Tryptophan interferes with the quorum sensing and cell surface hydrophobicity of Staphylococcus aureus: a promising approach to inhibit the biofilm development

Enhanced Efficacy of Ciprofloxacin and Tobramycin against Staphylococcus aureus When Combined with Corydalis Tuber and Berberine through Efflux Pump Inhibition

One way that bacteria develop antibiotic resistance is by reducing intracellular antibiotic concentrations through efflux pumps. Therefore, enhancing the efficacy of antibiotics using efflux pump inhibitors provides a way to overcome this type of resistance. Notably, an increasing number of pathogenic Staphylococcus aureus strains have efflux pump genes. In this study, the extract from Corydalis ternata Nakai tuber (Corydalis Tuber) at 512 mg/L was demonstrated to have an antibiotic synergistic effect with ciprofloxacin at 2 mg/L and tobramycin at 1024 mg/L against methicillin-resistant S. aureus (MRSA). Berberine, an isoquinoline alkaloid identified in Corydalis Tuber, was identified as contributing to this effect. Ethidium bromide efflux pump activity assays showed that Corydalis Tuber extract and berberine inhibited efflux, suggesting that they are efflux pump inhibitors. Molecular docking simulations suggested that berberine binds to S. aureus efflux pump proteins MepA, NorA, NorB, and SdrM. Additionally, berberine and Corydalis Tuber extract inhibit biofilm formation, which can confer antibiotic resistance. This study's findings suggest that Corydalis Tuber, a traditional herbal medicine, and berberine, a medicinal supplement, act as S. aureus efflux pump inhibitors, synergistically increasing the efficacy of ciprofloxacin and tobramycin and showing promise as a treatment for antibiotic-resistant S. aureus infections, including MRSA.

Application of cuminaldehyde and ciprofloxacin for the effective control of biofilm assembly of Pseudomonas aeruginosa: A combinatorial study

Pseudomonas aeruginosa is widely associated with biofilm-mediated antibiotic resistant chronic and acute infections which constitute a persistent healthcare challenges. Addressing this threat requires exploration of novel therapeutic strategies involving the combination of natural compounds and conventional antibiotics. Hence, our study has focused on two compounds; cuminaldehyde and ciprofloxacin, which were strategically combined to target the biofilm challenge of P. aeruginosa. The minimum inhibitory concentration (MIC) of cuminaldehyde and ciprofloxacin was found to be 400 μg/mL and 0.4 μg/mL, respectively. Moreover, the fractional inhibitory concentration index (FICI = 0.62) indicated an additive interaction prevailed between cuminaldehyde and ciprofloxacin. Subsequently, sub-MIC doses of cuminaldehyde (25 μg/mL) and ciprofloxacin (0.05 μg/mL) were selected for an array of antibiofilm assays which confirmed their biofilm inhibitory potential without exhibiting any antimicrobial activity. Furthermore, selected doses of the mentioned compounds could manage biofilm on catheter surface by inhibiting and disintegrating existing biofilm. Additionally, the test combination of the mentioned compounds reduced virulence factors secretion, accumulated reactive oxygen species and increased cell-membrane permeability. Thus, the combination of cuminaldehyde and ciprofloxacin demonstrates potential in combating biofilm-associated Pseudomonal threats.

Synthesis and molecular docking study of α-aminophosphonates as potential multi-targeting antibacterial agents

Antibacterial compounds that reduce extracellular polymeric substances (EPS) are needed to avoid bacterial biofilms in water pipelines. Herein, green one-pot synthesis of α-aminophosphonates (α-Amps) [A-G] was achieved by using ionic liquid (IL) as a Lewis acid catalyst. The synthesized α-Amp analogues were tested against different bacteria such as Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa. The representative [B] analogue showed an efficient antibacterial effect with MIC values of 3.13 μg/mL for E. coli, P. aeruginosa, and 6.25 μg/mL for B. subtilis. Additionally, a strong ability to eliminate the mature bacterial biofilm, with super-MIC values of 12.5 μg/mL for E. coli, P. aeruginosa, and 25 μg/mL for B. subtilis. Moreover, bacterial cell disruption by ROS formation was also tested, and the compound [B] revealed the highest ROS level compared to other compounds and the control, and efficiently destroyed the extracellular polymeric substances (EPS). The docking study confirmed strong interactions between [B] analogue and protein structures with a binding affinity of -6.65 kCal/mol for the lyase protein of gram-positive bacteria and -6.46 kCal/mol for DNA gyrase of gram-negative bacteria. The results showed that α-Amps moiety is a promising candidate for developing novel antibacterial and anti-biofilm agents for clean water supply.

