1,3-Oxazole derivatives of cytisine as potential inhibitors of glutathione reductase of Candida spp.: QSAR modeling,docking analysis and experimental study of new anti-Candida agents

Natural products as well as their derivatives play a significant role in the discovery of new biologically active compounds in the different areas of our life especially in the field of medicine. The synthesis of compounds produced from natural products including cytisine is one approach for the wider use of natural substances in the development of new drugs. QSAR modeling was used to predict and select of biologically active cytisine-containing 1,3-oxazoles. The eleven most promising compounds were identified, synthesized and tested. The activity of the synthesized compounds was evaluated using the disc diffusion method against C. albicans M 885 (ATCC 10,231) strain and clinical fluconazole-resistant Candida krusei strain. Molecular docking of the most active compounds as potential inhibitors of the Candida spp. glutathione reductase was performed using the AutoDock Vina. The built classification models demonstrated good stability, robustness and predictive power. The eleven cytisine-containing 1,3-oxazoles were synthesized and their activity against Candida spp. was evaluated. Compounds 10, 11 as potential inhibitors of the Candida spp. glutathione reductase demonstrated the high activity against C. albicans M 885 (ATCC 10,231) strain and clinical fluconazole-resistant Candida krusei strain. The studied compounds 10, 11 present the interesting scaffold for further investigation as potential inhibitors of the Candida spp. glutathione reductase with the promising antifungal properties. The developed models are publicly available online at http://ochem.eu/article/120720 and could be used by scientists for design of new more effective drugs.     

Design,synthesis and characterization of a series of 6-substituted-4-hydroxy-1-(2-substitutedthiazol-4-yl)quinolin-2(1H)-one derivatives and evaluation of their in vitro anticancer and antibacterial activity

The current research work deals with the design, synthesis and characterization of a series of 6-substituted-4-hydroxy-1-(2-substitutedthiazol-4-yl)quinolin-2(1H)-one derivatives [III(a-d)(1–3)] and evaluation of their in-vitro anticancer activity against MDA-MB (Breast cancer) and A549 (Lung cancer) cell lines based upon MTT assay and in-vitro antibacterial by the measurement of zone of inhibition and determining the Minimum Inhibitory Concentration (MIC). All the synthesized compounds were characterized by UV, IR, ¹H NMR and ¹³C NMR spectral data.Molecular docking studies of the title compounds were carried out using Molegro Virtual Docker (MVD-2013, 6.0) software. The synthesized compounds exhibited well conserved hydrogen bond interactions with one or more amino acid residues in the active pocket of EGFRK tyrosine kinase domain (PDB ID: 1m17) for docking study on anticancer activity and S. aureus DNA Gyrase domain complexed with a ciprofloxacin inhibitor (PDB ID: 2XCT) for antibacterial docking study. All synthesized derivatives were potent against A549 (Lung cancer) cell line as compared to MDA-MB (Breast cancer) cell line. Compound 2-(4-(4-hydroxy-6-methyl-2-oxoquinolin-1(2H)-yl)thiazol-2-yl)hydrazin-1-ium iodide (IIId-2) was found to be the most cytotoxic as compared to the other synthesized derivatives, with IC₅₀ values of 346.12 μg/mL against A549 (Lung cancer) cell line, however all synthesized derivatives were found to be a poor antibacterial agent when compared with standard ciprofloxacin.Thus, the synthesized derivatives possessed a potential to bind with some of the residues of the active site and can be further developed into potential pharmacological agents.     

