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Antimicrobial Agents That Inhibit the Outer Membrane Assembly Machines of Gram-Negative Bacteria
Department of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggido 17058, Republic of Korea
Correspondence to:J. Microbiol. Biotechnol. 2019; 29(1): 1-10
Published January 28, 2019 https://doi.org/10.4014/jmb.1804.03051
Copyright © The Korean Society for Microbiology and Biotechnology.
Abstract
Keywords
Introduction
The outer membrane (OM) of Gram-negative bacteria is a unique architecture with an asymmetric bilayer, which consists of phospholipids in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet [1]. In addition to phospholipids and LPS, there are a variety of bilayer-anchored lipoproteins and outer membrane β-barrel proteins (OMPs) in the OM [2]. Lipoproteins play an important role in several essential and non-essential functions, including the linkage between the OM and peptidoglycan [3], peptidoglycan synthesis [4, 5], pili and flagella assembly [6, 7], and protein and polysaccharide secretion [8, 9]. Porin, a major OMP of the OM, forms specific and non-specific channels that regulate the transport of hydrophilic molecules across the OM [10, 11].
The OM functions as an additional barrier that inhibits the transport of toxic molecules such as antimicrobial compounds. Therefore, compounds with a molecular weight (MW) of more than 600 Da cannot pass through the Gram-negative bacteria cell envelope. For example, vancomycin and daptomycin which have a MW of more than 1,400 Da are not able to penetrate the OM of Gram-negative bacteria [12]. This feature of Gram-negative bacteria is one of the major obstacles in novel antibiotic discovery targeting clinically important Gram-negative pathogens, such as
OM Assembly Machines
Lipoproteins and OMPs
Lipoproteins containing a so-called lipobox, a consensus sequence [LVI][ASTVI][GAS]C, are translocated across the inner membrane (IM) by the Sec or Tat system [15, 16]. The maturation of lipoprotein precursors occurs on the outer leaflet of the IM by sequential functions of phosphatidylglycerol/prolipoprotein diacylglyceryl transferase (Lgt), lipoprotein signal peptidase (LspA), and phospholipid/apolipoprotein transacylase (Lnt) [15]. Most mature lipoproteins are then transported to the OM by the LolABCDE pathway [3, 15, 16], and few lipoproteins with a so-called Lol avoidance signal (
The LolCD2E complex belonging to the ABC transporter superfamily extracts lipoproteins from the IM and transfers extracted lipoproteins to the periplasmic chaperone LolA, resulting in the formation of a soluble lipoprotein-LolA complex (Fig. 1) [16, 18]. This step depends on ATP hydrolysis of the cytoplasmic ATPase LolD [18, 19]. LolE and LolC, which have a significantly structural similarity, seem to play distinct roles, recognition and binding of lipoproteins [20] and the transfer of lipoproteins to LolA [21], respectively.
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Fig. 1. The outer membrane assembly machines in (A) The Lol pathway. After IM insertion of lipoprotein precursors by the Sec system, lipoprotein precursors are processed to lipoproteins. The lipoproteins extracted by the LolCD2E complex are transferred to LolB in the OM through the periplasmic protein LolA. Lipoproteins of LolB are released in the OM. (B) The Bam pathway. OMPs secreted by the Sec system are inserted into the OM by the Bam assembly machine. (C) The Lpt pathway. LPS extracted by the LptB2CFG complex are transferred to the LptDE complex in the OM through the transenvelope bridge of LptA that spans the entire periplasmic region. The LptDE complex inserts LPS into the outer leaflet of the OM. (D) Phospholipid transport systems. PbgA transports CL in the IM to the OM. The Mla pathway transports PG and PE in the OM to the IM.E. coli .E. coli has two systems (the Pqi and Yeb pathway) with a central channel capable of mediating phospholipid transport, but it has not been determined yet whether the Pqi and Yeb pathway mediate only retrograde transport of phospholipids or bidirectional migration of phospholipids.
