Compound Uptake into E. coli Can Be Facilitated by N-Alkyl Guanidiniums and Pyridiniums

Positive Charge in an Antimalarial Compound Unlocks Broad-Spectrum Antibacterial Activity

In this study, we synthesized a library of eNTRy-rule-compliant compounds by introducing ionizable nitrogen atoms to an antimalarial compound. These positively charged derivatives gained activity against both Gram-negative and -positive bacteria, Mycobacterium tuberculosis, and boosted Plasmodium falciparum inhibition to the double-digit nanomolar range. Overcoming and remaining inside the cell envelope of Gram-negative bacteria (GNB) is one of the major difficulties in antibacterial drug discovery and development. The eNTRy rules (N = ionizable nitrogen, T = low three-dimensionality, R = rigidity) can be a useful structural guideline to improve accumulation of small molecules in GNB. With the aim of unlocking Gram-negative activity, we added amines and (cyclic) N-alkyl guanidines to an already flat and rigid pyrazole-amide class as a representative example for our investigation. To test their performance, we compared these eNTRy-rule-compliant compounds to closely related noncompliant ones through phenotypic screening of various pathogens (P. falciparum, Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, and M. tuberculosis), obtaining a handful of broad-spectrum hits. The results support the working hypothesis and even extend its applicability. The studied pyrazole-amide class adheres to the eNTRy rules; noncompliant compounds do not kill any of the bacteria tested, while compliant compounds largely showed growth inhibition of Gram-negative, -positive, and M. tuberculosis bacteria in the single-digit micromolar range.

Seeking Correlation Among Porin Permeabilities and Minimum Inhibitory Concentrations Through Machine Learning: A Promising Route to the Essential Molecular Descriptors

Developing effective antibiotics against Gram-negative bacteria remains challenging due to their protective outer membrane. With this study, we investigated the relationship between antibiotic permeation through the OmpF porin of Escherichia coli and antimicrobial efficacy. We measured the relative permeability coefficients (RPCs) through the bacterial porin by liposome swelling assays, including non-antibacterial molecules, and the minimum inhibitory concentrations (MICs) against E. coli. We developed a machine learning (ML) approach by combining classification and regression models to correlate these data sets. Our strategy allowed us to quantify the negative correlation between RPC and MIC values, clearly indicating that increased permeability through OmpF generally leads to improved antimicrobial activity. Moreover, the correlation was remarkable only for compounds with significant permeability coefficients. Conversely, when permeation ability is low, other factors play the most significant role in antimicrobial potency. Importantly, the proposed ML-based approach was set by exploiting the available seminal information from previous investigations in order to keep the number of molecular descriptors to the minimum for greater interpretability. This provided valuable insights into the complex interplay between different molecular properties in defining the overall outer membrane permeation and, consequently, the antimicrobial efficacy. From a practical perspective, the presented approach does not aim at identifying the "golden rule" for boosting antibiotic potency. The automated protocol presented here could be used to inspect, in silico, many alternatives of a given molecular structure, with the output being the list of the best candidates to be then synthesized and tested. This could be a valuable in silico tool for researchers in both academia and industry to rapidly evaluate novel potential compounds and reduce costs and time during the early drug discovery stage.

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.

Synthesis, Antimicrobial Activities, and Model of Action of Indolyl Derivatives Containing Amino-Guanidinium Moieties

