Are the physicochemical properties of antibacterial compounds really different from other drugs?

Microbial community interactions on a chip

Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect the survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here, we report a Microbial Community Interaction (µCI) device to advance the systematic study of chemical and biological interactions within a microbial community. The µCI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing green fluorescent protein provided the "target" readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the "variables." The µCI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased the growth of B. cereus. The µCI device enables both strain-level and community-level insight. The scalable geometric design of the µCI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life.

Cerastecin Inhibition of the Lipooligosaccharide Transporter MsbA to Combat Acinetobacter baumannii: From Screening Impurity to In Vivo Efficacy

Acinetobacter baumannii, a commonly multidrug-resistant Gram-negative bacterium responsible for large numbers of bloodstream and lung infections worldwide, is increasingly difficult to treat and constitutes a growing threat to human health. Structurally novel antibacterial chemical matter that can evade existing resistance mechanisms is essential for addressing this critical medical need. Herein, we describe our efforts to inhibit the essential A. baumannii lipooligosaccharide (LOS) ATP-binding cassette (ABC) transporter MsbA. An unexpected impurity from a phenotypic screening was optimized as a series of dimeric compounds, culminating with 1 (cerastecin D), which exhibited antibacterial activity in the presence of human serum and a pharmacokinetic profile sufficient to achieve efficacy against A. baumannii in murine septicemia and lung infection models.

1,2,3-Triazol-5-ylidene- vs. 1,2,3-triazole-based tricarbonylrhenium(I) complexes: influence of a mesoionic carbene ligand on the electronic and biological properties

The tricarbonylrhenium complexes that incorporate a mesoionic carbene ligand represent an emerging and promising class of molecules, the solid-state optical properties of which have rarely been investigated. The aim of this comprehensive study is to compare three of these complexes with their 1,2,3-triazole-based analogues. The Hirshfeld surface analysis of the crystallographic data revealed that the triazolylidene derivatives are more prone to π-π interactions than their 1,2,3-triazole-based counterparts. The FT-IR and electrochemical data indicated a stronger electron donor effect from the organic ligand to the rhenium atom for triazolylidene derivatives, which was confirmed by DFT calculations. All compounds were phosphorescent in solution, where the 1,2,3-triazole-based complexes showed unusually strong dependence on dissolved oxygen. All compounds also emitted in the solid state, some of them exhibited marked solid-state luminescence enhancement (SLE) effect. The 1,2,3-triazole based complex Re-Phe even displayed astounding photoluminescence efficiency with quantum yield up to 0.69, and proved to be an excellent candidate for applications linked to aggregation-induced emission (AIE). Interestingly, one triazolylidene-based complex (Re-T-BOP) showed attractive antibacterial activity. This study highlights the potential of these new molecules for applications in the fields of photoluminescent and therapeutic materials, and provides the first bases for the design of efficient molecules in these research areas.

Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus

The application of computer-aided drug discovery (CADD) approaches has enabled the discovery of new antimicrobial therapeutic agents in the past. The high prevalence of methicillin-resistantStaphylococcus aureus(MRSA) strains promoted this pathogen to a high-priority pathogen for drug development. In this sense, modern CADD techniques can be valuable tools for the search for new antimicrobial agents. We employed a combination of a series of machine learning (ML) techniques to select and evaluate potential compounds with antibacterial activity against methicillin-susceptible S. aureus (MSSA) and MRSA strains. In the present study, we describe the antibacterial activity of six compounds against MSSA and MRSA reference (American Type Culture Collection (ATCC)) strains as well as two clinical strains of MRSA. These compounds showed minimal inhibitory concentrations (MIC) in the range from 12.5 to 200 μM against the different bacterial strains evaluated. Our results constitute relevant proven ML-workflow models to distinctively screen for novel MRSA antibiotics.

SAR investigation and optimization of benzimidazole-based derivatives as antimicrobial agents against Gram-negative bacteria

Antibiotic-resistant bacteria represent a serious threat to modern medicine and human life. Only a minority of antibacterial agents are active against Gram-negative bacteria. Hence, the development of novel antimicrobial agents will always be a vital need. In an effort to discover new therapeutics against Gram-negative bacteria, we previously reported a structure-activity-relationship (SAR) study on 1,2-disubstituted benzimidazole derivatives. Compound III showed a potent activity against tolC-mutant Escherichia coli with an MIC value of 2 μg/mL, representing a promising lead for further optimization. Building upon this study, herein, 49 novel benzimidazole compounds were synthesized to investigate their antibacterial activity against Gram-negative bacteria. Our design focused on three main goals, to address the low permeability of our compounds and improve their cellular accumulation, to expand the SAR study to the unexplored ring C, and to optimize the lead compound (III) by modification of the methanesulfonamide moiety. Compounds (25a-d, 25f-h, 25k, 25l, 25p, 25r, 25s, and 26b) exhibited potent activity against tolC-mutant E. coli with MIC values ranging from 0.125 to 4 μg/mL, with compound 25d displaying the highest potency among the tested compounds with an MIC value of 0.125 μg/mL. As its predecessor, III, compound 25d exhibited an excellent safety profile without any significant cytotoxicity to mammalian cells. Time-kill kinetics assay indicated that 25d exhibited a bacteriostatic activity and significantly reduced E. coli JW55031 burden as compared to DMSO. Additionally, combination of 25d with colistin partially restored its antibacterial activity against Gram-negative bacterial strains (MIC values ranging from 4 to 16 μg/mL against E. coli BW25113, K. pneumoniae, A. baumannii, and P. aeruginosa). Furthermore, formulation of III and 25d as lipidic nanoparticles (nanocapsules) resulted in moderate enhancement of their antibacterial activity against Gram-negative bacterial strains (A. Baumannii, N. gonorrhoeae) and compound 25d demonstrated superior activity to the lead compound III. These findings establish compound 25d as a promising candidate for treatment of Gram-negative bacterial infections and emphasize the potential of nano-formulations in overcoming poor cellular accumulation in Gram-negative bacteria where further optimization and investigation are warranted to improve the potency and broaden the spectrum of our compounds.

