Punicalagin, a pomegranate polyphenol sensitizes the activity of antibiotics against three MDR pathogens of the Enterobacteriaceae

BACKGROUND

Multidrug resistance (MDR) in the family Enterobacteriaceae is a perniciously increasing threat to global health security. The discovery of new antimicrobials having the reversing drug resistance potential may contribute to augment and revive the antibiotic arsenal in hand. This study aimed to explore the anti-Enterobacteriaceae capability of bioactive polyphenols from Punica granatum (P. granatum) and their co-action with antibiotics against clinical isolates of Enterobacteriaceae predominantly prevalent in South Asian countries.

METHODS

The Kandhari P. granatum (Pakistani origin) extracts were tested for anti-Enterobacteriaceae activity by agar well diffusion assay against MDR Salmonella enterica serovar Typhi, serovar Typhimurium and Escherichia coli. Predominant compounds of active extract were determined by mass spectrometry and screened for bioactivity by agar well diffusion and minimum inhibitory concentration (MIC) assay. The active punicalagin was further evaluated at sub-inhibitory concentrations (SICs) for coactivity with nine conventional antimicrobials using a disc diffusion assay followed by time-kill experiments that proceeded with SICs of punicalagin and antimicrobials.

RESULTS

Among all P. granatum crude extracts, pomegranate peel methanol extract showed the largest inhibition zones of 25, 22 and 19 mm, and the MICs as 3.9, 7.8 and 7.8 mg/mL for S. typhi, S. typhimurium and E. coli, respectively. Punicalagin and ellagic acid were determined as predominant compounds by mass spectrometry. In plate assay, punicalagin (10 mg/mL) was active with hazy inhibition zones of 17, 14, and 13 mm against S. typhi, S. typhimurium and E. coli, respectively. However, in broth dilution assay punicalagin showed no MIC up to 10 mg/mL. The SICs 30 μg, 100 μg, and 500 μg of punicalagin combined with antimicrobials i.e., aminoglycoside, β-lactam, and fluoroquinolone act in synergy against MDR strains with % increase in inhibition zone values varying from 3.4 ± 2.7% to 73.8 ± 8.4%. In time-kill curves, a significant decrease in cell density was observed with the SICs of antimicrobials/punicalagin (0.03-60 μg/mL/30, 100, 500 μg/mL of punicalagin) combinations.

CONCLUSIONS

The P. granatum peel methanol extract exhibited antimicrobial activity against MDR Enterobacteriaceae pathogens. Punicalagin, the bacteriostatic flavonoid act as a concentration-dependent sensitizing agent for antimicrobials against Enterobacteriaceae. Our findings for the therapeutic punicalagin-antimicrobial combination prompt further evaluation of punicalagin as a potent activator for drugs, which otherwise remain less or inactive against MDR strains.

Characterization of Salmonella enterica Biofilms and Antibiofilm Effect of Carvacrol and 2-Aminobenzimidazole

Biofilm-associated foodborne Salmonella infections in poultry have become increasingly challenging for veterinarians, particularly in developing countries, and warrant thorough investigation. We assessed the biofilm-forming tendency of poultry isolates of Salmonella enterica, namely Salmonella Typhimurium (n = 23), Salmonella Infantis (n = 28), and Salmonella Heidelberg (n = 18), in nutrient-rich Rappaport-Vassiliadis Soya (RVS) peptone broth and nutrient-deficient diluted Tryptone Soya Broth (TSB). Seven of the tested isolates exhibited moderate biofilm formation in diluted TSB, whereas two showed such formation in RVS. In addition, the Congo red agar assay revealed curli and cellulose production in seven isolates. Fourteen specific biofilm-associated genes were analyzed identifying sdiA and seqA to be the most prevalent (100%), and glyA the least prevalent (69.5%). The prevalence of the genes bcsA and csgA was significantly lower in moderate and weak biofilm formers, respectively, as compared with nonbiofilm formers in RVS peptone broth. Furthermore, the compounds carvacrol and 2-aminobenzimidazole (2-ABI) effectively inhibited biofilm formation by Salmonella serovars in RVS peptone and TSB media, respectively. Whereas the antibiofilm activity of 2-ABI against Salmonella has not been reported previously, we determined its most effective concentration at 1.5 mM among tested antibiofilm treatments. These findings indicate that Salmonella strains prevalent in poultry farms have the potential to form biofilms, and the tested compounds should be further explored as supportive or alternative antimicrobials.

