Antibiotic innovation for future public health needs

Evaluating the innovative potential of the global antibacterial pipeline

BACKGROUND

Resistance burden varies widely among WHO regions, and the potential impact of new antibiotics differs in addressing the WHO's critical priority pathogens' resistance challenge.

OBJECTIVES

To analyse the current global clinical pipeline in line with public and global health concerns and define innovation in antibacterial drug discovery.

SOURCES

Monitoring clinical pipelines since 2006, integrating peer-reviewed MEDLINE publications on clinical development of new antibacterial agents, supplemented with disclosed data from developers.

CONTENT

The current clinical pipeline is dominated by derivatives of established antibiotic classes, primarily β-lactamase inhibitor combinations in Phase 3 (six of ten which also include two beta-lactams without β-lactamase inhibitor). This pattern extends to Phase 1. Although incremental improvements in susceptibility rates among derivatives benefit patients in advanced health care systems within specific geographical regions, these concepts are not adequate for carbapenem-resistant strains of Enterobacterales (especially Klebsiella and Escherichia coli), Acinetobacter, and Pseudomonas. This limitation arises from the diverse distribution of resistance mechanisms across global regions. Innovation in this context refers to absence of cross-resistance because of class-specific resistance mechanisms. This can most likely be achieved by exploring new chemical classes and new targets/binding sites, and new mode of action. An initial glimpse of progress is evident as innovative agents progressed to Phase 1 clinical trials. However, an influx of more agents advancing to clinical development is essential given the inherent risks associated with novel chemistry and targets.

IMPLICATIONS

The limited innovation in the global clinical pipeline inadequately serves public and global health interests. The complexities of antibacterial drug discovery, from scientific challenges to financial constraints, underscore the need for collective researcher efforts and public support to drive innovation for patients globally.

A historical, economic, and technical-scientific approach to the current crisis in the development of antibacterial drugs: Promising role of antibacterial peptides in this scenario

The emergence of antibiotic resistance (AMR) is a global public health problem. According to estimates, drug-resistant bacteria infect 2 million patients and perish 23,000 annually. To overcome this problem, antimicrobial peptides became a potential solution based on a new mechanism of action against bacteria. This article addresses the phenomenon of antibacterial resistance in most of its nuances, responding to historical, technical-scientific, and economic aspects. Likewise, it explores new therapeutic approaches to combat multi-resistant pathogens, specifically concerning antibacterial peptides, as a potential therapeutic tool to mitigate the current crisis of antibacterial drugs. It is expected that, with technological advances, especially with the advent and adoption of artificial intelligence, there will be an increase in diversified synthetic peptide production, which can face the challenges that we have in terms of antibacterial drugs.

The role of drug regulatory authorities and health technology assessment agencies in shaping incentives for antibiotic R&D: a qualitative study

BACKGROUND

Few antibiotics have entered the market in recent years despite the need for new treatment options. Some of the challenges of bringing new antibiotics to market are linked to the marketing authorization and health technology assessment (HTA) processes. Research shows great variation in geographic availability of new antibiotics, suggesting that market introduction of new antibiotics is unpredictable. We aimed to investigate regulatory authorities' and HTA agencies' role in developing non-financial incentives to stimulate antibiotic research and development (R&D).

METHODS

We conducted individual, semi-structured, stakeholder interviews. Participants were recruited from regulatory authorities (EMA and FDA) and HTA agencies in Europe. Participants had to be experienced with assessment of antibiotics. The data were analyzed using a deductive and inductive approach to develop codes and identify key themes. Data were analyzed using thematic analysis including the constant comparison method to define concepts, and rival thinking to identify alternative explanations.

RESULTS

We found that (1) interpretation of key concepts guiding the understanding of what type of antibiotics are needed vary (2) lack of a shared approach on how to deal with limited clinical data in the marketing authorization and HTA processes is causing barriers to getting new antibiotics to market (3) necessary adaptations to the marketing authorization process causes uncertainties that transmit to other key stakeholders involved in delivering antibiotics to patients.