Elucidating the pivotal role of TSPO in porphyrin-related cellular processes, in Bacillus cereus

A structural homolog of the mammalian TSPO has been identified in the human pathogen Bacillus cereus. BcTSPO, in its recombinant form, has previously been shown to bind and degrade porphyrins. In this study, we generated a ΔtspO mutant strain in B. cereus ATCC 14579 and assessed the impact of the absence of BcTSPO on cellular proteomics and physiological characteristics. The proteomic analysis revealed correlations between the lack of BcTSPO and the observed growth defects, increased oxygen consumption, ATP deficiency, heightened tryptophan catabolism, reduced motility, and impaired biofilm formation in the ΔtspO mutant strain. Our results also suggested that BcTSPO plays a crucial role in regulating intracellular levels of metabolites from the coproporphyrin-dependent branch of the heme biosynthetic pathway. This regulation potentially underlies alterations in the metabolic landscape, emphasizing the pivotal role of BcTSPO in B. cereus aerobic metabolism. Notably, our study unveils, for the first time, the involvement of TSPO in tryptophan metabolism. These findings underscore the multifaceted role of TSPO, not only in metabolic pathways but also potentially in the microorganism's virulence mechanisms.

Design of a novel analogue peptide with potent antibiofilm activities against Staphylococcus aureus based upon a sapecin B-derived peptide

Nowadays, antimicrobial peptides are promising to confront the existing global crisis of antibiotic resistance. Here, a novel analogue peptide (mKLK) was designed based upon a D-form amidated sapecin B-derived peptide (KLK) by replacing two lysine residues with two tryptophan and one leucine by lysine, and inserting one alanine. The mKLK displayed superior amphipathic helixes in which the most of hydrophobic residues are confined to one face of the helix and had a higher hydrophobic moment compared with KLK. The mKLK retained its antibacterial activity and structure in human serum, suggesting its stability to proteolytic degradation. The values of MIC and MBC for mKLK were equal to those of KLK against clinical strains of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA). However, mKLK showed more capability of in vitro inhibiting, eradicating, and dispersing MRSA and MSSA biofilms compared with KLK. Furthermore, a remarkable inhibitory activity of mKLK against MRSA and MSSA biofilms was seen in the murine model of catheter-associated biofilm infection. Results of this study show that mKLK not only exhibits antibacterial activity and serum stability but also a potent biofilm inhibitory activity at sub-MIC concentrations, confirming its potential therapeutic advantage for preventing biofilm-associated MRSA and MSSA infections.

Regulation of σB-Dependent Biofilm Formation in Staphylococcus aureus through Strain-Specific Signaling Induced by Diosgenin

Staphylococcus aureus is a commensal skin bacterium and a causative agent of infectious diseases. Biofilm formation in S. aureus is a mechanism that facilitates the emergence of resistant strains. This study proposes a mechanism for the regulation of biofilm formation in S. aureus through strain-specific physiological changes induced by the plant steroid diosgenin. A comparison of diosgenin-induced changes in the expression of regulatory genes associated with physiological changes revealed the intracellular regulatory mechanisms involved in biofilm formation. Diosgenin reduced biofilm formation in S. aureus ATCC 6538 and methicillin-resistant S. aureus (MRSA) CCARM 3090 by 39% and 61%, respectively. Conversely, it increased biofilm formation in S. aureus ATCC 29213 and MRSA CCARM 3820 by 186% and 582%, respectively. Cell surface hydrophobicity and extracellular protein and carbohydrate contents changed in a strain-specific manner in response to biofilm formation. An assessment of the changes in gene expression associated with biofilm formation revealed that diosgenin treatment decreased the expression of icaA and spa and increased the expression of RNAIII, agrA, sarA, and sigB in S. aureus ATCC 6538 and MRSA CCARM 3090; however, contrasting gene expression changes were noted in S. aureus ATCC 29213 and MRSA CCARM 3820. These results suggest that a regulatory mechanism of biofilm formation is that activated sigB expression sequentially increases the expression of sarA, agrA, and RNAIII. This increased RNAIII expression decreases the expression of spa, a surface-associated adhesion factor. An additional regulatory mechanism of biofilm formation is that activated sigB expression decreases the expression of an unknown regulator that increases the expression of icaA. This in turn decreases the expression of icaA, which decreases the synthesis of polysaccharide intercellular adhesins and ultimately inhibits biofilm formation. By assessing strain-specific contrasting regulatory signals induced by diosgenin in S. aureus without gene mutation, this study elucidated the signal transduction mechanisms that regulate biofilm formation based on physiological and gene expression changes.

Identification of inhibitors for Agr quorum sensing system of Staphylococcus aureus by machine learning, pharmacophore modeling, and molecular dynamics approaches

CONTEXT

Staphylococcus aureus is a highly pathogenic organism that is the most common cause of postoperative complications as well as severe infections like bacteremia and infective endocarditis. By mediating the formation of biofilms and the expression of virulent genes, the quorum sensing (QS) mechanism is a major contributor to the development of these diseases. By hindering its QS network, an innovative approach to avoiding this bacterial infection is taken. Targeting the AgrA of the Agr system serves as beneficial in holding the top position in the QS system cascade.

