Design, molecular docking, and antimicrobial assessment of newly synthesized phytochemical thymol Mannich base derivatives

Antibacterial Activity of Selected Essential Oil Components and Their Derivatives: A Review

Essential oils (EOs) are gaining ground and have been intensively studied due to their widespread use in the pharmaceutical, food, and cosmetics industries. The essential components of EOs have been recognized for diverse therapeutic activities and have gained significant attention for their potential antibacterial activities. Despite the popularity of EOs and potent biological properties, their bioactive components and their derivatives are still not comprehensively characterized. This review explores the antibacterial efficacy of selected EO components and their derivatives, focusing on monoterpenes chosen (i.e., carvacrol, menthol, and thymol) and phenylpropanoids (i.e., cinnamaldehyde and eugenol). Furthermore, this review highlights recent advancements in developing derivatives of these EO components, which have shown improved antibacterial activity with reduced toxicity. By summarizing recent studies, this review reveals the potential of these natural compounds and their derivatives as promising candidates for pharmaceuticals, food preservation, and as alternatives to synthetic antibiotics in combating bacterial resistance.

Biogenic Synthesis and Characterization of Silver Nanoparticles With Cyanobacterium Oscillatoria salina Using Against MDR Pathogenic Bacteria and Their Antiproliferative and Toxicity Study

The biosynthesis of silver nanoparticles (AgNPs) using cyanobacteria has gained significant attention due to its cost-effective and eco-friendly advantages in green synthesis. Additionally, biogenic AgNPs show great potential for biological applications, particularly in combating infections caused by drug-resistant bacteria and fungi. This study synthesized using the cyanobacterium Oscillatoria salina (Os-AgNPs). The Os-AgNPs were characterized by a UV-vis spectral absorption peak at 447 nm, and their functional groups were identified through X-ray diffraction analysis, revealing a crystal structure with a 2θ value of 38°. Transmission electron microscopy (TEM) analysis showed an average nanoparticle size of 9.81 nm. The Os-AgNPs demonstrated remarkable antioxidant, antibacterial, and antifungal properties. Their antibacterial activity was tested against multidrug-resistant (MDR) Gram-positive bacteria, including Staphylococcus aureus, Streptococcus pyogenes, and Enterococcus faecalis, as well as Gram-negative bacteria such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, all isolated from clinical samples. The inhibition zones for bacterial strains ranged from 15 to 20 mm, as measured by the agar-well diffusion method. Similarly, the Os-AgNPs exhibited antifungal activity, with 20-30 mm inhibition zones against pathogenic fungi Trichophyton rubrum and Candida tropicalis. Additionally, the antiproliferative effects of the Os-AgNPs were evaluated on human cancer cell lines, including HeLa (cervical adenocarcinoma) and MD-AMB-231 (breast adenocarcinoma). In vivo toxicity studies were conducted using Swiss mouse models to assess the cytotoxic effects. Overall, the results suggest that Os-AgNPs, biosynthesized using O. salina, hold promise as potential antimicrobial and anticancer agents for pharmaceutical applications.

Multimodal antibacterial potency of newly designed and synthesized Schiff's/Mannich based coumarin derivatives: potential inhibitors of bacterial DNA gyrase and biofilm production

The briskened urge to develop potential antibacterial candidates against multidrug-resistant pathogens has motivated the present research study. Herein, newly synthesized coumarin derivatives with azomethine and amino-methylated as the functional groups have been focused on their antibacterial efficacy. The study proposed two distinct series: 3-acetyl substituted coumarin derivatives, followed by the Schiff base approach (5a-5i), and formaldehyde-secondary cyclic amine-based derivatives (7a-7g), using the Mannich base approach, further the compounds have been confirmed through various spectral studies. Further, target-specific binding affinity has been affirmed via in silico study. In vitro antibacterial study suggested compounds 5d and 5f to be most effective against S. aureus and multidrug-resistant K. pneumoniae, with MIC values of 8 and 16 μg mL-1. Among them, the compounds 5d and 5f showed excellent binding scores against different bacterial gyrase compared to the standard novobiocin. Based on RMRS, RMSF, Rg, and H-bond plots, MD simulation study at 100 ns also suggested better stability of 5d inside gyraseB of E. coli than the complex of E. coli-GyrB-novobiocin. The toxicity and pharmacokinetic profiles showed favorable drug-likeness. Overall, systematic in vitro and in silico assessment suggested that multimodal antibacterial derivatives 5d and 5f strongly inhibit both bacterial DNA gyrase and biofilm formation of drug-resistant pathogens, suggesting their potency in mainstream antibacterial therapy.