LolA interacts with lipoproteins through interaction between the large hydrophobic cavity of LolA and the acyl chains of lipoproteins, which shields the highly hydrophobic region of lipoprotein from the hydrophilic periplasm [22]. LolA transports lipoproteins to the OM lipoprotein LolB, which shares remarkably structural similarity with LolA [15]. The acyl chain transfer between LolA and LolB seems to be achieved by the directional mouth-to-mouth delivery driven by an affinity difference between the hydrophobic cavities of LolA and LolB for the acyl chain [21]. Lipoproteins of LolB are released in the OM, but its precise mechanism remains poorly understood [3]. The protruding loop of LolB seems to be important for lipoprotein insertion, as a LolB variant with a point mutation within this loop can receive lipoproteins from LolA, but is not able to mediate the OM insertion of lipoproteins [23]. All
OMPs
OMPs are OM transmembrane proteins with a β-barrel structure consisting of antiparallel β-sheets [24]. OMPs synthesized in the cytoplasm are transported to the periplasm by the Sec system. The nascent OMPs in the periplasm are guided by several periplasmic chaperones, such as SurA and Skp, which deliver OMPs to the β-barrel assembly machinery (BAM) complex in the OM (Fig. 1)[25]. The BAM complex is an insertase machinery consisting of five proteins (BamABCDF). BamA, an OMP itself, has a highly conserved D15 domain forming a 16-strand β-barrel, which is essential for the insertase activity of the BAM complex [26], and five periplasmic polypeptide transport associated domains (POTRA domains) in the N-terminal region, which function as protein-protein interaction domains [27]. BamA forms a tight complex with four lipoproteins (BamBCDE). Based on structural and functional studies, there are two working models: the assistance model of BamA for spontaneous insertion of OMPs (BamA-assisted model) and the conformational change model of OMPs within BamA followed by insertion into the OM via lateral opening of BamA (BamA-budding model) [25], but their precise mechanism remains unclear. Because BamA is itself an OMP, there is a “chicken-or-the-egg” question about BamA assembly. Recent studies suggest that BamB and BamD assist in the early assembly of BamA, and then the BAM complex containing all components may complete the BamA biogenesis [28, 29].
LPS
LPSs, which are composed of lipid A, core oligosaccharide, and O-antigen polysaccharide chains, are transported by the lipopolysaccharide transport (Lpt) pathway consisting of seven essential proteins (LptABCDEFG) (Fig. 1) [30]. The Lpt pathway is divided into two subassemblies, the nonconventional ABC transporter LptB2CFG located at the IM and LptDE located at the OM. Two sub-complexes are connected by the periplasmic chaperone LptA, which oligomerizes to form a transenvelope bridge that spans the entire periplasmic region from the IM to the OM [31]. LptA interacts with each other in a head-to-tail orientation [32] and their N-terminal and C-terminal regions interact with the C-terminal regions of LptC in the IM and the N-terminal regions of LptD in the OM, respectively [33]. Similar to the LolCD2E complex, the LptB2CFG complex extracts LPS from the outer leaflet of the IM using ATP hydrolysis and transfers it to LptC, an IM protein containing a single N-terminal transmembrane helix and a large soluble periplasmic domain [34]. LptC interacts with LptB2CFG complex and delivers LPS to LptA [34]. LptA has a highly structural similarity (a so-called Lpt-fold) with the periplasmic domain of LptC [35] and the Lpt-fold has a hydrophobic pocket for binding to the lipid moiety of LPS [34]. Similar to the transfer of lipoproteins between LolA and LolB [21], the transfer of LPS from LptC to LptA seems to be achieved by the spontaneous delivery driven by an affinity difference between LptC and LptA for the lipid moiety [35]. Although the exact delivery mechanism of LPS to the OM by LptA and the number of LptA present in the transenvelope bridge are not fully determined, several studies show that LptA oligomerization is necessary for the interaction with LPS and the delivery through periplasm [36, 37]. The LptDE complex, comprising the β-barrel protein LptD and the lipoprotein LptE, forms a so-called plug-and-barrel structure with the entire insertion of LptE inserted into the β-barrel of LptD [38]. The N-terminal periplasmic domain of LptD has an Lpt-fold for interaction with LPS and seems to be involved in the delivery of LPS from LptA to the LptDE complex [30]. Several studies suggest that LPS may laterally pass through the β-barrel lumen of LptsD and may be directly inserted into the outer leaflet of the OM [39-41]. LptE seems to play various important roles in controlling the correct maturation of the LptD disulfide bonds [42], plugging the too large lumen of LptD [30, 43, 44], and disaggregating LPS during transport through interaction with negative charges of LPS [45].
Phospholipids
The envelope of
Inhibitors Targeting the OM Assembly Machines
The development of antimicrobial agents inhibiting the transport of OM components, including lipoproteins, OMPs, LPS, and phospholipids, would provide an entirely new class of antimicrobial agents. We analyzed all studies on the development of inhibitors targeting OM assembly machines.
Inhibitors of Lipoprotein Transport
The identification of chemical compounds that inhibit the Lol pathway has been extensively researched (Table 1). The first identified compounds, CCT-00431 and CCT-00432, were found by an inhibition assay of the LolA-dependent release of L10P, an Lpp derivative, from the LolCDE-L10P complex [53]. CCT-00431 and CCT-00432 inhibited the formation of the LolA-L10P complex by 30% and 60%, respectively [53]. The minimal inhibitory concentrations (MICs) of CCT-00431 and CCT-00432 for
Several compounds inhibiting the LolCD2E complex were identified [57-59]. A pyrazole-containing compound was found by a high-throughput screen using an AmpC reporter assay [58]. The
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Table 1 . Antimicrobial inhibitors targeting the OM assembly machines.