On the ability of machine learning methods to discover novel scaffolds

The recent advances in the application of machine learning to drug discovery have made it a 'hot topic' for research, with hundreds of academic groups and companies integrating machine learning into their drug discovery projects. Nevertheless, there remains great uncertainty regarding the most appropriate ways to evaluate the relative performance of these powerful methods against more traditional cheminformatics approaches, and many pitfalls remain for the unwary. In 2020, researchers at MIT (Stokes et al., Cell 180(4), 688-702, 2020) reported the discovery of a new compound with antibacterial activity, halicin, through the use of a neural network machine learning method. A robust ability to identify new active chemotypes through computational methods would be very useful. In this study, we have used the Stokes et al. dataset to compare the performance of this method to two other approaches, Mapping of Activity Through Dichotomic Scores (MADS) by Todeschini et al. (J Chemom 32(4):e2994, 2018) and Random Matrix Theory (RMT) by Lee et al. (Proc Natl Acad Sci 116(9):3373-3378, 2019). Our results demonstrate that all three methods are capable of predicting halicin as an active antibacterial compound, but that this result is dependent on the dataset composition, pre-processing and the molecular fingerprint used. We have further assessed overall performance as determined by several performance metrics. We also investigated the scaffold hopping potential of the methods by modifying the dataset by removal of the β-lactam and fluoroquinolone chemotypes. MADS and RMT are able to identify actives in the test set that contained these substructures. This ability arises because of high scoring fragments of the withheld chemotypes that are in common with other active antibiotic classes. Interestingly, MADS is relatively better compared to the other two methods based on general predictive performance.

Acylhydrazones and Their Biological Activity: A Review

Due to the structure of acylhydrazones both by the pharmacophore -CO-NH-N= group and by the different substituents present in the molecules of compounds of this class, various pharmacological activities were reported, including antitumor, antimicrobial, antiviral, antiparasitic, anti-inflammatory, immunomodulatory, antiedematous, antiglaucomatous, antidiabetic, antioxidant, and actions on the central nervous system and on the cardiovascular system. This fragment is found in the structure of several drugs used in the therapy of some diseases that are at the top of public health problems, like microbial infections and cardiovascular diseases. Moreover, the acylhydrazone moiety is present in the structure of some compounds with possible applications in the treatment of other different pathologies, such as schizophrenia, Parkinson's disease, Alzheimer's disease, and Huntington's disease. Considering these aspects, we consider that a study of the literature data regarding the structural and biological properties of these compounds is useful.

Isatin Bis-Indole and Bis-Imidazothiazole Hybrids: Synthesis and Antimicrobial Activity

Isatin and its derivatives are important heterocycles found in nature and present in numerous bioactive compounds which possess various biological activities. Moreover, it is an essential building block in organic synthesis. The discovery of novel compounds active against human pathogenic bacteria and fungi is an urgent need, and the isatin may represent the suitable scaffold in the design of biologically relevant antimicrobials. A small library of 18 isatin hybrids was synthetized and evaluated for their antimicrobial potential on three reference strains: S. aureus, E. coli, both important human pathogens infamous for causing community- and hospital-acquired severe systemic infections; and C. albicans, responsible for devastating invasive infections, mainly in immunocompromised individuals. The study highlighted two lead compounds, 6k and 6m, endowed with inhibitory activity against S. aureus at very low concentrations (39.12 and 24.83 µg/mL, respectively).

Identification of potential non-nucleoside MraY inhibitors for tuberculosis chemotherapy using structure-based virtual screening

The efforts to limit the spread of the tuberculosis epidemic have been challenged by the rise of drug-resistant strains of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. It is critical to discover new chemical scaffolds acting on novel or unexploited targets to beat this drug-resistant pathogen. MraY (phospho-MurNAc-pentapeptide translocase or translocase I) is an in vivo validated target for antibacterials-discovery. MraY is inhibited by nucleoside-based natural products that suffer from poor in vivo efficacy. The current study is focused on discovering novel chemical entities, particularly, non-nucleoside small molecules, as MraYMtb inhibitors possessing antituberculosis activity. In the absence of any reported X-ray crystal structures of MraYMtb, we used a homology model-based virtual screening approach combined with the ligand-based e-pharmacophore screening. We screened ∼12 million commercially available compounds from the ZINC15 database using GOLD software. The resulting hits were filtered using a 2-pronged screening method comprising e-pharmacophore hypotheses and docking against the MraYMtb homology model using Glide. Further clustering based on Glide scores and optimal binding interactions resulted in 15 in silico hits. We performed molecular dynamics (MD) simulations for the three best-ranking compounds and one other poorer-ranking compound, out of the 15 in silico hits, to analyze the interaction modes in detail. The MD simulations indicated stable interactions between the compounds and key residues in the MraY active site that are crucial for maintaining the enzymatic activity. These in silico hits could advance the antibacterial drug discovery campaign to find new MraY inhibitors for tuberculosis treatment.Communicated by Ramaswamy H. Sarma.

