A Small-Molecule Screening Platform for the Discovery of Inhibitors of Undecaprenyl Diphosphate Synthase

Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations

Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer's randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, - 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein-ligand complexes, yielding five promising novel UPPS inhibitors.

Chemical genetic approaches for the discovery of bacterial cell wall inhibitors

Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.

Immunotargeting of Gram-Positive Pathogens via a Cell Wall Binding Tick Antifreeze Protein

Immunological agents that supplement or modulate the host immune response have proven to have powerful therapeutic potential, although this modality is less explored against bacterial pathogens. We describe the application of a bacterial binding protein to re-engage the immune system toward pathogenic bacteria. More specifically, a hapten was conjugated to a protein expressed by Ixodes scapularis ticks, called I. scapularis antifreeze glycoprotein (IAFGP), that has high affinity for the d-alanine residue on the bacterial peptidoglycan. We showed that a fragment of this protein retained high surface binding affinity. Moreover, conjugation of a hapten to this peptide led to the display of haptens on the cell surface of vancomycin-resistant Enterococcus faecalis. Hapten display then induced the recruitment of antibodies and promoted uptake of bacterial pathogens by immune cells. These results demonstrate the feasibility in using cell wall binding agents as the basis of a class of bacterial immunotherapies.

Antibacterial pyrazoles: tackling resistant bacteria

Bacterial resistance to antibiotics threatens our progress in healthcare, modern medicine, food production and ultimately life expectancy. Antibiotic resistance is a global concern, which spreads rapidly across borders and continents due to rapid travel of people, animals and goods. Derivatives of metabolically stable pyrazole nucleus are known for their wide range of pharmacological properties, including antibacterial activities. This review highlights recent reports of pyrazole derivatives targeting different bacterial strains focusing on the drug-resistant variants. Pyrazole derivatives target different metabolic pathways of both Gram-positive and Gram-negative bacteria.

Structural Insights into the Inhibition of Undecaprenyl Pyrophosphate Synthase from Gram-Positive Bacteria

The polyprenyl lipid undecaprenyl phosphate (C₅₅P) is the universal carrier lipid for the biosynthesis of bacterial cell wall polymers. C₅₅P is synthesized in its pyrophosphate form by undecaprenyl pyrophosphate synthase (UppS), an essential cis-prenyltransferase that is an attractive target for antibiotic development. We previously identified a compound (MAC-0547630) that showed promise as a novel class of inhibitor and an ability to potentiate β-lactam antibiotics. Here, we provide a structural model for MAC-0547630's inhibition of UppS and a structural rationale for its enhanced effect on UppS from Bacillus subtilis versus Staphylococcus aureus. We also describe the synthesis of a MAC-0547630 derivative (JPD447), show that it too can potentiate β-lactam antibiotics, and provide a structural rationale for its improved potentiation. Finally, we present an improved structural model of clomiphene's inhibition of UppS. Taken together, our data provide a foundation for structure-guided drug design of more potent UppS inhibitors in the future.

Systems-Level Chemical Biology to Accelerate Antibiotic Drug Discovery

Drug-resistant bacterial infections pose an imminent and growing threat to public health. The discovery and development of new antibiotics of novel chemical class and mode of action that are unsusceptible to existing resistance mechanisms is imperative for tackling this threat. Modern industrial drug discovery, however, has failed to provide new drugs of this description, as it is dependent largely on a reductionist genes-to-drugs research paradigm. We posit that the lack of success in new antibiotic drug discovery is due in part to a lack of understanding of the bacterial cell system as whole. A fundamental understanding of the architecture and function of bacterial systems has been elusive but is of critical importance to design strategies to tackle drug-resistant bacterial pathogens.Increasingly, systems-level approaches are rewriting our understanding of the cell, defining a dense network of redundant and interacting components that resist perturbations of all kinds, including by antibiotics. Understanding the network properties of bacterial cells requires integrative, systematic, and genome-scale approaches. These methods strive to understand how the phenotypic behavior of bacteria emerges from the many interactions of individual molecular components that constitute the system. With the ability to examine genomic, transcriptomic, proteomic, and metabolomic consequences of, for example, genetic or chemical perturbations, researchers are increasingly moving away from one-gene-at-a-time studies to consider the system-wide response of the cell. Such measurements are demonstrating promise as quantitative tools, powerful discovery engines, and robust hypothesis generators with great value to antibiotic drug discovery.In this Account, we describe our thinking and findings using systems-level studies aimed at understanding bacterial physiology broadly and in uncovering new antibacterial chemical matter of novel mechanism. We share our systems-level toolkit and detail recent technological developments that have enabled unprecedented acquisition of genome-wide interaction data. We focus on three types of interactions: gene-gene, chemical-gene, and chemical-chemical. We provide examples of their use in understanding cell networks and how these insights might be harnessed for new antibiotic discovery. By example, we show the application of these principles in mapping genetic networks that underpin phenotypes of interest, characterizing genes of unknown function, validating small-molecule screening platforms, uncovering novel chemical probes and antibacterial leads, and delineating the mode of action of antibacterial chemicals. We also discuss the importance of computation to these approaches and its probable dominance as a tool for systems approaches in the future. In all, we advocate for the use of systems-based approaches as discovery engines in antibacterial research, both as powerful tools and to stimulate innovation.