Discovery of novel piperidine-containing thymol derivatives as potent antifungal agents for crop protection

BACKGROUND

Plant fungal diseases pose a significant threat to crop production. The extensive use of chemical pesticides has led to growing environmental safety risks and pesticide resistance of various plant pathogens. Therefore, it is an urgent task to explore novel eco-friendly fungicidal agents with high efficacy to combat fungal infection.

RESULTS

In this study, we rationally designed a series of novel thymol derivatives by incorporation of the sulfonamide moiety and evaluated their biological activities against plant pathogenic fungi. The bioassay results underscored the remarkable in vitro antifungal activity of compounds 5m and 5t against Phytophthora capsici (P. capsici), with EC50 values of 8.420 and 8.414 μg/mL, respectively. Their efficacies were superior to that of widely used commercial fungicides azoxystrobin (AZO, 20.649 μg/mL) and cabendazim (CAB, 251.625 μg/mL). Furthermore, compound 5v exhibited excellent in vitro antifungal activity against Sclerotinia sclerotiorum (S. sclerotiorum), with an EC50 value of 12.829 μg/mL, significantly outperforming AZO (63.629 μg/mL). In vivo bioassays demonstrated the impactful activity of compound 5v against S. sclerotiorum, achieving over 98% curative and protective efficacies at the concentration of 200 μg/mL. Further mechanistic investigations unveiled that compound 5v induced mycelial shrinkage and collapse in S. sclerotiorum, resulting in organelle damage and the accumulation of antioxidant enzyme activity.

CONCLUSION

The significant antifungal efficacy of the prepared thymol derivatives shall encourage further exploration of compound 5v as a promising candidate to develop novel fungicides for crop protection. © 2024 Society of Chemical Industry.

Identifying p56lck SH2 Domain Inhibitors Using Molecular Docking and In-silico Scaffold Hopping

Bacterial infections are the second-leading cause of death, globally. The prevalence of antibacterial resistance has kept the demand strong for the development of new and potent drug candidates. It has been demonstrated that Src protein tyrosine kinases (TKs) play an important role in the regulation of inflammatory responses to tissue injury, which can trigger the onset of several severe diseases. We carried out a search for novel Src protein TK inhibitors, commencing from reported highly potent anti-bacterial compounds obtained using the Mannich reaction, using a combination of e-pharmacophore modeling, virtual screening, ensemble docking, and core hopping. The top-scoring compounds from ligand-based virtual screening were modified using protein structure-based design approaches and their binding to the Src homology-2 domain of p56lck TK was predicted using ensemble molecular docking. We have prepared a database of 202 small molecules and have identified 6 novel top hits that can be subjected to further investigation. We have also performed in silico ADMET property prediction for the hit compounds. This combined computer-aided drug design approach can serve as a starting point for identifying novel TK inhibitors that could be further subjected to in vitro studies and validation of antimicrobial activity.

Unveiling the antibacterial and antifungal potential of biosynthesized silver nanoparticles from Chromolaena odorata leaves

This research investigates the biogenic synthesis of silver nanoparticles (AgNPs) using the leaf extract of Chromolaena odorata (Asteraceae) and their potential as antibacterial and antifungal agents. Characterization techniques like ultraviolet-visible, Fourier transform infrared (FTIR), Dynamic light scattering and zeta potential (DLS), X-ray diffraction (XRD), transmission electron microscopy (TEM), and field emission scanning electron microscopy and energy-dispersive X-ray spectroscopy (FESEM-EDX) confirmed the formation of spherical (AgNPs). UV-vis spectroscopy reaffirms AgNP formation with a peak at 429 nm. DLS and zeta potential measurements revealed an average size of 30.77 nm and a negative surface charge (- 0.532 mV). Further, XRD analysis established the crystalline structure of the AgNPs. Moreover, the TEM descriptions indicate that the AgNPs are spherical shapes, and their sizes ranged from 9 to 22 nm with an average length of 15.27 nm. The X-ray photoelectron spectroscopy (XPS) analysis validated the formation of metallic silver and elucidated the surface state composition of AgNPs. Biologically, CO-AgNPs showed moderate antibacterial activity but excellent antifungal activity against Candida tropicalis (MCC 1559) and Trichophyton rubrum (MCC 1598). Low MIC values (0.195 and 0.390 mg/mL) respectively, suggest their potential as effective antifungal agents. This suggests potential applications in controlling fungal infections, which are often more challenging to treat than bacterial infections. Molecular docking results validated that bioactive compounds in C. odorata contribute to antifungal activity by interacting with its specific domain. Further research could pave the way for the development of novel and safe antifungal therapies based on biogenic nanoparticles.