The objectives of the study were to design, synthesize, and evaluate the antibacterial activity of a series of novel aminoguanidine-indole derivatives. Thirty-seven new compounds were effectively synthesized through nucleophilic substitution reaction and guanidinylation reaction. Chemical structures of all the desired compounds were identified by NMR and HR-MS spectroscopy. Most of the synthesized compounds showed significant antibacterial activity against ESKAPE pathogens and clinical resistant Klebsiella pneumoniae (K. pneumoniae) isolates. K. pneumoniae is an important opportunistic pathogen that often threatens the health of immunocompromised people such as the elderly, children, and ICU patients. The most active compound 4P showed rapid bactericidal activity against resistant K. pneumoniae 2108 with MIC and MBC values that were 4 and 8 µg/mL, respectively. The hemolytic activity of 4P was low, with an HC50 value of 123.6 µg/mL. Compound 4P induced the depolarization of the bacterial membrane and disrupted bacterial membrane integrity and was not prone to antibiotic resistance. The dihydrofolate reductase (DHFR) activity was also notably inhibited by 4P in vitro. Molecular docking revealed that the aminoguanidine moiety and indole structure of 4P played an important role in binding to the target site of the K. pneumoniae dihydrofolate reductase (DHFR) receptor. In the mouse pneumonia model caused by K. pneumoniae, 4P improved the survival rate of mice, reduced bacterial loads, and alleviated tissues' pathological injuries at a dosage of 4 mg/kg. Therefore, compound 4P may be a promising lead compound or drug candidate for antibacterial purposes against K. pneumoniae.

Advances in methods and concepts provide new insight into antibiotic fluxes across the bacterial membrane

The sophisticated envelope of Gram-negative bacteria modulates the uptake of small molecules in a side-chain-sensitive manner. Despite intensive theoretical and experimental investigations, a general set of pathways underpinning antibiotic uptake has not been identified. This manuscript discusses the passive influx versus active efflux of antibiotics, considering the responsible membrane proteins and the transported molecules. Recent methods have analyzed drug transport across the bacterial membrane in order to understand their activity. The combination of in vitro, in cellulo and in silico methods shed light on the key, mainly electrostatic, interactions between the molecule surface, porins and transporters during permeation. A key factor is the relationship between the dose of an active compound near its target and its antibacterial activity during the critical early window. Today, methodology breakthroughs provide fruitful tools to precisely dissect drug transport, identify key steps in drug resistance associated with membrane impermeability and efflux, and highlight key parameters to generate more effective drugs.

Screening Privileged Alkyl Guanidinium Motifs under Host-Mimicking Conditions Reveals a Novel Antibiotic with an Unconventional Mode of Action

Screening large molecule libraries against pathogenic bacteria is often challenged by a low hit rate due to limited uptake, underrepresentation of antibiotic structural motifs, and assays that do not resemble the infection conditions. To address these limitations, we present a screen of a focused library of alkyl guanidinium compounds, a structural motif associated with antibiotic activity and enhanced uptake, under host-mimicking infection conditions against a panel of disease-associated bacteria. Several hit molecules were identified with activities against Gram-positive and Gram-negative bacteria, highlighting the fidelity of the general concept. We selected one compound (L15) for in-depth mode of action studies that exhibited bactericidal activity against methicillin-resistant Staphylococcus aureus USA300 with a minimum inhibitory concentration of 1.5 μM. Structure-activity relationship studies confirmed the necessity of the guanidinium motif for antibiotic activity. The mode of action was investigated using affinity-based protein profiling with an L15 probe and identified the signal peptidase IB (SpsB) as the most promising hit. Validation by activity assays, binding site identification, docking, and molecular dynamics simulations demonstrated SpsB activation by L15, a recently described mechanism leading to the dysregulation of protein secretion and cell death. Overall, this study highlights the need for unconventional screening strategies to identify novel antibiotics.

Rational molecular design converting fascaplysin derivatives to potent broad-spectrum inhibitors against bacterial pathogens via targeting FtsZ