Genomic characterization and comparative genomic analysis of HS-associated Pasteurella multocida serotype B:2 strains from Pakistan

BACKGROUND

Haemorrhagic septicaemia (HS) is a highly fatal and predominant disease in livestock, particularly cattle and buffalo in the tropical regions of the world. Pasteurella multocida (P. multocida), serotypes B:2 and E:2, are reported to be the main causes of HS wherein serotype B:2 is more common in Asian countries including Pakistan and costs heavy financial losses every year. As yet, very little molecular and genomic information related to the HS-associated serotypes of P. multocida isolated from Pakistan is available. Therefore, this study aimed to explore the characteristics of novel bovine isolates of P. multocida serotype B:2 at the genomic level and perform comparative genomic analysis of various P. multocida strains from Pakistan to better understand the genetic basis of pathogenesis and virulence.

RESULTS

To understand the genomic variability and pathogenomics, we characterized three HS-associated P. multocida serotype B:2 strains isolated from the Faisalabad (PM1), Peshawar (PM2) and Okara (PM3) districts of Punjab, Pakistan. Together with the other nine publicly available Pakistani-origin P. multocida strains and a reference strain Pm70, a comparative genomic analysis was performed. The sequenced strains were characterized as serotype B and belong to ST-122. The strains contain no plasmids; however, each strain contains at least two complete prophages. The pan-genome analysis revealed a higher number of core genes indicating a close resemblance to the studied genomes and very few genes (1%) of the core genome serve as a part of virulence, disease, and defense mechanisms. We further identified that studied P. multocida B:2 strains harbor common antibiotic resistance genes, specifically PBP3 and EF-Tu. Remarkably, the distribution of virulence factors revealed that OmpH and plpE were not present in any P. multocida B:2 strains while the presence of these antigens was reported uniformly in all serotypes of P. multocida.

CONCLUSION

This study's findings indicate the absence of OmpH and PlpE in the analyzed P. multocida B:2 strains, which are known surface antigens and provide protective immunity against P. multocida infection. The availability of additional genomic data on P. multocida B:2 strains from Pakistan will facilitate the development of localized therapeutic agents and rapid diagnostic tools specifically targeting HS-associated P. multocida B:2 strains.

Highly sensitive fluorescent probes for selective detection of hypochlorite: Applications in blood serum and cell imaging

Being one of the vital reactive oxygen species (ROS), abnormal level of hypochlorite ion (ClO^-) may pose detrimental threats to living organisms. Therefore, highly selective, and rapid monitoring of ClO^- in living system is of prime importance to protect living organisms from its harmful effects. In this regard, design of synthetic fluorescent probes for ClO^- has garnered considerable attention. However less fluorescence emission in aggregated state and less photostability of several existing probes for ClO^- inspired us to design aggregation induced emission (AIE) active fluorescent probes SH1 and SH2. Probes were rationally designed by introducing thiourea moiety that selectively reacted through desulfurization reaction and resulted in highly selective detection of ClO^-. Hypochlorite induced desulfurization reaction was validated through ¹H NMR titration and DFT studies. Fine tuning of probes SH1 and SH2 prompted highly sensitive nanoscale (55 nM and 77 nM) and rapid (15 and 35 sec) detection of ClO^-. Probe SH1 displayed less cytotoxic effect to live cells before it was successfully applied for bioimaging of ClO^- in live MCF-7 cells. Moreover, probes displayed excellent sensing potential for ClO^- in blood serum and real water samples. Advantageously, probe coated portable fluorescent films were fabricated for the easy and fast monitoring of ClO^-. Of note, this work offers excellent design strategy for highly selective detection of ClO^- that may lead to clinical trials.

