation sites in a systematic fashion.
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Deng Y, Wang XZ, Huang SH, Li CH. Antibacterial activity evaluation of synthetic novel pleuromutilin derivatives in vitro and in experimental infection mice. Eur J Med Chem 2019; 162:194-202. [PMID: 30445267 DOI: 10.1016/j.ejmech.2018.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/09/2018] [Accepted: 11/04/2018] [Indexed: 11/22/2022]
Abstract
A series of novel pleuromutilin derivatives embracing 7H-pyrrolo[2,3-d]pyrimidine moiety were synthesized and evaluated for their in vitro antibacterial activity against Gram-positive and Gram-negative pathogens as well as in vivo efficacy in lethal systemic infected mice. Most compounds displayed good in vitro potency against MSSA, MRSA, MSSE, MRSE and E. faecium (MIC = 0.0625-4 μg/mL), especially 15a, 15b and 15o showed excellent activity that even more active than the comparator valnemulin. The in vivo efficacy investigation exhibited compound 15a (ED50 = 16.0 mg/kg) had comparable activity to valnemulin (ED50 = 13.5 mg/kg). The results provided by the dose-response study demonstrated 15a can supply infected mice with 70% survival rate at dose of 40 mg/kg via intragastric (i.g.) administration.
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Affiliation(s)
- Yu Deng
- Institute of Veterinary Sciences & Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, 402460, China
| | - Xiao-Zhong Wang
- Institute of Veterinary Sciences & Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, 402460, China
| | - Shu-Heng Huang
- College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Cheng-Hong Li
- Institute of Veterinary Sciences & Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, 402460, China.
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40
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Goethe O, Heuer A, Ma X, Wang Z, Herzon SB. Antibacterial properties and clinical potential of pleuromutilins. Nat Prod Rep 2019; 36:220-247. [PMID: 29979463 DOI: 10.1039/c8np00042e] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2018Pleuromutilins are a clinically validated class of antibiotics derived from the fungal diterpene (+)-pleuromutilin (1). Pleuromutilins inhibit bacterial protein synthesis by binding to the peptidyl transferase center (PTC) of the ribosome. In this review we summarize the biosynthesis and recent total syntheses of (+)-pleuromutilin (1). We review the mode of interaction of pleuromutilins with the bacterial ribosome, which involves binding of the C14 extension and the tricyclic core to the P and A sites of the PTC, respectively. We provide an overview of existing clinical agents, and discuss the three primary modes of bacterial resistance (mutations in ribosomal protein L3, Cfr methylation, and efflux). Finally we collect structure-activity relationships from publicly available reports, and close with some forward looking statements regarding future development.
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Affiliation(s)
- Olivia Goethe
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Abigail Heuer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Xiaoshen Ma
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Zhixun Wang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA. and Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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41
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Deng Y, Tang D, Wang QR, Huang S, Fu LZ, Li CH. Semi-synthesis, antibacterial activity, and molecular docking study of novel pleuromutilin derivatives bearing cinnamic acids moieties. Arch Pharm (Weinheim) 2019; 352:e1800266. [PMID: 30536467 DOI: 10.1002/ardp.201800266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 11/12/2022]
Abstract
To develop new antibiotics owning a special mechanism, we used the molecular assembly method to synthesize a series of novel pleuromutilin derivatives containing a cinnamic acid scaffold at the C-14 side chain. We evaluated their antibacterial activity and used in silico molecular docking to study their binding mode with the target. The structure-activity relationship (SAR) study suggested that compounds with NO2 (13e), OH (13u), and NH2 (13y) appeared more active (0.0625-2 µg/mL) in vitro against several penicillin-resistant Gram-positive bacteria and the position of the substituent on the benzene ring would affect the activity. The in vivo efficacy investigation of 13e, 13u, and 13y with once daily intragastric (i.g.) administration at 40 mg/kg for 3 consecutive days in a mouse systemic infection model showed that 13u had equal activity as valnemulin providing the mice with 60% survival, while 13e and 13y gave 30 and 40% survival, respectively. The molecular docking studies indicated that π-π stacking and hydrogen bond formation played important roles in improving the antibacterial activity.
