Targeting Bacterial Membranes: Identification of <i>Pseudomonas aeruginosa</i><scp>D</scp>‐Arabinose‐5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties

Airoldi, Cristina; Sommaruga, Silvia; Merlo, Silvia; Sperandeo, Paola; Cipolla, Laura; Polissi, Alessandra; Nicotra, Francesco

doi:10.1002/cbic.201000754

Cited by 26 publications

(12 citation statements)

References 43 publications

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“…1 H NMR-STD spectra clearly indicate that, in both cases, positions 1 and 3 are the most important for enzyme interactions as previously demon- strated for natural substrates. In addition, STD competitive binding experiments [16] performed in the presence of the natural substrates indicated that compounds 1 and 3 compete for enzyme binding with A5P and Ru5P suggestive of active-site binding by 1 and 3. In the case of compound 3 evaluation of the position 6 contribution to binding was not possible due to the absence of protons at the 6 position.…”

Section: Nmr Experimentsmentioning

confidence: 98%

“…Previous NMR studies of API [16] by our group showed that the acidic phosphate group is fundamental to enzyme binding. In particular, we speculate that a salt bridge between the negatively charged phosphate and a complementary basic residue in the catalytic pocket is the key interaction between substrate and enzyme.…”

Section: Introductionmentioning

confidence: 95%

“…[16,27] The presence of 1 H NMR signals corresponding to the tested compounds in the STD spectra is non-ambiguous evidence of enzyme binding. [16,27] The presence of 1 H NMR signals corresponding to the tested compounds in the STD spectra is non-ambiguous evidence of enzyme binding.…”

Section: Nmr Experimentsmentioning

confidence: 99%

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Phosphonate Analogues of Arabinose 5‐Phosphate: Putative Ligands for Arabinose 5‐Phosphate Isomerases

Gabrielli¹,

Airoldi²,

Sperandeo³

et al. 2013

Eur J Org Chem

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Metabolically stable arabinose 5‐phosphate analogues possessing phosphate mimetic groups at the 5‐position were synthesized and evaluated by saturation‐transfer‐difference (STD) NMR studies for their ability to interact with arabinose 5‐phosphate isomerase. Isosteric methylphosphonate 1 and (difluoromethyl)phosphonate 3 were recognised and bound by the catalytic pocket of the enzyme. The synthesized compounds were tested in vivo on E. coli and P. aeruginosa strains in order to evaluate their antibacterial activity.

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Section: Nmr Experimentsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 95%

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Phosphonate Analogues of Arabinose 5‐Phosphate: Putative Ligands for Arabinose 5‐Phosphate Isomerases

Gabrielli¹,

Airoldi²,

Sperandeo³

et al. 2013

Eur J Org Chem

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“…KdsD, the arabinose 5‐phosphate isomerase catalyzing the first step in the synthesis of Kdo, has also been investigated as a molecular target to design novel antimicrobials . Compounds able to inhibit KdsD activity have been rationally designed based on the available crystal structure of KdsD catalytic domain, and on the determination of KdsD structural requirements for substrate recognition and binding . While able to inhibit KdsD activity in vitro, none of the compounds displayed a significant MIC (minimal inhibitory concentration) against a selected panel of Gram‐negative pathogens, strongly suggesting that these molecules are not able to permeate across the OM.…”

Section: Targeting Lps Biogenesis Pathway For the Discovery Of Novel mentioning

confidence: 99%

Fat Matters for Bugs: How Lipids and Lipid Modifications Make the Difference in Bacterial Life

