Tyrosyl-tRNA synthetase inhibitors as antibacterial agents: Synthesis, molecular docking and structure–activity relationship analysis of 3-aryl-4-arylaminofuran-2(5H)-ones

Novel Insecticidal Butenolide-Containing Methylxanthine Derivatives: Synthesis, Crystal Structure, Biological Activity Evaluation, DFT Calculation and Molecular Docking

The design of novel agrochemicals starting from bioactive natural products is one of the most effective ways in the discovery and development of new pesticidal agents. In this paper, a series of novel butenolide-containing methylxanthine derivatives (Ia-Ir) were designed based on natural methylxanthine caffeine and stemofoline, and the derivatized insecticide flupyradifurone of the latter. The structures of the synthesized compounds were confirmed via 1H-NMR, 13C NMR, HRMS and X-ray single crystal diffraction analyses. The biological activities of the compounds were evaluated against a variety of agricultural pests including oriental armyworm, bean aphid, diamondback moth, fall armyworm, cotton bollworm, and corn borer; the results indicated that some of them have favorable insecticidal potentials, particularly toward diamondback moth. Among others, Ic and Iq against diamondback moth possessed LC50 values of 6.187 mg ⋅ L-1 and 3.269 mg ⋅ L-1, respectively, - 2.5- and 4.8-fold of relative insecticidal activity respectively to that of flupyradifurone (LC50=15.743 mg ⋅ L-1). Additionally, both the DFT theoretical calculation and molecular docking with acetylcholine binding protein were conducted for the highly bioactive compound (Ic). Ic and Iq derived from the integration of caffeine (natural methylxanthine) and butenolide motifs can serve as novel leading insecticidal compounds for further optimization.

Novel hybrid thiazoles, bis-thiazoles linked to azo-sulfamethoxazole: Synthesis, docking, and antimicrobial activity

The reaction of sulfamethoxazolehydrazonoyl chloride with thiosemicarbazones, bis-thiosemicarbazones, or 4-amino-3-mercapto-1,2,4-triazole in dioxane in the presence of triethylamine as a basic catalyst at reflux resulted in the regioselective synthesis of thiazoles and bis-thiazoles linked to azo-sulfamethoxazole as novel hybrid molecules. The structures of the new compounds were confirmed using a range of spectra. Each compound's antibacterial properties were evaluated using the agar well-diffusion technique, and most of them demonstrated significant potency. In silico investigations revealed that the described compounds had strong interactions with the binding sites of MurE ligase, tyrosyl-tRNA synthetase, and dihydropteroate synthase, demonstrating inhibitory activity.

In silico Identification of Potential Inhibitors against Staphylococcus aureus Tyrosyl-tRNA Synthetase

BACKGROUND

Drug-resistant Staphylococcus aureus (S. aureus) has spread from nosocomial to community-acquired infections. Novel antimicrobial drugs that are effective against resistant strains should be developed. S. aureus tyrosyl-tRNA synthetase (saTyrRS) is considered essential for bacterial survival and is an attractive target for drug screening.

OBJECTIVES

The purpose of this study was to identify potential new inhibitors of saTyrRS by screening compounds in silico and evaluating them using molecular dynamics (MD) simulations.

METHODS

A 3D structural library of 154,118 compounds was screened using the DOCK and GOLD docking simulations and short-time MD simulations. The selected compounds were subjected to MD simulations of a 75-ns time frame using GROMACS.

RESULTS

Thirty compounds were selected by hierarchical docking simulations. The binding of these compounds to saTyrRS was assessed by short-time MD simulations. Two compounds with an average value of less than 0.15 nm for the ligand RMSD were ultimately selected. The longtime (75 ns) MD simulation results demonstrated that two novel compounds bound stably to saTyrRS in silico.

CONCLUSION

Two novel potential saTyrRS inhibitors with different skeletons were identified by in silico drug screening using MD simulations. The in vitro validation of the inhibitory effect of these compounds on enzyme activity and their antibacterial effect on drug-resistant S. aureus would be useful for developing novel antibiotics.

