Design, synthesis, molecular docking, and antibacterial evaluation of some novel flouroquinolone derivatives as potent antibacterial agent

Genomic and Computational Analysis Unveils Bacteriocin Based Therapeutics against Clinical Mastitis Pathogens in Dairy Cows

Clinical mastitis (CM) remains a critical challenge in dairy production, exacerbated by the global rise of antibiotic-resistant pathogens, which threatens herd health and productivity. This study pioneers a dual genomic-computational strategy to develop bacteriocin-based therapeutics-a promising alternative to conventional antibiotics-by targeting conserved virulence mechanisms in CM-causing pathogens. We aimed to (i) identify essential core proteins in CM-causing pathogens of dairy cows using the genomic approach; and (ii) assess the efficacy of bacteriocin peptides (BPs) as novel therapeutic agents targeting the selected core proteins for sustainable management of mastitis. Through pan-genomic analysis of 16 clinically relevant pathogens, including Staphylococcus aureus, S. warneri, Streptococcus agalactiae, S. uberis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, P. putida, and P. asiatica, we identified 65 evolutionarily conserved core proteins. Prioritization based on essentiality, virulence, and resistance potential revealed Rho (transcription termination factor) and HupB (nucleoid-associated protein) as high-value therapeutic targets due to their critical roles in bacterial survival and pathogenicity. A computational screen of 70 BPs identified 14 candidates with high binding affinity for both Rho and HupB proteins. Molecular dynamics simulations demonstrated that BP8, a novel dual-action bacteriocin, competitively inhibits Rho-mediated transcription termination and disrupts HupB-DNA interactions, effectively crippling bacterial replication and virulence. BP8 exhibited superior structural stability and binding efficacy compared to other candidates, positioning it as a potent broad-spectrum agent against diverse CM pathogens, including multidrug-resistant strains. Our study underscores the untapped potential of bacteriocins in veterinary medicine, offering a sustainable solution to mitigate antibiotic overuse and resistance. The computational validation of BP8 provides a foundational framework for developing targeted therapies, with implications for reducing dairy industry losses and improving animal welfare. Further in vitro and in vivo studies are warranted to translate these insights into practical therapeutics.

A survey of isatin hybrids and their biological properties

The emergence of diverse infections worldwide, which is a serious global threat to human existence, necessitates the urgent development of novel therapeutic candidates that can combat these diseases with efficacy. Molecular hybridization has been established as an efficient technique in designing bioactive molecules capable of fighting infections. Isatin, a core nucleus of an array of compounds with diverse biological properties can be modified at different positions leading to the creation of novel drug targets, is an active area of medicinal chemistry. This review containing published articles from 2005 to 2022 highlights isatin hybrids which have been synthesized and reported in the literature alongside a discussion on their biological properties. The enriched structure-activity relationship studies discussed provides insights for the rational design of novel isatin hybrids with tailored biological properties as effective therapeutic candidates inspired by nature.

Synthesis and PASS-assisted evaluation of new heterocyclic compounds containing hydroquinoline scaffolds

