Type IIA topoisomerase inhibition by a new class of antibacterial agents

In vitro activity of gepotidacin against urinary tract infection isolates of Enterobacterales, Enterococcus faecalis, and Staphylococcus saprophyticus

Gepotidacin is a novel, bactericidal, first-in-class triazaacenaphthylene antibiotic that inhibits bacterial DNA replication through a distinct binding site and unique mechanism of action, providing well-balanced inhibition of two different type II topoisomerase enzymes for most uropathogens. Phase III clinical trials, NCT04020341 (EAGLE-2) and NCT04187144 (EAGLE-3), showed gepotidacin to be non-inferior and superior, respectively, to nitrofurantoin for the treatment of patients with uncomplicated urinary tract infections (uUTIs). To better define gepotidacin in vitro activity against pathogens that commonly cause UTIs, CLSI broth microdilution MICs were determined for gepotidacin and seven comparator agents, and agar dilution MICs were determined for fosfomycin, against 4,000 predominantly UTI isolates of Enterobacterales (3,250), Enterococcus faecalis (500), and Staphylococcus saprophyticus (250) collected globally from 2012 to 2020. Gepotidacin MIC90s against the Enterobacterales species tested were 4 µg/mL for Escherichia coli (1,000) and Klebsiella oxytoca (250), 8 µg/mL for Citrobacter spp. (250) and Klebsiella aerogenes (250), 16 µg/mL for Proteus mirabilis (250) and Providencia rettgeri (250), and 32 µg/mL for Enterobacter cloacae (500) and Klebsiella pneumoniae (500). Against the gram-positive species, gepotidacin MIC90s were 0.12 µg/mL and 4 µg/mL for S. saprophyticus (250) and E. faecalis (500), respectively. Gepotidacin MIC90s for ciprofloxacin not susceptible isolates ranged from 4 µg/mL for E. coli (352) to 128 µg/mL for P. rettgeri (48). Gepotidacin MIC90s for presumptive extended spectrum beta-laactamase (ESBL)-positive E. coli (228) and K. pneumoniae (145) were 8 µg/mL and 32 µg/mL, respectively. Gepotidacin was bactericidal (minimum bactericidal concentration [MBC]/MIC ratio ≤4) against 94% (47/50) of isolates tested.

Naturally inspired chimeric quinolone derivatives to reverse bacterial drug resistance

Antimicrobial resistance poses an urgent threat to global health, underscoring the critical need for new antibacterial drugs. Ciprofloxacin, a third-generation quinolone antibiotic, is used to treat different types of bacterial infections; however, it often results in the rapid emergence of resistance in clinical settings. Inspired by low susceptibility to antimicrobial resistance of natural antimicrobial peptides, we herein propose a host defense peptide-mimicking strategy for designing chimeric quinolone derivatives which may reduce the likelihood of antibacterial resistance. This strategy involves the incorporation of deliberately designed amphiphilic moieties into ciprofloxacin to mimic the structural characteristics and resistance-evading properties of host defense peptides. A resulting chimeric compound IPMCL-28b, carrying a rigid linker and three cationic amino acids along with a lipophilic acyl n-decanoyl tail, exhibited potent activity against a panel of multidrug-resistant bacterial strains by endowing the ciprofloxacin derivatives with additional ability to disrupt bacterial cell membranes. Molecular dynamics simulations showed that IPMCL-28b demonstrates significantly stronger disruptive interactions with cell membranes than ciprofloxacin. This compound not only demonstrated high selectivity with low hemolysis side effect, but also significantly reduced the likelihood of resistance development compared with ciprofloxacin. Excitingly, IPMCL-28b demonstrated highly enhanced in vivo antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) with a 99.99 % (4.4 log) reduction in skin bacterial load after a single dose. These findings highlight the potential of host defense peptides-mimicking amphiphilic ciprofloxacin derivatives to reverse antibiotic resistance and mitigate the development of antimicrobial resistance.

Novel Fluoroquinolones With Pinane Moiety: Synthesis and Antimicrobial Activity

Here, we report a synthesis of fluoroquinolones carrying a monoterpene moiety at the C7 position of aromatic structure. The minimal inhibitory concentrations of fluoroquinolone fused with trans-3-hydroxy-cis-myrtanylamine 18 against Staphylococcus aureus (MSSA isolates) were two- to eightfold lower compared to moxifloxacin, although fourfold higher against MRSA isolates. The fluoroquinolone fused with (-)-nopylamine 16 was four- to eightfold less active on MSSA compared to moxifloxacin, while had similar activity on MRSA. Against biofilms, both 16 and 18 were four times more active than both moxifloxacin and ciprofloxacin. Both 16 and 18 induced the drop of membrane potential and in silico exhibited similar binding energies with DNA gyrase of S. aureus (ΔG -13.44 to -13.17 kcal/mol), suggesting dual mechanism of action (topoisomerase inhibition by the fluoroquinolone core and membrane damage by the monoterpene fragment). Thus, our data demonstrate the perspectives of monoterpenes fusion to an antibiotic moiety to obtain dual-acting bipharmacophore antimicrobials with improved activity, including biofilm-associated infections.

Microwave-Assisted Synthesis of Bis-1,2,3-Triazole-Based Benzophenones, In Vitro Antimicrobial Activity, and Molecular Docking Studies

In this work, we have adopted an easy route to synthesize bis-1,2,3-triazole-based benzophenone compounds via a 1,3-dipolar cycloaddition reaction (Click chemistry). All the target compounds achieved better yields through the microwave-assisted method than the conventional method. Target compound structures were confirmed on the basis of the IR, 1H NMR, 13C NMR, and HR mass analysis. Additionally, we have carried out in vitro antibacterial and antifungal activities with ciprofloxacin and fluconazole standard drugs, respectively. Compounds 5b, 5f, 5i, 5k, and 5n were antibacterial, whereas 5a, 5e, 5g, 5i, and 5k showed promising antifungal activity with respect to standard drugs. Further, a molecular docking study performed against DNA gyrase and lanosterol 14-alpha demethylase envisioned promising binding interactions with a good docking score.

A stepwise dearomatization/nitration/enantioselective homoenolate reaction of quinolines to construct C3-nitro-substituted tetrahydroquinolines

Herein, we describe a stepwise 1,2-reductive dearomatization/selective C3-nitration of quinoline and a subsequent catalytic enantioselective homoenolate addition reaction using a NHC catalyst strategy to construct N-acetyl 3,4-disubstituted tetrahydroquinoline in good yields with remarkably high diastereo- and enantioselectivities (dr >99 : 1, ee up to >99%). An efficient metal- and base-free method for 3-nitroquinoline synthesis from readily accessible quinoline has also been realized.

Structural and Mechanistic Insights into Atypical Bacterial Topoisomerase Inhibitors

Novel bacterial topoisomerase inhibitors (NBTIs) targeting DNA gyrase and topoisomerase IV constitute a new antibacterial class for deadly pathogens such as MRSA. While most NBTIs induce gyrase-mediated single-strand DNA breaks, a subset of amide NBTIs induces both single-strand and double-strand DNA breaks. Here, we report the X-ray crystal structures of two such amide NBTIs, 148 and 185, and demonstrate an unusual binding mode characterized by engagement of both GyrA D83 and R122. The synthesis of two isosteric triazole NBTIs is also described, one of which (342) affords only single-strand DNA breaks, while the other (276) also induces both single- and double-strand DNA breaks. A combination of docking and molecular dynamics simulations is employed to further investigate the potential structural underpinnings of differences in DNA cleavage.

