1
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Quirke JCK, Sati GC, Sonousi A, Gysin M, Haldimann K, Bottger EC, Vasella A, Hobbie SN, Crich D. Structure-Activity Relationships for 5''-Modifications of 4,5-Aminoglycoside Antibiotics. ChemMedChem 2022; 17:e202200120. [PMID: 35385605 DOI: 10.1002/cmdc.202200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/06/2022] [Indexed: 11/08/2022]
Abstract
Modification at the 5''-position of 4,5-disubstituted aminoglycoside antibiotics (AGAs) to circumvent inactivation by the APH(3',5'') class of aminoglycoside modifying enzymes (AMEs) has been widely reported. Such modifications, however, impact activity against wild type bacteria and affect target selectivity in unpredictable ways thereby hindering drug development. We present a systematic survey of modifications to the 5''-position of the 4,5-AGAs and of the related 5- O -furanosyl apramycin derivatives. In the neomycin and the apralog series, all modifications were well-tolerated, but other 4,5-AGAs require the presence of a hydrogen bonding group at the 5''-position for maintenance of high antibacterial activity. Though the 5''-amino modification resulted in comparable activity to the parent compounds, reduced selectivity against the human cytosolic decoding A site renders this modification generally unfavorable in paromomycin, propylamycin, and ribostamycin. Installation of a 5''-formamido group and, to a lesser degree, a 5''-ureido group resulted in comparable activity to the parents without the selectivity cost of the 5''-amino modification. The lessons learned from this work will aid in the design of next-generation AGAs capable of circumventing susceptibility to AMEs while maintaining high antibacterial activity and target selectivity.
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Affiliation(s)
| | | | - Amr Sonousi
- Cairo University, Pharmaceutical Organic Chemistry, EGYPT
| | - Marina Gysin
- University of Zurich: Universitat Zurich, Medical Microbiology, SWITZERLAND
| | | | - Erik C Bottger
- University of Zurich: Universitat Zurich, Medical Microbiology, SWITZERLAND
| | - Andrea Vasella
- ETH-Zürich LOC: Eidgenossische Technische Hochschule Zurich Laboratorium fur Organische Chemie, Chemistry, SWITZERLAND
| | - Sven N Hobbie
- University of Zurich: Universitat Zurich, Medical Microbiology, SWITZERLAND
| | - David Crich
- University of Georgia, Pharmaceutical and Biomedical Sciences, 240 West Green Street, 30602, Athens, UNITED STATES
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2
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Yusupova G, Yusupov M. A Path to the Atomic-Resolution Structures of Prokaryotic and Eukaryotic Ribosomes. BIOCHEMISTRY (MOSCOW) 2021; 86:926-941. [PMID: 34488570 DOI: 10.1134/s0006297921080046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Resolving first crystal structures of prokaryotic and eukaryotic ribosomes by our group has been based on the knowledge accumulated over the decades of studies, starting with the first electron microscopy images of the ribosome obtained by J. Pallade in 1955. In 1983, A. Spirin, then a Director of the Protein Research Institute of the USSR Academy of Sciences, initiated the first study aimed at solving the structure of ribosomes using X-ray structural analysis. In 1999, our group in collaboration with H. Noller published the first crystal structure of entire bacterial ribosome in a complex with its major functional ligands, such as messenger RNA and three transport RNAs at the A, P, and E sites. In 2011, our laboratory published the first atomic-resolution structure of eukaryotic ribosome solved by the X-ray diffraction analysis that confirmed the conserved nature of the main ribosomal functional components, such as the decoding and peptidyl transferase centers, was confirmed, and eukaryote-specific elements of the ribosome were described. Using X-ray structural analysis, we investigated general principles of protein biosynthesis inhibition in eukaryotic ribosomes, along with the mechanisms of antibiotic resistance. Structural differences between bacterial and eukaryotic ribosomes that determine the differences in their inhibition were established. These and subsequent atomic-resolution structures of the functional ribosome demonstrated for the first time the details of binding of messenger and transport RNAs, which was the first step towards understanding how the ribosome structure ultimately determines its functions.