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Affiliation(s)
- Yu Deng
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Da Tang
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Qiu-Ru Wang
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Sheng Huang
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Li-Zhi Fu
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Cheng-Hong Li
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
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42
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Lin HC, Hewage RT, Lu YC, Chooi YH. Biosynthesis of bioactive natural products from Basidiomycota. Org Biomol Chem 2019; 17:1027-1036. [DOI: 10.1039/c8ob02774a] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The club fungi, Basidioycota, produce a wide range of bioactive compounds. Here, we describe recent studies on the biosynthetic pathways and enzymes of bioactive natural products from these fungi.
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Affiliation(s)
- Hsiao-Ching Lin
- Institute of Biological Chemistry
- Academia Sinica
- Taipei 115
- Republic of China
- Chemical Biology and Molecular Biophysics Program
| | - Ranuka T. Hewage
- Chemical Biology and Molecular Biophysics Program
- Taiwan International Graduate Program
- Academia Sinica
- Taipei 115
- Republic of China
| | - Yuan-Chun Lu
- Institute of Biological Chemistry
- Academia Sinica
- Taipei 115
- Republic of China
- Institute of Biochemical Sciences
| | - Yit-Heng Chooi
- School of Molecular Sciences
- The University of Western Australia
- Perth
- Australia
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43
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Yi Y, Fu Y, Wang K, Shui Y, Cai J, Jia Z, Niu B, Liang J, Shang R. Synthesis and antibacterial activities of novel pleuromutilin derivatives. Arch Pharm (Weinheim) 2018; 351:e1800155. [PMID: 30058185 DOI: 10.1002/ardp.201800155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 11/05/2022]
Abstract
Pleuromutilin derivatives 4a-h, 5a-g, and 6a-d were synthesized and characterized by IR, 1 H NMR, and 13 C NMR. All synthetic compounds were screened for their in vitro antibacterial activity against Staphylococcus aureus (ATCC 25923), methicillin-resistant S. aureus (MRSA, ATCC 43300), Pasteurella multocida (CVCC 408), Escherichia coli (ATCC 25922), and Salmonella typhimurium (ATCC 14028). Most compounds with quaternary amine showed higher antibacterial activities against both Gram-positive and Gram-negative bacteria strains. Among the screened compounds, compound 5a bearing an N,N,N-trimethyl group at the C-14 side chain of pleuromutilin was found to be the most active agent. Furthermore, preliminary molecular docking was performed to predict the binding interaction of the compounds in the binding pocket.
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Affiliation(s)
- Yunpeng Yi
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
| | - Yunxing Fu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
| | - Keli Wang
- Shangdong Qilu King-Phar Pharmaceutical Co., Ltd., Jinan, China
| | | | - Jing Cai
- Lanzhou Pulmonary Hospital, Lanzhou, China
| | - Zhong Jia
- Lanzhou Pulmonary Hospital, Lanzhou, China
| | - Biao Niu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
| | - Jianping Liang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
| | - Ruofeng Shang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
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Shang R, Zhang C, Yi Y, Liu Y, Pu W. Determination of a New Pleuromutilin Derivative in Broiler Chicken Plasma by RP-HPLC-UV and Its Application to a Pharmacokinetic Study. J Chromatogr Sci 2018; 56:604-610. [PMID: 29668863 DOI: 10.1093/chromsci/bmy033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 03/28/2018] [Indexed: 11/14/2022]
Abstract
A simple, sensitive and reproducible high-performance liquid chromatography method was developed and validated for the determination of 14-O-[(2-amino-1,3,4-thiadiazol-5-yl) thioacetyl] mutilin (ATTM), a new synthesized pleuromutilin derivative with potent antibacterial activity, in broiler chicken plasma after a single intravenous (i.v.), intramuscular (i.m.) or oral (p.o.) administration. Satisfactory separation was achieved on a ZORBAX Ecliplus C18 column (250 × 4.6, 5 μm) with UV detection at 279 nm, using a mobile phase comprising acetonitrile and ultrapure water (50:50, v/v). The elution was isocratic at ambient temperature with a flow rate of 1.0 mL/min. The method exhibited good linearity (R2 > 0.999) over the assayed concentration range (0.12-120.00 μg/mL) and demonstrated good intra- and inter-day precision and accuracy. The method was validated and successfully applied to the pharmacokinetic study of ATTM in chicken plasma after i.v. and p.o. administration.
