Bayesian Modeling and Intrabacterial Drug Metabolism Applied to Drug-Resistant Staphylococcus aureus

Identification of cysteine metabolism regulator (CymR)-derived pentapeptides as nanomolar inhibitors of Staphylococcus aureus O-acetyl-ʟ-serine sulfhydrylase (CysK)

The conditionally essential pathway of bacterial cysteine biosynthesis is gaining traction for the development of antibiotic adjuvants. Bacterial cysteine biosynthesis is generally facilitated by two enzymes possessing O-acetyl-ʟ-serine sulfhydrylase (OASS) activity, CysK and CysM. CysK enzymes can also form functional complexes with other proteins that regulate cysteine metabolism. In Staphylococcus aureus there exists a single OASS homologue, herein termed Sa CysK. Knockout of Sa CysK was found to increase sensitivity to oxidative stress, making it a relevant target for inhibitor development. Sa CysK forms two functional complexes via interaction with the preceding enzyme in the pathway serine acetyltransferase (CysE) or the transcriptional regulator of cysteine metabolism (CymR). These interactions occur through the insertion of a C-terminal peptide of CysE or CymR into the active site of Sa CysK, inhibiting OASS activity, and therefore represent an excellent starting point for developing Sa CysK inhibitors. Here we detail the characterization of CysE and CymR-derived C-terminal peptides as inhibitors of Sa CysK. First, interactions between CysE or CymR-derived C-terminal decapeptides and Sa CysK were assessed by X-ray crystallography. While both peptides occupied the active site of Sa CysK, the alternate sidechains of the CymR decapeptide formed more extensive interactions. Surface plasmon resonance binding assays and Sa CysK inhibition assays revealed that the CymR decapeptide bound to Sa CysK with nanomolar affinity (K D = 25 nM) and inhibited Sa CysK activity (IC 50 = 180 nM), making it a promising lead for the development of Sa CysK inhibitors. To understand the determinants of this high affinity interaction the structure-activity relationships of 16 rationally designed peptides were also investigated. This identified that the C-terminal pentapeptide of CymR alone facilitates the high affinity interaction with Sa CysK, and that subtle structural modification of the pentapeptide is possible without impacting potency. Ultimately, this work has identified CymR pentapeptides as a promising scaffold for the development of antibiotic adjuvants targeting Sa CysK.

Author summary

There is increasing interest in the investigation of non-essential pathways including bacterial cysteine metabolism for developing antibiotic adjuvants. Within this pathway the O-acetyl-ʟ-serine sulfhydrylase (OASS) enzymes CysK and CysM have been a focus. As such, the OASS enzyme of Staphylococcus aureus , Sa CysK, gained our interest. Previous efforts to inhibit CysK enzymes have mimicked the interaction between CysK and the C-terminus of serine acetyltransferase (CysE) which occurs inside the CysK active site and inhibits OASS activity. CysE peptides have only moderate potency, typically binding with micromolar affinity. In S. aureus another complex forms between Sa CysK and a transcriptional regulator CymR, but the ability of CymR peptides to inhibit CysK enzymes has not been investigated. We noticed there is variation between the C-terminus of CysE and CymR, suggesting that CymR peptides make distinct interactions with Sa CysK and may be superior inhibitors. Here we characterized CysE and CymR peptides as Sa CysK inhibitors. We found CymR peptides make more extensive molecular interactions with Sa CysK and bind with higher affinity, being the most potent peptide inhibitors of a CysK enzyme to date. A CymR pentapeptide is the minimal length required for this potency and provides a promising scaffold for developing antibiotic adjuvants targeting Sa CysK.

Novel anionic surfactant-modified chlorhexidine and its potent antimicrobial properties

Chlorhexidine dodecyl sulfate (CHX-DS) was synthesized and characterized via single-crystal X-ray diffraction (SC-XRD), 1H nuclear magnetic resonance (NMR) spectroscopy, 1H nuclear Overhauser effect spectroscopy (NOESY), and attenuated total reflectance Fourier-transform infrared spectroscopy (ATR-FTIR). The solid-state structure, comprising a 1 : 2 stoichiometric ratio of chlorhexidine cations [C22H30Cl2N10]2+ to dodecyl sulfate anions [C12H25SO4]-, is the first report of chlorhexidine isolated with a surfactant. CHX-DS exhibits broad-spectrum antibacterial activity and demonstrates superior efficacy for reducing bacteria-generated volatile sulfur compounds (VSCs) as compared to chlorhexidine gluconate (CHG). The minimum inhibitory concentrations (MICs) of CHX-DS were 7.5, 2.5, 2.5, and 10 μM for S. enterica, E. coli, S. aureus, and S. mutans, respectively. Furthermore, MIC assays for E. coli and S. mutans demonstrate that CHX-DS and CHX exhibit a statistically significant efficacy enhancement in 2.5 μM treatment as compared to CHG. CHX-DS was incorporated into SBA-15, a mesoporous silica nanoparticle (MSN) framework, and its release was qualitatively measured via UV-vis in aqueous media, which suggests its potential as an advanced functional material for drug delivery applications.