Development of xanthone derivatives as effective broad-spectrum antimicrobials: Disrupting cell wall and inhibiting DNA synthesis

Discovering potent antibiotics is of critical importance due to the substantial increases of microbial resistance. Xanthones are intriguing sources of antimicrobials, despite a scarcity of extensive investigations into their mechanisms of action. Here, we reported the development of a series of xanthone derivatives, among which compound XT17 displayed strong broad-spectrum antibacterial activity, weak hemolytic activity, and low cytotoxicity against mammalian cell lines, low frequencies of drug resistance, and potent in vivo efficacy in Staphylococcu aureus- or Pseudomonas aeruginosa-induced murine corneal infection models. Compound XT17 presented a multifaceted mode of actions, involving the disruption of cell wall by interacting with lipoteichoic acid or lipopolysaccharides and the suppression of DNA synthesis. A further docking study confirmed the capability of compound XT17 to form a stable complex with the bacterial gyrase enzyme. This work could offer an innovative design strategy for developing broad-spectrum therapeutic agents against drug-resistant bacteria.

Novel 2-Alkoxy-3-Cyanopyridine Derivatives as Cholinesterase Inhibitors: Synthesis, Biological Evaluation, and In Silico Investigations

Alzheimer's disease remains a major challenge in neuroscience and medicine. Cholinesterase inhibitors provide symptomatic relief but do not alter disease progression. While significant progress has been made in understanding its biology, there is an urgent need for effective therapies. In this study, a series of 2-alkoxy-3-cyanopyridine derivatives (1-7) were prepared and evaluated as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). Among the compounds, 3 and 4 were identified as good inhibitors of AChE and BuChE with relatively low IC50 values. 3 inhibited AChE with an IC50 of 53.95 ± 4.29 µM, while 4 had a greater potency for BuChE with an IC50 of 31.79 ± 0.38 µM. Kinetic studies revealed that 3 and 4 are competitive inhibitors with Ki values of 14.23 ± 0.42 and 19.80 ± 3.38 µM for AChE and BuChE, respectively. In silico investigations, including docking studies, DFT calculations, and ADME/drug-likeness properties, were carried out to understand the mode of interaction of 3 and 4 toward the AChE and BuChE enzymes, as well as to determine their molecular geometry, chemical reactivity, and pharmacokinetic properties. This study highlights the potential of 3-cyanopyridine derivatives in the treatment of AD and provides a solid foundation for further optimization and exploration of their therapeutic applications.

Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research

In the fight against bacterial infections, particularly those caused by multi-resistant pathogens known as "superbugs", the need for new antibacterials is undoubted in scientific communities and is by now also widely perceived by the general population. However, the antibacterial research landscape has changed considerably over the past years. With few exceptions, the majority of big pharma companies has left the field and thus, the decline in R&D on antibacterials severely impacts the drug pipeline. In recent years, antibacterial research has increasingly relied on smaller companies or academic research institutions, which mostly have only limited financial resources, to carry a drug discovery and development process from the beginning and through to the beginning of clinical phases. This review formulates the requirements for an antibacterial in regard of targeted pathogens, resistance mechanisms and drug discovery. Strategies are shown for the discovery of new antibacterial structures originating from natural sources, by chemical synthesis and more recently from artificial intelligence approaches. This is complemented by principles for the computer-aided design of antibacterials and the refinement of a lead structure. The second part of the article comprises a compilation of antibacterial molecules classified according to bacterial target structures, e.g. cell wall synthesis, protein synthesis, as well as more recently emerging target classes, e.g. fatty acid synthesis, proteases and membrane proteins. Aspects of the origin, the antibacterial spectrum, resistance and the current development status of the presented drug molecules are highlighted.

Antibacterials with Novel Chemical Scaffolds in Clinical Development

The rise of antimicrobial resistance represents a significant global health threat, driven by the diminishing efficacy of existing antibiotics, a lack of novel antibacterials entering the market, and an over- or misuse of existing antibiotics, which accelerates the evolution of resistant bacterial strains. This review focuses on innovative therapies by highlighting 19 novel antibacterials in clinical development as of June 2024. These selected compounds are characterized by new chemical scaffolds, novel molecular targets, and/or unique mechanisms of action, which render their potential to break antimicrobial resistance particularly high. A detailed analysis of the scientific foundations behind each of these compounds is provided, including their pharmacodynamic profiles, current development state, and potential for overcoming existing limitations in antibiotic therapy. By presenting this subset of chemically novel antibacterials, the review highlights the ability to innovate in antibiotic drug development to counteract bacterial resistance and improve treatment outcomes.

Addressing urgent priorities in antibiotic development: insights from WHO 2023 antibacterial clinical pipeline analyses

Antimicrobial resistance continues to evolve and remains a leading cause of death worldwide, with children younger than 5 years being among those at the highest risk. Addressing antimicrobial resistance requires a comprehensive response, including infection prevention efforts, surveillance, stewardship, therapy appropriateness and access, and research and development. However, antimicrobial research and development is limited and lags behind the output of other fields, such as that of cancer or HIV research. The 2023 WHO analysis of the global antibacterial clinical pipeline serves as a tool to monitor and guide research and development efforts. The analysis emphasises the remaining gaps in developing a robust and effective antibacterial drug pipeline, drawing insights from trend analyses and assessment of the innovation potential of candidate antimicrobials. In the present analysis, we evaluated the activity of antibiotics against the new WHO bacterial priority pathogens list 2024, which reflects changing trends in resistance patterns, distribution of bacterial infections, and the emergence of new resistance mechanisms.

Anti-Mycobacterial Activity of Bacterial Topoisomerase Inhibitors with Dioxygenated Linkers

Developing new classes of drugs that are active against infections caused by Mycobacterium tuberculosis is a priority for treating and managing this deadly disease. Here, we describe screening a small library of 20 DNA gyrase inhibitors and identifying new lead compounds. Three structurally diverse analogues were identified with minimal inhibitory concentrations of 0.125 μg/mL against both drug-susceptible and drug-resistant strains of M. tuberculosis. These lead compounds also demonstrated antitubercular activity in ex vivo studies using infected THP-1 macrophages with minimal cytotoxicity in THP-1, HeLa, and HepG2 cells (IC50 ≥ 128 μg/mL). The molecular target of the lead compounds was validated through biochemical studies of select analogues with purified M. tuberculosis gyrase and the generation of resistant mutants. The lead compounds were assessed in combination with bedaquiline and pretomanid to determine the clinical potential, and the select lead (158) demonstrated in vivo efficacy in an acute model of TB infection in mice, reducing the lung bacterial burden by approximately 3 log10 versus untreated control mice. The advancement of DNA gyrase inhibitors expands the field of innovative therapies for tuberculosis and may offer an alternative to fluoroquinolones in future therapeutic regimens.

Management and prevention of Neisseria meningitidis and Neisseria gonorrhoeae infections in the context of evolving antimicrobial resistance trends

PURPOSE

To describe the relationships between Neisseria meningitidis (NM) and Neisseria gonorrhoeae (NG) at genetic, population, and individual levels; to review historical trends in antimicrobial resistance (AMR); to review the treatment and preventive landscapes and explore their potential impact on AMR.

METHODS

A narrative literature search was conducted in PubMed, with searches restricted to 2003-2023 and additional articles included based on expertise.

RESULTS

NM and NG are closely related bacterial pathogens causing invasive meningococcal disease (IMD) and gonorrhea, respectively. NM can currently be treated with most antibiotics and generally has a wild-type susceptibility profile, whereas NG is increasingly resistant even in the first line of treatment. These pathogens share 80-90% genetic identity and can asymptomatically cohabit the pharynx. While AMR has historically been rare for NM, recent reports show this to be an emerging clinical concern. Extensively drug-resistant NG are reported globally, with data available from 73 countries, and can lead to treatment failure. Importantly, Neisseria commensals within the normal microbiota in the pharynx can act as a genetic reservoir of resistance to extended-spectrum cephalosporins. Novel oral antibiotics are urgently needed to treat a growing threat from antibiotic-resistant NG, recognized as a major global concern to public health by the World Health Organization. Numerous vaccines are available to prevent IMD, but none are approved for gonorrhea. Research to identify suitable candidates is ongoing.

CONCLUSION

Holistic management of AMR in IMD and gonorrhea should couple judicious use of existing antibiotics, optimization of vaccination programs, and development of novel antibiotics and vaccines.

Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics

Urinary tract infections (UTIs), which include any infection of the urethra, bladder or kidneys, account for an estimated 400 million infections and billions of dollars in health-care spending per year. The most common bacterium implicated in UTI is uropathogenic Escherichia coli, but diverse pathogens including Klebsiella, Enterococcus, Pseudomonas, Staphylococcus and even yeast such as Candida species can also cause UTIs. UTIs occur in both women and men and in both healthy and immunocompromised patients. However, certain patient factors predispose to disease: for example, female sex, history of prior UTI, or the presence of a urinary catheter or other urinary tract abnormality. The current clinical paradigm for the treatment of UTIs involves the use of antibiotics. Unfortunately, the efficacy of this approach is dwindling as the prevalence of antimicrobial resistance rises among UTI isolates, and the immense quantity of antibiotics prescribed annually for these infections contributes to the emergence of resistant pathogens. Therefore, there is an urgent need for new antibiotics and non-antibiotic treatment and prevention strategies. In this Review, we discuss how recent studies of bacterial pathogenesis, recurrence, persistence, host-pathogen interactions and host susceptibility factors have elucidated new and promising targets for the treatment and prevention of UTIs.

Microwave-assisted synthesis and in vitro and in silico studies of pyrano[3,2-c]quinoline-3-carboxylates as dual acting anti-cancer and anti-microbial agents and potential topoisomerase II and DNA-gyrase inhibitors

A microwave-assisted method was utilized to synthesize novel pyranoquinolone derivatives as dual acting topoisomerase II/DNA gyrase inhibitors with apoptosis induction ability for halting lung cancer and staphylococcal infection. Herein, the designed rationale was directed toward mimicking the structural features of both topoisomerase II and DNA gyrase inhibitors as well as endowing them with apoptosis induction potential. The absolute configuration of the series was assigned using X-ray diffraction analysis. Cytotoxic activity against NSCLC A549 cells showed that ethyl 2-amino-9-bromo-4-(furan-2-yl)-5-oxo-5,6-dihydro-4H-pyrano[3,2-c]quinoline-3-carboxylate (IC50 ≈ 35 μM) was the most potent derivative in comparison to the positive control Levofloxacin and was selected for further investigation to assess its selectivity (SI = 1.23). Furthermore, in vitro antibacterial screening revealed the potential activity of this bromo derivative against Staphylococcus aureus. Mechanistic studies showed that the aforementioned compound exhibited promising inhibitory activity against topoisomerase II (IC50 = 45.19 μM) and DNA gyrase (IC50 = 40.76 μM) compared to reference standards. In addition, the previous compound induced a A549 cell apoptosis by 38.49-fold and it also increased the total apoptosis by 20.4% compared to a 0.53% increase in the control. Docking simulations postulated its interactions and suggested well fitting into its molecular targets.

Synthesis and antibacterial evaluation of quinoline-sulfonamide hybrid compounds: a promising strategy against bacterial resistance

Antibiotic-resistant bacteria are a serious global health threat, making infections harder to treat and increasing medical costs and mortality rates. To combat resistant bacterial strains, a series of compounds (QS1-12) were synthesized with an excellent yield of 85-92%. Initial assessments of these analogues as potential antibacterial agents were conducted through a preliminary screening against a panel of diverse bacterial strains. The results identified compound QS-3 as the most effective antibacterial candidate, exhibiting exceptional inhibitory activity against P. aeruginosa with a minimum inhibitory concentration (MIC) of 64 μg mL-1. Furthermore, QS-3 demonstrated a favorable synergistic effect when combined with ciprofloxacin. Notably, the compound displayed minimal cytotoxicity, inducing less than 5% lysis of red blood cells (RBCs). Significantly, QS-3 exhibited enhanced inhibitory activity, particularly against the antibiotic-resistant strains AA202 and AA290. In silico predictions of physicochemical properties underscored the drug-like qualities of the designed compounds. Additionally, molecular docking poses, ligPlot images, and a binding affinity of -8.0 kcal mol-1 further reinforced their potential as promising antibacterial agents. Briefly, the reported compound QS3 may be a future broad-range antibacterial agent.

Isolation and Analysis of Rare Enzymatic Events with Multiplex Flow Magnetic Tweezers

Our understanding of biomolecular dynamics has been revolutionized with the advent of techniques that enable the manipulation of forces and torques at the single-molecule level. However, the characterization of rare intermediates has proven challenging due to limited throughput. In this chapter, we present a method that dramatically enhances the throughput of force spectroscopy measurements with topological control. The method allows for routine imaging of tens of thousands of individual molecules undergoing millions of reaction cycles in parallel. The improvement in throughput enables the discovery of rare enzymatic events. Here, we describe the experimental procedures for the observation and analysis of supercoiling dynamics by DNA gyrase. To efficiently quantify diverse dynamic behaviors and rare events, we introduce a software platform with an incorporated automated feature classification pipeline. This method and accompanying software can be freely adapted for investigations into a wide array of complex, multistep enzymatic pathways where the characterization of rare intermediates has been hindered by limited throughput.

Exploring the Antimicrobial Potential of Novel 1,2,4-Triazole Conjugates with Pyrazole: Synthesis, Biological Activity and In Silico Docking

In the present study, a new series of 1,2,4-triazole linked pyrazole hybrids (5 a-5 l) were synthesized from dimethyl amino pyrazole (1) in good yield by three-step reaction. The chemical structures of the resulted compounds were thoroughly elucidated using spectral analyses such as IR, 1H-NMR, 13C-NMR, mass spectra and elemental analysis. The target compounds were screened for their antimicrobial activity against the various standard pathogenic Gram-(-ve) (E. coli, P. aeruginosa, K. pneumoniae, A. baumannii), and Gram-(+ve) (S. aureus, S. faecalis) microorganisms. According to the results obtained, in particular, compounds 5 b, 5 f, 5 h and 5 j was effective at inhibiting the antibacterial growth of all the bacteria's, having MIC values ranging 0.983-14.862 mg/mL and compared to moxifloxacin (1.391-22.01 mg mL-1). The most active compounds were chosen to interact with the DNA gyrase and topoisomerase-IV targets via molecular docking. These selected ligands interacted with 2XCO, 1S16 targets and docked into the active site of amino acids Ala-269, Gly-413, Asn-405, Ser-1182, Thr-1185, His-1186, His-1186, Lys-1189, and Trp-1213. Computational studies were carried out to design the precursor compounds to support the experimental part of the study. The pharmacokinetic properties, stability, and drug-likeness parameters of all target molecules were estimated using SwissADME and PkCSM protocols. The current study used in silico approaches combining e-pharmacophore modeling and structure-based molecular docking of targets to identify antimicrobial agents.

Antimicrobial resistance: a concise update

Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately 5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted and cohesive approach that ranges from increased understanding of mechanisms and drivers at the individual and population levels, AMR surveillance, antimicrobial stewardship, improved infection prevention and control measures, and strengthened global policies and funding to development of novel antimicrobial therapeutic strategies. In this rapidly advancing field, this Review provides a concise update on AMR, encompassing epidemiology, evolution, underlying mechanisms (primarily those related to last-line or newer generation of antibiotics), infection prevention and control measures, access to antibiotics, antimicrobial stewardship, AMR surveillance, and emerging non-antibiotic therapeutic approaches. The Review also discusses the potential roles of artificial intelligence in addressing AMR, including antimicrobial susceptibility testing, AMR surveillance, antimicrobial stewardship, diagnosis, and antimicrobial drug discovery and development. This Review highlights the urgent need for addressing the global effects of AMR and for rapid advancement of relevant technology in this dynamic field.

