Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Review Article

Prospects for new antibiotics: a molecule-centered perspective

Abstract

There is a continuous need for iterative cycles of antibiotic discovery and development to deal with the selection of resistant pathogens that emerge as therapeutic application of an antibiotic becomes widespread. A short golden age of antibiotic discovery from nature followed by a subsequent golden half century of medicinal chemistry optimization of existing molecular scaffolds emphasizes the need for new antibiotic molecular frameworks. We bring a molecule-centered perspective to the questions of where will new scaffolds come from, when will chemogenetic approaches yield useful new antibiotics and what existing bacterial targets merit contemporary re-examination.

A personal pathway to antibiotics research

For one of us (CTW), a career-long interest in antibiotics1 was spurred by discussions on the mechanism of action of D-fluoroalanine2, 3 during a seminar visit, as a second year assistant professor, at Merck in 1974. This visit led to examination of the mechanism of action of mono-, di- and trifluoroalanines as mechanism-based inactivators for the bacterial pyridoxal phosphate-dependent alanine racemase, the first step in assembly of the muramyl pentapeptide of the bacterial peptidoglycan layer.4, 5, 6, 7 In turn, that led to analysis of other muramyl peptide biosynthetic enzymes, including MurA8, 9, 10, 11 (the target of fosfomycin) and MurB,12, 13, 14, 15, 16, 17, 18 which together build the lactyl ether moiety of UDP muramic acid. We progressed on to the enzyme MurF,19 the D-Ala-D-Ala ligase that adds this D-D-dipeptide to UDP-muramyl tripeptide, to yield UDP-muramyl pentatopeptide as the last step in the cytoplasmic phase of peptidoglycan assembly.20, 21

A second phase of interest was initiated when CTW was the CEO of the Dana Farber Cancer Institute in the early 1990s at a time when vancomycin was being used as the antibiotic of last resort for treatment of life-threatening Gram-positive bacterial infections of patients undergoing cycles of chemotherapy. The molecular mechanism of resistance of pathogenic vancomycin-resistant enterococci (VRE) turned out to be replacement of the D-Ala-D-Ala termini of muramyl pentapeptide intermediates with D-Ala-D-Lactate, which had 1000-fold lower affinity to vancomycin.22 We established the the VanA enzyme in VRE was not the classic D-Ala-D-Ala ligase but a D-Ala-D-Lac ligase22, 23, 24, 25, 26 and thus determined the molecular basis of drug resistance in VRE.27, 28, 29

The rise of VRE through the 1990s focused our attention on how natural product antibiotic scaffolds such as those of vancomycin and the related teicoplanin were assembled,29, 30 in part to decipher the chemical logic and molecular machinery and, in part, with the hope that one might learn to reprogram natural antibiotic assembly lines to engineer improved molecular variants.

We have subsequently deciphered many of the rules for nonribosomal peptide (NRP) synthetase assembly lines, including post-translational priming of carrier protein domains by phosphopantetheinylation, and the nature of the chain initiation, elongation and termination steps.30, 31, 32, 33, 34, 35 These efforts have allowed us and many other groups to undertake full reconstitution of NRP synthetase assembly lines, especially in siderophore biosynthesis.36 From our extensive work on characterization of natural product biosynthesis catalytic machinery and molecular logic, we have had a continued interest in new natural products and the underlying chemistry of molecular scaffold assembly.37

Antibiotics as a special class of therapeutics

One could argue that antibiotics represent a special class of therapeutic agents whose misuse affects not just the individual patient but the broader community. This is due to the almost inevitable selection for antibiotic-resistant bacteria that arise in clinically significant waves at some point after widespread introduction and use of a new antibiotic (both in veterinary and human populations). As Table 1 (modified from a review by Palumbi)38 shows, resistance is inevitable.39, 40, 41, 42, 43, 44, 45 It is not a question of if but rather a question of when. Much effort in recent years has gone into definition of the resistome,46, 47 the collection of antibiotic-resistant genomes harbored in both bacterial pathogens and in environmental bacterial populations. The origins of vancomycin resistance, for example, derive from transfer of vanHAX genes from intrinsically resistant soil microbes such as lactobacilli and leuconostoc strains to enterococci where they often reside on transposable elements.46, 48, 49 The depth of the resistome resevoir was powerfully demonstrated in the findings of D’Costa et al.50 in 2006 showing that collections of soil actinomycetes had, on average, resistance genes to 7 antibiotics while some isolates were resistant to 15 drugs.

Table 1 Evolution of resistance to clinical antibiotics

Because of the mobilization of resistome genes into opportunistic and professional bacterial pathogens, there is always a need for the next generation of antibiotics. There are parallels to antiviral and anticancer therapeutics where the rapid proliferation and the large number of viruses and tumor cells in a patient can mirror the rapid growth and titer of bacterial pathogens. Mutations rates of 10−6 per cell divison are problematic in all the three therapeutic arenas. We shall return later to a distinction in therapeutic regimens: in antiviral and anticancer drug regimens, combination therapy is the norm while for bacterial infections monotherapy has been the default historical prescribing pattern.

Gram-positive and Gram-negative pathogens present overlapping but distinct target profiles. While Gram-positive pathogens such as VRE and methicillin-resistant Staphylococcus aureus (MRSA) have rightly drawn attention over the past two decades, the Gram-negatives, underlined, in the list of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa and Enterobacter species), are in many cases more of a pressing treatment challenge.51 The approvals of synercid and daptomycin were largely in response to VRE and MRSA challenges52, 53 but there has not been a new antibiotic scaffold for Gram-negative pathogens in decades. As a consequence polymyxins (for example, colistin) have become front-line therapy in recent years,54, 55 even though they were eschewed as too toxic when discovered 40 years ago. Multidrug-resistant tuberculosis pose their own crises for therapy around the world but, finally, promising new molecules (for example, benzothiazinone BTZ04356, 57, 58, 59, 60, 61 in late preclinical GLP/Tox funded by the European Commission, sponsored by New Medicines for Tuberculosis, and in development by Alere in Germany; nitroimidazole PA-82462, 63 in Phase II sponsored by the TB Alliance; ethylenediamine SQ10964 in Phase II sponsored by Sequella Inc and OOO Infectex; and Sutezolid65 (also known as PNU-100480) a thiooxazolidinone in Phase II under Pfizer) are progressing through late stage clinical trials or have recently been approved by the Food and Drug Administration (FDA; bedaquiline,45 a diarylquinoline inhibitor of ATP-synthase developed by J&J).66, 67

This essay is not encyclopedic and doubtless has important omissions about promising molecules in both discovery and development phases. Rather, the choices reflect the particular perspective of the authors about emerging science that seems intriguing and worthy of follow up. In consideration of the underexploited targets noted below, there is a chemocentric set of prejudices: that the availability of promising chemical matter, from Nature or from initial screening campaigns is an important precondition for finding hits, developing them into leads and conducting lead optimization for compounds to be selected as development candidates. Figure 1 is a variant of a typical drug discovery/development flow chart adapted for antibiotics;68 the low success rate emphasizes the importance of starting with molecular frameworks that can stand up to the rigors of development. The focus of the remarks in this chapter are all on discovery, not development.

Figure 1
figure 1

Antibiotic drug discovery and development flow chart adapted from literature versions.68

A pressing need for new antibiotic scaffolds

Over the past century of antibiotic discovery and development, two parallel and independent lines of discovery have been fruitful. One route has been the identification of antimicrobial chemical weaponry in Nature as small-molecule natural products were observed to have clinically useful antibacterial activity. Among these scaffolds were the penicillins and cephalosporins, the macrolides such as erythromycin, the glycopeptides exemplified by vancomycin and teicoplanin, the tetracylines and the aminoglycosides. A separate track is represented by the discovery that aromatic sulfa scaffolds originally from the chemical dyes industry frameworks had antibiotic activity.69 The resultant sulfa drugs have been in continuous use in one incarnation or another for 80 years. The second example of man-made ‘magic bullets’ as widely used antibiotics were the fluoroquinolones, first introduced clinically in the 1960s. A third distinct synthetically derived scaffold is represented by the first-generation oxazolidinone linezolid approved in the US in 2000.

The ‘golden age’ of discovery of natural antibiotics of clinical significance was actually a short two decades (Figure 2), between 1940 and 1960. One could argue that the ensuing 50 years has been a ‘golden age’ of antibiotic medicinal chemistry where chemical tailoring of the periphery of major antibiotic classes, while leaving the core intact, has been successful in dealing with successive waves of resistant bacterial pathogens. As illustrated in Figure 3, successive generations of cephalosporins, fluoroquinolones, macrolides and tetracyclines have been developed and commercialized with significant usage. In the tetracycline arena, new synthetic methodologies have enabled synthesis of pentacyclines,70 which may become a fourth generation of this antibiotic class. Analogously, while the informal designation of generations of an antibiotic class are somewhat in the eye of the beholder, one could argue that molecules such as prulifloxacin71 represent a fifth generation of fluoroquinolones. It is unlikely that medicinal chemistry modifications of these four antibiotic classes can go indefinitely. That prediction argues for a pressing need for new antibiotic scaffolds, either from natural products or from the many strands of modern synthetic chemistries. In the short term, it is understandable that antibiotic development groups and companies choose to reduce risk by working on known scaffolds and known targets, but in the longer term, new molecules and new targets will need to be identified72 as bacterial pathogens become multidrug resistant as exemplified by some of the ESKAPE pathogens.51

Figure 2
figure 2

Timeline showing the ‘Golden Age’ of antibiotic discovery (1940–1960) and the ‘Golden Age’ of antibiotic medicinal chemistry (from 1960 to present). No new structural classes of antibiotics were introduced between 1962 and 2000, representing a serious innovation gap during the genomic era.

Figure 3
figure 3

Synthetic tailoring of antibiotic core structures leading to successive generations of antibiotic classes has been the mainstay of antibiotic drug development for the past 50 years. New antibiotic core scaffolds are desperately needed. Core scaffolds are shown in black and peripheral chemical derivatizations are shown in white. The quinolone/fluoroquinolone scaffolds are of synthetic origin, while all other scaffolds are natural products or their semisynthetic derivatives.

A 2011 survey of 21 antibiotics launched since 200073 revealed that the two lines of discovery and development, natural products vs synthetic chemicals, are still operant with two new natural product classes, represented by daptomycin as a stem loop lipopeptide and retapamulin as a member of the terpenoid pleuromutilins. Of the nine antibiotics of synthetic origin launched in the past 12 years, other than the oxazolidinone linezolid, the other eight are fluoroquinolones, stressing the need for scaffold diversification away from such over-reliance on the F-quinolone framework. In that same 2011 survey of five antibiotic candidates in phase III trials, the one synthetic molecule was a second-generation oxazolidinone torezolid phosphate.74, 75, 76 Another second-generation oxazolidinone, radezolid, is progressing through late stage trials.77, 78, 79, 80

Where will new scaffolds come from

The two historical lines of discovery, synthetic chemical efforts vs isolation of new natural product scaffolds are both still in play. Two contemporary lines of chemical efforts are high throughput screening of chemical libraries and target structure-guided efforts.