Retraction Note: Screening and identification of bioactive compounds from citrus against non-structural protein 3 protease of hepatitis C virus genotype 3a by fluorescence resonance energy transfer assay and mass spectrometry

Retraction note: Khan M, Rauf W, Habib F, Rahman M, Iqbal M. Screening and identification of bioactive compounds from citrus against non-structural protein 3 protease of hepatitis C virus genotype 3a by fluorescence resonance energy transfer assay and mass spectrometry. World J Hepatol 2020; 12(11): 976-992 PMID: 33312423 DOI: 10.4254/wjh.v12.i11.976. The online version of the original article can be found at https://www.wjgnet.com/1948-5182/full/v12/i11/976.htm.

LC-MS/MS based appraisal of multi-mycotoxin co-occurrence in poultry feeds from different regions of Punjab, Pakistan

Mycotoxins, being a threat to animal and human health, contribute significantly towards economic losses in the poultry sector. A liquid chromatography-mass spectrometry-based study was conducted on poultry feed samples collected from Punjab, Pakistan to evaluate the prevalence, contamination levels, and co-occurrence of multi-mycotoxins across different processed forms of the feed, types of utilities and sampling regions. All samples were found to be contaminated with aflatoxin B1 (AFB1) and fumonisin B1 (FB1). The European Commission (EC) maximum level for AFB1 in complete feedingstuffs in poultry and guidance values for FB1 and zearalenone (ZEN) were exceeded in 73%, 2%, and 14% of the contaminated samples, respectively. The corresponding median values were 39.9 µg/kg, 205 µg/kg, and 34.5 µg/kg. In addition to exceeding contamination levels, a varying co-occurrence of three to fourteen mycotoxins was observed in each of the feed samples that calls for mitigation measures to safeguard the feed and its ingredients.

Aggregation-Induced Emission of Quinoline Based Fluorescent and Colorimetric Sensors for Rapid Detection of Fe3+ and 4-Nitrophenol in Aqueous Medium

New quinoline based fluorescent sensors 4 and 5 were rationally synthesized that exhibited excellent aggregation induced emission (AIE) in an aqueous medium. High fluorescence emission of sensors was accompanied by a noticeable redshift in their absorption and emission spectra that corresponds to the formation of J-aggregates. An AIE feature of sensors 4 and 5 was used for selective detection of Fe³⁺ and 4-NP in an aqueous medium that is attributed to the involvement of intermolecular charge transfer (ICT). The interaction mechanism of sensors with Fe³⁺ and 4-NP was investigated through ¹H NMR titration, Jobs plots, dynamic light scattering (DLS), and DFT analysis. The fluorescence quenching response of sensors 4 and 5 displayed distinguished linear behavior with the concentrations of Fe³⁺ and limits of detection (LOD) were calculated to be 15 and 10 nM, respectively. Further, LOD of sensors 4 and 5 for 4-NP (7.3 and 4.1 nM, respectively) was very low compared to previously reported sensors. Moreover, sensors' coated test strips were fabricated for solid-supported detection of Fe³⁺ and 4-NP. Sensors were successfully applied for the detection and quantification of Fe³⁺ and 4-NP in real water samples. Additionally, sensors were used for the determination of trace amounts of Fe³⁺ in the human serum sample.

Hesperidin identified from Citrus extracts potently inhibits HCV genotype 3a NS3 protease

Background

Hepatitis C virus infection is the main cause of liver ailments across the globe. Several HCV genotypes have been identified in different parts of the world. Effective drugs for combating HCV infections are available but not affordable, particularly to infected individuals from resource-limited countries. Hence, cost-effective drugs need to be developed against important HCV drug targets. As Citrus fruits naturally contain bioactive compounds with antiviral activities, the current study was designed to identify antiviral inhibitors from Citrus fruit extracts against an important drug target, NS3 protease, of HCV genotype 3a which is found predominantly in South Asian countries.