Insights into the antimicrobial efficacy of Coleus aromaticus essential oil against food-borne microbes: Biochemical and molecular simulation approaches

The study reported the antimicrobial efficacy of chemically characterized Coleus aromaticus essential oil (CEO) against food-borne bacteria, molds (Aspergillus flavus), aflatoxin B1 (AFB1) and explored its mechanism of action using biochemical and molecular simulation approaches. The chemical profile of CEO was explored by Gas chromatography-mass spectrometry (GC-MS) analysis, which revealed thymol (46.0%) as the major compound. The minimum inhibitory concentration values of CEO for bacterial species Escherichia coli, Salmonella enterica, Bacillus cereus, and Shigella flexneri was found to be 0.9 μl/ml, 0.7 μl/ml, 0.16 μl/ml, and 0.12 μl/ml respectively. The MIC value for A. flavus and AFB1 contamination was 0.6 μl/ml. The DPPH radical scavenging activity of CEO was recorded with IC50 0.32 μl/ml. Biochemical and computational approaches (docking and dynamics simulation) have been performed to explore the multi-faceted antimicrobial inhibitory effects of CEO at the molecular level, which shows the impairment in membrane functioning, leakage of cellular contents, release of 260-nm absorbing materials, antioxidative defense, carbon catabolism and vital genes (7AP3, Nor1, Omt1, and Vbs). The findings indicated that CEO could be used as natural antimicrobial agents against food-spoilage bacteria, A. flavus and AFB1 contamination to extend the shelf-life of food product and prevention of food-borne diseases.

Molecular docking, dynamics simulation and pharmacokinetic studies of Cyperus articulatus essential oil metabolites as inhibitors of Staphylococcus aureus

Cyperus articulatus has been extensively studied for its essential oil (EO), active components and antibacterial activities against a wide range of bacteria such as Bacillus megaterium, Streptococcus pyogenes, Staphylococcus epidermidis, Escherichia coli and Staphylococcus aureus. However, knowledge of the biomolecular interaction of the individual EO metabolites responsible for its inhibition activities is lacking. The multi-drug-resistant bacteria S. aureus, which is of prime concern, has been reported to be inhibited by Cyperus articulatus rhizome EO. The present work analyzed the molecular interactions of the major Cyperus articulatus rhizome EO metabolites with the target enzyme TyrRS of S. aureus and studied the conformational dynamics and stability of the protein-ligand complexes. Molecular docking studies of selected EO metabolites such as mustakone, longifolenaldehyde, cyperotundone, α-copaene, β-calacorene, α-calacorene and khusinol were conducted along with standard drug chloramphenicol for comparative analysis of their binding affinity with S. aureus TyrRS. The metabolites khusinol, mustakone, β-calacorene and α-calacorene generated comparable docking scores (-6.4, -6.2, -6.1 and -6.2 kcal/mol, respectively) with that of the drug chloramphenicol (-6.3 kcal/mol). Most EO metabolites did not exhibit H-bonding with the S. aureus TyrRS residues and were stabilized through pi-interactions. The MD simulation study illustrated that compounds like mustakone could effectively bind to the receptors of S. aureus TyrRS with high stability and integrity. Pharmacokinetic, drug-like properties and toxicity analysis of the EO metabolites supported the candidature of mustakone and khusinol as pharmacologically important antibacterial drug ingredients. The study envisaged the structural framework of the EO metabolites for antibacterial drug design.Communicated by Ramaswamy H. Sarma.

Antibiofilm, Antimicrobial, Anti-Quorum Sensing, and Antioxidant Activities of Saudi Sidr Honey: In Vitro and Molecular Docking Studies

Sidr honey is a valuable source of bioactive compounds with promising biological properties. In the present study, antimicrobial, antioxidant, and anti-quorum sensing properties of Saudi Sidr honey were assessed, along with phytochemical analysis, via gas chromatography-mass spectrometry (GC-MS). In silico study was also carried out to study the drug-likeness properties of the identified compounds and to study their affinity with known target proteins assessed using molecular docking approach. The results showed that Saudi Sidr honey exhibited promising antibacterial activity, with MIC values ranging from 50 to 400 mg/mL and MBC values from 50 to >450 mg/mL. Interestingly, the Saudi Sidr honey was active against Candida auris and Candida neoformans, with an MIC value of about 500 mg/mL. Moreover, the Sidr honey showed important antioxidant activities (ABTS assay: IC50 5.41 ± 0.045 mg/mL; DPPH assay: IC50 7.70 ± 0.065 mg/mL) and β-carotene bleaching test results (IC50 ≥ 20 mg/mL). In addition, the Saudi Sidr honey was able to inhibit biofilm formation on glass slides at 1/2 MIC by 77.11% for Bacillus subtilis, 70.88% for Staphylococcus aureus, 61.79% for Escherichia coli, and 56.64% for Pseudomonas aeruginosa. Similarly, violacein production by Chromobacterium violaceum was reduced by about 56.63%, while the production of pyocyanin by P. aeruginosa was decreased to 46.27% at a low concentration of Saudi Sidr honey. ADMET properties showed that five identified compounds, namely, 1-cyclohexylimidazolidin-2-one, 3-Butyl-3-methylcyclohexanone, 4-butyl-3-methoxy-2-cyclo penten-1-one, 2,2,3,3-Tetramethyl cyclopropane carboxylic acid, and 3,5-dihydroxy-2-(3-methylbut-2-en-1-yl showed promising drug-likeness properties. The compound 3,5-dihydroxy-2-(3-methylbut-2-en-1-yl exhibited the highest binding energy against antimicrobial and antioxidant target proteins (1JIJ, 2VAM, 6B8A, 6F86, 2CDU, and 1OG5). Overall, the obtained results highlighted the promising potential of Saudi Sidr honey as a rich source of bioactive compounds that can be used as food preservatives and antimicrobial, antioxidant, and anti-quorum sensing molecules.