Assembly machine Inhibitor Cellular target IC50a MIC (μg/ml) MIC in the resistant mutant Reference The Lol pathway CCT-00431 and CCT-00432 LolA N.D.b 16 ( E. coli NIHJ JC-2)
8 (E. coli M101)8 (Parent)
32 or 128 (Δlpp )[53] MAC13243 LolA N.D. 16 ( E. coli ATCC25922)
4 (Pseudomonas aeruginosa PAO1)N.D. [54] S -(4-chlorobenzyl)iso-thiourea andS -(3,4-dichlorobenzyl)iso-thiourea (A22)LolA IC50=150 μM [ S -(4-chlo-robenzyl)isothiourea]
IC50=200 μM (A22)2 ( E. coli MG1655)N.D. [55] Pyrazole-containing compound LolC and LolE N.D. 8 ( E. coli ATCC25922)
0.125 (E. coli ATCC25922 ΔtolC )
32 (Haemophilus influenza ATCC49247)
>64 (Pseudomonas aeruginosa PAO1)0.125 (Parent)
>128 [LolC(G254V)]
>128 [LolE(G195S)]
>128 [LolE(P365C)]
>128 [LolE(P367Y)][58] Pyridineimidazole-containing compound 1 LolC and LolE N.D. 32 ( E. coli ATCC25922)
0.25 (E. coli ATCC25922 ΔtolC )
2 (Haemophilus influenza ATCC49247)
>64 (Pseudomonas aeruginosa PAO1)0.125 (Parent)
>64 [LolC(N265K)]
>64 [LolE(I59N)]
64 [LolE(P372L)]
>64 [LolE(L371P)][57] Pyridineimidazole-containing compound 2 LolC and N.D. 4 ( E. coli ATCC25922)
<0.06 (E. coli ATCC25922 ΔtolC )
0.25 (Haemophilus influenza ATCC49247)
>64 (Pseudomonas aeruginosa PAO1)<0.06 (Parent)
>64 [LolC(N265K)]
>64 [LolE(I59N)]
8 [LolE(P372L)]
>64 [LolE(L371P)][57] Pyrrolopyrimidinedione compound G507 LolCDE N.D. >64 ( E. coli MG1655)
0.5 (E. coli MG1655 ΔtolC )
1 (E. coli MG1655imp4213 )
16 (TQ/he MIC of G0793 againstE. coli MG1655)N.D. [59] The Lpt pathway Compound 1 and 2 LptB IC50=25 μM (compound 1) IC50=17 μM N.D. N.D. [63] 4-Phenylpyrrolocarba-zole derivatives, 1a and 1b LptB IC50=119 μM >100 ( E. coli MC4100) 25
(E. coli NR698)N.D. [64] Peptidomimetic compound L27-11 LptD N.D. 0.01 ( Pseudomonas aeruginosa ATCC27853)
0.004 (Pseudomonas aeruginosa PAO1)0.06 (Parent)
>64 (Duplication of residues 210-215 of LptD)[68] β-hairpin-shaped peptidomimetic compound LB-01 LptD N.D. 0.008 ( Pseudomonas aeruginosa ATCC27853)
0.015 (Pseudomonas aeruginosa PAO1)N.D. [71] β-hairpin-shaped peptidomimetic compound Dab4NMe LptD N.D. 0.005 ( Pseudomonas aeruginosa ATCC27853)
0.009 (Pseudomonas aeruginosa PAO1)N.D. [71] The BAM pathway β-hairpin macrocyclic peptide JB-95 BamA and LptD N.D. 0.25 ( E. coli ATCC25922)
1 (Acinetobacter baumannii ATCC17978)
4 (Pseudomonas aeruginosa PAO1)
2 (Staphylococcus aureus ATCC29213)N.D. [73] aThe half maximal inhibitory concentration.
bNot determined.