Facile synthesis and biological evaluation of chrysin derivatives

In this paper, novel synthetic methods, including microwave O-alkylation, were used to produce several chrysin derivatives. These compounds were purified, characterised and tested on different cell lines and bacterial strains. From this family, 7-(2,4-dinitrophenoxy)-5-hydroxy-3-phenyl-4H-chromen-4-one (C3) was shown to be extremely active on bacterial strains methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa and Klebsiella pneumoniae as well as having anticancer activity on a range of cancer cell lines with IC50 values less than 30 µM. Chrysin has been known for their anticancer and antimicrobial properties, and this study not only corroborates this but also shows that it is possible to synthesise new improved derivatives with therapeutic possibilities.

Towards machine learning discovery of dual antibacterial drug-nanoparticle systems

Artificial Intelligence/Machine Learning (AI/ML) algorithms may speed up the design of DADNP systems formed by Antibacterial Drugs (AD) and Nanoparticles (NP). In this work, we used IFPTML = Information Fusion (IF) + Perturbation-Theory (PT) + Machine Learning (ML) algorithm for the first time to study of a large dataset of putative DADNP systems composed by >165 000 ChEMBL AD assays and 300 NP assays vs. multiple bacteria species. We trained alternative models with Linear Discriminant Analysis (LDA), Artificial Neural Networks (ANN), Bayesian Networks (BNN), K-Nearest Neighbour (KNN) and other algorithms. IFPTML-LDA model was simpler with values of Sp ≈ 90% and Sn ≈ 74% in both training (>124 K cases) and validation (>41 K cases) series. IFPTML-ANN and KNN models are notably more complicated even when they are more balanced Sn ≈ Sp ≈ 88.5%-99.0% and AUROC ≈ 0.94-0.99 in both series. We also carried out a simulation (>1900 calculations) of the expected behavior for putative DADNPs in 72 different biological assays. The putative DADNPs studied are formed by 27 different drugs with multiple classes of NP and types of coats. In addition, we tested the validity of our additive model with 80 DADNP complexes experimentally synthetized and biologically tested (reported in >45 papers). All these DADNPs show values of MIC < 50 μg mL^-1 (cutoff used) better that MIC of AD and NP alone (synergistic or additive effect). The assays involve DADNP complexes with 10 types of NP, 6 coating materials, NP size range 5-100 nm vs. 15 different antibiotics, and 12 bacteria species. The IFPTML-LDA model classified correctly 100% (80 out of 80) DADNP complexes as biologically active. IFPMTL additive strategy may become a useful tool to assist the design of DADNP systems for antibacterial therapy taking into consideration only information about AD and NP components by separate.

Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-β-lactamase inhibitors

Production of metallo-β-lactamases (MBLs) in bacterial pathogens is an important cause of resistance to the 'last-resort' carbapenem antibiotics. Development of effective MBL inhibitors to reverse carbapenem resistance in Gram-negative bacteria is still needed. We herein report X-ray structure-guided optimization of 1H-imidazole-2-carboxylic acid (ICA) derivatives by considering how to engage with the active-site flexible loops and improve penetration into Gram-negative bacteria. Structure-activity relationship studies revealed the importance of appropriate substituents at ICA 1-position to achieve potent inhibition to class B1 MBLs, particularly the Verona Integron-encoded MBLs (VIMs), mainly by involving ingenious interactions with the flexible active site loops as observed by crystallographic analyses. Of the tested ICA inhibitors, 55 displayed potent synergistic antibacterial activity with meropenem against engineered Escherichia coli strains and even intractable clinically isolated Pseudomonas aeruginosa producing VIM-2 MBL. The morphologic and internal structural changes of bacterial cells after treatment further demonstrated that 55 crossed the outer membrane and reversed the activity of meropenem. Moreover, 55 showed good pharmacokinetic and safety profile in vivo, which could be a potential candidate for combating VIM-mediated Gram-negative carbapenem resistance.

Challenges in Drug Discovery for Intracellular Bacteria

Novel drugs are needed to treat a variety of persistent diseases caused by intracellular bacterial pathogens. Virulence pathways enable many functions required for the survival of these pathogens, including invasion, nutrient acquisition, and immune evasion. Inhibition of virulence pathways is an established route for drug discovery; however, many challenges remain. Here, we propose the biggest problems that must be solved to advance the field meaningfully. While it is established that we do not yet understand the nature of chemicals capable of permeating into the bacterial cell, this problem is compounded when targeting intracellular bacteria because we are limited to only those chemicals that can permeate through both human and bacterial outer envelopes. Unfortunately, many chemicals that permeate through the outer layers of mammalian cells fail to penetrate the bacterial cytoplasm. Another challenge is the lack of publicly available information on virulence factors. It is virtually impossible to know which virulence factors are clinically relevant and have broad cross-species and cross-strain distribution. In other words, we have yet to identify the best drug targets. Yes, standard genomics databases have much of the information necessary for short-term studies, but the connections with patient outcomes are yet to be established. Without comprehensive data on matters such as these, it is difficult to devise broad-spectrum, effective anti-virulence agents. Furthermore, anti-virulence drug discovery is hindered by the current state of technologies available for experimental investigation. Antimicrobial drug discovery was greatly advanced by the establishment and standardization of broth microdilution assays to measure the effectiveness of antimicrobials. However, the currently available models used for anti-virulence drug discovery are too broad, as they must address varied phenotypes, and too expensive to be generally adopted by many research groups. Therefore, we believe drug discovery against intracellular bacterial pathogens can be advanced significantly by overcoming the above hurdles.

