1
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Mohamed H, Child SA, Doherty DZ, Bruning JB, Bell SG. Structural determination and characterisation of the CYP105Q4 cytochrome P450 enzyme from Mycobacterium marinum. Arch Biochem Biophys 2024; 754:109950. [PMID: 38430969 DOI: 10.1016/j.abb.2024.109950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
The cytochrome P450 family of heme metalloenzymes (CYPs) catalyse important biological monooxygenation reactions. Mycobacterium marinum contains a gene encoding a CYP105Q4 enzyme of unknown function. Other members of the CYP105 CYP family have key roles in bacterial metabolism including the synthesis of secondary metabolites. We produced and purified the cytochrome P450 enzyme CYP105Q4 to enable its characterization. Several nitrogen-donor atom-containing ligands were found to bind to CYP105Q4 generating type II changes in the UV-vis absorbance spectrum. Based on the UV-vis absorbance spectra none of the potential substrate ligands we tested with CYP105Q4 were able to displace the sixth distal aqua ligand from the heme, though there was evidence for binding of oleic acid and amphotericin B. The crystal structure of CYP105Q4 in the substrate-free form was determined in an open conformation. A computational structural similarity search (Dali) was used to find the most closely related characterized relatives within the CYP105 family. The structure of CYP105Q4 enzyme was compared to the GfsF CYP enzyme from Streptomyces graminofaciens which is involved in the biosynthesis of a macrolide polyketide. This structural comparison to GfsF revealed conformational changes in the helices and loops near the entrance to the substrate access channel. A disordered B/C loop region, usually involved in substrate recognition, was also observed.
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Affiliation(s)
- Hebatalla Mohamed
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - Stella A Child
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - Daniel Z Doherty
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA, 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA, 5005, Australia.
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2
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Bian C, Zhang J, Zheng X, Qiao M, Li Y, Chen X, Si S. Synthesis and structure-activity relationships of novel 14-membered 2-fluoro ketolides with structural modification at the C11 position. Eur J Med Chem 2024; 267:116181. [PMID: 38354519 DOI: 10.1016/j.ejmech.2024.116181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
A series of novel C11 substituted 14-membered 2-fluoro ketolides were synthesized and evaluated for their antibacterial activity against erythromycin-resistant and erythromycin-susceptible clinical isolates and strains from ATCC. The overall antibacterial spectra of the semi-synthetic antibiotics are similar to that of telithromycin (TEL) and most of them exhibited excellent activity against Gram-positive bacteria (S. epidermidis, S. pneumoniae, S. aureus) and several Gram-negative bacteria (M. catarrhalis, H. influenza). Compounds 11c, 11g, 11h, 11q, 12a, 12b, 12d and 12e displayed 4-16 fold more potency than TEL against all the tested erythromycin-resistant S. epidermidis strains and S. pneumonia SPN19-8 and SPN19-8. Compounds 11b, 11c, 11e, 11g, 11h, 11q, 12a, 12b and 12c showed at least 8 fold potency than TEL against erythromycin-resistant M. catarrhalis BCA19-5 and BCA19-6. Molecular docking suggested compound 12d oriented the macrolide ring and side chain similarly to solithromycin (SOL). Noticeably an additional hydrogen bond was observed between the Lys90 residue of ribosome protein L22 and the carbamate group at the C11 position, which might provide a rational explanation for the enhanced antibacterial activity of target compounds. Therefore this research would offer a new perspective for further structural optimization of the C11 side chain. Based on the results of antibacterial activity, cytotoxicity and structural diversity, 5 compounds (11a, 11b, 11h, 12d and 12i) were selected for the stability testing of human liver microsomes and compound 11a exhibited preferable metabolic stability.
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Affiliation(s)
- Cong Bian
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Jing Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Xiao Zheng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Mengqian Qiao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China
| | - Yan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
| | - Xiaofang Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1 TiantanXili, Beijing 100050, China.
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3
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Dhindwal P, Myziuk I, Ruzzini A. Macrolide esterases: current threats and opportunities. Trends Microbiol 2023; 31:1199-1201. [PMID: 37689489 DOI: 10.1016/j.tim.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/11/2023]
Abstract
Antibiotics often contain ester bonds. The macrocyclic lactones of macrolides are pre-eminent examples in which ester bonds are essential to the form and function of antibiotics. Bacterial macrolide esterases that hydrolyze these macrocyclic lactones to confer antimicrobial resistance (AMR) are the topic of this forum. We provide insight into their role in agricultural systems and discuss their emergence and their potential extensibility to bioremediation efforts.
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Affiliation(s)
- Poonam Dhindwal
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5B4
| | - Iryna Myziuk
- Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5
| | - Antonio Ruzzini
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5B4; Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5E5.
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4
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Umeda K, Iwasaki A, Taguchi R, Kurisawa N, Jeelani G, Nozaki T, Suenaga K. Isolation and Structure Determination of Akunolides, Macrolide Glycosides from a Marine Okeania sp. Cyanobacterium. J Nat Prod 2023; 86:2529-2538. [PMID: 37945375 DOI: 10.1021/acs.jnatprod.3c00742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Akunolides A (1), B (2), C (3), and D (4), new macrolide glycosides, were isolated from a marine Okeania sp. cyanobacterium. Their structures were elucidated by spectroscopic analyses and derivatization reactions. Akunolides A-D (1-4) are classified as 16-membered macrolide glycosides, which are relatively rare structures for marine cyanobacterium-derived natural products. Akunolides A-D (1-4) showed moderate antitrypanosomal activities against Trypanosoma brucei rhodesiense, with IC50 values ranging from 11 to 14 μM. Furthermore, akunolides A (1) and C (3) exhibited no cytotoxicity against normal human WI-38 cells even at a concentration of 150 μM.
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Affiliation(s)
- Kairi Umeda
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Arihiro Iwasaki
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Raimu Taguchi
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Naoaki Kurisawa
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Ghulam Jeelani
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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5
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Sahana MH, Paul D, Sharma H, Goswami RK. Total Synthesis of Antibacterial Macrolide Sorangiolide A. Org Lett 2023; 25:7827-7831. [PMID: 37856450 DOI: 10.1021/acs.orglett.3c03066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A convergent route for the asymmetric total synthesis of antibacterial macrolide sorangiolide A has been developed for the first time. The key feature of this synthesis includes Krische iridium-catalyzed anti-diastereoselective carbonyl crotylation, Crimmins acetate aldol, Yamaguchi esterification, Julia-Kocienski olefination, Horner-Wadsworth-Emmons olefination, and ring-closing metathesis. The origin of the low intensity of the 13C{1H} NMR signals of the C1 and C2 centers of the natural product has been investigated, disclosing possible forms of existence for the natural product in the solution phase.
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Affiliation(s)
- Moinul Haque Sahana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, West Bengal 700032, India
| | - Debobrata Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, West Bengal 700032, India
| | - Himangshu Sharma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, West Bengal 700032, India
| | - Rajib Kumar Goswami
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, West Bengal 700032, India
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6
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Umaña CA, Henry JL, Saltzman CT, Sackett DL, Jenkins LM, Taylor RE. Linear (-)-Zampanolide: Flexibility in Conformation-Activity Relationships. ChemMedChem 2023; 18:e202300292. [PMID: 37552215 PMCID: PMC10615712 DOI: 10.1002/cmdc.202300292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
Through an understanding of the conformational preferences of the polyketide natural product (-)-zampanolide, and the structural motifs that control these preferences, we developed a linear zampanolide analogue that exhibits potent cytotoxicity against cancer cell lines. This discovery provides a set of three structural handles for further structure-activity relationship (SAR) studies of this potent microtubule-stabilizing agent. Moreover, it provides additional evidence of the complex relationship between ligand preorganization, conformational flexibility, and biological potency. In contrast to medicinal chemistry dogma, these results demonstrate that increased overall conformational flexibility is not necessarily detrimental to protein binding affinity and biological activity.
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Affiliation(s)
- Christian A Umaña
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Jeffrey L Henry
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Claire T Saltzman
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa M Jenkins
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard E Taylor
- Department of Chemistry and Biochemistry and the Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, IN 46556-5670, USA
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7
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Wang R, Bao Y, Dong Y, Dong Y, Li H. Genome-directed discovery of antiproliferative bafilomycins from a deepsea-derived Streptomyces samsunensis. Bioorg Chem 2023; 138:106599. [PMID: 37320913 DOI: 10.1016/j.bioorg.2023.106599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Genomic bioinformatics analysis identified a bafilomycin biosynthetic gene cluster (named bfl) in the deepsea-derived S. samsunensis OUCT16-12, from which two new (1 and 2, named bafilomycins R and S) along with four known (3-6) bafilomycins were targetly obtained. The structure of 3 was clearly identified for the first time, thus named bafilomycin T herein. Differ from the fumarate substitution at C-21 of known bafilomycins, its location on C-23 is a unique feature of 1 and 2. The stereochemistry of the compounds was established based on NOE correlations, ketoreductase (KR)-types in PKS modules of bfl, and ECD calculations. Moreover, a detailed biosynthetic model of 1-6 in S. samsunensis OUCT16-12 was provided based on the gene function prediction and sequence identity. Compared with the positive control doxorubicin, 1-6 showed more potent antiproliferative activities against drug-resistant lung cancer cell line A549-Taxol, with IC50 values ranging from 0.07 μM to 1.79 μM, which arrested cell cycle in G0/G1 phase to hinder proliferation.