Inhibitors of LPS Transport
Chemicals inhibiting the ATPase activity of the ATPase component LptB of the LptB2CFG complex were screened by a continuous assay that couples ATP hydrolysis to NADH oxidation [63]. Two compounds, 1 and 2, that have different structural classes, inhibited the ATPase activity of LptB with an IC50 of 25 and 17 μM, respectively [63]. The value of the MICs of these compounds was not determined. In 2013, other inhibitors of LptB were identified by the same biochemical assay, the continuous assay coupling ATP hydrolysis to NADH oxidation [64]. A compound 4-phenylpyrrolocarbazole derivative that had previously been known as a potent inhibitor of a eukaryotic kinase Wee1, which regulates mitosis entry [65], was identified as an inhibitor of LptA [64]. Several derivatives of 4- phenylpyrrolocarbazole were additionally tested for inhibition of the ATPase activity of LptB. Compounds 1a and 1b showed a weak antimicrobial activity (MIC of >100 μg/ml) against the
Several β-hairpin-shaped peptidomimetics (small protein- like chains designed to mimic a peptide) targeting the β- barrel OM protein LptD were developed by optimization of peptidomimetics based on the antimicrobial peptide protegrin I (PG-I) [66]. PG-I is a broad-spectrum antimicrobial peptide against Gram-negative and Gram-positive bacteria [67], but optimized peptidomimetics, L26-19 and L27-11, display a narrow-spectrum antimicrobial effect only against
Inhibitors of OMP Transport
One study investigated an inhibitor that targets the BAM complex. Similar to L27-11, a β-hairpin macrocyclic peptidomimetic JB-95 was identified as an inhibitor of β-barrel OM proteins BamA and LptD [73]. JB-95 induced no cellular lytic activity like L27-11, but selectively disrupted the OM integrity, but not the IM, and induced rapid depletion of β-barrel OM proteins [73]. Photolabeling experiments revealed the interaction of JB-96 with BamA and LptD. The MICs of JB-95 against
Upon the revelation of a more complete picture of the transport system of OM components, the possibility of developing antimicrobial agents targeting OM transport machines was examined. The most successful case is Murepavadin, an L27-11-based peptidomimetic inhibitor of LptD, which has successfully completed phase-II clinical trials [72]. Because several additional optimization procedures of L27-11 have been suggested [70, 71], there is the possibility of developing more potent antimicrobial agents. Although there have been various attempts at developing new antibiotics targeting the Lol system, an inhibitor with an MIC in the nanomolar range has not yet been developed. The high-throughput screen of inhibitors based on peptidomimetics may be useful for the development of inhibitors of the Lol system. Because the transport system of phospholipids from the IM to the OM remains undetermined, extensive studies are required in this field. The phospholipid transport system has potential to be a novel target for the development of new antimicrobial agents against Gram-negative bacteria.
Acknowledgements
This work was supported by research grants from the Advanced Biomass R&D Center (ABC) of the Global Frontier Project funded by the Ministry of Science, ICT and Future Planning (ABC-2015M3A6A2065700), and the Bio & Medical Technology Development Program of the NRF funded by the Korean government, MSIT (NRF-2017M3A9E4078017).
Conflict of Interest
The authors have no financial conflicts of interest to declare.
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Related articles in JMB
Article
Review
J. Microbiol. Biotechnol. 2019; 29(1): 1-10
Published online January 28, 2019 https://doi.org/10.4014/jmb.1804.03051
Copyright © The Korean Society for Microbiology and Biotechnology.
Antimicrobial Agents That Inhibit the Outer Membrane Assembly Machines of Gram-Negative Bacteria
Umji Choi and Chang-Ro Lee *
Department of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggido 17058, Republic of Korea
Correspondence to:Chang-Ro Lee
crlee@mju.ac.kr
Abstract
Gram-negative pathogens, such as Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, pose a serious threat to public health worldwide, due to high rates of antibiotic resistance and the lack of development of novel antimicrobial agents targeting Gram-negative bacteria. The outer membrane (OM) of Gram-negative bacteria is a unique architecture that acts as a potent permeability barrier against toxic molecules, such as antibiotics. The OM is composed of phospholipids, lipopolysaccharide (LPS), outer membrane β-barrel proteins (OMP), and lipoproteins. These components are synthesized in the cytoplasm or in the inner membrane, and are then selectively transported to the OM by the specific transport machines, including the Lol, BAM, and Lpt pathways. In this review, we summarize recent studies on the assembly systems of OM components and analyze studies for the development of inhibitors that target these systems. These analyses show that OM assembly machines have the potential to be a novel attractive drug target of Gram-negative bacteria.
Keywords: Antimicrobial agents, outer membrane assembly machine, lipoprotein, LPS, OMP, phospholipid
Introduction
The outer membrane (OM) of Gram-negative bacteria is a unique architecture with an asymmetric bilayer, which consists of phospholipids in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet [1]. In addition to phospholipids and LPS, there are a variety of bilayer-anchored lipoproteins and outer membrane β-barrel proteins (OMPs) in the OM [2]. Lipoproteins play an important role in several essential and non-essential functions, including the linkage between the OM and peptidoglycan [3], peptidoglycan synthesis [4, 5], pili and flagella assembly [6, 7], and protein and polysaccharide secretion [8, 9]. Porin, a major OMP of the OM, forms specific and non-specific channels that regulate the transport of hydrophilic molecules across the OM [10, 11].
