Discovery of Antibacterial Agents Inhibiting the Energy-Coupling Factor (ECF) Transporters by Structure-Based Virtual Screening

Here, we report on the virtual screening, design, synthesis and structure–activity relationships (SARs) of the first class of selective, antibacterial agents against the energy-coupling factor (ECF) transporters. The ECF transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. Because of their central role in the metabolism of bacteria and their absence in humans, ECF transporters are novel potential antimicrobial targets to tackle infection. The hit compound’s metabolic and plasma stability, the potency (20, MIC Streptococcus pneumoniae = 2 µg/mL), the absence of cytotoxicity and a lack of resistance development under the conditions tested here suggest that this scaffold may represent a promising starting point for the development of novel antimicrobial agents with an unprecedented mechanism of action.<br>

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Discovery of Antibacterial Agents Inhibiting the Energy-Coupling Factor (ECF) Transporters by Structure-Based Virtual Screening

10.26434/chemrxiv.11728710.v1 ◽

2020 ◽

Author(s):

Eleonora Diamanti ◽

Inda Setyawati ◽

Spyridon Bousis ◽

leticia mojas ◽

lotteke Swier ◽

...

Keyword(s):

Virtual Screening ◽

Antibacterial Agents ◽

Antimicrobial Agents ◽

Energy Coupling ◽

Coupling Factor ◽

Design Synthesis ◽

Screening Design ◽

Starting Point ◽

Wide Range ◽

Vitamin Uptake

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Targeting the energy-coupling factor (ECF) transporters: identification of new tool compounds

10.26434/chemrxiv-2021-xq08b-v2 ◽

2021 ◽

Author(s):

Eleonora Diamanti ◽

Inda Setyawati ◽

Spyridon Bousis ◽

Paulo C. T. Souza ◽

leticia mojas ◽

...

Keyword(s):

Energy Coupling ◽

Coupling Factor ◽

Coarse Grained ◽

Design Synthesis ◽

Screening Design ◽

Wide Range ◽

Pharmaceutical Properties ◽

Vitamin Uptake ◽

Dynamics Simulations ◽

Chemical Class

The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. Their central role in the metabolism of bacteria and absence in humans make the ECF transporters a potential antibacterial target, which can be further investigated making use of a selective chemical probe. Here, we report on the virtual screening, design, synthesis, structure–activity relationships (SARs) and coarse-grained molecular dynamics simulations of the first class of inhibitors of the ECF transporters. We investigated the mechanism of action of this chemical class and profiled the best hit compounds regarding their pharmaceutical properties. The optimized hit has a minimum inhibitory concentration (MIC) value of 2 µg/mL against Streptococcus pneumoniae, which opens up the possibility to use this chemical class to investigate the role of the ECF transporters in health and disease.

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Scorpion Venom Antimicrobial Peptides Induce Siderophore Biosynthesis and Oxidative Stress Responses in Escherichia coli

mSphere ◽

10.1128/msphere.00267-21 ◽

2021 ◽

Vol 6 (3) ◽

Author(s):

Mohamed M. Tawfik ◽

Magnus Bertelsen ◽

Mohamed A. Abdel-Rahman ◽

Peter N. Strong ◽

Keith Miller

Keyword(s):

Escherichia Coli ◽

Antimicrobial Peptides ◽

Antimicrobial Agents ◽

Venom Gland ◽

Cation Transport ◽

Content Type ◽

Starting Point ◽

Wide Range ◽

Initial Starting ◽

Increased Susceptibility

ABSTRACT The increasing development of microbial resistance to classical antimicrobial agents has led to the search for novel antimicrobials. Antimicrobial peptides (AMPs) derived from scorpion and snake venoms offer an attractive source for the development of novel therapeutics. Smp24 (24 amino acids [aa]) and Smp43 (43 aa) are broad-spectrum AMPs that have been identified from the venom gland of the Egyptian scorpion Scorpio maurus palmatus and subsequently characterized. Using a DNA microarray approach, we examined the transcriptomic responses of Escherichia coli to subinhibitory concentrations of Smp24 and Smp43 peptides following 5 h of incubation. Seventy-two genes were downregulated by Smp24, and 79 genes were downregulated by Smp43. Of these genes, 14 genes were downregulated in common and were associated with bacterial respiration. Fifty-two genes were specifically upregulated by Smp24. These genes were predominantly related to cation transport, particularly iron transport. Three diverse genes were independently upregulated by Smp43. Strains with knockouts of differentially regulated genes were screened to assess the effect on susceptibility to Smp peptides. Ten mutants in the knockout library had increased levels of resistance to Smp24. These genes were predominantly associated with cation transport and binding. Two mutants increased resistance to Smp43. There was no cross-resistance in mutants resistant to Smp24 or Smp43. Five mutants showed increased susceptibility to Smp24, and seven mutants showed increased susceptibility to Smp43. Of these mutants, formate dehydrogenase knockout (fdnG) resulted in increased susceptibility to both peptides. While the electrostatic association between pore-forming AMPs and bacterial membranes followed by integration of the peptide into the membrane is the initial starting point, it is clear that there are numerous subsequent additional intracellular mechanisms that contribute to their overall antimicrobial effect. IMPORTANCE The development of life-threatening resistance of pathogenic bacteria to the antibiotics typically in use in hospitals and the community today has led to an urgent need to discover novel antimicrobial agents with different mechanisms of action. As an ancient host defense mechanism of the innate immune system, antimicrobial peptides (AMPs) are attractive candidates to fill that role. Scorpion venoms have proven to be a rich source of AMPs. Smp24 and Smp43 are new AMPs that have been identified from the venom gland of the Egyptian scorpion Scorpio maurus palmatus, and these peptides can kill a wide range of bacterial pathogens. By better understanding how these AMPs affect bacterial cells, we can modify their structure to make better drugs in the future.