CONCLUSIONS

A shared understanding of limited clinical data and how to deal with this issue is needed amongst stakeholders involved in antibiotic R&D, marketing authorization, and market introduction to ensure antibiotics reach the market before resistance levels are out of control. Regulatory authorities and HTA agencies could play an active role in aligning the view of what constitutes an unmet medical need, and direct new economic models towards stimulating greater diversity in the antibiotic armamentarium.

Membrane-Active Nonivamide Derivatives as Effective Broad-Spectrum Antimicrobials: Rational Design, Synthesis, and Biological Evaluation

Antibiotic resistance is emerging as a "global public health concern". To address the growing epidemic of multidrug-resistant pathogens, the development of novel antimicrobials is urgently needed. In this study, by biomimicking cationic antibacterial peptides, we designed and synthesized a series of new membrane-active nonivamide and capsaicin derivatives as peptidomimetic antimicrobials. Through modulating charge/hydrophobicity balance and rationalizing structure-activity relationships of these peptidomimetics, compound 51 was identified as the lead compound. Compound 51 exhibited potent antibacterial activity against both Gram-positive bacteria (MICs = 0.39-0.78 μg/mL) and Gram-negative bacteria (MICs = 1.56-6.25 μg/mL), with low hemolytic activity and low cytotoxicity. Compound 51 displayed a faster bactericidal action through a membrane-disruptive mechanism and avoided bacterial resistance development. Furthermore, compound 51 significantly reduced the microbial burden in a murine model of keratitis infected by Staphylococcus aureus or Pseudomonas aeruginosa. Hence, this design strategy can provide a promising and effective solution to overcome antibiotic resistance.

Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials

Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20^th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.

Computational Target-Based Screening of Anti-MRSA Natural Products Reveals Potential Multitarget Mechanisms of Action through Peptidoglycan Synthesis Proteins

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of bacterial infections in both healthcare and community settings. MRSA can acquire resistance to any current antibiotic, which has major implications for its current and future treatment options. As such, it is globally a major focus for infection control efforts. The mechanical rigidity provided by peptidoglycans in the bacteria cell walls makes it a promising target for broad-spectrum antibacterial drug discovery. The development of drugs that can target different stages of the synthesis of peptidoglycan in MRSA may compromise the integrity of its cell wall and consequently result in the rapid decline of diseases associated with this drug-resistant bacteria. The present study is aimed at screening natural products with known in vitro activities against MRSA to identify their potential to inhibit the proteins involved in the biosynthesis of the peptidoglycan cell wall. A total of 262 compounds were obtained when a literature survey was conducted on anti-MRSA natural products (AMNPs). Virtual screening of the AMNPs was performed against various proteins (targets) that are involved in the biosynthesis of the peptidoglycan (PPC) cell wall using Schrödinger software (release 2020-3) to determine their binding affinities. Nine AMNPs were identified as potential multitarget inhibitors against peptidoglycan biosynthesis proteins. Among these compounds, DB211 showed the strongest binding affinity and interactions with six protein targets, representing three stages of peptidoglycan biosynthesis, and thus was selected as the most promising compound. The MD simulation results for DB211 and its proteins indicated that the protein-ligand complexes were relatively stable over the simulation period of 100 ns. In conclusion, DB211 showed the potential to inhibit six proteins involved in the biosynthesis of the peptidoglycan cell wall in MRSA, thus reducing the chance of MRSA developing resistance to this compound. Therefore, DB211 provided a starting point for the design of new compounds that can inhibit multiple targets in the biosynthesis of the peptidoglycan layer in MRSA.

Efficacy and appropriateness of novel antibiotics in response to antimicrobial-resistant Gram-negative bacteria in patients with sepsis in the ICU

INTRODUCTION

There is an ever-increasing range of antibiotic-resistant pathogens that have led to higher community-acquired infections, and substantial mortality rates in critically ill patients.

AREAS COVERED

We have critically appraised available evidence through a structured literature review, investigating effective empiric antibiotic administration and appropriateness on outcomes of critically ill patients with an increased risk of developing resistant pathogens. The use of new antibiotics should be determined based on relevant knowledge of their spectrum and properties to provide effective mode of action for critically ill patients.