Currently, there is a growing interest in the synthesis of heterocyclic compounds containing hydroquinoline fragments. This surge can be attributed to the broad range of pharmaceutical and industrial applications that these compounds possess. In this study, the synthesis of both linear and fused heterocyclic systems that incorporate hydroquinoline fragments was described. Furthermore, the pharmacological activity spectra of the synthesized compounds were predicted using the in silico method, employing the Prediction of Activity Spectra of Substances (PASS) program. Hydroquinolines containing the nitrile functionality 7 and 8 were synthesized through the reaction of the corresponding hydroquinolinecarbaldehyde 5a, 6b with hydroxylamine hydrochloride and iodine in aqueous ammonia under ambient conditions, respectively. 2-Phenyl-1,3-oxazol-5(4 H)-ones 9a, b and 10a, b were synthesized via the condensation of compounds 5a, b and 6a, b with hippuric acid in acetic acid in 30-60% yield. When the methyl activated 7-methylazolopyrimidines 11a, b were reacted with N-alkyl-2,2,4-trimethyl-1,2,3,4-tetrahydroquinoline-6-carbaldehydes 6a, b, 60-70% yield of triazolo/pyrazolo[1,5-a]pyrimidin-6-yl carboxylic acids 12a, b were obtained. The condensation of 7-hydroxy-1,2,3,4-tetramethyl-1,2-dihydroquinoline 3 h with dimethylacetylenedicarboxylate (DMAD) and ethyl acetoacetate afforded cyclic products 16 and 17, respectively. The condensation reaction of 6-formyl-7-hydroxy-1,2,2,4-tetramethyl-1,2-dihydroquinoline 5e with methylene-active compounds such as ethyl cyanoacetate/dimethyl-3-oxopentanedioate/ethyl acetoacetate/diethylmalonate/Meldrum's acid afforded 3-substituted coumarins 19 and 21 containing dihydroquinoline moiety. The pentacyclic coumarin 22 was obtained via the tandom condensation reaction of malononitrile with 5e in the presence of a catalytic amount of piperidine in ethanol. The biological activities of the synthesized compounds were predicted using the PASS program. Based on the prognosis, compounds 13a, b, and 14 exhibited a high likelihood of being active as inhibitors of gluconate 2-dehydrogenase, as well as possessing antiallergic, antiasthmatic, and antiarthritic properties, with a probability value (Pa) ranging from 0.849 to 0.870. Furthermore, it was discovered that compounds 7 and 8 tended to act as effective progesterone antagonists and displayed antiallergic, antiasthmatic, and antiarthritic effects (Pa = 0.276-0.827). Among the hydroquinolines containing coumarin moieties, compounds 17, 19a, and 19c were predicted to be potent progesterone antagonists, with Pa values of 0.710, 0.630, and 0.615, respectively.

Antibacterial activity of natural flavones against bovine mastitis pathogens: in vitro, SAR analysis, and computational study

Bovine mastitis is a worldwide disease affecting dairy cattle and causes major economic losses in the dairy industry. Recently, the emergence of microbial resistance to the current antibiotics complicates the treatment protocol which necessitates antibiotic stewardship and further research to find new active compounds. Recently, phytobiotics have gained interest in being used as an alternative to antibiotics in the poultry industry as an antibiotic stewardship intervention. This study evaluated the in vitro antibacterial activity of 16 flavonoids against bovine mastitis pathogens. Two flavones: 2-(4-methoxyphenyl)chromen-4-one (1) and 2-(3-hydroxyphenyl)chromen-4-one (4) showed inhibition of the growth of Klebsiella oxytoca with MIC values range (25-50 µg mL- 1) followed by a structure-activity relationship (SAR) study indicating that the presence of a hydroxyl group at C-3` or methoxy at C-4` increases the activity against Klebsiella oxytoca while the presence of hydroxyl group at C-7 decreases the activity. Furthermore, a structure-based drug development approach was applied using several in silico tools to understand the interactions of active flavones at the active site of the DNA gyrase protein. Compound (4) showed a higher docking score than quercetin (standard) which is known to have antibacterial activity by inhibiting the DNA gyrase. In addition, the structure-based pharmacophores of compound (4) and quercetin showed similar pharmacophoric features and interactions with DNA gyrase. Based on our findings, compounds (1) and (4) are promising for further study as potential anti-microbial phytochemicals that can have a role in controlling bovine mastitis as well as to investigate their mechanism of action further.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00253-w.

Bioactive plant waste components targeting oral bacterial pathogens as a promising strategy for biofilm eradication

The significance of this study lies in its exploration of bioactive plant extracts as a promising avenue for combating oral bacterial pathogens, offering a novel strategy for biofilm eradication that could potentially revolutionize oral health treatments. Oral bacterial infections are common in diabetic patients; however, due to the development of resistance, treatment options are limited. Considering the excellent antimicrobial properties of phenolic compounds, we investigated them against isolated oral pathogens using in silico and in vitro models. We performed antibiogram studies and minimum inhibitory concentration (MIC), antibiofilm, and antiquorum sensing activities covering phenolic compounds. Bacterial strains were isolated from female diabetic patients and identified by using 16S rRNA sequencing as Pseudomonas aeruginosa, Bacillus chungangensis, Bacillus paramycoides, and Paenibacillus dendritiformis. Antibiogram studies confirmed that all strains were resistant to most tested antibiotics except imipenem and ciprofloxacin. Molecular docking analysis revealed the significant interaction of rutin, quercetin, gallic acid, and catechin with transcription regulator genes 1RO5, 4B2O, and 5OE3. All tested molecules followed drug-likeness rules except rutin. The MIC values of the tested compounds varied from 0.0625 to 0.5 mg/mL against clinical isolates. Significant antibiofilm activity was recorded in the case of catechin (73.5% ± 1.6% inhibition against B. paramycoides), cinnamic acid (80.9% ± 1.1% inhibition against P. aeruginosa), and vanillic acid and quercetin (65.5% ± 1.7% and 87.4% ± 1.4% inhibition, respectively, against B. chungangensis) at 0.25-0.125 mg/mL. None of the phenolic compounds presented antiquorum sensing activity. It was, therefore, concluded that polyphenolic compounds may have the potential to be used against oral bacterial biofilms, and further detailed mechanistic investigations should be performed.