Design, synthetic approach, in silico molecular docking and antibacterial activity of quinazolin-2,4-dione hybrids bearing bioactive scaffolds

Antimicrobial resistance (AMR) is one of ten global public health threats facing humanity. This created the need to identify and develop effective inhibitors as antimicrobial agents. In this respect, quinazolin-2,4-dione hybrids bearing N-heterocyclic cores such as pyrrolidine-2,5-dione, pyrazole and oxadiazole and/or bioactive scaffolds such as hydrazone, amide, sulfonamide, azomethine, and thiourea linkage are described for design, synthesis, antibacterial investigation, and in silico studies. The characterization of the target compounds was accomplished by elemental analysis and various spectroscopic data like FT-IR, ¹H-NMR, ¹³C-NMR and MS. The antibacterial evaluation was achieved for the newly synthesized compounds using two G -ve bacteria (Escherichia coli ATCC 25955 and Pseudomonas aeruginosa ATCC 10145), and two G +ve bacteria (Bacillus subtilis ATCC 6633 and Staphylococcus aureus NRRL B-767). Synthesized compounds exhibited various activities against the tested pathogens, the results revealed that compound 3c exhibited a characteristic antimicrobial efficacy against all the tested pathogenic strains at a concentration lower than the tested standard drug ranging from 2.5 to 10 μg ml^-1. Moreover, the molecular docking study against the target S. aureus tyrosyl-tRNA synthetase (PDB ID: 1JIJ) was carried out to investigate the mechanism of action of the prepared compounds, which is in line with an in vitro study. Most new compounds exhibited zero violation of Lipinski's rule (Ro5). These candidate molecules have shown promising antibacterial activity. Among these molecules, compound 3c with di-hydroxyl groups on two phenyl rings at position-4 exhibited a promising potent antibacterial inhibitory effect. Further SAR analysis reveals that a greater number of hydroxyl groups in an organic compound might be crucial for antibacterial efficacy. These findings demonstrate the potential activity of compound 3c as an antibacterial agent.

Synthesis and medicinal chemistry of tetronamides: Promising agrochemicals and antitumoral compounds

Butenolides and tetronic acids occupy a prominent position in synthetic chemistry due to their ubiquitous distribution in nature. This has stimulated investigations firstly in the synthesis of such systems and, laterly, the interest has turned to the understanding of the quantum structure of such systems, allowing a deeper understanding of the mechanism and reactivity of this cyclic scaffold. In contrast, tetronamides, which consist of compounds bearing a 4-aminofuran-2(5H)-one backbone, are relatively rare in nature and synthetic routes to such compounds are poorly explored. This review highlights both the importance of the tetronamide scaffold in medicinal chemistry and the most relevant recondite synthetic strategies for obtaining compounds of this class.