A comprehensive screening effort against genetically validated essential targets, on the part of many companies, most notably detailed by a GSK group in 2007,81 effectively failed to find new chemical matter worthy of development. This has properly dampened enthusiasm for continued screening campaigns. On the other hand, the development of focused libraries, more suited for specific target classes, could hold more promise. A Pfizer group repurposed a library built for eukaryotic kinase projects and identified hits and optimized leads against the bacterial form of the ATP-dependent biotin carboxylase, which generates malonyl CoA from acetyl CoA at the start of fatty acid biosynthesis.82

Chemical libraries that mimic the scaffold complexity of natural products in three dimensional architectures, regiochemical constraints, multiple stereogenic centers and high density of functional groups have not been available over the first two decades of combichem efforts. Such libraries, even relatively small and focused around particular scaffolds, may be requisite for screening efforts to increase in success rates against bacterial targets.83, 84, 85, 86

A recent report of a structure-guided antibiotic discovery effort comes from an Astra Zeneca team on thymidylate kinase inhibition. Reasoning that this kinase lies at the intersection of both salvage and de novo formation of dTMP, essential for DNA synthesis, Keating et al.87, 88 designed scaffolds to bind to the dTMP subsite rather than the ATP subsite, using the X-ray structure of the enzyme as guide. TK-666 (Figure 4a) represents a thymine-sugar mimic with fragment coupling to two additional rings. The molecule is rapidly bacteriocidal against Gram-positives such as S. aureus, with MIC of 0.25 μg ml−1 and a Ki against pure S. aureus dTMP kinase of 0.33 nM. Inhibition of thymidylate kinase from a variety of pathogenic microbes is being pursued by several groups using modified thymidine scaffolds and mimetics.89, 90, 91, 92, 93

Figure 4
figure 4

(a) Structure of TK-666, a potent synthetic inhibitor of bacterial thymidylate kinase developed by researchers at AstraZeneca. (b) Structure of platensimycin, a potent inhibitor of bacterial β-ketoacyl-ACP synthase type I/II (FabF/B) isolated from Streptomyces platensis by a group at Merck. (c) Structure of kibdelomycin, an inhibitor of DNA gyrase subunit A isolated from Kibdelosporangium sp. MA7385 by a group at Merck. (d) Structure of abyssomycin C, an isoprenoid inhibitor of p-aminobenzoate biosynthesis in the folate biosynthetic pathway. (e) Structure of tetarimycin A, an anti-MRSA tetracyclic molecule discovered through heterologous expression of a gene cluster found in environmental DNA.

The parallel search for new scaffolds in Nature bears fruit when new assays are developed, new cultivation methods established94, 95, 96 and new niches explored.97, 98 As will be noted in a subsequent section, the platensin and platensimycin scaffolds (Figure 4b) were discovered99, 100 in antisense screens that made FabF the rate-limiting step in S. aureus lipid biosynthesis and made bacterial growth sensitive to inhibition of this step. The initial enthusiasm over these potent Fab enzyme inhibitors has been partially muted by the observation that some bacteria can scavenge host lipids during infection.101 With a collection of 245 S. aureus strains similarly manipulated to lower the bacterial cell levels of encoded enzymes, a Merck group102 reported the isolation of kibdelomycin (Figure 4c) as a DNA gyrase subunit A inhibitor, the first new natural product scaffold against gyrase in the past several decades. This antisense approach is discussed further in a subsequent section.

Exploration of new niches has traditionally yielded new molecular frameworks. In this vein, isolation of microbes from the abyss in the Sea of Japan led to the novel isoprenoid abyssomycins, which inhibit para-aminobenzoate biosynthesis in the folate biosynthetic pathway103 (Figure 4d). The genome sequences of several thousand bacteria reveal up to two dozen silent clusters for natural product biosynthesis, typically polyketide (PK), NRP and hybrid PK-NRP frameworks.104, 105, 106, 107, 108, 109, 110 Fungi similarly harbor multiple biosynthetic gene clusters that are cryptic under normal laboratory culture conditons.111 A variety of approaches have been used to turn on silent biosynthetic gene clusters to evaluate the novelty and activity of the resultant small molecules.111, 112, 113

Progress also continues in examination of the genomes of uncultivated microbes through induced expression of environmental DNA gene clusters.96, 98, 114 One recent example is the isolation of tetarimycin A (Figure 4e), a tetracyclic molecule active against MRSA. This was accomplished by insertion of e-DNA containing the PK gene cluster along with a regulatory protein promoter, into the generic host Streptomyces albus under the control of a constitutive erythromycin-resistance promoter.115

Challenges of a target-poor therapeutic arena

Historically, the treatment of human bacterial infections by antibiotics has been a target-poor therapeutic arena. Despite thousands of molecules shown to have antibiotic properties, there are essentially five major clinically validated antibacterial targets/pathways.1 As schematized in Figure 5, these include bacterial peptidoglycan/cell wall biosynthesis, targeted by both the β-lactams and the vancomcyin-type glycopeptides. A second set of targets is encompassed by bacterial protein synthesis, with most antibiotics targeting the ribosome. Daniel Wilson has provided an elegant, structurally oriented compendium of the A–Z of molecules targeting the small and large ribosomal subunits and the interface between them.116 A third target area is the blockade of DNA replication and transcription to RNA, most notably the targeting of DNA gyrase and RNA polymerase. The fourth is the folate biosynthetic pathway, which provides the one carbon unit required for the deoxythymidylate building block for DNA synthesis. The sulfa drugs and the folate analogs, used in combination, block two sequential steps in that biosynthetic pathway.117 The fifth and perhaps the most recent target of widespread clinical utility has been daptomycin disruption of bacterial membrane integrity.118, 119

Figure 5
figure 5

The five major clinically validated antibacterial targets/pathways. (a) Inhibition of cell wall biosynthesis. (b) Inhibition of protein synthesis. (c) Inhibition of DNA or RNA synthesis. (d) Inhibition of folate biosynthesis. (e) Disruption of membrane integrity. Modified from the cover of Walsh.1

When will chemogenetic approaches pay off?

Over the decades since the 1960s, the antibiotics research community has sought to broaden the number of clinically validated targets, using many rational as well as screening approaches. A particularly concerted effort went on with the advent of genome sequences of the most common bacterial pathogens and the determination of essential genes. Their protein products were intensively examined in a first wave of screens in the chemogenetics era. The hallmark paper from the GSK group in 200781 noted above, summarizing more than 100 screens, starkly described the failure of that first wave. Among the resultant questions were the utility of in vitro screening of a target vs whole-cell assays and also the utility of chemical library collections in pharmaceutical companies for screening prokaryotic rather than the eukaryotic targets, for which many of those libraries were biased.

Smart screens: leads for combination therapies?

Among the smart screens to be employed in recent years are a series of publications102, 120, 121, 122, 123 from the Merck groups on a 245 siRNA collection to lower the levels of essential gene expressions in MRSA, one at a time. These siRNAs may thereby render that particular step in a pathway sufficiently rate determining to give a growth impairment signal when inhibited by a small molecule. Screening of such strains with these and related gene knock-down collections in other pathogens has turned up new scaffolds from both natural and synthetic sources. This approach led to discovery of the platensin and platensimycin (Figure 4b) novel terpenoid architectural frameworks that target fatty acid biosynthesis,96, 99 although their clinical utility has been questioned.101 This approach also turned up kibdelomycin (Figure 4c) as the first new natural product scaffold for gyrase inhibition in 60 years.102 The coumarin antibiotics (which are not used in human bacterial infections) target the ATPase domain in the GyrB subunit of DNA gyrase.1 Although structurally related to the coumarin antibiotics, kibdelomycin shows no cross resistance indicating that it targets a distinct subsite of DNA gyrase, possibly within the GyrA subunit or the catalytic active site of GyrB.102 The kibdelomycin scaffold is forbiddingly complex for structure-activity relationship (SAR) work, but there is the eribulin anticancer drug precedent86, 124 to show that a complex (32 step) synthesis can be commercially viable.

The Merck 245 siRNA collection targeting MRSA screens may also be useful in finding rational choices for new combination therapies.122, 123 Interactome analysis in such collections challenged with different subsets of β-lactam antibiotics turned up molecules that resensitize MRSA to carbapenems. A 256-fold gain in sensitivity to imipenem was seen in the presence of a small-molecule inhibitor of glucosamine synthase.121 For example, L-norvaline-N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid (Nva-FMDP) is a mimetic of the natural product dapdiamide, which captures the active site Cys thiolate of the glutaminase domain of glucosamine synthase.125, 126 Deprivation of glucosamine units required for peptidoglycan assembly generates a defective cell wall that shows synergistic suceptibility to imipenem. A distinct but parallel approach to resensitize MRSA to β-lactam antibiotics is conferred by tunicamycin, which blocks wall teichoic acid biosynthesis.127 A third example involved a screen for inhibitors of lipid II flippase, with a synthetic library.122 Again, a molecule was detected that was read out as a regain of sensitivity to carbapenems.

Inter alia, these results, with both natural product and synthetic chemical libraries, bring into high relief the whole issue of default monotherapy for treatment of bacterial infections vs combinations of antibiotics. These sensitization-screening approaches may offer good algorithms for choice of the combinations and might be extended; for example, to molecules that could combine with colistin for treating MDR Gram-negative pathogens. Although consecutive deployment of antibiotics one at a time to treat persistent bacterial infections has been a long held approach, there are multiple examples reflecting combination therapy with antibiotics that may presage a future where combinations are applied simultaneously, with real-time knowledge of the pathogen genotypes as a guide. Those combinations include β-lactams and β-lactamase inhibitors such as augmentin (amoxicillin and clavulanate), sulfa drugs plus trimethoprim to block two consecutive steps in folate biosynthesis and the standard drug cocktails used in front-line tuberculosis therapy which include rifampin, isoniazid, pyrazinamide and ethambutol.1

Second-generation combinations of β-lactam and β-lactamase inhibitor are progressing through clinical trials. The lactamase inhibitors are not clavulanate or the penicillin sulfones used in the first- and second-generation combinations but rather bicyclic diazabycyclooctanes (Figure 6) in which the warhead is not the traditional four membered β-lactam but instead a five member γ-lactam bearing an O-sulfate substituent on the nitrogen128 in the clinical candidates avibactam and MK-7655. Studies on avibactam with purified lactamase show that γ-lactam is opened by the active site Ser-OH to yield a variant of the typical O-acyl-lactamase covalent intermediate.129 Over time, the lactam ring can reform and induce deacylation and regain lactamase activity, but the residence time suffices for either ceftaroline or ceftazidime, cephalosporins administered in combination with avibactam to reach their penicillin-binding proteins and function as killing antibiotics. Merck’s MK-7655 is being clinically evaluated in combination with the carbapenem imipenem.128

Figure 6
figure 6

Next generation ‘non-β-lactam’ β-lactamase inhibitors (diazabicyclooctanes; DBOs) in clinical development.

Should some underexplored targets be revisited?

Peptidoglycan biosynthesis

In peptidoglycan assembly, the nascent disaccharyl pentapeptide units are incorporated into existing cell wall by two kinds of enzymes, the PG transpeptidases (TPases), long the targets of clinically useful β-lactam and glycopeptides antibiotics, and the PG transglycosylases (TGases; Figure 7a). The transpeptidases are robust targets, in part, because their active sites are accessible from the periplasmic face in Gram-negative membranes and from the outside environment in Gram-positives. Bifunctional versions of the TPases and TGases are common killing targets in many bacteria, where inhibition of the TPase leaves mechanically weakened cell wall layers.1

Figure 7
figure 7

(a) Inhibition of PG transglycosylases (TGases) by moenomycin and inhibition of PG transpeptidases (TPases) by β-lactams. (b) X-ray crystal structure of a moenomycin analog containing a 10-carbon neryl chain bound to the TGase domain of PBP1A from Aquifex aeolicus.134 The α-amino-β-hydroxy-cyclopentenol ring of the moenomycin analog was highly distorted and is therefore omitted from the structure. Image was generated from PDB entry 3D3H134 using PyMOL (The PyMOL Molecular Graphics System, Version 1.4, Schrödinger, LLC).

