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Tevyashova AN, Shapovalova KS. Potential for the Development of a New Generation of Aminoglycoside Antibiotics. Pharm Chem J 2022; 55:860-875. [PMID: 35039693 PMCID: PMC8754558 DOI: 10.1007/s11094-021-02510-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Indexed: 11/29/2022]
Abstract
The present review summarizes recent publications devoted to aminoglycosides that study the main types of resistance to antibiotics of this class and the main directions of chemical modification aimed at overcoming the resistance or changing the spectrum of biological activity. Conjugates of aminoglycosides with various pharmacophores including amino acids, peptides, peptide nucleic acids, nucleic bases, and several other biologically active molecules and modifications resulting in other types of biological activity of this class of antibiotics are described. It is concluded that a promising research direction aimed at increasing the activity of antibiotics against resistant strains is the search for selective inhibitors of aminoglycoside-modifying enzymes. This would allow renewal of the use of antibiotics already meeting widespread resistance and would increase the potential of a new generation of antibiotics.
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Affiliation(s)
- A. N. Tevyashova
- G. F. Gause Institute of New Antibiotics, 11/1 B. Pirogovskaya St, Moscow, 119021 Russia
| | - K. S. Shapovalova
- G. F. Gause Institute of New Antibiotics, 11/1 B. Pirogovskaya St, Moscow, 119021 Russia
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2
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Paul A, Huang J, Han Y, Yang X, Vuković L, Král P, Zheng L, Herrmann A. Photochemical control of bacterial gene expression based on trans encoded genetic switches. Chem Sci 2021; 12:2646-2654. [PMID: 34164033 PMCID: PMC8179269 DOI: 10.1039/d0sc05479h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/07/2021] [Indexed: 12/02/2022] Open
Abstract
Controlling gene expression by light with fine spatiotemporal resolution not only allows understanding and manipulating fundamental biological processes but also fuels the development of novel therapeutic strategies. In complement to exploiting optogenetic tools, photochemical strategies mostly rely on the incorporation of photo-responsive small molecules into the corresponding biomacromolecular scaffolds. Therefore, generally large synthetic effort is required and the switching of gene expression in both directions within a single system remains a challenge. Here, we report a trans encoded ribo-switch, which consists of an engineered tRNA mimicking structure (TMS), under control of small photo-switchable signalling molecules. The signalling molecules consist of two amino glycoside molecules that are connected via an azobenzene unit. The light responsiveness of our system originates from the photo-switchable noncovalent interactions between the signalling molecule and the TMS switch, leading to the demonstration of photochemically controlled expression of two different genes. We believe that this modular design will provide a powerful platform for controlling the expression of other functional proteins with high spatiotemporal resolution employing light as a stimulus.
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Affiliation(s)
- Avishek Paul
- Zernike Institute for Advanced Materials, Dept. of Polymer Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
| | - Jingyi Huang
- Zernike Institute for Advanced Materials, Dept. of Polymer Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Yanxiao Han
- Department of Chemistry, University of Illinois at Chicago Chicago Illinois 60607 USA
| | - Xintong Yang
- Zernike Institute for Advanced Materials, Dept. of Polymer Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
| | - Lela Vuković
- Department of Chemistry, University of Texas at El Paso El Paso Texas 79968-0513 USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago Chicago Illinois 60607 USA
- Department of Physics, University of Illinois at Chicago Chicago Illinois 60607 USA
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago Chicago Illinois 60612 USA
| | - Lifei Zheng
- Zernike Institute for Advanced Materials, Dept. of Polymer Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University Worringerweg 2 52074 Aachen Germany
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials, Dept. of Polymer Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstr. 50 52056 Aachen Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University Worringerweg 2 52074 Aachen Germany
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3
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Bastian AA, Gruszka A, Jung P, Herrmann A. Aptamer protective groups tolerate different reagents and reactions for regioselective modification of neomycin B. Org Biomol Chem 2020; 18:9606-9610. [PMID: 33237073 DOI: 10.1039/d0ob02104k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aptameric protective group strategy for the one-step regioselective transformation of aminoglycoside antibiotics was found to be compatible with diverse reagents and reaction conditions. New derivatives of neomycin B were synthesized with regioselectivities of >99%. This result extends the scope of applicability of APGs facilitating access to novel aminoglycoside derivatives.
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Affiliation(s)
- Andreas A Bastian
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany.
