Solvent-Free Synthesis, In Vitro and In Silico Studies of Novel Potential 1,3,4-Thiadiazole-Based Molecules against Microbial Pathogens

In silico and in vitro prediction of new synthesized N-heterocyclic compounds as anti-SARS-CoV-2

Computer-aided drug design has been employed to get the medicinal effects against Corona virus from different pyridine derivatives after synthesizing the new compounds. Additionally, various computational studies are also employed between the newly prepared pyridine derivatives and three controls against three proteins (6Y2E, 6M71 and 6M3M). Different methods were employed to synthesize new pyridine derivatives according to the literature using different reaction mediums. MTT was performed for cytotoxicity study and IC50 for inhibitory concentration. Additionally, in-silico studies including DFT, molecular docking, molecular dynamics, MMPBSA, ADME, pharmacokinetics and Lipinski rules were evaluated. The chemical structures of all new compounds were elucidated based on spectroscopic investigation. A molecular docking study demonstrated that compounds 5, 11, and 12 have the best binders of the SARS-CoV-2 main protease enzyme, with energy scores of - 7.5 kcal/mol, - 7.2 kcal/mol, and - 7.9 kcal/mol, respectively. The net binding energy values of the 11-Mpro, 12-Mpro, and 5-Mpro complexes revealed their highly stable nature in terms of both intermolecular interactions and docked conformation across the simulation time. ADME properties, besides the pharmacokinetics and Lipinski rules, showed that all seven newly synthesized compounds follow Lipinski rules with high GI absorption. The In Vitro antiviral study against SARS-CoV-2 using MTT methods confirms that compound 5 has more potential and is safer than other tested compounds. The study shows that the newly synthesized pyridine derivatives have medicinal properties against SARS-CoV-2 without violating Lipinski rules. Compounds 5, 11, and 12, particularly compound 5, may serve as promising potential candidate for COVID-19.

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.

Antibacterial Activity of Quinoline-Based Derivatives against Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa: Design, Synthesis, DFT and Molecular Dynamic Simulations

Bacterial virulence becomes a significant challenge for clinical treatments, particularly those characterized as Multi-Drug-Resistant (MDR) strains. Therefore, the preparation of new compounds with active moieties could be a successful approach for eradication of MDR strains. For this purpose, newly synthesized quinoline compounds were prepared and tested for their antimicrobial activity against Methicillin-Resistant Staphylococcus Aureus (MRSA) and Pseudomonas Aeruginosa (PA). Among the synthesized derivatives, compounds 1-(quinolin-2-ylamino)pyrrolidine-2,5-dione (8) and 2-(2-((5-methylfuran-2-yl)methylene)hydrazinyl)quinoline (12) were shown to possess the highest antimicrobial activity with the minimum inhibitory concentration with the values of 5±2.2 and10±1.5 μg/mL towards Pseudomonas aeruginosa without any activity towards MRSA. Interestingly, compounds 2-(2-((1H-indol-3-yl)methylene)hydrazinyl)quinoline (13) and 2-(4-bromophenyl)-3-(quinolin-2-ylamino)thiazolidin-4-one (16c) showed significant inhibition activity against Staphylococcus aureus MRSA and Pseudomonas aeruginosa. Compound 13 (with indole moiety) particularly displayed excellent bactericidal activity with low MIC values 20±3.3 and 10±1.5 μg/mL against Staphylococcus aureus MRSA and Pseudomonas aeruginosa, respectively. Effects molecular modelling was used to determine the mode of action for the antimicrobial effect. The stability of complexes formed by docking and target-ligand pairing was evaluated using molecular dynamics simulations. The compounds were also tested for binding affinity to the target protein using MM-PBSA. Density-functional theory (DFT) calculations were also used to investigate the electrochemical properties of various compounds.

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.

Towards Covid-19 TMPRSS2 enzyme inhibitors and antimicrobial agents: Synthesis, antimicrobial potency, molecular docking, and drug-likeness prediction of thiadiazole-triazole hybrids

1,3,4-Thiadiazole analogues 3 and 4 were synthesised via the reaction of 1-(5-methyl-1-(5-(methylthio)-1,3,4-thiadiazol-2-yl)-1H-1,2,3-triazol-4-yl)ethan-1one 2 with vanillin or thiophene-2-carboxaldhyde, respectively through chalcone reaction. Compounds 3 and 4 were submitted to react with thiosemicarbazide affording 5-(4‑hydroxy-3-methoxyphenyl)-3-(5-methyl-1-(5-(methylthio)-1,3,4-thiadiazol-2-yl)-1H-1,2,3-triazol-4-yl)-4,5-dihydro-1H-pyrazole-1-carbothioamide (5) give 3-(5-methyl-1-(5-(methylthio)-1,3,4-thiadiazol-2-yl)-1H-1,2,3-triazol-4-yl)-5-(thiophen-2-yl)-4,5 dihydro-1H-pyrazole-1-carbothioamide (6), respectively. The letters were reacted with N-(4-chlorophenyl)-2-oxopropanehydrazonoyl chloride to give compounds 7 and 8. The chemical compositions of the novel compounds were affirmed by spectral and microanalytical data. Meanwhile, all the newly synthesized compounds have been screened for their ability to prevent the proliferation of different pathogens named Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, and Candida albicans in vitro. Additionally, the potency of the newly synthesized compounds to be anti-COVID-19 candidates was studied through a molecular docking study. The newly prepared molecules 2-8 were studied in silico against transmembrane serine protease 2 (TMPRSS2) to identify their potential therapeutic activity against Coronavirus. Moreover, the drug-likeness of the compounds was tested theoretically by ADMET studies. Compound 8 exhibited a better binding affinity (-9.1 kcal/mol) against the target enzyme TMPRSS2. Additionally, it respects Lipinski's rule of five and has acceptable ADMET properties, indicating that compound 8 could be interesting for the treatment of Covid-19.

