Drug-resistant bacterial infections have been one of the critical health issues encountered worldwide currently because most conventional antibiotics are losing their effectiveness in clinical treatments. It is thus urgently to identify new antibiotics or alternatives against drug-resistant bacteria. For this purpose, we attempted to seek active compounds from commercially available natural products, which may be one of the fast-tracks to address the drug-resistant bacterial infections. In the present study, we investigated the antibacterial activity, antibacterial mechanism and synergistic effects of carvacrol against a panel of drug-resistant bacteria, including some clinical isolates. The results show that carvacrol (cymophenol), a monoterpenoid phenol, has excellent antibacterial activity. The MIC values against the bacteria examined are found to be 4-16 μg/mL. Our results also suggested that carvacrol might not likely to induce drug-resistance. More importantly, when carvacrol combined with first-line antibiotics, it exhibited good synergistic effects against drug-resistant bacteria. Moreover, in morphological studies, carvacrol could cause B. subtilis 168 elongation and S. aureus BAA-41 enlargement, which may suggest an antibacterial mechanism possibly correlated with the inhibition of bacterial cell division. We further demonstrated that carvacrol facilitated the polymerization of FtsZ that is a critically important protein for regulating bacterial cell division. Furthermore, molecular modeling predicted that carvacrol could interact with T7-loop of FtsZ. The findings of this study suggest that carvacrol may be a potential inhibitor of FtsZ and it could be utilized to combat drug-resistant bacteria in combination with existing antibiotics.

The emergence of multiple drug-resistant bacteria poses critical health threats worldwide. It is urgently needed to develop potent and safe antibacterial agents with novel bactericidal mechanisms to treat these infections. In this study, magnolol was identified as a potential bacterial cell division inhibitor by a cell-based screening approach. This compound showed good antibacterial activity against a number of Gram-positive pathogens (minimum inhibitory concentration 8-16 µg/mL) including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. Further results obtained from biochemical experiments demonstrated that magnolol could markedly disrupt GTPase activity and filamentous temperature-sensitive mutant Z (FtsZ) polymerization, consistent with the impediment to cell division in the bacteria tested. The in vivo antibacterial activity of magnolol was evaluated with a Galleria mellonella larvae model. The results showed that magnolol significantly increased the survival rate of larvae infected with methicillin-resistant S. aureus. The interaction pattern of magnolol with FtsZ was investigated through molecular docking. The finding may offer meaningful insights into the mechanism of action of the compound. The results point to magnolol as a promising antimicrobial compound that inhibits cell division by affecting FtsZ polymerization and has the potential to be developed into an effective antimicrobial drug by further structure modification.

Multidrug resistant bacteria have been a global health threat currently and frontline clinical treatments for these infections are very limited. To develop potent antibacterial agents with new bactericidal mechanisms is thus needed urgently to address this critical antibiotic resistance challenge. Natural products are a treasure of small molecules with high bioactive and low toxicity. In the present study, we demonstrated that a natural compound, honokiol, showed potent antibacterial activity against a number of Gram-positive bacteria including MRSA and VRE. Moreover, honokiol in combination with clinically used β-lactam antibiotics exhibits strong synergistic antimicrobial effects against drug-resistant S. aureus strains. Biochemical studies further reveal that honokiol may disrupt the GTPase activity, FtsZ polymerization, cell division. These biological impacts induced by honokiol may ultimately cause bacterial cell death. The in vivo antibacterial activity of honokiol against S. aureus infection was also verified with a biological model of G. mellonella larvae. The in vivo results support that honokiol is low toxic against the larvae and effectively increases the survival rate of the larvae infected with S. aureus. These findings demonstrate the potential of honokiol for further structural advancement as a new class of antibacterial agents with high potency against multidrug-resistant bacteria.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common multi-resistant organisms found in hospital-acquired infections and is associated with high morbidity and mortality. The development of new drugs and promising therapeutic strategies against MRSA is thus an urgent request. In recent years, some natural products have been demonstrated to show great potential in improving the efficacy of antibiotics to treat various drug-resistant bacteria, particularly MRSA. In this context, we aimed to analyze systematically from the prior arts that investigated the synergy between natural products and antibiotics against MRSA. These findings not only give us a better understanding on the mechanism of actions but also shed light on the bioactive molecular scaffolds identified from diverse natural products. In the present study, we concentratedly reviewed the studies that utilized natural products to enhance the potency of conventional antibiotics against MRSA in the last decade. The timely information reported herein may give meaningful insights into the molecular design of novel and potent antibacterial agents and/or effective therapeutics to combat MRSA for practical applications.