Discovery of natural berberine-derived nitroimidazoles as potentially multi-targeting agents against drug-resistant <Emphasis Type="Italic">Escherichia coli</Emphasis>

A series of natural berberine-derived nitroimidazoles as novel antibacterial agents were designed, synthesized and characterized by nuclear magnetic resonance (NMR), infrared spectra (IR), and high resolution mass spectra (HRMS) spectra. The antimicrobial evaluation showed that some target molecules exhibited moderate to good inhibitory activities against the tested bacteria and fungi including clinical drug-resistant strains isolated from infected patients. Especially, 2-fluorobenzyl derivative 8f not only gave strong activity against drug-resistant E. coli with the minimal inhibitory concentration (MIC) value of 0.003 mM, 33-fold more active than norfloxacin, but also exhibited low toxicity toward RAW 264.7 cells and less propensity to trigger resistance. The aqueous solubility and ClogP values of target compounds were investigated to elucidate the structureactivity relationships. Molecular docking and quantum chemical studies for compound 8f rationally explained its antibacterial effect. The further exploration of antibacterial mechanism revealed that the highly active compound 8f could effectively permeabilize E. coli cell membrane and intercalate into DNA isolated from resistant E. coli to form 8f-DNA complex that might block DNA replication to exert the powerful bioactivities. Compound 8f could also selectively address resistant E. coli from a mixture of various strains.     

Synthesis,in-silico antiviral screening and in-vitro antibacterial screening of a novel chalcone derivatives

A new series of novel chalcones was synthesized and subjected to screening of theoretical molecular and biological properties. For evaluating the theoretical molecular properties of these molecules Molinspiration and Osiris software were used. It was concluded from data that the majority of molecules exhibited theoretical molecular and biological properties similar to that of standard drugs. Role of Hemagglutinin is vital during the attack of virus on cells so Hemagglutinin inhibitors may act as potent antiviral agents. Considering this fact in-silico studies were performed using the SwissDock screening engine on Hemagglutinin target PDB code 1HGH. Hemagglutinin inhibition potential in terms of binding affinity was expressed as ΔG values ranging from −8.71 kcal/mol to −7.39 kcal/mol. Compound IIIm showed maximum binding affinity with ΔG value −8.71 kcal/mol followed by compound IIIj ΔG value −8.31 kcal/mol. It's prudent from ΔG values that compounds may act as potent antiviral agents. Compounds were also screened for in-vitro antibacterial activity against five pathogenic strains. Most of the compounds exhibited low to moderate activity against strains under study. Compound IIIn demonstrated good activity against four pathogenic strains with highest zone of inhibition of 16 mm against K. pneumoniae and S. typhi.     

Thiazolidin-4-Ones as Potential Antimicrobial Agents: Experimental and In Silico Evaluation

Herein, we report computational and experimental evaluations of the antimicrobial activity of twenty one 2,3-diaryl-thiazolidin-4-ones. All synthesized compounds exhibited an antibacterial activity against six Gram-positive and Gram-negative bacteria to different extents. Thus, the MIC was in the range of 0.008–0.24 mg/mL, while the MBC was 0.0016–0.48 mg/mL. The most sensitive bacterium was S. Typhimurium, whereas S. aureus was the most resistant. The best antibacterial activity was observed for compound 5 (MIC at 0.008–0.06 mg/mL). The three most active compounds 5, 8, and 15, as well as compound 6, which were evaluated against three resistant strains, MRSA, P. aeruginosa, and E. coli, were more potent against all bacterial strains used than ampicillin. The antifungal activity of some compounds exceeded or were equipotent with those of the reference antifungal agents bifonazole and ketoconazole. The best activity was expressed by compound 5. All compounds exhibited moderate to good drug-likeness scores ranging from −0.39 to 0.39. The docking studies indicated a probable involvement of E. coli Mur B inhibition in the antibacterial action, while CYP51 inhibition is likely responsible for the antifungal activity of the tested compounds. Finally, the assessment of cellular cytotoxicity of the compounds in normal human MRC-5 cells revealed that the compounds were not toxic.     