METHODS

Using known AgrA inhibitors, the machine learning algorithms (artificial neural network, naïve Bayes, random forest, and support vector machine) and pharmacophore model were developed. The potential lead compounds were screened against the Zinc and COCONUT databases using the best pharmacophore hypothesis. The hits were then subjected second screening process using the best machine learning model. The predicted active compounds were then reranked based on the docking score. The stability of AgrA-lead compounds was studied using molecular dynamics approaches, and an ADME profile was also carried out. Five lead compounds, namely, CNP02386963,4,5-trihydroxy-2-[({7,13,14-trihydroxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.04,16.011,15]hexadeca-1(14),4,6,8(16),11(15),12-hexaen-6-yl}oxy)methyl]benzoic acid, CNP0129274 4-(dimethylamino)-1,5,6,10,12,12a-hexahydroxy-6-methyl-3,11-dioxo-3,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, CNP0242717 3-Hydroxyasebotin, CNP0361624 3,4,5-trihydroxy-6-[(2,4,5,6,7-pentahydroxy-1-oxooctan-3-yl)oxy]oxane-2-carboxylic acid, and CNP0285058 2-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]oxan-2-yl]oxy}-2-(4-hydroxyphenyl)acetonitrile were obtained using the two-step virtual screening process. The molecular dynamics study revealed that the CNP0238696 was found to be stable in the binding pocket of AgrA. ADME profiles show that this compound has two Lipinski violations and low bioavailability. Further studies should be performed to assess the anti-biofilm activity of the lead compound in vitro.

Piperine Exhibits Potential Antibiofilm Activity Against Pseudomonas aeruginosa by Accumulating Reactive Oxygen Species, Affecting Cell Surface Hydrophobicity and Quorum Sensing

Gram-positive and Gram-negative bacteria often develop biofilm through different mechanisms in promoting pathogenicity. Hence, the antibiofilm molecule needs to be examined separately on both organisms to manage the biofilm threat. Since the antibiofilm activity of piperine against Staphylococcus aureus was already reported; here, we aimed to examine the antibiofilm activity of it against Pseudomonas aeruginosa. P. aeruginosa is an opportunistic Gram-negative pathogen that can cause several healthcare-associated infections by exploiting biofilm. Several experiments like crystal violet assay, estimation of total protein, measurement of extracellular polymeric substance, and microscopic analysis confirmed that lower concentrations (8 and 16 µg/mL) of piperine could inhibit the microbial biofilm formation considerably. Besides, it could also reduce the secretion of virulence factors from P. aeruginosa. Further investigation showed that the cell surface hydrophobicity and microbial motility of the test organism got reduced under the influence of piperine. Piperine exposure was found to increase the accumulation of reactive oxygen species (ROS) that resulted in the inhibition of biofilm formation. Furthermore, the molecular simulation studies suggested that piperine could affect the quorum sensing network of P. aeruginosa. Towards this direction, we noticed that piperine treatment could decrease the expression of the quorum sensing gene (lasI) that resulted in the inhibition of biofilm formation. Besides biofilm inhibition, piperine was also found to disintegrate the pre-existing biofilm of P. aeruginosa without showing any antimicrobial property to the test organism. Thus, piperine could be used for the sustainable protection of public-healthcare by compromising the biofilm assembly of P. aeruginosa.

Immobilized arginine/tryptophan-rich cyclic dodecapeptide on reduced graphene oxide anchored with manganese dioxide for microbial biofilm eradication

To avoid the accumulation of bacterial biofilms in water pipelines, it is critical to develop potent antimicrobial agents with good ability to reduce extracellular polymeric substances (EPS). In this study, cyclic dodecapeptides were synthesized, and different mutations for increasing the ratio of arginine (Arg) and tryptophan (Trp) were introduced. Separately, the synthesized dodecapeptides were immobilized on a reduced graphene oxide nanocomposite anchored with a hierarchical β-MnO₂ (RGO/β-MnO₂) hybrid. With a minimum inhibitory concentration of 0.97 g/mL, the immobilized Arg-Trp rich antimicrobial peptides (AMP) on RGO/MnO₂ nanocomposite, Cdp-4/RGO/MnO₂, showed superior efficacy against multidrug-resistant Pseudomonas aeruginosa ATCC 15692 (P. aeruginosa) planktonic cells. The immobilized Cdp-4/RGO/β-MnO₂ also eradicated the mature biofilm by 99% with a minimum inhibitory concentration value of 62.5 µg/mL with significant reduction of EPS. These characteristics allow the use of the immobilized Arg-Trp rich AMP as a promising antimicrobial agent against microbial biofilms, present in water distribution systems.