Impact of the pentose phosphate pathway on metabolism and pathogenesis of Staphylococcus aureus

Staphylococcus aureus is an important pathogen that leads to significant disease through multiple routes of infection. We recently published a transposon sequencing (Tn-seq) screen in a mouse acute pneumonia model and identified a hypothetical gene (SAUSA300_1902, pgl) with similarity to a lactonase of Escherichia coli involved in the pentose phosphate pathway (PPP) that was conditionally essential. Limited studies have investigated the role of the PPP in physiology and pathogenesis of S. aureus. We show here that mutation of pgl significantly impacts ATP levels and respiration. RNA-seq analysis of the pgl mutant and parent strains identified compensatory changes in gene expression for glucose and gluconate as well as reductions in the pyrimidine biosynthesis locus. These differences were also evident through unbiased metabolomics studies and 13C labeling experiments that showed mutation of pgl led to reductions in pyrimidine metabolism including decreases in ribose-5P, UMP and GMP. These nucleotide reductions impacted the amount of extracellular DNA in biofilms and reduced biofilm formation. Mutation also limited the capacity of the strain to resist oxidant damage induced by hydrogen peroxide and paraquat and subsequent intracellular survival inside macrophages. Changes in wall teichoic acid impacted susceptibility to hydrogen peroxide. We demonstrated the importance of these changes on virulence in three different models of infection, covering respiratory, skin and septicemia, demonstrating the need for proper PPP function in all models. This work demonstrates the multifaceted role metabolism can play in multiple aspects of S. aureus pathogenesis.

Copper ions inhibit pentose phosphate pathway function in Staphylococcus aureus

To gain a better insight of how Copper (Cu) ions toxify cells, metabolomic analyses were performed in S. aureus strains that lacks the described Cu ion detoxification systems (ΔcopBL ΔcopAZ; cop-). Exposure of the cop- strain to Cu(II) resulted in an increase in the concentrations of metabolites utilized to synthesize phosphoribosyl diphosphate (PRPP). PRPP is created using the enzyme phosphoribosylpyrophosphate synthetase (Prs) which catalyzes the interconversion of ATP and ribose 5-phosphate to PRPP and AMP. Supplementing growth medium with metabolites requiring PRPP for synthesis improved growth in the presence of Cu(II). A suppressor screen revealed that a strain with a lesion in the gene coding adenine phosphoribosyltransferase (apt) was more resistant to Cu. Apt catalyzes the conversion of adenine with PRPP to AMP. The apt mutant had an increased pool of adenine suggesting that the PRPP pool was being redirected. Over-production of apt, or alternate enzymes that utilize PRPP, increased sensitivity to Cu(II). Increasing or decreasing expression of prs resulted in decreased and increased sensitivity to growth in the presence of Cu(II), respectively. We demonstrate that Prs is inhibited by Cu ions in vivo and in vitro and that treatment of cells with Cu(II) results in decreased PRPP levels. Lastly, we establish that S. aureus that lacks the ability to remove Cu ions from the cytosol is defective in colonizing the airway in a murine model of acute pneumonia, as well as the skin. The data presented are consistent with a model wherein Cu ions inhibits pentose phosphate pathway function and are used by the immune system to prevent S. aureus infections.

Liquid chromatography-mass spectrometry-based protocol to measure drug accumulation in Mycobacterium tuberculosis and its host cell

The extent to which a drug accumulates in Mycobacterium tuberculosis (Mtb) and its host cell can affect treatment efficacy. We describe protocols measuring drug accumulation in Mtb, macrophages, and Mtb-infected macrophages. The method leverages drug extraction from the cellular lysate and drug-level quantification by liquid chromatography-mass spectrometry. The general methodology has broad applicability and can quantify drug accumulation in other cell types, while being extended to quantification of drug metabolites formed within the cell under study. For complete details on the use and execution of this protocol, please refer to Lavin et al. (2021).1.

Random Forest Model Predictions Afford Dual-Stage Antimalarial Agents

The need for novel antimalarials is apparent given the continuing disease burden worldwide, despite significant drug discovery advances from the bench to the bedside. In particular, small-molecule agents with potent efficacy against both the liver and blood stages of Plasmodium parasite infection are critical for clinical settings as they would simultaneously prevent and treat malaria with a reduced selection pressure for resistance. While experimental screens for such dual-stage inhibitors have been conducted, the time and cost of these efforts limit their scope. Here, we have focused on leveraging machine learning approaches to discover novel antimalarials with such properties. A random forest modeling approach was taken to predict small molecules with in vitro efficacy versus liver-stage Plasmodium berghei parasites and a lack of human liver cell cytotoxicity. Empirical validation of the model was achieved with the realization of hits with liver-stage efficacy after prospective scoring of a commercial diversity library and consideration of structural diversity. A subset of these hits also demonstrated promising blood-stage Plasmodium falciparum efficacy. These 18 validated dual-stage antimalarials represent novel starting points for drug discovery and mechanism of action studies with significant potential for seeding a new generation of therapies.

Rickettsia Aglow: A Fluorescence Assay and Machine Learning Model to Identify Inhibitors of Intracellular Infection

Rickettsia is a genus of Gram-negative bacteria that has for centuries caused large-scale morbidity and mortality. In recent years, the resurgence of rickettsial diseases as a major cause of pyrexias of unknown origin, bioterrorism concerns, vector movement, and concerns over drug resistance is driving a need to identify novel treatments for these obligate intracellular bacteria. Utilizing an uvGFP plasmid reporter, we developed a screen for identifying anti-rickettsial small molecule inhibitors using Rickettsia canadensis as a model organism. The screening data were utilized to train a Bayesian model to predict growth inhibition in this assay. This two-pronged methodology identified anti-rickettsial compounds, including duartin and JSF-3204 as highly specific, efficacious, and noncytotoxic compounds. Both molecules exhibited in vitro growth inhibition of R. prowazekii, the causative agent of epidemic typhus. These small molecules and the workflow, featuring a high-throughput phenotypic screen for growth inhibitors of intracellular Rickettsia spp. and machine learning models for the prediction of growth inhibition of an obligate intracellular Gram-negative bacterium, should prove useful in the search for new therapeutic strategies to treat infections from Rickettsia spp. and other obligate intracellular bacteria.