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4
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Aradi K, Di Giorgio A, Duca M. Aminoglycoside Conjugation for RNA Targeting: Antimicrobials and Beyond. Chemistry 2020; 26:12273-12309. [PMID: 32539167 DOI: 10.1002/chem.202002258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Indexed: 01/04/2023]
Abstract
Natural aminoglycosides are therapeutically useful antibiotics and very efficient RNA ligands. They are oligosaccharides that contain several ammonium groups able to interfere with the translation process in prokaryotes upon binding to bacterial ribosomal RNA (rRNA), and thus, impairing protein synthesis. Even if aminoglycosides are commonly used in therapy, these RNA binders lack selectivity and are able to bind to a wide number of RNA sequences/structures. This is one of the reasons for their toxicity and limited applications in therapy. At the same time, the ability of aminoglycosides to bind to various RNAs renders them a great source of inspiration for the synthesis of new binders with improved affinity and specificity toward several therapeutically relevant RNA targets. Thus, a number of studies have been performed on these complex and highly functionalized compounds, leading to the development of various synthetic methodologies toward the synthesis of conjugated aminoglycosides. The aim of this review is to highlight recent progress in the field of aminoglycoside conjugation, paying particular attention to modifications performed toward the improvement of affinity and especially to the selectivity of the resulting compounds. This will help readers to understand how to introduce a desired chemical modification for future developments of RNA ligands as antibiotics, antiviral, and anticancer compounds.
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Affiliation(s)
- Klara Aradi
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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Chandrika NT, Garneau-Tsodikova S. A review of patents (2011-2015) towards combating resistance to and toxicity of aminoglycosides. MEDCHEMCOMM 2015; 7:50-68. [PMID: 27019689 PMCID: PMC4806794 DOI: 10.1039/c5md00453e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Since the discovery of the first aminoglycoside (AG), streptomycin, in 1943, these broad-spectrum antibiotics have been extensively used for the treatment of Gram-negative and Gram-positive bacterial infections. The inherent toxicity (ototoxicity and nephrotoxicity) associated with their long-term use as well as the emergence of resistant bacterial strains have limited their usage. Structural modifications of AGs by AG-modifying enzymes, reduced target affinity caused by ribosomal modification, and decrease in their cellular concentration by efflux pumps have resulted in resistance towards AGs. However, the last decade has seen a renewed interest among the scientific community for AGs as exemplified by the recent influx of scientific articles and patents on their therapeutic use. In this review, we use a non-conventional approach to put forth this renaissance on AG development/application by summarizing all patents filed on AGs from 2011-2015 and highlighting some related publications on the most recent work done on AGs to overcome resistance and improving their therapeutic use while reducing ototoxicity and nephrotoxicity. We also present work towards developing amphiphilic AGs for use as fungicides as well as that towards repurposing existing AGs for potential newer applications.
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Affiliation(s)
- Nishad Thamban Chandrika
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. Fax: 859-257-7585; Tel: 859-218-1686
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. Fax: 859-257-7585; Tel: 859-218-1686
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Kuil J, Buckle T, van Leeuwen FWB. Imaging agents for the chemokine receptor 4 (CXCR4). Chem Soc Rev 2012; 41:5239-61. [PMID: 22743644 DOI: 10.1039/c2cs35085h] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interaction between the chemokine receptor 4 (CXCR4) and stromal cell-derived factor-1 (SDF-1, also known as CXCL12) is a natural regulatory process in the human body. However, CXCR4 over-expression is also found in diseases such as cancer, where it plays a role in, among others, the metastatic spread. For this reason it is an interesting biomarker for the field of diagnostic oncology, and therefore, it is gaining increasing interest for applications in molecular imaging. Especially "small-molecule" imaging agents based on T140, FC131 and AMD3100 have been extensively studied. SDF-1, antibodies, pepducins and bioluminescence have also been used to visualize CXCR4. In this critical review reported CXCR4 targeting imaging agents are described based on their affinity, specificity and biodistribution. The level wherein CXCR4 is up-regulated in cancer patients and its relation to the different cell lines and animal models used to evaluate the efficacy of the imaging agents is also discussed (221 references).