An Insight into All Tested Small Molecules against Fusarium oxysporum f. sp. Albedinis: A Comparative Review

Bayoud disease affects date palms in North Africa and the Middle East, and many researchers have used various methods to fight it. One of those methods is the chemical use of synthetic compounds, which raises questions centred around the compounds and common features used to prepare targeted molecules. In this review, 100 compounds of tested small molecules, collected from 2002 to 2022 in Web of Sciences, were divided into ten different classes against the main cause of Bayoud disease pathogen Fusarium oxysporum f. sp. albedinis (F.o.a.) with structure-activity relationship (SAR) interpretations for pharmacophore site predictions as (δ^-···δ^-), where 12 compounds are the most efficient (one compound from each group). The compounds, i.e., (Z)-1-(1.5-Dimethyl-1H-pyrazole-3-yl)-3-hydroxy but-2-en-1-one 7, (Z)-3-(phenyl)-1-(1,5-dimethyl-1H-pyrazole-3-yl)-3-hydroxyprop-2-en-1-one 23, (Z)-1-(1,5-Dimethyl-1H-pyrazole-3-yl)-3-hydroxy-3-(pyridine-2-yl)prop-2-en-1-one 29, and 2,3-bis-[(2-hydroxy-2-phenyl)ethenyl]-6-nitro-quinoxaline 61, have antifungal pharmacophore sites (δ^-···δ^-) in common in N1---O4, whereas other compounds have only one δ^- pharmacophore site pushed by the donor effect of the substituents on the phenyl rings. This specificity interferes in the biological activity against F.o.a. Further understanding of mechanistic drug-target interactions on this subject is currently underway.

A Phytochemical Analysis, Microbial Evaluation and Molecular Interaction of Major Compounds of Centaurea bruguieriana Using HPLC-Spectrophotometric Analysis and Molecular Docking

Centaurea is one of the most important genera within the family Asteraceae. An investigation of the phytochemical composition of Centaurea bruguieriana using Gas-Chromatography coupled to Mass spectrometry (GC-MS) was performed. Antimicrobial activity was evaluated using the minimum inhibitory concentration method (MIC) and validated by molecular docking for the major compounds of the most active fraction (1,10-di-epi-cubenol and methyl 8-oxooctanoate) of C. bruguieriana against three bacterial receptors (TyrRS, DNA gyrase, and dihydrofolate reductase (DHFR)). Evaluation of antioxidant activity was conducted using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assays. High-performance liquid chromatography (HPLC) was used to identify and quantify the contents of major compounds from ethyl acetate fraction (luteolin 7-O-glucoside, chlorogenic acid, kaempferol and isorhamnetin). The antimicrobial activity test showed that the chloroform fraction was more active against all microbial strains. The results of the molecular docking of two major compounds from chloroform fraction showed that good affinities were made between 1,10-di-epi-cubenol and the three selected receptors (TyrRs: −6.0 Kcal/mol against −8.2 Kcal/mol obtained with clorobiocin (standard); DNA gyrase: −6.6 Kcal/mol against −9.1 Kcal/mole obtained with clorobiocin; DHFR: −7.4 Kcal/mol against −6.3 Kcal/mol obtained with SCHEMBL2181345 Standard). Antioxidant evaluation showed that the ethyl acetate fraction was the most active fraction in DPPH (IC50 49.4 µg/mL) and ABTS (IC50 52.8 µg/mL) models. HPLC results showed the contents of luteolin 7-O-glucoside (7.4 µg/mg), and chlorogenic acid (3.2 µg/mg). Our study demonstrated that C. bruguierana is a promising source of bioactive compounds.

In-Vitro Catalytic and Antibacterial Potential of Green Synthesized CuO Nanoparticles against Prevalent Multiple Drug Resistant Bovine Mastitogen Staphylococcus aureus

Nanoparticles prepared from bio-reduction agents are of keen interest to researchers around the globe due to their ability to mitigate the harmful effects of chemicals. In this regard, the present study aims to synthesize copper oxide nanoparticles (CuO NPs) by utilizing root extracts of ginger and garlic as reducing agents, followed by the characterization and evaluation of their antimicrobial properties against multiple drug resistant (MDR) S. aureus. In this study, UV-vis spectroscopy revealed a reduced degree of absorption with an increase in the extract amount present in CuO. The maximum absorbance for doped NPs was recorded around 250 nm accompanying redshift. X-ray diffraction analysis revealed the monoclinic crystal phase of the particles. The fabricated NPs exhibited spherical shapes with dense agglomeration when examined with FE-SEM and TEM. The crystallite size measured by using XRD was found to be within a range of 23.38-46.64 nm for ginger-doped CuO and 26-56 nm for garlic-doped CuO. Green synthesized NPs of ginger demonstrated higher bactericidal tendencies against MDR S. aureus. At minimum and maximum concentrations of ginger-doped CuO NPs, substantial inhibition areas for MDR S. aureus were (2.05-3.80 mm) and (3.15-5.65 mm), and they were measured as (1.1-3.55 mm) and (1.25-4.45 mm) for garlic-doped NPs. Conventionally available CuO and crude aqueous extract (CAE) of ginger and garlic roots reduced MB in 12, 21, and 38 min, respectively, in comparison with an efficient (100%) reduction of dye in 1 min and 15 s for ginger and garlic doped CuO NPs.

Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study

An endophytic fungus isolated from healthy leaf tissues of Houttuynia cordata Thunb., an ethnomedicinal plant of North East India, showed a considerable amount of antimicrobial activity. The ethyl acetate extract of the fungal culture filtrates displayed promising antimicrobial activity against a panel of clinically significant pathogens including Candida albicans, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Bioassay guided purification of the organic extract using column and thin layer chromatography yielded a pure homogenous compound which was identified using spectroscopic methods (essentially by ¹H NMR and MS) as tyrosol, a well-known phenylethanoid present in several natural sources. Besides, molecular docking studies against tyrosyl tRNA synthetases (TyrRS) of S. aureus (PDB ID: 1JIL) and E. coli (PDB ID: 1VBM), and CYP45014α-lanosterol demethylase (CYP51) of C. albicans (PDB ID: 5FSA) revealed tyrosol has a strong binding affinity with the enzyme active site residues. The fungus was identified as Colletotrichum sp. and characterized by its genomic ITS rDNA and ITS2 sequences. Phylogenetic analyses showed clustering of our isolate with Colletotrichum coccodes. Species of Colletotrichum are also reported to be plant pathogens. Therefore, to confirm the endophytic lifestyle of the isolate, ITS2 RNA secondary structure study was undertaken. The result indicated our isolate exhibited differences in the folding pattern as well as in motif structures when compared to those of pathogenic C. coccodes. The findings indicated that endophytic fungi harboring H. cordata could be explored as a potent source of antimicrobial agents.

Aminoacyl-tRNA synthetases as drug targets

Aminoacyl-tRNA synthetases (AARSs) have been considered very attractive drug-targets for decades. This interest probably emerged with the identification of differences in AARSs between prokaryotic and eukaryotic species, which provided a rationale for the development of antimicrobials targeting bacterial AARSs with minimal effect on the homologous human AARSs. Today we know that AARSs are not only attractive, but also valid drug targets as they are housekeeping proteins that: (i) play a fundamental role in protein translation by charging the corresponding amino acid to its cognate tRNA and preventing mistranslation mistakes [1], a critical process during fast growing conditions of microbes; and (ii) present significant differences between microbes and humans that can be used for drug development [2]. Together with the vast amount of available data on both pathogenic and mammalian AARSs, it is expected that, in the future, the numerous reported inhibitors of AARSs will provide the basis to develop new therapeutics for the treatment of human diseases. In this chapter, a detailed summary on the state-of-the-art in drug discovery and drug development for each aminoacyl-tRNA synthetase will be presented.

Synthesis, characterization, antibacterial evaluation, 2D-QSAR modeling and molecular docking studies for benzocaine derivatives

Possible application of incorporating a well-known drug (benzocaine) with cyanoacetamide function to get a powerful synthon ethyl 4-cyanoacetamido benzoate. This synthetic intermediate was used as a precursor for the synthesis of triazine, pyridone, thiazolidinone, thiazole and thiophene scaffolds containing the benzocaine core. Facile coupling, Michael addition, condensation and nucleophilic attack reactions were used to synthesize our targets. The structural features of the synthesized scaffolds were characterized using IR, ¹H NMR, ¹³C NMR and mass spectroscopy. The antibacterial activities against Gram-positive (Staphylococcus aureus, Bacillus subtilis) and Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa) were evaluated using ampicillin as a reference drug. DNA/methyl-green colorimetric assay of the DNA-binding compounds was also performed. Theoretical studies of the newly synthesized compounds based on molecular docking and QSAR study were conducted. The molecular docking studies were screened by MOE software for the more potent antibacterial agent 28b and each native ligand against four of S. aureus proteins 1jij, 2xct, 2w9s and 3t07.

Synthesis of new tetronamides displaying inhibitory activity against bloom-forming cyanobacteria

BACKGROUND

The increasing frequency and intensity of cyanobacterial blooms pose a serious threat to aquatic ecosystems. These blooms produce potent toxins that can contaminate drinking water and endanger the life of wild and domestic animals as well as humans. Consequently, the development of effective methods for their control is a matter of high priority. We have previously shown that some γ-benzylidenebutenolides, related to the rubrolide family of natural products, are capable of inhibiting the photosynthetic electron transport chain (Hill reaction), a target of commercial herbicides. Here we report the synthesis and biological properties of a new class of rubrolide-inspired molecules featuring a tetronamide motif.