How Do Gepotidacin and Zoliflodacin Stabilize DNA-Cleavage Complexes with Bacterial Type IIA Topoisomerases? 2. A Single Moving Metal Mechanism

DNA gyrase is a bacterial type IIA topoisomerase that can create temporary double-stranded DNA breaks to regulate DNA topology and an archetypical target of antibiotics. The widely used quinolone class of drugs use a water-metal ion bridge in interacting with the GyrA subunit of DNA gyrase. Zoliflodacin sits in the same pocket as quinolones but interacts with the GyrB subunit and also stabilizes lethal double-stranded DNA breaks. Gepotidacin has been observed to sit on the twofold axis of the complex, midway between the two four-base-pair separated DNA-cleavage sites and has been observed to stabilize singe-stranded DNA breaks. Here, we use information from three crystal structures of complexes of Staphlococcus aureus DNA gyrase (one with a precursor of gepotidacin and one with the progenitor of zoliflodacin) to propose a simple single moving metal-ion-catalyzed DNA-cleavage mechanism. Our model explains why the catalytic tyrosine is in the tyrosinate (negatively charged) form for DNA cleavage. Movement of a single catalytic metal-ion (Mg2+ or Mn2+) guides water-mediated protonation and cleavage of the scissile phosphate, which is then accepted by the catalytic tyrosinate. Type IIA topoisomerases need to be able to rapidly cut the DNA when it becomes positively supercoiled (in front of replication forks and transcription bubbles) and we propose that the original purpose of the small Greek Key domain, common to all type IIA topoisomerases, was to allow access of the catalytic metal to the DNA-cleavage site. Although the proposed mechanism is consistent with published data, it is not proven and other mechanisms have been proposed. Finally, how such mechanisms can be experimentally distinguished is considered.

Ammar Y, A. Abu Ali O, Ragab A, Mahfoz AM, Abusaif MS. Fluorinated indeno-quinoxaline bearing thiazole moieties as hypoglycaemic agents targeting α-amylase, and α-glucosidase: synthesis, molecular docking, and ADMET studies

Inhibition of α-glucosidase and α-amylase are key tactics for managing blood glucose levels. Currently, stronger, and more accessible inhibitors are needed to treat diabetes. Indeno[1,2-b] quinoxalines-carrying thiazole hybrids 1-17 were created and described using NMR. All analogues were tested for hypoglycaemic effect against STZ-induced diabetes in mice. Compounds 4, 6, 8, and 16 were the most potent among the synthesised analogues. These hybrids were examined for their effects on plasma insulin, urea, creatinine, GSH, MDA, ALT, AST, and total cholesterol. Moreover, these compounds were tested against α-glucosidase and α-amylase enzymes in vitro. The four hybrids 4, 6, 8, and 16 represented moderate to potent activity with IC50 values 0.982 ± 0.04, to 10.19 ± 0.21 for α-glucosidase inhibition and 17.58 ± 0.74 to 121.6 ± 5.14 μM for α-amylase inhibition when compared to the standard medication acarbose with IC50=0.316 ± 0.02 μM for α-glucosidase inhibition and 31.56 ± 1.33 μM for α-amylase inhibition. Docking studies as well as in silico ADMT were done.

Quinolone antibiotics stimulate bacterial mercury methylation by Geobacter metallireducens GS-15

Bacterial mercury (Hg) methylation is critical for bioremediating Hg pollution, but the impact of emerging antibiotics on this process has rarely been reported. This study innovatively investigated the interactions between Hg-methylating bacteria of Geobacter metallireducens GS-15 and two quinolone antibiotics: lomefloxacin (LOM) and ciprofloxacin (CIP) at 5 μg/L. Short-term LOM exposure increased methylmercury (MeHg) yield by 36 % compared to antibiotic-free conditions, caused by hormesis to alter bioactivities of single GS-15 cells. Long-term CIP exposure led to more antibiotic resistance and mercury tolerance in GS-15 cells, doubling MeHg productivity and significantly increasing expression of Hg methylation (hgcA by 95 folds) and antibiotic resistance (gyrA by 54 folds) genes, while mercury resistance gene merA only increased by 2.5 folds than without selective pressure. These results suggest quinolone antibiotics at environmentally contaminated concentrations stimulate bacterial Hg methylation to form highly toxic MeHg, raising considerable concern for the Hg-antibiotic complex in contaminated environments.

Novel tetrazolyl-1,2,3-triazole derivatives as potent antimicrobial targets: design, synthesis and molecular docking techniques

The main objective of this study is to produce novel triazoles-loaded tetrazoles, which are crucial in the development of prospective therapeutic agents in medicinal chemistry. Recent investigations have found a wide range of uses for these derivatives, and they are prospective lead molecules for the synthesis of substances with enormous therapeutic utility for various diseases, especially for bacterial therapy. New series of 1,2,3-triazole derivatives have been synthesized from methyl (2S,4S)-4-azido-1-(2,4-difluoro-3-methylbenzoyl)pyrrolidine-2-carboxylate (5) using a well-established click reaction that has several advantages to afford a novel heterocyclic compound based on tetrazole moieties. The structures of the new compounds were ascertained by spectral means (IR, NMR: 1H and 13C) and mass spectrum. All the synthesized compounds were assessed in vitro antimicrobial activity against Gram-+ve (S. pyogenes, S. aureus and B. subtilis), Gram-negative (E. coli and P. aeruginosa) bacterial and fungal strains A. flavus and C. albicans. The prepared compounds 7b and7f proved to have strong impact on S. aureus and S. pyogenes strains with MICs of 2.5 µg/mL and 1.5 µg/mL respectively. Among the tested compounds, hybrids 7b, 7f, 7h, and 7i exhibited exceptional antifungal susceptibilities against C. albicans with zone of inhibition 25 ± 0.2, 30 ± 0.3, 30 ± 0.1, and 28 ± 0.2 mm respectively, which is stronger than fluconazole (28 ± 0.1 mm). The capacity of ligand 7f to form a stable compound on the active site of S. aureus complex with DNA Gyrase (2XCT) was confirmed by docking studies using amino acids Ala233(A), Arg234(A), Gly283(A), Ser286(A), Lys52(A), His280(A), Gly51(A), His282(A) and Val246(A). Furthermore, the physicochemical and ADME (absorption, distribution, metabolism, and excretion) filtration molecular properties, estimation of toxicity, and bioactivity scores of these scaffolds were evaluated.

Advancing Topoisomerase Research Using DNA Nanotechnology

In this Perspective, the use of DNA nanotechnology is explored as a powerful tool for studying a family of enzymes known as topoisomerases. These enzymes regulate DNA topology within a living cell and play a major role in the pharmaceutical field, serving as anti-cancer and anti-bacterial targets. This Perspective will provide a short historical overview of the methods employed in studying these enzymes and emphasizing recent advancements in assays using DNA nanotechnology. These innovations have substantially improved accuracy and expanded the understanding of enzyme activity. This perspective will showcase the versatile utility of DNA nanotechnology in advancing scientific knowledge and its application in exploring new drug candidates, particularly in the study of topoisomerase enzymes.

Recent developments of topoisomerase inhibitors: Clinical trials, emerging indications, novel molecules and global sales

The nucleic acid topoisomerases (TOP) are an evolutionary conserved mechanism to solve topological problems within DNA and RNA that have been historically well-established as a chemotherapeutic target. During investigation of trends within clinical trials, we have identified a very high number of clinical trials involving TOP inhibitors, prompting us to further evaluate the current status of this class of therapeutic agents. In total, we have identified 233 unique molecules with TOP-inhibiting activity. In this review, we provide an overview of the clinical drug development highlighting advances in current clinical uses and discussing novel drugs and indications under development. A wide range of bacterial infections, along with solid and hematologic neoplasms, represent the bulk of clinically approved indications. Negative ADR profile and drug resistance among the antibacterial TOP inhibitors and anthracycline-mediated cardiotoxicity in the antineoplastic TOP inhibitors are major points of concern, subject to continuous research efforts. Ongoing development continues to focus on bacterial infections and cancer; however, there is a degree of diversification in terms of novel drug classes and previously uncovered indications, such as glioblastoma multiforme or Clostridium difficile infections. Preclinical studies show potential in viral, protozoal, parasitic and fungal infections as well and suggest the emergence of a novel target, TOP IIIβ. We predict further growth and diversification of the field thanks to the large number of experimental TOP inhibitors emerging.