Synthesis, characterization, PXRD studies, and theoretical calculation of the effect of gamma irradiation and antimicrobial studies on novel Pd(II), Cu(II), and Cu(I) complexes

The main objective of this study is to synthesize and characterize of a new three complexes of Pd (II), Cu (II), and Cu (I) metal ions with novel ligand ((Z)-2-(phenylamino)-N'-(thiophen-2-ylmethylene)acetohydrazide) H2LB. The structural composition of new compounds was assessed using several analytical techniques including FT-IR, 1H-NMR, electronic spectra, powder X-ray diffraction, and thermal behavior analysis. The Gaussian09 program employed the Density Functional Theory (DFT) approach to optimize the geometry of all synthesized compounds, therefore obtaining the most favorable structures and crucial parameters. An investigation was conducted to examine the impact of γ-irradiation on ligands and complexes. Before and after γ-irradiation, the antimicrobial efficiency was investigated for the activity of ligands and their chelates. The Cu(I) complex demonstrated enhanced antibacterial activity after irradiation, as well as other standard medications such as ampicillin and gentamicin. Similarly, the Cu(I) complex exhibited superior activity against antifungal species relative to the standard drug Nystatin. The docking investigation utilized the target location of the topoisomerase enzyme (2xct) chain A.

Fluoroquinolones' Biological Activities against Laboratory Microbes and Cancer Cell Lines

Development of novel derivatives to rein in and fight bacteria have never been more demanding, as microbial resistance strains are alarmingly increasing. A multitude of new fluoroquinolones derivatives with an improved spectrum of activity and/or enhanced pharmacokinetics parameters have been widely explored. Reporting novel antimicrobial agents entails comparing their potential activity to their parent drugs; hence, parent fluoroquinolones have been used in research as positive controls. Given that these fluoroquinolones possess variable activities according to their generation, it is necessary to include parent compounds and market available antibiotics of the same class when investigating antimicrobial activity. Herein, we provide a detailed guide on the in vitro biological activity of fluoroquinolones based on experimental results published in the last years. This work permits researchers to compare and analyze potential fluoroquinolones as positive control agents and to evaluate changes occurring in their activities. More importantly, the selection of fluoroquinolones as positive controls by medicinal chemists when investigating novel FQs analogs must be correlated to the laboratory pathogen inquest for reliable results.

A Novel In Silico Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery

Simple Summary

Protein interactions govern the majority of an organism’s biological processes. Therefore, to fully understand the functionality of an organism, we must know how proteins work at a molecular level. This study assembled a protocol that enables scientists to construct a protein’s tertiary structure easily and subsequently to investigate its mechanism and function. Each step involved in prediction, validation, and functional analysis of a protein is crucial to obtain an accurate result. We have dubbed this the trifecta analysis. It was clear early in our research that no single study in the literature had previously encompassed the complete trifecta analysis. In particular, studies that recommend free, open-source tools that have been benchmarked for each step are lacking. The present study ensures that predictions are accurate and validated and will greatly benefit new and experienced scientists alike in obtaining a strong understanding of the trifecta analysis, resulting in a domino effect that could lead to drug development.