The OM functions as an additional barrier that inhibits the transport of toxic molecules such as antimicrobial compounds. Therefore, compounds with a molecular weight (MW) of more than 600 Da cannot pass through the Gram-negative bacteria cell envelope. For example, vancomycin and daptomycin which have a MW of more than 1,400 Da are not able to penetrate the OM of Gram-negative bacteria [12]. This feature of Gram-negative bacteria is one of the major obstacles in novel antibiotic discovery targeting clinically important Gram-negative pathogens, such as
OM Assembly Machines
Lipoproteins and OMPs
Lipoproteins containing a so-called lipobox, a consensus sequence [LVI][ASTVI][GAS]C, are translocated across the inner membrane (IM) by the Sec or Tat system [15, 16]. The maturation of lipoprotein precursors occurs on the outer leaflet of the IM by sequential functions of phosphatidylglycerol/prolipoprotein diacylglyceryl transferase (Lgt), lipoprotein signal peptidase (LspA), and phospholipid/apolipoprotein transacylase (Lnt) [15]. Most mature lipoproteins are then transported to the OM by the LolABCDE pathway [3, 15, 16], and few lipoproteins with a so-called Lol avoidance signal (
The LolCD2E complex belonging to the ABC transporter superfamily extracts lipoproteins from the IM and transfers extracted lipoproteins to the periplasmic chaperone LolA, resulting in the formation of a soluble lipoprotein-LolA complex (Fig. 1) [16, 18]. This step depends on ATP hydrolysis of the cytoplasmic ATPase LolD [18, 19]. LolE and LolC, which have a significantly structural similarity, seem to play distinct roles, recognition and binding of lipoproteins [20] and the transfer of lipoproteins to LolA [21], respectively.
-
Figure 1. The outer membrane assembly machines in (A) The Lol pathway. After IM insertion of lipoprotein precursors by the Sec system, lipoprotein precursors are processed to lipoproteins. The lipoproteins extracted by the LolCD2E complex are transferred to LolB in the OM through the periplasmic protein LolA. Lipoproteins of LolB are released in the OM. (B) The Bam pathway. OMPs secreted by the Sec system are inserted into the OM by the Bam assembly machine. (C) The Lpt pathway. LPS extracted by the LptB2CFG complex are transferred to the LptDE complex in the OM through the transenvelope bridge of LptA that spans the entire periplasmic region. The LptDE complex inserts LPS into the outer leaflet of the OM. (D) Phospholipid transport systems. PbgA transports CL in the IM to the OM. The Mla pathway transports PG and PE in the OM to the IM.E. coli .E. coli has two systems (the Pqi and Yeb pathway) with a central channel capable of mediating phospholipid transport, but it has not been determined yet whether the Pqi and Yeb pathway mediate only retrograde transport of phospholipids or bidirectional migration of phospholipids.
LolA interacts with lipoproteins through interaction between the large hydrophobic cavity of LolA and the acyl chains of lipoproteins, which shields the highly hydrophobic region of lipoprotein from the hydrophilic periplasm [22]. LolA transports lipoproteins to the OM lipoprotein LolB, which shares remarkably structural similarity with LolA [15]. The acyl chain transfer between LolA and LolB seems to be achieved by the directional mouth-to-mouth delivery driven by an affinity difference between the hydrophobic cavities of LolA and LolB for the acyl chain [21]. Lipoproteins of LolB are released in the OM, but its precise mechanism remains poorly understood [3]. The protruding loop of LolB seems to be important for lipoprotein insertion, as a LolB variant with a point mutation within this loop can receive lipoproteins from LolA, but is not able to mediate the OM insertion of lipoproteins [23]. All
OMPs
OMPs are OM transmembrane proteins with a β-barrel structure consisting of antiparallel β-sheets [24]. OMPs synthesized in the cytoplasm are transported to the periplasm by the Sec system. The nascent OMPs in the periplasm are guided by several periplasmic chaperones, such as SurA and Skp, which deliver OMPs to the β-barrel assembly machinery (BAM) complex in the OM (Fig. 1)[25]. The BAM complex is an insertase machinery consisting of five proteins (BamABCDF). BamA, an OMP itself, has a highly conserved D15 domain forming a 16-strand β-barrel, which is essential for the insertase activity of the BAM complex [26], and five periplasmic polypeptide transport associated domains (POTRA domains) in the N-terminal region, which function as protein-protein interaction domains [27]. BamA forms a tight complex with four lipoproteins (BamBCDE). Based on structural and functional studies, there are two working models: the assistance model of BamA for spontaneous insertion of OMPs (BamA-assisted model) and the conformational change model of OMPs within BamA followed by insertion into the OM via lateral opening of BamA (BamA-budding model) [25], but their precise mechanism remains unclear. Because BamA is itself an OMP, there is a “chicken-or-the-egg” question about BamA assembly. Recent studies suggest that BamB and BamD assist in the early assembly of BamA, and then the BAM complex containing all components may complete the BamA biogenesis [28, 29].
