Elsevier

Current Opinion in Biotechnology

Volume 48, December 2017, Pages 33-41
Current Opinion in Biotechnology

Biosynthetic pathways of aminoglycosides and their engineering

https://doi.org/10.1016/j.copbio.2017.03.019Get rights and content

Highlights

  • Aminoglycosides have been and will be treasured anti-infective against ‘superbugs’.

  • Aminoglycosides’ defensive structural features are clues for antibiotic discovery.

  • Understanding aminoglycoside biosynthesis is a key for its pathway engineering.

  • Engineered biosynthesis will be an efficient tool to generate new aminoglycosides.

Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature’s gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature’s biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging ‘superbugs’ but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.

Introduction

Aminoglycosides (AGs) are one of the oldest classes of essential antibiotic agents. They possess two or three uncommon amino-sugars, which are attached by glycosidic bonds to the amino-substituted cyclohexane scaffold aminocyclitol (Figure 1). The first discovered AG streptomycin contains streptamine as the core aminocyclitol, whereas other pharmaceutically valuable AGs have 2-deoxystreptamine (2DOS) as the core [1, 2, 3, 4, 5]. The 2DOS-containing AGs are appended with amino-sugars at the C4 and C5 or C4 and C6 positions, thus yielding 4,5-disubstituted AGs (e.g., butirosin and neomycin), or 4,6-disubstituted AGs (e.g., kanamycin, tobramycin and gentamicin) (see Figure 1).

The AGs interfere with protein biosynthesis by acting on the smaller 30S subunit of the bacterial ribosome, causing bactericidal effects against the pathogens [6, 7, 8]. Moreover, their potential for the treatment of human immunodeficiency virus infection and human genetic diseases have also been recently demonstrated [9, 10, 11, 12]. Therefore, the structural modification of AG scaffolds with diverse chemical motifs to improve or alter their activities along with the reduced toxicity can greatly expand their utility [13, 14, 15].

Widespread bacterial resistance to the AGs has limited their clinical use [6, 7]. Deactivation of AGs by AG-modifying enzymes (AMEs) is the most common resistance mechanism and causes severe clinical problems [16]. Fortunately, some 2DOS–containing AGs possess natural defensive structural features active against these AMEs, including the N-aminoacyl moiety in butirosin (e.g., 4-amino-2-hydroxybutyrate (AHBA) substituent on the C1-amine of the 2DOS core) and the 3′,4′- or 3′-deoxygenation in gentamicin or tobramycin, respectively. These naturally occurring AG modifications have thus been applied to generate second-generation semi-synthetic AGs (e.g., amikacin, dibekacin and arbekacin) (see Figure 1). Despite the historical success of these conventional chemical modification approaches [17, 18], biotechnological approaches such as combinatorial biosynthesis or pathway engineering can be attractive alternatives to invent structurally diverse AGs [2, 19, 20, 21, 22]. Herein, we discuss the up-to-date findings on 2DOS-containing AG biosynthetic pathways which provide the knowledge to guide rational biosynthetic efforts aimed at producing novel AG analogs, recent examples of their pathway engineering, and some pivotal advances in the development of semi-synthetic AG leads. The potential of pathway engineering for the revitalization of this old class of antibiotics are also addressed.

Section snippets

State-of-the-art research in aminoglycoside biosynthetic pathways

The AHBA side chain of 4,5-disubstituted butirosin is one of the critical structural traits utilized to circumvent the resistance mechanisms of AMEs, hence giving birth to semi-synthetic AGs [23]. The function of seven genes in the butirosin cluster involved in the biosynthesis and installation of the AHBA moiety onto butirosin have been elucidated (Figure 2a) [24, 25]. These findings allowed for the incorporation of the AHBA biosynthetic machinery into the different AG biosynthetic pathways to

Pathway engineering challenges

Several recent studies have demonstrated that the engineering of AG biosynthetic pathways can provide an efficient tool for producing the valuable AG congeners as major products, or generating novel AG analogs with potentially improved activities. Kanamycin B is a starting AG for the manufacture of semi-synthetic arbekacin and dibekacin [23]. Streptomyces tenebrarius H6 has been known to contain both apramycin and tobramycin biosynthetic gene clusters, and two sets of homologous genes (e.g.,

Semi-synthetic aminoglycoside leads

Gratifyingly, a few semi-synthetic AG leads have been developed for next-generation anti-infective therapies to overcome the AG resistance mechanisms. Plazomicin was designed to avoid almost all clinically relevant AMEs by the chemical modification of the natural 3′,4′-deoxy sisomicin by affixing both an AHBA moiety at the C1-amine position and a hydroxyethyl chain at the C6′-amine [45] (Figure 4). Plazomicin displays superior activity against a broad range of Gram-negative pathogens that have

Perspective

The semi-synthesis of new AG derivatives will undoubtedly continue to play a role in developing anti-infective therapeutics against multidrug-resistant and life-threatening pathogens. However, biotechnological strategies will become efficient alternatives for producing currently desired AGs and for developing new AGs that will be indispensable in the post-antibiotic era. Recent insights into the biosynthesis of natural AG’s defensive structural elements, including both the 1-N-aminoacyl and

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

We thank Dr Kris Rathwell for critically reading this manuscript. This work was supported by the National Research Foundation of Korea grants (2016R1A2A1A05005078, 2015R1A2A2A01002524 [J.W.P.]) funded by the Ministry of Science, ICT and Future Planning (MISP), and the Intelligent Synthetic Biology Center of the Global Frontier Project funded by MISP (20110031961), Advanced Production Technology Development Program (114048-03-3-CG000) and High Value-added Food Technology Development Program

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