Facile one-pot synthesis of N-pyridinylaminonaphthol derivatives and their antibacterial evaluation against multidrug-resistant Staphylococcus aureus

The escalating severity of the menace posed by bacterial resistance has rendered the existing antibiotics less effective, thus necessitating the discovery of new antibacterial agents. The current study reports the exploration of substituted N-pyridinylaminonaphthols produced by a straightforward, one-pot multicomponent reaction process as antibacterial agents. The synthesized derivatives were assessed in vitro for their antibacterial properties against a panel of bacterial pathogens. The analogs 4b, 4g, 4h, 4i, 4j, 4l, 4r, and 4t exhibited potent inhibitory activity with minimum inhibitory concentration (MIC) values of 1-2 µg/mL. Notably, 4b, 4l, and 4t displayed an excellent selectivity index. Additionally, they were active against the multidrug-resistant bacterial strains, with 4l exhibiting the best activity against methicillin-resistant Staphylococcus aureus and vancomycin resistant staphylococcus aureus with a MIC of 1 µg/mL. 4l showed synergism with gentamycin and showed bactericidal property in a concentration-dependent manner. Furthermore, the molecule 4l inhibited the DNA gyrase supercoiling activity. Absorption, distribution, metabolism, excretion/toxicity parameters and pharmacokinetic properties were assessed via in silico techniques, which elucidate the potential mode of action. These findings demonstrate the potential of the N-pyridinylaminonaphthol derivatives as antibacterial agents against multidrug-resistant S. aureus.

Introducing of novel class of pyrano[2,3-c]pyrazole-5-carbonitrile analogs with potent antimicrobial activity, DNA gyrase inhibition, and prominent pharmacokinetic and CNS toxicity profiles supported by molecular dynamic simulation

Microbiological DNA gyrase is recognized as an exceptional microbial target for the innovative development of low-resistant and more effective antimicrobial drugs. Hence, we introduced a one-pot facile synthesis of a novel pyranopyrazole scaffold bearing different functionalities; substituted aryl ring, nitrile, and hydroxyl groups. All new analogs were characterized with full spectroscopic data. The antimicrobial screening for all analogs was assessed against standard strains of Gm + ve and Gm-ve through in vitro considers. The screened compounds displayed very promising MIC/MBC values against some of the bacterial strains with broad or selective antibacterial effects. Of these, 4j biphenyl analog showed 0.5-2/2-8 µg/mL MIC/MBC for suppression and killing of Gm + ve and Gm-ve strains. Moreover, the antimicrobial screening was assessed for the most potent analogs against certain highly resistant microbial strains. Consequently, DNA gyrase supercoiling assay was done for all analogs using ciprofloxacin as reference positive control. Obviously, the results showed a different activity profile with potent analog 4j with IC50 value 6.29 µg/mL better than reference drug 10.2 µg/mL. Additionally, CNS toxicity testing was done using the HiB5 cell line for attenuation of GABA/NMDA expression to both 4j and ciprofloxacin compounds that revealed better neurotransmitter modulation by novel scaffold. Importantly, docking and dynamic simulations were performed for the most active 4j analog to investigate its interaction with DNA binding sites, which supported the in vitro observations and compound stability with binding pocket. Finally, a novel scaffold pyranopyrazole was introduced as a DNA gyrase inhibitor with prominent antibacterial efficacy and low CNS side effect toxicity better than quinolones.Communicated by Ramaswamy H. Sarma.

How Do Gepotidacin and Zoliflodacin Stabilize DNA Cleavage Complexes with Bacterial Type IIA Topoisomerases? 1. Experimental Definition of Metal Binding Sites

One of the challenges for experimental structural biology in the 21st century is to see chemical reactions happen. Staphylococcus aureus (S. aureus) DNA gyrase is a type IIA topoisomerase that can create temporary double-stranded DNA breaks to regulate DNA topology. Drugs, such as gepotidacin, zoliflodacin and the quinolone moxifloxacin, can stabilize these normally transient DNA strand breaks and kill bacteria. Crystal structures of uncleaved DNA with a gepotidacin precursor (2.1 Å GSK2999423) or with doubly cleaved DNA and zoliflodacin (or with its progenitor QPT-1) have been solved in the same P61 space-group (a = b ≈ 93 Å, c ≈ 412 Å). This suggests that it may be possible to observe the two DNA cleavage steps (and two DNA-religation steps) in this P61 space-group. Here, a 2.58 Å anomalous manganese dataset in this crystal form is solved, and four previous crystal structures (1.98 Å, 2.1 Å, 2.5 Å and 2.65 Å) in this crystal form are re-refined to clarify crystal contacts. The structures clearly suggest a single moving metal mechanism-presented in an accompanying (second) paper. A previously published 2.98 Å structure of a yeast topoisomerase II, which has static disorder around a crystallographic twofold axis, was published as containing two metals at one active site. Re-refined coordinates of this 2.98 Å yeast structure are consistent with other type IIA topoisomerase structures in only having one metal ion at each of the two different active sites.

Molecular mechanism of a triazole-containing inhibitor of Mycobacterium tuberculosis DNA gyrase

Antimicrobial resistance remains a persistent and pressing public health concern. Here, we describe the synthesis of original triazole-containing inhibitors targeting the DNA gyrase, a well-validated drug target for developing new antibiotics. Our compounds demonstrate potent antibacterial activity against various pathogenic bacteria, with notable potency against Mycobacterium tuberculosis (Mtb). Moreover, one hit, compound 10a, named BDM71403, was shown to be more potent in Mtb than the NBTI of reference, gepotidacin. Mechanistic enzymology assays reveal a competitive interaction of BDM71403 with fluoroquinolones within the Mtb gyrase cleavage core. High-resolution cryo-electron microscopy structural analysis provides detailed insights into the ternary complex formed by the Mtb gyrase, double-stranded DNA, and either BDM71403 or gepotidacin, providing a rational framework to understand the superior in vitro efficacy on Mtb. This study highlights the potential of triazole-based scaffolds as promising gyrase inhibitors, offering new avenues for drug development in the fight against antimicrobial resistance.

Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R

The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.

A Review of Antibacterial Candidates with New Modes of Action

There is a lack of new antibiotics to combat drug-resistant bacterial infections that increasingly threaten global health. The current pipeline of clinical-stage antimicrobials is primarily populated by "new and improved" versions of existing antibiotic classes, supplemented by several novel chemical scaffolds that act on traditional targets. The lack of fresh chemotypes acting on previously unexploited targets (the "holy grail" for new antimicrobials due to their scarcity) is particularly unfortunate as these offer the greatest opportunity for innovative breakthroughs to overcome existing resistance. In recognition of their potential, this review focuses on this subset of high value antibiotics, providing chemical structures where available. This review focuses on candidates that have progressed to clinical trials, as well as selected examples of promising pioneering approaches in advanced stages of development, in order to stimulate additional research aimed at combating drug-resistant infections.

Role of DNA Double-Strand Break Formation in Gyrase Inhibitor-Mediated Killing of Nonreplicating Persistent Mycobacterium tuberculosis in Caseum

Tuberculosis is the leading cause of mortality by infectious agents worldwide. The necrotic debris, known as caseum, which accumulates in the center of pulmonary lesions and cavities is home to nonreplicating drug-tolerant Mycobacterium tuberculosis that presents a significant hurdle to achieving a fast and durable cure. Fluoroquinolones such as moxifloxacin are highly effective at killing this nonreplicating persistent bacterial population and boosting TB lesion sterilization. Fluoroquinolones target bacterial DNA gyrase, which catalyzes the negative supercoiling of DNA and relaxes supercoils ahead of replication forks. In this study, we investigated the potency of several other classes of gyrase inhibitors against M. tuberculosis in different states of replication. In contrast to fluoroquinolones, many other gyrase inhibitors kill only replicating bacterial cultures but produce negligible cidal activity against M. tuberculosis in ex vivo rabbit caseum. We demonstrate that while these inhibitors are capable of inhibiting M. tuberculosis gyrase DNA supercoiling activity, fluoroquinolones are unique in their ability to cleave double-stranded DNA at low micromolar concentrations. We hypothesize that double-strand break formation is an important driver of gyrase inhibitor-mediated bactericidal potency against nonreplicating persistent M. tuberculosis populations in the host. This study provides general insight into the lesion sterilization potential of different gyrase inhibitor classes and informs the development of more effective chemotherapeutic options against persistent mycobacterial infections.

