Structure- and Ligand-Dynamics-Based Design of Novel Antibiotics Targeting Lipid A Enzymes LpxC and LpxH in Gram-Negative Bacteria

A combined in silico and MD simulation approach to discover novel LpxC inhibitors targeting multiple drug resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa), a member of the ESKAPE family, is the major cause of infections leading to increased morbidity and mortality due to multidrug resistance (MDR). One of the main proteins involved in the Raetz pathway is LpxC, which plays a significant role in anti-microbial resistance (AMR). Our study aimed to identify a novel compound to combat MDR due to the LpxC protein. It involved in silico methods comprising molecular docking, simulations, ADMET profiling, and DFT calculations. First, an ADMET and bioactivity evaluation of the 25 top-hit compounds retrieved from ligand-based virtual screening was performed, followed by molecular docking. The results revealed compound P-2 as the lead compound, which was further subjected to DFT analysis and molecular dynamics (MD) simulations. With these analyses, our in silico study identified P-2, 3-[(dimethylamino)methyl]-N-[(2 S)-1-(hydroxyamino)-1-oxobutan-2-yl]benzamide as a potential lead compound that may behave as a very potent inhibitor of LpxC for the development of targeted therapies against MDR P. aeruginosa.

Antibacterial Effect and Mechanism of Chelerythrine on Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) is a biotrophic bacterial pathogen, which causes devastating bacterial blight disease worldwide. In this study, we thoroughly investigated the antimicrobial effect of the plant-derived extract chelerythrine against Xanthomonas oryzae pv. oryzae (Xoo) and elucidated its mechanism. Chelerythrine is a quaternary ammonium alkaloid with a 2,3,7,8-tetrasubstituted phenanthridine structure, extracted from plants, such as the whole plant of Chelidonium majus, and the roots, stems, and leaves of Macleaya cordata. We found that chelerythrine significantly inhibited the growth of Xoo at a concentration of 1.25 μg/mL. Further experiments revealed that chelerythrine interfered with the division and reproduction of the bacterium, leading to its filamentous growth. Additionally, it increased the permeability of Xoo cell membranes and effectively decreased the pathogenicity of Xoo, including the inhibition of extracellular polysaccharide production, cellulase secretion, and biofilm formation. Chelerythrine induced the accumulation of reactive oxygen species in the bacterium, triggering oxidative stress. The result showed that chelerythrine inhibited the formation of the Z-ring of Xoo, interfered with the synthesis of pyrimidine and purine nucleotides, inhibited DNA damage repair, and inhibited the formation of peptidoglycan and lipid-like A, thus interfering with cell membrane permeability, inhibiting carbohydrate metabolism and phosphorylation of sugars, reducing pathogenicity, and ultimately inhibiting bacterial growth and leading to the destruction or lysis of bacterial cells. Altogether, our results suggest that the antimicrobial effect of chelerythrine on Xoo exhibits multi-target properties. Additionally, its effective inhibitory concentration is low. These findings provide a crucial theoretical basis and guidance for the development of novel and efficient plant-derived antimicrobial compounds.

Novel Antibacterial Approaches and Therapeutic Strategies

The increase in multidrug-resistant organisms worldwide is a major public health threat driven by antibiotic overuse, horizontal gene transfer (HGT), environmental drivers, and deficient infection control in hospitals. In this article, we discuss these factors and summarize the new drugs and treatment strategies suggested to combat the increasing challenges of multidrug-resistant (MDR) bacteria. New treatments recently developed involve targeting key processes involved in bacterial growth, such as riboswitches and proteolysis, and combination therapies to improve efficacy and minimize adverse effects. It also tackles the challenges of the Gram-negative bacterial outer membrane, stressing that novel strategies are needed to evade permeability barriers, efflux pumps, and resistance mechanisms. Other approaches, including phage therapy, AMPs, and AI in drug discovery, are also discussed as potential alternatives. Finally, this review points out the urgency for continued research and development (R&D), industry-academic partnerships, and financial engines to ensure that MDR microbes do not exceed the value of antibacterial therapies.