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Affiliation(s)
- Runyi Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yilei Bao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yujing Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yun Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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8
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Kumar P, Nalli Y, Singh S, Wakchaure PD, Gor R, Ghadge VA, Kim E, Ramalingam S, Azger Dusthackeer VN, Yoon YJ, Ganguly B, Shinde PB. Dactylides A-C, three new bioactive 22-membered macrolides produced by Dactylosporangium aurantiacum. J Antibiot (Tokyo) 2023; 76:503-510. [PMID: 37208457 DOI: 10.1038/s41429-023-00632-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/15/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023]
Abstract
Three new 22-membered polyol macrolides, dactylides A-C (1-3), were isolated from Dactylosporangium aurantiacum ATCC 23491 employing repeated chromatographic separations, and their structures were established based on detailed analysis of NMR and MS data. The relative configurations at the stereocenters were established via vicinal 1H-1H coupling constants, NOE correlations, and by application of Kishi's universal NMR database. In order to get insights into the biosynthetic pathway of 1-3, the genome sequence of the producer strain D. aurantiacum was obtained and the putative biosynthetic gene cluster encoding their biosynthesis was identified through bioinformatic analysis using antiSMASH. Compounds 1-3 showed significant in-vitro antimycobacterial and cytotoxic activity.
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Affiliation(s)
- Pankaj Kumar
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Yedukondalu Nalli
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Sanju Singh
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Padmaja D Wakchaure
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Computation and Simulation Unit, Analytical and Environmental Science Division and Centralized Instrument Facility, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
| | - Ravi Gor
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Vishal A Ghadge
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Satish Ramalingam
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - V N Azger Dusthackeer
- Department of Bacteriology, National Institute for Research in Tuberculosis, ICMR, Sathyamoorty road, Chetpet, Chennai, 600031, Tamil Nadu, India
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bishwajit Ganguly
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Computation and Simulation Unit, Analytical and Environmental Science Division and Centralized Instrument Facility, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
| | - Pramod B Shinde
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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9
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Takada K, Oku N, Peach ML, Ransom TT, Henrich CJ, Gustafson KR. Enigmazole Phosphomacrolides from the Marine Sponge Cinachyrella enigmatica. J Org Chem 2023; 88:10996-11002. [PMID: 37471139 DOI: 10.1021/acs.joc.3c00963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Enigmazole B (1) and four new analogues, cis-enigmazole B (2), dehydroenigmazole B (3), enigmimide B (4), and enigmimide A (5), were isolated from the marine sponge Cinachyrella enigmatica. Their planar structures were elucidated by detailed NMR and MS data analyses, which established 1-3 to be oxazole-substituted 18-membered phosphomacrolides, while 4 and 5 were oxazole ring-opened congeners. The relative and absolute configurations in 1 were determined by a combination of chemical transformations and spectroscopic analyses. Photooxidation of the oxazole moiety in 1 gave enigmimide B (4), thus establishing that 4 has the same absolute configuration of 1. Enigmazole B (1) along with analogues 2 and 3 showed cytotoxicity against murine IC-2 mast cells with IC50 values of 3.6-7.0 μM. The enigmimides (4 and 5) and dephosphoenigmazoles did not show cytotoxicity (IC50 > 10 μM), implying that both the oxazole moiety and the phosphate group are necessary for the cytotoxicity of the enigmazole class macrolides.
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Affiliation(s)
- Kentaro Takada
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Naoya Oku
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Megan L Peach
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United States
| | - Tanya T Ransom
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Curtis J Henrich
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United States
| | - Kirk R Gustafson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
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10
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Harris CM, Hintze L, Gaillard S, Tanniou S, Small H, Reece KS, Tillmann U, Krock B, Harris TM. Mass spectrometric characterization of the seco acid formed by cleavage of the macrolide ring of the algal metabolite goniodomin A. Toxicon 2023; 231:107159. [PMID: 37210046 DOI: 10.1016/j.toxicon.2023.107159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Goniodomin A (GDA) is a polyketide macrolide produced by multiple species of the marine dinoflagellate genus Alexandrium. GDA is unusual in that it undergoes cleavage of the ester linkage under mild conditions to give mixtures of seco acids (GDA-sa). Ring-opening occurs even in pure water although the rate of cleavage accelerates with increasing pH. The seco acids exist as a dynamic mixture of structural and stereo isomers which is only partially separable by chromatography. Freshly prepared seco acids show only end absorption in the UV spectrum but a gradual bathochromic change occurs, which is consistent with formation of α,β-unsaturated ketones. Use of NMR and crystallography is precluded for structure elucidation. Nevertheless, structural assignments can be made by mass spectrometric techniques. Retro-Diels-Alder fragmentation has been of value for independently characterizing the head and tail regions of the seco acids. The chemical transformations of GDA revealed in the current studies help clarify observations made on laboratory cultures and in the natural environment. GDA has been found to reside mainly within the algal cells while the seco acids are mainly external with the transformation of GDA to the seco acids occurring largely outside the cells. This relationship, plus the fact that GDA is short-lived in growth medium whereas GDA-sa is long-lived, suggests that the toxicological properties of GDA-sa in its natural environment are more important for the survival of the Alexandrium spp. than those of GDA. The structural similarity of GDA-sa to that of monensin is noted. Monensin has strong antimicrobial properties, attributed to its ability to transport sodium ions across cell membranes. We propose that toxic properties of GDA may primarily be due to the ability of GDA-sa to mediate metal ion transport across cell membranes of predator organisms.
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Affiliation(s)
- Constance M Harris
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
| | - Luisa Hintze
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung (AWI), 27570, Bremerhaven, Germany
| | - Sylvain Gaillard
- Department of Aquatic Health Sciences, Virginia Institute of Marine Science (VIMS), William & Mary, Gloucester Point, VA, 23062, USA
| | - Simon Tanniou
- Ifremer, PHYTOX, Laboratoire METALG, F-44000, Nantes, France
| | - Hamish Small
- Department of Aquatic Health Sciences, Virginia Institute of Marine Science (VIMS), William & Mary, Gloucester Point, VA, 23062, USA
| | - Kimberly S Reece
- Department of Aquatic Health Sciences, Virginia Institute of Marine Science (VIMS), William & Mary, Gloucester Point, VA, 23062, USA
| | - Urban Tillmann
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung (AWI), 27570, Bremerhaven, Germany
| | - Bernd Krock
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung (AWI), 27570, Bremerhaven, Germany
| | - Thomas M Harris
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
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11
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Caradec T, Trivelli X, Desmecht E, Peucelle V, Khalife J, Hartkoorn RC. Dactylosporolides: Glycosylated Macrolides from Dactylosporangium fulvum. J Nat Prod 2022; 85:2714-2722. [PMID: 36512509 PMCID: PMC9791991 DOI: 10.1021/acs.jnatprod.2c00484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 05/30/2023]
Abstract
A series of novel macrolides were discovered from the culture supernatant of the rare soil actinobacteria Dactylosporangium fulvum and named dactylosporolides A-C. The structure and absolute configuration of these dactylosporolides were defined using a combination of NMR structural elucidation and analysis of the dactylosporolide biosynthetic gene cluster. Together these data revealed dactylosporolides to be composed of a central 22-membered macrolactone with an internal hemiketal ring and a protruding ketide tail that were (poly)glycosylated at two distal parts. While bearing no antibiotic activity, these dactylosporolides displayed activity against Plasmodium falciparum 3D7.
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Affiliation(s)
- Thibault Caradec
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Xavier Trivelli
- Univ.
Lille, CNRS, INRAE, Centrale Lille, Univ. Artois, FR 2638—IMEC—Institut
Michel-Eugène Chevreul, Lille 59000, France
| | - Eva Desmecht
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Veronique Peucelle
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jamal Khalife
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ruben C. Hartkoorn
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
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12
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Lu S, Zhou T, Fukaya K, Harunari E, Oku N, Urabe D, Igarashi Y. Krasilnikolides A and B and Detalosylkrasilnikolide A, Cytotoxic 20-Membered Macrolides from the Genus Krasilnikovia: Assignment of Anomeric Configuration by J-Based Configuration Analysis. J Nat Prod 2022; 85:2796-2803. [PMID: 36482689 DOI: 10.1021/acs.jnatprod.2c00781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A chemical investigation of strain RD003821, belonging to the underexplored actinomycetes genus Krasilnikovia, led to the discovery of three novel polyketides: two 20-membered glycomacrolides, krasilnikolides A (1) and B (2), and an aglycone of 1, detalosylkrasilnikolide A (3). A major challenge in the structure elucidation of 1 was to determine the anomeric configuration of the α-l-6-deoxytalose (6dTal) unit, which was achieved by J-based configuration analysis (JBCA) that incorporated anomeric carbon- and proton-specific two-bond 13C-1H spin-spin coupling constants as diagnostic parameters. The updated criteria for the conformation/configuration assignment facilitated discrimination of three out of four stereochemical variants at the anomeric and the adjacent C2 positions, which expanded the scope of the JBCA method to determination of the anomeric configuration of aldohexopyranoses. Compounds 1 and 2 are the first macrolides decorated by 6dTal. Compounds 1-3 exhibited cytotoxicity against P388 murine leukemia cells with IC50 values of 14, 8.4, and 3.9 μM, respectively. In addition, 1-3 were antibacterial against the Gram-positive bacterium Kocuria rhizophila with MIC values of 25, 50, and 100 μg/mL. 1 was inhibitory against Staphylococcus aureus with an MIC of 50 μg/mL.
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Affiliation(s)
- Shiyang Lu
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Tao Zhou
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Keisuke Fukaya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Daisuke Urabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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13
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Liu J, Chen Y, Luesch H, Ye T. Total Synthesis of des-Thiomethyllooekeyolide A. Org Lett 2022; 24:7260-7264. [PMID: 36150127 PMCID: PMC9635982 DOI: 10.1021/acs.orglett.2c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first asymmetric total synthesis and validation of the structural assignment of des-thiomethyllooekeyolide A (3) is described, which features a Shiina macrolactonization and a late-stage pyran-hemiketal formation. The eight stereogenic centers of the C16-polyketide chain were installed by sequential aldol and crotylation reactions.