LPS
LPSs, which are composed of lipid A, core oligosaccharide, and O-antigen polysaccharide chains, are transported by the lipopolysaccharide transport (Lpt) pathway consisting of seven essential proteins (LptABCDEFG) (Fig. 1) [30]. The Lpt pathway is divided into two subassemblies, the nonconventional ABC transporter LptB2CFG located at the IM and LptDE located at the OM. Two sub-complexes are connected by the periplasmic chaperone LptA, which oligomerizes to form a transenvelope bridge that spans the entire periplasmic region from the IM to the OM [31]. LptA interacts with each other in a head-to-tail orientation [32] and their N-terminal and C-terminal regions interact with the C-terminal regions of LptC in the IM and the N-terminal regions of LptD in the OM, respectively [33]. Similar to the LolCD2E complex, the LptB2CFG complex extracts LPS from the outer leaflet of the IM using ATP hydrolysis and transfers it to LptC, an IM protein containing a single N-terminal transmembrane helix and a large soluble periplasmic domain [34]. LptC interacts with LptB2CFG complex and delivers LPS to LptA [34]. LptA has a highly structural similarity (a so-called Lpt-fold) with the periplasmic domain of LptC [35] and the Lpt-fold has a hydrophobic pocket for binding to the lipid moiety of LPS [34]. Similar to the transfer of lipoproteins between LolA and LolB [21], the transfer of LPS from LptC to LptA seems to be achieved by the spontaneous delivery driven by an affinity difference between LptC and LptA for the lipid moiety [35]. Although the exact delivery mechanism of LPS to the OM by LptA and the number of LptA present in the transenvelope bridge are not fully determined, several studies show that LptA oligomerization is necessary for the interaction with LPS and the delivery through periplasm [36, 37]. The LptDE complex, comprising the β-barrel protein LptD and the lipoprotein LptE, forms a so-called plug-and-barrel structure with the entire insertion of LptE inserted into the β-barrel of LptD [38]. The N-terminal periplasmic domain of LptD has an Lpt-fold for interaction with LPS and seems to be involved in the delivery of LPS from LptA to the LptDE complex [30]. Several studies suggest that LPS may laterally pass through the β-barrel lumen of LptsD and may be directly inserted into the outer leaflet of the OM [39-41]. LptE seems to play various important roles in controlling the correct maturation of the LptD disulfide bonds [42], plugging the too large lumen of LptD [30, 43, 44], and disaggregating LPS during transport through interaction with negative charges of LPS [45].
Phospholipids
The envelope of
Inhibitors Targeting the OM Assembly Machines
The development of antimicrobial agents inhibiting the transport of OM components, including lipoproteins, OMPs, LPS, and phospholipids, would provide an entirely new class of antimicrobial agents. We analyzed all studies on the development of inhibitors targeting OM assembly machines.
Inhibitors of Lipoprotein Transport
The identification of chemical compounds that inhibit the Lol pathway has been extensively researched (Table 1). The first identified compounds, CCT-00431 and CCT-00432, were found by an inhibition assay of the LolA-dependent release of L10P, an Lpp derivative, from the LolCDE-L10P complex [53]. CCT-00431 and CCT-00432 inhibited the formation of the LolA-L10P complex by 30% and 60%, respectively [53]. The minimal inhibitory concentrations (MICs) of CCT-00431 and CCT-00432 for
Several compounds inhibiting the LolCD2E complex were identified [57-59]. A pyrazole-containing compound was found by a high-throughput screen using an AmpC reporter assay [58]. The
-
Table 1 . Antimicrobial inhibitors targeting the OM assembly machines..