Dynamics-based drug discovery by time-resolved cryo-EM

Rational structure-based drug design (SBDD) depends on high-resolution structural models of target macromolecules or their complexes. However, the lack of atomic-level functional molecular dynamics hinders the applications of SBDD and limits their effective translation into clinically successful therapeutics. Time-resolved cryo-electron microscopy (cryo-EM) has emerged as a powerful tool in structural biology, capable of capturing high-resolution snapshots of biomolecular machines in action. Unlike molecular dynamics (MD) simulations, time-resolved cryo-EM can visualize rare intermediate states across a broader range of timescales, providing invaluable insights into drug-binding kinetics, dynamic protein-ligand interactions, and allosteric regulation. Integration of time-resolved cryo-EM with machine learning (ML) and artificial intelligence (AI) expands SBDD into a dynamics-based approach, allowing for more accurate pharmacological modeling of challenging drug targets that are beyond the reach of MD simulations. Time-resolved cryo-EM can help researchers to identify novel druggable conformations, overcome drug resistance, and reduce the time and cost of clinical translations. Despite current challenges, the future development of time-resolved cryo-EM with AI and in situ imaging strategy, such as cryo-electron tomography, holds the potential to revolutionize drug discovery by revealing in vivo molecular dynamics of drug actions at an unprecedented spatiotemporal scale.

Global health perspectives on antibacterial drug discovery and the preclinical pipeline

Antibacterial resistance is a global challenge that requires a coordinated international response. The current clinical pipeline largely consists of derivatives of established antibiotic classes, whereas the discovery and preclinical pipeline is diverse and innovative including new direct-acting agents with no cross-resistance with existing antibiotics. These novel compounds target pathways such as lipoprotein synthesis, lipopolysaccharide biosynthesis and transport, outer membrane assembly, peptidoglycan biosynthesis, fatty acid biosynthesis and isoprenoid biosynthesis. If these agents can be developed into safe, effective and affordable drugs, they could address a broad range of infections worldwide, benefiting large patient populations without geographical limitations. However, strategies such as indirect-acting or pathogen-specific treatments are likely to benefit small patient groups, primarily in high-income countries that have advanced health-care systems and diagnostic infrastructure. Although encouraging, the discovery and preclinical pipeline remains insufficiently robust to offset the high attrition rates typical of early-stage drug innovation and to meet global health needs.

Evaluation of a potent LpxC inhibitor for post-exposure prophylaxis treatment of antibiotic-resistant Burkholderia pseudomallei in a murine infection model

LPC-233 (a.k.a. VB-233) is a potent antibiotic targeting the essential enzyme LpxC in Gram-negative bacteria. We present herein the pharmacokinetics and pharmacodynamics data of LPC-233 for treating murine infections caused by Burkholderia pseudomallei, a potential biodefense pathogen. A range of doses was evaluated in a post-aerosol exposure model of B. pseudomallei-infected mice. After the aerosol challenge with the B. pseudomallei strain K96243, treatment was initiated with 10, 30, or 90 mg/kg of LPC-233 orally every 12 h (q12h) or 90 mg/kg intraperitoneally q12h for 14 days. A vehicle-control arm and a positive-control arm consisting of one of the recommended standards of care, ceftazidime (150 mg/kg, q6h) injected subcutaneously, were included. LPC-233 significantly and dose-dependently rescued mice from B. pseudomallei infection in comparison with the vehicle (P < 0.0001). At dose levels of 30 mg/kg or higher, the survival rate with LPC-233 was significantly higher than that from the ceftazidime arm (P range: 0.001-0.05). LPC-233 reversed the murine body weight loss caused by the B. pseudomallei infection more rapidly than ceftazidime did, suggesting that it is a faster-acting antibiotic in this dosing regimen. Despite the outstanding survival advantage of LPC-233 over ceftazidime, no significant differences in tissue burdens (liver, lung, spleen, and blood) were observed among any of the treatment groups surviving to the termination of the experiment, suggesting that similar to commercial antibiotics, LPC-233 treatment for lethal B. pseudomallei infection may likely require both an acute phase of intensive treatment and an eradication phase of prolonged treatment.