RESULTS

A total of 47 N-aryl tetronamides, including 38 aldol adducts, were prepared bearing phenyl, biphenyl, naphthyl, aliphatic and heteroaromatic groups. Some of the aldol adducts were dehydrated to the corresponding γ-benzylidenetetronamides, although satisfactory yields were obtained in only three cases (52-97%). None of the synthesized compounds were capable of blocking the Hill reaction. This notwithstanding, several aldol adducts equipped with a biphenyl substituent displayed excellent inhibitory activity against Synechococcus elongatus and other cyanobacterial strains (IC₅₀  = 1-5 μM). Further, these tetronamides were found to be essentially inactive against eukaryotic microorganisms.

CONCLUSION

Several newly synthesized biphenyl-containing tetronamides were shown to display potent and selective inhibitory activity against cyanobacteria. These compounds appear to exert their biological effects without interfering with the Hill reaction. As such, they represent novel leads in the search of environmentally benign agents for controlling cyanobacterial blooms. © 2019 Society of Chemical Industry.

Toward a structome of Acinetobacter baumannii drug targets

Acinetobacter baumannii is well known for causing hospital-associated infections due in part to its intrinsic antibiotic resistance as well as its ability to remain viable on surfaces and resist cleaning agents. In a previous publication, A. baumannii strain AB5075 was studied by transposon mutagenesis and 438 essential gene candidates for growth on rich-medium were identified. The Seattle Structural Genomics Center for Infectious Disease entered 342 of these candidate essential genes into our pipeline for structure determination, in which 306 were successfully cloned into expression vectors, 192 were detectably expressed, 165 screened as soluble, 121 were purified, 52 crystalized, 30 provided diffraction data, and 29 structures were deposited in the Protein Data Bank. Here, we report these structures, compare them with human orthologs where applicable, and discuss their potential as drug targets for antibiotic development against A. baumannii.

Next-generation strategy for treating drug resistant bacteria: Antibiotic hybrids

Resistance against nearly all antibiotics used clinically have been documented in bacteria. There is an ever-increasing danger caused by multidrug-resistant Gram-negative bacteria in both hospital and community settings. In Gram-negative bacteria, intrinsic resistance to currently available antibiotics is mainly due to overexpressed efflux pumps which are constitutively present and also presence of protective outer membrane. Combination therapy, i.e., use of two or more antibiotics, was thought to be an effective strategy because it took advantage of the additive effects of multiple antimicrobial mechanisms, lower risk of resistance development and lower mortality and improved clinical outcome. However, none of the benefits were seen in in vivo studies. Antibiotic hybrids are being used to challenge the growing drug resistance threat and increase the usefulness of current antibiotic arsenal. Antibiotic hybrids are synthetic constructs of two molecules which are covalently linked. These could be two antibiotics or antibiotic with an adjuvant (efflux pump inhibitor, siderophore, etc.) which increases the access of the antibiotics to the target. The concepts, developments and challenges in the future use of antibiotic hybrids are discussed here. Majority of the studies have been conducted on fluoroquinolones and aminoglycosides molecules. The antibiotic tobramycin has the property to enhance the action of antimicrobial agents against which the multidrug-resistant Gram-negative bacteria were earlier resistant, and thus potentiating the action of legacy antibiotics. Antibiotic hybrids may have a role as the silver bullet in Gram-negative bacteria to overcome drug resistance as well as extend the spectrum of existing antibiotics.

Antibacterial Activity and Molecular Docking Studies of a Selected Series of Hydroxy-3-arylcoumarins

Antibiotic resistance is one of the main public health concerns of this century. This resistance is also associated with oxidative stress, which could contribute to the selection of resistant bacterial strains. Bearing this in mind, and considering that flavonoid compounds are well known for displaying both activities, we investigated a series of hydroxy-3-arylcoumarins with structural features of flavonoids for their antibacterial activity against different bacterial strains. Active compounds showed selectivity against the studied Gram-positive bacteria compared to Gram-negative bacteria. 5,7-Dihydroxy-3-phenylcoumarin (compound 8) displayed the best antibacterial activity against Staphylococcus aureus and Bacillus cereus with minimum inhibitory concentrations (MICs) of 11 g/mL, followed by Staphylococcus aureus (MRSA strain) and Listeria monocytogenes with MICs of 22 and 44 g/mL, respectively. Moreover, molecular docking studies performed on the most active compounds against Staphylococcus aureus tyrosyl-tRNA synthetase and topoisomerase II DNA gyrase revealed the potential binding mode of the ligands to the site of the appropriate targets. Preliminary structure-activity relationship studies showed that the antibacterial activity can be modulated by the presence of the 3-phenyl ring and by the position of the hydroxyl groups at the coumarin scaffold.