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Affiliation(s)
- Joeri Kuil
- Department of Radiology, Interventional Molecular Imaging, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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Berchanski A, Kalinkovich A, Ludin A, Lapidot T, Lapidot A. Insights into the mechanism of enhanced mobilization of hematopoietic progenitor cells and release of CXCL12 by a combination of AMD3100 and aminoglycoside-polyarginine conjugates. FEBS J 2011; 278:4150-65. [PMID: 21910828 DOI: 10.1111/j.1742-4658.2011.08348.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mobilization of hematopoietic stem and progenitor cells (HSPCs) from the bone marrow to the peripheral blood is utilized in clinical HSPC transplantation protocols. Retention of HSPCs in the bone marrow is determined by relationships between the chemokine chemokine (C-X-C motif) ligand 12 (CXCL12) and its major receptor C-X-C chemokine receptor type 4 (CXCR4), and disruption of this retention by CXCR4 antagonists such as AMD3100 induces rapid HSPC mobilization. Here, we report that aminoglycoside-polyarginine conjugates (APACs) and N-α-acetyl-nona-D-arginine (r9) induce mobilization of white blood cells and, preferentially, immature hematopoietic progenitor cells (HPCs) in mice, similarly to AMD3100. Remarkably, administration of AMD3100 with each one of the APACs or r9 caused additional HPC mobilization. The mobilizing activity of APACs and r9 was accompanied by a significant elevation in plasma CXCL12 levels. To further understand how APACs, r9 and their combinations with AMD3100 compete with CXCL12 binding to CXCR4, as well with antibody against CXCR4 for CXCR4 binding, we have undertaken an approach combining experimental validation and docking to determine plausible binding modes for these ligands. On the basis of our biological and docking findings, and recently published NMR data, we suggest that combination of pairs of compounds such as APACs (or r9) with AMD3100 induces more efficient disruption of the CXCL12-CXCR4 interaction than AMD3100 alone, resulting in enhanced HPC mobilization.
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Affiliation(s)
- Alexander Berchanski
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Houghton JL, Green KD, Chen W, Garneau-Tsodikova S. The future of aminoglycosides: the end or renaissance? Chembiochem 2010; 11:880-902. [PMID: 20397253 DOI: 10.1002/cbic.200900779] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Indexed: 11/05/2022]
Abstract
Although aminoglycosides have been used as antibacterials for decades, their use has been hindered by their inherent toxicity and the resistance that has emerged to these compounds. It seems that such issues have relegated a formerly front-line class of antimicrobials to the proverbial back shelf. However, recent advances have demonstrated that novel aminoglycosides have a potential to overcome resistance as well as to be used to treat HIV-1 and even human genetic disorders, with abrogated toxicity. It is not the end for aminoglycosides, but rather, the challenges faced by researchers have led to ingenuity and a change in how we view this class of compounds, a renaissance.
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Affiliation(s)
- Jacob L Houghton
- Department of Medicinal Chemistry in the College of Pharmacy, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
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Tan JJ, Cong XJ, Hu LM, Wang CX, Jia L, Liang XJ. Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection. Drug Discov Today 2010; 15:186-97. [PMID: 20096804 DOI: 10.1016/j.drudis.2010.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 11/21/2009] [Accepted: 01/14/2010] [Indexed: 11/28/2022]
Abstract
The HIV replication cycle offers multiple targets for chemotherapeutic intervention, including the viral exterior envelope glycoprotein, gp120; viral co-receptors CXCR4 and CCR5; transmembrane glycoprotein, gp41; integrase; reverse transcriptase; protease and so on. Most currently used anti-HIV drugs are reverse transcriptase inhibitors or protease inhibitors. The expanding application of simulation to drug design combined with experimental techniques have developed a large amount of novel inhibitors that interact specifically with targets besides transcriptase and protease. This review presents details of the anti-HIV inhibitors discovered with computer-aided approaches and provides an overview of the recent five-year achievements in the treatment of HIV infection and the application of computational methods to current drug design.