Introduction: Obesity, which is associated with gut microbiota dysbiosis, low-grade chronic inflammation and intestinal barrier dysfunction, can cause a variety of chronic metabolic diseases. Phytochemical flavonoids have a variety of biological activities, among which there may be safe and effective anti-obesity solutions. Methods: We tested a plant-derived flavonoid hesperidin and fecal microbiota transplantation (FMT) to alleviate diet-induced obesity. High-fat diet (HFD)-fed mice were treated with hesperidin (100 and 200 mg/kg BW) and FMT. Results: Results indicated that hesperidin had the effects of reducing obesity as indicated by reduction of body weight, fat accumulation and blood lipids, reducing inflammation as indicated by reduction of pro-inflammation factors including TNF alpha, IL-6, IL-1 beta and iNOS, and improving gut integrity as indicated by increasing colon length, reducing plasma gut permeability indicators iFABP and LBP, increased mRNA expression of mucus protein Muc2, tight junction p Claudin 2, Occludin and ZO-1 in the HFD-fed mice. The anti-obesity effects of hesperidin treatment have a dose-dependent manner. In addition, 16S rRNA-based gut microbiota analysis revealed that hesperidin selectively promoted the growth of Lactobacillus salivarius, Staphylococcus sciuri and Desulfovibrio C21_c20 while inhibiting Bifidobacterium pseudolongum, Mucispirillum schaedleri, Helicobacter ganmani and Helicobacter hepaticus in the HFD-fed mice. Horizontal feces transfer from the normal diet (ND)-fed mice to the HFD-fed mice conferred anti-obesity effects and transmitted some of the HFD-modulated microbes. Conclusion: We concluded that hesperidin and FMT both affect the reduction of body weight and improve HFD-related disorders in the HFD-fed mice possibly through modulating the composition of the gut microbiota.

Cyclic dimeric guanosine monophosphate (c-di-GMP) is an important second messenger in bacteria. It regulates a wide range of bacterial functions and behaviors including biofilm formation that causes chronic infections and antibiotic resistance. C-di-GMP being as a signal transducer in bacteria is known to exist in monomer and dimer form. Recent studies also discover that c-di-GMP can form higher-order oligomers, such as tetramer and octamer, which may have physiological roles in bacterial cells. Moreover, the tetrameric c-di-GMP structure was reported to link two subunits of a transcription factor (BldD), which controls the progression of multicellular differenti-ation in sporulating actinomycete bacteria and then mediates the dimerization process. Current understanding on higher-order oligomers of c-di-GMP is relatively limited compared to its monomer or dimer structure. To probe and visualize the higher-order structure of c-di-GMP and its associated biofunctions in live bacterial cells with fluorescence techniques for mechanistic study and cellular investigation is important. Nonetheless, the sensitive and selective fluorescent probe with a rapid signal response for higher-order oligomers of c-di-GMP is currently lacking. In the present study, a series of fluorescent probes that preferentially interacted with tetrameric c-di-GMP and generated red fluorescence signal promptly were synthesized and investigated. The interaction mechanism was studied with 1H NMR and molecular docking. In addition, the ligand was demonstrated as an excellent molecular fluorescent probe for bioimaging of tetrameric c-di-GMP structure and monitoring of biofilm formation on both biotic and abiotic surfaces with pathogenic bacteria including Pseudomonas aeruginosa PAO1 and Bacillus subtilis 168.