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Affiliation(s)
- Ruofeng Shang
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, Gansu Province, China
| | - Chao Zhang
- Lianyungang Animal Health Inspection Institute, Lianyungang, Jiangsu Province, China
| | - Yunpeng Yi
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, Gansu Province, China
| | - Yu Liu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, Gansu Province, China
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project of Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, Gansu Province, China
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Saftić D, Ban Ž, Matić J, Tumirv LM, Piantanida I. Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications. Curr Med Chem 2018; 26:5609-5624. [PMID: 29737251 DOI: 10.2174/0929867325666180508090640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/27/2018] [Accepted: 04/10/2018] [Indexed: 11/22/2022]
Abstract
Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder - nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.
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Affiliation(s)
- Dijana Saftić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Željka Ban
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Josipa Matić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Lidija-Marija Tumirv
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
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46
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Ma X, Kucera R, Goethe OF, Murphy SK, Herzon SB. Directed C-H Bond Oxidation of (+)-Pleuromutilin. J Org Chem 2018; 83:6843-6892. [PMID: 29664634 DOI: 10.1021/acs.joc.8b00462] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibiotics derived from the diterpene fungal metabolite (+)-pleuromutilin (1) are useful agents for the treatment Gram-positive infections in humans and farm animals. Pleuromutilins elicit slow rates of resistance development and minimal cross-resistance with existing antibiotics. Despite efforts aimed at producing new derivatives by semisynthesis, modification of the tricyclic core is underexplored, in part due to a limited number of functional group handles. Herein, we report methods to selectively functionalize the methyl groups of (+)-pleuromutilin (1) by hydroxyl-directed iridium-catalyzed C-H silylation, followed by Tamao-Fleming oxidation. These reactions provided access to C16, C17, and C18 monooxidized products, as well as C15/C16 and C17/C18 dioxidized products. Four new functionalized derivatives were prepared from the protected C17 oxidation product. C6 carboxylic acid, aldehyde, and normethyl derivatives were prepared from the C16 oxidation product. Many of these sequences were executed on gram scales. The efficiency and practicality of these routes provides an easy method to rapidly interrogate structure-activity relationships that were previously beyond reach. This study will inform the design of fully synthetic approaches to novel pleuromutilins and underscores the power of the hydroxyl-directed iridium-catalyzed C-H silylation reaction.
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Paukner S, Gruss A, Jensen JS. In Vitro Activity of Lefamulin against Sexually Transmitted Bacterial Pathogens. Antimicrob Agents Chemother 2018; 62:e02380-17. [PMID: 29530863 PMCID: PMC5923106 DOI: 10.1128/aac.02380-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/08/2018] [Indexed: 11/20/2022] Open
Abstract
The pleuromutilin antibiotic lefamulin demonstrated in vitro activity against the most relevant bacterial pathogens causing sexually transmitted infections (STI), including Chlamydia trachomatis (MIC50/90, 0.02/0.04 mg/liter; n = 15), susceptible and multidrug-resistant Mycoplasma genitalium (MIC range, 0.002 to 0.063 mg/liter; n = 6), and susceptible and resistant Neisseria gonorrhoeae (MIC50/90, 0.12/0.5 mg/liter; n = 25). The results suggest that lefamulin could be a promising first-line antibiotic for the treatment of STI, particularly in populations with high rates of resistance to standard-of-care antibiotics.