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Affiliation(s)
- Jian J Tan
- College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100124, China
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Teixeira C, Serradji N, Maurel F, Barbault F. Docking and 3D-QSAR studies of BMS-806 analogs as HIV-1 gp120 entry inhibitors. Eur J Med Chem 2009; 44:3524-32. [DOI: 10.1016/j.ejmech.2009.03.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 01/27/2009] [Accepted: 03/19/2009] [Indexed: 10/21/2022]
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12
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Xu Y, Jin H, Yang Z, Zhang L, Zhang L. Synthesis and biological evaluation of novel neamine–nucleoside conjugates potentially targeting to RNAs. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.04.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Synthesis and evaluation of novel neamine derivatives effectively targeting to RNA. Bioorg Med Chem Lett 2009; 19:2103-6. [DOI: 10.1016/j.bmcl.2009.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 02/18/2009] [Accepted: 03/09/2009] [Indexed: 11/21/2022]
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Computer-based design of novel HIV-1 entry inhibitors: neomycin conjugated to arginine peptides at two specific sites. J Mol Model 2008; 15:281-94. [DOI: 10.1007/s00894-008-0401-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 10/03/2008] [Indexed: 10/21/2022]
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Lapidot A, Berchanski A, Borkow G. Insight into the mechanisms of aminoglycoside derivatives interaction with HIV-1 entry steps and viral gene transcription. FEBS J 2008; 275:5236-57. [PMID: 18803669 DOI: 10.1111/j.1742-4658.2008.06657.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In recent years, based on peptide models of HIV-1 RNA binding, NMR structures of Tat-responsive element-ligand complexes and aminoglycoside-RNA interactions, and HIV-1 Tat structure, we have designed and synthesized aminoglycoside-arginine conjugates (AACs) and aminoglycoside poly-arginine conjugates (APACs), to serve as Tat mimetics. These novel molecules inhibit HIV-1 infectivity with 50% effective concentration values in the low micromolar range, the most potent compounds being the hexa-arginine-neomycin B and nona-D-arginine-neomycin conjugates. Importantly, these compounds, in addition to acting as Tat antagonists, inhibit HIV-1 infectivity by blocking several steps in HIV-1 cell entry. The AACs and APACs inhibit HIV-1 cell entry by interacting with gp120 at the CD4-binding site, by interacting with CXCR4 at the binding site of the CXCR4 mAb 12G5, and apparently by interacting with transient structures of the ectodomain of gp41. In the current review, we discuss the mechanisms of anti-HIV-1 activities of these AACs, APACs and other aminoglycoside derivatives in detail. Targeting several key processes in the viral life cycle by the same compound not only may increase its antiviral efficacy, but more importantly, may reduce the capacity of the virus to develop resistance to the compound. AACs and APACs may thus serve as leading compounds for the development of multitargeting novel HIV-1 inhibitors.
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Affiliation(s)
- Aviva Lapidot
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
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Berchanski A, Lapidot A. Bacterial RNase P RNA is a drug target for aminoglycoside-arginine conjugates. Bioconjug Chem 2008; 19:1896-906. [PMID: 18712898 DOI: 10.1021/bc800191u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ribonuclease P (RNase P) holoenzymes are RNPs composed of RNase P RNA (PRNA) and a variable number of P protein subunits. Primary differences in structure and function between bacterial and eukaryotic RNase P and its indispensability for cell viability make the bacterial enzyme an attractive drug target. On the basis of our previous studies, aminoglycoside-arginine conjugates (AACs) bind to HIV-1 TAR and Rev responsive element (RRE) RNAs significantly more efficiently than neomycin B. Their specific inhibition of bacterial rRNA as well as the findings that the hexa-arginine neomycin derivative (NeoR6) is 500-fold more potent than neomycin B in inhibiting bacterial RNase P, led us to explore the structure-function relationships of AACs in comparison to a new set of aminoglycoside-polyarginine conjugates (APACs). We here present predicted binding modes of AACs and APACs to PRNA. We used a multistep docking approach comprising rigid docking full scans and final refinement of the obtained complexes. Our docking results suggest three possible mechanisms of RNase P inhibition by AACs and APACs: competition with the P protein and pre-tRNA on binding to P1-P4 multihelix junction and to J19/4 region (probably including displacement of Mg2+ ions from the P4 helix) of PRNA; competition with Mg2+ ions near the P15 loop; and competition with the P protein and/or pre-tRNA near the P15 helix and interfering with interactions between the P protein and pre-tRNA at this region. The APACs revealed about 10-fold lower intermolecular energy than AACs, indicating stronger interactions of APACs than AACs with PRNA.
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Affiliation(s)
- Alexander Berchanski
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Lapidot A, Peled A, Berchanski A, Pal B, Kollet O, Lapidot T, Borkow G. NeoR6 inhibits HIV-1-CXCR4 interaction without affecting CXCL12 chemotaxis activity. Biochim Biophys Acta Gen Subj 2008; 1780:914-20. [DOI: 10.1016/j.bbagen.2008.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Revised: 03/05/2008] [Accepted: 03/07/2008] [Indexed: 11/30/2022]
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