EXPERT OPINION

Restricting severely ill patients access to new broad-spectrum empirical drugs is not the answer. Rather there should be a focus on identifying host response to infection to differentiate between colonization or contamination and true infection, and the sensitivity to antibiotics used in the intensive care unit (ICU).

Management relies on adequate antibiotic administration, the ability to monitor response, and facilitate the cessation of antibiotic treatment. The major determinant of patient success in a patient with a severe infection is the 'right' antibiotic or complementary course of treatment. As an overarching criterion, the following 3 appropriate "Ds" should be considered: Dosing, Duration and De-escalation to empirically assess the right antibiotic optimal antimicrobial selection.

Antimicrobial and biofilm inhibiting potential of an amide derivative [N-(2', 4'-dinitrophenyl)-3β-hydroxyurs-12-en-28-carbonamide] of ursolic acid by modulating membrane potential and quorum sensing against colistin resistant Acinetobacter baumannii

Acinetobacter baumannii is Gram-negative, an opportunistic pathogen responsible for life-threatening ventilator-associated pneumonia. World Health Organization (WHO) enlisted it as a priority pathogen for which therapeutic options need speculations. Biofilm further benefits this pathogen and aids 100-1000 folds more resistant against antimicrobials and the host immune system. In this study, ursolic acid (1) and its amide derivatives (2-4) explored for their antimicrobial and antibiofilm potential against colistin-resistant A. baumannii (CRAB) reference and clinical strains. Viability, crystal violet, microscopic, and gene expression assays further detailed the active compounds' antimicrobial and biofilm inhibition potential. Compound 4 [N-(2',4'-dinitrophenyl)-3β-hydroxyurs-12-en-28-carbonamide)], a synthetic amide derivate of ursolic acid significantly inhibits bacterial growth with MIC in the range of 78-156 μg/mL against CRAB isolates. This compound failed to completely kill the CRAB isolates even at 500 μg/mL concentration, suggesting the compound's anti-virulence and bacteriostatic nature. Short and prolonged exposure of 4 inhibited or delayed the bacterial growth at sub MIC, MIC, and 2× MIC, as evident in time-kill and post-antibacterial assay. It significantly inhibited and eradicated >70% of biofilm formation at MIC and sub MIC levels compared to colistin required in high concentrations. Microscopic analysis showed disintegrated biofilm after treatment with the 4 further strengthened its antibiofilm potential. Atomic force microscopy (AFM) hinted the membrane disrupting effect of 4 at MIC's. Further it was confirmed by DiBAC4 using fluorescence-activating cells sorting (FACS), suggesting a depolarized membrane at MIC. Gene expression analysis also supported our data as it showed reduced expression of biofilm-forming (bap) and quorum sensing (abaR) genes after treatment with sub MIC of 4. The results suggest that 4 significantly inhibit bacterial growth and biofilm mode of colistin-resistant A. baumannii. Thus, further studies are required to decipher the complete mechanism of action to develop 4 as a new pharmacophore against A. baumannii.

A call for action to the biomaterial community to tackle antimicrobial resistance

The global surge of antimicrobial resistance (AMR) is a major concern for public health and proving to be a key challenge in modern disease treatment, requiring action plans at all levels. Microorganisms regularly and rapidly acquire resistance to antibiotic treatments and new drugs are continuously required. However, the inherent cost and risk to develop such molecules has resulted in a drying of the pipeline with very few compounds currently in development. Over the last two decades, efforts have been made to tackle the main sources of AMR. Nevertheless, these require the involvement of large governmental bodies, further increasing the complexity of the problem. As a group with a long innovation history, the biomaterials community is perfectly situated to push forward novel antimicrobial technologies to combat AMR. Although this involvement has been felt, it is necessary to ensure that the field offers a united front with special focus in areas that will facilitate the development and implementation of such systems. This paper reviews state of the art biomaterials strategies striving to limit AMR. Promising broad-spectrum antimicrobials and device modifications are showcased through two case studies for different applications, namely topical and implantables, demonstrating the potential for a highly efficacious physical and chemical approach. Finally, a critical review on barriers and limitations of these methods has been developed to provide a list of short and long-term focus areas in order to ensure the full potential of the biomaterials community is directed to helping tackle the AMR pandemic.