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Affiliation(s)
- Junyang Liu
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529020, China
| | - Ying Chen
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, University Town, Xili, Shenzhen, 518055, China
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, USA
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, University Town, Xili, Shenzhen, 518055, China
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14
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Ghosh AK, Yuan H. Total Syntheses of the Proposed Structure of Iriomoteolide-1a, -1b and Synthesis of Three Derivatives for Structural Studies. Mar Drugs 2022; 20:587. [PMID: 36286411 PMCID: PMC9605196 DOI: 10.3390/md20100587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 12/10/2023] Open
Abstract
Iriomoteolide-1a and iriomoteolide-1b are very potent cytotoxic agents, isolated from marine dinoflagellates. We carried out the enantioselective syntheses of the proposed structures of these natural products. However, our analysis of the NMR spectra of the synthetic iriomoteolide-1a and the natural products revealed that the structures of iriomoteolide-1a and iriomoteolide-1b were assigned incorrectly. Based upon our detailed analysis of the spectral data of the synthetic iriomoteolide-1a and the natural products, we rationally designed three diastereomers of the proposed structure of 1 in an effort to assign the correct structures. The key steps of our syntheses of the proposed structures of iriomoteolides involved a highly diastereoselective ene reaction, a carbocupration that utilized a Gilman reagent, a Julia-Kocienski olefination to couple fragments, and Yamaguchi macrolactonization to form the target macrolactone. This synthetic route was then utilized to carry out syntheses of three diastereomers to the proposed structure of 1. These diastereomeric structures show close similarities to natural iriomoteolide-1a; however, there were differences in their spectral data. While natural iriomoteolides exhibited potent cytotoxicies, our preliminary biological evaluation of synthetic iriomoteolide-1a, iriomoteolide-1b, and all three synthetic derivatives did not show any appreciable cytotoxic properties.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry, Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hao Yuan
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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15
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Tarazona G, Fernández R, Pérez M, Millán RE, Jiménez C, Rodríguez J, Cuevas C. Enigmazole C: A Cytotoxic Macrocyclic Lactone and Its Ring-Opened Derivatives from a New Species of Homophymia Sponge. J Nat Prod 2022; 85:1059-1066. [PMID: 35234467 PMCID: PMC9040057 DOI: 10.1021/acs.jnatprod.1c01179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Indexed: 06/14/2023]
Abstract
A new macrolide, enigmazole C (1), and two additional analogues, enigmazoles E (2) and D (3), were obtained from a new species of the Homophymia genus as part of an ongoing discovery program at PharmaMar to study cytotoxic substances from marine sources. The structures were fully characterized by cumulative analyses of NMR, IR, and MS spectra, along with density functional theory computational calculations. All three of the new compounds feature an unusual 2,3-dihydro-4H-pyran-4-one moiety, but only enigmazoles C (1) and D (3) showed cytotoxic activity in the micromolar range against A-549 (lung), HT-29 (colon), MDA-MB-231 (breast), and PSN-1 (pancreas) tumor cells.
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Affiliation(s)
- Guillermo Tarazona
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
| | - Rogelio Fernández
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
| | - Marta Pérez
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
| | - Ramón E. Millán
- Departmento
de Química, Facultad de Ciencias and Centro de Investigacions
Científicas Avanzadas (CICA), Universidade
de A Coruña, 15071 A Coruña, Spain
| | - Carlos Jiménez
- Departmento
de Química, Facultad de Ciencias and Centro de Investigacions
Científicas Avanzadas (CICA), Universidade
de A Coruña, 15071 A Coruña, Spain
| | - Jaime Rodríguez
- Departmento
de Química, Facultad de Ciencias and Centro de Investigacions
Científicas Avanzadas (CICA), Universidade
de A Coruña, 15071 A Coruña, Spain
| | - Carmen Cuevas
- R&D, PharmaMar, Avenida De los Reyes, 1, Pol. Ind. La Mina-Norte, 28770-Colmenar Viejo, Madrid, Spain
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16
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An JS, Lim HJ, Lee JY, Jang YJ, Nam SJ, Lee SK, Oh DC. Hamuramicin C, a Cytotoxic Bicyclic Macrolide Isolated from a Wasp Gut Bacterium. J Nat Prod 2022; 85:936-942. [PMID: 35362983 DOI: 10.1021/acs.jnatprod.1c01075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A new bicyclic macrolide, hamuramicin C (1), was isolated from Streptomyces sp. MBP16, a gut bacterial strain of the wasp Vespa crabro flavofasciata. Its 22-membered macrocyclic lactone structure was determined by NMR and mass spectrometry. The relative configurations of hamuramicin C (1) were assigned by J-based configuration analysis utilizing 1H rotating frame Overhauser effect spectroscopy and heteronuclear long-range coupling NMR spectroscopy. Genomic and bioinformatic analyses of the bacterial strain enabled identification of the type-I polyketide synthase pathway, which employs a trans-acyltransferase system. The absolute configurations of 1 were proposed based on the analysis of the sequences of ketoreductases in the modular gene cluster. Moreover, hamuramicin C (1) demonstrated significant inhibitory activity against diverse human cancer cell lines (HCT116, A549, SNU-638, SK-HEP-1, and MDA-MB-231).
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyung-Ju Lim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Yun Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Joon Jang
- Natura Center of Life and Environment, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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17
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Abstract
We report the first total syntheses of strasseriolide A and B. Strasseriolide B shows potent activity against the wild-type malaria parasite Plasmodium falciparum and good activity against a chloroquine-resistant strain. A convergent strategy was envisioned with an aldehyde-acid fragment and a vinyl iodide-alcohol fragment. Both fragments were prepared using chiral pool starting materials. They were combined with a Yamaguchi esterification and cyclized with a Nozaki-Hiyama-Kishi reaction. Strasseriolide B was assembled in a 16-step LLS.
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Affiliation(s)
- Leah J Salituro
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Jessica E Pazienza
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Scott D Rychnovsky
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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18
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Kragol G, Steadman VA, Marušić Ištuk Z, Čikoš A, Bosnar M, Jelić D, Ergović G, Trzun M, Bošnjak B, Bokulić A, Padovan J, Glojnarić I, Eraković Haber V. Unprecedented Epimerization of an Azithromycin Analogue: Synthesis, Structure and Biological Activity of 2'-Dehydroxy-5″-Epi-Azithromycin. Molecules 2022; 27:1034. [PMID: 35164298 PMCID: PMC8838534 DOI: 10.3390/molecules27031034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 11/30/2022] Open
Abstract
Certain macrolide antibiotics, azithromycin included, possess anti-inflammatory properties that are considered fundamental for their efficacy in the treatment of chronic inflammatory diseases, such as diffuse pan-bronchiolitis and cystic fibrosis. In this study, we disclose a novel azithromycin analog obtained via Barton-McCombie oxidation during which an unprecedented epimerization on the cladinose sugar occurs. Its structure was thoroughly investigated using NMR spectroscopy and compared to the natural epimer, revealing how the change in configuration of one single stereocenter (out of 16) profoundly diminished the antimicrobial activity through spatial manipulation of ribosome binding epitopes. At the same time, the anti-inflammatory properties of parent macrolide were retained, as demonstrated by inhibition of LPS- and cigarette-smoke-induced pulmonary inflammation. Not surprisingly, the compound has promising developable properties including good oral bioavailability and a half-life that supports once-daily dosing. This novel anti-inflammatory candidate has significant potential to fill the gap in existing anti-inflammatory agents and broaden treatment possibilities.
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Affiliation(s)
- Goran Kragol
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | | | - Zorica Marušić Ištuk
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Ana Čikoš
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Martina Bosnar
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Dubravko Jelić
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Gabrijela Ergović
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Marija Trzun
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Berislav Bošnjak
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Ana Bokulić
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Jasna Padovan
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Ines Glojnarić
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
| | - Vesna Eraković Haber
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (Z.M.I.); (A.Č.); (M.B.); (D.J.); (G.E.); (M.T.); (B.B.); (A.B.); (J.P.); (I.G.); (V.E.H.)
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19
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Hikima A, Asamizu S, Onaka H, Zhang H, Tomoda H, Koyama N. Kimidinomycin, a new antibiotic against Mycobacterium avium complex, produced by Streptomyces sp. KKTA-0263. J Antibiot (Tokyo) 2022; 75:72-76. [PMID: 34949834 DOI: 10.1038/s41429-021-00494-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 02/08/2023]
Abstract
During our screening for antibiotics against Mycobacterium avium complex (MAC) with a mass spectrometry network-based indexing approach, a new compound named kimidinomycin was isolated from the culture broth of Streptomyces sp. KKTA-0263 by solvent extraction, HP20 column chromatography, and preparative HPLC. From the structural elucidation, the compound possesses a 38-membered macrolide structure with an N-methylguanidyl group at the terminal side chain. The compound exhibited antimycobacterial activity against M. avium, M. intracellulare, M. smegmatis, and M. bovis BCG with respective MIC values of 12.5, 0.78, 12.5, and 25.0 µg ml-1.
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Affiliation(s)
- Ayumi Hikima
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Huiping Zhang
- RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroshi Tomoda
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
- Drug Discovery Laboratory, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Nobuhiro Koyama
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
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20
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Al-Fadhli AA, Threadgill MD, Mohammed F, Sibley P, Al-Ariqi W, Parveen I. Macrolides from rare actinomycetes: Structures and bioactivities. Int J Antimicrob Agents 2022; 59:106523. [PMID: 35041941 DOI: 10.1016/j.ijantimicag.2022.106523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 11/19/2022]
Abstract
Rare actinomycetes are the sources of numerous biologically active secondary metabolites with diverse structures. Among them are macrolides, which have been shown to display several antibiotic activities. In this review, twenty-six groups of macrolides from rare actinomycetes are presented, with their bioactivities and structures of representatives from each group. It has been divided according to the classes of macrolides. The most interesting groups with a wide range of biological activities are ammocidins, bafilomycins, neomaclafungins, rosaramicins, spinosyns, and tiacumicins. Most macrolides are obtained from the genus, Micromonospora, with smaller contributions from genera such as Saccharothrix, Amycolatopsis, Nocardiopsis and Catenulispora. These macrolides display unique cytotoxic, antibacterial, antifungal, antimicrobial, insecticidal, anti-trypanosomal, antimalarial, antiprotozoal, antimycobacterial and anti-herpetic activity. Based on their noticeable bioactivities and diverse structures, macrolides from rare actinomycetes deserve to be investigated further for future applications in medicine. This work highlights the bioactivities and structures of important classes of macrolides from rare actinomycetes, which could be used in medicine in the future or which are already in the market.