Although β-lactam antibiotics have been in use for 70 years, by contrast, no TGase inhibitors, which would have the same outcome in accumulation of uncrosslinked peptidoglycan units, are in human clinical use. Nature has turned up one TGase-targeting scaffold in the glycolipid moenomycins, metabolites from streptomycetes. Moenomycins are structurally complex natural products with five sugars and an isoprenoid C25 lipid tail connected by a glycerol phosphate linker.130 They are used in veterinary medicine but have poor pharmacokinetic properties, which curtail their use in humans.130 Nonetheless, recent advances of note are the determination of the X-ray structure of the PG transglycosylase, now from three different research groups131, 132, 133, 134, 135, 136 working with three distinct organisms (E. coli, S. aureus, A. aeolius), some with moenomycin bound131, 134, 135, 136 (Figure 7b). This structural information along with advances in chemical synthesis,137 biosynthesis138 and assay development139 should enable structure-driven optimization/simplification of the moenomycin scaffold (by synthesis and/or by pathway engineering) to get to a minimal structural core with potential amelioration of physical and pharmacodynamic properties that would move a moenomycin framework from veterinary to human indications.

Lipid II

Lipid II, at a few thousand molecules per bacterial cell, is the C55 isoprenoid carrier that receives the muramyl pentapeptide at the end of the cytoplasmic phase of peptidoglycan biosynthesis. While still on the inner face of the cytoplasmic membrane, the muramyl-pentapeptidyl-lipid II is a substrate for glycosylation by MurG. Then the disaccharyl-pentapeptidyl-lipid II is translocated by membrane flippases140 to the outer face of the cytoplasmic membrane. On the outward membrane face, it can be a substrate for the TPases and TGases that add these peptidoglycan-building blocks to existing PG strands. When the disaccharyl-pentapeptidyl-lipid II (Figure 8) is exposed at the outer surface of the membrane, the lipid II moiety is targeted at different subregions of its scaffold by two kinds of antibiotics.141 The vancomycin family glycopeptide antibiotics interact with the D-Ala-D-Ala terminus29, 142 while the antibiotics, such as the food preservative nisin, instead bind to the pyrophosphate subregion143 of Lipid II. A third class of natural molecules, the defensin family of peptides/small proteins, also bind to lipid II; the interaction of plectasin with lipid II has been characterized by NMR,144 and this structure may serve as starting point for peptidomimetics that may span multiple subregions of lipid II. These antimicrobial peptides by themselves have presented challenges for development,145 but we shall return to the peptidomimetic approach in a subsequent section on LptD in the lipopolysaccharide (LPS) export pathway.

Figure 8
figure 8

Structure of disaccharyl-pentapeptidyl-lipid II with the D-Ala-D-Ala-vancomycin and the nisin-pyrophosphate binding sites highlighted. Images were created using PyMOL from PDB entries 1FVM142 (vancomycin-Di-acetyl-L-Lys-D-Ala-D-Ala complex) and IWCO143 (nisin-lipid II complex).

One recent advance of note is the work of Boger’s group to generate the aglycone form of an amidine derivative of vancomycin146, 147 (Figure 9). The synthetic design took inspiration from the fact that VRE lower the affinity of vancmycin family glycopeptides for the uncrosslinked PG termini by substitution of D-Ala-D-Ala for D-Ala-D-lactate.22 The loss of one H-bond and the electronic repulsion of the D-Ala-D-Lac lone pair on the oxygen of the ester can be compensated in the amidine derivative. Not only did the amidine regain activity against VRE but also maintained acceptable activity against the wild-type D-Ala-D-Ala PG terminus. Addition of the glucosyl-1,2-vancosamine disaccharide moiety to the amidine aglycone, by chemical or enzymatic means, might result in a useful third-generation glycopeptide antibiotic (where the recently approved telavancin148 would be considered a second-generation molecule).

Figure 9
figure 9

Diagram of the vancomycin-D-Ala-D-Lactate (a) and Boger’s synthetic amidine vancomycin aglycone-D-Ala-D-Lactate (b) hydrogen bonding networks. Boger’s amidine vancomycin aglycone increases the binding affinity for the uncrosslinked D-Ala-D-Lactate moiety found in modified lipid II of the peptidoglycan (normal lipid II contains a terminal D-Ala-D-Ala) by restoring a key hydrogen bond and compensating for electrostatic repulsion created by this increasingly common resistance conferring lipid II structural modification.

More natural lipopeptides and variants

With the success of the lipodepsipeptide daptomycin (Figure 10a) in treatment of bacterial infections in humans over the past decade,118, 119 there has been renewed interest in natural and semisynthetic versions of other lipopeptides as antibiotics. We take up acyldepsipeptides (ADEPS) below in the context of ATP-utilizing bacterial enzymes but note here the inhibition of signal peptidases (SPs) by arylomycins,149, 150 actinocarbasins,151 krisynomycin,151 the polyketide macrolactone antibiotic TA152 (also known as myxovirescin) and globomycin153, 154 (Figures 10b and c). Each of these natural products has a constrained conformation due to macrocyclization that is imposed during biosynthesis. The arylomycins and actinocarbasins have a dihydroxybiphenyl moiety that arises from coupling of two tyrosine side chains in the precursor peptide, presumably through a radical coupling mediated by an iron-enzyme that can make high valent oxo-iron intermediates.155 This C-C coupling is reminiscent of the coupling of residues 5 and 7 in vancomycin. The natural fatty acyl chain in the N-terminal tail of the actinocarbasins can be replaced semisynthetically with typical med chem biphenyl chains.151, 156 Gram-negative bacteria have two signal peptidases.157 Type I signal peptidase (SPI) is a serine protease with a catalytic mechanism distinct from eukaryotic serine proteases for trimming the signal sequence from secreted proteins, outer membrane proteins and periplasmic proteins. Type II signal peptidase (SPII) are completely absent in eukaryotes, making this an ideal antibiotic target, and function as an aspartyl protease that trims the precursor forms of lipoproteins found in the outer membranes of Gram-negative bacteria. While arylomycins target SPI, antibiotic TA and globomycin target SPII and are bacteriocidal at low concentrations.152 One feature of potential interest is that arylomycins synergize with aminoglycosides150 while actinocarbasins and krisynomycin do so with β-lactams.151 These natural products may therefore serve as starting points for further semisynthetic modifications of the frameworks through synthesis156, 158, 159, 160, 161 and pathway engineering,155, 162, 163, 164, 165, 166 with an eye towards combination therapy.

Figure 10
figure 10

(a) Structure of daptomycin, a lipodepsipeptide antibiotic produced by Streptomyces roseosporus, discovered by Eli Lilly and Co. in the late 1980s, acquired and developed by Cubist Pharmaceuticals in 1997 and FDA approved in 2003. (b) Structures of the arylomycin, actinocarbasin and krisynomycin macrocyclic antibiotics that target type I bacterial signal peptidases. (c) Structures of antibiotic TA (also known as myxovirescin) and globomycin macrolactone antibiotics that target type II bacterial signal peptidases.

LPS: is the time ripe for a renewed assault on those enzymes?

One of the holy grails of antibiotic discovery efforts in Gram-negative pathogens has been the search for a broadly active inhibitor of lps biosynthesis and/or export. For decades, investigators have focused on the rate-determining step in lps biogenesis, the second committed step catalyzed by the zinc-dependent deacetylase LpxC (Figure 11a).167 The central metabolite UDP-GlcNAc undergoes long chain acylation at the 3′-OH of the GlcNAc by LpxA and then LpxC mediates deacetylation of the acetyl moiety on the 2′-amino group. A series of acylations, glycosylations and phosphoryl transfers then ensue on the way to the lipid A core of lps.168 A prototype alkynyl hydroxamate CHIR-090 has been characterized for mechanism and structure with LpxC,169 but narrow spectrum and pathogen mutation to resistance have been problematic for its development. Recent structure–function analysis has led to a diacetylenic congener LPC-009,170 which overcome the loss of affinity in point mutations that negate CHIR-090 binding (Figure 11b). Perhaps there is finally momentum towards a clinical candidate, at which point toxicology and pharmacology in human hosts will become crucial gating parameters.

Figure 11
figure 11

(a) LpxC inhibitors block the first committed step of lipid A biosynthesis, a pathway specific to Gram-negative bacteria. (b) Structure-guided efforts inspired by the prototype alkynyl hydroxamate LpxC inhibitor CHIR-090 revealed the next generation diacetylenic inhibitor LPC-009, which overcomes point mutations (G214 to S214 in Rhzobium leguminosarum) associated with CHIR-090 resistance in Gram-negative pathogens. Images were created using PyMOL from PDB entries 2JT2169 (LpxC-CHIR-090 complex) and 3P3C170 (LpxC-LPC-009 complex). For both the cases, the structure was solved for WT LpxC from Aquifex aeolicus complexed to the inhibitor and a point mutation of G198 to S198 was inserted computationally into the PyMOL structure to demonstrate in this figure how this mutation leads to steric repulsion in the LpxC-CHIR-090 complex.

There has also been dramatic progress in recent years in delineation of the roles and structures of the periplasmic and outer membrane proteins LptA-E that function as chaperones for lps molecules to get across the periplasmic space.171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182 The Lpt protein machinery also effects insertion of the translocated lps molecules and localization in the outer leaflet of the outer membrane in most Gram-negatives. In that context, the outer membrane β-barrel protein LptD has been known to be inhibited by an 18 residue antimicrobial peptide (AMP) protegrin I from porcine leukocytes.183 John Robinson and coworkers used this as a starting point for building a peptidomimetic scaffold (Figure 12).183, 184, 185 The natural bridging disulfide was removed, the rest of protegrin β-sheet was used as template and the framework cyclized with a diproline insert to give a potent inhibitor of lps trafficking in pseudomonas.183 Challenges remain to optimize broad spectrum Gram-negative activity. If the peptide framework is not sufficiently stable to protease breakdown, there is the traditionally difficult challenge to go from a peptide-based to a nonpeptidic scaffold to improve in vivo lifetimes while preserving activity. Although LptD is in the outer membrane and perhaps thereby particularly accessible to external agents, the other components of the Lpt assembly pathway also seem reasonable targets, and structural information is accruing on their bridge functions, architecture and roles in moving Lps through the periplasm.171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182

Figure 12
figure 12

Protegrin I is a naturally occurring disulfide-stabilized beta-turn antimicrobial peptide that targets LptD and served as inspiration for the rational design of template-stabilized beta-turn peptidomimetic scaffolds, such as POL7001, progressing towards clinically useful antimicrobial peptides targeting LptD.

Bacterial RNA polymerase: many natural products bind in adjacent subsites

Bacterial RNA polymerase has been a validated antibacterial target for decades. It is the target for rifampicin and derivatives as front-line agents in combination therapy against Mycobacterium tuberculosis. In fact, a wide range of natural product scaffolds have been examined and found to inhibit bacterial transcription by targeting RNA polymerase.186 One of the most recently approved antibiotics fidaxomicin, an 18 membered polyketide macrolactone (Figure 13a) from Dactylosporangium auranticum187 likewise blocks RNA transcription and has been approved by the FDA for the treatment of Clostridium difficile infections.188 The drug is poorly adsorbed from the gastrointestinal tract, supporting its use against C. difficile. As shown in Figure 13b, rifamycins189 and the natural product sorangicin190 bind to almost identical subsites of the enzyme while streptolydigin191 and myxopyronin192 bind in separate subsites.193 The bicyclic phosphate metabolite tagetitoxin from the phytopathogenic Pseudomonas syringae pv tagetis binds in yet a fourth subsite coordinating the Mg2+ in the active site.194 Nature clearly presents a rich variety of small molecular frameworks to target different pockets in RNAP. The specific binding subsite for fidaxomycin is not yet determined. One anticipates that other scaffolds may be found for additional or overlapping RNAP subsites and that structure-based evaluation might guide combinations directed against RNAP beyond Tb and C. difficile colitis.