Discovery of aminopiperidine based potent & novel topoisomerase inhibitor with broad spectrum anti-bacterial activity

Bacterial DNA gyrase and topoisomerase IV inhibition has emerged as a promising strategy for the cure of infections caused by antibiotic-resistant bacteria. The Novel Bacterial Topoisomerase Inhibitors (NBTIs) bind to a different site from that of the quinolones with novel mechanism of action. This evades the existing target-mediated bacterial resistance associated with quinolones. This article presents our efforts to identify in vitro potent and broad-spectrum antibacterial agent 4l.

Pyrimidine-based sulfonamides and acetamides as potent antimicrobial Agents: Synthesis, Computational Studies, and biological assessment

A series of novel sulfonamide and acetamide derivatives of pyrimidine were synthesized and their antimicrobial activities were assessed. Based on the Microbroth dilution method, the minimum inhibitory concentration (MIC) of the synthesized compounds demonstrated moderate to good levels of antifungal and antibacterial activity. Structure-activity relationship analysis suggested that the presence of electron-withdrawing groups, such as halogens, nitrile, and nitro groups, on the pyrimidine ring contributed to the enhanced antimicrobial potency, while electron-donating substituents led to a decrease in activity. Computational studies, including density functional theory (DFT), frontier molecular orbitals (FMO), and molecular electrostatic potential (MEP) analysis, provided insights into the electronic properties and charge distribution of the compounds. Drug-likeness evaluation using ADME/Tox analysis indicated that the synthesized compounds possess favorable physicochemical properties and could be potential drug candidates. Molecular docking against the Mycobacterium TB protein tyrosine phosphatase B (MtbPtpB) revealed that the synthesized compounds exhibited strong binding affinities (-46 kcal/mol to - 61 kcal/mol) and formed stable protein-ligand complexes through hydrogen bonding and π-π stacking interactions with key residues in the active site. The observed interactions from the docking simulations were consistent with the predicted interaction sites identified in the FMO and MEP analyses. These findings suggest that the synthesized pyrimidine derivatives could serve as promising antimicrobial agents and warrant further investigation for drug development.

Identification of potential Escherichia coli DNA gyrase B inhibitors targeting antibacterial therapy: an integrated docking and molecular dynamics simulation study

The alarming rise in the rate of antibiotic resistance is a matter of significant concern. DNA gyrase B (GyrB), a critical bacterial enzyme involved in DNA replication, transcription, and recombination, has emerged as a promising target for antibacterial agents. Inhibition of GyrB disrupts bacterial DNA replication, leading to cell death, making it an attractive candidate for antibiotic development. Although several classes of antibiotics targeting GyrB are currently in clinical use, the emergence of antibiotic resistance necessitates the exploration of novel inhibitors. In this study, we aimed to identify potential Escherichia coli GyrB inhibitors from a database of phytoconstituents sourced from Indian medicinal plants. Utilizing virtual screening, we performed a rigorous search to identify compounds with the most promising inhibitory properties against GyrB. Two compounds, namely Zizogenin and Cucurbitacin S, were identified based on their favorable drug likeliness and pharmacokinetic profiles. Employing advanced computational techniques, we analyzed the binding interactions of Zizogenin and Cucurbitacin S with the ATP-binding site of GyrB through molecular docking simulations. Both compounds exhibited robust binding interactions, evidenced by their high docking energy scores. To assess the stability of these interactions, we conducted extensive 100 ns molecular dynamics (MD) simulations, which confirmed the stability of Zizogenin and Cucurbitacin S when bound to GyrB. In conclusion, our study highlights Zizogenin and Cucurbitacin S as promising candidates for potential antibacterial agents targeting GyrB. Experimental validation of these compounds is warranted to further explore their efficacy and potential as novel antibiotics to combat antibiotic-resistant bacteria.Communicated by Ramaswamy H. Sarma.

BWC0977, a broad-spectrum antibacterial clinical candidate to treat multidrug resistant infections

The global crisis of antimicrobial resistance (AMR) necessitates the development of broad-spectrum antibacterial drugs effective against multi-drug resistant (MDR) pathogens. BWC0977, a Novel Bacterial Topoisomerase Inhibitor (NBTI) selectively inhibits bacterial DNA replication via inhibition of DNA gyrase and topoisomerase IV. BWC0977 exhibited a minimum inhibitory concentration (MIC90) of 0.03-2 µg/mL against a global panel of MDR Gram-negative bacteria including Enterobacterales and non-fermenters, Gram-positive bacteria, anaerobes and biothreat pathogens. BWC0977 retains activity against isolates resistant to fluoroquinolones (FQs), carbapenems and colistin and demonstrates efficacy against multiple pathogens in two rodent species with significantly higher drug levels in the epithelial lining fluid of infected lungs. In healthy volunteers, single-ascending doses of BWC0977 administered intravenously ( https://clinicaltrials.gov/study/NCT05088421 ) was found to be safe, well tolerated (primary endpoint) and achieved dose-proportional exposures (secondary endpoint) consistent with modelled data from preclinical studies. Here, we show that BWC0977 has the potential to treat a range of critical-care infections including MDR bacterial pneumonias.

Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq

Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability and a number of clinically important anticancer and antibacterial drugs, e.g. quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50-fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e. negative versus positive supercoiling. SHAN-seq's exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.

Structural insights into the assembly of type IIA topoisomerase DNA cleavage-religation center

The ability to catalyze reversible DNA cleavage and religation is central to topoisomerases' role in regulating DNA topology. In type IIA topoisomerases (Top2), the formation of its DNA cleavage-religation center is driven by DNA-binding-induced structural rearrangements. These changes optimally position key catalytic modules, such as the active site tyrosine of the WHD domain and metal ion(s) chelated by the TOPRIM domain, around the scissile phosphodiester bond to perform reversible transesterification. To understand this assembly process in detail, we report the catalytic core structures of human Top2α and Top2β in an on-pathway conformational state. This state features an in trans formation of an interface between the Tower and opposing TOPRIM domain, revealing a groove for accommodating incoming G-segment DNA. Structural superimposition further unveils how subsequent DNA-binding-induced disengagement of the TOPRIM and Tower domains allows a firm grasp of the bound DNA for cleavage/religation. Notably, we identified a previously undocumented protein-DNA interaction, formed between an arginine-capped C-terminus of an α-helix in the TOPRIM domain and the DNA backbone, significantly contributing to Top2 function. This work uncovers a previously unrecognized role of the Tower domain, highlighting its involvement in anchoring and releasing the TOPRIM domain, thus priming Top2 for DNA binding and cleavage.

In silico gepotidacin target mining among 33 213 global Neisseria gonorrhoeae genomes from 1928 to 2023 combined with gepotidacin MIC testing of 22 gonococcal isolates with different GyrA and ParC substitutions

OBJECTIVES

The novel dual-target triazaacenaphthylene, gepotidacin, recently showed promising results in its Phase III randomized controlled trial for the treatment of gonorrhoea. We investigated alterations in the gepotidacin GyrA and ParC targets in gonococci by in silico mining of publicly available global genomes (n = 33 213) and determined gepotidacin MICs in isolates with GyrA A92 alterations combined with other GyrA and/or ParC alterations.