Assembly machine Inhibitor Cellular target IC50a MIC (μg/ml) MIC in the resistant mutant Reference The Lol pathway CCT-00431 and CCT-00432 LolA N.D.b 16 ( E. coli NIHJ JC-2)8 ( E. coli M101)8 (Parent) 32 or 128 (Δ lpp )[53] MAC13243 LolA N.D. 16 ( E. coli ATCC25922)4 ( Pseudomonas aeruginosa PAO1)N.D. [54] S -(4-chlorobenzyl)iso-thiourea andS -(3,4-dichlorobenzyl)iso-thiourea (A22)LolA IC50=150 μM [ S -(4-chlo-robenzyl)isothiourea]IC50=200 μM (A22) 2 ( E. coli MG1655)N.D. [55] Pyrazole-containing compound LolC and LolE N.D. 8 ( E. coli ATCC25922)0.125 ( E. coli ATCC25922 ΔtolC )32 ( Haemophilus influenza ATCC49247)>64 ( Pseudomonas aeruginosa PAO1)0.125 (Parent) >128 [LolC(G254V)] >128 [LolE(G195S)] >128 [LolE(P365C)] >128 [LolE(P367Y)] [58] Pyridineimidazole-containing compound 1 LolC and LolE N.D. 32 ( E. coli ATCC25922)0.25 ( E. coli ATCC25922 ΔtolC )2 ( Haemophilus influenza ATCC49247)>64 ( Pseudomonas aeruginosa PAO1)0.125 (Parent) >64 [LolC(N265K)] >64 [LolE(I59N)] 64 [LolE(P372L)] >64 [LolE(L371P)] [57] Pyridineimidazole-containing compound 2 LolC and N.D. 4 ( E. coli ATCC25922)<0.06 ( E. coli ATCC25922 ΔtolC )0.25 ( Haemophilus influenza ATCC49247)>64 ( Pseudomonas aeruginosa PAO1)<0.06 (Parent) >64 [LolC(N265K)] >64 [LolE(I59N)] 8 [LolE(P372L)] >64 [LolE(L371P)] [57] Pyrrolopyrimidinedione compound G507 LolCDE N.D. >64 ( E. coli MG1655)0.5 ( E. coli MG1655 ΔtolC )1 ( E. coli MG1655imp4213 )16 (TQ/he MIC of G0793 against E. coli MG1655)N.D. [59] The Lpt pathway Compound 1 and 2 LptB IC50=25 μM (compound 1) IC50=17 μM N.D. N.D. [63] 4-Phenylpyrrolocarba-zole derivatives, 1a and 1b LptB IC50=119 μM >100 ( E. coli MC4100) 25( E. coli NR698)N.D. [64] Peptidomimetic compound L27-11 LptD N.D. 0.01 ( Pseudomonas aeruginosa ATCC27853)0.004 ( Pseudomonas aeruginosa PAO1)0.06 (Parent) >64 (Duplication of residues 210-215 of LptD) [68] β-hairpin-shaped peptidomimetic compound LB-01 LptD N.D. 0.008 ( Pseudomonas aeruginosa ATCC27853)0.015 ( Pseudomonas aeruginosa PAO1)N.D. [71] β-hairpin-shaped peptidomimetic compound Dab4NMe LptD N.D. 0.005 ( Pseudomonas aeruginosa ATCC27853)0.009 ( Pseudomonas aeruginosa PAO1)N.D. [71] The BAM pathway β-hairpin macrocyclic peptide JB-95 BamA and LptD N.D. 0.25 ( E. coli ATCC25922)1 ( Acinetobacter baumannii ATCC17978)4 ( Pseudomonas aeruginosa PAO1)2 ( Staphylococcus aureus ATCC29213)N.D. [73] aThe half maximal inhibitory concentration..
bNot determined..
Inhibitors of LPS Transport
Chemicals inhibiting the ATPase activity of the ATPase component LptB of the LptB2CFG complex were screened by a continuous assay that couples ATP hydrolysis to NADH oxidation [63]. Two compounds, 1 and 2, that have different structural classes, inhibited the ATPase activity of LptB with an IC50 of 25 and 17 μM, respectively [63]. The value of the MICs of these compounds was not determined. In 2013, other inhibitors of LptB were identified by the same biochemical assay, the continuous assay coupling ATP hydrolysis to NADH oxidation [64]. A compound 4-phenylpyrrolocarbazole derivative that had previously been known as a potent inhibitor of a eukaryotic kinase Wee1, which regulates mitosis entry [65], was identified as an inhibitor of LptA [64]. Several derivatives of 4- phenylpyrrolocarbazole were additionally tested for inhibition of the ATPase activity of LptB. Compounds 1a and 1b showed a weak antimicrobial activity (MIC of >100 μg/ml) against the
Several β-hairpin-shaped peptidomimetics (small protein- like chains designed to mimic a peptide) targeting the β- barrel OM protein LptD were developed by optimization of peptidomimetics based on the antimicrobial peptide protegrin I (PG-I) [66]. PG-I is a broad-spectrum antimicrobial peptide against Gram-negative and Gram-positive bacteria [67], but optimized peptidomimetics, L26-19 and L27-11, display a narrow-spectrum antimicrobial effect only against
Inhibitors of OMP Transport
One study investigated an inhibitor that targets the BAM complex. Similar to L27-11, a β-hairpin macrocyclic peptidomimetic JB-95 was identified as an inhibitor of β-barrel OM proteins BamA and LptD [73]. JB-95 induced no cellular lytic activity like L27-11, but selectively disrupted the OM integrity, but not the IM, and induced rapid depletion of β-barrel OM proteins [73]. Photolabeling experiments revealed the interaction of JB-96 with BamA and LptD. The MICs of JB-95 against
Upon the revelation of a more complete picture of the transport system of OM components, the possibility of developing antimicrobial agents targeting OM transport machines was examined. The most successful case is Murepavadin, an L27-11-based peptidomimetic inhibitor of LptD, which has successfully completed phase-II clinical trials [72]. Because several additional optimization procedures of L27-11 have been suggested [70, 71], there is the possibility of developing more potent antimicrobial agents. Although there have been various attempts at developing new antibiotics targeting the Lol system, an inhibitor with an MIC in the nanomolar range has not yet been developed. The high-throughput screen of inhibitors based on peptidomimetics may be useful for the development of inhibitors of the Lol system. Because the transport system of phospholipids from the IM to the OM remains undetermined, extensive studies are required in this field. The phospholipid transport system has potential to be a novel target for the development of new antimicrobial agents against Gram-negative bacteria.