The filamentous temperature-sensitive mutant Z protein (FtsZ), a key player in bacterial cell division machinery, emerges as an attractive target to tackle the plight posed by the ever growing antibiotic resistance over the world. Therefore in this regard, agents with scaffold diversities and broad-spectrum antibacterial activity against Gram-positive and Gram-negative pathogens are highly needed. In this study, a new class of marine-derived fascaplysin derivatives has been designed and synthesized by Suzuki-Miyaura cross-coupling. Some compounds exhibited potent bactericidal activities against a panel of Gram-positive (MIC = 0.024-6.25 μg/mL) and Gram-negative (MIC = 1.56-12.5 μg/mL) bacteria including methicillin-resistant S. aureus (MRSA). They exerted their effects by dual action mechanism via disrupting the integrity of the bacterial cell membrane and targeting FtsZ protein. These compounds stimulated polymerization of FtsZ monomers and bundling of the polymers, and stabilized the resulting polymer network, thus leading to the dysfunction of FtsZ in cell division. In addition, these agents showed negligible hemolytic activity and low cytotoxicity to mammalian cells. The studies on docking and molecular dynamics simulations suggest that these inhibitors bind to the hydrophilic inter-domain cleft of FtsZ protein and the insights obtained in this study would facilitate the development of potential drugs with broad-spectrum bioactivities.

The Hybrid Antibiotic Thiomarinol A Overcomes Intrinsic Resistance in Escherichia coli Using a Privileged Dithiolopyrrolone Moiety

An impermeable outer membrane and multidrug efflux pumps work in concert to provide Gram-negative bacteria with intrinsic resistance against many antibiotics. These resistance mechanisms reduce the intracellular concentrations of antibiotics and render them ineffective. The natural product thiomarinol A combines holothin, a dithiolopyrrolone antibiotic, with marinolic acid A, a close analogue of mupirocin. The hybridity of thiomarinol A converts the mupirocin scaffold from inhibiting Gram-positive bacteria to inhibiting both Gram-positive and -negative bacteria. We found that thiomarinol A accumulates significantly more than mupirocin within the Gram-negative bacterium Escherichia coli, likely contributing to its broad-spectrum activity. Antibiotic susceptibility testing of E. coli mutants reveals that thiomarinol A overcomes the intrinsic resistance mechanisms that render mupirocin inactive. Structure-activity relationship studies suggest that the dithiolopyrrolone is a privileged moiety for improving the accumulation and antibiotic activity of the mupirocin scaffold without compromising binding to isoleucyl-tRNA synthetase. These studies also highlight that accumulation is required but not sufficient for antibiotic activity. Our work reveals a role of the dithiolopyrrolone moiety in overcoming intrinsic mupirocin resistance in E. coli and provides a starting point for designing dual-acting and high-accumulating hybrid antibiotics.

Amine Basicity of Quinoline ATP Synthase Inhibitors Drives Antibacterial Activity against Pseudomonas aeruginosa

Pseudomonas aeruginosa (PA), a Gram-negative pathogen, is a common cause of nosocomial infections, especially in immunocompromised and cystic fibrosis patients. PA is intrinsically resistant to many currently prescribed antibiotics due to its tightly packed, anionic lipopolysaccharide outer membrane, efflux pumps, and ability to form biofilms. PA can acquire additional resistance through mutation and horizontal gene transfer. PA ATP synthase is an attractive target for antibiotic development because it is essential for cell survival even under fermentation conditions. Previously, we developed two lead quinoline compounds that were capable of selectively inhibiting PA ATP synthase and acting as antibacterial agents against multidrug-resistant PA. Herein we conduct a structure-activity relationship analysis of the lead compounds through the synthesis and evaluation of 18 quinoline derivatives. These compounds function as new antibacterial agents while providing insight into the balance of physical properties needed to promote cellular entry while maintaining PA ATP synthase inhibition.

Guiding the Way: Traditional Medicinal Chemistry Inspiration for Rational Gram-Negative Drug Design

The discovery and development of small-molecule therapeutics effective against Gram-negative pathogens are highly challenging tasks. Most compounds that are active in biochemical settings fail to exhibit whole-cell activity. The major reason for this lack of activity is the effectiveness of bacterial cell envelopes as permeability barriers. These barriers originate from the nutrient-selective outer membranes, which act synergistically with polyspecific efflux pumps. Guiding principles to enable rational optimization of small molecules for efficient penetration and intracellular accumulation in Gram-negative bacteria would have a transformative impact on the discovery and design of chemical probes and therapeutics. In this Perspective, we draw on inspiration from traditional medicinal chemistry approaches for eukaryotic drug design to present a broader call for action in developing comparable approaches for Gram-negative bacteria.