Leveraging Cryptic Ligand Envelopes through Enhanced Molecular Simulations

Protein-bound ligands can adopt a range of different conformations, collectively defining a ligand envelope that has proven to be crucial for the design of potent and selective drugs. Yet, the cryptic nature of this ligand envelope makes it difficult to visualize, characterize, and ultimately exploit for drug design. Using enhanced molecular dynamics simulations, here, we provide a general framework to reconstruct the cryptic ligand envelope that is dynamically accessible by protein-bound small molecules in solution. We apply this approach to quantify hidden conformational heterogeneity in structurally complex ligands including the marine natural product plitidepsin. The computed conformational heterogeneity expands the small-molecule footprint beyond that typically observed in experiments, also revealing key thermodynamic and kinetic properties of single ligand-target interactions. The model agrees quantitatively with solution NMR, X-ray crystallography, and biochemical measurements, showcasing a versatile strategy to integrate receptor-bound ligand conformational ensembles in molecular design.

New avenues of combating antibiotic resistance by targeting cryptic pockets

Antibiotic resistance is a global health concern that is rapidly spreading among human and animal pathogens. Developing novel antibiotics is one of the most significant approaches to surmount antibiotic resistance. Given the difficult in identifying novel targets, cryptic binding sites provide new pockets for compounds design to combat antibiotic resistance. However, there exists a lack of comprehensive analysis and discussion on the successful utilization of cryptic pockets in overcoming antibiotic resistance. Here, we systematically analyze the crucial role of cryptic pockets in neutralizing antibiotic resistance. First, antibiotic resistance development and associated resistance mechanisms are summarized. Then, the advantages and mechanisms of cryptic pockets for overcoming antibiotic resistance were discussed. Specific cryptic pockets in resistant proteins and successful case studies of designed inhibitors are exemplified. This review provides insight into the discovery of cryptic pockets for drug design as an approach to overcome antibiotic resistance.

Design and Evaluation of Pyridinyl Sulfonyl Piperazine LpxH Inhibitors with Potent Antibiotic Activity Against Enterobacterales

Enterobacterales, a large order of Gram-negative bacteria, including Escherichia coli and Klebsiella pneumoniae, are major causes of urinary tract and gastrointestinal infections, pneumonia, and other diseases in healthcare settings and communities. ESBL-producing Enterobacterales and carbapenem-resistant Enterobacterales can break down commonly used antibiotics, with some strains being resistant to all available antibiotics. This public health threat necessitates the development of novel antibiotics, ideally targeting new pathways in these bacteria. Gram-negative bacteria possess an outer membrane enriched with lipid A, a saccharolipid that serves as the membrane anchor of lipopolysaccharides and the active component of the bacterial endotoxin, causing septic shock. The biosynthesis of lipid A is crucial for the viability of Gram-negative bacteria, and as an essential enzyme in this process, LpxH has emerged as a promising target for developing novel antibiotics against multidrug-resistant Gram-negative pathogens. Here, we report the development of pyridinyl sulfonyl piperazine LpxH inhibitors. Among them, ortho-substituted pyridinyl compounds significantly boost LpxH inhibition and antibiotic activity over the original phenyl series. Structural and QM/MM analyses reveal that these improved activities are primarily due to the enhanced interaction between F141 of the LpxH insertion lid and the pyridinyl group. Incorporation of the N-methyl-N-phenyl-methanesulfonamide moiety into the pyridinyl sulfonyl piperazine backbone results in JH-LPH-106 and JH-LPH-107, both of which exhibit potent antibiotic activity against wild-type Enterobacterales such as K. pneumoniae and E. coli. JH-LPH-107 exhibits a low rate of spontaneous resistance and a high safety window in vitro, rendering it an excellent lead for further clinical development.

Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors

New antibacterial compounds are urgently needed, especially for infections caused by the top-priority Gram-negative bacteria that are increasingly difficult to treat. Lipid A is a key component of the Gram-negative outer membrane and the LpxH enzyme plays an important role in its biosynthesis, making it a promising antibacterial target. Inspired by previously reported ortho-N-methyl-sulfonamidobenzamide-based LpxH inhibitors, novel benzamide substitutions were explored in this work to assess their in vitro activity. Our findings reveal that maintaining wild-type antibacterial activity necessitates removal of the N-methyl group when shifting the ortho-N-methyl-sulfonamide to the meta-position. This discovery led to the synthesis of meta-sulfonamidobenzamide analogs with potent antibacterial activity and enzyme inhibition. Moreover, we demonstrate that modifying the benzamide scaffold can alter blocking of the cardiac voltage-gated potassium ion channel hERG. Furthermore, two LpxH-bound X-ray structures show how the enzyme-ligand interactions of the meta-sulfonamidobenzamide analogs differ from those of the previously reported ortho analogs. Overall, our study has identified meta-sulfonamidobenzamide derivatives as promising LpxH inhibitors with the potential for optimization in future antibacterial hit-to-lead programs.