Modifications of quinolones and fluoroquinolones: hybrid compounds and dual-action molecules

ABSTRACT

This review is aimed to provide extensive survey of quinolones and fluoroquinolones for a variety of applications ranging from metal complexes and nanoparticle development to hybrid conjugates with therapeutic uses. The review covers the literature from the past 10 years with emphasis placed on new applications and mechanisms of pharmacological action of quinolone derivatives. The following are considered: metal complexes, nanoparticles and nanodrugs, polymers, proteins and peptides, NO donors and analogs, anionic compounds, siderophores, phosphonates, and prodrugs with enhanced lipophilicity, phototherapeutics, fluorescent compounds, triazoles, hybrid drugs, bis-quinolones, and other modifications. This review provides a comprehensive resource, summarizing a broad range of important quinolone applications with great utility as a resource concerning both chemical modifications and also novel hybrid bifunctional therapeutic agents.

GRAPHICAL ABSTRACT

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.

Bifunctional antimicrobial conjugates and hybrid antimicrobials

Covering: up to the end of 2016Novel antimicrobial drugs are continuously needed to counteract bacterial resistance development. An innovative molecular design strategy for novel antibiotic drugs is based on the hybridization of an antibiotic with a second functional entity. Such conjugates can be grouped into two major categories. In the first category (antimicrobial hybrids), both functional elements of the hybrid exert antimicrobial activity. Due to the dual targeting, resistance development can be significantly impaired, the pharmacokinetic properties can be superior compared to combination therapies with the single antibiotics, and the antibacterial potency is often enhanced in a synergistic manner. In the second category (antimicrobial conjugates), one functional moiety controls the accumulation of the other part of the conjugate, e.g. by mediating an active transport into the bacterial cell or blocking the efflux. This approach is mostly applied to translocate compounds across the cell envelope of Gram-negative bacteria through membrane-embedded transporters (e.g. siderophore transporters) that provide nutrition and signalling compounds to the cell. Such 'Trojan Horse' approaches can expand the antibacterial activity of compounds against Gram-negative pathogens, or offer new options for natural products that could not be developed as standalone antibiotics, e.g. due to their toxicity.

Thermodynamically driven, syn-selective vinylogous aldol reaction of tetronamides

A stereoselective vinylogous aldol reaction of N-monosubstituted tetronamides with aldehydes is described.

Targeting druggable enzymome by exploiting natural medicines: An in silico-in vitro integrated approach to combating multidrug resistance in bacterial infection

CONTEXT

Antibiotic resistance is a major clinical and public health problem. Development of new therapeutic approaches to prevent bacterial multidrug resistance during antimicrobial chemotherapy has thus been becoming a primary consideration in the medicinal chemistry community.

OBJECTIVE

We described a new strategy that combats multidrug resistance by using natural medicines to target the druggable enzymome (i.e., enzymatic proteome) of Staphylococcus aureus.

MATERIALS AND METHODS

A pipeline of integrating in silico analysis and in vitro assay was purposed to identify antibacterial agents from a large library of natural products with diverse structures, high drug-likeness, and relatively low flexibility, with which a systematic interactome of 826 natural product candidates with 125 functionally essential S. aureus enzymes was constructed via a high-throughput cross-docking approach. The obtained docking score matrix was then converted into an array of synthetic scores; each corresponds to a natural product candidate. By systematically examining the docking results, a number of highly promising candidates with potent antibacterial activity were suggested.

RESULTS

Three natural products, i.e., radicicol, jorumycin, and amygdalin, have been determined to possess strong broad-spectrum potency combating both the drug-resistant and drug-sensitive strains (MIC value <10 μg/ml). In addition, some natural products such as tetrandrine, bilobalide, and arbutin exhibited selective inhibition on different strains.

DISCUSSION AND CONCLUSION

Combined quantum mechanics/molecular mechanics analysis revealed diverse non-bonded interactions across the complex interfaces of newly identified antibacterial agents with their putative targets GyrB ATPase and tyrosyl-tRNA synthetase.