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Affiliation(s)
- Ammar A Al-Fadhli
- Department of Chemistry, Faculty of Science, Sana'a University, Sana'a, Republic of Yemen; Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom.
| | - Michael D Threadgill
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom; Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Faez Mohammed
- School of Environmental Sciences, University of Guelph, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada; Faculty of Applied Science-Arhab, Sana'a University, Sana'a, Yemen.
| | - Paul Sibley
- School of Environmental Sciences, University of Guelph, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada
| | - Wadie Al-Ariqi
- Department of Chemistry, Faculty of Science, Sana'a University, Sana'a, Republic of Yemen
| | - Ifat Parveen
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom
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21
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Alihodžić S, Čipčić Paljetak H, Čikoš A, Elenkov IJ. New Bicyclic Azalide Macrolides Obtained by Tandem Palladium Catalyzed Allylic Alkylation/Conjugated Addition Reaction. Molecules 2022; 27:molecules27020432. [PMID: 35056746 PMCID: PMC8781410 DOI: 10.3390/molecules27020432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/27/2021] [Accepted: 12/31/2021] [Indexed: 01/27/2023] Open
Abstract
Unprecedented tandem allylic alkylation/intermolecular Michael addition was used in the preparation of novel bicyclic azalides. NMR spectroscopy was used not only to unambiguously determine and characterize the structures of these unexpected products of chemical reaction but also to investigate the effect the rigid bicyclic modification has on the conformation of the whole molecule. Thus, some of the macrolides prepared showed antibacterial activity in the range of well-known antibiotic drug azithromycin.
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Affiliation(s)
- Sulejman Alihodžić
- Department of Chemistry, Fidelta Ltd. (Selvita Group), Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia;
| | - Hana Čipčić Paljetak
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, Šalata 2, 10000 Zagreb, Croatia;
| | - Ana Čikoš
- NMR Center, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia;
| | - Ivaylo Jivkov Elenkov
- Department of Chemistry, Fidelta Ltd. (Selvita Group), Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia;
- Correspondence:
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22
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Barone ME, Murphy E, Parkes R, Fleming GTA, Campanile F, Thomas OP, Touzet N. Antibacterial Activity and Amphidinol Profiling of the Marine Dinoflagellate Amphidinium carterae (Subclade III). Int J Mol Sci 2021; 22:ijms222212196. [PMID: 34830076 PMCID: PMC8618426 DOI: 10.3390/ijms222212196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 12/24/2022] Open
Abstract
Microalgae have received growing interest for their capacity to produce bioactive metabolites. This study aimed at characterising the antimicrobial potential of the marine dinoflagellate Amphidinium carterae strain LACW11, isolated from the west of Ireland. Amphidinolides have been identified as cytotoxic polyoxygenated polyketides produced by several Amphidinium species. Phylogenetic inference assigned our strain to Amphidinium carterae subclade III, along with isolates interspersed in different geographic regions. A two-stage extraction and fractionation process of the biomass was carried out. Extracts obtained after stage-1 were tested for bioactivity against bacterial ATCC strains of Staphylococcus aureus, Enterococcus faecalis, Escherichia coli and Pseudomonas aeruginosa. The stage-2 solid phase extraction provided 16 fractions, which were tested against S. aureus and E. faecalis. Fractions I, J and K yielded minimum inhibitory concentrations between 16 μg/mL and 256 μg/mL for both Gram-positive. A targeted metabolomic approach using UHPLC-HRMS/MS analysis applied on fractions G to J evidenced the presence of amphidinol type compounds AM-A, AM-B, AM-22 and a new derivative dehydroAM-A, with characteristic masses of m/z 1361, 1463, 1667 and 1343, respectively. Combining the results of the biological assays with the targeted metabolomic approach, we could conclude that AM-A and the new derivative dehydroAM-A are responsible for the detected antimicrobial bioactivity.
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Affiliation(s)
- Maria Elena Barone
- Centre for Environmental Research, Sustainability and Innovation, Department of Environmental Science, School of Science, Institute of Technology Sligo, Ash Ln, Ballytivnan, F91 YW50 Sligo, Ireland; (M.E.B.); (R.P.)
| | - Elliot Murphy
- Marine Biodiversity, School of Chemistry, Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland;
| | - Rachel Parkes
- Centre for Environmental Research, Sustainability and Innovation, Department of Environmental Science, School of Science, Institute of Technology Sligo, Ash Ln, Ballytivnan, F91 YW50 Sligo, Ireland; (M.E.B.); (R.P.)
| | - Gerard T. A. Fleming
- Discipline of Microbiology, School of Natural Science, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland;
| | - Floriana Campanile
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia n. 97, 95123 Catania, Italy;
| | - Olivier P. Thomas
- Marine Biodiversity, School of Chemistry, Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland;
- Correspondence: (O.P.T.); (N.T.)
| | - Nicolas Touzet
- Centre for Environmental Research, Sustainability and Innovation, Department of Environmental Science, School of Science, Institute of Technology Sligo, Ash Ln, Ballytivnan, F91 YW50 Sligo, Ireland; (M.E.B.); (R.P.)
- Correspondence: (O.P.T.); (N.T.)
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23
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Harris CM, Krock B, Tillmann U, Tainter CJ, Stec DF, Andersen AJC, Larsen TO, Reece KS, Harris TM. Alkali Metal- and Acid-Catalyzed Interconversion of Goniodomin A with Congeners B and C. J Nat Prod 2021; 84:2554-2567. [PMID: 34520205 DOI: 10.1021/acs.jnatprod.1c00586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Goniodomin A (GDA, 1) is a phycotoxin produced by at least four species of Alexandrium dinoflagellates that are found globally in brackish estuaries and lagoons. It is a linear polyketide with six oxygen heterocyclic rings that is cyclized into a macrocyclic structure via lactone formation. Two of the oxygen heterocycles in 1 comprise a spiro-bis-pyran, whereas goniodomin B (GDB) contains a 2,7-dioxabicyclo[3.3.1]nonane ring system fused to a pyran. When H2O is present, 1 undergoes facile conversion to isomer GDB and to an α,β-unsaturated ketone, goniodomin C (GDC, 7). GDB and GDC can be formed from GDA by cleavage of the spiro-bis-pyran ring system. GDA, but not GDB or GDC, forms a crown ether-type complex with K+. Equilibration of GDA with GDB and GDC is observed in the presence of H+ and of Na+, but the equilibrated mixtures revert to GDA upon addition of K+. Structural differences have been found between the K+ and Na+ complexes. The association of GDA with K+ is strong, while that with Na+ is weak. The K+ complex has a compact, well-defined structure, whereas Na+ complexes are an ill-defined mixture of species. Analyses of in vitro A. monilatum and A. hiranoi cultures indicate that only GDA is present in the cells; GDB and GDC appear to be postharvest transformation products.
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Affiliation(s)
- Constance M Harris
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Bernd Krock
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung (AWI), Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Urban Tillmann
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung (AWI), Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Craig J Tainter
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Donald F Stec
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Aaron J C Andersen
- Department of Biotechnology and Biomedicine, Søltofts Plads, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Søltofts Plads, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Kimberly S Reece
- Virginia Institute of Marine Science (VIMS), William & Mary, Gloucester Point, Virginia 23062, United States
| | - Thomas M Harris
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Virginia Institute of Marine Science (VIMS), William & Mary, Gloucester Point, Virginia 23062, United States
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24
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Breiner-Goldstein E, Eyal Z, Matzov D, Halfon Y, Cimicata G, Baum M, Rokney A, Ezernitchi A, Lowell A, Schmidt J, Rozenberg H, Zimmerman E, Bashan A, Valinsky L, Anzai Y, Sherman D, Yonath A. Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida. Nucleic Acids Res 2021; 49:9560-9573. [PMID: 34417608 PMCID: PMC8450085 DOI: 10.1093/nar/gkab684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 02/02/2023] Open
Abstract
Macrolides have been effective clinical antibiotics for over 70 years. They inhibit protein biosynthesis in bacterial pathogens by narrowing the nascent protein exit tunnel in the ribosome. The macrolide class of natural products consist of a macrolactone ring linked to one or more sugar molecules. Most of the macrolides used currently are semi-synthetic erythromycin derivatives, composed of a 14- or 15-membered macrolactone ring. Rapidly emerging resistance in bacterial pathogens is among the most urgent global health challenges, which render many antibiotics ineffective, including next-generation macrolides. To address this threat and advance a longer-term plan for developing new antibiotics, we demonstrate how 16-membered macrolides overcome erythromycin resistance in clinically isolated Staphylococcus aureus strains. By determining the structures of complexes of the large ribosomal subunit of Deinococcus radiodurans (D50S) with these 16-membered selected macrolides, and performing anti-microbial studies, we identified resistance mechanisms they may overcome. This new information provides important insights toward the rational design of therapeutics that are effective against drug resistant human pathogens.