A merged molecular docking,ADME-T and dynamics approaches towards the genus of Arisaema as herpes simplex virus type 1 and type 2 inhibitors

An attempt toward screening of phytoconstituents (Arisaema genus) against herpes viruses (HSV-1 and HSV-2) was carried out using in silico approaches. Human HSV-1 and HSV-2 are accountable for cold sores genital herpes, respectively. Two drug targets, namely thymidine kinase (TK; PDB: 2ki5) serine protease (PDB: 1at3) were selected for HSV-1 and HSV-2. Initially, molecular docking tool was employed to screened apex hits phytoconstituents against herpes infections. ADME-T studies of top ranked were also further highlighted to achieve their effectiveness. Following, molecular dynamics studies were also examined to further optimize the stability of ligands. Glide scores and binding interactions of phytoconstituents were compared with Acyclovir, the main drug used in treatment of HSV, the screened top hits exhibited more glide scores and better binding for both HSV-1 and HSV-2 receptors. Additionally, ADME-T showed an ideal range for top hits while molecular dynamics results also illustrated stability of models. Ultimately, the whole efforts reveal to top three most promising hits for HSV-1 (39, 21, 19) and HSV-2 (20, 51, 19) receptors which can be explored further in wet lab experiments as promising agents against HSV infections.     

Synthesis and Antimicrobial Activity Screening of Piperazines Bearing N,N′-Bis(1,3,4-thiadiazole) Moiety as Probable Enoyl-ACP Reductase Inhibitors

A new N,N′-disubstituted piperazine conjugated with 1,3,4-thiadiazole and 1,2,4-triazole was prepared and the chemical structures were identified by IR, NMR and elemental analysis. All the prepared compounds were tested for their antimicrobial activity. The antimicrobial results indicated that the tested compounds showed significant antibacterial activity against gram-negative strains, especially E. coli, relative to gram-positive bacteria. Docking analysis was performed to support the biological results; binding modes with the active site of enoyl reductase amino acids from E. coli showed very good scores, ranging from −6.1090 to −9.6184 kcal/mol. Correlation analysis was performed for the inhibition zone (nm) and the docking score.     

Molecular docking,HOMO-LUMO and quantum chemical computation analysis of anti-glyoximehydrazone derivatives containing pyrazolone moiety and their transition metal complexes

In this study, in order to obtain biologically active compounds, a series of anti-glyoximehydrazone ligands bearing vic-dioxime, hydrazone, and pyrazole moieties and their (O•••H–O) bridged nickel(II), cobalt(II) and copper(II) metal complexes were prepared. Further, the molecular docking studies were carried out on those ligands and their nickel(II), cobalt(II) and copper(II) metal complexes to analyze the interaction with EGFR Kinase domain complexed with tak-285 (PDB ID: 3POZ) and human androgen receptor T877A mutant (PDB ID:2OZ7). In addition, the compounds were optimized by using B3LYP/6-311G+(d,p) level of Density Functional Theory (DFT) to evaluate the HOMO–LUMO contours and quantum chemical parameters. Also, bioactivity analysis were performed.Metal complexes had higher binding affinities against 3POZ and 2OZ7. The most promising compounds for 3POZ were nickel(II) and copper(II) metal complexes. However, for the 2OZ7 target receptor, cobalt(II) and copper(II) metal complexes were the possible hit compounds. Furthermore, cobalt(II) metal complex of ligand two was found to be the most reactive one among others. Moreover, it had the highest ω which is related to a potent higher electrophilic character. It was determined that all the compounds had moderate bioactivity.In conclusion, nickel(II), cobalt(II), and copper(II) complexes could be powerful hit compounds for anti-cancer drug discovery studies.     

Synthesis,characterization, biological applications,and molecular docking studies of amino-phenol-derived mixed-ligand complexes with Fe(III), Cr(III), and La(III) ions

A new series of Fe(III), Cr(III), and La(III) mixed-ligand complexes, resulting from the interaction of 2-aminophenol with 2-hydroxy acetophenone (HL₁) as primary ligand and L- histidine (L₂) as a secondary ligand, has been investigated using various physicochemical studies such as elemental analyses, molar conductivity, magnetic moment, infrared, UV/Vis, ¹H NMR, and mass spectroscopic techniques. The microanalytical results indicate that the mixed ligand complexes were designed in a 1:1:1 M ratio. The electronic spectral data indicated that all the synthesized complexes have an octahedral structure. The disc diffusion assay was used to determine the disc inhibition zone (IZ, mm) and minimum inhibitory concentration (MIC, g/mL) of the investigated compounds against the growth of the pathogenic bacterial strains S. aureus, E. faecalis, P. aeruginosa, Klebsiella sp., and E. coli. The MTT test was used to determine the cytotoxicity of these reported compounds against the human hepatocellular liver cancer (HEPG-2) cell lines. The molecular docking study for the compounds against the EGFR tyrosine kinase receptor (PDB code: 1 M17) was conducted to examine the interactions in protein–ligand complexes. Furthermore, the biological activity of the ligand was investigated using quantitative structure–activity relationship studies (QSAR).     