Investigations into the Antibacterial Mechanism of Action of Viridicatumtoxins

Viridicatumtoxins are a rare class of tetracycline-like antibiotics that strongly inhibit drug-resistant Gram-positive bacteria. Although reported to exhibit in vitro inhibition activity to undecaprenyl pyrophosphate synthase (UPPS), an essential enzyme in bacterial cell wall synthesis, the biological targets and mechanism of action of viridicatumtoxins, especially the drug-target interactions, remain largely unknown. In this study, the structure of Enterococcus faecalis UPPS (EfaUPPS) was first determined, uncovering that EfaUPPS can form not only a typical functional dimer but also an unexpected atypical dimer. We then observed that viridicatumtoxins A (VirA) and B (VirB) are able to bind to UPPSs of E. faecalis, S. aureus, and E. coli in a direct and high-affinity manner as evidenced by in vitro enzyme inhibition assay, surface plasmon resonance (SPR) binding analysis, and in vivo growth inhibition assay, demonstrating that viridicatumtoxins exert antibacterial effects through UPPS binding. The key amino acid residues involved in the interactions with VirA and VirB in EfaUPPS binding pocket were revealed by molecular docking studies, and further validated by site-directed mutagenesis. A single mutation of EfaUPPS at D29A, N31A, and R42A can obviously increase their affinities to VirA, while a single mutation at W228A conferred significant resistance to VirA. Moreover, translation inhibition assay showed that VirA and VirB can weakly inhibit E. coli 70S ribosome. The weak inhibition of ribosome was proposed to be attributed to steric hindrance between viridicatumtoxin ring F and 70S ribosome helix 34 by molecular docking study. Our structural, biochemical, and computational investigations on the interactions of viridicatumtoxins with UPPS and 70S ribosome not only disclosed the potential biological targets of viridicatumtoxins, but also provided a theoretical basis for structural optimization to make new viridicatumtoxin derivatives with improved antimicrobial activities.

A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid

The biosynthesis of bacterial cell envelope polysaccharides such as peptidoglycan relies on the use of a dedicated carrier lipid both for the assembly of precursors at the cytoplasmic face of the plasma membrane and for the translocation of lipid linked oligosaccharides across the plasma membrane into the periplasmic space. This dedicated carrier lipid, undecaprenyl phosphate, results from the dephosphorylation of undecaprenyl pyrophosphate, which is generated de novo in the cytoplasm by undecaprenyl pyrophosphate synthase and released as a by-product when newly synthesized glycans are incorporated into the existing cell envelope. The de novo synthesis of undecaprenyl pyrophosphate has been thoroughly characterized from a structural and mechanistic standpoint; however, its dephosphorylation to the active carrier lipid form, both in the course of de novo synthesis and recycling, has only been begun to be studied in depth in recent years. This review provides an overview of bacterial carrier lipid synthesis and presents the current state of knowledge regarding bacterial carrier lipid recycling.

Discovery of an antivirulence compound that reverses β-lactam resistance in MRSA

Staphylococcus aureus is the leading cause of infections worldwide, and methicillin-resistant strains (MRSA) are emerging. New strategies are urgently needed to overcome this threat. Using a cell-based screen of ~45,000 diverse synthetic compounds, we discovered a potent bioactive, MAC-545496, that reverses β-lactam resistance in the community-acquired MRSA USA300 strain. MAC-545496 could also serve as an antivirulence agent alone; it attenuates MRSA virulence in Galleria mellonella larvae. MAC-545496 inhibits biofilm formation and abrogates intracellular survival in macrophages. Mechanistic characterization revealed MAC-545496 to be a nanomolar inhibitor of GraR, a regulator that responds to cell-envelope stress and is an important virulence factor and determinant of antibiotic resistance. The small molecule discovered herein is an inhibitor of GraR function. MAC-545496 has value as a research tool to probe the GraXRS regulatory system and as an antibacterial lead series of a mechanism to combat drug-resistant Staphylococcal infections.