Compound Prioritization through Meta-Analysis Enhances the Discovery of Antimicrobial Hits against Bacterial Pathogens

The development of informatic tools to improve the identification of novel antimicrobials would significantly reduce the cost and time of drug discovery. We previously screened several plant (Xanthomonas sp., Clavibacter sp., Acidovorax sp., and Erwinia sp.), animal (Avian pathogenic Escherichia coli and Mycoplasma sp.), and human (Salmonella sp. and Campylobacter sp.) pathogens against a pre-selected small molecule library (n = 4182 SM) to identify novel SM (hits) that completely inhibited the bacterial growth or attenuated at least 75% of the virulence (quorum sensing or biofilm). Our meta-analysis of the primary screens (n = 11) using the pre-selected library (approx. 10.2 ± 9.3% hit rate per screen) demonstrated that the antimicrobial activity and spectrum of activity, and type of inhibition (growth versus virulence inhibitors) correlated with several physico-chemical properties (PCP; e.g., molecular weight, molar refraction, Zagreb group indexes, Kiers shape, lipophilicity, and hydrogen bond donors and acceptors). Based on these correlations, we build an in silico model that accurately classified 80.8% of the hits (n = 1676/2073). Therefore, the pre-selected SM library of 4182 SM was narrowed down to 1676 active SM with predictable PCP. Further, 926 hits affected only one species and 1254 hits were active against specific type of pathogens; however, no correlation was detected between PCP and the type of pathogen (29%, 34%, and 46% were specific for animal, human foodborne and plant pathogens, respectively). In conclusion, our in silico model allowed rational identification of SM with potential antimicrobial activity against bacterial pathogens. Therefore, the model developed in this study may facilitate future drug discovery efforts by accelerating the identification of uncharacterized antimicrobial molecules and predict their spectrum of activity.

Empirical Analysis Revealing Privileged Chemical Space of Cosmetic Preservatives

Most cosmetic products require preservation to prevent microbial contamination and to ensure consumer safety. Due to regulatory restrictions and rejection by consumers, preservative options have become limited and the development of novel solutions is needed. This search can be guided by knowledge about favorable chemical space for cosmetic preservatives. Therefore, we used preservatives allowed in the EU as training set and calculated various molecular properties. Empirical analysis revealed two separated areas of privileged chemical space with the net charge as distinctive property. The first area comprises the group of neutral and anionic preservatives and is characterized by low molecular size as well as limited hydrogen-bonding capacity, polarity, and flexibility. The second area includes cationic preservatives, which are rather diffusely distributed regarding molecular weight and hydrogen-bonding, however, all members share high flexibility. Both groups significantly differ from antibiotics, reflecting the specific requirement of cosmetic preservation. The molecular properties defining the privileged chemical space are easy to calculate, and thus, can provide guidance for the development of novel preservatives.

Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds

The growing antimicrobial resistance (AMR) of pathogenic organisms to currently prescribed drugs has resulted in the failure to treat various infections caused by these superbugs. Therefore, to keep pace with the increasing drug resistance, there is a pressing need for novel antimicrobial agents, especially from non-conventional sources. Several natural products (NPs) have been shown to display promising in vitro activities against multidrug-resistant pathogens. Still, only a few of these compounds have been studied as prospective drug candidates. This may be due to the expensive and time-consuming process of conducting important studies on these compounds. The present review focuses on applying cheminformatics strategies to characterize, prioritize, and optimize NPs to develop new lead compounds against antimicrobial resistance pathogens. Moreover, case studies where these strategies have been used to identify potential drug candidates, including a few selected open-access tools commonly used for these studies, are briefly outlined.

U.S. FDA Approved Drugs from 2015-June 2020: A Perspective

In the present work, we report compilation and analysis of 245 drugs, including small and macromolecules approved by the U.S. FDA from 2015 until June 2020. Nearly 29% of the drugs were approved for the treatment of various types of cancers. Other major therapeutic areas of focus were infectious diseases (14%); neurological conditions (12%); and genetic, metabolic, and cardiovascular disorders (7-8% each). Itemization of the approved drugs according to the year of approval, sponsor, target, chemical class, major drug-metabolizing enzyme(s), route of administration/elimination, and drug-drug interaction liability (perpetrator or/and victim) is presented and discussed. An effort has been made to analyze the pharmacophores to identify the structural (e.g., aromatic, heterocycle, and aliphatic), elemental (e.g., boron, sulfur, fluorine, phosphorus, and deuterium), and functional group (e.g., nitro drugs) diversity among the approved drugs. Further, descriptor-based chemical space analysis of FDA approved drugs and several strategies utilized for optimizing metabolism leading to their discoveries have been emphasized. Finally, an analysis of drug-likeness for the approved drugs is presented.

The Demand for New Antibiotics: Antimicrobial Peptides, Nanoparticles, and Combinatorial Therapies as Future Strategies in Antibacterial Agent Design

The inappropriate use of antibiotics and an inadequate control of infections have led to the emergence of resistant strains which represent a major threat to public health and the global economy. Therefore, research and development of a new generation of antimicrobials to mitigate the spread of antibiotic resistance has become imperative. Current research and technology developments have promoted the improvement of antimicrobial agents that can selectively interact with a target site (e.g., a gene or a cellular process) or a specific pathogen. Antimicrobial peptides and metal nanoparticles exemplify a novel approach to treat infectious diseases. Nonetheless, combinatorial treatments have been recently considered as an excellent platform to design and develop the next generation of antibacterial agents. The combination of different drugs offers many advantages over their use as individual chemical moieties; these include a reduction in dosage of the individual drugs, fewer side effects compared to the monotherapy, reduced risk for the development of drug resistance, a better combined response compared to the effect of the individual drugs (synergistic effects), wide-spectrum antibacterial action, and the ability to attack simultaneously multiple target sites, in many occasions leading to an increased antibacterial effect. The selection of the appropriate combinatorial treatment is critical for the successful treatment of infections. Therefore, the design of combinatorial treatments provides a pathway to develop antimicrobial therapeutics with broad-spectrum antibacterial action, bactericidal instead of bacteriostatic mechanisms of action, and better efficacy against multidrug-resistant bacteria.

Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C β-Lactamase from Escherichia coli

Resistance to β-lactam antibacterials, importantly via production of β-lactamases, threatens their widespread use. Bicyclic boronates show promise as clinically useful, dual-action inhibitors of both serine- (SBL) and metallo- (MBL) β-lactamases. In combination with cefepime, the bicyclic boronate taniborbactam is in phase 3 clinical trials for treatment of complicated urinary tract infections. We report kinetic and crystallographic studies on the inhibition of AmpC, the class C β‑lactamase from Escherichia coli, by bicyclic boronates, including taniborbactam, with different C-3 side chains. The combined studies reveal that an acylamino side chain is not essential for potent AmpC inhibition by active site binding bicyclic boronates. The tricyclic form of taniborbactam was observed bound to the surface of crystalline AmpC, but not at the active site, where the bicyclic form was observed. Structural comparisons reveal insights into why active site binding of a tricyclic form has been observed with the NDM-1 MBL, but not with other studied β-lactamases. Together with reported studies on the structural basis of inhibition of class A, B and D β‑lactamases, our data support the proposal that bicyclic boronates are broad-spectrum β‑lactamase inhibitors that work by mimicking a high energy 'tetrahedral' intermediate. These results suggest further SAR guided development could improve the breadth of clinically useful β-lactamase inhibition.

Hepatitis C Virus NS3 Protease and Helicase Inhibitors from Red Sea Sponge (Amphimedon) Species in Green Synthesized Silver Nanoparticles Assisted by in Silico Modeling and Metabolic Profiling

Background

Hepatitis C virus (HCV) infection is a major cause of hepatic diseases all over the world. This necessitates the need to discover novel anti-HCV drugs to overcome emerging drug resistance and liver complications.

Purpose

Total extract and petroleum ether fraction of the marine sponge (Amphimedon spp.) were used for silver nanoparticle (SNP) synthesis to explore their HCV NS3 helicase- and protease-inhibitory potential.

Methods

Characterization of the prepared SNPs was carried out with ultraviolet-visible spectroscopy, transmission electron microscopy, and Fourier-transform infrared spectroscopy. The metabolomic profile of different Amphimedon fractions was assessed using liquid chromatography coupled with high-resolution mass spectrometry. Fourteen known compounds were isolated and their HCV helicase and protease activities assessed using in silico modeling of their interaction with both HCV protease and helicase enzymes to reveal their anti-HCV mechanism of action. In vitro anti-HCV activity against HCV NS3 helicase and protease was then conducted to validate the computation results and compared to that of the SNPs.

Results

Transmission electron–microscopy analysis of NPs prepared from Amphimedon total extract and petroleum ether revealed particle sizes of 8.22–14.30 nm and 8.22–9.97 nm, and absorption bands at λ_max of 450 and 415 nm, respectively. Metabolomic profiling revealed the richness of Amphimedon spp. with different phytochemical classes. Bioassay-guided isolation resulted in the isolation of 14 known compounds with anti-HCV activity, initially revealed by docking studies. In vitro anti–HCV NS3 helicase and protease assays of both isolated compounds and NPs further confirmed the computational results.

Conclusion

Our findings indicate that Amphimedon, total extract, petroleum ether fraction, and derived NPs are promising biosources for providing anti-HCV drug candidates, with nakinadine B and 3,4-dihydro-6-hydroxymanzamine A the most potent anti-HCV agents, possessing good oral bioavailability and penetration power.

Perspective on Antibacterial Lead Identification Challenges and the Role of Hypothesis-Driven Strategies

For the past three decades, the pharmaceutical industry has undertaken many diverse approaches to discover novel antibiotics, with limited success. We have witnessed and personally experienced many mistakes, hurdles, and dead ends that have derailed projects and discouraged scientists and business leaders. Of the many factors that affect the outcomes of screening campaigns, a lack of understanding of the properties that drive efflux and permeability requirements across species has been a major barrier for advancing hits to leads. Hits that possess bacterial spectrum have seldom also possessed druglike properties required for developability and safety. Persistence in solving these two key barriers is necessary for the reinvestment into discovering antibacterial agents. This perspective narrates our experience in antibacterial discovery-our lessons learned about antibacterial challenges as well as best practices for screening strategies. One of the tenets that guides us is that drug discovery is a hypothesis-driven science. Application of this principle, at all steps in the antibacterial discovery process, should improve decision making and possibly the odds of what has become, in recent decades, an increasingly challenging endeavor with dwindling success rates.