Binding Free Energy (BFE) Calculations and Quantitative Structure–Activity Relationship (QSAR) Analysis of Schistosoma mansoni Histone Deacetylase 8 (smHDAC8) Inhibitors

Histone-modifying proteins have been identified as promising targets to treat several diseases including cancer and parasitic ailments. In silico methods have been incorporated within a variety of drug discovery programs to facilitate the identification and development of novel lead compounds. In this study, we explore the binding modes of a series of benzhydroxamates derivatives developed as histone deacetylase inhibitors of Schistosoma mansoni histone deacetylase (smHDAC) using molecular docking and binding free energy (BFE) calculations. The developed docking protocol was able to correctly reproduce the experimentally established binding modes of resolved smHDAC8–inhibitor complexes. However, as has been reported in former studies, the obtained docking scores weakly correlate with the experimentally determined activity of the studied inhibitors. Thus, the obtained docking poses were refined and rescored using the Amber software. From the computed protein–inhibitor BFE, different quantitative structure–activity relationship (QSAR) models could be developed and validated using several cross-validation techniques. Some of the generated QSAR models with good correlation could explain up to ~73% variance in activity within the studied training set molecules. The best performing models were subsequently tested on an external test set of newly designed and synthesized analogs. In vitro testing showed a good correlation between the predicted and experimentally observed IC₅₀ values. Thus, the generated models can be considered as interesting tools for the identification of novel smHDAC8 inhibitors.     

Synthesis and Structure–Activity Relationship of Thioacetamide-Triazoles against Escherichia coli

Infections due to Gram-negative bacteria are increasingly dangerous due to the spread of multi-drug resistant strains, emphasizing the urgent need for new antibiotics with alternative modes of action. We have previously identified a novel class of antibacterial agents, thioacetamide-triazoles, using an antifolate targeted screen and determined their mode of action which is dependent on activation by cysteine synthase A. Herein, we report a detailed examination of the anti-E. coli structure–activity relationship of the thioacetamide-triazoles. Analogs of the initial hit compounds were synthesized to study the contribution of the aryl, thioacetamide, and triazole sections. A clear structure–activity relationship was observed generating compounds with excellent inhibition values. Substitutions to the aryl ring were generally best tolerated, including the introduction of thiazole and pyridine heteroaryl systems. Substitutions to the central thioacetamide linker section were more nuanced; the introduction of a methyl branch to the thioacetamide linker substantially decreased antibacterial activity, but the isomeric propionamide and N-benzamide systems retained activity. Changes to the triazole portion of the molecule dramatically decreased the antibacterial activity, further indicating that 1,2,3-triazole is critical for potency. From these studies, we have identified new lead compounds with desirable in-vitro ADME properties and in-vivo pharmacokinetic properties.     

FWAVina: A novel optimization algorithm for protein-ligand docking based on the fireworks algorithm

Protein-ligand docking is an essential process that has accelerated drug discovery. How to accurately and effectively optimize the predominant position and orientation of ligands in the binding pocket of a target protein is a major challenge. This paper proposed a novel ligand binding pose search method called FWAVina based on the fireworks algorithm, which combined the fireworks algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon local search method adopted in AutoDock Vina to address the pose search problem in docking. The FWA was used as a global optimizer to rapidly search promising poses, and the Broyden-Fletcher-Goldfarb-Shannon method was incorporated into FWAVina to perform an exact local search. FWAVina was developed and tested on the PDBbind and DUD-E datasets. The docking performance of FWAVina was compared with the original Vina program. The results showed that FWAVina achieves a remarkable execution time reduction of more than 50 % than Vina without compromising the prediction accuracies in the docking and virtual screening experiments. In addition, the increase in the number of ligand rotatable bonds has almost no effect on the efficiency of FWAVina. The higher accuracy, faster convergence and improved stability make the FWAVina method a better choice of docking tool for computer-aided drug design. The source code is available at https://github.com/eddyblue/FWAVina/.     