Combined in vitro/in silico approaches, molecular dynamics simulations and safety assessment of the multifunctional properties of thymol and carvacrol: A comparative insight

Bioactive compounds derived from medicinal plants have acquired immense attentiveness in drug discovery and development. The present study investigated in vitro and predicted in silico the antibacterial, antifungal, and antiviral properties of thymol and carvacrol, and assessed their safety. The performed microbiological assays against Pseudomonas aeruginosa, Escherichia coli, Salmonella enterica Typhimurium revealed that the minimal inhibitory concentration values ranged from (0.078 to 0.312 mg/mL) and the minimal fungicidal concentration against Candida albicans was 0.625 mg/mL. Molecular docking simulations, stipulated that these compounds could inhibit bacterial replication and transcription functions by targeting DNA and RNA polymerases receptors with docking scores varying between (-5.1 to -6.9 kcal/mol). Studied hydroxylated monoterpenes could hinder C. albicans growth by impeding lanosterol 14α-demethylase enzyme and showed a (ΔG=-6.2 and -6.3 kcal/mol). Computational studies revealed that thymol and carvacrol could target the SARS-Cov-2 spike protein of the Omicron variant RBD domain. Molecular dynamics simulations disclosed that these compounds have a stable dynamic behavior over 100 ns as compared to remdesivir. Chemo-computational toxicity prediction using Protox II webserver indicated that thymol and carvacrol could be safely and effectively used as drug candidates to tackle bacterial, fungal, and viral infections as compared to chemical medication.

Protein interactions, molecular docking, antimicrobial and antifungal studies of terpyridine ligands

Resistance to antibiotics/antibacterials/antifungals in pathogenic microbes has been developing over the past few decades and has recently become a commonplace public-health peril. Thus, alternative nontoxic potent antibiotic agents are covertly needed to control antibiotic-resistant outbreaks. In an effort to combat the challenges posed by the co-occurrence of multidrug resistance, two terpyridine ligands 4'-(4-N,N'-dimethylaminophenyl)-2,2':6',2″-terpyridine (L1) and 4'-(4-tolyl)-2,2':6',2″-terpyridine (L2) have been designed, prepared and confirmed their structure by spectral studies. Thereafter, antimicrobial assay was performed against gram positive and negative bacterial strains along with fungal strains. Both compounds L1 and L2 exhibited remarkable inhibitory activities against bacteria, Escherichia coli and Staphylococcus aureus at MIC values 6.25 and 3.125 µg/ml, respectively. In addition, in silico molecular docking studies were ascertained with bacterial DNA gyrase and fungal demethylase. Furthermore, both L1 and L2 could bind Bovine Serum Albumin (BSA) protein and binding interaction has been studied with the help of UV-Visible and fluorescence spectroscopy. While fluorescence of BSA unperturbed in the presence of L2, an addition of L1 to the solution of BSA resulted significant quenching. The binding constant calculations at different temperature confirmed that the fluorescence quenching between BSA and L1 is predominantly static in nature. The toxicity of L1 and L2 was checked using Drosophila melanogaster. The toxicity analysis suggest both the dyes are non-cytotoxic in nature.Communicated by Ramaswamy H. Sarma.

Antifungal Activities of Natural Products and Their Hybrid Molecules

The increasing cases of drug resistance and high toxicity associated with the currently used antifungal agents are a worldwide public health concern. There is an urgent need to develop new antifungal drugs with unique target mechanisms. Plant-based compounds, such as carvacrol, eugenol, coumarin, cinnamaldehyde, curcumin, thymol, etc., have been explored for the development of promising antifungal agents due to their diverse biological activities, lack of toxicity, and availability. However, researchers around the world are unable to fully utilize the potential of natural products due to limitations, such as their poor bioavailability and aqueous solubility. The development of hybrid molecules containing natural products is a promising synthetic approach to overcome these limitations and control microbes' capability to develop resistance. Based on the potential advantages of hybrid compounds containing natural products to improve antifungal activity, there have been different reported synthesized hybrid compounds. This paper reviews different literature to report the potential antifungal activities of hybrid compounds containing natural products.