Enabling design of screening libraries for antibiotic discovery by modeling ChEMBL data

It is critical to identify novel antibiotics. Yet, the scientific community has struggled in this pursuit because we do not understand which molecules will penetrate the bacterial outer envelope. In this work, we have identified a large dataset of compounds known to reach their targets in bacterial cells (penetrators) and compared them with molecules that do not (non-penetrators). Our dataset, extracted from the ChEMBL database, is a useful tool to guide the selection of molecules for antibiotic screening. Simple random forest classification models are able to correctly identify penetrators from non-penetrators. The model demonstrated ~87% accuracy, with high precision (~88%) and recall (~97%) in identifying penetrators of Gram-positive bacteria. A paucity of data for non-penetrators was a major hurdle to model-building; we observed a ~86% negative predictive value, but only a ~57% specificity. Accumulation of data on non-penetrators is therefore necessary. Data for Gram-negative bacteria was also sparse, but a larger fraction of these data represented non-penetrators. Correspondingly, the resultant models performed well in predicting those molecules that would fail to enter Gram-negative cells, but were relatively weaker in correctly predicting penetrators. A comparison of physicochemical properties of penetrators and non-penetrators suggests only marginal differences exist. Therefore, it may be difficult to identify overarching rules for generation of screening libraries for antibiotic discovery, based purely on physicochemical properties alone. Instead, models such as ours should be of use. Our models are highly preliminary and based on phenotypic data, but a similar large dataset directly addressing accumulation of chemical matter in bacterial cells is currently unavailable. Hence, our models represent the cutting edge in design of screening libraries for antibiotic discovery until appropriate data can be compiled.

Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold

Multidrug efflux is a major contributor to antibiotic resistance in Gram-negative bacterial pathogens. Inhibition of multidrug efflux pumps is a promising approach for reviving the efficacy of existing antibiotics. Previously, inhibitors targeting both the efflux transporter AcrB and the membrane fusion protein AcrA in the Escherichia coli AcrAB-TolC efflux pump were identified. Here we use existing physicochemical property guidelines to generate a filtered library of compounds for computational docking. We then experimentally test the top candidate coumpounds using in vitro binding assays and in vivo potentiation assays in bacterial strains with controllable permeability barriers. We thus identify a new class of inhibitors of E. coli AcrAB-TolC. Six molecules with a shared scaffold were found to potentiate the antimicrobial activity of erythromycin and novobiocin in hyperporinated E. coli cells. Importantly, these six molecules were also active in wild-type strains of both Acinetobacter baumannii and Klebsiella pneumoniae, potentiating the activity of erythromycin and novobiocin up to 8-fold.

Testicular Caspase-3 and β-Catenin Regulators Predicted via Comparative Metabolomics and Docking Studies

Many routes have been explored to search for effective, safe, and affordable alternatives to hazardous female contraceptives. Herbal extracts and their secondary metabolites are some of the interesting research areas to address this growing issue. This study aims to investigate the effects of ten different plant extracts on testicular spermatogenesis. The correlation between the chemical profile of these extracts and their in vivo effect on male reproductive system was evaluated using various techniques. Approximately 10% of LD₅₀ of hydro-methanolic extracts were orally administrated to rats for 60 days. Semen parameters, sexual organ weights, and serum levels of male sex hormones in addition to testes histopathology, were evaluated. Moreover, metabolomic analysis using (LC-HRESIMS), multivariate analysis (PCA), immunohistochemistry (caspase-3 and β-catenin), and a docking study were performed. Results indicated that three plant extracts significantly decreased epididymal sperm density and motility. Moreover, their effects on testicular cells were also assured by histopathological evaluations. Metabolomic profiling of the bioactive plant extracts showed the presence of diverse phytochemicals, mostly oleanane saponins, phenolic diterpenes, and lupane triterpenes. A docking study on caspase-3 enzyme showed that oleanane saponins possessed the highest binding affinity. An immunohistochemistry assay on β-catenin and caspase-3 indicated that Albizzia lebbeck was the most active extract for decreasing immunoexpression of β-catenin, while Rosmarinus officinalis showed the highest activity for increasing immunoexpression of caspase-3. The spermatogenesis decreasing the activity of A. lebbeck, Anagallis arvensis, and R. officinalis can be mediated via up-regulation of caspase-3 and down-regulation of β-catenin existing in testis cells.

Small Polar Hits against S. aureus: Screening, Initial Hit Optimization, and Metabolomic Studies

The global prevalence of antibacterial resistance requires new antibacterial drugs with novel chemical scaffolds and modes of action. It is also vital to design compounds with optimal physicochemical properties to permeate the bacterial cell envelope. We described an approach of combining and integrating whole cell screening and metabolomics into early antibacterial drug discovery using a library of small polar compounds. Whole cell screening of a diverse library of small polar compounds against Staphylococcus aureus gave compound 2. Hit expansion was carried out to determine structure-activity relationships. A selection of compounds from this series, together with other screened active compounds, was subjected to an initial metabolomics study to provide a metabolic fingerprint of the mode of action. It was found that compound 2 and its analogues have a different mode of action from some of the known antibacterial compounds tested. This early study highlighted the potential of whole cell screening and metabolomics in early antibacterial drug discovery. Future works will require improving potency and performing orthogonal studies to confirm the modes of action.

Synthesis of Disulfide-Bridged N-Phenyl-N'-(alkyl/aryl/heteroaryl)urea Derivatives and Evaluation of Their Antimicrobial Activities

The discovery of new antimicrobial agents is extremely needed to overcome multidrug-resistant bacterial and tuberculosis infections. In the present study, eight novel substituted urea derivatives (10a-10h) containing disulfide bond were designed, synthesized and screened for their in vitro antimicrobial activities on standard strains of Gram-positive and Gram-negative bacteria as well as on Mycobacterium tuberculosis. According to the obtained results, antibacterial effects of the compounds were found to be considerably better than their antimycobacterial activities along with their weak cytotoxic effects. Molecular docking studies were performed to gain insights into the antibacterial activity mechanism of the synthesized compounds. The interactions and the orientation of compound 10a (1,1'-((disulfanediylbis(methylene))bis(2,1-phenylene))bis(3-phenylurea)) were found to be highly similar to the original ligand within the binding pocket E. faecalis β-ketoacyl acyl carrier protein synthase III (FabH). Finally, a theoretical study was established to predict the physicochemical properties of the compounds.