Novel Stapling by Lysine Tethering Provides Stable and Low Hemolytic Cationic Antimicrobial Peptides

Cationic antimicrobial peptides (CAMPs) are potent therapeutics for drug-resistant bacterial infections. However, the clinical application of CAMPs is hampered by its poor proteolytic stability and hemolytic activity toward eukaryotic cells. Great efforts have been made to design and generate derivatives of CAMPs with improved pharmacological properties. Here, we report a novel stapling protocol, which tethers two ε-amino groups of the lysine residue by the N-alkylation reaction on the hydrophilic face of amphiphilic antimicrobial peptides. A series of lysine-tethered stapled CAMPs were synthesized, employing the antimicrobial peptide OH-CM6 as a model. Biological screening of the stapled CAMPs provided an analogue with strong antimicrobial activity, high proteolytic stability, and low hemolytic activity. This novel stapling approach offers an important chemical tool for developing CAMP-based antibiotics.

Antibiotics targeting bacterial ribosomal subunit biogenesis

This article describes 20 years of research that investigated a second novel target for ribosomal antibiotics, the biogenesis of the two subunits. Over that period, we have examined the effect of 52 different antibiotics on ribosomal subunit formation in six different microorganisms. Most of the antimicrobials we have studied are specific, preventing the formation of only the subunit to which they bind. A few interesting exceptions have also been observed. Forty-one research publications and a book chapter have resulted from this investigation. This review will describe the methodology we used and the fit of our results to a hypothetical model. The model predicts that inhibition of subunit assembly and translation are equivalent targets for most of the antibiotics we have investigated.

Critical analysis of antibacterial agents in clinical development

The antibacterial agents currently in clinical development are predominantly derivatives of well-established antibiotic classes and were selected to address the class-specific resistance mechanisms and determinants that were known at the time of their discovery. Many of these agents aim to target the antibiotic-resistant priority pathogens listed by the WHO, including Gram-negative bacteria in the critical priority category, such as carbapenem-resistant Acinetobacter, Pseudomonas and Enterobacterales. Although some current compounds in the pipeline have exhibited increased susceptibility rates in surveillance studies that depend on geography, pre-existing cross-resistance both within and across antibacterial classes limits the activity of many of the new agents against the most extensively drug-resistant (XDR) and pan-drug-resistant (PDR) Gram-negative pathogens. In particular, cross-resistance to unrelated classes may occur by co-selection of resistant strains, thus leading to the rapid emergence and subsequent spread of resistance. There is a continued need for innovation and new-class antibacterial agents in order to provide effective therapeutic options against infections specifically caused by XDR and PDR Gram-negative bacteria.

Abundant Extractable Metabolites from Temperate Tree Barks: The Specific Antimicrobial Activity of Prunus Avium Extracts

Tree barks are mainly considered as wood wastes from forestry activities, but represent valuable resources as they may contain antimicrobial compounds. Here, we aimed to evaluate the possible antimicrobial activities of bark extracts and to characterize the chemical composition of the most active extract. Ten methanol bark extracts were tested in vitro against 17 bacterial strains and 5 yeast strains, through minimum inhibitory concentration (MIC) and minimum bactericidal (or fungicidal) concentration (MBC/MFC) assays. The extract from Prunus avium (E2-4) displayed the largest bactericidal activity against Gram-positive bacteria, with a lethal effect on 6 out of 8 strains. Antibiofilm assays of E2-4 were performed by crystal violet staining and enumeration of adhered bacteria. Assays demonstrated a biofilm inhibitory effect of E2-4 against Staphylococcus aureus CIP 53.154 at concentrations equal to or higher than 250 µg/mL. Chemical profiling of E2-4 by ¹³C nuclear magnetic resonance (NMR) revealed the presence of dihydrowogonin as a major constituent of the extract. E2-4 was fractionated by centrifugal partition chromatography and the three fractions containing dihydrowogonin were tested for their antibacterial and antibiofilm activities, revealing similar activities to those of E2-4. Dihydrowogonin was positively assessed as an interesting antimicrobial compound, which could be valued from wastes of Prunus avium barks.

Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing

The selective regulation of bacteria in complex microbial populations is key to controlling pathogenic bacteria. CRISPR nucleases can be programmed to kill bacteria, but require an efficient and broad-host range delivery system to be effective. Here, using an Escherichia coli and Salmonella enterica co-culture system, we show that plasmids based on the IncP RK2 conjugative system can be used as delivery vectors for a TevSpCas9 dual nuclease. Notably, a cis-acting plasmid that encodes the conjugation and CRISPR machinery conjugates from E. coli to S. enterica with high frequency compared to a trans system that separates conjugation and CRISPR machinery. In culture conditions that enhance cell-to-cell contact, conjugation rates approach 100% with the cis-acting plasmid. Targeting of single or multiplexed sgRNAs to non-essential genes results in high S. enterica killing efficiencies. Our data highlight the potential of cis-acting conjugative plasmids as a delivery system for CRISPR nucleases or other microbial-altering agents for targeted bacterial killing.

Discovery and development of DNA polymerase IIIC inhibitors to treat Gram-positive infections

Despite the growing global crisis caused by antimicrobial drug resistance among pathogenic bacteria, the number of new antibiotics, especially new chemical class of antibiotics under development is insufficient to tackle the problem. Our review focuses on an emerging class of antibacterial therapeutic agents that holds a completely novel mechanism of action, namely, inhibition of bacterial DNA polymerase IIIC. The recent entry of this new class into human trials may herald the introduction of novel drugs whose novel molecular target precludes cross-resistance with existing antibiotic classes. This review therefore examines the evolution of DNA pol IIIC inhibitors from the discovery of 6-(p-hydroxyphenylazo)uracil (HPUra) in the 1960s to the development of current first-in-class N7-substituted guanine drug candidate ACX-362E, now under clinical development for the treatment of Clostridioides difficile infection.

High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB

The permeation of most antibiotics through the outer membrane of Gram-negative bacteria occurs through porin channels. To design drugs with increased activity against Gram-negative bacteria in the face of the antibiotic resistance crisis, the strict constraints on the physicochemical properties of the permeants imposed by these channels must be better understood. Here we show that a combination of high-resolution electrophysiology, new noise-filtering analysis protocols and atomistic biomolecular simulations reveals weak binding events between the β-lactam antibiotic ampicillin and the porin PorB from the pathogenic bacterium Neisseria meningitidis. In particular, an asymmetry often seen in the electrophysiological characteristics of ligand-bound channels is utilised to characterise the binding site and molecular interactions in detail, based on the principles of electro-osmotic flow through the channel. Our results provide a rationale for the determinants that govern the binding and permeation of zwitterionic antibiotics in porin channels.

Analysis of the clinical antibacterial and antituberculosis pipeline

This analysis of the global clinical antibacterial pipeline was done in support of the Global Action Plan on Antimicrobial Resistance. The study analysed to what extent antibacterial and antimycobacterial drugs for systemic human use as well as oral non-systemic antibacterial drugs for Clostridium difficile infections were active against pathogens included in the WHO priority pathogen list and their innovativeness measured by their absence of cross-resistance (new class, target, mode of action). As of July 1, 2018, 30 new chemical entity (NCE) antibacterial drugs, ten biologics, ten NCEs against Mycobacterium tuberculosis, and four NCEs against C difficile were identified. Of the 30 NCEs, 11 are expected to have some activity against at least one critical priority pathogen expressing carbapenem resistance. The clinical pipeline is dominated by derivatives of established classes and most development candidates display limited innovation. New antibacterial drugs without pre-existing cross-resistance are under-represented and are urgently needed, especially for geographical regions with high resistance rates among Gram-negative bacteria and M tuberculosis.

Probing key elements of teixobactin-lipid II interactions in membranes

Two binding poses of the teixobactin–lipid II complex were captured with MD simulations at the membrane surface.