Bacteria can form biofilms in natural and clinical environments on both biotic and abiotic surfaces. The bacterial aggregates embedded in biofilms are formed by their own produced extracellular matrix. Staphylococcus aureus (S. aureus) is one of the most common pathogens of biofilm infections. The formation of biofilm can protect bacteria from being attacked by the host immune system and antibiotics and thus bacteria can be persistent against external challenges. Therefore, clinical treatments for biofilm infections are currently encountering difficulty. To address this critical challenge, a new and effective treatment method needs to be developed. A comprehensive understanding of bacterial biofilm formation and regulation mechanisms may provide meaningful insights against antibiotic resistance due to bacterial biofilms. In this review, we discuss an overview of S. aureus biofilms including the formation process, structural and functional properties of biofilm matrix, and the mechanism regulating biofilm formation.

Recent advancements in unsupervised protein language models (ProteinLMs), like ESM-1b and ESM-2, have shown promise in different protein prediction tasks. However, these models face challenges due to their high computational demands, significant memory needs, and latency, restricting their usage on devices with limited resources. To tackle this, we explore post-training quantization (PTQ) for ProteinLMs, focusing on ESMFold, a simplified version of AlphaFold based on ESM-2 ProteinLM. Our study is the first attempt to quantize all weights and activations of ProteinLMs. We observed that the typical uniform quantization method performs poorly on ESMFold, causing a significant drop in TM-Score when using 8-bit quantization. We conducted extensive quantization experiments, uncovering unique challenges associated with ESMFold, particularly highly asymmetric activation ranges before Layer Normalization, making representation difficult using low-bit fixed-point formats. To address these challenges, we propose a new PTQ method for ProteinLMs, utilizing piecewise linear quantization for asymmetric activation values to ensure accurate approximation. We demonstrated the effectiveness of our method in protein structure prediction tasks, demonstrating that ESMFold can be accurately quantized to low-bit widths without compromising accuracy. Additionally, we applied our method to the contact prediction task, showcasing its versatility. In summary, our study introduces an innovative PTQ method for ProteinLMs, addressing specific quantization challenges and potentially leading to the development of more efficient ProteinLMs with significant implications for various protein-related applications.

Background:Staphylococcus haemolyticus is an opportunistic pathogen that belongs to coagulase-negative Staphylococci (CoNS). Increasing infection and multi-drug resistance cases caused by this strain have been reported and thus it poses a great health threat.Methods:The third-generation sequencing technology was performed on a S. haemolyticus SH-1 isolated from a clinical sample to analyze the drug resistance genes, which included vancomycin resistance related genes. In addition, antimicrobial susceptibility tests, transmission electron microscopy and Triton X-100 stimulated autolysis were conducted to understand its biological characteristics.Results:The study shows that this clinical isolate is a vancomycin intermediate-resistant strain. Genome comparison also revealed that WalK(N70K) and WalK(R280Q) mutations may contribute to the vancomycin resistant phenotype. Besides, S. haemolyticus SH-1 exhibit common features of thicker cell wall and decreased autolytic activity.Conclusion:S. haemolyticus SH-1 with WalKR mutations shows typical characteristics of vancomycin resistant strains. Combining the genome features and biological properties, our findings may provide important information for the understanding of the molecular mechanism of S. haemolyticus to vancomycin intermediate-resistance.

The emerging of drug resistant Pseudomonas aeruginosa is a critical challenge and renders an urgent action to discover innovative antimicrobial interventions. One of these interventions is to disrupt the pseudomonas quinolone signal (pqs) quorum sensing (QS) system, which governs multiple virulence traits and biofilm formation. This study aimed to investigate the QS inhibitory activity of a series of new PqsR inhibitors bearing a quinoline scaffold against Ps. aeruginosa.

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 role in bacterial cell division. In the present study, potential inhibitors of FtsZ were identified by virtual screening followed by in vivo and in vitro bioassays. One of the candidates, Dacomitinib (S2727), shows for the first time its potent inhibitory activity against the MRSA strains. The binding mode of Dacomitinib in FtsZ was analyzed by docking, and Asp199 and Thr265 are thought to be essential residues involved in the interactions.