Bisbenzamidine and Bisbenzguanidine Ureas Act as Antibacterial Agents against Pseudomonas aeruginosa

Due to the global rise in the number of antibiotic resistant bacterial infections over the past 20 years, there is a dire need for the development of small molecule antibiotics capable of overcoming resistance mechanisms in pathogenic bacteria. Antibiotic development against Gram-negative pathogens, such as Pseudomonas aeruginosa, is especially challenging due to their additional outer membrane which reduces antibiotic entry. Recently, it has been shown that a broad range of nitrogen functionality, including guanidines, amidines, primary amines, imidazolines, and imidazoles, promote antibiotic and adjuvant activity in Gram-negative bacteria, but few of these have been targeted towards Pseudomonas aeruginosa specifically despite this pathogen being deemed a critical threat by the United States Centers for Disease Control and Prevention. Herein, we examined a small series of known and unknown nitrogenous dimers, with guanidine, amidine, dimethyl amine, and pyridine functionality, for antibacterial activity against multidrug resistant Pseudomonas aeruginosa. We found that two, with bisbenzguanidine and bisbenzamidine functionality, are potent against clinical isolates of multidrug resistant and biofilm forming Pseudomonas aeruginosa.

Porin-independent accumulation in Pseudomonas enables antibiotic discovery

Gram-negative antibiotic development has been hindered by a poor understanding of the types of compounds that can accumulate within these bacteria1,2. The presence of efflux pumps and substrate-specific outer-membrane porins in Pseudomonas aeruginosa renders this pathogen particularly challenging3. As a result, there are few antibiotic options for P. aeruginosa infections4 and its many porins have made the prospect of discovering general accumulation guidelines seem unlikely5. Here we assess the whole-cell accumulation of 345 diverse compounds in P. aeruginosa and Escherichia coli. Although certain positively charged compounds permeate both bacterial species, P. aeruginosa is more restrictive compared to E. coli. Computational analysis identified distinct physicochemical properties of small molecules that specifically correlate with P. aeruginosa accumulation, such as formal charge, positive polar surface area and hydrogen bond donor surface area. Mode of uptake studies revealed that most small molecules permeate P. aeruginosa using a porin-independent pathway, thus enabling discovery of general P. aeruginosa accumulation trends with important implications for future antibiotic development. Retrospective antibiotic examples confirmed these trends and these discoveries were then applied to expand the spectrum of activity of a gram-positive-only antibiotic, fusidic acid, into a version that demonstrates a dramatic improvement in antibacterial activity against P. aeruginosa. We anticipate that these discoveries will facilitate the design and development of high-permeating antipseudomonals.

The mechanism of an electrostatic nanofilter: overcoming entropy with electrostatics

General porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. These biological nanopores have been designed to protect the interior of the bacterial cell from leakage of toxic compounds while selectively allowing the entry of the molecules needed for cell growth and function. The mechanism of transport through porins is of utmost and direct interest for drug discovery, extending toward nanotechnology applications for blue energy, separations, and sequencing. Here we present a theoretical framework for analysing the filter of general porins in relation to translocating molecules with the aid of enhanced molecular simulations quantitatively. Using different electrostatic probes in the form of a series of related molecules, we describe the nature of this filter and how to finely tune permeability by exploiting electrostatic interactions between the pore and the translocating molecule. Eventually, we show how enhanced simulations constitute today a valid tool for characterising the mechanism and quantifying energetically the transport of molecules through nanopores.