Synthesis, X-ray crystallography and antimicrobial activity of 2-cyanoguanidinophenytoin

The optimized synthesis of [5-oxo-4,4-diphenylimidazolidin-2-ylidene]cyanamide, which is known as 2-cyanoguanidinophenytoin (CNG-DPH) (3), and (imidazo[4,5-d]imidazole-2,5-diylidine)dicyanamide (4) has been reported in the present work. Furthermore, new Mannich bases derived from CNG-DPH were synthesized via its reaction with formaldehyde and using the corresponding amines, piperidine (base 5), and morpholine (base 6). Also, the antimicrobial activity and X-ray crystal structures for CNG-DPH and their Mannich bases were studied. The bases 3 and 6 crystallized in a monoclinic system; the crystal structure of 3 containing four molecules in the unit cell with a P21/c space group. The unit cell of 6 has eight molecules with a C2/c space group. The inter and intra hydrogen bond contacts packed and stabilized both of the structures. The morpholine ring of base 6 demonstrated a distinctive chair configuration. Mannich bases 5 and 6 showed promising antimicrobial effects. base 4 has a greater percentage for in vitro cytotoxicity (IC50) against normal cells, whereas 3 has the lowest ratio.

In-vitro anticancer evaluation of newly designed and characterized tri/tetra-substituted imidazole congeners- maternal embryonic leucine zipper kinase inhibitors: Molecular docking and MD simulation approaches

Our cascading attempt to develop new potent molecules now involves designing a series of imidazole derivatives and synthesizing two sets of 2,4,5- tri-substituted (4a-4d) and 1,2,4,5-tetra-substituted (6a-6d) imidazole by the principle of Debus-Radziszewski multicomponent synthesis reaction. The structures of the obtained compounds were confirmed by 1H/13C NMR, FT-IR, elemental analysis, purity and the retention time was analyzed by HPLC. Based upon the binding affinity in the molecular docking studies, we have synthesized different imidazole derivatives from which compound 6c have been found to show more anti-proliferative activity by inducing apoptosis at a higher rate than the other compounds corroborating the in-silico prediction. The structure and crystallinity of compound 4d have been confirmed by single XRD analysis. The synthesized molecules were screened for their in vitro anti-cancer properties in triple negative breast cancer cell line (MDA-MB-231), pancreatic cancer cell lines (MIA PaCa-2) and oral squamous cell carcinoma cell line (H357) and results indicated that all the compounds inhibited the cell proliferation in a concentration-dependent manner at different time points. The compounds 4b and 6d were found to be effective against the S. aureus bacterial strain whereas only compound 4d fairly inhibited the fungal strain of T. rubrum with a MIC 12.5 μg/mL. Molecular docking study reveals good interaction of the synthesized compounds with known target MELK involved in oncogenesis having high binding profiles. The lead compound 6c was further analyzed by the detailed molecular dynamics study to establish the stability of the ligand-enzyme complex.

Coumaryl-sulfonamide moiety: Unraveling their synthetic strategy and specificity toward hCA IX/XII, facilitating anticancer drug development

Currently, cancer is the most grieving threat to society. The cancer-related death rate has had an ascending trend, despite the implementation of numerous treatment strategies or the discovery of an array of potent molecules against several pathways of cancer growth. The need of the hour is to prevent the multidrug resistance toll, and the current efforts have been bestowed upon a versatile small molecule scaffold, coumarin (benz[α]pyrone), a natural compound possessing interesting affinity toward the cancer target human carbonic anhydrase (hCA), focusing on hCA I, II, IX, and XII. Along with coumarin, the age-old known antibacterial drug sulfonamide, when conjugated at positions 3, 7, and 8 of coumarin either with a linker group or as a single entity, has been reported to enhance the affinity of coumarin toward the overexpressed enzymes in tumor cell lines. The sulfonamides have been listed as obsolete drugs due to the severe side effects caused by them; however, their affinity toward the hCA-zinc-binding core has attracted the attention of researchers. Hence, in the process of drug development, coumarin and sulfonamides have remained the choice of last resort. To unveil the synthetic strategy of coumarin-sulfonamide conjugation, their rationale for inhibiting cancer cells/enzymes, and their affinity toward various types of carcinoma have been the sole goal of the researchers. This review specifically focuses on the mechanism of action and the structure-activity relationship through synthetic strategies and the binding affinity of coumaryl-sulfonamide conjugates with the anticancer targets possessing the highest enzyme affinity, since 2008.