The discovery of small molecular inhibitors targeting essential and conserved bacterial drug targets such as FtsZ protein is a promising approach to fight against multi-drug resistant bacteria. In the present study, two new series of FtsZ inhibitors based on a 1-methylquinolinium scaffold were synthesized. The inhibitors possess a variety of substituent groups including the cyclic or linear amine skeleton at the 2 and 4-position of the quinolinium ring for structure-activity relationship study. In general, the inhibitors bearing a cyclic amine substituent at the 4-position of the quinolinium ring showed better antibacterial activity (MIC down to 0.25 mu g/mL) than that at the 2-position, especially against Gram-positive bacteria. Among the twenty FtsZ inhibitors examined in various assays, A3 was identified to exhibit excellent antibacterial activity against S. aureus (MIC = 0.5-1 mu g/mL), S. epidermidis (MIC = 0.25 mu g/mL) and E. faecium (MIC = 1-8 mu g/mL). More importantly, A3 showed low hemolytic toxicity (IC5 = 64 mu g/mL) and was found not readily to induce drug resistance. A3 at 2-8 mu g/mL promoted the polymerization of FtsZ and interrupted the bacterial division. Furthermore, the ligand-FtsZ interaction study conducted with circular dichroism and molecular docking revealed that A3 induced secondary structure changes of FtsZ protein upon binding to the interdomain cleft of the protein. A3 is thus a potent inhibitor of FtsZ and shows potential to be used as a new antibacterial agent against drug-resistant bacteria. (C) 2022 Elsevier Masson SAS. All rights reserved.

A series of conformationally constrained novel benzo[1,3]oxazinyloxazolidinones were designed, synthesized, and evaluated on their activities against Mycobacterium tuberculosis, Gram-positive bacteria, and Gram-negative bacteria. The studies identified a new compound 20aa that displayed good to excellent antibacterial and antitubercular profiles against drug-resistant TB strains (MIC = 0.48-0.82 μg/mL), MRSA (MIC = 0.25-0.5 μg/mL), MRSE (MIC = 1 μg/mL), VISA (MIC = 0.25 μg/mL), and VRE (MIC = 0.25 μg/mL) and some linezolid-resistant strains (MIC 1-2 μg/mL). Compound 20aa was demonstrated as a promising candidate through ADME/T evaluation including microsomal stability, cytotoxicity, and inhibition of hERG and monoamine oxidase. Notably, 20aa showed excellent mouse PK profile with high plasma exposure (AUC0-∞ = 78 669 h·ng/mL), high peak plasma concentration (Cmax = 10 253 ng/mL), appropriate half-life of 3.76 h, and superior oral bioavailability (128%). The present study not only successfully provides a novel benzo[1,3]oxazinyloxazolidinone scaffold with superior druggability but also lays a good foundation for new antibacterial drug development.

During infections, bacteria stimulate host cells to produce and release histamine, which is a key mediator of vital cellular processes in animals. However, the mechanisms underlying the bacterial cell's ability to sense and respond to histamine are poorly understood. Herein, we show that HinK, a LysR-type transcriptional regulator, is required to evoke responses to histamine in Pseudomonas aeruginosa, an important human pathogen. HinK directly binds to and activates the promoter of genes involved in histamine uptake and metabolism, iron acquisition, and Pseudomonas quinolone signal (PQS) biosynthesis. The transcriptional regulatory activity of HinK is induced when histamine is present, and it occurs when HinK binds with imidazole-4-acetic acid (ImAA), a histamine metabolite whose production in P. aeruginosa depends on the HinK-activated histamine uptake and utilization operon hinDAC-pa0222. Importantly, the inactivation of HinK inhibits diverse pathogenic phenotypes of P. aeruginosa. These results suggest that histamine acts as an interkingdom signal and provide insights into the mechanism used by pathogenic bacteria to exploit host regulatory signals to promote virulence.