METHODS

We examined gonococcal gyrA and parC alleles available at the European Nucleotide Archive. MICs were determined using the agar dilution method (gepotidacin) or Etest (four antimicrobials). Models of DNA gyrase and topoisomerase IV were obtained from AlphaFold and used to model gepotidacin in the binding site.

RESULTS

GyrA A92 alterations were identified in 0.24% of genomes: GyrA A92P/S/V + S91F + D95Y/A/N (0.208%), A92P + S91F (0.024%) and A92P (0.003%), but no A92T (previously associated with gepotidacin resistance) was found. ParC D86 alterations were found in 10.6% of genomes: ParC D86N/G (10.5%), D86N + S87I (0.051%), D86N + S88P (0.012%) and D86G + E91G (0.003%). One isolate had GyrA A92P + ParC D86N alterations, but remained susceptible to gepotidacin (MIC = 0.125 mg/L). No GyrA plus ParC alterations resulted in a gepotidacin MIC > 4 mg/L. Modelling of gepotidacin binding to GyrA A92/A92T/A92P suggested that gepotidacin resistance due to GyrA A92T might be linked to the formation of a new polar contact with DNA.

CONCLUSIONS

In silico mining of 33 213 global gonococcal genomes (isolates from 1928 to 2023) showed that A92 is highly conserved in GyrA, while alterations in D86 of ParC are common. No GyrA plus ParC alterations caused gepotidacin resistance. MIC determination and genomic surveillance of potential antimicrobial resistance determinants are imperative.

Discovery of new quaternized norharmane dimers as potential anti-MRSA agents

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA)-caused infections greatly threaten public health. The discovery of natural-product-based anti-MRSA agents for treating infectious diseases has become one of the current research focuses.

OBJECTIVES

This study aims to identify promising anti-MRSA agents with a clear mechanism based on natural norharmane modified by quaternization or dimerization.

METHODS

A total of 32 norharmane analogues were prepared and characterized. Their antibacterial activities and resistance development propensity were tested by the broth double-dilution method. Cell counting kit-8 and hemolysis experiments were used to assess their biosafety. The plasma stability, bactericidal mode, and biofilm disruption effects were examined by colony counting and crystal violet staining assays. Fluorescence microscopy, metabolomic analysis, docking simulation and spectra titration revealed its anti-MRSA mechanisms. The mouse skin infection model was used to investigate the in vivo efficacy.

RESULTS

Compound 5a was selected as a potential anti-MRSA agent, which exhibited potent anti-MRSA activity in vitro and in vivo, low cytotoxicity and hemolysis under an effective dose. Moreover, compound 5a showed good stability in 50% plasma, a low tendency of resistance development and capabilities to disrupt bacterial biofilms. The mechanism studies revealed that compound 5a could inhibit the biosynthesis of bacteria cell walls, damage the membrane, disturb energy metabolism and amino acid metabolism pathways, and interfere with protein synthesis and nucleic acid function.

CONCLUSIONS

These results suggested that compound 5a is a promising candidate for combating MRSA infections, providing valuable information for further exploiting a new generation of therapeutic antibiotics.

An in silico molecular docking, ADMET and molecular dynamics simulations studies of azolyl-2H-chroman-4-ones as potential inhibitors against pathogenic fungi and bacteria

Antimicrobial resistance is a major global threat. In an attempt to discover new compounds with improved efficiency and to overcome drug resistance, a library of 3960 compounds was designed as conformationally rigid analogues of oxiconazole with 2H-chroman-4-one, azole and substituted phenyl fragments. The antifungal and antibacterial activity of the compounds was evaluated using molecular docking studies in the active site of six fungal and four bacterial proteins to establish the binding affinity of the designed ligands. In-silico ADME and Lipinski's rule were used to establish the drug-likeness properties of the compounds. This study revealed that all the designed compounds had a high binding affinity with the target proteins and formed H-bond and π-π interactions. The identified hits have been subjected to molecular dynamics simulations to study protein-ligand complex stability. This study has led to the identification of important compounds that can be developed further as therapeutic agents against pathogenic fungi and bacteria.Communicated by Ramaswamy H. Sarma.

Antibacterial activity of natural flavones against bovine mastitis pathogens: in vitro, SAR analysis, and computational study

Bovine mastitis is a worldwide disease affecting dairy cattle and causes major economic losses in the dairy industry. Recently, the emergence of microbial resistance to the current antibiotics complicates the treatment protocol which necessitates antibiotic stewardship and further research to find new active compounds. Recently, phytobiotics have gained interest in being used as an alternative to antibiotics in the poultry industry as an antibiotic stewardship intervention. This study evaluated the in vitro antibacterial activity of 16 flavonoids against bovine mastitis pathogens. Two flavones: 2-(4-methoxyphenyl)chromen-4-one (1) and 2-(3-hydroxyphenyl)chromen-4-one (4) showed inhibition of the growth of Klebsiella oxytoca with MIC values range (25-50 µg mL- 1) followed by a structure-activity relationship (SAR) study indicating that the presence of a hydroxyl group at C-3` or methoxy at C-4` increases the activity against Klebsiella oxytoca while the presence of hydroxyl group at C-7 decreases the activity. Furthermore, a structure-based drug development approach was applied using several in silico tools to understand the interactions of active flavones at the active site of the DNA gyrase protein. Compound (4) showed a higher docking score than quercetin (standard) which is known to have antibacterial activity by inhibiting the DNA gyrase. In addition, the structure-based pharmacophores of compound (4) and quercetin showed similar pharmacophoric features and interactions with DNA gyrase. Based on our findings, compounds (1) and (4) are promising for further study as potential anti-microbial phytochemicals that can have a role in controlling bovine mastitis as well as to investigate their mechanism of action further.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00253-w.

Interactions between Zoliflodacin and Neisseria gonorrhoeae Gyrase and Topoisomerase IV: Enzymological Basis for Cellular Targeting

Gyrase and topoisomerase IV are the cellular targets for fluoroquinolones, a critically important class of antibacterial agents used to treat a broad spectrum of human infections. Unfortunately, the clinical efficacy of the fluoroquinolones has been curtailed by the emergence of target-mediated resistance. This is especially true for Neisseria gonorrhoeae, the causative pathogen of the sexually transmitted infection gonorrhea. Spiropyrimidinetriones (SPTs), a new class of antibacterials, were developed to combat the growing antibacterial resistance crisis. Zoliflodacin is the most clinically advanced SPT and displays efficacy against uncomplicated urogenital gonorrhea in human trials. Like fluoroquinolones, the primary target of zoliflodacin in N. gonorrhoeae is gyrase, and topoisomerase IV is a secondary target. Because unbalanced gyrase/topoisomerase IV targeting has facilitated the evolution of fluoroquinolone-resistant bacteria, it is important to understand the underlying basis for the differential targeting of zoliflodacin in N. gonorrhoeae. Therefore, we assessed the effects of this SPT on the catalytic and DNA cleavage activities of N. gonorrhoeae gyrase and topoisomerase IV. In all reactions examined, zoliflodacin displayed higher potency against gyrase than topoisomerase IV. Moreover, zoliflodacin generated more DNA cleavage and formed more stable enzyme-cleaved DNA-SPT complexes with gyrase. The SPT also maintained higher activity against fluoroquinolone-resistant gyrase than topoisomerase IV. Finally, when compared to zoliflodacin, the novel SPT H3D-005722 induced more balanced double-stranded DNA cleavage with gyrase and topoisomerase IV from N. gonorrhoeae, Escherichia coli, and Bacillus anthracis. This finding suggests that further development of the SPT class could yield compounds with a more balanced targeting against clinically important bacterial infections.