Fast prediction of antibiotic permeability through membrane channels using Brownian dynamics

The efficient permeation across the Gram-negative bacterial membrane is an important step in the overall process of antibacterial action of a molecule and the one that has posed a significant hurdle on the way toward approved antibiotics. Predicting the permeability for a large library of molecules and assessing the effect of different molecular transformations on permeation rates of a given molecule is critical to the development of effective antibiotics. We present a computational approach for obtaining estimates of molecular permeability through a porin channel in a matter of hours using a Brownian dynamics approach. The fast sampling using a temperature acceleration scheme enables the approximate estimation of permeability using the inhomogeneous solubility diffusion model. Although the method is a significant approximation to similar all-atom approaches tested previously, we show that the present approach predicts permeabilities that correlate fairly well with the respective experimental permeation rates from liposome swelling experiments and accumulation rates from antibiotic accumulation assays, and is significantly, i.e., about 14 times, faster compared with a previously reported approach. The possible applications of the scheme in high-throughput screening for fast permeators are discussed.

Structure-Uptake Relationship Studies of Oxazolidinones in Gram-Negative ESKAPE Pathogens

The clinical success of linezolid for treating Gram-positive infections paired with the high conservation of bacterial ribosomes predicts that if oxazolidinones were engineered to accumulate in Gram-negative bacteria, then this pharmacological class would find broad utility in eradicating infections. Here, we report an investigative study of a strategically designed library of oxazolidinones to determine the effects of molecular structure on accumulation and biological activity. Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa strains with varying degrees of compromise (in efflux and outer membrane) were used to identify motifs that hinder permeation across the outer membrane and/or enhance efflux susceptibility broadly and specifically between species. The results illustrate that small changes in molecular structure are enough to overcome the efflux and/or permeation issues of this scaffold. Three oxazolidinone analogues (3e, 8d, and 8o) were identified that exhibit activity against all three pathogens assessed, a biological profile not observed for linezolid.

Design and evaluation of poly-nitrogenous adjuvants capable of potentiating antibiotics in Gram-negative bacteria

Antibiotic resistance has been a growing public health crisis since the 1980s. Therefore, it is essential not only to continue to develop novel antibiotics but also to develop new methods for overcoming resistance mechanisms in pathogenic bacteria so antibiotics can be reactivated towards these resistant strains. One common cause of antibiotic resistance in Gram-negative bacteria is reduced permeability of the tightly packed, negatively charged lipopolysaccharide outer membrane (OM), which dramatically reduces or even prevents antibiotic accumulation within the cell. Adjuvants that promote passive diffusion through the OM, including phenylalanine-arginine-β-naphthylamide, tobramycin, and pentamidine, have proven useful in potentiating antibiotics against Gram-negative bacteria. Structural evaluation of these adjuvants, which all include multiple nitrogenous groups, indicates that the entry rules developed for improving antibiotic accumulation in Escherichia coli (EC), could also be used to guide adjuvant development. To this end, a series of structurally simple poly-nitrogenous diphenylsuccinamide compounds have been prepared and evaluated for their ability to potentiate a panel of classic antibiotics in wild-type EC and Pseudomonas aeruginosa (PA). Modest adjuvant activity was observed for all compounds surveyed when co-administered with known antibiotics to inhibit either wild-type EC or PA, and all were able to accumulate in both EC and PA.

Total Synthesis and Antibacterial Evaluation of Empetroxepins A and B and related analogs

Empetroxepins A and B, which are 10,11-dihydrodibenz[b,f]oxepins produced by the Black Crowberry (Empetrum nigrum), displayed weak anti-tubercular activity upon isolation, but have not been explored for antibiotic activity despite their molecular similarity to other phenolic antibacterial natural products. Herein we detail the first total synthesis of Empetroxepins A and B via a selective demethylation strategy and antibacterial structure activity relationship (SAR) study of the natural products and related analogs. Empetroxepin A was found to be weakly active against susceptible strains of Staphylococcus aureus (SA) and Bacillus subtilis (BS) with MICs = 256 μg/mL against both, whereas Empetroxepin B was found to be weakly active against only BS (MIC = 256 μg/mL). Neither natural product was active against Escherichia coli (EC). Antibiotic activity was improved through derivatization of the 10,11-dihydrodibenz[b,f]oxepin core with the best compound of the SAR series, 9-chloro-10,11-dihydrodibenzo[b,f]oxepine-2,3,4-triol, having MICs of 8 μg/mL, 16 μg/mL, and 256 μg/mL against SA, BS, and EC respectively.