Discovery of a Novel DNA Gyrase-Targeting Antibiotic through the Chemical Perturbation of Streptomyces venezuelae Sporulation

Common approaches to antibiotic discovery include small-molecule screens for growth inhibition in target pathogens and screens for inhibitors of purified enzymes. These approaches have a shared intent of seeking to directly target a vital Achilles heel in a pathogen of interest. Here, we report the first screen against a sporulation pathway in a non-pathogenic bacterium as a means of discovering novel antibiotics—this effort has resulted in two important discoveries. First, we show that the sporulation program of Streptomyces venezuelae is exquisitely sensitive to numerous forms of DNA damage. Second, we have identified a DNA gyrase inhibitor. This molecule, EN-7, is active against pathogenic species that are resistant to ciprofloxacin and other clinically important antibiotics. We suggest that this strategy could be applied to other morphogenetic pathways in prokaryotes or eukaryotes as a means of identifying novel chemical matter having scientific and clinical utility.

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Streptomyces sporulation is sensitive to chemically induced DNA damage

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Screening 3,705 synthetic molecules uncovered novel sporulation inhibitors

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Lead molecule, EN-7, is an inhibitor of extensively resistant Gram-positive pathogens

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EN-7 targets DNA gyrase

High-Throughput Screening for Inhibitors of Wall Teichoic Acid Biosynthesis in Staphylococcus aureus

The world is heading toward a dangerous post-antibiotic era where antibiotics fail to treat infections. Staphylococcus aureus is the leading cause of healthcare-associated infections worldwide, and an ever-increasing percentage of them are methicillin-resistant (MRSA). New strategies are urgently needed to combat this pathogen. Wall teichoic acids (WTA) in S. aureus are polyribitol phosphate polymers that play important roles in virulence and resistance to β-lactam antibiotics. Here, we describe a high-throughput whole-cell screening platform for inhibitors targeting WTA biosynthesis. This platform takes advantage of the unique dispensability patterns of genes encoding WTA biosynthesis. We further describe follow-up dose-response assays to identify WTA inhibitors among the primary bioactives. WTA inhibitors offer an exciting opportunity for the development of novel antibacterial leads of unique mechanism in the fight against drug-resistant staphylococcal infections.

Membrane activity profiling of small molecule B. subtilis growth inhibitors utilizing novel duel-dye fluorescence assay

Small molecule disruption of the bacterial membrane is both a challenge and interest for drug development. While some avoid membrane activity due to toxicity issues, others are interested in leveraging the effects for new treatments. Existing assays are available for measuring disruption of membrane potential or membrane permeability, two key characteristics of the bacterial membrane, however they are limited in their ability to distinguish between these properties. Here, we demonstrate a high throughput assay for detection and characterization of membrane active compounds. The assay distinguishes the effect of small molecules on either the membrane potential or membrane permeability using the fluorescent dyes TO-PRO-3 iodide and DiOC2(3) without the need for secondary assays. We then applied this assay to a library of 3520 synthetic molecules previously shown to inhibit growth of B. subtilis in order to determine the frequency of membrane activity within such a biologically active library. From the library, we found 249 compounds that demonstrated significant membrane activity, suggesting that synthetic libraries of this kind do not contain a plurality of membrane active molecules.

Synthesis and shift-reagent-assisted full NMR assignment of bacterial (Z8,E2,ω)-undecaprenol

The repeating isoprene unit is a fundamental biosynthetic motif. The repetitive structure presents challenges both for synthesis and for structural characterization. In this synthesis of the (Z8,E2,ω)-undecaprenol of prokaryotic glycobiology, we exemplify solutions to these challenges. Allylation of sulfone-derived carbanions controlled the stereochemistry, and its proof-of-structure was secured by Eu(hfc)3 complexation to disperse the overlaid resonances of its 1H NMR spectrum.

Bacterial Cell Growth Inhibitors Targeting Undecaprenyl Diphosphate Synthase and Undecaprenyl Diphosphate Phosphatase

We synthesized a series of benzoic acids and phenylphosphonic acids and investigated their effects on the growth of Staphylococcus aureus and Bacillus subtilis. One of the most active compounds, 5-fluoro-2-(3-(octyloxy)benzamido)benzoic acid (7, ED50 ∼0.15 μg mL-1 ) acted synergistically with seven antibiotics known to target bacterial cell-wall biosynthesis (a fractional inhibitory concentration index (FICI) of ∼0.35, on average) but had indifferent effects in combinations with six non-cell-wall biosynthesis inhibitors (average FICI∼1.45). The most active compounds were found to inhibit two enzymes involved in isoprenoid/bacterial cell-wall biosynthesis: undecaprenyl diphosphate synthase (UPPS) and undecaprenyl diphosphate phosphatase (UPPP), but not farnesyl diphosphate synthase, and there were good correlations between bacterial cell growth inhibition, UPPS inhibition, and UPPP inhibition.