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Affiliation(s)
- Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Donna Matzov
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Moti Baum
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Assaf Rokney
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Analia V Ezernitchi
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Andrew N Lowell
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Jennifer J Schmidt
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Haim Rozenberg
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
| | - Lea Valinsky
- Government Central Laboratories, Ministry of Health, Jerusalem 91342, Israel
| | - Yojiro Anzai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-0072, Japan
| | - David H Sherman
- Life Sciences Institute and Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel
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25
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Grell T, Barbero M, Pattarino F, Giovenzana GB, Colombo V. Solvatomorphism of Moxidectin. Molecules 2021; 26:molecules26164869. [PMID: 34443452 PMCID: PMC8398095 DOI: 10.3390/molecules26164869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/02/2021] [Accepted: 08/07/2021] [Indexed: 11/16/2022] Open
Abstract
The solvatomorphism of the anthelmintic drug moxidectin is investigated, and a new solvatomorph with nitromethane is reported. Moreover, the hitherto unknown crystal structures of the solvatomorphs with ethanol and 2-propanol are reported and discussed. The thermal characterization of these solvatomorphs through variable-temperature powder X-ray diffraction analysis (VT-PXRD) is also described, providing new insights into the crystallochemistry of this active pharmaceutical ingredient.
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Affiliation(s)
- Toni Grell
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, I-20133 Milano, Italy;
| | - Mauro Barbero
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale A. Avogadro, Largo Donegani 2/3, I-28100 Novara, Italy; (M.B.); (F.P.); (G.B.G.)
| | - Franco Pattarino
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale A. Avogadro, Largo Donegani 2/3, I-28100 Novara, Italy; (M.B.); (F.P.); (G.B.G.)
| | - Giovanni Battista Giovenzana
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale A. Avogadro, Largo Donegani 2/3, I-28100 Novara, Italy; (M.B.); (F.P.); (G.B.G.)
| | - Valentina Colombo
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, I-20133 Milano, Italy;
- Correspondence: ; Tel.: +39-02-5031-4450
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26
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Shi P, Li Y, Zhu J, Shen Y, Wang H. Targeted Discovery of the Polyene Macrolide Hexacosalactone A from Streptomyces by Reporter-Guided Selection of Fermentation Media. J Nat Prod 2021; 84:1924-1929. [PMID: 34170140 DOI: 10.1021/acs.jnatprod.1c00144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
New approaches are still needed to fully explore the biosynthetic potential of microbes. We recently devised a melC reporter-guided fermentation media screening approach for targeted activation of cryptic gene clusters. Using this approach, we successfully activated the expression of the hcl gene cluster in Streptomyces sp. LZ35 and discovered a novel polyene macrolide hexacosalactone A (1).
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Affiliation(s)
- Peng Shi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, People's Republic of China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, People's Republic of China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
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27
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Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmüller H, Mankin AS, Innis CA, Vázquez-Laslop N, Wilson DN. Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Nat Commun 2021; 12:4466. [PMID: 34294725 PMCID: PMC8298421 DOI: 10.1038/s41467-021-24674-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/30/2021] [Indexed: 12/23/2022] Open
Abstract
Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.
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Affiliation(s)
- Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Elodie C Leroy
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael Graf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Stefan Arenz
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Maha Abdelshahid
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Britta Seip
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - C Axel Innis
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France.
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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28
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Otranto D, Colella V, Bezerra-Santos MA, Mendoza-Roldan JA, Cavalera MA, Pereira A, Schaper R, Maia C. Efficacy of a spot-on formulation containing moxidectin 2.5%/imidacloprid 10% for the treatment of Cercopithifilaria spp. and Onchocerca lupi microfilariae in naturally infected dogs from Portugal. Parasit Vectors 2021; 14:199. [PMID: 33849643 PMCID: PMC8042703 DOI: 10.1186/s13071-021-04704-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/28/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Onchocerca lupi and Cercopithifilaria spp. are vector-borne filarioids of dogs, which harbour skin microfilariae (mfs), the former being of zoonotic concern. Proper treatment studies using compounds with microfilaricidal activity have not been performed. Therefore, this study aimed to assess the efficacy of a commercially available spot-on formulation containing moxidectin 2.5%/imidacloprid 10% for the treatment of O. lupi or Cercopithifilaria spp. skin-dwelling mfs in naturally infected dogs. METHODS Privately owned dogs (n = 393) from southern Portugal were sampled via skin biopsies to identify and count mfs in 20 µl of skin sediment. A total of 22 mfs-positive dogs were allocated to treatment group (n = 11; G1) or left untreated as a control (n = 11; G2). As a pilot investigation to test the treatment efficacy, five dogs assigned to G1 were treated four times at monthly intervals with moxidectin 2.5%/imidacloprid 10% spot-on formulation on SDs 0, 28 (± 2), 56 (± 2), and 84 (± 2). Based on the negative results for both O. lupi and/or Cercopithifilaria spp. mfs of dogs in the pilot study from SD28 onwards, the remaining six dogs in G1 were treated at SD0 and assessed only at SD28. RESULTS Of the 393 animals sampled, 78 (19.8%) scored positive for skin-dwelling mfs. At the pilot investigation, a mean number of 19.6 mfs for O. lupi was recorded among five infected dogs whereas no mfs were detected at SD28. At SD0, the mean number of Cercopithifilaria spp. larvae was 12.6 for G1 and 8.7 for G2. The mean number of mfs for G2 was 20.09. CONCLUSIONS Results herein obtained suggest that a single treatment with moxidectin 2.5%/imidacloprid 10% spot-on formulation is efficacious against skin-dwelling mfs in dogs. The microfilaricidal effect of moxidectin could also be useful in reducing the risk of O. lupi infection for humans.
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Affiliation(s)
- Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Valenzano, 70010, Italy.
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran.
| | - Vito Colella
- Department of Veterinary Medicine, University of Bari, Valenzano, 70010, Italy
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | | | | | | | - André Pereira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene E Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisboa, Portugal
| | | | - Carla Maia
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene E Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisboa, Portugal
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29
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Abstract
Pharmacological inhibition of vacuolar-type H+-ATPase (V-ATPase) by its specific inhibitor can abrogate tumor metastasis, prevent autophagy, and reduce cellular signaling responses. Bafilomycin A1, a member of macrolide antibiotics and an autophagy inhibitor, serves as a specific and potent V-ATPases inhibitor. Although there are many V-ATPase structures reported, the molecular basis of specific inhibitors on V-ATPase remains unknown. Here, we report the cryo-EM structure of bafilomycin A1 bound intact bovine V-ATPase at an overall resolution of 3.6-Å. The structure reveals six bafilomycin A1 molecules bound to the c-ring. One bafilomycin A1 molecule engages with two c subunits and disrupts the interactions between the c-ring and subunit a, thereby preventing proton translocation. Structural and sequence analyses demonstrate that the bafilomycin A1-binding residues are conserved in yeast and mammalian species and the 7'-hydroxyl group of bafilomycin A1 acts as a unique feature recognized by subunit c.
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Affiliation(s)
- Rong Wang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jin Wang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abdirahman Hassan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiao-Song Xie
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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30
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Abstract
Macrolides are a class of antibiotics widely used in both medicine and agriculture. Unsurprisingly, as a consequence of their exensive usage a plethora of resistance mechanisms have been encountered in pathogenic bacteria. One of these resistance mechanisms entails the enzymatic cleavage of the macrolides' macrolactone ring by erythromycin esterases (Eres). The most frequently identified Ere enzyme is EreA, which confers resistance to the majority of clinically used macrolides. Despite the role Eres play in macrolide resistance, research into this family enzymes has been sparse. Here, we report the first three-dimensional structures of an erythromycin esterase, EreC. EreC is an extremely close homologue of EreA, displaying more than 90% sequence identity. Two structures of this enzyme, in conjunction with in silico flexible docking studies and previously reported mutagenesis data allowed for the proposal of a detailed catalytic mechanism for the Ere family of enzymes, labeling them as metal-independent hydrolases. Also presented are substrate spectrum assays for different members of the Ere family. The results from these assays together with an examination of residue conservation for the macrolide binding site in Eres, suggests two distinct active site archetypes within the Ere enzyme family.
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Affiliation(s)
- Michał Zieliński
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Department of Biochemistry, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Barry Sleno
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montréal, QC, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
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31
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Li H, Zhang M, Li H, Yu H, Chen S, Wu W, Sun P. Discovery of Venturicidin Congeners and Identification of the Biosynthetic Gene Cluster from Streptomyces sp. NRRL S-4. J Nat Prod 2021; 84:110-119. [PMID: 33356258 DOI: 10.1021/acs.jnatprod.0c01177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical screening of Streptomyces sp. NRRL S-4 with liquid chromatography-mass spectrometry (LC-MS) and the following chromatographic isolation led to the discovery of four 20-membered macrolides, venturicidin A (4) and three new congeners venturicidins D-F (1-3). Genome sequencing of strain S-4 revealed the presence of a biosynthetic gene cluster (BGC) encoding glycosylated type I polyketides (PKS). The BGC designated to venturicidin biosynthesis (ven) was supported by the proposed biosynthetic pathway and confirmed by inactivation of the core PKS gene of venK. Bioinformatic analyses on the conserved motifs and known stereospecificities in PKS modules are consistent with the structure and absolute configuration. This is the first report of venturicidin BGC since the discovery of the macrolide in 1961. In the biological assays, venturicidin A (4) and E (2) displayed a high selective cytotoxicity against acute monocytic leukemia MV-4-11 cells with IC50 values of 0.09 and 0.94 μM, respectively. Venturicidin A (4) also showed a weak inhibitory activity on FMS-like-tyrosine kinase.