Figure 13
figure 13

(a) Structure of fidaxomycin, an 18-membered polyketide macrolactone bacterial RNAP inhibitor produced by Dactylosporangium auranticum approved by the FDA in 2011 for the treatment of C. difficile infections. (b) Surface structure of bacterial RNA polymerase from Thermus aquaticus showing the binding sites of a representative panel of natural product inhibitors (rifampin, sorangicin, streptolydigin, myxopyronin and tagetitoxin). Image was generated from PDB entries 1YNN189 (RNAP-rifampin complex; used for alignment of all structures), 1YNJ190 (RNAP-sorangicin complex), 1ZYR191 (RNAP-streptolydigin complex), 3DXJ192 (RNAP-myxopyronin complex) and 2BE5194 (RNAP-tagetitoxin complex) using PyMOL software.

ATP-dependent enzyme targets

For the past 15 years, inhibition of eukaryotic ATP-dependent protein kinases has been a mainstay of pharmaceutical and biotech research and development activity across a broad swath of human disease areas.195, 196 Although protein tyrosine kinase equivalent catalysts are almost absent in bacterial life, Ser/Thr kinases have become more prominent with knowledge of bacterial genomes. The histidine kinases that are the front end of dozens of two component signaling systems in bacteria have been investigated multiple times but, as yet, no robust, optimizable chemical scaffolds have emerged.197 Nonetheless, the ATP-dependent biotin carboxylase component of bacterial acetyl CoA carboxylase, the first committed step in fatty acid biosynthesis, has been targeted with specificity and potency by repurposed kinase libraries by a team at Pfizer.82 There is no a priori reason to think this need be an isolated success against a bacterial ATP-generating/consuming enzyme (for example, the Lps kinases that install the phosphates on lipid A)168 but does suggest investment in library design may be required.

Figure 14 introduces three additional such targets in bacteria. DNA gyrase, with type II topoisomerase activity for unwinding concatenated DNA at the end of replication, could be considered the grandfather of this ATP-targeting paradigm. In these topoisomerases, ATP hydrolysis powers the mechanical work of strand cleavage, passage and repair.1 The venerable and contemporary fluoroquinolones block the GyrA subunit and possibly the newly identified kibdelomycin family of natural products targets this same gyrase subunit,102 while the coumarin1 and cyclothialidine198 families of natural products inhibit the ATPase activity conferred by the GyrB subunit.

Figure 14
figure 14

Molecular scaffolds targeting bacterial ATP-dependent enzymes as potential antibiotic therapeutic approaches.

A second successful example of an antibiotic targeting an ATP-dependent bacterial enzyme is bedaquiline, a diarylquinoline identified in a screening campaign for molecules that could kill M. tuberculosis.199 The mechanism of action was determined by generation of resistant mutants and mapping them by whole-genome sequencing, allowing identification of the Fo subunit of the Mtb ATP synthase.200, 201 The molecule is specific for mycobacterial ATP synthase202 and has proven efficacy through phase II trials,199, 203 with a new drug application filed in July 2012 and approval granted at the start of 2013.45 Perhaps there are still more ATP-utilizing proteins within the Mtb proteome that might surface as valid therapeutic targets.204

The third potential antibacterial target, the chambered proteases of the ClpP family,205, 206 are acted on by a family of related lipopeptidolactones, known as ADEPS,207, 208 originally isolated from Streptococcus hawaiiensis in 1985 by scientists at Eli Lilly and Co.209 Semisynthetic tailoring of the scaffold has led to increased potency; for example, in ADEP2 (Figure 14).205 These bacterial chambered proteases, in mechanistic and structural analogy to eukaryotic chambered proteasomes, require ATP hydrolysis to unfold and thread protein substrates into the central cavity containing the protease sites. ADEPS are intriguing because they are actually activators, not inhibitors, of the basal protease activity of ClpP and so uncouple protease activity from ATP hydrolysis.205, 206 This occurs by allosteric activation207, 208 on the outer surface of the multisubunit proteases. Turning up unregulated protease activity is harmful to cells that contain active ClpPs. Of recent note is the connection of ADEP-mediated ClpP activity to disruption of cell division. One of the early key structural proteins to form the cell division ring is FtsZ. It is poorly folded and subject to the inappropriately activated ClpP-mediated degradation in ADEP-treated cells.210 In turn, the cell division septum does not form and/or is degraded and cell division abrogated. Although ADEPS may have liabilities in monotherapy, such as rates of mutation of the allosteric site to insensitivity, they may have value in combination regimens.

FtsZ itself is a homolog of eukyaryotic tubulin and shows GTPase activity involved in assembly of the divisome components.211 A molecule known as PC19073212 (Figure 15) has been reported to be an FtsZ inibitor by polymerization assays213 and X-ray crystallography.214 However, more recently, Shaw and coworkers215 failed to detect inhibition of GTPase activity. They also noted that many structures cited in preliminary reports as FtsZ inhibitors are either aggregators and/or nonspecific GTPase inhibitors. They pointed out zantrin Z3 (Figure 15) as a bona fide, specific albeit weak (IC50=20 μM) starting lead for future SAR work.215

Figure 15
figure 15

Inhibitors of FtsZ, a bacterial homolog of eukaryotic tubulin with GTPase activity.

Protein synthesis inhibitors

We noted previously that inhibition of protein synthesis is one of the five major clinically validated antibacterial pathways (Figure 5), with most antibiotics in this class targeting the ribosome.116 These have spurred at least one company Ribex to use structure-based approaches to design next-generation ribosome-directed antibiotics. We also noted new developments in tetracycline chemistry70 and still more structural information is being reported on this class of antibiotics.216 The clinical progression of second-generation oxazolidinones into phase II studies was also mentioned.74, 75, 76, 77, 78, 79, 80 Achaogen is working to bring forward new aminoglycoside protein synthesis inhibitors, such as plazomicin (ACHN-490), which successfully completed a phase II trial for urinary tract infections.217 Novartis has converted the natural thiopeptide GE2270A, an inhibitor of elongation factor Tu,218 to a semisynthetic version with a 105 increase in aqueous solubility and moved it into phase II trials for C. difficile infections.219 Other protein synthesis halting antibacterials currently in various stages of clinical development include members of the pleuromutilin (BC-3781, BC-7013, BC-3205) and macrolide (Cethromycin) structural classes.73

Summary thoughts

This perspective has argued that there is a continuing need for new cycles of antibiotic discovery and development. The genes found in the global resistomes are mobilizable with different frequencies to propel waves of resistant bacteria to each generation of newly introduced antibiotics. Given that the past half century has turned up few new molecular scaffolds, the fine tuning of existing frameworks by medicinal chemists may be approaching an asymptotic limit.

One small surprise has been the rise in usage/rediscovery of lipopeptides made by NRP synthetase machineries as antibiotics. Although daptomycin is the poster child of the past decade, ADEPS show unanticipated mechanisms, not working through membrane disruption. Even the polymyxins have come back into prominence, given the multidrug-resistant profiles of Gram-negative pathogens. There are certainly many more lipopeptide natural products in the biosphere, and they may be starting points for combination therapies. New approaches to interrogation of the biosynthetic capacity of the microbial world for conditional metabolites suggests new scaffolds will be found, presumably opening up additional rounds of both chemical and bioengineering optimization of those novel molecular scaffolds. Different approaches to synthetic library design may also enrich the hit rates in whole bacterial screens, especially to combat the permeability barriers and efflux pumps of the ESKAPE pathogens.

In parallel, we have opined on a select, possibly representative set of targets that we suggest are underexploited based on chemocentric past experience that promising, specific chemical matter has been identified, often in the form of natural product scaffolds. Improvements in biological assay designs and configurations almost always turn up new molecules. Smart screens have already shown that activity-guided isolation of novel natural molecular architectures is still possible. Several of these screens have assayed for resensitization and/or synergy with existing antibiotics to which pathogens have become insensitive. These augur for early guidance for combination therapies against particular pathogens.

More combination therapy seems a likely way forward, paralleling the trend of therapeutic modalities in viral infections and in cancer treatments. In that eventuality, coupling real-time diagnostics of the pathogen population in each patient to a proven or predictively effective combination of antibiotics may be a way forward, although Kishony and coworkers have noted the downside potential for resistance development in combination approaches.220

References

  1. Walsh, C. Antibiotics: Actions, origins, and resistance, ASM Press: Washington DC, USA, (2003).

    Book  Google Scholar 

  2. Kollonitsch, J., Barash, L., Kahan, F. M. & Kropp, H. New antibacterial agent via photofluorination of a bacterial cell wall constituent. Nature 243, 346–347 (1973).

    Article  CAS  PubMed  Google Scholar 

  3. Kollonitsch, J. & Barash, L. Organofluorine synthesis via photofluorination: 3-fluoro-D-alanine and 2-deuterio analogue, antibacterials related to the bacterial cell wall. J. Am. Chem. Soc. 98, 5591–5593 (1976).

    Article  CAS  PubMed  Google Scholar 

  4. Wang, E. & Walsh, C. Suicide substrates for the alanine racemase of Escherichia coli B. Biochemistry 17, 1313–1321 (1978).

    Article  CAS  PubMed  Google Scholar 

  5. Wang, E. A. & Walsh, C. Characteristics of β,β-difluoroalanine and β,β,β-trifluoroalanine as suicide substrates for Escherichia coli B alanine racemase. Biochemistry 20, 7539–7546 (1981).

    Article  CAS  PubMed  Google Scholar 

  6. Walsh, C. T. Suicide substrates, mechanism-based enzyme inactivators: recent developments. Ann. Rev. Biochem. 53, 493–535 (1984).

    Article  CAS  PubMed  Google Scholar 

  7. Faraci, W. S. & Walsh, C. T. Mechanism of inactivation of alanine racemase by β,β,β-trifluoroalanine. Biochemistry 28, 431–437 (1989).

    Article  CAS  PubMed  Google Scholar 

  8. Brown, E. D., Vivas, E. I., Walsh, C. T. & Kolter, R. MurA (MurZ), the enzyme that catalyzes the first committed step in peptidoglycan biosynthesis, is essential in Escherichia coli. J. Bacteriol. 177, 4194–4197 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kim, D. H., Tucker-Kellogg, G. W., Lees, W. J. & Walsh, C. T. Analysis of fluoromethyl group chirality establishes a common stereochemical course for the enolpyruvate transfers catalyzed by EPSP synthase and UDP-GlcNAc enolpyruvyl transferase. Biochemistry 35, 5435–5440 (1996).

    Article  CAS  PubMed  Google Scholar 

  10. Skarzynski, T., Kim, D. H., Lees, W. J., Walsh, C. T. & Duncan, K. Stereochemical course of enzymatic enolpyruvyl transfer and catalytic conformation of the active site revealed by the crystal structure of the fluorinated analogue of the reaction tetrahedral intermediate bound to the active site of the C115A mutant of MurA. Biochemistry 37, 2572–2577 (1998).

    Article  CAS  PubMed  Google Scholar 

  11. Kim, D. H. et al. Characterization of a Cys115 to Asp substitution in the Escherichia coli cell wall biosynthetic enzyme UDP-GlcNAc enolpyruvyl transferase (MurA) that confers resistance to inactivation by the antibiotic fosfomycin. Biochemistry 35, 4923–4928 (1996).