Targeting the Bacterial Membrane with a New Polycyclic Privileged Structure: A Powerful Tool To Face Staphylococcus aureus Infections

In this paper, a small series of anthracene-maleimide-based compounds was prepared and evaluated to assess the antimicrobial potential of this polycyclic core, a scaffold previously unexplored for new antibiotic development. Some of the new compounds showed appreciable anti-Staphylococcus aureus activity, together with good safety profiles. In particular, compound 13 proved to be the most promising of the series, showing remarkable antimicrobial activity toward planktonic and sessile bacterial cells within a mature preformed biofilm. The mechanism of action seems to be related to the ability of this compound to interfere with bacterial membrane functionality, probably through the targeting of key enzymes responsible for membrane redox homeostasis and energy production. The data reported confirm the ability of this polycyclic nucleus to behave as a new "privileged structure", suitable to be further exploited in the antimicrobial field.

The assemblage of covalent and metal binding dual functional scaffold for cross-class metallo-β-lactamases inhibition

Aim: The discovery and development of novel broad-spectrum MβLs inhibitors are urgent to overcome antibiotic resistance mediated by MβLs. Methods & results: Herein, the synthesized 21 compounds exhibited potent inhibition to the clinically important MβLs (NDM-1, IMP-1 and ImiS) and effectively restored the antibacterial efficacy of cefazolin and imipenem against Escherichia coli harboring MβLs. 5b was first identified to be dual functional broad-spectrum MβLs inhibitor through assemblage of covalent and metal binding scaffold, which irreversibly inhibited B1, B2 MβLs via forming a Se–S covalent bond, and competitively inhibited B3 MβLs by coordinating the metals at active site. Conclusion: The designed compounds can serve as potent broad-spectrum MβLs inhibitors and combat MβLs-producing ‘superbug’ in combination with β-lactams.

Potential of marine natural products against drug-resistant bacterial infections

Natural products have been a rich source of compounds with structural and chemical diversity for drug discovery. However, antibiotic resistance in bacteria has been reported for nearly every antibiotic once it is used in clinical practice. In the past decade, pharmaceutical companies have reduced their natural product discovery projects because of challenges, such as high costs, low return rates, and high rediscovery rates. The largely unexplored marine environment harbours substantial diversity and is a large resource to discover novel compounds with novel modes of action, which is essential for the treatment of drug-resistant bacterial infections. In this Review, we report compounds derived from marine sources that have shown in-vivo and in-vitro efficacy against drug-resistant bacteria. Analysis of the physicochemical properties of these marine natural products with activity against drug-resistant bacteria showed that 60% of the compounds have oral bioavailability potential. Their overall distribution pattern of drug characteristics agrees with the observation that marketed antibacterial drugs have a polar distribution, with a lower median calculated logP. The aim of this Review is to summarise the diversity of these marine natural products, with a special focus on analysis of drug bioavailability. Such biologically active compounds, with high degrees of bioavailability, have the potential to be developed as effective drugs against infectious diseases.

Novel narrow spectrum benzyl thiophene sulfonamide derivatives to control Campylobacter

Campylobacter is a leading cause of bacterial foodborne gastroenteritis worldwide, and poultry are a major source of human campylobacteriosis. The control of Campylobacter from farm to fork is challenging due to emergence of microbial resistance and lack of effective control methods. We identified a benzyl thiophene sulfonamide based small molecule (compound 1) with a minimal inhibitory concentration (MIC) of 100 μM against Campylobacter jejuni 81-176 and Campylobacter coli ATCC33559, good drug-like properties, and low toxicity on eukaryotic cells. Compound 1 was used as a lead for the preparation of 13 analogues. Two analogues, compounds 4 and 8 (TH-4 and TH-8), were identified with better antimicrobial properties than compound 1. TH-4 and TH-8 had a MIC of 12.5 μM and 25 μM for C. coli and 50 μM and 100 μM for C. jejuni, respectively. Cytological studies revealed that both compounds affected C. jejuni envelope integrity. Further, both compounds had no effect on other foodborne pathogens. TH-4 and TH-8 had a minimal impact on the chicken cecal microbiota and were not toxic to colon epithelial cells and chicken macrophages, and red blood cells at 200 µM. Further, TH-4 and TH-8 reduced the Campylobacter load in chicken ceca (up to 2-log reduction) when infected chickens were orally treated for 5 days with 0.254 mg kg^-1; as well as against internalized Campylobacter in Caco-2 cells at 12.5 µM and higher. Our study identified two novel specific and safe benzyl thiophene sulfonamide derivatives having potential for control of Campylobacter in chickens and humans.

Efficient discovery of novel antimicrobials through integration of synthesis and testing in crude ribosome extract

Discovery of novel ribosomal inhibitors using an integration method of synthesis and activity testing.