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.

A comprehensive review of recent developments in the gram-negative bacterial UDP-2,3-diacylglucosamine hydrolase (LpxH) enzyme

The emergence of multidrug resistance has provided a great challenge to treat nosocomial infections, which have become a major health threat around the globe. Lipid A (an active endotoxin component), the final product of the Raetz lipid A metabolism pathway, is a membrane anchor of lipopolysaccharide (LPS) of the gram-negative bacterial outer membrane. It shields bacterial cells and serves as a protective barrier from antibiotics, thereby eliciting host response and making it difficult to destroy. UDP-2,3-diacylglucosamine pyrophosphate hydrolase (LpxH), a crucial peripheral membrane enzyme of the Raetz pathway, turned out to be the potential target to inhibit the production of Lipid A. This review provides a comprehensive compilation of information regarding the structural and functional aspects of LpxH, as well as its analogous LpxI and LpxG. In addition, apart from by providing a broader understanding of the enzyme-inhibitor mechanism, this review facilitates the development of novel drug candidates that can inhibit the pathogenicity of the lethal bacterium.

Signaling through the Salmonella PbgA-LapB regulatory complex activates LpxC proteolysis and limits lipopolysaccharide biogenesis during stationary-phase growth

Salmonella enterica serovar Typhimurium (S. Typhimurium) controls lipopolysaccharide (LPS) biosynthesis by regulating proteolysis of LpxC, the rate-limiting enzyme and target of preclinical antibiotics. PbgA/YejM/LapC regulates LpxC levels and controls outer membrane (OM) LPS composition at the log-to-stationary phase transition. Suppressor substitutions in LPS assembly protein B (LapB/YciM) rescue the LPS and OM integrity defects of pbgA-mutant S. Typhimurium. We hypothesized that PbgA regulates LpxC proteolysis by controlling LapB's ability to bind LpxC as a function of the growth phase. According to existing models, when nutrients are abundant, PbgA binds and restricts LapB from interacting with LpxC and FtsH, which limits LpxC proteolysis. However, when nutrients are limited, there is debate whether LapB dissociates from PbgA to bind LpxC and FtsH to enhance degradation. We sought to examine these models and investigate how the structure of LapB enables salmonellae to control LpxC proteolysis and LPS biosynthesis. Salmonellae increase LapB levels during the stationary phase to promote LpxC degradation, which limits lipid A-core production and increases their survival. The deletion of lapB, resulting in unregulated lipid A-core production and LpxC overabundance, leads to bacterial growth retardation. Tetratricopeptide repeats near the cytosol-inner membrane interface are sufficient for LapB to bind LpxC, and remarkably, LapB and PbgA interact in both growth phases, yet LpxC only associates with LapB in the stationary phase. Our findings support that PbgA-LapB exists as a constitutive complex in S. Typhimurium, which differentially binds LpxC to control LpxC proteolysis and limit lipid A-core biosynthesis in response to changes in the environment.IMPORTANCEAntimicrobial resistance has been a costly setback for human health and agriculture. Continued pursuit of new antibiotics and targets is imperative, and an improved understanding of existing ones is necessary. LpxC is an essential target of preclinical trial antibiotics that can eliminate multidrug-resistant Gram-negative bacterial infections. LapB is a natural LpxC inhibitor that targets LpxC for degradation and limits lipopolysaccharide production in Enterobacteriaceae. Contrary to some studies, findings herein support that LapB remains in complex instead of dissociating from its presumed negative regulator, PbgA/YejM/LapC, under conditions where LpxC proteolysis is enhanced. Advanced comprehension of this critical protein-lipid signaling network will lead to future development and refinement of small molecules that can specifically interfere.

Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria

Here, we describe the identification of an antibiotic class acting via LpxH, a clinically unexploited target in lipopolysaccharide synthesis. The lipopolysaccharide synthesis pathway is essential in most Gram-negative bacteria and there is no analogous pathway in humans. Based on a series of phenotypic screens, we identified a hit targeting this pathway that had activity on efflux-defective strains of Escherichia coli. We recognized common structural elements between this hit and a previously published inhibitor, also with activity against efflux-deficient bacteria. With the help of X-ray structures, this information was used to design inhibitors with activity on efflux-proficient, wild-type strains. Optimization of properties such as solubility, metabolic stability and serum protein binding resulted in compounds having potent in vivo efficacy against bloodstream infections caused by the critical Gram-negative pathogens E. coli and Klebsiella pneumoniae. Other favorable properties of the series include a lack of pre-existing resistance in clinical isolates, and no loss of activity against strains expressing extended-spectrum-β-lactamase, metallo-β-lactamase, or carbapenemase-resistance genes. Further development of this class of antibiotics could make an important contribution to the ongoing struggle against antibiotic resistance.

LpxC inhibition: Potential and opportunities with carbohydrate scaffolds

Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a key enzyme involved in the biosynthesis of lipid A, an essential building block, for the construction and assembly of the outer membrane (OM) of Gram-negative bacteria. The enzyme is highly conserved in almost all Gram-negative bacteria and hence has emerged as a promising target for drug discovery in the fight against multi-drug resistant Gram-negative infections. Since the first nanomolar LpxC inhibitor, L-161,240, an oxazoline-based hydroxamate, the two-decade-long ongoing search has provided valuable information regarding essential features necessary for inhibition. Although the design and structure optimization for arriving at the most efficacious inhibitor of this enzyme has made good use of different heterocyclic moieties, the use of carbohydrate scaffold is scant. This review briefly covers the advancement and progress made in LpxC inhibition. The field awaits the use of potential associated with carbohydrate-based scaffolds for LpxC inhibition and the discovery of anti-bacterial agents against Gram-negative infections.

Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action

One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.

Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections

Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.

"AMP plus": Immunostimulant-Inspired Design Based on Chemotactic Motif-(PhHAhPH)n

Ability to stimulate antimicrobial immunity has proven to be a useful therapeutic strategy in treating infections, especially in the face of increasing antibiotic resistance. Natural antimicrobial peptides (AMPs) exhibiting immunomodulatory functions normally encompass complex activities, which make it difficult to optimize their therapeutic benefits. Here, a chemotactic motif was harnessed as a template to design a series of AMPs with immunostimulatory activities plus bacteria-killing activities ("AMP plus"). An amphipathic peptide ((PhHAhPH)n) was employed to improve the antimicrobial impact and expand the therapeutic potential of the chemotactic motif that lacked obvious bacteria-killing properties. A total of 18 peptides were designed and evaluated for their structure-activity relationships. Among the designed, KWH2 (1) potently killed bacteria and exhibited a narrow antimicrobial spectrum against Gram-negative bacteria and (2) activated macrophages (i.e., inducing Ca2+ influx, cell migration, and reactive oxygen species production) as a macrophage chemoattractant. Membrane permeabilization is the major antimicrobial mechanism of KWH2. Furthermore, the mouse subcutaneous abscess model supported the dual immunomodulatory and antimicrobial potential of KWH2 in vivo. The above results confirmed the efficiency of KWH2 in treating bacterial infection and provided a viable approach to develop immunomodulatory antimicrobial materials with desired properties.

Quaternized carbon dots with enhanced antimicrobial ability towards Gram-negative bacteria for the treatment of acute peritonitis caused by E. coli