Methods

The full-length NS3 protease alone and the NS3 protease domain in fusion with the cognate NS4A cofactor were expressed in Escherichia coli, and purified by chromatographic techniques. Using the purified protein as a drug target, Citrus extracts were evaluated in a FRET assay, and active ingredients, identified using ESI–MS/MS, were docked to observe the interaction with active site residues of NS3. The best interacting compound was further confirmed through the FRET assay as the inhibitor of NS3 protease.

Results

Fusion of the NS3 protease domain to the NS4A cofactor significantly improved the purification yield, and NS3-NS4A was functionally more active than the full-length NS3 alone. The purified protein (NS3-NS4A) was successfully employed in a validated FRET assay to evaluate 14 Citrus fruit extracts, revealing that the mesocarp extract of Citrus paradisi, and whole fruit extracts of C. sinesis, C. aurantinum, and C. reticulata significantly inhibited the protease activity of HCV NS3 protease (IC₅₀ values of 5.79 ± 1.44 µg/mL, 37.19 ± 5.92 µg/mL, 42.62 ± 6.89 µg/mL, and 57.65 ± 3.81 µg/mL, respectively). Subsequent ESI-MSⁿ analysis identified a flavonoid, hesperidin, abundantly present in all the afore-mentioned Citrus extracts. Importantly, docking studies suggested that hesperidin interacts with active site residues, and acts as a potent inhibitor of NS3 protease, exhibiting an IC₅₀ value of 11.34 ± 3.83 µg/mL.

Conclusions

A FRET assay was developed using NS3-NS4A protease, which was successfully utilized for the evaluation of Citrus fruit extracts. Hesperidin, a compound present in the Citrus extracts, was identified as the main flavonoid, which can serve as a cost-effective potent inhibitor of NS3 protease, and could be developed as a drug for antiviral therapy against HCV genotype 3a.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03578-1.

A recessive variant in TFAM causes mtDNA depletion associated with primary ovarian insufficiency, seizures, intellectual disability and hearing loss

Mitochondrial disorders are collectively common, genetically heterogeneous disorders in both pediatric and adult populations. They are caused by molecular defects in oxidative phosphorylation, failure of essential bioenergetic supply to mitochondria, and apoptosis. Here, we present three affected individuals from a consanguineous family of Pakistani origin with variable seizures and intellectual disability. Both females display primary ovarian insufficiency (POI), while the male shows abnormal sex hormone levels. We performed whole exome sequencing and identified a recessive missense variant c.694C > T, p.Arg232Cys in TFAM that segregates with disease. TFAM (mitochondrial transcription factor A) is a component of the mitochondrial replisome machinery that maintains mtDNA transcription and replication. In primary dermal fibroblasts, we show depletion of mtDNA and significantly altered mitochondrial function and morphology. Moreover, we observed reduced nucleoid numbers with significant changes in nucleoid size or shape in fibroblasts from an affected individual compared to controls. We also investigated the effect of tfam impairment in zebrafish; homozygous tfam mutants carrying an in-frame c.141_149 deletion recapitulate the mtDNA depletion and ovarian dysgenesis phenotypes observed in affected humans. Together, our genetic and functional data confirm that TFAM plays a pivotal role in gonad development and expands the repertoire of mitochondrial disease phenotypes.

Screening and identification of bioactive compounds from citrus against non-structural protein 3 protease of hepatitis C virus genotype 3a by fluorescence resonance energy transfer assay and mass spectrometry

BACKGROUND

Hepatitis C virus genotype 3a (HCV G3a) is highly prevalent in Pakistan. Due to the elevated cost of available Food and Drug Administration-approved drugs against HCV, medicinal natural products of potent antiviral activity should be screened for the cost-effective treatment of the disease. Furthermore, from natural products, active compounds against vital HCV proteins like non-structural protein 3 (NS3) protease could be identified to prevent viral proliferation in the host.

AIM

To develop cost-effective HCV genotype 3a NS3 protease inhibitors from citrus fruit extracts.