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Affiliation(s)
- Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, 67404, France
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, Illkirch, 67404, France. .,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
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3
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Hendrickx S, Reis-Cunha JL, Forrester S, Jeffares DC, Caljon G. Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms. Microorganisms 2021; 9:microorganisms9081546. [PMID: 34442625 PMCID: PMC8398221 DOI: 10.3390/microorganisms9081546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 01/07/2023] Open
Abstract
The relatively high post-treatment relapse rates of paromomycin (PMM) in visceral leishmaniasis treatment and the swift emergence of experimental drug resistance challenge its broad application and urge for rational use and monitoring of resistance. However, no causal molecular mechanisms to Leishmania PMM resistance have been identified so far. To gain insights into potential resistance mechanisms, twelve experimentally selected Leishmania donovani clonal lines and the non-cloned preselection population, with variable degrees of PMM resistance, were subjected to whole genome sequencing. To identify genomic variations potentially associated with resistance, SNPs, Indels, chromosomal somy and gene copy number variations were compared between the different parasite lines. A total of 11 short nucleotide variations and the copy number alterations in 39 genes were correlated to PMM resistance. Some of the identified genes are involved in transcription, translation and protein turn-over (transcription elongation factor-like protein, RNA-binding protein, ribosomal protein L1a, 60S ribosomal protein L6, eukaryotic translation initiation factor 4E-1, proteasome regulatory non-ATP-ase subunit 3), virulence (major surface protease gp63, protein-tyrosine phosphatase 1-like protein), mitochondrial function (ADP/ATP mitochondrial carrier-like protein), signaling (phosphatidylinositol 3-related kinase, protein kinase putative and protein-tyrosine phosphatase 1-like protein) and vesicular trafficking (ras-related protein RAB1). These results indicate that, in Leishmania, the aminoglycoside PMM affects protein translational processes and underlines the complex and probably multifactorial origin of resistance.
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Affiliation(s)
- Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Antwerp, Belgium;
| | - João Luís Reis-Cunha
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
| | - Sarah Forrester
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
| | - Daniel C. Jeffares
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
- Correspondence: (D.C.J.); (G.C.); Tel.: +32-3-265-26-01 (G.C.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Antwerp, Belgium;
- Correspondence: (D.C.J.); (G.C.); Tel.: +32-3-265-26-01 (G.C.)
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4
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Martinez-Peinado N, Cortes-Serra N, Sherman J, Rodriguez A, Bustamante JM, Gascon J, Pinazo MJ, Alonso-Padilla J. Identification of Trypanosoma cruzi Growth Inhibitors with Activity In Vivo within a Collection of Licensed Drugs. Microorganisms 2021; 9:microorganisms9020406. [PMID: 33669310 PMCID: PMC7920067 DOI: 10.3390/microorganisms9020406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/08/2021] [Accepted: 02/13/2021] [Indexed: 11/17/2022] Open
Abstract
Chagas disease, caused by the parasite Trypanosoma cruzi (T. cruzi), affects more than six million people worldwide, with its greatest burden in Latin America. Available treatments present frequent toxicity and variable efficacy at the chronic phase of the infection, when the disease is usually diagnosed. Hence, development of new therapeutic strategies is urgent. Repositioning of licensed drugs stands as an attractive fast-track low-cost approach for the identification of safer and more effective chemotherapies. With this purpose we screened 32 licensed drugs for different indications against T. cruzi. We used a primary in vitro assay of Vero cells infection by T. cruzi. Five drugs showed potent activity rates against it (IC50 < 4 µmol L−1), which were also specific (selectivity index >15) with respect to host cells. T. cruzi inhibitory activity of four of them was confirmed by a secondary anti-parasitic assay based on NIH-3T3 cells. Then, we assessed toxicity to human HepG2 cells and anti-amastigote specific activity of those drugs progressed. Ultimately, atovaquone-proguanil, miltefosine, and verapamil were tested in a mouse model of acute T. cruzi infection. Miltefosine performance in vitro and in vivo encourages further investigating its use against T. cruzi.