Abstract

Current in silico proteomics require the trifecta analysis, namely, prediction, validation, and functional assessment of a modeled protein. The main drawback of this endeavor is the lack of a single protocol that utilizes a proper set of benchmarked open-source tools to predict a protein’s structure and function accurately. The present study rectifies this drawback through the design and development of such a protocol. The protocol begins with the characterization of a novel coding sequence to identify the expressed protein. It then recognizes and isolates evolutionarily conserved sequence motifs through phylogenetics. The next step is to predict the protein’s secondary structure, followed by the prediction, refinement, and validation of its three-dimensional tertiary structure. These steps enable the functional analysis of the macromolecule through protein docking, which facilitates the identification of the protein’s active site. Each of these steps is crucial for the complete characterization of the protein under study. We have dubbed this process the trifecta analysis. In this study, we have proven the effectiveness of our protocol using the cystatin C and AChE proteins. Beginning with just their sequences, we have characterized both proteins’ structures and functions, including identifying the cystatin C protein’s seven-residue active site and the AChE protein’s active-site gorge via protein–protein and protein–ligand docking, respectively. This process will greatly benefit new and experienced scientists alike in obtaining a strong understanding of the trifecta analysis, resulting in a domino effect that could expand drug development.

In Vitro and In Silico Toxicological Properties of Natural Antioxidant Therapeutic Agent Azimatetracantha. LAM

Plant-derived antioxidants are a large group of natural products with the capacity to reduce radical-scavenging. Due to their potent therapeutic and preventive actions, these compounds receive a lot of attention from scientists, particularly pharmacologists. The pharmacological activities of the Azima tetracantha Lam. (AT) plant, belonging to the Salvadoraceae family, reported here justifies its traditional use in treating several diseases or disorders. This study aims to look at the propensity of certain plant compounds found in natural AT plant extracts that might play a critical role as a secondary metabolite in cervical cancer treatment. There is a shortage of information on the plant’s phytochemical and biological characteristics. Methanol (MeOH) solvent extracts of the dried AT plant were screened phytochemically. Its aqueous extract was tested for antioxidant, antiseptic, anti-inflammatory, and anticancerous properties. Absorption Distribution Metabolism and Excretion (ADME/T), Docking, and HPLC were also performed. In clinical treatment, the plant shown no adverse effects. The antioxidant activity was evaluated and showed the highest concentration at 150 µg/mL (63.50%). MeOH leaf extract of AT exhibited the highest and best inhibitory activity against Staphylococcus aureus (15.3 mm/1000) and displayed a high antiseptic potential. At a 200 µg/mL concentration, MeOH leaves-extract inhibited red blood cells (RBC) hemolysis by 66.56 ± 0.40, compared with 62.33 ± 0.40 from the standard. Albumin’s ability to suppress protein denaturation ranged from 16.75 ± 0.65 to 62.35 ± 0.20 inhibitions in this test, providing even more support for its favorable anti-inflammatory properties. The ADME/T studies were considered for a potential cancer drug molecule, and one of our compounds from MeOH extract fills the ADME and toxicity parameters. The forms of compound 4 showed a strong hydrogen-bonding interaction with the vital amino acids (ASN923, THR410, LEU840TRY927, PHE921, and GLY922). A total of 90% of cell inhibition was observed when HeLa cell lines were treated with 300 µg/mL of compound 4 (7-acetyl-3a¹-methyl- 4,14-dioxo-1,2,3a,3a¹,4,5,5a,6,8a,9b,10,11,11a-tetradecahydro-2,5a epoxy5,6a (methanooxymethano)phenaleno[1′,9′:5,6,7]indeno[1,7a-b]oxiren-2-yl acetate). The polyphenol compounds demonstrated significant advances in anticancer drug properties, and it could lead to activation of cancer cell apoptosis.

Synthesis, biological evaluation and QSAR studies of new thieno[2,3-d]pyrimidin-4(3H)-one derivatives as antimicrobial and antifungal agents