    Article  CAS  PubMed  Google Scholar 

  12. Benson, T. E., Marquardt, J. L., Marquardt, A. C., Etzkorn, F. A. & Walsh, C. T. Overexpression, purification, and mechanistic study of UDP-N-acetylpyruvylglucosamine reductase. Biochemistry 32, 2024–2030 (1993).

    Article  CAS  PubMed  Google Scholar 

  13. Benson, T. E., Walsh, C. T. & Hogle, J. M. Crystallization and preliminary X-ray crystallographic studies of UDP-N-acetylpyruvylglucosamine reductase. Protein Sci. 3, 1125–1127 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Benson, T. E., Filman, D. J., Walsh, C. T. & Hogle, J. M. An enzyme-substrate complex involved in bacterial cell wall biosynthesis. Nat. Struct. Biol. 2, 644–653 (1995).

    Article  CAS  PubMed  Google Scholar 

  15. Benson, T. E., Walsh, C. T. & Hogle, J. M. The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls. Structure 4, 47–54 (1996).

    Article  CAS  PubMed  Google Scholar 

  16. Lees, W. J., Benson, T. E., Hogle, J. M. & Walsh, C. T. (E)-Enolbutyryl-UDP-N-acetylglucosamine as a mechanistic probe of UDP-N-acetylenolpyruvylglucosamine reductase (MurB). Biochemistry 35, 1342–1351 (1996).

    Article  CAS  PubMed  Google Scholar 

  17. Benson, T. E., Walsh, C. T. & Massey, V. Kinetic characterization of wild-type and S229A mutant MurB: evidence for the role of Ser 229 as a general acid. Biochemistry 36, 796–805 (1997).

    Article  CAS  PubMed  Google Scholar 

  18. Benson, T. E., Walsh, C. T. & Hogle, J. M. X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-Å resolution. Biochemistry 36, 806–811 (1997).

    Article  CAS  PubMed  Google Scholar 

  19. Duncan, K., van Heijenoort, J. & Walsh, C. T. Purification and characterization of the D-alanyl-D-alanine-adding enzyme from Escherichia coli. Biochemistry 29, 2379–2386 (1990).

    Article  CAS  PubMed  Google Scholar 

  20. Walsh, C. T. Enzymes in the D-alanine branch of bacterial cell wall peptidoglycan assembly. J. Biol. Chem. 264, 2393–2396 (1989).

    CAS  PubMed  Google Scholar 

  21. Bugg, T. D. H. & Walsh, C. T. Intracellular steps of bacterial cell wall peptidoglycan biosynthesis: enzymology, antibiotics, and antibiotic resistance. Nat. Prod. Rep. 9, 199–215 (1992).

    Article  CAS  PubMed  Google Scholar 

  22. Bugg, T. D. H. et al. Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA. Biochemistry 30, 10408–10415 (1991).

    Article  CAS  PubMed  Google Scholar 

  23. Chang, F., Moews, P. C., Walsh, C. T. & Knox, J. R. Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 Å resolution. Science 266, 439–443 (1994).

    Article  Google Scholar 

  24. Shi, Y. & Walsh, C. T. Active site mapping of Escherichia coli D-Ala-D-Ala ligase by structure-based mutagenesis. Biochemistry 34, 2768–2776 (1995).

    Article  CAS  PubMed  Google Scholar 

  25. Lessard, I. A., Healy, V. L., Park, I. S. & Walsh, C. T. Determinants for differential effects on D-Ala-D-lactate vs D-Ala-D-Ala formation by the VanA ligase from vancomycin-resistant enterococci. Biochemistry 38, 14006–14022 (1999).

    Article  CAS  PubMed  Google Scholar 

  26. Kuzin, A. P. et al. Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides. Structure 8, 463–470 (2000).

    Article  CAS  PubMed  Google Scholar 

  27. Walsh, C. T., Fisher, S. L., Park, I. S., Prahalad, M. & Wu, Z. Bacterial resistance to vancomycin: fve genes and one missing hydrogen bond tell the story. Chem. Biol. 3, 21–28 (1996).

    Article  CAS  PubMed  Google Scholar 

  28. Healy, V. L., Lessard, I. A., Roper, D. I., Knox, J. R. & Walsh, C. T. Vancomycin resistance in enterococci: reprogramming of the D-Ala-D-Ala ligases in bacterial peptidoglycan biosynthesis. Chem. Biol. 7, R109–R119 (2000).

    Article  CAS  PubMed  Google Scholar 

  29. Kahne, D., Leimkuhler, C., Lu, W. & Walsh, C. Glycopeptide and lipoglycopeptide antibiotics. Chem. Rev. 105, 425–448 (2005).

    Article  CAS  PubMed  Google Scholar 

  30. Hubbard, B. K. & Walsh, C. T. Vancomycin assembly: nature’s way. Angew. Chem. Int. Ed. Engl. 42, 730–765 (2003).

    Article  CAS  PubMed  Google Scholar 

  31. Walsh, C. T. et al. Tailoring enzymes that modify nonribosomal peptides during and after chain elongation on NRPS assembly lines. Curr. Opin. Chem. Biol. 5, 525–534 (2001).

    Article  CAS  PubMed  Google Scholar 

  32. Walsh, C. T. Polyketide and nonribosomal peptide antibiotics: modularity and versatility. Science 303, 1805–1810 (2004).

    Article  CAS  PubMed  Google Scholar 

  33. Fischbach, M. A. & Walsh, C. T. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem. Rev. 106, 3468–3496 (2006).

    Article  CAS  PubMed  Google Scholar 

  34. Walsh, C. T. The chemical versatility of natural-product assembly lines. Acc. Chem. Res. 41, 4–10 (2008).

    Article  CAS  PubMed  Google Scholar 

  35. Sattely, E. S., Fischbach, M. A. & Walsh, C. T. Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat. Prod. Rep. 25, 757–793 (2008).

    Article  CAS  PubMed  Google Scholar 

  36. Crosa, J. H. & Walsh, C. T. Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol. Mol. Biol. Rev. 66, 223–249 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Walsh, C. T. & Fischbach, M. A. Natural products version 2.0: connecting genes to molecules. J. Am. Chem. Soc. 132, 2469–2493 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Palumbi, S. R. Humans as the world's greatest evolutionary force. Science 293, 1786–1790 (2001).

    Article  CAS  PubMed  Google Scholar 

  39. Ronald, A. R., Turck, M. & Petersdorf, R. G. A critical evaluation of nalidixic acid in urinary-tract infections. New Engl. J. Med. 275, 1081–1089 (1966).

    Article  CAS  PubMed  Google Scholar 

  40. Kresken, M. & Wiedemann, B. Development of resistance to nalidixic acid and the fluoroquinolones after the introduction of norfloxacin and ofloxacin. Antimicrob. Agents Chemother. 32, 1285–1288 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Tsiodras, S. et al. Linezolid resistance in a clinical isolate of Staphylococcus aureus. Lancet 358, 207–208 (2001).

    Article  CAS  PubMed  Google Scholar 

  42. Sabol, K. et al. Emergence of daptomycin resistance in Enterococcus faecium during daptomycin therapy. Antimicrob. Agents Chemother. 49, 1664–1665 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Gentry, D. R. et al. Genetic characterization of Vga ABC proteins conferring reduced susceptibility to pleuromutilins in Staphylococcus aureus. Antimicrob. Agents Chemother. 52, 4507–4509 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Goldstein, E. J. C. et al. Comparative suscpetibilities to fidaxomicin (OPT-80) of isolates collected as baseline, recurrence, and failure from patients in two phase III trials of fidaxomicin against Clostridium difficile infection. Antimicrob. Agents Chemother. 55, 5194–5199 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Cohen, J. Approval of novel TB drug celebrated—with restraint. Science 339, 130 (2013).

    Article  CAS  PubMed  Google Scholar 

  46. Wright, G. D. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 5, 175–186 (2007).

    Article  CAS  PubMed  Google Scholar 

  47. Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Walsh, C. T. Vancomycin resistance: decoding the molecular logic. Science 261, 308–309 (1993).

    Article  CAS  PubMed  Google Scholar 

  49. Arthur, M. & Courvalin, P. Genetics and mechanisms of glycopeptide resistance in enterococci. Antimicrob. Agents Chemother. 37, 1563–1571 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. D'Costa, V. M., McGrann, K. M., Hughes, D. W. & Wright, G. D. Sampling the antibiotic resistome. Science 311, 374–377 (2006).

    Article  PubMed  Google Scholar 

  51. Boucher, H. W. et al. Bad bugs, no drugs: no ESKAPE! an update from the Infectious Diseases Society of America. Clin. Infect. Dis. 48, 1–12 (2009).

    Article  PubMed  Google Scholar 

  52. Allington, D. R. & Rivey, M. P. Quinupristin/dalfopristin: a therapeutic review. Clin. Ther. 23, 24–44 (2001).

    Article  CAS  PubMed  Google Scholar 

  53. Tally, F. P. & DeBruin, M. F. Development of daptomycin for Gram-positive infections. J. Antimicrob. Chemother. 46, 523–526 (2000).

    Article  CAS  PubMed  Google Scholar 

  54. Falagas, M. E. & Kasiakou, S. K. Colistin: the revival of polymyxins for the management of multidrug-resistant Gram-negative bacterial infections. Clin. Infect. Dis. 40, 1333–1341 (2005).

    Article  CAS  PubMed  Google Scholar 

  55. Fernández, L. et al. Characterization of the polymyxin B resistome of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 57, 110–119 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Makarov, V. et al. Benzothiazinones kill Mycobacterium tuberculosis by blocking Arabinan synthesis. Science 324, 801–804 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Trefzer, C. et al. Benzothiazinones: prodrugs that covalently modify the decaprenylphosphoryl-β-D-ribose 2′-epimerase DprE1 of Mycobacterium tuberculosis. J. Am. Chem. Soc. 132, 13663–13665 (2010).

    Article  CAS  PubMed  Google Scholar 

  58. Trefzer, C. et al. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2'-oxidase DprE1. J. Am. Chem. Soc. 134, 912–915 (2012).

    Article  CAS  PubMed  Google Scholar 

  59. Batt, S. M. et al. Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors. Proc. Natl Acad. Sci. USA 109, 11354–11359 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Neres, J. et al. Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis. Sci. Transl. Med. 4, 150ra121 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Tiwari, R. et al. Thiolates chemically induce redox activation of BTZ043 and related potent nitroaromatic anti-tuberculosis agents. J. Am. Chem. Soc. 135, 3539–3549 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Stover, C. K. et al. A small-molecule nitroimidazopyran drug cndidate for the treatment of tuberculosis. Nature 405, 962–966 (2000).

    Article  CAS  PubMed  Google Scholar 

  63. Ginsberg, A. M., Laurenzi, M. W., Rouse, D. J., Whitney, K. D. & Spigelman, M. K. Safety, tolerability, and pharmacokinetics of PA-824 in healthy subjects. Antimicrob. Agents Chemother. 53, 3720–3725 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Sacksteder, K. A., Protopopova, M., Barry, C. E. 3rd, Andries, K. & Nacy, C. A. Discovery and development of SQ109: a new antituberculosis drug with a novel mechanism of action. Future Microbiol. 7, 823–837 (2012).

    Article  CAS  PubMed  Google Scholar 

  65. Williams, K. N. et al. Promising antituberculosis activity of the oxazolidinone PNU-100480 relative to that of linezolid in a murine model. Antimicrob. Agents Chemother. 53, 1314–1319 (2009).