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Affiliation(s)
- Huanhuan Li
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Mengxue Zhang
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Hongji Li
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
| | - Hai Yu
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
| | - Shuo Chen
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Wenhui Wu
- College of Food Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, People's Republic of China
| | - Peng Sun
- School of Pharmacy, Second Military Medical University, 325 Guo-He Road, Shanghai 200433, People's Republic of China
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Bassanini I, Parapini S, Ferrandi EE, Gabriele E, Basilico N, Taramelli D, Sparatore A. Design, Synthesis and In Vitro Investigation of Novel Basic Celastrol Carboxamides as Bio-Inspired Leishmanicidal Agents Endowed with Inhibitory Activity against Leishmania Hsp90. Biomolecules 2021; 11:56. [PMID: 33466300 PMCID: PMC7824787 DOI: 10.3390/biom11010056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
The natural triterpene celastrol (CE) is here used as lead compound for the design and synthesis of a panel of eleven CE carboxamides that were tested in vitro for their growth inhibitory activity against Leishmania infantum and L.tropica parasites. Among them, in vitro screening identified four basic CE carboxamides endowed with nanomolar leishmanicidal activity, against both the promastigotes and the intramacrophage Leishmania amastigotes forms. These compounds also showed low toxicity toward two human (HMEC-1 and THP-1) and one murine (BMDM) cell lines. Interestingly, the most selective CE analogue (compound 3) was also endowed with the ability to inhibit the ATPase activity of the Leishmania protein chaperone Hsp90 as demonstrated by the in vitro assay conducted on a purified, full-length recombinant protein. Preliminary investigations by comparing it with the naturally occurring Hsp90 active site inhibitor Geldanamycin (GA) in two different in vitro experiments were performed. These promising results set the basis for a future biochemical investigation of the mode of interaction of celastrol and CE-inspired compounds with Leishmania Hsp90.
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Affiliation(s)
- Ivan Bassanini
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy;
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy;
| | - Silvia Parapini
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Via Mangiagalli 31, 20133 Milano, Italy;
- Centro Interuniversitario di Ricerca sulla Malaria-Italian Malaria Network (CIRM-IMN), Università degli Studi di Milano, 20133 Milano, Italy
| | - Erica E. Ferrandi
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy;
| | - Elena Gabriele
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy;
| | - Nicoletta Basilico
- Centro Interuniversitario di Ricerca sulla Malaria-Italian Malaria Network (CIRM-IMN), Università degli Studi di Milano, 20133 Milano, Italy
- Dipartimento di Scienze Biomediche, Chirurgiche e Odontoiatriche, Università degli Studi di Milano, Via Pascal 36, 20133 Milano, Italy;
| | - Donatella Taramelli
- Centro Interuniversitario di Ricerca sulla Malaria-Italian Malaria Network (CIRM-IMN), Università degli Studi di Milano, 20133 Milano, Italy
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano Via Pascal, 36, 20133 Milano, Italy;
| | - Anna Sparatore
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy;
- Centro Interuniversitario di Ricerca sulla Malaria-Italian Malaria Network (CIRM-IMN), Università degli Studi di Milano, 20133 Milano, Italy
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Abstract
Total synthesis allowed the constitution of the cytotoxic marine macrolides of the formosalide family to be confirmed and their previously unknown stereostructure to be assigned with confidence. The underlying blueprint was inherently modular to ensure that each conceivable isomer could be reached. This flexibility derived from the use of strictly catalyst controlled transformations to set the stereocenters, except for the anomeric position, which is under thermodynamic control; as an extra safety measure, all stereogenic centers were set prior to ring closure to preclude any interference of the conformation adopted by the macrolactone rings of the different diastereomers. Late-stage macrocyclization by ring-closing alkyne metathesis was followed by a platinum-catalyzed transannular 6-exo-dig hydroalkoxylation/ketalization to craft the polycyclic frame. The side chain featuring a very labile unsaturation pattern was finally attached to the core by Stille coupling.
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Affiliation(s)
| | | | - Marc Heinrich
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
| | - Yonghoon Kwon
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
| | - Conny Wirtz
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
| | - Alois Fürstner
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
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Abstract
An enantioselective synthesis of the C(1)-C(15) segment of the marine natural product amphidinolide C has been accomplished by a route that includes a stereoselective boron-Wittig reaction to furnish a trisubstituted alkenylboronate. In addition, the route employs enantioselective alkene diboration to install the C(6) hydroxyl group which undergoes intramolecular conjugate addition to establish a tetrahydrofuran ring. Lastly, a catalytic Suzuki-Miyaura cross-coupling is accomplished to construct the C(9)-C(10) bond.
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Affiliation(s)
- Sheila Namirembe
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Lu Yan
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - James P. Morken
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, United States
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Abstract
Natural products possess a wide range of bioactivities with potential for therapeutic usage. While the distribution of these molecules can vary greatly there is some correlation that exists between the biodiversity of an environment and the uniqueness and concentration of natural products found in that region or area. The Caribbean and pan-Caribbean area is home to thousands of species of endemic fauna and flora providing huge potential for natural product discovery and by way, potential leads for drug development. This can especially be said for marine natural products as many of are rapidly diluted through diffusion once released and therefore are highly potent to achieve long reaching effects. This review seeks to highlight a small selection of marine natural products from the Caribbean region which possess antiproliferative, anti-inflammatory and antipathogenic properties while highlighting any synthetic efforts towards bioactive analogs.
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Affiliation(s)
- Adrian Demeritte
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - William M Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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36
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Fogarty S, Ouyang Y, Li L, Chen YC, Rane H, Manoni F, Parra KJ, Rutter J, Harran PG. Callyspongiolide Is a Potent Inhibitor of the Vacuolar ATPase. J Nat Prod 2020; 83:3381-3386. [PMID: 33151675 DOI: 10.1021/acs.jnatprod.0c00813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Callyspongiolide is a marine-derived macrolide that kills cells in a caspase-independent manner. NCI COMPARE analysis of human tumor cell line toxicity data for synthetic callyspongiolide indicated that its pattern of cytotoxicity correlated with that seen for concanamycin A, an inhibitor of the vacuolar-type H+-ATPase (V-ATPase). Using yeast as a model system, we report that treatment with synthetic callyspongiolide phenocopied a loss of V-ATPase activity including (1) inability to grow on a nonfermentable carbon source, (2) rescue of cell growth via supplementation with Fe2+, (3) pH-sensitive growth, and (4) a vacuolar acidification defect visualized using the fluorescent dye quinacrine. Crucially, in an in vitro assay, callyspongiolide was found to dose-dependently inhibit yeast V-ATPase (IC50 = 10 nM). Together, these data identify callyspongiolide as a new and highly potent V-ATPase inhibitor. Notably, callyspongiolide is the first V-ATPase inhibitor known to be expelled by Pdr5p.
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Affiliation(s)
- Sarah Fogarty
- Howard Hughes Medical Institute and Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
| | - Yeyun Ouyang
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
| | - Liubo Li
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Yu-Chan Chen
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
| | - Hallie Rane
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Francesco Manoni
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Karlett J Parra
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Jared Rutter
- Howard Hughes Medical Institute and Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
| | - Patrick G Harran
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
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Yang S, DeMars MD, Grandner JM, Olson NM, Anzai Y, Sherman DH, Houk KN. Computational-Based Mechanistic Study and Engineering of Cytochrome P450 MycG for Selective Oxidation of 16-Membered Macrolide Antibiotics. J Am Chem Soc 2020; 142:17981-17988. [PMID: 33030347 PMCID: PMC7720209 DOI: 10.1021/jacs.0c04388] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MycG is a cytochrome P450 that performs two sequential oxidation reactions on the 16-membered ring macrolide M-IV. The enzyme evolved to oxidize M-IV preferentially over M-III and M-VI, which differ only by the presence of methoxy vs free hydroxyl groups on one of the macrolide sugar moieties. We utilized a two-pronged computational approach to study both the chemoselective reactivity and substrate specificity of MycG. Density functional theory computations determined that epoxidation of the substrate hampers its ability to undergo C-H abstraction, primarily due to a loss of hyperconjugation in the transition state. Metadynamics and molecular dynamics simulations revealed a hydrophobic sugar-binding pocket that is responsible for substrate recognition/specificity and was not apparent in crystal structures of the enzyme/substrate complex. Computational results also led to the identification of other interactions between the enzyme and its substrates that had not previously been observed in the cocrystal structures. Site-directed mutagenesis was then employed to test the effects of mutations hypothesized to broaden the substrate scope and alter the product profile of MycG. The results of these experiments validated this complementary effort to engineer MycG variants with improved catalytic activity toward earlier stage mycinamicin substrates.
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Affiliation(s)
- Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Matthew D DeMars
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jessica M Grandner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Noelle M Olson
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yojiro Anzai
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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Jednačak T, Mikulandra I, Novak P. Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics. Int J Mol Sci 2020; 21:E7799. [PMID: 33096889 PMCID: PMC7589898 DOI: 10.3390/ijms21207799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.
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Affiliation(s)
- Tomislav Jednačak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
| | | | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
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39
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Liniger M, Neuhaus CM, Altmann KH. Ring-Closing Metathesis Approaches towards the Total Synthesis of Rhizoxins. Molecules 2020; 25:E4527. [PMID: 33023218 PMCID: PMC7582377 DOI: 10.3390/molecules25194527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 02/01/2023] Open
Abstract
Efforts are described towards the total synthesis of the bacterial macrolide rhizoxin F, which is a potent tubulin assembly and cancer cell growth inhibitor. A significant amount of work was expanded on the construction of the rhizoxin core macrocycle by ring-closing olefin metathesis (RCM) between C(9) and C(10), either directly or by using relay substrates, but in no case was ring-closure achieved. Macrocycle formation was possible by ring-closing alkyne metathesis (RCAM) at the C(9)/C(10) site. The requisite diyne was obtained from advanced intermediates that had been prepared as part of the synthesis of the RCM substrates. While the direct conversion of the triple bond formed in the ring-closing step into the C(9)-C(10) E double bond of the rhizoxin macrocycle proved to be elusive, the corresponding Z isomer was accessible with high selectivity by reductive decomplexation of the biscobalt hexacarbonyl complex of the triple bond with ethylpiperidinium hypophosphite. Radical-induced double bond isomerization, full elaboration of the C(15) side chain, and directed epoxidation of the C(11)-C(12) double bond completed the total synthesis of rhizoxin F.
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Affiliation(s)
| | | | - Karl-Heinz Altmann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, 8093 Zürich, Switzerland; (M.L.); (C.M.N.)