A series of new thieno[2,3-d]pyrimidin-4(3H)-one derivatives were synthesized and evaluated for their activity against four gram-positive and four gram-negative bacterial and eight fungal species. The majority of the compounds exhibited excellent antimicrobial and antifungal activity, being more potent than the control compounds. Compound 22, bearing a m-methoxyphenyl group and an ethylenediamine side chain anchored at C-2 of the thienopyrimidinone core, is the most potent antibacterial compound with broad antimicrobial activity with MIC values in the range of 0.05-0.13 mM, being 6 to 15 fold more potent than the controls, streptomycin and ampicillin. Furthermore, compounds 14 and 15 which bear a p-chlorophenyl and m-methoxyphenyl group, respectively, and share a 2-(2-mercaptoethoxy)ethan-1-ol side chain showed the best antifungal activity, being 10-15 times more potent than ketoconazole or bifonazole with MIC values 0.013-0.026 and 0.027 mM, respectively. Especially in the case of compound 15 the low MIC values were accompanied by excellent MFC values ranging from 0.056 to 0.058 mM. Evaluation of toxicity in vitro on HFL-1 human embryonic primary cells and in vivo in the nematode C. elegans revealed no toxic effects for both compounds 15 and 22 tested at the MIC concentrations. Ligand-based similarity search and molecular docking predicted that the antibacterial activity of analogue 22 is related to inhibition of the topoisomerase II DNA gyrase enzyme and the antifungal activity of compound 15 to CYP51 lanosterol demethylase enzyme. R-Group analysis as a means of computational structure activity relationship tool, highlighted the compounds' crucial pharmacophore features and their impact on the antibacterial and antifungal activity. The presence of a N-methyl piperidine ring fused to the thienopyrimidinone core plays an important role in both activities.

Optimization Rules for SARS-CoV-2 Mpro Antivirals: Ensemble Docking and Exploration of the Coronavirus Protease Active Site

Coronaviruses are viral infections that have a significant ability to impact human health. Coronaviruses have produced two pandemics and one epidemic in the last two decades. The current pandemic has created a worldwide catastrophe threatening the lives of over 15 million as of July 2020. Current research efforts have been focused on producing a vaccine or repurposing current drug compounds to develop a therapeutic. There is, however, a need to study the active site preferences of relevant targets, such as the SARS-CoV-2 main protease (SARS-CoV-2 M^pro), to determine ways to optimize these drug compounds. The ensemble docking and characterization work described in this article demonstrates the multifaceted features of the SARS-CoV-2 M^pro active site, molecular guidelines to improving binding affinity, and ultimately the optimization of drug candidates. A total of 220 compounds were docked into both the 5R7Z and 6LU7 SARS-CoV-2 M^pro crystal structures. Several key preferences for strong binding to the four subsites (S1, S1′, S2, and S4) were identified, such as accessing hydrogen binding hotspots, hydrophobic patches, and utilization of primarily aliphatic instead of aromatic substituents. After optimization efforts using the design guidelines developed from the molecular docking studies, the average docking score of the parent compounds was improved by 6.59 −log₁₀(Kd) in binding affinity which represents an increase of greater than six orders of magnitude. Using the optimization guidelines, the SARS-CoV-2 M^pro inhibitor cinanserin was optimized resulting in an increase in binding affinity of 4.59 −log₁₀(Kd) and increased protease inhibitor bioactivity. The results of molecular dynamic (MD) simulation of cinanserin-optimized compounds CM02, CM06, and CM07 revealed that CM02 and CM06 fit well into the active site of SARS-CoV-2 M^pro [Protein Data Bank (PDB) accession number 6LU7] and formed strong and stable interactions with the key residues, Ser-144, His-163, and Glu-166. The enhanced binding affinity produced demonstrates the utility of the design guidelines described. The work described herein will assist scientists in developing potent COVID-19 antivirals.

SYNTHESIS, ANTIBACTERIAL ACTIVITY AND DOCKING STUDIES OF BENZYL ALCOHOL DERIVATIVES

Benzyl alcohol derivatives were synthesized, and characterized using NMR and FTIR spectroscopic techniques. For the first time, the antibacterial activities of the synthesized compounds were examined using disc diffusion method by measuring the diameter of the zones of inhibition against Staphylococcus aureus and Pseudomonas aeruginosa. The results demonstrated that the activity was concentration dependant, and that the compounds were generally potent against P. aeruginosa. Only two of the compounds were active against S. aureus. In terms of broad spectrum activity, compound 2d (35 mm) was found to exhibit a promising efficacy which surpassed that of the standard drug (amoxicillin).The binding of compounds 2a-e to the glucosamine-6-phosphate synthase (GlcN-6-P) active-site revealed that all the synthesized compounds fitted into the GlcN-6-P active-site receptor cavity, exhibited potential hydrogen-bonding interactions with the proximal amino acid residues and aligned similar to amoxicillin. Interestingly, it has been found that the most active compound, 2d also appeared to have a relatively low binding energy (-52.8901 kcal/mol).