    Article  CAS  PubMed  Google Scholar 

  66. Villemagne, B. et al. Tuberculosis: the drug development pipeline at a glance. Eur. J. Med. Chem. 51, 1–16 (2012).

    Article  CAS  PubMed  Google Scholar 

  67. Lienhardt, C. et al. New drugs for the treatment of tuberculosis: needs, challenges, promise, and prospects for the future. J. Infect. Dis. 205, s241–s249 (2012).

    Article  PubMed  Google Scholar 

  68. Drug Discovery and Development. Understanding the R & D Process, Pharmaceutical Research and Manufacturers of America: Washington, DC, USA, (2007).

  69. Amyes, S. G. B. Magic Bullets, Lost Horizons: The Rise and Fall of Antibiotics, Taylor and Francis, (2001).

    Book  Google Scholar 

  70. Sun, C. et al. Synthesis and antibacterial activity of pentacyclines: a novel class of tetracycline analogs. J. Med. Chem. 54, 3704–3731 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Rafailidis, P. I., Polyzos, K. A., Sgouros, K. & Falagas, M. E. Prulifloxacin: a review focusing on its use beyond respiratory and urinary tract infections. Int. J. Antimicrob. Agents 37, 283–290 (2011).

    Article  CAS  PubMed  Google Scholar 

  72. Fischbach, M. A. & Walsh, C. T. Antibiotics for emerging pathogens. Science 325, 1089–1093 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Butler, M. S. & Cooper, M. A. Antibiotics in the clinical pipeline in 2011. J. Antibiot. 64, 413–425 (2011).

    Article  CAS  Google Scholar 

  74. Bin Im, W. et al. Discovery of torezolid as a novel 5-hydroxymethyl-oxazolidinone antibacterial agent. Eur. J. Med. Chem. 46, 1027–1039 (2011).

    Article  CAS  Google Scholar 

  75. Brown, S. D. & Traczewski, M. M. Comparative in vitro antimicrobial activities of torezolid (TR-700), the active moiety of a new oxazolidinone, torezolid phosphate (TR-701), determination of tentative disk diffusion interpretive criteria, and quality control ranges. Antimicrob. Agents Chemother. 54, 2063–2069 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Prokocimer, P. et al. Phase 2, randomized, double-blind, dose-ranging study evaluating the safety, tolerability, population pharmacokinetics, and efficacy of oral torezolid phosphate in patients with complicated skin and skin structure infections. Antimicrob. Agents Chemother. 55, 583–592 (2011).

    Article  CAS  PubMed  Google Scholar 

  77. Skripkin, E. et al. RX-01, a new family of oxazolidinones that overcome ribosome-based linezolid resistance. Antimicrob. Agents Chemother. 52, 3550–3557 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Zhou, J. et al. Design at the atomic level: design of biaryloxazolidinones as potent orally active antibiotics. Bioorg. Med. Chem. Lett. 18, 6175–6178 (2008).

    Article  CAS  PubMed  Google Scholar 

  79. Lemaire, S., Tulkens, P. M. & Van Bambeke, F. Cellular pharmacokinetics of the novel biaryloxazolidinone radezolid in phagocytic cells: studies with macrophages and polymorphonuclear neutrophils. Antimicrob. Agents Chemother. 54, 2540–2548 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Lemaire, S. et al. Cellular pharmacodynamics of the novel biaryloxazolidinone radezolid: studies with infected phagocytic and nonphagocytic cells, using Staphylococcus aureus, Staphylococcus epidermidis, Listeria monocytogenes, and Legionella pneumophila. Antimicrob. Agents Chemother. 54, 2549–2559 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Payne, D. J., Gwynn, M. N., Holmes, D. J. & Pompliano, D. L. Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat. Rev. Drug Discov. 6, 29–40 (2007).

    Article  CAS  PubMed  Google Scholar 

  82. Mochalkin, I. et al. Discovery of antibacterial biotin carboxylase inhibitors by virtual screening and fragment-based approaches. ACS Chem. Biol. 4, 473–483 (2009).

    Article  CAS  PubMed  Google Scholar 

  83. Schreiber, S. L. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 287, 1964–1969 (2000).

    Article  CAS  PubMed  Google Scholar 

  84. Galloway, W. R. J. D., Bender, A., Welch, M. & Spring, D. R. The discovery of antibacterial agents using diversity-oriented synthesis. Chem. Commun. 2446–2462 (2009).

  85. Nielsen, T. E. & Schreiber, S. L. Towards the optimal screening collection: a synthesis strategy. Angew. Chem. Int. Ed. Engl. 47, 48–56 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Schreiber, S. L. Organic synthesis toward small-molecule probes and drugs. Proc. Natl Acad. Sci. USA 108, 6699–6702 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  87. Martínez-Botella, G. et al. Discovery of selective and potent inhibitors of Gram-positive bacterial thymidylate kinase (TMK). J. Med. Chem. 55, 10010–10021 (2012).

    Article  CAS  PubMed  Google Scholar 

  88. Keating, T. A. et al. In vivo validation of thymidylate kinase (TMK) with a rationally designed, selective antibacterial compound. ACS Chem. Biol. 7, 1866–1872 (2012).

    Article  CAS  PubMed  Google Scholar 

  89. Yong Choi, J. et al. Structure guided development of novel thymidine mimetics targeting Pseudomonas aeruginosa thymidylate kinase: from hit to lead generation. J. Med. Chem. 55, 852–870 (2012).

    Article  CAS  Google Scholar 

  90. Van Poecke, S., Munier-Lehmann, H., Helynck, O., Froeyen, M. & Van Calenbergh, S. Synthesis and inhibitory activity of thymidine analogues targeting Mycobacterium tuberculosis thymidine monophosphate kinase. Bioorg. Med. Chem. 19, 7603–7611 (2011).

    Article  CAS  PubMed  Google Scholar 

  91. Cui, H. et al. Synthesis and evaluation of α-thymidine analogues as novel antimalarials. J. Med. Chem. 55, 10948–10957 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Martínez-Botella, G. et al. Sulfonylpiperidine as novel, antibacterial inhibitors of Gram-positive thymidylate kinase (TMK). Bioorg. Med. Chem. Lett. 23, 169–173 (2013).

    Article  CAS  PubMed  Google Scholar 

  93. Toti, K. S. et al. Synthesis and evaluation of 5′-modified thymidines and 5-hydroxymethyl-2′-deoxyuridines as Mycobacterium tuberculosis thymidylate kinase inhibitors. Bioorg. Med. Chem. 21, 257–268 (2013).

    Article  CAS  PubMed  Google Scholar 

  94. Kaeberlein, T., Lewis, K. & Epstein, S. S. Isolating ‘uncultivable’ microorganisms in pure culture in a simulated natural environment. Science 296, 1127–1129 (2002).

    Article  CAS  PubMed  Google Scholar 

  95. D'Onofrio, A. et al. Siderophores from neighboring organisms promote the growth of uncultured bacteria. Chem. Biol. 17, 254–264 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Lewis, K., Epstein, S., D'Onofrio, A. & Ling, L. L. Uncultured microorganisms as a source of secondary metabolites. J. Antibiot. 63, 468–476 (2010).

    Article  CAS  Google Scholar 

  97. Clardy, J., Fischbach, M. A. & Walsh, C. T. New antibiotics from bacterial natural products. Nat. Biotechnol. 24, 1541–1550 (2006).

    Article  CAS  PubMed  Google Scholar 

  98. Bode, H. B. & Müller, R. The impact of bacterial genomics on natural product research. Angew. Chem. Int. Ed. Engl. 44, 6828–6846 (2005).

    Article  CAS  PubMed  Google Scholar 

  99. Wang, J. et al. Platensimycin is a selective FabF inhibitor with potent antibiotic properties. Nature 441, 358–361 (2006).

    Article  CAS  PubMed  Google Scholar 

  100. Young, K. et al. Discovery of FabH/FabF inhibitors from natural products. Antimicrob. Agents Chemother. 50, 519–526 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Brinster, S. et al. Type II fatty acid synthesis is not a suitable antibiotic target for Gram-positive pathogens. Nature 458, 83–87 (2009).

    Article  CAS  PubMed  Google Scholar 

  102. Phillips, J. W. et al. Discovery of kibdelomycin, a potent new class of bacterial type II topoisomerase inhibitor by chemical-genetic profiling in Staphylococcus aureus. Chem. Biol. 18, 955–965 (2011).

    Article  CAS  PubMed  Google Scholar 

  103. Bister, B. et al. Abyssomycin C-A polycyclic antibiotic from a marine Verrucosispora strain as an inhibitor of the p-aminobenzoic acid/tetrahydrofolate biosynthesis pathway. Angew. Chem. Int. Ed. Engl. 43, 2574–2576 (2004).

    Article  CAS  PubMed  Google Scholar 

  104. Watve, M. G., Tickoo, R., Jog, M. M. & Bhole, B. D. How many antibiotics are produced by the genus Streptomyces? Arch. Microbiol. 176, 386–390 (2001).

    Article  CAS  PubMed  Google Scholar 

  105. Challis, G. L. Genome mining for novel natural product discovery. J. Med. Chem. 51, 2618–2628 (2008).

    Article  CAS  PubMed  Google Scholar 

  106. Challis, G. L. Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology 154, 1555–1569 (2008).

    Article  CAS  PubMed  Google Scholar 

  107. McAlpine, J. B. Advances in the understanding and use of the genomic base of microbial secondary metabolite biosynthesis for the discovery of new natural products. J. Nat. Prod. 72, 566–572 (2009).

    Article  CAS  PubMed  Google Scholar 

  108. Banskota, A. H. et al. Genomic analyses lead to novel secondary metabolites. J. Antibiot. 59, 533–542 (2006).

    Article  CAS  Google Scholar 

  109. Udwary, D. W. et al. Significant natural product biosynthetic potential of actinorhizal symbionts of the genus Frankia, as revealed by comparative genomic and proteomic analyses. Appl. Environ. Microbiol. 77, 3617–3625 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Letzel, A.-C., Pidot, S. J. & Hertweck, C. A genomic approach to the cryptic secondary metabolome of the anaerobic world. Nat. Prod. Rep. 30, 392–428 (2013).

    Article  CAS  PubMed  Google Scholar 

  111. Brakhage, A. A. & Schroeckh, V. Fungal secondary metabolites—strategies to activate silent gene clusters. Fungal Genet. Biol. 48, 15–22 (2011).

    Article  CAS  PubMed  Google Scholar 

  112. Cichewicz, R. H. Epigenome manipulation as a pathway to new natural product scaffolds and their congeners. Nat. Prod. Rep. 27, 11–22 (2010).

    Article  CAS  PubMed  Google Scholar 

  113. Chiang, Y.-M., Chang, S.-L., Oakley, B. R. & Wang, C. C. C. Recent advances in awakening silent biosynthetic gene clusters and linking orphan clusters to natural products in microorganisms. Curr. Opin. Chem. Biol. 15, 137–143 (2011).

    Article  CAS  PubMed  Google Scholar 

  114. Brady, S. F., Simmons, L., Kim, J. H. & Schmidt, E. W. Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat. Prod. Rep. 26, 1488–1503 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Kallifidas, D., Kang, H.-S. & Brady, S. F. Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters. J. Am. Chem. Soc. 134, 19552–19555 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Wilson, D. N. The A-Z of bacterial translation inhibitors. Crit. Rev. Biochem. Mol. Biol. 44, 393–433 (2009).

    Article  CAS  PubMed  Google Scholar 

  117. Scholar, E. M. & Pratt, W. B. The Antimicrobial Drugs 2nd ed. Oxford University Press: New York, NY, USA, (2000).

    Google Scholar 

  118. Baltz, R. H. Daptomycin: mechanisms of action and resistance, and biosynthetic engineering. Curr. Opin. Chem. Biol. 13, 144–151 (2009).