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Affiliation(s)
- Nieves Martinez-Peinado
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (N.M.-P.); (N.C.-S.); (J.G.)
| | - Nuria Cortes-Serra
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (N.M.-P.); (N.C.-S.); (J.G.)
| | - Julian Sherman
- Department of Microbiology, New York University School of Medicine, New York, NY 10010, USA; (J.S.); (A.R.)
| | - Ana Rodriguez
- Department of Microbiology, New York University School of Medicine, New York, NY 10010, USA; (J.S.); (A.R.)
| | - Juan M. Bustamante
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA;
| | - Joaquim Gascon
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (N.M.-P.); (N.C.-S.); (J.G.)
| | - Maria-Jesus Pinazo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (N.M.-P.); (N.C.-S.); (J.G.)
- Correspondence: (M.-J.P.); (J.A.-P.); Tel.: +1-0034-932275400 (ext. 1802) (M.-J.P.); +1-0034-932275400 (ext. 4569) (J.A.-P.)
| | - Julio Alonso-Padilla
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (N.M.-P.); (N.C.-S.); (J.G.)
- Correspondence: (M.-J.P.); (J.A.-P.); Tel.: +1-0034-932275400 (ext. 1802) (M.-J.P.); +1-0034-932275400 (ext. 4569) (J.A.-P.)
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5
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Quirke JCK, Rajasekaran P, Sarpe VA, Sonousi A, Osinnii I, Gysin M, Haldimann K, Fang QJ, Shcherbakov D, Hobbie SN, Sha SH, Schacht J, Vasella A, Böttger EC, Crich D. Apralogs: Apramycin 5- O-Glycosides and Ethers with Improved Antibacterial Activity and Ribosomal Selectivity and Reduced Susceptibility to the Aminoacyltranserferase (3)-IV Resistance Determinant. J Am Chem Soc 2019; 142:530-544. [PMID: 31790244 DOI: 10.1021/jacs.9b11601] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Apramycin is a structurally unique member of the 2-deoxystreptamine class of aminoglycoside antibiotics characterized by a monosubstituted 2-deoxystreptamine ring that carries an unusual bicyclic eight-carbon dialdose moiety. Because of its unusual structure, apramycin is not susceptible to the most prevalent mechanisms of aminoglycoside resistance including the aminoglycoside-modifying enzymes and the ribosomal methyltransferases whose widespread presence severely compromises all aminoglycosides in current clinical practice. These attributes coupled with minimal ototoxocity in animal models combine to make apramycin an excellent starting point for the development of next-generation aminoglycoside antibiotics for the treatment of multidrug-resistant bacterial infections, particularly the ESKAPE pathogens. With this in mind, we describe the design, synthesis, and evaluation of three series of apramycin derivatives, all functionalized at the 5-position, with the goals of increasing the antibacterial potency without sacrificing selectivity between bacterial and eukaryotic ribosomes and of overcoming the rare aminoglycoside acetyltransferase (3)-IV class of aminoglycoside-modifying enzymes that constitutes the only documented mechanism of antimicrobial resistance to apramycin. We show that several apramycin-5-O-β-d-ribofuranosides, 5-O-β-d-eryrthofuranosides, and even simple 5-O-aminoalkyl ethers are effective in this respect through the use of cell-free translation assays with wild-type bacterial and humanized bacterial ribosomes and of extensive antibacterial assays with wild-type and resistant Gram negative bacteria carrying either single or multiple resistance determinants. Ex vivo studies with mouse cochlear explants confirm the low levels of ototoxicity predicted on the basis of selectivity at the target level, while the mouse thigh infection model was used to demonstrate the superiority of an apramycin-5-O-glycoside in reducing the bacterial burden in vivo.