METHODS

Full-length NS3 without co-factor non-structural protein 4A (NS4A) and codon optimized NS3 protease in fusion with NS4A were expressed in Escherichia coli. The expressed protein was purified by metal ion affinity chromatography and gel filtration. Citrus fruit extracts were screened using fluorescence resonance energy transfer (FRET) assay against the protease and polyphenols were identified as potential inhibitors using electrospray ionization-mass spectrometry (MS)/MS technique. Among different polyphenols, highly potent compounds were screened using molecular modeling approaches and consequently the most active compound was further evaluated against HCV NS4A-NS3 protease domain using FRET assay.

RESULTS

NS4A fused with NS3 protease domain gene was overexpressed and the purified protein yield was high in comparison to the lower yield of the full-length NS3 protein. Furthermore, in enzyme kinetic studies, NS4A fused with NS3 protease proved to be functionally active compared to full-length NS3. So it was concluded that co-factor NS4A fusion is essential for the purification of functionally active protease. FRET assay was developed and validated by the half maximal inhibitory concentration (IC₅₀) values of commercially available inhibitors. Screening of citrus fruit extracts against the native purified fused NS4A-NS3 protease domain showed that the grapefruit mesocarp extract exhibits the highest percentage inhibition 91% of protease activity. Among the compounds identified by LCMS analysis, hesperidin showed strong binding affinity with the protease catalytic triad having S-score value of -10.98.

CONCLUSION

Fused NS4A-NS3 protease is functionally more active, which is effectively inhibited by hesperidin from the grapefruit mesocarp extract with an IC₅₀ value of 23.32 µmol/L.

Mass spectrometric analysis of lipid A obtained from the lipopolysaccharide ofPasteurella multocida

LC/MS-based variant profiling of lipid A component of endotoxic lipopolysaccharides ofPasteurella multocidatype B:2, a causative agent of haemorrhagic septicaemia in water buffalo and cattle.

Regioselective, one-pot, multi-component, green synthesis of substituted benzo[c]pyrazolo[2,7]naphthyridines

An efficient and environmentally benign synthetic protocol has been developed for the synthesis of benzo[c]pyrazolo[2,7]naphthyridine derivatives through regioselective multi-component “on-water” reaction of isatin, malononitrile and 3-aminopyrazole. The Knoevenagel condensation of isatin with malononitrile resulted in the formation of arylidene, which subsequently underwent Michael addition with 3-aminopyrazole followed by basic hydrolysis, cyclization, decarboxylation and aromatization to give the target naphthyridines in good to excellent yields. The one-pot multi-component protocol was also employed to obtain the said naphthyridines in a lower yield (10–15%) than obtained by basic hydrolysis of spiro-intermediates. The present study shows attractive features such as the use of water as a green solvent, short reaction time, reduced waste products and transition metal free C–C and C–N bond formation. The structures of the synthesized derivatives were established through FTIR, ¹H-NMR, ¹³C-NMR spectroscopy and ESI-mass spectrometry.

An efficient and environmentally benign synthetic protocol has been developed for the synthesis of benzo[c]pyrazolo[2,7]naphthyridine derivatives through regioselective multi-component “on-water” reaction of isatin, malononitrile and 3-aminopyrazole.

A facile and concise route to (hydroxybenzoyl)pyrido[2,3-d]pyrimidine heterocycle derivatives: synthesis, and structural, spectral and computational exploration