Exploration of the Antimicrobial Effects of Benzothiazolylthiazolidin-4-One and In Silico Mechanistic Investigation

Background: Infectious diseases still affect large populations causing significant morbidity and mortality. Bacterial and fungal infections for centuries were the main factors of death and disability of millions of humans. Despite the progress in the control of infectious diseases, the appearance of resistance of microbes to existing drugs creates the need for the development of new effective antimicrobial agents. In an attempt to improve the antibacterial activity of previously synthesized compounds modifications to their structures were performed. Methods: Nineteen thiazolidinone derivatives with 6-Cl, 4-OMe, 6-CN, 6-adamantan, 4-Me, 6-adamantan substituents at benzothiazole ring were synthesized and evaluated against panel of four bacterial strains S. aureus, L. monocytogenes, E. coli and S. typhimirium and three resistant strains MRSA, E. coli and P. aeruginosa in order to improve activity of previously evaluated 6-OCF₃-benzothiazole-based thiazolidinones. The evaluation of minimum inhibitory and minimum bactericidal concentration was determined by microdilution method. As reference compounds ampicillin and streptomycin were used. Results: All compounds showed antibacterial activity with MIC in range of 0.12–0.75 mg/mL and MBC at 0.25–>1.00 mg/mL The most active compound among all tested appeared to be compound 18, with MIC at 0.10 mg/mL and MBC at 0.12 mg/mL against P. aeruginosa. as well as against resistant strain P. aeruginosa with MIC at 0.06 mg/mL and MBC at 0.12 mg/mL almost equipotent with streptomycin and better than ampicillin. Docking studies predicted that the inhibition of LD-carboxypeptidase is probably the possible mechanism of antibacterial activity of tested compounds. Conclusion: The best improvement of antibacterial activity after modifications was achieved by replacement of 6-OCF₃ substituent in benzothiazole moiety by 6-Cl against S. aureus, MRSA and resistant strain of E. coli by 2.5 folds, while against L. monocytogenes and S. typhimirium from 4 to 5 folds.     

Phytochemical Analysis,Antibacterial Activity and Modulating Effect of Essential Oil from Syzygium cumini (L.) Skeels

One of the main global problems that affect human health is the development of bacterial resistance to different drugs. As a result, the growing number of multidrug-resistant pathogens has contributed to an increase in resistant infections and represents a public health problem. The present work seeks to investigate the chemical composition and antibacterial activity of the essential oil of Syzygium cumini leaves. To identify its chemical composition, gas chromatography coupled to mass spectrometry was used. The antibacterial activity test was performed with the standard strains Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 25853 and Staphylococcus aureus ATCC 25923 and multidrug-resistant clinical isolates E. coli 06, P. aeruginosa 24 and S. aureus 10. The minimum inhibitory concentration (MIC) was determined by serial microdilution as well as the verification of the modulating effect of the antibiotic effect. In this test, the oil was used in a subinhibitory concentration. The test reading was performed after 24 h of incubation at 37 °C. The results show that the major chemical constituent is α-pinene (53.21%). The oil showed moderate activity against E. coli ATCC 25922, with the MIC of 512 µg/mL; there was no activity against the other strains. The oil potentiated the effect of antibiotics demonstrating possible synergism when associated with gentamicin, erythromycin and norfloxacin against E. coli 06 and S. aureus 10.     