In Silico Evaluation of the Antimicrobial Activity of Thymol-Major Compounds in the Essential Oil of Lippia thymoides Mart. & Schauer (Verbenaceae)

In this paper, we evaluated the drug-receptor interactions responsible for the antimicrobial activity of thymol, the major compound present in the essential oil (EO) of Lippia thymoides (L. thymoides) Mart. & Schauer (Verbenaceae). It was previously reported that this EO exhibits antimicrobial activity against Candida albicans (C. albicans), Staphylococcus aureus (S. aureus), and Escherichia coli (E. coli). Therefore, we used molecular docking, molecular dynamics simulations, and free energy calculations to investigate the interaction of thymol with pharmacological receptors of interest to combat these pathogens. We found that thymol interacted favorably with the active sites of the microorganisms’ molecular targets. MolDock Score results for systems formed with CYP51 (C. albicans), Dihydrofolate reductase (S. aureus), and Dihydropteroate synthase (E. coli) were −77.85, −67.53, and −60.88, respectively. Throughout the duration of the MD simulations, thymol continued interacting with the binding pocket of the molecular target of each microorganism. The van der Waals (ΔE_vdW = −24.88, −26.44, −21.71 kcal/mol, respectively) and electrostatic interaction energies (ΔE_ele = −3.94, −11.07, −12.43 kcal/mol, respectively) and the nonpolar solvation energies (ΔG_NP = −3.37, −3.25, −2.93 kcal/mol, respectively) were mainly responsible for the formation of complexes with CYP51 (C. albicans), Dihydrofolate reductase (S. aureus), and Dihydropteroate synthase (E. coli).

Recent progression of cyanobacteria and their pharmaceutical utility: an update

Cyanobacteria (blue-green algae) are Gram-negative photosynthetic eubacteria that are found everywhere. This largest group of photosynthetic prokaryotes is rich in structurally novel and biologically active compounds; several of which have been utilized as prospective drugs against cancer and other ailments, as well. Consequently, the integument of nanoparticles-synthetic approaches in cyanobacterial extracts should increase pharmacological activity. Moreover, silver nanoparticles (AgNPs) are small materials with diameters below 100 nm that are classified into different classes based on their forms, sizes, and characteristics. Indeed, the biosynthesized AgNPs are generated with a variety of organisms, algae, plants, bacteria, and a few others, for the medicinal purposes, as the bioactive compounds of curio and some proteins from cyanobacteria have the potentiality in the treatment of a wide range of infectious diseases. The critical focus of this review is on the antimicrobial, antioxidant, and anticancer properties of cyanobacteria. This would be useful in the pharmaceutical industries in the future drug development cascades.Communicated by Ramaswamy H. Sarma.

Design, molecular docking study of synthesised N-heteroaryl substituted gallamide derivatives and their antibacterial assessment

A series of N-heteroaryl substituted Gallamide derivatives 3a-3g were synthesised and the obtained structures were further confirmed by different spectral studies. For in-vitro antibacterial activity, the synthesised compounds were evaluated against three UTI (Urinary Tract Infection) bacterial strains including Staphylococcus aureus, Escherichia coli, and Streptococcus pyogenes. Furthermore, the designed compounds were docked with bacterial DNA gyrase and dihydropteroate synthase. All the compounds had shown good inhibition against S. aureus whereas compound 3e has produced significant inhibition at 28 and 26 mm against S.aureus and E.coli, respectively. The MIC value of the conjugate 3e and 3d was 3.12 and 6.25 μg/mL against S. aureus andE.coli, respectively. Compound 3,4,5-trihydroxy-N-(4-(N-(5-methyl isoxazol-3-yl) sulfamoyl) phenyl)benzamide 3d had shown the highest binding energy against both the targets along with good antibacterial action.