Teixobactin (Txb) is a recently discovered antibiotic against Gram-positive bacteria that induces no detectable resistance. The bactericidal mechanism is believed to be the inhibition of cell wall biosynthesis by Txb binding to lipid II and lipid III. Txb binding specificity likely arises from targeting of the shared lipid component, the pyrophosphate moiety. Despite synthesis and functional assessment of numerous chemical analogs of Txb, and consequent identification of the Txb pharmacophore, the detailed structural information of Txb–substrate binding is still lacking. Here, we use molecular modeling and microsecond-scale molecular dynamics simulations to capture the formation of Txb–lipid II complexes at a membrane surface. Two dominant binding conformations were observed, both showing characteristic lipid II phosphate binding by the Txb backbone amides near the C-terminal cyclodepsipeptide (d-Thr8–Ile11) ring. Additionally, binding by Txb also involved the side chain hydroxyl group of Ser7, as well as a secondary phosphate binding provided by the side chain of l-allo-enduracididine. Interestingly, those conformations differ by swapping two groups of hydrogen bond donors that coordinate the two phosphate moieties of lipid II, resulting in opposite orientations of lipid II binding. In addition, residues d-allo-Ile5 and Ile6 serve as the membrane anchors in both Txb conformations, regardless of the detailed phosphate binding interactions near the cyclodepsipeptide ring. The role of hydrophobic residues in Txb activity is primarily for its membrane insertion, and subsidiarily to provide non-polar interactions with the lipid II tail. Based on the Txb–lipid II interactions captured in their complexes, as well as their partitioning depths into the membrane, we propose that the bactericidal mechanism of Txb is to arrest cell wall synthesis by selectively inhibiting the transglycosylation of peptidoglycan, while possibly leaving the transpeptidation step unaffected. The observed “pyrophosphate caging” mechanism of lipid II inhibition appears to be similar to some lantibiotics, but different from that of vancomycin or bacitracin.

In Vitro Synergism of Silver Nanoparticles with Antibiotics as an Alternative Treatment in Multiresistant Uropathogens

The increase in the prevalence of bacterial resistance to antibiotics has become one of the main health problems worldwide, thus threatening the era of antibiotics most frequently used in the treatment of infections. The need to develop new therapeutic strategies against multidrug resistant microorganisms, such as the combination of selected antimicrobials, can be considered as a suitable alternative. The in vitro activities of two groups of conventional antimicrobial agents alone and in combination with silver nanoparticles (AgNPs) were investigated against a set of ten multidrug resistant clinical isolate and two references strains by MIC assays and checkerboard testing, as well as their cytotoxicity, which was evaluated on human fibroblasts by MTT assay at the same concentration of the antimicrobial agents alone and in combination. Interesting results were achieved when the AgNPs and their combinations were characterized by Dynamic Light Scattering (DLS), Zeta Potential, Transmission Electron Microscopy (TEM), UV⁻visible spectroscopy and Fourier Transforms Infrared (FTIR) spectroscopy. The in vitro activities of ampicillin, in combination with AgNPs, against the 12 microorganisms showed one Synergy, seven Partial Synergy and four Additive effects, while the results with amikacin and AgNPs showed three Synergy, eight Partial Synergy and one Additive effects. The cytotoxic effect at these concentrations presented a statistically significant decrease of their cytotoxicity (p < 0.05). These results indicate that infections caused by multidrug resistant microorganisms could be treated using a synergistic combination of antimicrobial drugs and AgNPs. Further studies are necessary to evaluate the specific mechanisms of action, which could help predict undesirable off-target interactions, suggest ways of regulating a drug&rsquo;s activity, and identify novel therapeutic agents in this health problem.

Antibiotic Pipeline Coordinators

The World Health Organization (WHO) has published a global priority list of antibiotic-resistant bacteria to guide research and development (R&D) of new antibiotics. Every pathogen on this list requires R&D activity, but some are more attractive for private sector investments, as evidenced by the current antibacterial pipeline. A "pipeline coordinator" is a governmental/non-profit organization that closely tracks the antibacterial pipeline and actively supports R&D across all priority pathogens employing new financing tools.