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Local antibiotic therapy of bacterial infectious and inflammatory diseases of the anterior segment of the eye (literature review)

POINT OF VIEW EAST – WEST ◽

10.25276/2410-1257-2021-2-89-93 ◽

2021 ◽

pp. 89-93

Author(s):

A.E. Babushkin ◽

Keyword(s):

Antibacterial Agents ◽

Antimicrobial Agents ◽

High Efficiency ◽

Inflammatory Diseases ◽

Anterior Segment ◽

Eye Diseases ◽

Good Tolerability ◽

Wide Range ◽

Local Antibiotic ◽

Topical Antimicrobial

Inflammatory eye diseases are one of the most important problems of ophthalmology. They can be caused by various pathogens of the infection, which is still more often bacterial. Therapy of bacterial inflammatory diseases of the eye involves the use of antibacterial drugs (sulfonamides, antiseptics, nitrofurans, etc.), among which antibiotics are of primary importance. Of this group of drugs, in this review article, special attention is paid to quinolones, mainly synthetic fluoroquinolones, which are distinguished by a wide range of bactericidal action, fairly high efficiency, low level of resistance of microorganisms to it and the frequency of side effects, as well as good tolerability by patients, i.e. they best meet the requirements for modern topical antimicrobial agents. In certain clinical situations and indications, it is advisable to use ophthalmic antiseptics and combined preparations containing several antibiotics of different effects at once, or an antibiotic and a corticosteroid. Key words: infectious and inflammatory eye diseases, antibacterial agents, antibiotics, combined preparations, antiseptics.

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Two Essential Arginine Residues in the T Components of Energy-Coupling Factor Transporters

Journal of Bacteriology ◽

10.1128/jb.00965-09 ◽

2009 ◽

Vol 191 (21) ◽

pp. 6482-6488 ◽

Cited By ~ 34

Author(s):

Olivia Neubauer ◽

Anja Alfandega ◽

Janna Schoknecht ◽

Ulrich Sternberg ◽

Anne Pohlmann ◽

...

Keyword(s):

Atpase Activity ◽

Transmembrane Protein ◽

Energy Coupling ◽

Coupling Factor ◽

Single Mutation ◽

Modular Assembly ◽

Double Mutation ◽

Arginine Residues ◽

Uptake Activity ◽

Vitamin Uptake

ABSTRACT Energy-coupling factor (ECF) transporters, a recently discovered class of importers of micronutrients, are composed of a substrate-specific transmembrane component (S component) and a conserved energy-coupling module consisting of a transmembrane protein (T component) and pairs of ABC ATPases (A proteins). Based on utilization of a dedicated (subclass I) or shared (subclass II) energy-coupling module, ECF systems fall into two subclasses. The T components are the least-characterized proteins of ECF importers, and their function is essentially unknown. Using RcBioN and LmEcfT, the T units of the subclass I biotin transporter (RcBioMNY) of a gram-negative bacterium and of the subclass II folate, pantothenate, and riboflavin transporters of a lactic acid bacterium, respectively, we analyzed the role of two strongly conserved short motifs, each containing an arginine residue. Individual replacement of the two Arg residues in RcBioN reduced ATPase activity, an indicator of the transporter function, by two-thirds without affecting the modular assembly of the RcBioMNY complex. A double Arg-to-Glu replacement destroyed the complex and abolished ATPase activity. The corresponding single mutation in motif II of LmEcfT, as well as a double mutation, led to loss of the T unit from the subclass II ECF transporters and inactivated these systems. A single Arg-to-Glu replacement in motif I, however, abolished vitamin uptake activity without affecting assembly of the modules. Our results indicate that the conserved motif I in T components is essential for intramolecular signaling and, in cooperation with motif II, for subunit assembly of modular ECF transporters.