Background: The Coronavirus disease 2019 pneumonia broke out in 2019 (COVID-19) and spread rapidly, which causes serious harm to the health of people and a huge economic burden around the world. Purpose: In this study, the network pharmacology, molecular docking and surface plasmon resonance technology (SPR) were used to explore the potential compounds and interaction mechanism in the Toujie Quwen Granules (TQG) for the treatment of coronavirus pneumonia 2019. Study design: The chemical constituents and compound targets of Lonicerae Japonicae Flos, Pseudostellariae Radix, Artemisia Annua L, Peucedani Radix, Forsythiae Fructus, Scutellariae Radix, Hedysarum Multijugum Maxim, Isatidis Folium, Radix Bupleuri, Fritiliariae Irrhosae Bulbus, Cicadae Periostracum, Poria Cocos Wolf, Pseudobulbus Cremastrae Seu Pleiones, Mume Fructus, Figwort Root and Fritillariae Thunbrgii Bulbus in TQG were searched. The target name was translated to gene name using the UniProt database and then the Chinese medicine-compound-target network was constructed. Protein-protein interaction network (PPI), Gene ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the core targets were performed in the Metascape to predict its mechanism. The top 34 compounds in the Chinese medicine-compound-target network were docked with SARS-CoV-2 3CL enzyme and SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and then the 13 compounds with lowest affinity score were docked with angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 Spike protein and interleukin 6 to explore its interaction mechanism. Lastly, SPR experiments were done using the quercetin, astragaloside IV, rutin and isoquercitrin, which were screened from the Chinese medicine-compound-target network and molecular docking. Results: The Chinese medicine-compound-target network includes 16 medicinal materials, 111 compounds and 298 targets, in which the degree of PTGS2, TNF and IL-6 is higher compared with other targets and which are the disease target exactly. The result of GO function enrichment analysis included the response to the molecule of bacterial origin, positive regulation of cell death, apoptotic signaling pathway, cytokine-mediated signaling pathway, cytokine receptor binding and so on. KEGG pathway analysis enrichment revealed two pathways: signaling pathway- IL-17 and signaling pathway- TNF. The result of molecular docking showed that the affinity score of compounds including quercetin, isoquercitrin, astragaloside IV and rutin is higher than other compounds. In addition, the SPR experiments revealed that the quercetin and isoquercitrin were combined with SARS-CoV-2 Spike protein rather than Angiotensin-converting enzyme 2, while astragaloside IV and rutin were combined with ACE2 rather than SARS-CoV-2 Spike protein. Conclusion: TQG may have therapeutic effects on COVID-19 by regulating viral infection, immune and inflammation related targets and pathways, in the way of multi-component, multi-target and multi-pathway.

Benefit from the efficient energy transfer, aggregation-induced emission (AIE) and host-guest recognition as strategies of signal amplification and specific binding have been applied to establish the sensing system; however, the application of these two attractive strategies in one system is rare. Herein, we propose a "turn-on" to "turn-off' fluorescent strategy for sensitive detection of beta-galactosidase (beta-Gal) based on the application of AIE and host-guest recognition. In this work, a novel red-emitted (635 nm) copper nanoclusters (CuNCs) protected by dithioerythritol (DTE) and beta-cyclodextrin (beta-CD) has been found to possess AIE property induced by aluminum cations to achieve the "turn-on" process, and the coordinated behavior between aluminum cations and DTE/beta-CD CuNCs is also discussed. As the hydrolysis product of beta-Gal and 4-nitrophenyl-D-galactopyranoside, p-nitrophenol can combine with beta-CD in DTE/beta-CD CuNCs by the host-guest recognition to realize the efficient photoelectron transfer to "turn-off' the fluorescence. This strategy performs the exciting linear range of 0.0-50.0 U/L and detection limit of 0.56 U/L (S/N = 3) for sensitive detection of beta-Gal and further applies in biologic samples successfully. As far as we know, this is the first work to combine AIE and host-guest recognition in one system to construct the sensing platform, which can achieve efficient and specific energy transfer to improve the sensitivity of the system.