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40
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An JS, Lee JY, Kim E, Ahn H, Jang YJ, Shin B, Hwang S, Shin J, Yoon YJ, Lee SK, Oh DC. Formicolides A and B, Antioxidative and Antiangiogenic 20-Membered Macrolides from a Wood Ant Gut Bacterium. J Nat Prod 2020; 83:2776-2784. [PMID: 32892623 DOI: 10.1021/acs.jnatprod.0c00772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Two new macrolides, formicolides A (1) and B (2), were isolated from Streptomyces sp. BA01, a gut bacterial strain of the wood ant (Formica yessensis). Their 20-membered macrocyclic lactone structures were established using NMR and mass spectrometric data. The relative configurations of the formicolides were determined by J-based configuration analysis utilizing ROESY, HETLOC, and HECADE NMR spectroscopic data. Genomic and bioinformatics analysis of the bacterial strain enabled us to identify the type-I polyketide synthase pathway employing a trans-acyltransferase system. The absolute configurations of 1 and 2 are proposed based on detailed analysis of the sequences of the ketoreductases in the modular gene cluster and statistical comparative analysis of the experimental NMR chemical shifts and quantum mechanical calculations. Formicolides A and B (1 and 2) induced quinone reductase activity in murine Hepa-1c1c7 cells and antiangiogenic activity by suppression of tube formation in human umbilical vein endothelial cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Yun Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyungju Ahn
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Joon Jang
- Natura Center of Life and Environment, Seoul 08826, Republic of Korea
| | - Bora Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Teshima A, Hadae N, Tsuda N, Arakawa K. Functional Analysis of P450 Monooxygenase SrrO in the Biosynthesis of Butenolide-Type Signaling Molecules in Streptomyces rochei. Biomolecules 2020; 10:biom10091237. [PMID: 32854353 PMCID: PMC7564063 DOI: 10.3390/biom10091237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
Streptomyces rochei 7434AN4 produces two structurally unrelated polyketide antibiotics lankacidin and lankamycin, and their biosynthesis is tightly controlled by butenolide-type signaling molecules SRB1 and SRB2. SRBs are synthesized by SRB synthase SrrX, and induce lankacidin and lankamycin production at 40 nM concentration. We here investigated the role of a P450 monooxygenase gene srrO (orf84), which is located adjacent to srrX (orf85), in SRB biosynthesis. An srrO mutant KA54 accumulated lankacidin and lankamycin at a normal level when compared with the parent strain. To elucidate the chemical structures of the signaling molecules accumulated in KA54 (termed as KA54-SRBs), this mutant was cultured (30 L) and the active components were purified. Two active components (KA54-SRB1 and KA54-SRB2) were detected in ESI-MS and chiral HPLC analysis. The molecular formulae for KA54-SRB1 and KA54-SRB2 are C15H26O4 and C16H28O4, whose values are one oxygen smaller and two hydrogen larger when compared with those for SRB1 and SRB2, respectively. Based on extensive NMR analysis, the signaling molecules in KA54 were determined to be 6'-deoxo-SRB1 and 6'-deoxo-SRB2. Gel shift analysis indicated that a ligand affinity of 6'-deoxo-SRB1 to the specific receptor SrrA was 100-fold less than that of SRB1. We performed bioconversion of the synthetic 6'-deoxo-SRB1 in the Streptomyces lividans recombinant carrying SrrO-expression plasmid. Substrate 6'-deoxo-SRB1 was converted through 6'-deoxo-6'-hydroxy-SRB1 to SRB1 in a time-dependent manner. Thus, these results clearly indicated that SrrO catalyzes the C-6' oxidation at a final step in SRB biosynthesis.
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Affiliation(s)
- Aiko Teshima
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; (A.T.); (N.H.); (N.T.)
| | - Nozomi Hadae
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; (A.T.); (N.H.); (N.T.)
| | - Naoto Tsuda
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; (A.T.); (N.H.); (N.T.)
| | - Kenji Arakawa
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan; (A.T.); (N.H.); (N.T.)
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Correspondence: ; Tel./Fax: +81-82-424-7767
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Shigdel UK, Lee SJ, Sowa ME, Bowman BR, Robison K, Zhou M, Pua KH, Stiles DT, Blodgett JAV, Udwary DW, Rajczewski AT, Mann AS, Mostafavi S, Hardy T, Arya S, Weng Z, Stewart M, Kenyon K, Morgenstern JP, Pan E, Gray DC, Pollock RM, Fry AM, Klausner RD, Townson SA, Verdine GL. Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface. Proc Natl Acad Sci U S A 2020; 117:17195-17203. [PMID: 32606248 PMCID: PMC7382241 DOI: 10.1073/pnas.2006560117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of "undruggability" for an intracellular target. Structural studies reveal extensive protein-WDB002 and protein-protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise "undruggable" targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.
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Affiliation(s)
| | | | | | | | | | - Minyun Zhou
- Warp Drive Bio, Inc., Redwood City, CA 94063
| | | | | | | | | | | | - Alan S Mann
- Warp Drive Bio, Inc., Redwood City, CA 94063
| | | | - Tara Hardy
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Sukrat Arya
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | | | | | - Kyle Kenyon
- Warp Drive Bio, Inc., Redwood City, CA 94063
| | | | - Ende Pan
- Warp Drive Bio, Inc., Redwood City, CA 94063
| | | | | | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, LE1 7RH Leicester, United Kingdom
| | | | | | - Gregory L Verdine
- Warp Drive Bio, Inc., Redwood City, CA 94063;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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43
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Goto T, Yamazoe Y, Tohkin M. Applications of a grid-based CYP3A4 Template system to understand the interacting mechanisms of large-size ligands; part 4 of CYP3A4 Template study. Drug Metab Pharmacokinet 2020; 35:485-496. [PMID: 32967779 DOI: 10.1016/j.dmpk.2020.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/11/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023]
Abstract
Catalytic interactions of CYP3A4 with large-size ligands have been studied on the Template established in our previous studies using polyaromatic hydrocarbon and steroid ligands (DMPK 34: 113-125 and 351-364 2019 and in press 2020). Typical CYP3A4-substrates including erythromycin, cyclosporin A (ca.1200 Da), ivermectin B1a and taxanes were applied successfully and regioselective metabolisms of these ligands were reconstituted faithfully on Template. These results suggest the applicability of CYP3A4 Template throughout broadened sizes of CYP3A4 ligands. Macrolide antibiotics showed distinct degrees of tight sittings in Width-gauge, a tool for accommodation measure. The observed differences were associated with different inhibitory/inactivation potentials of troleandomycin, erythromycin, clarithromycin and azithromycin, suggesting CYP3A4 Template also as a tool for drug-interaction mechanisms. Slight expansion of Template area was made at near Site of oxidation from simulation results of antitumor agent, rilpivirine, in the present study. Ligand entry from left side of Template is also suggested from macrolide interactions. Broadened applicability of the refined CYP3A4 Template were assured with experiments with various large-size ligands.
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Affiliation(s)
- Takahiro Goto
- Regulation and Prequalification, Access to Medicines and Health Products, World Health Organization, Avenue Appia 20, 1211, Geneva 27, Switzerland; Regulatory Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1, Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Yasushi Yamazoe
- Division of Drug Metabolism and Molecular Toxicology, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aramaki-Aoba, Aoba-ku, Sendai, 980-8578, Japan; Division of Risk Assessment, National Institute of Health Sciences, Tonomachi 3-25-26, Kawasaki-ku, Kanagawa, 210-9501, Japan.
| | - Masahiro Tohkin
- Regulatory Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1, Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
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44
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Ndukwe IE, Wang X, Lam NYS, Ermanis K, Alexander KL, Bertin MJ, Martin GE, Muir G, Paterson I, Britton R, Goodman JM, Helfrich EJN, Piel J, Gerwick WH, Williamson RT. Synergism of anisotropic and computational NMR methods reveals the likely configuration of phormidolide A. Chem Commun (Camb) 2020; 56:7565-7568. [PMID: 32520016 PMCID: PMC7436192 DOI: 10.1039/d0cc03055d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Characterization of the complex molecular scaffold of the marine polyketide natural product phormidolide A represents a challenge that has persisted for nearly two decades. In light of discordant results arising from recent synthetic and biosynthetic reports, a rigorous study of the configuration of phormidolide A was necessary. This report outlines a synergistic effort employing computational and anisotropic NMR investigation, that provided orthogonal confirmation of the reassigned side chain, as well as supporting a further correction of the C7 stereocenter.
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Affiliation(s)
- Ikenna E Ndukwe
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Xiao Wang
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, USA
| | - Nelson Y S Lam
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kristaps Ermanis
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kelsey L Alexander
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA and Department of Chemistry, University of California, San Diego, CA, USA
| | - Matthew J Bertin
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
| | - Gary E Martin
- Department of Chemistry, Seton Hall University, South Orange, NJ, USA
| | - Garrett Muir
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Ian Paterson
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | | | - Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - William H Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - R Thomas Williamson
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, NC, USA.
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45
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Yamada T, Kogure H, Kataoka M, Kikuchi T, Hirano T. Halosmysin A, a Novel 14-Membered Macrodiolide Isolated from the Marine-Algae-Derived Fungus Halosphaeriaceae sp. Mar Drugs 2020; 18:E320. [PMID: 32570727 PMCID: PMC7344848 DOI: 10.3390/md18060320] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Halosmysin A, a new 14-membered macrodiolide with an unprecedented skeleton, was isolated from the fungus Halosphaeriaceae sp. OUPS-135D-4, which, in turn, was obtained from the marine algae Sargassum thunbergii. The chemical structure of the macrodiolide was elucidated using 1D and 2D NMR, as well as high resolution fast atom bombardment mass (HRFABMS) spectral analysis. The absolute stereochemistry was determined via chemical derivatization and comparison with a known compound, (6R,11R,12R,14R)-colletodiol. Additionally, halosmysin A was shown to be very potent against murine P388 leukemia, human HL-60 leukemia, and murine L1210 leukemia cell lines, with IC50 values ranging from 2.2 ± 3.1 to 11.7 ± 2.8 μM.