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Energy Coupling Factor-Type ABC Transporters for Vitamin Uptake in Prokaryotes

Biochemistry ◽

10.1021/bi300504v ◽

2012 ◽

Vol 51 (22) ◽

pp. 4390-4396 ◽

Cited By ~ 36

Author(s):

Guus B. Erkens ◽

Maria Majsnerowska ◽

Josy ter Beek ◽

Dirk Jan Slotboom

Keyword(s):

Abc Transporters ◽

Energy Coupling ◽

Coupling Factor ◽

Factor Type ◽

Vitamin Uptake

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A Novel Class of Modular Transporters for Vitamins in Prokaryotes

Journal of Bacteriology ◽

10.1128/jb.01208-08 ◽

2008 ◽

Vol 191 (1) ◽

pp. 42-51 ◽

Cited By ~ 181

Author(s):

Dmitry A. Rodionov ◽

Peter Hebbeln ◽

Aymerick Eudes ◽

Josy ter Beek ◽

Irina A. Rodionova ◽

...

Keyword(s):

Abc Transporters ◽

Transmembrane Protein ◽

Energy Coupling ◽

Coupling Factor ◽

Human Pathogens ◽

Gram Positive Bacteria ◽

New Class ◽

Vitamin Uptake ◽

Genome Context ◽

Nucleotide Binding Proteins

ABSTRACT The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have yet to be identified, including the vitamin transporters in various human pathogens, whose growth depends strictly on vitamin uptake. Comparative analysis of the ever-growing collection of microbial genomes coupled with experimental validation enables the discovery of such transporters. Here, we used this approach to discover an abundant class of vitamin transporters in prokaryotes with an unprecedented architecture. These transporters have energy-coupling modules comprised of a conserved transmembrane protein and two nucleotide binding proteins similar to those of ATP binding cassette (ABC) transporters, but unlike ABC transporters, they use small integral membrane proteins to capture specific substrates. We identified 21 families of these substrate capture proteins, each with a different specificity predicted by genome context analyses. Roughly half of the substrate capture proteins (335 cases) have a dedicated energizing module, but in 459 cases distributed among almost 100 gram-positive bacteria, including numerous human pathogens, different and unrelated substrate capture proteins share the same energy-coupling module. The shared use of energy-coupling modules was experimentally confirmed for folate, thiamine, and riboflavin transporters. We propose the name energy-coupling factor transporters for the new class of membrane transporters.

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Discovery of FtsZ inhibitors by virtual screening as antibacterial agents and study of the inhibition mechanism

RSC Medicinal Chemistry ◽

10.1039/d1md00249j ◽

2021 ◽

Author(s):

Ruo-Lan Du ◽

Ning Sun ◽

Yik-Hong Fung ◽

Yuanyuan Zheng ◽

Yu Wai Chen ◽

...

Keyword(s):

Cell Division ◽

Virtual Screening ◽

Bacterial Cell ◽

Drug Target ◽

Antibacterial Agents ◽

Antimicrobial Agents ◽

Inhibition Mechanism ◽

Bacterial Cell Division ◽

Ftsz Protein ◽

Ftsz Inhibitors

Inhibition of bacterial cell division is a novel mechanistic action in the development of new antimicrobial agents. The FtsZ protein is an important antimicrobial drug target because of its essential...

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Design, Synthesis and Antimicrobial Evaluation of Novel Benzimidazole-incorporated Naphthalimide Derivatives As Salmonella typhimurium DNA Intercalators, and Combination Researches

Medicinal Chemistry ◽

10.2174/1573406417666210712105922 ◽

2021 ◽

Vol 17 ◽

Author(s):

Zhi-Wei Ning ◽

Hui-Zhen Zhang ◽

Cheng-He Zhou

Keyword(s):

Salmonella Typhimurium ◽

Antimicrobial Agents ◽

Antimicrobial Activities ◽

Design Synthesis ◽

Reference Drug ◽

Naphthalic Anhydride ◽

Antimicrobial Efficiency ◽

Starting Point ◽

Clinical Drugs

Objective: A series of novel benzimidazole-incorporated naphthalimide derivatives were designed and prepared to overcome the increasing antibiotic resistance. Method: The target novel benzimidazole-incorporated naphthalimide derivatives were synthesized from commercial 4-bromo-1,8-naphthalic anhydride and o-phenylene diamine by aminolysis, N-alkylation, and so on. The antimicrobial activity of the synthesized compounds was evaluated in vitro by a two-fold serial dilution technique. The interaction of compound 10g with Salmonella typhimurium DNA was studied using UV-vis spectroscopic methods. Results: Compound 10g bearing a 2,4-dichlorobenzyl moiety exhibited the best antimicrobial activities in this series relatively, especially it gave the comparable action against Salmonella typhimurium compared to the reference drug Norfloxacin (MIC = 4 mg/mL). Further research showed that compound 10g could effectively intercalate into the Salmonella typhimurium DNA to form the 10g–DNA complex, which might correlate with the inhibitory activity. Molecular docking results demonstrated that naphthalimide compound 10g could interact with base-pairs of DNA hexamer duplex by p–p stacking. Additionally, the combinations of the solid active combination with clinical drugs gave better antimicrobial efficiency with less dosage and broader antimicrobial spectrum than the separated use alone. Notably, these combined systems were more sensitive to Fluconazole-insensitive M. ruber. Conclusion: This work opened up a good starting point to optimize the structures of benzimidazole-incorporated naphthalimide derivatives as potent antimicrobial agents.

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