Infections caused by Gram-negative bacteria still pose a clinical challenge. Although nanomaterials have been developed for antibacterial treatments, a systematic evaluation of the mechanisms and intervention models of antibacterial materials toward Gram-negative bacteria is still lacking. Herein, antibacterial quaternized carbon dots (QCDs) were synthesized via a one-step melting method using anhydrous citric acid and diallyl dimethyl ammonium chloride (DDA). The QCDs exhibited effective broad-spectrum antibacterial activity and enhanced inhibitory ability towards Gram-negative bacteria. The antibacterial mechanism of the QCDs with respect to Gram-negative bacteria was investigated through the characterization of bacterial morphology changes, the absorption modes of the QCDs on bacteria, and the potential generation of reactive oxygen species by the QCDs. The QCDs showed low toxicity in different cells, and did not cause hemolysis. The QCDs were administered via intraperitoneal injection to treat acute peritonitis in mice infected with E. coli. Routine blood examination, magnetic resonance imaging, and pathological analysis were undertaken and it was found that, similar to the positive control group treated with gentamicin sulfate, the QCDs exhibited a therapeutic effect that eliminated infection and inflammation. This study explores a controllable synthetic strategy for the synthesis of active carbon dots with antibacterial activity, a material that is a promising candidate for new treatments of Gram-negative bacterial infections.

Preclinical safety and efficacy characterization of an LpxC inhibitor against Gram-negative pathogens

The UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosamine deacetylase LpxC is an essential enzyme in the biosynthesis of lipid A, the outer membrane anchor of lipopolysaccharide and lipooligosaccharide in Gram-negative bacteria. The development of LpxC-targeting antibiotics toward clinical therapeutics has been hindered by the limited antibiotic profile of reported non-hydroxamate inhibitors and unexpected cardiovascular toxicity observed in certain hydroxamate and non-hydroxamate-based inhibitors. Here, we report the preclinical characterization of a slow, tight-binding LpxC inhibitor, LPC-233, with low picomolar affinity. The compound is a rapid bactericidal antibiotic, unaffected by established resistance mechanisms to commercial antibiotics, and displays outstanding activity against a wide range of Gram-negative clinical isolates in vitro. It is orally bioavailable and efficiently eliminates infections caused by susceptible and multidrug-resistant Gram-negative bacterial pathogens in murine soft tissue, sepsis, and urinary tract infection models. It displays exceptional in vitro and in vivo safety profiles, with no detectable adverse cardiovascular toxicity in dogs at 100 milligrams per kilogram. These results establish the feasibility of developing oral LpxC-targeting antibiotics for clinical applications.

In-silico assay of a dosing vehicle based on chitosan-TiO2 and modified benzofuran-isatin molecules against Pseudomonas aeruginosa

A high priority of the World Health Organization (WHO) is the study of drugs against Pseudomonas aeruginosa, which has developed antibiotic resistance. In this order, recent research is analyzing biomaterials and metal oxide nanoparticles, such as chitosan (QT) and TiO2 (NT), which can transport molecules with biological activity against bacteria, to propose them as drug carrier candidates. In the present work, 10 modified benzofuran-isatin molecules were studied through computational simulation using density functional theory (DFT) and molecular docking assays against Hfq and LpxC (proteins of P. aeruginosa). The results show that the ligand efficiency of commercial drugs C-CP and C-AZI against Hfq is low compared with the best-designed molecule MOL-A. However, we highlight that the influence of NT promotes a better interaction of some molecules, where MOL-E generates a better interaction by 0.219 kcal/mol when NT is introduced in Hfq, forming the system Hfq-NT (Target-NT). Similar behavior is observed in the LpxC target, in which MOL-J is better at 0.072 kcal/mol. Finally, two pharmacophoric models for Hfq and LpxC implicate hydrophobic and aromatic-hydrophobic fragments.

Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance

Gram-negative bacteria pose a major threat to human health in an era fraught with multi-drug resistant bacterial infections. Despite extensive drug discovery campaigns over the past decades, no new antibiotic target class effective against gram-negative bacteria has become available to patients since the advent of the carbapenems in 1985. Antibiotic discovery efforts against gram-negative bacteria have been hampered by limited intracellular accumulation of xenobiotics, in large part due to the impermeable cell envelope comprising lipopolysaccharide (LPS) in the outer leaflet of the outer membrane, as well as a panoply of efflux pumps. The biosynthesis and transport of LPS are essential to the viability and virulence of most gram-negative bacteria. Thus, both LPS biosynthesis and transport are attractive pathways to target therapeutically. In this review, we summarize the LPS biosynthesis and transport pathways and discuss efforts to find small molecule inhibitors against targets within these pathways.