Acknowledgements
This work was supported by research grants from the Advanced Biomass R&D Center (ABC) of the Global Frontier Project funded by the Ministry of Science, ICT and Future Planning (ABC-2015M3A6A2065700), and the Bio & Medical Technology Development Program of the NRF funded by the Korean government, MSIT (NRF-2017M3A9E4078017).
Conflict of Interest
The authors have no financial conflicts of interest to declare.
Fig 1.
-
Table 1 . Antimicrobial inhibitors targeting the OM assembly machines..
Assembly machine Inhibitor Cellular target IC50a MIC (μg/ml) MIC in the resistant mutant Reference The Lol pathway CCT-00431 and CCT-00432 LolA N.D.b 16 ( E. coli NIHJ JC-2)8 ( E. coli M101)8 (Parent) 32 or 128 (Δ lpp )[53] MAC13243 LolA N.D. 16 ( E. coli ATCC25922)4 ( Pseudomonas aeruginosa PAO1)N.D. [54] S -(4-chlorobenzyl)iso-thiourea andS -(3,4-dichlorobenzyl)iso-thiourea (A22)LolA IC50=150 μM [ S -(4-chlo-robenzyl)isothiourea]IC50=200 μM (A22) 2 ( E. coli MG1655)N.D. [55] Pyrazole-containing compound LolC and LolE N.D. 8 ( E. coli ATCC25922)0.125 ( E. coli ATCC25922 ΔtolC )32 ( Haemophilus influenza ATCC49247)>64 ( Pseudomonas aeruginosa PAO1)0.125 (Parent) >128 [LolC(G254V)] >128 [LolE(G195S)] >128 [LolE(P365C)] >128 [LolE(P367Y)] [58] Pyridineimidazole-containing compound 1 LolC and LolE N.D. 32 ( E. coli ATCC25922)0.25 ( E. coli ATCC25922 ΔtolC )2 ( Haemophilus influenza ATCC49247)>64 ( Pseudomonas aeruginosa PAO1)0.125 (Parent) >64 [LolC(N265K)] >64 [LolE(I59N)] 64 [LolE(P372L)] >64 [LolE(L371P)] [57] Pyridineimidazole-containing compound 2 LolC and N.D. 4 ( E. coli ATCC25922)<0.06 ( E. coli ATCC25922 ΔtolC )0.25 ( Haemophilus influenza ATCC49247)>64 ( Pseudomonas aeruginosa PAO1)<0.06 (Parent) >64 [LolC(N265K)] >64 [LolE(I59N)] 8 [LolE(P372L)] >64 [LolE(L371P)] [57] Pyrrolopyrimidinedione compound G507 LolCDE N.D. >64 ( E. coli MG1655)0.5 ( E. coli MG1655 ΔtolC )1 ( E. coli MG1655imp4213 )16 (TQ/he MIC of G0793 against E. coli MG1655)N.D. [59] The Lpt pathway Compound 1 and 2 LptB IC50=25 μM (compound 1) IC50=17 μM N.D. N.D. [63] 4-Phenylpyrrolocarba-zole derivatives, 1a and 1b LptB IC50=119 μM >100 ( E. coli MC4100) 25( E. coli NR698)N.D. [64] Peptidomimetic compound L27-11 LptD N.D. 0.01 ( Pseudomonas aeruginosa ATCC27853)0.004 ( Pseudomonas aeruginosa PAO1)0.06 (Parent) >64 (Duplication of residues 210-215 of LptD) [68] β-hairpin-shaped peptidomimetic compound LB-01 LptD N.D. 0.008 ( Pseudomonas aeruginosa ATCC27853)0.015 ( Pseudomonas aeruginosa PAO1)N.D. [71] β-hairpin-shaped peptidomimetic compound Dab4NMe LptD N.D. 0.005 ( Pseudomonas aeruginosa ATCC27853)0.009 ( Pseudomonas aeruginosa PAO1)N.D. [71] The BAM pathway β-hairpin macrocyclic peptide JB-95 BamA and LptD N.D. 0.25 ( E. coli ATCC25922)1 ( Acinetobacter baumannii ATCC17978)4 ( Pseudomonas aeruginosa PAO1)2 ( Staphylococcus aureus ATCC29213)N.D. [73] aThe half maximal inhibitory concentration..
bNot determined..
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