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Affiliation(s)
- Jonathan C K Quirke
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Parasuraman Rajasekaran
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Vikram A Sarpe
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Amr Sonousi
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Ivan Osinnii
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Marina Gysin
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Klara Haldimann
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Qiao-Jun Fang
- Department of Pathology and Laboratory Medicine , Medical University of South Carolina , Walton Research Building, Room 403-E, 39 Sabin Street , Charleston , South Carolina 29425 , United States
| | - Dimitri Shcherbakov
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Sven N Hobbie
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - Su-Hua Sha
- Department of Pathology and Laboratory Medicine , Medical University of South Carolina , Walton Research Building, Room 403-E, 39 Sabin Street , Charleston , South Carolina 29425 , United States
| | - Jochen Schacht
- Kresge Hearing Research Institute, Department of Otolaryngology , University of Michigan , 1150 West Medical Center Drive , Ann Arbor , Michigan 48109 , United States
| | - Andrea Vasella
- Organic Chemistry Laboratory , ETH Zürich , Vladimir-Prelog-Weg 1-5/10 , 8093 Zürich , Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology , University of Zurich , Gloriastrasse 28 , 8006 Zürich , Switzerland
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences , University of Georgia , 250 West Green Street , Athens , Georgia 30602 , United States.,Department of Chemistry , University of Georgia , 140 Cedar Street , Athens , Georgia 30602 , United States.,Complex Carbohydrate Research Center , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States.,Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
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6
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Sati GC, Sarpe VA, Furukawa T, Mondal S, Mantovani M, Hobbie SN, Vasella A, Böttger EC, Crich D. Modification at the 2'-Position of the 4,5-Series of 2-Deoxystreptamine Aminoglycoside Antibiotics To Resist Aminoglycoside Modifying Enzymes and Increase Ribosomal Target Selectivity. ACS Infect Dis 2019; 5:1718-1730. [PMID: 31436080 PMCID: PMC6788953 DOI: 10.1021/acsinfecdis.9b00128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
A series
of derivatives of the 4,5-disubstituted class of 2-deoxystreptamine
aminoglycoside antibiotics neomycin, paromomycin, and ribostamycin
was prepared and assayed for (i) their ability to inhibit protein
synthesis by bacterial ribosomes and by engineered bacterial ribosomes
carrying eukaryotic decoding A sites, (ii) antibacterial activity
against wild type Gram negative and positive pathogens, and (iii)
overcoming resistance due to the presence of aminoacyl transferases
acting at the 2′-position. The presence of five suitably positioned
residual basic amino groups was found to be necessary for activity
to be retained upon removal or alkylation of the 2′-position
amine. As alkylation of the 2′-amino group overcomes the action
of resistance determinants acting at that position and in addition
results in increased selectivity for the prokaryotic over eukaryotic
ribosomes, it constitutes an attractive modification for introduction
into next generation aminoglycosides. In the neomycin series, the
installation of small (formamide) or basic (glycinamide) amido groups
on the 2′-amino group is tolerated.
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Affiliation(s)
- Girish C. Sati
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Vikram A. Sarpe
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Takayuki Furukawa
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Sujit Mondal
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Matilde Mantovani
- Institute of Medical Microbiology, University of Zurich, 28 Gloriastrasse, 8006 Zürich, Switzerland
| | - Sven N. Hobbie
- Institute of Medical Microbiology, University of Zurich, 28 Gloriastrasse, 8006 Zürich, Switzerland
| | - Andrea Vasella
- Organic Chemistry Laboratory, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Erik C. Böttger
- Institute of Medical Microbiology, University of Zurich, 28 Gloriastrasse, 8006 Zürich, Switzerland
| | - David Crich
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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7
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Pramanik PK, Alam MN, Roy Chowdhury D, Chakraborti T. Drug Resistance in Protozoan Parasites: An Incessant Wrestle for Survival. J Glob Antimicrob Resist 2019; 18:1-11. [PMID: 30685461 DOI: 10.1016/j.jgar.2019.01.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/04/2019] [Accepted: 01/15/2019] [Indexed: 11/19/2022] Open
Abstract
Nowadays, drug resistance in parasites is considered to be one of the foremost concerns in health and disease management. It is interconnected worldwide and undermines the health of millions of people, threatening to grow worse. Unfortunately, it does not receive serious attention from every corner of society. Consequently, drug resistance in parasites is gradually complicating and challenging the treatment of parasitic diseases. In this context, we have dedicated ourselves to review the incidence of drug resistance in the protozoan parasites Plasmodium, Leishmania, Trypanosoma, Entamoeba and Toxoplasma gondii. Moreover, understanding the role of ATP-binding cassette (ABC) transporters in drug resistance is essential in the control of parasitic diseases. Therefore, we also focused on the involvement of ABC transporters in drug resistance, which will be a superior approach to find ways for better regulation of diseases caused by parasitic infections.