Modeling allosteric mechanisms of eukaryotic type II topoisomerases

Type II topoisomerases (TopoIIs) are ubiquitous enzymes that are involved in crucial nuclear processes such as genome organization, chromosome segregation, and other DNA metabolic processes. These enzymes function as large, homodimeric complexes that undergo a complex cycle of binding and hydrolysis of two ATP molecules in their ATPase domains, which regulates the capture and passage of one DNA double-helix through a second, cleaved DNA molecule. This process requires the transmission of information about the state of the bound nucleotide over vast ranges in the TopoII complex. How this information is transmitted at the molecular level to regulate TopoII functions and how protein substitutions disrupt these mechanisms remains largely unknown. Here, we employed extensive microsecond-scale molecular dynamics simulations of the yeast TopoII enzyme in multiple nucleotide-bound states and with amino acid substitutions near both the N and C termini of the complex. Simulation results indicate that the ATPase domains are remarkably flexible on the sub-microsecond timescale and that these dynamics are modulated by the identity of the bound nucleotides and both local and distant amino acid substitutions. Network analyses point toward specific allosteric networks that transmit information about the hydrolysis cycle throughout the complex, which include residues in both the protein and the bound DNA molecule. Amino acid substitutions weaken many of these pathways. Together, our results provide molecular level details on how the TopoII catalytic cycle is controlled through nucleotide binding and hydrolysis and how mutations may disrupt this process.

In vitro activity of gepotidacin and comparator antimicrobials against isolates of nontuberculous mycobacteria (NTM)

Novel antimicrobials are needed to treat rising nontuberculous mycobacteria (NTM) infections. Using standard broth microdilution methods, 68 NTM isolates were tested against gepotidacin, a new, first-in-class, oral triazaacenaphthylene bacterial topoisomerase inhibitor. MICs varied (0.25 to >64 µg/mL) with the lowest being M. fortuitum complex (0.25-8 µg/mL), M. mucogenicum complex (1-2 µg/mL), M. kansasii (0.25-8 µg/mL), and M. marinum (4-16 µg/mL). Testing greater numbers of some species is suggested to better understand gepotidacin activity against NTM.

Management of Neisseria gonorrhoeae infection: from drug resistance to drug repurposing

INTRODUCTION

Neisseria gonorrhoeae is a common sexually transmitted disease connected with extensive drug resistance to many antibiotics. Presently, only expanded spectrum cephalosporins (ceftriaxone and cefixime) and azithromycin remain useful for its management.

AREAS COVERED

New chemotypes for the classical antibiotic drug target gyrase/topoisomerase IV afforded inhibitors with potent binding to these enzymes, with an inhibition mechanism distinct from that of fluoroquinolones, and thus less prone to mutations. The α-carbonic anhydrase from the genome of this bacterium (NgCAα) was also validated as an antibacterial target.

EXPERT OPINION

By exploiting different subunits from the gyrase/topoisomerase IV as well as new chemotypes, two new antibiotics reached Phase II/III clinical trials, zoliflodacin and gepotidacin. They possess a novel inhibition mechanism, binding in distinct parts of the enzyme compared to the fluoroquinolones. Other chemotypes with inhibitory activity in these enzymes were also reported. NgCAα inhibitors belonging to a variety of classes were obtained, with several sulfonamides showing MIC values in the range of 0.25-4 µg/mL and significant activity in animal models of this infection. Acetazolamide and similar CA inhibitors might thus be repurposed as antiinfectives. The scientific/patent literature has been searched for on PubMed, ScienceDirect, Espacenet, and PatentGuru, from 2016 to 2024.

Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq

Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seq's exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.

Dynamic Profiling and Binding Affinity Prediction of NBTI Antibacterials against DNA Gyrase Enzyme by Multidimensional Machine Learning and Molecular Dynamics Simulations

Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs) are a newly disclosed class of antibacterials. Prediction of their binding affinity to these enzymes would be beneficial for de novo design/optimization of new NBTIs. Utilizing in vitro NBTI experimental data, we constructed two comprehensive multidimensional DNA gyrase surrogate models for Staphylococcus aureus (q2 = 0.791) and Escherichia coli (q2 = 0.806). Both models accurately predicted the IC50s of 26 NBTIs from our recent studies. To investigate the NBTI's dynamic profile and binding to both targets, 10 selected NBTIs underwent molecular dynamics (MD) simulations. The analysis of MD production trajectories confirmed key hydrogen-bonding and hydrophobic contacts that NBTIs establish in both enzymes. Moreover, the binding free energies of selected NBTIs were computed by the linear interaction energy (LIE) method employing an in-house derived set of fitting parameters (α = 0.16, β = 0.029, γ = 0.0, and intercept = -1.72), which are successfully applicable to DNA gyrase of Gram-positive/Gram-negative pathogens. Both methods offer accurate predictions of the binding free energies of NBTIs against S. aureus and E. coli DNA gyrase. We are confident that this integrated modeling approach could be valuable in the de novo design and optimization of efficient NBTIs for combating resistant bacterial pathogens.

Target-Mediated Fluoroquinolone Resistance in Neisseria gonorrhoeae: Actions of Ciprofloxacin against Gyrase and Topoisomerase IV

Fluoroquinolones make up a critically important class of antibacterials administered worldwide to treat human infections. However, their clinical utility has been curtailed by target-mediated resistance, which is caused by mutations in the fluoroquinolone targets, gyrase and topoisomerase IV. An important pathogen that has been affected by this resistance is Neisseria gonorrhoeae, the causative agent of gonorrhea. Over 82 million new cases of this sexually transmitted infection were reported globally in 2020. Despite the impact of fluoroquinolone resistance on gonorrhea treatment, little is known about the interactions of this drug class with its targets in this bacterium. Therefore, we investigated the effects of the fluoroquinolone ciprofloxacin on the catalytic and DNA cleavage activities of wild-type gyrase and topoisomerase IV and the corresponding enzymes that harbor mutations associated with cellular and clinical resistance to fluoroquinolones. Results indicate that ciprofloxacin interacts with both gyrase (its primary target) and topoisomerase IV (its secondary target) through a water-metal ion bridge that has been described in other species. Moreover, mutations in amino acid residues that anchor this bridge diminish the susceptibility of the enzymes for the drug, leading to fluoroquinolone resistance. Results further suggest that ciprofloxacin primarily induces its cytotoxic effects by enhancing gyrase-mediated DNA cleavage as opposed to inhibiting the DNA supercoiling activity of the enzyme. In conclusion, this work links the effects of ciprofloxacin on wild-type and resistant gyrase to results reported for cellular and clinical studies and provides a mechanistic explanation for the targeting and resistance of fluoroquinolones in N. gonorrhoeae.

Interactions between Gepotidacin and Escherichia coli Gyrase and Topoisomerase IV: Genetic and Biochemical Evidence for Well-Balanced Dual-Targeting

Antimicrobial resistance is a global threat to human health. Therefore, efforts have been made to develop new antibacterial agents that address this critical medical issue. Gepotidacin is a novel, bactericidal, first-in-class triazaacenaphthylene antibacterial in clinical development. Recently, phase III clinical trials for gepotidacin treatment of uncomplicated urinary tract infections caused by uropathogens, including Escherichia coli, were stopped for demonstrated efficacy. Because of the clinical promise of gepotidacin, it is important to understand how the compound interacts with its cellular targets, gyrase and topoisomerase IV, from E. coli. Consequently, we determined how gyrase and topoisomerase IV mutations in amino acid residues that are involved in gepotidacin interactions affect the susceptibility of E. coli cells to the compound and characterized the effects of gepotidacin on the activities of purified wild-type and mutant gyrase and topoisomerase IV. Gepotidacin displayed well-balanced dual-targeting of gyrase and topoisomerase IV in E. coli cells, which was reflected in a similar inhibition of the catalytic activities of these enzymes by the compound. Gepotidacin induced gyrase/topoisomerase IV-mediated single-stranded, but not double-stranded, DNA breaks. Mutations in GyrA and ParC amino acid residues that interact with gepotidacin altered the activity of the compound against the enzymes and, when present in both gyrase and topoisomerase IV, reduced the antibacterial activity of gepotidacin against this mutant strain. Our studies provide insights regarding the well-balanced dual-targeting of gyrase and topoisomerase IV by gepotidacin in E. coli.