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Affiliation(s)
| | | | - Jørgen Skov Jensen
- Statens Serum Institut, Microbiology and Infection Control, Copenhagen, Denmark
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Sharkey LKR, O’Neill AJ. Antibiotic Resistance ABC-F Proteins: Bringing Target Protection into the Limelight. ACS Infect Dis 2018; 4:239-246. [PMID: 29376318 DOI: 10.1021/acsinfecdis.7b00251] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Members of the ATP-binding cassette (ABC)-F protein subfamily collectively mediate resistance to a broader range of clinically important antibiotic classes than any other group of resistance proteins and are widespread in pathogenic bacteria. Following over 25 years' of controversy regarding the mechanism by which these proteins work, it has recently been established that they provide antibiotic resistance through the previously recognized but underappreciated phenomenon of target protection; they bind to the ribosome to effect the release of ribosome-targeted antibiotics, thereby rescuing the translation apparatus from antibiotic-mediated inhibition. Here we review the ABC-F resistance proteins with an emphasis on their mechanism of action, first exploring the history of the debate about how these proteins work and outlining our current state of knowledge and then considering key questions to be addressed in understanding the molecular detail of their function.
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Affiliation(s)
- Liam K. R. Sharkey
- Antimicrobial Research Centre and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Alex J. O’Neill
- Antimicrobial Research Centre and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
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Haque F, Pi F, Zhao Z, Gu S, Hu H, Yu H, Guo P. RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:10.1002/wrna.1452. [PMID: 29105333 PMCID: PMC5739991 DOI: 10.1002/wrna.1452] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/25/2017] [Accepted: 09/01/2017] [Indexed: 12/23/2022]
Abstract
In recent years, RNA has attracted widespread attention as a unique biomaterial with distinct biophysical properties for designing sophisticated architectures in the nanometer scale. RNA is much more versatile in structure and function with higher thermodynamic stability compared to its nucleic acid counterpart DNA. Larger RNA molecules can be viewed as a modular structure built from a combination of many 'Lego' building blocks connected via different linker sequences. By exploiting the diversity of RNA motifs and flexibility of structure, varieties of RNA architectures can be fabricated with precise control of shape, size, and stoichiometry. Many structural motifs have been discovered and characterized over the years and the crystal structures of many of these motifs are available for nanoparticle construction. For example, using the flexibility and versatility of RNA structure, RNA triangles, squares, pentagons, and hexagons can be constructed from phi29 pRNA three-way-junction (3WJ) building block. This review will focus on 2D RNA triangles, squares, and hexamers; 3D and 4D structures built from basic RNA building blocks; and their prospective applications in vivo as imaging or therapeutic agents via specific delivery and targeting. Methods for intracellular cloning and expression of RNA molecules and the in vivo assembly of RNA nanoparticles will also be reviewed. WIREs RNA 2018, 9:e1452. doi: 10.1002/wrna.1452 This article is categorized under: RNA Methods > RNA Nanotechnology RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Farzin Haque
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Fengmei Pi
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Zhengyi Zhao
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Shanqing Gu
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Haibo Hu
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Hang Yu
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute; Comprehensive Cancer Center; and Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
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Matzov D, Eyal Z, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A. Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus. Nucleic Acids Res 2017; 45:10284-10292. [PMID: 28973455 PMCID: PMC5622323 DOI: 10.1093/nar/gkx658] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/18/2017] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus. Lincosamide antibiotics were proved to be effective against this pathogen. This small, albeit important group of antibiotics is mostly active against Gram-positive bacteria, but also used against selected Gram-negative anaerobes and protozoa. S. aureus resistance to lincosamides can be acquired by modifications and/or mutations in the rRNA and rProteins. Here, we present the crystal structures of the large ribosomal subunit of S. aureus in complex with the lincosamides lincomycin and RB02, a novel semisynthetic derivative and discuss the biochemical aspects of the in vitro potency of various lincosamides. These results allow better understanding of the drugs selectivity as well as the importance of the various chemical moieties of the drug for binding and inhibition.
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Eyal
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raphael I Benhamou
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehuda Halfon
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Micha Fridman
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
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