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Affiliation(s)
- Pijush Kanti Pramanik
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Md Nur Alam
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Dibyapriya Roy Chowdhury
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Tapati Chakraborti
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India.
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8
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Abstract
Aminoglycosides are well known as antibiotics that target the bacterial ribosome. However, they also impact the eukaryotic translation mechanism to promote read-through of premature termination codons (PTCs) in mRNA. Aminoglycosides are therefore considered as potential therapies for PTC-associated human diseases. Here, we performed a comprehensive study of the mechanism of action of aminoglycosides in eukaryotes by applying a combination of structural and functional approaches. Our findings reveal complex interactions of aminoglycosides with eukaryotic 80S ribosome caused by their multiple binding sites, which lead to inhibition of intersubunit movement within the human ribosome that impact nearly every aspect of protein synthesis. Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukaryotic translation remain largely unexplored. Here, we use the combination of X-ray crystallography and single-molecule FRET analysis to reveal the interactions of distinct classes of aminoglycosides with the 80S eukaryotic ribosome. Crystal structures of the 80S ribosome in complex with paromomycin, geneticin (G418), gentamicin, and TC007, solved at 3.3- to 3.7-Å resolution, reveal multiple aminoglycoside-binding sites within the large and small subunits, wherein the 6′-hydroxyl substituent in ring I serves as a key determinant of binding to the canonical eukaryotic ribosomal decoding center. Multivalent binding interactions with the human ribosome are also evidenced through their capacity to affect large-scale conformational dynamics within the pretranslocation complex that contribute to multiple aspects of the translation mechanism. The distinct impacts of the aminoglycosides examined suggest that their chemical composition and distinct modes of interaction with the ribosome influence PTC read-through efficiency. These findings provide structural and functional insights into aminoglycoside-induced impacts on the eukaryotic ribosome and implicate pleiotropic mechanisms of action beyond decoding.
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9
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Yusupova G, Yusupov M. Crystal structure of eukaryotic ribosome and its complexes with inhibitors. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0184. [PMID: 28138070 DOI: 10.1098/rstb.2016.0184] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 01/26/2023] Open
Abstract
A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS/INSERM, University of Strasbourg, BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS/INSERM, University of Strasbourg, BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France
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10
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Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin. Nat Commun 2017; 8:1589. [PMID: 29150609 PMCID: PMC5693986 DOI: 10.1038/s41467-017-01664-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/05/2017] [Indexed: 12/25/2022] Open
Abstract
Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL). The structure reveals the mechanism by which the drug induces its deleterious effects on the parasite. We further show that PAR interferes with several aspects of cytosolic translation, thus highlighting the cytosolic rather than the mitochondrial ribosome as the primary drug target. The results also highlight unique as well as conserved elements in the PAR-binding pocket that can serve as hotspots for the development of novel therapeutics.
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11
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Zhang X, Lai M, Chang W, Yu I, Ding K, Mrazek J, Ng HL, Yang OO, Maslov DA, Zhou ZH. Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes. Nat Commun 2016; 7:13223. [PMID: 27752045 PMCID: PMC5071889 DOI: 10.1038/ncomms13223] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/13/2016] [Indexed: 11/17/2022] Open
Abstract
The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. Here, by direct electron-counting cryoEM, we have determined the structures of the Leishmania donovani and human ribosomes at 2.9 Å and 3.6 Å, respectively. Our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rRNA (as opposed to a single 28S rRNA in most eukaryotes, including humans) and reveals atomic details of a unique 20 amino acid extension of the uL13 protein that pins down the ends of three of the rRNA fragments. The structure also fashions many large rRNA expansion segments. Direct comparison of our human and leishmanial ribosome structures at the decoding A-site sheds light on how the bacterial ribosome-targeting drug paromomycin selectively inhibits the eukaryotic L. donovani, but not human, ribosome.