Synthesis and Evaluation of Pseudomonas aeruginosa ATP Synthase Inhibitors

New antibiotics with unique biological targets are desperately needed to combat the growing number of resistant bacterial pathogens. ATP synthase, a critical protein found in all life, has recently become a target of interest for antibiotic development due to the success of the anti-tuberculosis drug bedaquiline, and while many groups have worked on developing drugs to target bacterial ATP synthase, few have been successful at inhibiting Pseudomonas aeruginosa (PA) ATP synthase specifically. PA is one of the leading causes of resistant nosocomial infections across the world and is extremely challenging to treat due to its various antibiotic resistance mechanisms for most commonly used antibiotics. Herein, we detail the synthesis and evaluation of a series of C1/C2 quinoline analogues for their ability to inhibit PA ATP synthase and act as antibiotics against wild-type PA. From this survey, we found six compounds capable of inhibiting PA ATP synthase in vitro showing that bulky/hydrophobic C1/C2 substitutions are preferred. The strongest inhibitor showed an IC₅₀ of 10 μg/mL and decreased activity of PA ATP synthase to 24% relative to the control. While none of the compounds were able to inhibit wild-type PA in cell culture, two showed improved inhibition of PA growth when permeability of the outer membrane was increased or efflux was knocked out, thus demonstrating that these compounds could be further developed into efficacious antibiotics.

Three-Dimensional Structure and Optimization of the Metallo-β-Lactamase Inhibitor Aspergillomarasmine A

The aminopolycarboxylic acid aspergillomarasmine A (AMA) is a natural Zn²⁺ metallophore and inhibitor of metallo-β-lactamases (MBLs) which reverses β-lactam resistance. The first crystal structure of an AMA coordination complex is reported and reveals a pentadentate ligand with distorted octahedral geometry. We report the solid-phase synthesis of 23 novel analogs of AMA involving structural diversification of each subunit (l-Asp, l-APA1, and l-APA2). Inhibitory activity was evaluated in vitro using five strains of Escherichia coli producing globally prevalent MBLs. Further in vitro assessment was performed with purified recombinant enzymes and intracellular accumulation studies. Highly constrained structure-activity relationships were demonstrated, but three analogs revealed favorable characteristics where either Zn²⁺ affinity or the binding mode to MBLs were improved. This study identifies compounds that can further be developed to produce more potent and broader-spectrum MBL inhibitors with improved pharmacodynamic/pharmacokinetic properties.

Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge

Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and form favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.

An LC-MS/MS assay and complementary web-based tool to quantify and predict compound accumulation in E. coli

Novel classes of broad-spectrum antibiotics have been extremely difficult to discover, largely due to the impermeability of the Gram-negative membranes coupled with a poor understanding of the physicochemical properties a compound should possess to promote its accumulation inside the cell. To address this challenge, numerous methodologies for assessing intracellular compound accumulation in Gram-negative bacteria have been established, including classic radiometric and fluorescence-based methods. The recent development of accumulation assays that utilize liquid chromatography-tandem mass spectrometry (LC-MS/MS) have circumvented the requirement for labeled compounds, enabling assessment of a substantially broader range of small molecules. Our unbiased study of accumulation trends in Escherichia coli using an LC-MS/MS-based assay led to the development of the eNTRy rules, which stipulate that a compound is most likely to accumulate in E. coli if it has an ionizable Nitrogen, has low Three-dimensionality and is relatively Rigid. To aid in the implementation of the eNTRy rules, we developed a complementary web tool, eNTRyway, which calculates relevant properties and predicts compound accumulation. Here we provide a comprehensive protocol for analysis and prediction of intracellular accumulation of small molecules in E. coli using an LC-MS/MS-based assay (which takes ~2 d) and eNTRyway, a workflow that is readily adoptable by any microbiology, biochemistry or chemical biology laboratory.