In recent years, the abuse of antibiotics has caused the emergence of drug-resistant bacteria, which is now widely spread around the world. It is currently a critical issue that seriously threats to human health due to the lack of effective clinical drugs to treat the multidrug-resistant bacterial infections. With such a serious shortage of drugs and means for clinical treatment against multidrug-resistant bacterial infections, it is urgently needed to develop new antibacterial drugs, especially those molecules possessing new mechanisms of action to combat the drug-resistant bacteria. Filamenting temperature-sensitive mutant Z (FtsZ) is an essential protein for bacterial division and has been one of the most popular targets for new drug discovery. FtsZ is a highly conserved protein and it plays a key role in cell division in most prokaryotic cells. In this article, we reviewed the structural characteristics and biological functions of bacterial cell division proteins and the recent research progress on antibacterial drugs development targeting FtsZ.

The recent outbreak of coronavirus disease 2019 caused by the new coronavirus, SARS-CoV-2, has become an international emergency. Since there is no effective therapy for the treatment of this disease, drugs or vaccine that can prevent or cure the SARS-CoV-2 infection are urgently needed. The viral 3-chymotrypsin-like cysteine protease (3CLpro), which plays a key role in the replication of coronavirus, is a potential drug target for the development of anti-SARS-CoV-2 drugs. With the crystal structure of 3CLpro, we performed virtual screening from a small chemical library of a Traditional Chinese Medicine recipe- FuFang Zhenzhu Tiaozhi (FTZ). Five compounds with the best scores were screened and could be considered as potential hit compounds to be investigated further with bioassays for their anti-virus effects.

Novel antibacterial agents are urgently needed to address the infections caused by multi-drug resistant bacteria. Urinary tract infections are common infectious diseases in clinical. Most of these infections are caused by drug-resistant uropathogenic Escherichia coli. PPK1 is an essential kinase for bacterial motility, biofilm formation, quorum sensing, and virulence factors in the expression of uropathogenic E. coli. In the present study, two small molecules potentially targeting PPK1 were discovered through virtual screening and biological assays. The in vitro and in vivo results suggested that the interaction of these compounds with PPK1 can disrupt biofilm formation of uropathogenic E. coli and reduce invasive ability and resistance to oxidative stress of this strain. Moreover, the compounds exhibit good antibacterial bacterial activity in the mice with urinary tract infection. Taken together, our findings could provide a new chemotype for the development of antibacterials targeting PPK1.

New antimicrobial agents are urgently needed to address the emergence of multi-drug resistant organisms, especially those active compounds with new mechanisms of action. Based on the molecular structures of the FtsZ inhibitors reported, a variety of thiazole-quinolinium derivatives with aliphatic amino and/or styrene substituents were synthesized from benzothiazolidine derivatives. In the present study, to further explore the antibacterial potential of thiazole-quinolinium derivatives, several Gram-positive and Gram-negative bacteria were treated with the newly modified compounds and the biological effects were studied in detail in order to understand the bactericidal action of the compounds. Our findings reveal that some of these derivatives possess good potent bactericidal activity as they can inhibit Gram-positive methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus and also some Gram-negative organisms and NDM-1 Escherichia coli. Furthermore, compounds 4a1-4a4 and 4b1-4b4 altered the morphology of bacterial cells and the cells displayed a more-elongated shape compared to the untreated cells. Biochemical assays showed that 4a4 and 4b4 stimulate FtsZ polymerization in bacterial cells, which eventually disrupts its dynamic assembly and Z-ring formation. The inhibition of this crucial step in bacterial cell division could potentially represent their main mechanism of antibacterial activity. Cytotoxicity assay and hemolysis assay suggested that 4a4 and 4b4 possess low cytotoxicity. In summary, these results further highlight the importance of 4a4 and 4b4 that could be developed as potent and effective bacteriostatic agents against multi-drug resistant bacteria.