Identification of Therapeutic Targets in an Emerging Gastrointestinal Pathogen Campylobacter ureolyticus and Possible Intervention through Natural Products

Campylobacter ureolyticus is a Gram-negative, anaerobic, non-spore-forming bacteria that causes gastrointestinal infections. Being the most prevalent cause of bacterial enteritis globally, infection by this bacterium is linked with significant morbidity and mortality in children and immunocompromised patients. No information on pan-therapeutic drug targets for this species is available yet. In the current study, a pan-genome analysis was performed on 13 strains of C. ureolyticus to prioritize potent drug targets from the identified core genome. In total, 26 druggable proteins were identified using subtractive genomics. To the best of the authors’ knowledge, this is the first report on the mining of drug targets in C. ureolyticus. UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) was selected as a promiscuous pharmacological target for virtual screening of two bacterial-derived natural product libraries, i.e., postbiotics (n = 78) and streptomycin (n = 737) compounds. LpxC inhibitors from the ZINC database (n = 142 compounds) were also studied with reference to LpxC of C. ureolyticus. The top three docked compounds from each library (including ZINC26844580, ZINC13474902, ZINC13474878, Notoginsenoside St-4, Asiaticoside F, Paraherquamide E, Phytoene, Lycopene, and Sparsomycin) were selected based on their binding energies and validated using molecular dynamics simulations. To help identify potential risks associated with the selected compounds, ADMET profiling was also performed and most of the compounds were considered safe. Our findings may serve as baseline information for laboratory studies leading to the discovery of drugs for use against C. ureolyticus infections.

Checkpoints That Regulate Balanced Biosynthesis of Lipopolysaccharide and Its Essentiality in Escherichia coli

The outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step in LPS biosynthesis mediated by LpxC through its turnover by FtsH and HslUV proteases in coordination with LPS assembly factors LapB and LapC. After the synthesis of LPS on the inner leaflet of the inner membrane (IM), LPS is flipped by the IM-located essential ATP-dependent transporter to the periplasmic face of IM, where it is picked up by the LPS transport complex spanning all three components of the cell envelope for its delivery to OM. MsbA exerts its intrinsic hydrocarbon ruler function as another checkpoint to transport hexa-acylated LPS as compared to underacylated LPS. Additional checkpoints in LPS assembly are: LapB-assisted coupling of LPS synthesis and translocation; cardiolipin presence when LPS is underacylated; the recruitment of RfaH transcriptional factor ensuring the transcription of LPS core biosynthetic genes; and the regulated incorporation of non-stoichiometric modifications, controlled by the stress-responsive RpoE sigma factor, small RNAs and two-component systems.

Genomic and Transcriptomic Analysis of Bovine Pasteurella multocida Serogroup A Strain Reveals Insights Into Virulence Attenuation

Pasteurella multocida is one of the primary pathogens of bovine respiratory disease (BRD), and causes huge losses in the cattle industry. The Pm3 strain was a natural isolate, which is a strong form of pathogen and is sensitive to fluoroquinolones antibiotics. A high fluoroquinolone resistant strain, Pm64 (MIC = 64 μg/mL), was formed after continuous induction with subinhibitory concentration (1/2 MIC) of enrofloxacin, with the enhanced growth characteristics and large attenuation of pathogenicity in mice. This study reports the whole genome sequence and the transcription profile by RNA-Seq of strain Pm3/Pm64. The results showed an ineffective difference between the two strains at the genome level. However, 32 genes could be recognized in the gene islands (GIs) of Pm64, in which 24 genes were added and 8 genes were lost. Those genes are involved in DNA binding, trehalose metabolism, material transportation, capsule synthesis, prophage, amino acid metabolism, and other functions. In Pm3 strain, 558 up-regulated and 568 down-regulated genes were found compared to Pm64 strain, from which 20 virulence factor-related differentially expressed genes (DEGs) were screened. Mainly differentially transcribed genes were associated with capsular polysaccharide (CPS), lipopolysaccharide (LPS), lipooligosaccharide (LOS). Iron utilization, and biofilm composition. We speculated that the main mechanism of virulence attenuation after the formation of resistance of Pm64 comes from the change of the expression profile of these genes. This report elucidated the toxicity targets of P. multocida serogroup A which provide fundamental information toward the understanding of the pathogenic mechanism and to decreasing antimicrobial drugs resistance.