The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes

Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".

Donnan Potential across the Outer Membrane of Gram-Negative Bacteria and Its Effect on the Permeability of Antibiotics

The cell envelope structure of Gram-negative bacteria is unique, composed of two lipid bilayer membranes and an aqueous periplasmic space sandwiched in between. The outer membrane constitutes an extra barrier to limit the exchange of molecules between the cells and the exterior environment. Donnan potential is a membrane potential across the outer membrane, resulted from the selective permeability of the membrane, which plays a pivotal role in the permeability of many antibiotics. In this review, we discussed factors that affect the intensity of the Donnan potential, including the osmotic strength and pH of the external media, the osmoregulated periplasmic glucans trapped in the periplasmic space, and the displacement of cell surface charges. The focus of our discussion is the impact of Donnan potential on the cellular permeability of selected antibiotics including fluoroquinolones, tetracyclines, β-lactams, and trimethoprim.

Dreams, False Starts, Dead Ends, and Redemption: A Chronicle of the Evolution of a Chemoinformatic Workflow for the Optimization of Enantioselective Catalysts

Catalyst design in enantioselective catalysis has historically been driven by empiricism. In this endeavor, experimentalists attempt to qualitatively identify trends in structure that lead to a desired catalyst function. In this body of work, we lay the groundwork for an improved, alternative workflow that uses quantitative methods to inform decision making at every step of the process. At the outset, we define a library of synthetically accessible permutations of a catalyst scaffold with the philosophy that the library contains every potential catalyst we are willing to make. To represent these chiral molecules, we have developed general 3D representations, which can be calculated for tens of thousands of structures. This defines the total chemical space of a given catalyst scaffold; it is constructed on the basis of catalyst structure only without regard to a specific reaction or mechanism. As such, any algorithmic subset selection method, which is unsupervised (i.e., only considers catalyst structure), should provide an ideal initial screening set for any new reaction that can be catalyzed by that scaffold. Notably, because this design strategy, the same set of catalysts can be used for any reaction that can be catalyzed with that parent catalyst scaffold. These are tested experimentally, and statistical learning tools can be used to create a model relating catalyst structure to catalyst function. Further, this model can be used to predict the performance of each catalyst candidate in the greater database of virtual catalyst candidates. In this way, it is possible estimate the performance of tens of thousands of catalysts by experimentally testing a smaller subset. Using error assessment metrics, it is possible to understand the confidence in new predictions. An experimentalist using this tool can balance the predicted results (reward) with the prediction confidence (risk) when deciding which catalysts to synthesize next in an optimization campaign. These catalysts are synthesized and tested experimentally. At this stage, either the optimization is a success or the predicted values were incorrect and further optimization is required. In the case of the latter, the information can be fed back into the statistical learning model to refine the model, and this iterative process can be used to determine the optimal catalyst. In this body of work, we not only establish this workflow but quantitatively establish how best to execute each step. Herein, we evaluate several 3D molecular representations to determine how best to represent molecules. Several selection protocols are examined to best decide which set of molecules can be used to represent the library of interest. In addition, the number of reactions needed to make accurate, statistical learning models is evaluated. Taken together these components establish a tool ready to progress from the development stage to the utility stage. As such, current research endeavors focus on applying these tools to optimize new reactions.

Designing Inhibitors of β-Lactamase Enzymes to Overcome Carbapenem Resistance in Gram-Negative Bacteria