    Article  CAS  PubMed  Google Scholar 

  119. Robbel, L. & Marahiel, M. A. Daptomycin, a bacterial lipopeptide synthesized by a nonribosomal machinery. J. Biol. Chem. 285, 27501–27508 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Donald, R. G. K. et al. A Staphylococcus aureus fitness test platform for mechanism-based profiling of antibacterial compounds. Chem. Biol. 16, 826–836 (2009).

    Article  CAS  PubMed  Google Scholar 

  121. Ho Lee, S. et al. Antagonism of chemical genetic interaction networks resensitize MRSA to β-lactam antibiotics. Chem. Biol. 18, 1379–1389 (2011).

    Article  CAS  Google Scholar 

  122. Huber, J. et al. Chemical genetic identification of peptidoglycan inhibitors potentiating carbapenem activity against methicillin-resistant Staphylococcus aureus. Chem. Biol. 16, 837–848 (2009).

    Article  CAS  PubMed  Google Scholar 

  123. Roemer, T., Davies, J., Giaever, G. & Nislow, C. Bugs, drugs and chemical genomics. Nat. Chem. Biol. 8, 46–56 (2012).

    Article  CAS  Google Scholar 

  124. Kim, D.-S. et al. New syntheses of E7389 C14-C35 and halichondrin C14-C38 building blocks: double-inversion approach. J. Am. Chem. Soc. 131, 15636–15641 (2009).

    Article  CAS  PubMed  Google Scholar 

  125. Hollenhorst, M. A., Ntai, I., Badet, B., Kelleher, N. L. & Walsh, C. T. A head-to-head comparison of eneamide and epoxyamide inihbitors of glucosamine-6-phosphate synthase from the dapdiamide biosynthetic pathway. Biochemistry 50, 3859–3861 (2011).

    Article  CAS  PubMed  Google Scholar 

  126. Milewski, S. et al. Mechanism of action of anticandidal dipeptides containing inhibitors of glucosamine-6-phosphate synthase. Antimicrob. Agents Chemother. 35, 36–43 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Campbell, J. et al. Synthetic lethal compound combinations reveal a fundamental connection between wall teichoic acid and peptidoglycan biosyntheses in Staphylococcus aureus. ACS Chem. Biol. 6, 106–116 (2011).

    Article  CAS  PubMed  Google Scholar 

  128. Coleman, K. Diazabicyclooctanes (DBOs): a potent new class of non-β-lactam β-lactamase inhibitors. Curr. Opin. Microbiol. 14, 550–555 (2011).

    Article  CAS  PubMed  Google Scholar 

  129. Ehmann, D. E. et al. Avibactam is a covalent, reversible, non-β-lactam β-lactamase inhibitor. Proc. Natl Acad. Sci. USA 109, 11663–11668 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  130. Ostash, B. & Walker, S. Moenomycin family antibiotics: chemical synthesis, biosynthesis, and biological activity. Nat. Prod. Rep. 27, 1594–1617 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Lovering, A. L., de Castro, L. H., Lim, D. & Strynadka, N. C. J. Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis. Science 315, 1402–1405 (2007).

    Article  CAS  PubMed  Google Scholar 

  132. Yuan, Y. et al. Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis. Proc. Natl Acad. Sci. USA 104, 5348–5353 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Sung, M.-T. et al. Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli. Proc. Natl Acad. Sci. USA 106, 8824–8829 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  134. Yuan, Y. et al. Structural analysis of the contacts anchoring moenomycin to peptidoglycan glycosyltransferases and implications for antibiotic design. ACS Chem. Biol. 3, 429–436 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Heaslet, H., Shaw, B., Mistry, A. & Miller, A. A. Characterization of the active site of S. aureus monofunctional glycosyltransferas (Mtg) by site-directed mutation and structural analysis of the protein complexed with moenomycin. J. Struct. Biol. 167, 129–135 (2009).

    Article  CAS  PubMed  Google Scholar 

  136. Fuse, S. et al. Functional and structural analysis of a key region of the cell wall inhibitor moenomycin. ACS Chem. Biol. 5, 701–711 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Taylor, J. G., Li, X., Oberthür, M., Zhu, W. & Kahne, D. E. The total synthesis of moenomycin A. J. Am. Chem. Soc. 128, 15084–15085 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Ostash, B. et al. Complete characterization of the seventeen step moenomycin biosynthetic pathway. Biochemistry 48, 8830–8841 (2009).

    Article  CAS  PubMed  Google Scholar 

  139. Gampe, C. M., Tsukamoto, H., Doud, E. H., Walker, S. & Kahne, D. Tuning the moenomycin pharmacophore to enable discovery of bacterial cell wall synthesis inhibitors. J. Am. Chem. Soc. 135, 3776–3779 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Mohammadi, T. et al. Identification of FtsW as a transporter of lipid-linked cell wall precursors across the membrane. EMBO J. 30, 1425–1432 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Breukink, E. & de Kruijff, B. Lipid II as a target for antibiotics. Nat. Rev. Drug Discov. 5, 321–332 (2006).

    Article  CAS  PubMed  Google Scholar 

  142. Nitanai, Y. et al. Crystal structures of the complexes between vancomycin and cell-wall precursor analogs. J. Mol. Biol. 385, 1422–1432 (2009).

    Article  CAS  PubMed  Google Scholar 

  143. Hsu, S.-T. D. et al. The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics. Nat. Struct. Mol. Biol. 11, 963–967 (2004).

    Article  CAS  PubMed  Google Scholar 

  144. Schneider, T. et al. Plectasin, a fungal defensin, targets the bacterial cell wall precursor lipid II. Science 328, 1168–1172 (2010).

    Article  CAS  PubMed  Google Scholar 

  145. Fjell, C. D., Hiss, J. A., Hancock, R. E. W. & Schneider, G. Designing antimicrobial peptides: form follows function. Nat. Rev. Drug Discov. 11, 37–51 (2012).

    Article  CAS  Google Scholar 

  146. Xie, J., Pierce, J. G., James, R. C., Okano, A. & Boger, D. L. A redesigned vancomycin engineered for dual D-Ala-D-Ala and D-Ala-D-Lac binding exhibits potent antimicrobial activity against vancomycin-resistant bacteria. J. Am. Chem. Soc. 133, 13946–13949 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. James, R. C., Pierce, J. G., Okano, A., Xie, J. & Boger, D. L. Redesign of glycopeptide antibiotics: back to the future. ACS Chem. Biol. 7, 797–804 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Ralph Corey, G., Stryjewski, M. E., Weyenberg, W., Yasothan, U. & Kirkpatrick, P. Telavancin. Nat. Rev. Drug Discov. 8, 929–930 (2009).

    Article  CAS  PubMed  Google Scholar 

  149. Liu, J. et al. Synthesis and characterization of the arylomycin lipoglycopeptide antibiotics and the crystallographic analysis of their complex with signal peptidase. J. Am. Chem. Soc. 133, 17869–17877 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Smith, P. A. & Romesberg, F. E. Mechanism of action of the arylomycin antibiotics and effects of signal peptidase I inihbition. Antimicrob. Agents Chemother. 56, 5054–5060 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Therien, A. G. et al. Broadening the spectrum of β-lactam antibiotics through inhibition of signal peptidase type I. Antimicrob. Agents Chemother. 56, 4662–4670 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Xiao, Y., Gerth, K., Müller, R. & Wall, D. Myxobacterium-produced antibiotic TA (Myxovirescin) inhibits type II signal peptidase. Antimicrob. Agents Chemother. 56, 2014–2021 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Dev, I. K., Harvey, R. J. & Ray, P. H. Inhibition of prolipoprotein signal peptidase by globomycin. J. Biol. Chem. 260, 5891–5894 (1985).

    CAS  PubMed  Google Scholar 

  154. Kogen, H. et al. Crystal structure and total synthesis of globomycin: establishment of relative and absolute configurations. J. Am. Chem. Soc. 122, 10214–10215 (2000).

    Article  CAS  Google Scholar 

  155. Liu, W.-T., Kersten, R. D., Yang, Y.-L., Moore, B. S. & Dorrestein, P. C. Imaging mass spectrometry and genome mining via short sequence tagging identified the anti-infective agent arylomycin in Streptomyces roseosporus. J. Am. Chem. Soc. 133, 18010–18013 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Roberts, T. C., Schallenberger, M. A., Liu, J., Smith, P. A. & Romesberg, F. E. Initial efforts toward the optimization of arylomycins for antibiotic activity. J. Med. Chem. 54, 4954–4963 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Paetzel, M., Karla, A., Strynadka, N. C. J. & Dalbey, R. E. Signal peptidases. Chem. Rev. 102, 4549–4579 (2002).

    Article  CAS  PubMed  Google Scholar 

  158. Content, S., Dutton, C. J. & Roberts, L. Myxovirescin analogues via macrocyclic ring-closing metathesis. Bioorg. Med. Chem. Lett. 13, 321–325 (2003).

    Article  CAS  PubMed  Google Scholar 

  159. Fürstner, A. et al. Total synthesis of Myxovirescin A1 . Chem. Eur. J. 13, 8762–8783 (2007).

    Article  CAS  PubMed  Google Scholar 

  160. Kiho, T. et al. Structure-activity relationships of globomycin analogues as antibiotics. Bioorg. Med. Chem. 12, 337–361 (2004).

    Article  CAS  PubMed  Google Scholar 

  161. Sarabia, F., Chammaa, S. & García-Ruiz, C. Solid phase synthesis of globomycin and SF-1902 A5 . J. Org. Chem. 76, 2132–2144 (2011).

    Article  CAS  PubMed  Google Scholar 

  162. Jin, X. et al. Biosynthesis of new lipopentapeptides by an engineered strain of Streptomyces sp. Biotechnol. Lett. 34, 2283–2289 (2012).

    Article  CAS  PubMed  Google Scholar 

  163. Simunovic, V. et al. Myxovirescin A biosynthesis is directed by hybrid polyketide synthases/nonribosomal peptide synthetase, 3-hydroxy-3-methylglutaryl-CoA synthases, and trans-acting acyltransferases. ChemBioChem 7, 1206–1220 (2006).

    Article  CAS  PubMed  Google Scholar 

  164. Simunovic, V. & Müller, R. 3-Hydroxy-3-methylglutaryl-CoA-like synthases direct the formation of methyl and ethyl side groups in the biosynthesis of the antibiotic Myxovirescin A. ChemBioChem 8, 497–500 (2007).

    Article  CAS  PubMed  Google Scholar 

  165. Simunovic, V. & Müller, R. Mutational analysis of the Myxovirescin biosynthetic gene cluster reveals novel insights into the functional elaboration of polyketide backbones. ChemBioChem 8, 1273–1280 (2007).

    Article  CAS  PubMed  Google Scholar 

  166. Calderone, C. T., Iwig, D. F., Dorrestein, P. C., Kelleher, N. L. & Walsh, C. T. Incorporation of nonmethyl branches by isoprenoid-like logic: multiple β-alkylation events in the biosynthesis of Myxovirescin A1. Chem. Biol. 14, 835–846 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Anderson, M. S., Robertson, A. D., Macher, I. & Raetz, C. R. H. Biosynthesis of lipid A in Escherichia coli: identification of UDP-3-O-[(R)-3-hydroxymyristoyl]-α-D-glucosamine as a precursor of UDP-N2,O3-bis[(R)-3-hydroxymyristoyl]-α-D-glucosamine. Biochemistry 27, 1908–1917 (1988).