Sperandeo

Polissi

Fabiani

2019

Euro J Lipid Sci & Tech

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Lipids are building blocks of biological membranes in the three domains of life and are endowed with several important biological functions. Lipopolysaccharide (LPS) is a peculiar glycolipid that represents the hallmark of the cell envelope of Gram‐negative bacteria, a group comprising several important human pathogens. The presence of LPS in the outer membrane (OM) of Gram‐negative bacteria correlates not only with the intrinsic resistance of this group of bacteria toward several antibiotics currently in use, but also with the worrisome increase in antibiotic resistance that is depleting the arsenal of efficacious molecules to cure bacterial infections. LPS consists of a conserved internal moiety decorated by a more variable distal unit. Several modifications occur at the canonical LPS structure during bacterial infection which are exploited by the microorganism to co‐evolve with the host thus evading its immune system. This viewpoint article discusses the current knowledge on LPS biogenesis and modification systems and their consequences on recognition by immune cells and antimicrobial resistance. It also discusses how knowledge on LPS biogenesis can be exploited to develop molecules able to dismantle the Gram‐negative protective barrier and to interfere with the interaction with the mammalian host. Practical Applications: Antibiotic resistance is a major threat for human health leading to inefficacy of many antibiotics to treat infectious diseases. Resistance to antibiotics causes around 25 000 deaths per year in the European Union alone and 700 000 deaths per year globally. This results in an increase of 1.5 billion euros per year in healthcare costs and productivity losses for illness. Gram‐negative bacteria are intrinsically resistant to many antibiotics, due to their LPS‐coated cell surface that protects them from the environment. LPS is sensed by the host immune system as a signal of bacterial infection, moreover bacteria exploit the complexity of LPS modifications to modulate the host immune response and eventually escape it. A deep understanding of the molecular mechanisms underlying LPS biogenesis, including the physico‐chemical and biological consequences of its lipid modifications, will be instrumental to develop novel antibiotic treatments aimed at dismantling the Gram‐negative bacteria barrier and restoring drug sensitivity. The hallmark of Gram‐negative bacteria is the presence of an asymmetric outer membrane (OM) surrounding the cytoplasmic membrane (inner membrane, IM), whose outer leaflet is made by lipopolysaccharide (LPS). A layer of peptidoglycan (PG) is sandwiched in between. LPS endows the bacteria with increased resistance to many antibiotics and is the first line of interaction with the host cell immune system. Chemical modifications of the canonical LPS structure determine different stimulatory effects of the immune response and allow the bacteria to escape from the killing action of effector molecules such as antimicrobial peptides.

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“…These components are synthesized in the cytoplasm or in the IM, and are then selectively transported to the OM by specific transport machines. Recent reviews on the transport and assembly systems of OM components have been published with the aim of developing inhibitors targeting these systems [ 21 , 22 , 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

Amphiphilic Aminoglycosides as Medicinal Agents

Dezanet

Kempf

Mingeot‐Leclercq

et al. 2020

IJMS

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The conjugation of hydrophobic group(s) to the polycationic hydrophilic core of the antibiotic drugs aminoglycosides (AGs), targeting ribosomal RNA, has led to the development of amphiphilic aminoglycosides (AAGs). These drugs exhibit numerous biological effects, including good antibacterial effects against susceptible and multidrug-resistant bacteria due to the targeting of bacterial membranes. In the first part of this review, we summarize our work in identifying and developing broad-spectrum antibacterial AAGs that constitute a new class of antibiotic agents acting on bacterial membranes. The target-shift strongly improves antibiotic activity against bacterial strains that are resistant to the parent AG drugs and to antibiotic drugs of other classes, and renders the emergence of resistant Pseudomonas aeruginosa strains highly difficult. Structure–activity and structure–eukaryotic cytotoxicity relationships, specificity and barriers that need to be crossed in their development as antibacterial agents are delineated, with a focus on their targets in membranes, lipopolysaccharides (LPS) and cardiolipin (CL), and the corresponding mode of action against Gram-negative bacteria. At the end of the first part, we summarize the other recent advances in the field of antibacterial AAGs, mainly published since 2016, with an emphasis on the emerging AAGs which are made of an AG core conjugated to an adjuvant or an antibiotic drug of another class (antibiotic hybrids). In the second part, we briefly illustrate other biological and biochemical effects of AAGs, i.e., their antifungal activity, their use as delivery vehicles of nucleic acids, of short peptide (polyamide) nucleic acids (PNAs) and of drugs, as well as their ability to cleave DNA at abasic sites and to inhibit the functioning of connexin hemichannels. Finally, we discuss some aspects of structure–activity relationships in order to explain and improve the target selectivity of AAGs.

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Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosaD‐Arabinose‐5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties

Cited by 26 publications

References 43 publications

Phosphonate Analogues of Arabinose 5‐Phosphate: Putative Ligands for Arabinose 5‐Phosphate Isomerases

Phosphonate Analogues of Arabinose 5‐Phosphate: Putative Ligands for Arabinose 5‐Phosphate Isomerases

Fat Matters for Bugs: How Lipids and Lipid Modifications Make the Difference in Bacterial Life

Amphiphilic Aminoglycosides as Medicinal Agents

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