Ever since the first β-lactam antibiotic, penicillin, was introduced into the clinic over 70 years ago, resistance has been observed because of the presence of β-lactamase enzymes, which hydrolyze the β-lactam ring of β-lactam antibiotics. Early β-lactamase enzymes were all of the serine β-lactamase (SBL) type, but more recently, highly resistant Gram-negative strains have emerged in which metallo-β-lactamase (MBL) enzymes are responsible for resistance. The two types of β-lactamase enzymes are structurally and mechanistically different but serve the same purpose in bacteria. The SBLs use an active serine group as a nucleophile to attack the β-lactamase ring, forming a covalent intermediate that is subsequently hydrolyzed. In contrast, the MBLs use a zinc ion to activate the β-lactam toward nucleophilic attack by a hydroxide anion held between two zinc ions. In this Account, we review our recent contribution to the field of β-lactamase inhibitor design in terms of both SBL and MBL inhibitors. We describe how we have approached these challenges from the particular perspective of a small biotechnology company, identifying new inhibitors when faced with either a paucity of starting points for medicinal chemistry (MBL inhibitors) or else an abundance of prior research necessitating a search for novelty, improvement, and differentiation (SBL inhibitors). During the journey from the beginning of lead optimization to successful identification of a preclinical candidate for development, we encountered and solved a range of issues. For example, in the MBL inhibitor series we were able to prevent metabolic cleavage of a glycinamide moiety by circulating amidases while still retaining the activity by converting the amino group into a guanidine. In the SBL inhibitor series, the structure-activity relationship led us to consider introducing a fluorine substituent adjacent to a urea functionality. At first sight this grouping would appear to be chemically unstable. However, deeper theoretical considerations suggested that this would not be the case, and in practice the compound is remarkably stable. Both examples serve to illustrate the importance of scientific insight and the necessity to explore speculative hypotheses as part of the creative medicinal chemistry process.

Facilitating Compound Entry as a Means to Discover Antibiotics for Gram-Negative Bacteria

It has been over half a century since the last class of antibiotics active against the most problematic Gram-negative bacteria was approved by the Food and Drug Administration (FDA). The major challenge with developing antibiotics to treat these infections is not drug-target engagement but rather the inability of most small molecules to traverse the Gram-negative membranes, be retained, and accumulate within the cell. Despite an abundance of lead compounds, limited understanding of the physicochemical properties needed for compound accumulation (or avoidance of efflux) in Gram-negative bacteria has precluded a generalizable approach for developing Gram-negative antibiotics. Indeed, in many instances, despite years of intensive derivatization efforts and the synthesis of hundreds of compounds aimed at building in Gram-negative activity, little or no progress has been made in expanding the spectrum of activity for many Gram-positive-only antibiotics. In this Account, we describe the discovery and successful applications of a promising strategy for enhancing the accumulation of Gram-positive-only antibiotics as a means of imbuing compounds with broad-spectrum activity.Utilizing a prospective approach examining the accumulation in Escherichia coli for more than 180 diverse compounds, we found that small molecules have an increased likelihood to accumulate in E. coli when they contain an ionizable Nitrogen, have low Three-dimensionality, and are Rigid. Implementing these guidelines, codified as the "eNTRy rules" and assisted by web application www.entry-way.org, we have facilitated compound entry and systematically built Gram-negative activity into Gram-positive-only antibiotics. Though each antibiotic will have case-specific considerations, we describe a set of important criteria to consider when selecting candidate Gram-positive-only antibiotics for conversion to Gram-negative-active versions via the eNTRy rules. As detailed herein, using this blueprint the spectrum of activity was expanded for three antibiotic classes that engage three different biological targets: DNA gyrase inhibitor 6DNM, FabI inhibitor Debio-1452, and FMN riboswitch inhibitor Ribocil C. In each scenario, the eNTRy rules guided the synthesis of key analogues predisposed to accumulate in Gram-negative bacteria leading to compounds that display antibiotic activity (minimum inhibitory concentrations (MIC) ≤8 μg mL^-1) against E. coli and other Gram-negative ESKAPE pathogens. While the eNTRy rules will continue to be refined and enhanced as more accumulation data is gathered, on the basis of these collective results and on other examples not covered herein it is clear that the eNTRy rules are actionable for the development of novel broad-spectrum antibiotics from Gram-positive-only compounds. By enabling the prediction of compound accumulation, the eNTRy rules should facilitate the process of discovering and developing novel antibiotics active against Gram-negative bacteria.