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Affiliation(s)
- Xing Zhang
- Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
| | - Mason Lai
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Winston Chang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Iris Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Ke Ding
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Jan Mrazek
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Hwee L. Ng
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Otto O. Yang
- California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Dmitri A. Maslov
- Department of Biology, University of California, Riverside, California 91521, USA
| | - Z. Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA
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12
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Shalev M, Rozenberg H, Smolkin B, Nasereddin A, Kopelyanskiy D, Belakhov V, Schrepfer T, Schacht J, Jaffe CL, Adir N, Baasov T. Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics. Nucleic Acids Res 2015; 43:8601-13. [PMID: 26264664 PMCID: PMC4787808 DOI: 10.1093/nar/gkv821] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/01/2015] [Indexed: 11/13/2022] Open
Abstract
Leishmaniasis comprises an array of diseases caused by pathogenic species of Leishmania, resulting in a spectrum of mild to life-threatening pathologies. Currently available therapies for leishmaniasis include a limited selection of drugs. This coupled with the rather fast emergence of parasite resistance, presents a dire public health concern. Paromomycin (PAR), a broad-spectrum aminoglycoside antibiotic, has been shown in recent years to be highly efficient in treating visceral leishmaniasis (VL)—the life-threatening form of the disease. While much focus has been given to exploration of PAR activities in bacteria, its mechanism of action in Leishmania has received relatively little scrutiny and has yet to be fully deciphered. In the present study we present an X-ray structure of PAR bound to rRNA model mimicking its leishmanial binding target, the ribosomal A-site. We also evaluate PAR inhibitory actions on leishmanial growth and ribosome function, as well as effects on auditory sensory cells, by comparing several structurally related natural and synthetic aminoglycoside derivatives. The results provide insights into the structural elements important for aminoglycoside inhibitory activities and selectivity for leishmanial cytosolic ribosomes, highlighting a novel synthetic derivative, compound 3, as a prospective therapeutic candidate for the treatment of VL.
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Affiliation(s)
- Moran Shalev
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Smolkin
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Abedelmajeed Nasereddin
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dmitry Kopelyanskiy
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Valery Belakhov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Thomas Schrepfer
- Kresge Hearing Research Institute, Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jochen Schacht
- Kresge Hearing Research Institute, Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Charles L Jaffe
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | - Timor Baasov
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
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13
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Structural basis for the inhibition of the eukaryotic ribosome. Nature 2014; 513:517-22. [DOI: 10.1038/nature13737] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/06/2014] [Indexed: 11/08/2022]
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14
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Fosso MY, Li Y, Garneau-Tsodikova S. New trends in aminoglycosides use. MEDCHEMCOMM 2014; 5:1075-1091. [PMID: 25071928 PMCID: PMC4111210 DOI: 10.1039/c4md00163j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite their inherent toxicity and the acquired bacterial resistance that continuously threaten their long-term clinical use, aminoglycosides (AGs) still remain valuable components of the antibiotic armamentarium. Recent literature shows that the AGs' role has been further expanded as multi-tasking players in different areas of study. This review aims at presenting some of the new trends observed in the use of AGs in the past decade, along with the current understanding of their mechanisms of action in various bacterial and eukaryotic cellular processes.