A Computer-Driven Approach to Discover Natural Product Leads for Methicillin-Resistant Staphylococcus aureus Infection Therapy

The risk of methicillin-resistant Staphylococcus aureus (MRSA) infection is increasing in both the developed and developing countries. New approaches to overcome this problem are in need. A ligand-based strategy to discover new inhibiting agents against MRSA infection was built through exploration of machine learning techniques. This strategy is based in two quantitative structure–activity relationship (QSAR) studies, one using molecular descriptors (approach A) and the other using descriptors (approach B). In the approach A, regression models were developed using a total of 6645 molecules that were extracted from the ChEMBL, PubChem and ZINC databases, and recent literature. The performance of the regression models was successfully evaluated by internal and external validation, the best model achieved R² of 0.68 and RMSE of 0.59 for the test set. In general natural product (NP) drug discovery is a time-consuming process and several strategies for dereplication have been developed to overcome this inherent limitation. In the approach B, we developed a new NP drug discovery methodology that consists in frontloading samples with 1D NMR descriptors to predict compounds with antibacterial activity prior to bioactivity screening for NPs discovery. The NMR QSAR classification models were built using 1D NMR data (¹H and ¹³C) as descriptors, from crude extracts, fractions and pure compounds obtained from actinobacteria isolated from marine sediments collected off the Madeira Archipelago. The overall predictability accuracies of the best model exceeded 77% for both training and test sets.

Meeting the discovery challenge of drug-resistant infections: progress and focusing resources

Following multiple warnings from governments and health organisations, there has been renewed investment, led by the public sector, in the discovery of novel antimicrobials to meet the challenge of rising levels of drug-resistant infection, particularly in the case of resistance to antibiotics. Initiatives have also been announced to support and enable the antibiotic discovery process. In January 2018, the Medicines Discovery Catapult, UK, hosted a symposium: Next Generation Antibiotics Discovery, to consider the latest initiatives and any remaining challenges to inform and guide the international research community and better focus resources to yield a novel class of antibiotic.

Cheminformatics in the Service of GPCR Drug Discovery

Cheminformatics is a broad discipline covering a wide range of computational approaches, including the characterization of molecular similarity, pattern recognition, and predictive modeling. The unifying theme that these apparently disparate methods have in common is the aim of extracting useable information from the increasing amounts of data that are associated with contemporary drug discovery projects. Both proprietary and publically available data can be exploited to help inform and improve the process of developing novel therapeutic molecules targeting the GPCR family of proteins.

Overcoming problems of poor drug penetration into bacteria: challenges and strategies for medicinal chemists

INTRODUCTION

Bacterial cell walls and membranes provide essential protection for bacteria against environmental influences. Different bacteria possess different cell envelopes and understanding each of these structures is crucial for the design of effective antibacterial drugs whose targets are intracellular. Optimal properties of drugs that are required for their entry into bacteria are still hard to predict. The guidelines that are suitable and well established for the penetration of a drug into eukaryotic cells are poorly adaptable to the complex world of pathogens. Areas covered: The factors that govern the penetration of anti-infection drugs into bacteria are examined and the available strategies to overcome this therapeutically very important barrier are reviewed. The areas covered include optimization of the physicochemical properties of compounds, utilization of iron-chelating compounds, i.e. siderophores, the use of efflux pump inhibitors, and of carriers such as liposomes. Expert opinion: Although several rules governing permeation have recently been proposed for effective antibacterial drugs, none of them has been so far established as the 'golden' rule. Thus, new research is needed to find a more general approach on how to increase the concentration of antibacterial compounds in bacterial cells.

Antibiotic Hybrids: the Next Generation of Agents and Adjuvants against Gram-Negative Pathogens?

The global incidence of drug-resistant Gram-negative bacillary infections has been increasing, and there is a dire need to develop novel strategies to overcome this problem. Intrinsic resistance in Gram-negative bacteria, such as their protective outer membrane and constitutively overexpressed efflux pumps, is a major survival weapon that renders them refractory to current antibiotics. Several potential avenues to overcome this problem have been at the heart of antibiotic drug discovery in the past few decades. We review some of these strategies, with emphasis on antibiotic hybrids either as stand-alone antibacterial agents or as adjuvants that potentiate a primary antibiotic in Gram-negative bacteria. Antibiotic hybrid is defined in this review as a synthetic construct of two or more pharmacophores belonging to an established agent known to elicit a desired antimicrobial effect. The concepts, advances, and challenges of antibiotic hybrids are elaborated in this article. Moreover, we discuss several antibiotic hybrids that were or are in clinical evaluation. Mechanistic insights into how tobramycin-based antibiotic hybrids are able to potentiate legacy antibiotics in multidrug-resistant Gram-negative bacilli are also highlighted. Antibiotic hybrids indeed have a promising future as a therapeutic strategy to overcome drug resistance in Gram-negative pathogens and/or expand the usefulness of our current antibiotic arsenal.

1,3,5-triazaspiro[5.5]undeca-2,4-dienes as selective Mycobacterium tuberculosis dihydrofolate reductase inhibitors with potent whole cell activity

The emergence of multi- and extensively-drug resistant tubercular (MDR- and XDR-TB) strains of mycobacteria has limited the use of existing therapies, therefore new drugs are needed. Dihydrofolate reductase (DHFR) has recently attracted much attention as a target for the development of anti-TB agents. This study aimed to develop selective M. tuberculosis DHFR inhibitors using rationale scaffolding design and synthesis, phenotype-oriented screening, enzymatic inhibitory study, whole cell on-target validation, molecular modeling, and in vitro DMPK determination to derive new anti-TB agents. 2,4-diamino-1-phenyl-1,3,5-triazaspiro[5.5]undeca-2,4-dienes 20b and 20c were identified as selective M. tuberculosis DHFR inhibitors, showing promising antimycobacterial activities (MIC₅₀: 0.01 μM and MIC₉₀: 0.025 μM on M. tuberculosis H37Rv). This study provided compelling evidence that compound 20b and 20c exerted whole cell antimycobacterial activity through DHFR inhibition. In addition, these two compounds exhibited low cytotoxicity and low hemolytic activity. The in vitro DMPK and physiochemical properties suggested their potential in vivo efficacy.