Synthesis and Anticancer Evaluation of New Thiazole and Thiadiazole Derivatives Bearing Acetanilide Moiety

New thiazole and thiadiazole derivatives bound to the acetanilide moiety were synthesized and evaluated for their cytotoxic activity. The precursor N-(4-acetamidophenyl)-N'-phenylthiourea (2) was cyclocondensed with ethyl bromoacetate to afford a mixture of the two isomers, 2-(4-acetamidophenylimino)-3-phenylthiazolidin-4-one (3a, 23%) and 3-(4-acetamidophenyl)-2-phenyliminothiazolidin-4-one (3b, 71%). The Knoevenagel reaction of 3b with various aromatic aldehydes afforded 5-arylidene-2-phenyliminothiazolidin-4-one derivatives 5a-5e. Intramolecular cyclization of thiourea scaffold 2 with chloroacetone and/or phenacyl chloride gave the conforming thiazole derivatives 6a and 6b. A new series of thiadiazole derivatives 9a-9c and 11a-11c was synthesized by the reaction of N-(4-acetamidophenyl)-N'-phenylthiourea (2) with selected derivatives of hydrazonoyl halide in ethanol and triethylamine. The structures of the synthesized thiazole and thiadiazole compounds were elucidated by their compatible spectral data. The cytotoxic activity of the synthesized thiazole and thiadiazole derivatives was screened against four human cancer cell lines and showed promising results. Thiazolidin-4-one compound 5d showed the strongest cytotoxic effects on hepatocellular carcinoma (IC50 = 8.80 ± 0.31 μg/mL), mammary gland breast cancer (IC50 = 7.22 ± 0.65 μg/mL) and colorectal carcinoma (IC50 = 9.35 ± 0.61 μg/mL) cell lines.

In silico study to identify novel potential thiadiazole-based molecules as anti-Covid-19 candidates by hierarchical virtual screening and molecular dynamics simulations

In the present study, a new category of 1,3,4-thiadiazoles was developed by submitting methyl 2-(4-hydroxy-3-methoxybenzylidene) hydrazine-1-carbodithioate to react with the appropriate hydrazonoyl halides in presence of few drops of diisopropyl ethyl amine. The chemical structures of the newly synthesized derivatives were inferred by means of their micro-analytical and spectral data. Utilizing combined molecular docking and molecular dynamics techniques, the binding affinities and features of the synthesized compounds were evaluated against four SARS-CoV-2 target enzymes, namely, main protease (M^pro), papain-like protease (PL^pro), RNA-dependent RNA polymerase (RdRp), and receptor-binding domain (RBD) of the spike protein. Compound 7 demonstrated promising binding affinities with the target enzymes M^pro, PL^pro, RdRp, and RBD with docking scores of −11.4, −9.4, −8.2, and −6.8 kcal/mol, respectively. In addition, compound 7 exhibited MM-GBSA//100 ns MD docking score of −35.9 kcal/mol against M^pro. Structural and energetic analyses revealed the stability of the 7-M^pro complex over 100 ns MD simulations. In addition, compound 7 obeyed Lipinski’s rule of five, as it has acceptable absorption, distribution, and oral bioavailability inside the body. Therefore, compound 7 is considered as a promising starting point for designing potential therapeutic agents against Covid-19.

Novel Thiadiazole-Based Molecules as Promising Inhibitors of Black Fungi and Pathogenic Bacteria: In Vitro Antimicrobial Evaluation and Molecular Docking Studies

Novel 1,3,4-thiadiazole derivatives were synthesized through the reaction of methyl 2-(4-hydroxy-3-methoxybenzylidene) hydrazine-1-carbodithioate and the appropriate hydrazonoyl halides in the presence of a few drops of diisopropylethylamine. The chemical structure of the newly fabricated compounds was inferred from their microanalytical and spectral data. With the increase in microbial diseases, fungi remain a devastating threat to human health because of the resistance of microorganisms to antifungal drugs. COVID-19-associated pulmonary aspergillosis (CAPA) and COVID-19-associated mucormycosis (CAM) have higher mortality rates in many populations. The present study aimed to find new antifungal agents using the disc diffusion method, and minimal inhibitory concentration (MIC) values were estimated by the microdilution assay. An in vitro experiment of six synthesized chemical compounds exhibited antifungal activity against Rhizopus oryzae; compounds with an imidazole moiety, such as the compound 7, were documented to have energetic antibacterial, antifungal properties. As a result of these findings, this research suggests that the synthesized compounds could be an excellent choice for controlling black fungus diseases. Furthermore, a molecular docking study was achieved on the synthesized compounds, of which compounds 2, 6, and 7 showed the best interactions with the selected protein targets.