Adenosine analogs as inhibitors of tyrosyl-tRNA synthetase: Design, synthesis and antibacterial evaluation

Herein we describe the synthesis and evaluation of a series of adenosine analogs for in vitro antibacterial activity against Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. Out of these compounds, compound c6 has much stronger antibacterial potency against Pseudomonas aeruginosa than ciprofloxacin, and was determined to target tyrosyl-tRNA synthetase with IC50 of 0.8±0.07 μM. Structure-activity relationship analysis suggested that introduction of a fluorine atom at the 3'-position of benzene ring of the phenylacetyl moiety significantly increased affinities to the enzyme. In comparison with isopropylidene analogs, 2',3'-deprotected compounds displayed higher inhibitory activity. Molecular dockings provided an explanation for observations in biological assays.

A continuous spectrophotometric assay for monitoring adenosine 5'-monophosphate production

A number of biologically important enzymes release adenosine 5'-monophosphate (AMP) as a product, including aminoacyl-tRNA synthetases, cyclic AMP (cAMP) phosphodiesterases, ubiquitin and ubiquitin-like ligases, DNA ligases, coenzyme A (CoA) ligases, polyA deadenylases, and ribonucleases. In contrast to the abundance of assays available for monitoring the conversion of adenosine 5'-triphosphate (ATP) to ADP, there are relatively few assays for monitoring the conversion of ATP (or cAMP) to AMP. In this article, we describe a homogeneous assay that continuously monitors the production of AMP. Specifically, we have coupled the conversion of AMP to inosine 5'-monophosphate (IMP) (by AMP deaminase) to the oxidation of IMP (by IMP dehydrogenase). This results in the reduction of oxidized nicotine adenine dinucleotide (NAD(+)) to reduced nicotine adenine dinucleotide (NADH), allowing AMP formation to be monitored by the change in the absorbance at 340 nm. Changes in AMP concentrations of 5 μM or more can be reliably detected. The ease of use and relatively low expense make the AMP assay suitable for both high-throughput screening and kinetic analyses.

Synthesis of furo[3,4-c]quinolin-3(1H)-one derivatives through TMG catalyzed intramolecular aza-MBH reaction based on the furanones

The first TMG catalyzed intramolecular aza-MBH reaction based on furanone derivatives for the construction of furo[3,4-c]quinolin-3(1H)-ones scaffold.

Novel 3-arylfuran-2(5H)-one-fluoroquinolone hybrid: design, synthesis and evaluation as antibacterial agent

3-Arylfuran-2(5H)-one, a novel antibacterial pharmacophore targeting tyrosyl-tRNA synthetase (TyrRS), was hybridized with the clinically used fluoroquinolones to give a series of novel multi-target antimicrobial agents. Thus, twenty seven 3-arylfuran-2(5H)-one-fluoroquinolone hybrids were synthesized and evaluated for their antimicrobial activities. Some of the hybrids exhibited merits from both parents, displaying a broad spectrum of activity against resistant strains including both Gram-negative and Gram-positive bacteria. The most potent compound (11) in antibacterial assay shows MIC50 of 0.11μg/mL against Multiple drug resistant Escherichia coli, being about 51-fold more potent than ciprofloxacin. The enzyme assays reveal that 11 is a potent multi-target inhibitor with IC50 of 1.15±0.07μM against DNA gyrase and 0.12±0.04μM against TyrRS, respectively. Its excellent inhibitory activities against isolated enzymes and intact cells strongly suggest that 11 deserves to further research as a novel antibiotic.

Design, synthesis, and evaluation of novel fluoroquinolone-flavonoid hybrids as potent antibiotics against drug-resistant microorganisms

Based on a rationally conceived pharmacophore model to build a multi-target bacterial topoisomerase inhibitor, twenty-one fluoroquinolone-flavonoid hybrids were synthesized. Some obtained hybrids show excellent antibacterial activity against drug-resistant microorganisms with narigenin-ciprofloxacin being the most active, showing 8, 43, 23 and 88 times better activity than ciprofloxacin against Escherichia coli ATCC 35218, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 25923 and Candida albicans ATCC 90873, respectively. Drug accumulation and DNA supercoiling assays of two active analogues revealed potent inhibition of both the DNA gyrase and efflux pump, confirming the desired dual mode of action. Molecular docking study disclosed that the introduced flavonoid moiety not only provides several additional interactions but also does not disturb the binding mode of the floxacin moiety. Our data also demonstrated that development of antifungals is possible from fluoroquinolones modified at C-7 position.