In this work, we report the efficient synthesis of novel (hydroxybenzoyl)pyrido[2,3-d]pyrimidine heterocycle derivatives: 6-(2-hydroxy-5-methylbenzoyl)-1-methylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione (6a), 6-(5-fluoro-2-hydroxybenzoyl)-1-methylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione (6b), 6-(5-ethyl-2-hydroxybenzoyl)-1-methylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione (6c) and 6-(2-hydroxy-5-isopropylbenzoyl)-1-methylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione (6d). The chemical structures of the title compounds were ascertained by spectral techniques including ¹H, ¹³C NMR, UV-visible and FT-IR spectroscopy as well as single-crystal X-ray diffraction analysis. Additionally, density functional theory (DFT) and time-dependent (TD-DFT) computation were adopted to analyze the electronic structures of 6a-d. Compounds 6a-d were computed in the ground state for FT-IR spectroscopic and natural bond orbital (NBO) analysis by DFT/B3LYP with the 6-311+G(d,p) basis set. UV-vis spectroscopic and HOMO and LUMO energy values for 6a-d were determined via TD-DFT/B3LYP with the 6-311+G(d,p) basis set. The optimized geometric parameters, UV-vis findings, and vibrational frequencies indicate good consistency with the experimental data. NBO analysis was conducted to explore the interactions and charge transfer among different orbitals in the title compounds. The HOMO and LUMO band gap (ΔE) values for 6a-d were found to be 3.93, 3.91, 4.10 and 3.91 eV, respectively. Molecular electrostatic potential (MEP) analysis explored the reactivity of the title compounds by predicting their nucleophilic as well as electrophilic sites.

Restraining the multidrug efflux transporter STY4874 of Salmonella Typhi by reserpine and plant extracts

Efflux-mediated multidrug resistance is a well-known phenomenon facilitated by multidrug resistant (MDR) transporters. One of the approaches to counteract efflux-mediated resistance is the use of MDR pump inhibitors, and thus be used in combination with the conventional antibiotics to treat deadly diseases like typhoid fever. We have previously reported that STY4874, an efflux transporter of Salmonella serotype Typhi, exhibited promising characteristics as MDR pump. In this study, we aimed to get an insight into possible STY4874 inhibitors of plant origin. STY4874 was overexpressed in Escherichia coli and extracts from pomegranate peel, milk thistle seeds and reserpine, a synthetic plant alkaloid, were screened for inhibition of ciprofloxacin efflux. The extracts of milk thistle seeds and reserpine when incubated with ciprofloxacin showed statistically significant STY4874-mediated inhibitory activity, rendering the efflux pump inactive and hence early growth inhibition of host cells compared with cells expressing efflux pump and incubated only with ciprofloxacin. This efflux pump inhibitory activity was further confirmed by time-kill experiments. This study is the first to report on efflux pump inhibition of S. Typhi STY4874 and results can be extended towards its close homologues such as MdfA and MdtM from E. coli. SIGNIFICANCE AND IMPACT OF THE STUDY: Understanding and combating resistance governed by multidrug efflux transporters is an ongoing research intensive area, affecting treatment of various nosocomial and endemic/epidemic infections. Confronting drug resistance requires that inhibitors debilitating the underlying mechanisms should be included in combination therapy. One such example is the prescription of clavulanic acid as combination therapy with amoxicillin, collectively called as co-amoxiclav to combat β-lactamase-mediated resistance. However, research related to finding the inhibitors of efflux transporters, the resistance mechanism distinct from β-lactamase mediated resistance is at an early stage. The current study finds that plant-derived inhibitors can be an option towards restraining efflux-mediated resistance.

Mechanisms for C(sp2)-Si activation of aryltrimethylsilyl groups in palladium-catalysed couplings

Silyl-substituted aromatic compounds can participate as the electrophilic component in palladium-catalysed cross-couplings, and reactivity is enhanced by a neighbouring silyl-group. Products analogous to those obtained from C-H activation chemistry are accessible by this means with the additional benefit of regiochemistry defined by the site of silyl substitution. DFT studies described here show that the mechanism of C-Si cleavage is distinct from previously recognised mechanisms for C-H cleavage, with a cascade of silyl intermediates en route to a stable product. The amide directing-groups are involved only in the stabilisation of palladacyclic intermediates, and are never disposed to activate silicon directly. 5-Membered and 6-membered palladacycles are known to behave differently in coupling reactions and the calculations reveal underlying reasons in the cationic pathways studied here.

Palladium-catalysed directed C–H activation by anilides and ureas; water participation in a general base mechanism

A general-base pathway for CH-activation in anilides and ureas en route to palladacycles was developed through DFT calculations and fits available evidence.