    Article  CAS  PubMed  Google Scholar 

  168. Raetz, C. R. H. & Whitfield, C. Lipopolysaccharide endotoxins. Annu. Rev. Biochem. 71, 635–700 (2002).

    Article  CAS  PubMed  Google Scholar 

  169. Barb, A. W., Jiang, L., Raetz, C. R. H. & Zhou, P. Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: time-dependent inhibition and specificity in ligand binding. Proc. Natl Acad. Sci. USA 104, 18433–18438 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  170. Lee, C.-J. et al. Species-specific and inhibitor-dependent conformations of LpxC: implications for antibiotic design. Chem. Biol. 18, 38–47 (2011).

    Article  CAS  PubMed  Google Scholar 

  171. Villa, R. et al. The Escherichia coli Lpt transenvelope protein complex for lipopolysaccharide export is assembled via conserved structurally homologous domains. J. Bacteriol. 195, 1100–1108 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Okuda, S., Freinkman, E. & Kahne, D. Cytoplasmic ATP hydrolysis powers transport of lipopolysaccharide across the periplasm in E. coli. Science 338, 1214–1217 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Chng, S.-S. et al. Disulfide rearrangement triggered by translocon assembly controls lipopolysaccharide export. Science 337, 1665–1668 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Freinkman, E., Okuda, S., Ruiz, N. & Kahne, D. Regulated assembly of the transenvelope protein complex required for lipopolysaccharide export. Biochemistry 51, 4800–4806 (2012).

    Article  CAS  PubMed  Google Scholar 

  175. Chimalakonda, G. et al. Lipoprotein LptE is required for the assembly of LptD by the β-barrel assembly machine in the outer membrane of Escherichia coli. Proc. Natl Acad. Sci. USA 108, 2492–2497 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  176. Freinkman, E., Chng, S.-S. & Kahne, D. The complex that inserts lipopolysaccharide into the bacterial outer membrane forms a two-protein plug-and-barrel. Proc. Natl Acad. Sci. USA 108, 2486–2491 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  177. Ruiz, N., Chng, S.-S., Hiniker, A., Kahne, D. & Silhavy, T. J. Nonconsecutive disulfide bond formation in an essential integral outer membrane protein. Proc. Natl Acad. Sci. USA 107, 12245–12250 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  178. Chng, S.-S., Ruiz, N., Chimalakonda, G., Silhavy, T. J. & Kahne, D. Characterization of the two-protein complex in Escherichia coli responsible for lipopolysaccharide assembly at the outer membrane. Proc. Natl Acad. Sci. USA 107, 5363–5368 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  179. Gronenberg, L. S. & Kahne, D. Development of an activity assay for discovery of inhibitors of lipopolysaccharide transport. J. Am. Chem. Soc. 132, 2518–2519 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Ruiz, N., Kahne, D. & Silhavy, T. J. Transport of lipopolysaccharide across the cell envelope: the long road of discovery. Nat. Rev. Microbiol. 7, 677–683 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Chng, S.-S., Gronenberg, L. S. & Kahne, D. Proteins required for lipopolysaccharide assembly in Escherichia coli form a transenvelope complex. Biochemistry 49, 4565–4567 (2010).

    Article  CAS  PubMed  Google Scholar 

  182. Kim, S. et al. Structure and function of an essential component of the outer membrane protein assembly machine. Science 317, 961–964 (2007).

    Article  CAS  PubMed  Google Scholar 

  183. Srinivas, N. et al. Peptidomimetic antibiotics target outer-membrane biogenesis in Pseudomonas aeruginosa. Science 327, 1010–1013 (2010).

    Article  CAS  PubMed  Google Scholar 

  184. Shankaramma, S. C. et al. Macrocyclic hairpin mimetics of the cationic antimicrobial peptide protegrin I: a new family of broad-spectrum antibiotics. ChemBioChem 3, 1126–1133 (2002).

    Article  CAS  PubMed  Google Scholar 

  185. Robinson, J. A. et al. Properties and structure-activity studies of cyclic β-haripin peptidomimetics based on the cationic antimicrobial peptide protegrin I. Bioorg. Med. Chem. 13, 2055–2064 (2005).

    Article  CAS  PubMed  Google Scholar 

  186. Mariani, R. & Maffioli, S. I. Bacterial RNA polymerase inhibitors: an organized overview of their structures, derivatives, biological activity and current clinical development status. Curr. Med. Chem. 16, 430–454 (2009).

    Article  CAS  PubMed  Google Scholar 

  187. Erb, W. & Zhu, J. From natural product to marketed drug: the tiacumicin odyssey. Nat. Prod. Rep. 30, 161–174 (2013).

    Article  CAS  PubMed  Google Scholar 

  188. Venugopal, A. A. & Johnson, S. Fidaxomicin: a novel macrocyclic antibiotic approved for treatment of Clostridium difficile infection. Clin. Infect. Dis. 54, 568–574 (2012).

    Article  CAS  PubMed  Google Scholar 

  189. Campbell, E. A. et al. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 104, 901–912 (2001).

    Article  CAS  PubMed  Google Scholar 

  190. Campbell, E. A. et al. Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J. 24, 674–682 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Tuske, S. et al. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 122, 541–552 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Mukhopadhyay, J. et al. The RNA polymerase ‘switch region’ is a target for inhibitors. Cell 135, 295–307 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Ho, M. X., Hudson, B. P., Das, K., Arnold, E. & Ebright, R. H. Structures of RNA polymerase-antibiotic complexes. Curr. Opin. Struct. Biol. 19, 715–723 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Vassylyev, D. G. et al. Structural basis for transcription inhibition by tagetitoxin. Nat. Struct. Mol. Biol. 12, 1086–1093 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Cohen, P. Protein kinases—the major drug targets of the twenty-first century? Nat. Rev. Drug Discov. 1, 309–315 (2002).

    Article  CAS  PubMed  Google Scholar 

  196. Karaman, M. W. et al. A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 26, 127–132 (2008).

    Article  CAS  PubMed  Google Scholar 

  197. Škedelj, V., Tomašić, T., Peterlin Mašič, L. & Zega, A. ATP-binding bite of bacterial enzymes as a target for antibacterial drug design. J. Med. Chem. 54, 915–929 (2011).

    Article  CAS  PubMed  Google Scholar 

  198. Angehrn, P. et al. A new DNA gyrase inhibitor subclass of the cyclothialidine family based on a bicyclic dilactam-lactone scaffold. Synthesis and antibacterial properties. J. Med. Chem. 54, 2207–2224 (2011).

    Article  CAS  PubMed  Google Scholar 

  199. Diacon, A. H. et al. The diarylquinolone TMC207 for multidrug-resistant tuberculosis. N. Engl. J. Med. 360, 2397–2405 (2009).

    Article  CAS  PubMed  Google Scholar 

  200. Andries, K. et al. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307, 223–227 (2005).

    Article  CAS  PubMed  Google Scholar 

  201. Koul, A. et al. Diarylquinolines target subunit C of mycobacterial ATP synthase. Nat. Chem. Biol. 3, 323–324 (2007).

    Article  CAS  PubMed  Google Scholar 

  202. Haagsma, A. C. et al. Selectivity of TMC207 towards mycobacterial ATP synthase compared with that towards the eukaryotic homologue. Antimicrob. Agents Chemother. 53, 1290–1292 (2009).

    Article  CAS  PubMed  Google Scholar 

  203. Rustomjee, R. et al. Early bactericidal activity and pharmacokinetics of the diarylquinoline TMC207 in treatment of pulmonary tuberculosis. Antimicrob. Agents Chemother. 52, 2831–2835 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Wolfe, L. M. et al. A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis. Mol. Cell. Proteomics (e-pub ahead of print 5 March 2013; doi:10.1074/mcp.M112.025635) (2013).

  205. Brötz-Oesterhelt, H. et al. Dysregulation of bacterial proteolytic machinery by a new class of antibiotics. Nat. Med. 11, 1082–1087 (2005).

    Article  CAS  PubMed  Google Scholar 

  206. Frees, D., Savijoki, K., Varmanen, P. & Ingmer, H. Clp ATPases and ClpP proteolytic complexes regulate vital biological processes in low GC, Gram-positive bacteria. Mol. Microbiol. 63, 1285–1295 (2007).

    Article  CAS  PubMed  Google Scholar 

  207. Lee, B.-G. et al. Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism. Nat. Struct. Mol. Biol. 17, 471–479 (2010).

    Article  CAS  PubMed  Google Scholar 

  208. Shun, L. i.,D. H. et al. Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: a model for the ClpX/ClpA-bound state of ClpP. Chem. Biol. 17, 959–969 (2010).

    Article  CAS  Google Scholar 

  209. Michel, K. H. & Kastner, R. E. A54556 antibiotics and process for production thereof. US Patent 4492650 (1985).

  210. Sass, P. et al. Antibiotic acyldepsipeptides activate ClpP peptidase to degrade the cell division protein FtsZ. Proc. Natl Acad. Sci. USA 108, 17474–17479 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  211. Erickson, H. P., Anderson, D. E. & Osawa, M. FtsZ in bacterial cytokinesis: cytoskeleton and force generator all in one. Microbiol. Mol. Biol. Rev. 74, 504–528 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Haydon, D. J. et al. An inhibitor of FtsZ with potent and selective anti-Staphylococcal activity. Science. 321, 1673–1675 (2008).

    Article  CAS  PubMed  Google Scholar 

  213. Andreu, J. M. et al. The antibacterial cell division inhibitor PC190723 is an FtsZ polymer-stabilizing agent that induces filament assembly and condensation. J. Biol. Chem. 285, 14239–14246 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Tan, C. M. et al. Restoring methicillin-resistant Staphylococcus aureus susceptibility to β-lactam antibiotics. Sci. Transl. Med. 4, 126ra135 (2012).

    Google Scholar 

  215. Anderson, D. E. et al. Comparison of small molecule inhibitors of the bacterial cell division protein FtsZ and identification of a reliable cross-species inhibitor. ACS Chem. Biol. 7, 1918–1928 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Jenner, L. et al. Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis. Proc. Natl Acad. Sci. USA 110, 3812–3816 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  217. Becker, B. & Cooper, M. A. Aminoglycoside antibiotics in the 21st century. ACS Chem. Biol. 8, 105–115 (2013).

    Article  CAS  PubMed  Google Scholar 

  218. Parmeggiani, A. et al. Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu. Biochemistry 45, 6846–6857 (2006).

    Article  CAS  PubMed  Google Scholar 

  219. LaMarche, M. J. et al. Discovery of LFF571: an investigational agent for Clostridium difficile infection. J. Med. Chem. 55, 2376–2387 (2012).

    Article  CAS  PubMed  Google Scholar 

  220. Chait, R., Vetsigian, K. & Kishony, R. What counters antibiotic resistance in nature? Nat. Chem. Biol. 8, 2–5 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We sincerely thank Gerry Wright for thinking up this issue and all the authors who contribute articles in it. We acknowledge research efforts in our laboratory supported by NIH Grants GM 20011 and GM 49338 and the many colleagues in the Walsh group, some of whom are noted in specific references.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Christopher T Walsh.

Ethics declarations

Competing interests

CTW is on the Board of Directors of Achaogen, which has plazomicin in clinical trials.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Walsh, C., Wencewicz, T. Prospects for new antibiotics: a molecule-centered perspective. J Antibiot 67, 7–22 (2014). https://doi.org/10.1038/ja.2013.49

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ja.2013.49

Keywords

  • antibiotics
  • mechanism of action
  • natural products
  • resistance

Further reading

Search

Quick links