Synthesis,Molecular Docking,and Biofilm Formation Inhibitory Activity of Bis(Indolyl)Pyridines Analogues of the Marine Alkaloid Nortopsentin

An efficient and simple protocol for the synthesis of a new class of diverse bis(indolyl)pyridines analogues of the marine alkaloid nortopsentin has been reported. A one-pot four-component condensation of 3-cyanocarbomethylindole, various aldehyde, 3-acetylindole, and ammonium acetate in glacial acetic acid led to the formation of 2,6-bis(1H-indol-3-yl)-4-(substituted-phenyl)pyridine-5-carbonitriles. Additionally, 2,6-bis(1H-indol-3-yl)-4-(benzofuran) pyridine-5-carbonitriles were prepared via a one-pot four-component condensation of 3-cyanocarbomethylindole, various N-substituted-indole-3-aldehydes, 2-acetylbenzofuran, and ammonium acetate. The synthesized compounds were evaluated for their ability to inhibit biofilm formation against the Gram-positive bacterial reference strains Staphylococcus aureus ATCC 6538 and the Gram-negative strain Escherichia coli ATCC 25922. Some of the new compounds showed a marked selectivity against the Gram-positive and Gram-negative strains. Remarkably, five compounds 4b, 7a, 7c, 7d and 8e demonstrated good antibiofilm formation against S. aureus and E. coli. On the other hand, the release of reducing sugars and proteins from the treated bacterial strains over the untreated strains was considered to explain the disruption effect of the selected compound on the contact cells of S. aureus and E. coli. Out of all studied compounds, the binding energies and binding mode of bis-indole derivatives 7c and 7d were theoretically the best thymidylate kinase, DNA gyrase B and DNA topoisomerase IV subunit B inhibitors.     

SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction

Predicting the binding of T cell receptors (TCRs) to epitopes plays a vital role in the immunotherapy, because it guides the development of therapeutic vaccines and cancer treatments. Many prediction methods attempted to explain the relationship between TCR repertoires from different aspects such as the V(D)J gene locus and the biophysical features of amino acids molecules, but the extraction of these features is time consuming and the performance of these models are limited. Few studies have investigated how k-mers formed by adjacent amino acids in TCR sequences direct the epitope recognition, and the specific mechanism of TCR epitope binding is still unclear. Motivated by these, we presented SETE (Sequence-based Ensemble learning approach for TCR Epitope binding prediction), a novel model to predict the TCR epitope binding accurately. The model deconstructed the CDR3β sequence to short amino acid chains as features and learned the pattern of them between different TCR repertoires with gradient boosting decision tree algorithm. Experiments have demonstrated that SETE can be helpful in predicting the TCRs’ corresponding epitopes and it outperforms other state-of-the-art methods in predicting the epitope specificity of TCR on VDJdb data set. The source codes have been uploaded at https://github.com/wonanut/SETE for academic usage only.     

QSAR Evaluations to Unravel the Structural Features in Lysine-Specific Histone Demethylase 1A Inhibitors for Novel Anticancer Lead Development Supported by Molecular Docking,MD Simulation and MMGBSA

Using 84 structurally diverse and experimentally validated LSD1/KDM1A inhibitors, quantitative structure–activity relationship (QSAR) models were built by OECD requirements. In the QSAR analysis, certainly significant and understated pharmacophoric features were identified as critical for LSD1 inhibition, such as a ring Carbon atom with exactly six bonds from a Nitrogen atom, partial charges of lipophilic atoms within eight bonds from a ring Sulphur atom, a non-ring Oxygen atom exactly nine bonds from the amide Nitrogen, etc. The genetic algorithm–multi-linear regression (GA-MLR) and double cross-validation criteria were used to create robust QSAR models with high predictability. In this study, two QSAR models were developed, with fitting parameters like R² = 0.83–0.81, F = 61.22–67.96, internal validation parameters such as Q²_LOO = 0.79–0.77, Q²_LMO = 0.78–0.76, CCC_cv = 0.89–0.88, and external validation parameters such as, R2ext = 0.82 and CCCex = 0.90. In terms of mechanistic interpretation and statistical analysis, both QSAR models are well-balanced. Furthermore, utilizing the pharmacophoric features revealed by QSAR modelling, molecular docking experiments corroborated with the most active compound’s binding to the LSD1 receptor. The docking results are then refined using Molecular dynamic simulation and MMGBSA analysis. As a consequence, the findings of the study can be used to produce LSD1/KDM1A inhibitors as anticancer leads.