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Affiliation(s)
- Takeshi Yamada
- Department of Medicinal Molecular Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1, Nasahara, Takatsuki, Osaka 569-1094, Japan; (H.K.); (M.K.); (T.K.); (T.H.)
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46
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Warryn L, Dangy JP, Gersbach P, Gehringer M, Schäfer A, Ruf MT, Ruggli N, Altmann KH, Pluschke G. Development of an ELISA for the quantification of mycolactone, the cytotoxic macrolide toxin of Mycobacterium ulcerans. PLoS Negl Trop Dis 2020; 14:e0008357. [PMID: 32589646 PMCID: PMC7347236 DOI: 10.1371/journal.pntd.0008357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 07/09/2020] [Accepted: 05/04/2020] [Indexed: 01/04/2023] Open
Abstract
Mycolactones, macrolide cytotoxins, are key virulence factors of Mycobacterium ulcerans, the etiological agent of the chronic necrotizing skin disease Buruli ulcer. There is urgent need for a simple point-of-care laboratory test for Buruli ulcer and mycolactone represents a promising target for the development of an immunological assay. However, for a long time, all efforts to generate mycolactone-specific antibodies have failed. By using a protein conjugate of a truncated non-toxic synthetic mycolactone derivative, we recently described generation of a set of mycolactone-specific monoclonal antibodies. Using the first mycolactone-specific monoclonal antibodies that we have described before, we were able to develop an antigen competition assay that detects mycolactones. By the systematic selection of a capturing antibody and a reporter molecule, and the optimization of assay conditions, we developed an ELISA that detects common natural variants of mycolactone with a limit of detection in the low nanomolar range. The mycolactone-specific ELISA described here will be a very useful tool for research on the biology of this macrolide toxin. After conversion into a simple point-of-care test format, the competition assay may have great potential as laboratory assay for both the diagnosis of Buruli ulcer and for the monitoring of treatment efficacy.
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Affiliation(s)
- Louisa Warryn
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jean-Pierre Dangy
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Philipp Gersbach
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Matthias Gehringer
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Anja Schäfer
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Marie-Thérèse Ruf
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicolas Ruggli
- The Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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47
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Yamano A, Natsume N, Yamada M, Sumimoto S, Iwasaki A, Suenaga K, Teruya T. Irijimasides A-E, Macrolide Glycosides from an Okeania sp. Marine Cyanobacterium. J Nat Prod 2020; 83:1585-1591. [PMID: 32267694 DOI: 10.1021/acs.jnatprod.0c00042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Irijimasides A-E (1-5), a series of new 14-membered macrolide glycosides, were isolated from a marine cyanobacterium collected in Okinawa. The gross structures of 1-5 were established by spectroscopic analysis, including 2D NMR, while absolute stereostructures were determined based on NOESY spectra, chemical derivatization, and ECD data. All five macrolides suppressed receptor activator of nuclear factor-κB ligand (RANKL)-induced tartrate-resistant acid phosphatase (TRAP) activity in mouse RAW264 macrophage cells, indicating that these compounds inhibit osteoclast formation.
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Affiliation(s)
- Aki Yamano
- Faculty of Education, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Noriyuki Natsume
- Graduate School of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Miki Yamada
- Faculty of Education, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Shimpei Sumimoto
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Arihiro Iwasaki
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Toshiaki Teruya
- Faculty of Education, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
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48
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Naineni SK, Itoua Maïga R, Cencic R, Putnam AA, Amador LA, Rodriguez AD, Jankowsky E, Pelletier J. A comparative study of small molecules targeting eIF4A. RNA 2020; 26:541-549. [PMID: 32014999 PMCID: PMC7161356 DOI: 10.1261/rna.072884.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/30/2020] [Indexed: 05/13/2023]
Abstract
The PI3K/Akt/mTOR kinase pathway is extensively deregulated in human cancers. One critical node under regulation of this signaling axis is eukaryotic initiation factor (eIF) 4F, a complex involved in the control of translation initiation rates. eIF4F-dependent addictions arise during tumor initiation and maintenance due to increased eIF4F activity-generally in response to elevated PI3K/Akt/mTOR signaling flux. There is thus much interest in exploring eIF4F as a small molecule target for the development of new anticancer drugs. The DEAD-box RNA helicase, eIF4A, is an essential subunit of eIF4F, and several potent small molecules (rocaglates, hippuristanol, pateamine A) affecting its activity have been identified and shown to demonstrate anticancer activity in vitro and in vivo in preclinical models. Recently, a number of new small molecules have been reported as having the capacity to target and inhibit eIF4A. Here, we undertook a comparative analysis of their biological activity and specificity relative to the eIF4A inhibitor, hippuristanol.
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Affiliation(s)
- Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Rayelle Itoua Maïga
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Andrea A Putnam
- School of Medicine, Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Luis A Amador
- Department of Chemistry, Faculty of Natural Sciences, University of Puerto Rico, San Juan, 00931-3346, Puerto Rico
| | - Abimael D Rodriguez
- Department of Chemistry, Faculty of Natural Sciences, University of Puerto Rico, San Juan, 00931-3346, Puerto Rico
| | - Eckhard Jankowsky
- School of Medicine, Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Québec H3G 1Y6, Canada
- Department of Oncology, McGill University, Montreal, Québec H4A 3T2, Canada
- Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, Québec H3A 1A3, Canada
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49
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Tainter CJ, Schley ND, Harris CM, Stec DF, Song AK, Balinski A, May JC, McLean JA, Reece KS, Harris TM. Algal Toxin Goniodomin A Binds Potassium Ion Selectively to Yield a Conformationally Altered Complex with Potential Biological Consequences. J Nat Prod 2020; 83:1069-1081. [PMID: 32083860 PMCID: PMC9290314 DOI: 10.1021/acs.jnatprod.9b01094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The marine toxin goniodomin A (GDA) is a polycyclic macrolide containing a spiroacetal and three cyclic ethers as part of the macrocycle backbone. GDA is produced by three species of the Alexandrium genus of dinoflagellates, blooms of which are associated with "red tides", which are widely dispersed and can cause significant harm to marine life. The toxicity of GDA has been attributed to stabilization of the filamentous form of the actin group of structural proteins, but the structural basis for its binding is not known. Japanese workers, capitalizing on the assumed rigidity of the heavily substituted macrolide ring, assigned the relative configuration and conformation by relying on NMR coupling constants and NOEs; the absolute configuration was assigned by degradation to a fragment that was compared with synthetic material. We have confirmed the absolute structure and broad features of the conformation by X-ray crystallography but have found GDA to complex with alkali metal ions in spite of two of the heterocyclic rings facing outward. Such an arrangement would have been expected to impair the ability of GDA to form a crown-ether-type multidentate complex. GDA shows preference for K+, Rb+, and Cs+ over Li+ and Na+ in determinations of relative affinities by TLC on metal-ion-impregnated silica gel plates and by electrospray mass spectrometry. NMR studies employing the K+ complex of GDA, formed from potassium tetrakis[pentafluorophenyl]borate (KBArF20), reveal a major alteration of the conformation of the macrolide ring. These observations argue against the prior assumption of rigidity of the ring. Alterations in chemical shifts, coupling constants, and NOEs indicate the involvement of most of the molecule other than ring F. Molecular mechanics simulations suggest K+ forms a heptacoordinate complex involving OA, OB, OC, OD, OE, and the C-26 and C-27 hydroxy groups. We speculate that complexation of K+ with GDA electrostatically stabilizes the complex of GDA with filamentous actin in marine animals due to the protein being negatively charged at physiological pH. GDA may also cause potassium leakage through cell membranes. This study provides insight into the structural features and chemistry of GDA that may be responsible for significant ecological damage associated with the GDA-producing algal blooms.
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Affiliation(s)
- Craig J. Tainter
- Department of Chemistry, Vanderbilt University, Nashville,
TN 37235, USA
| | - Nathan D. Schley
- Department of Chemistry, Vanderbilt University, Nashville,
TN 37235, USA
| | | | - Donald F. Stec
- Department of Chemistry, Vanderbilt University, Nashville,
TN 37235, USA
| | - Anna K. Song
- Department of Aquatic Health Sciences, Virginia Institute
of Marine Science, Gloucester Point, VA 23062, USA
| | - Andrzej Balinski
- Department of Chemistry, Vanderbilt University, Nashville,
TN 37235, USA
| | - Jody C. May
- Department of Chemistry, Vanderbilt University, Nashville,
TN 37235, USA
| | - John A. McLean
- Department of Chemistry, Vanderbilt University, Nashville,
TN 37235, USA
| | - Kimberly S. Reece
- Department of Aquatic Health Sciences, Virginia Institute
of Marine Science, Gloucester Point, VA 23062, USA
| | - Thomas M. Harris
- Department of Chemistry, Vanderbilt University, Nashville,
TN 37235, USA
- Department of Aquatic Health Sciences, Virginia Institute
of Marine Science, Gloucester Point, VA 23062, USA
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50
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Abstract
Macrolactones, macrocyclic lactones with at least twelve atoms within the core ring, include diverse natural products such as macrolides with potent bioactivities (e.g. antibiotics) and useful drug-like characteristics. We have developed MacrolactoneDB, which integrates nearly 14,000 existing macrolactones and their bioactivity information from different public databases, and new molecular descriptors to better characterize macrolide structures. The chemical distribution of MacrolactoneDB was analyzed in terms of important molecular properties and we have utilized three targets of interest (Plasmodium falciparum, Hepatitis C virus and T-cells) to demonstrate the value of compiling this data. Regression machine learning models were generated to predict biological endpoints using seven molecular descriptor sets and eight machine learning algorithms. Our results show that merging descriptors yields the best predictive power with Random Forest models, often boosted by consensus or hybrid modeling approaches. Our study provides cheminformatics insights into this privileged, underexplored structural class of compounds with high therapeutic potential.
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Affiliation(s)
- Phyo Phyo Kyaw Zin
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Gavin J Williams
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Sean Ekins
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA.
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