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Affiliation(s)
- Marina Y. Fosso
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Yijia Li
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
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15
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Guha K, Bhandari D, Sen T, Saha P. Ubiquitination-mediated interaction among domains is responsible for inhibition of RNA endonuclease activity of mRNA cycling sequence binding protein from L. donovani (LdCSBP). Parasitol Res 2014; 113:2941-9. [PMID: 24908431 DOI: 10.1007/s00436-014-3956-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 05/20/2014] [Indexed: 11/25/2022]
Abstract
In nearly complete absence of transcriptional regulation, messenger RNA (mRNA) turnover mediated through specific cis-elements plays a predominant role in the control of differential gene expression for the disease causing trypanosomatid parasites. In these organisms, the periodic accumulation of S-phase messages during cell cycle is determined by the presence of one or more copies of a conserved CAUAGAAG octanucleotide motif in the untranslated regions of mRNAs. In our previous studies, a multi-domain cycling sequence binding protein LdCSBP from Leishmania donovani was characterized, which binds specifically to the octamer-containing RNAs via its uniquely arranged CCCH-type Zn fingers and degrades them through its small MutS-related (Smr) endonuclease domain, indicative of its potential role in the turnover of the S-phase mRNAs. Interestingly, the protein is modified by the incorporation of a monoubiquitin residue, and the posttranslational modification inhibits its riboendonuclease activity. However, the mechanism of such inhibition was previously unknown. Here, we establish that the CCCH-type Zn finger domain is the site of ubiquitination in LdCSBP and the interaction of CUE domain of the protein with the ubiquitinated Zn finger domain is responsible for inhibition of its riboendonuclease activity. The findings elucidate an inhibitory mechanism of RNA cleavage through ubiquitination-mediated intramolecular interaction among domains of the enzyme. Furthermore, the riboendonuclease activity is inhibited by anti-leishmanial drug paromomycin suggesting that the regulation of RNA metabolism could be a target of the drug.
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Affiliation(s)
- Kasturi Guha
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India
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16
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Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Böttger EC. 4'-O-substitutions determine selectivity of aminoglycoside antibiotics. Nat Commun 2014; 5:3112. [PMID: 24473108 PMCID: PMC3942853 DOI: 10.1038/ncomms4112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023] Open
Abstract
Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.
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Affiliation(s)
- Déborah Perez-Fernandez
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
- These authors contributed equally to this work
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
- These authors contributed equally to this work
| | - Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Ng Chyan Leong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- These authors contributed equally to this work
| | - Iwona Kudyba
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashmi Patak
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Srinivas Reddy Dubbaka
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Kathrin Lang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Pietro Freihofer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Swapna Vaddi
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - Pia Thommes
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
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17
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Identification of the molecular attributes required for aminoglycoside activity against Leishmania. Proc Natl Acad Sci U S A 2013; 110:13333-8. [PMID: 23898171 DOI: 10.1073/pnas.1307365110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Leishmaniasis, a parasitic disease caused by protozoa of the genus Leishmania, affects millions of people worldwide. Aminoglycosides are mostly known as highly potent, broad-spectrum antibiotics that exert their antibacterial activity by selectively targeting the decoding A site of the bacterial ribosome, leading to aberrant protein synthesis. Recently, some aminoglycosides have been clinically approved and are currently used worldwide for the treatment of leishmaniasis; however the molecular details by which aminoglycosides induce their deleterious effect on Leishmaina is still rather obscure. Based on high conservation of the decoding site among all kingdoms, it is assumed that the putative binding site of these agents in Leishmania is the ribosomal A site. However, although recent X-ray crystal structures of the bacterial ribosome in complex with aminoglycosides shed light on the mechanism of aminoglycosides action as antibiotics, no such data are presently available regarding their binding site in Leishmania. We present crystal structures of two different aminoglycoside molecules bound to a model of the Leishmania ribosomal A site: Geneticin (G418), a potent aminoglycoside for the treatment of leishmaniasis at a 2.65-Å resolution, and Apramycin, shown to be a strong binder to the leishmanial ribosome lacking an antileishmanial activity at 1.4-Å resolution. The structural data, coupled with in vitro inhibition measurements on two strains of Leishmania, provide insight as to the source of the difference in inhibitory activity of different Aminoglycosides. The combined structural and physiological data sets the ground for rational design of new, and more specific, aminoglycoside derivatives as potential therapeutic agents against leishmaniasis.
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18
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Poulikakos P, Falagas ME. Aminoglycoside therapy in infectious diseases. Expert Opin Pharmacother 2013; 14:1585-97. [DOI: 10.1517/14656566.2013.806486] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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