Virtual screening, ADME study, and molecular dynamic simulation of chalcone and flavone derivatives as 5-Lipoxygenase (5-LO) inhibitor

Design, Synthesis, Biocompatibility, molecular docking and molecular dynamics studies of novel Benzo[b]thiophene-2-carbaldehyde derivatives targeting human IgM Fc Domains

In this study, three novel derivatives of benzo[b]thiophene-2-carbaldehyde (BTAP1, BTAP2, and BTAP3) were successfully synthesized and comprehensively characterized using spectroscopic techniques including FTIR, UV-VIS, 1HNMR, and 13CNMR. Thermal analysis through TGA and DTA demonstrated remarkable thermal stability with a maximum threshold at 270 °C. Spectroscopic investigations revealed π → π* transitions in all compounds, attributed to the conjugated system comprising benzothiophene rings connected to bromophenyl/ aminophenyl/phenol rings via α, β-unsaturated ketone bridges. Quantum chemical calculations indicated varying molecular stabilities, with BTAP3 exhibiting the highest energy gap (ΔE = 3.59 eV) and global hardness (η = 1.8), while BTAP2 showed enhanced reactivity potential with the lowest energy gap (ΔE = 3.22 eV) and highest global softness (S = 0.62). Virtual screening and molecular docking studies identified protein target 4JVW as the most favorable interaction partner, with binding energies of -8.0, -7.5, and -7.6 kcal/mol for BTAP1, BTAP2, and BTAP3, respectively. Molecular dynamics simulations revealed stable protein-ligand complexes, characterized by minimal RMSD and RMSF fluctuations, optimal Rg values, sustained hydrogen bonding networks and favorable solvent accessible surface area values. MMGBSA analysis highlighted the significance of Coulombic, van der Waals, and lipophilic interactions in complex stabilization. Toxicological evaluations demonstrated favorable safety profiles with minimal ocular and dermal irritation potential compared to allicin, coupled with low lethal dose values. These findings collectively position these novel compounds as promising candidates for pharmaceutical applications, warranting further investigation into their therapeutic potential.

Scaffold-Hopping Strategies in Aurone Optimization: A Comprehensive Review of Synthetic Procedures and Biological Activities of Nitrogen and Sulfur Analogues

Aurones, particular polyphenolic compounds belonging to the class of minor flavonoids and overlooked for a long time, have gained significative attention in medicinal chemistry in recent years. Indeed, considering their unique and outstanding biological properties, they stand out as an intriguing reservoir of new potential lead compounds in the drug discovery context. Nevertheless, several physicochemical, pharmacokinetic, and pharmacodynamic (P3) issues hinder their progression in more advanced phases of the drug discovery pipeline, making lead optimization campaigns necessary. In this context, scaffold hopping has proven to be a valuable approach in the optimization of natural products. This review provides a comprehensive and updated picture of the scaffold-hopping approaches directed at the optimization of natural and synthetic aurones. In the literature analysis, a particular focus is given to nitrogen and sulfur analogues. For each class presented, general synthetic procedures are summarized, highlighting the key advantages and potential issues. Furthermore, the biological activities of the most representative scaffold-hopped compounds are presented, emphasizing the improvements achieved and the potential for further optimization compared to the aurone class.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes

The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography-mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product-enzyme interaction.Communicated by Ramaswamy H. Sarma.

Identification of a Prenyl Chalcone as a Competitive Lipoxygenase Inhibitor: Screening, Biochemical Evaluation and Molecular Modeling Studies

Cyclooxygenase (COX) and lipoxygenase (LOX) are key targets for the development of new anti-inflammatory agents. LOX, which is involved in the biosynthesis of mediators in inflammation and allergic reactions, was selected for a biochemical screening campaign to identify LOX inhibitors by employing the main natural product library of Brazilian biodiversity. Two prenyl chalcones were identified as potent inhibitors of LOX-1 in the screening. The most active compound, (E)-2-O-farnesyl chalcone, decreased the rate of oxygen consumption to an extent similar to that of the positive control, nordihydroguaiaretic acid. Additionally, studies on the mechanism of the action indicated that (E)-2-O-farnesyl chalcone is a competitive LOX-1 inhibitor. Molecular modeling studies indicated the importance of the prenyl moieties for the binding of the inhibitors to the LOX binding site, which is related to their pharmacological properties.

Synthesis and characterization of chitosan silver nanoparticle decorated with benzodioxane coupled piperazine as an effective anti-biofilm agent against MRSA: A validation of molecular docking and dynamics

Biomaterial research has improved the delivery and efficacy of drugs over a wide range of pharmaceutical applications. The objective of this study was to synthesize benzodioxane coupled piperazine decorated chitosan silver nanoparticle (Bcp*C@AgNPs) against methicillin-resistant Staphylococcus aureus (MRSA) and to assess the nanoparticle as an effective candidate for antibacterial and anti-biofilm care. Antibacterial activity of the compound was examined and minimum inhibitory concentration (MIC) was observed at (10.21 ± 0.03 ZOI) a concentration of 200 μg/mL. The Bcp*C@AgNPs interferes with surface adherence of MRSA, suggesting an anti-biofilm distinctive property that is verified for the first time by confocal laser microscopic studies. By ADMET studies the absorption, distribution, metabolism, excretion and toxicity of the compound was examined. The interaction solidity and the stability of the compound when surrounded by water molecules were analyzed by docking and dynamic simulation analysis. The myoblast cell line (L6) was considered for toxicity study and was observed that the compound exhibited less toxic effect. This current research highlights the biocidal efficiency of Bcp*C@AgNPs with their bactericidal and anti-biofilm properties over potential interesting clinical trial targets in future.

4-acetamido-3-nitrobenzoic acid - structural, quantum chemical studies, ADMET and molecular docking studies of SARS-CoV2

In December 2019, a new type of SARS corona virus emerged from China and caused a globally pandemic corona virus disease (COVID-19). This highly infectious virus has been named as SARS-CoV-2 by the International Committee of the Taxonomy of Viruses. It has severely affected a large population and economy worldwide. Globally various scientific communities have been involved in studying this newly emerged virus and is lifecycle. Multiple diverse studies are in progress to design novel therapeutic agents, in which understanding of interactions between the target and drug ligand is a significant key for this challenge. Structures of proteins involved in the life cycle of the virus have been revealed in RCSB PDB by researchers. In this study, we employed molecular docking study of 4-Acetamido-3-nitrobenzoic acid (ANBA) with corona virus proteins (spike protein, spike binding domain with ACE2 receptor and Main protease, RNA-dependent RNA polymerase). Single crystal X-ray analysis and density functional theory calculations were carried out for ANBA to explore the structural and chemical-reactive parameters. Intermolecular interactions which are involved in the ligand-protein binding process are validated by Hirshfeld surface analysis. To study the behaviour of ANBA in a living organism and to calculate the physicochemical parameters, ADMET analysis was done using SwissADME and Osiris data warrior tools. Further, Toxicity of ANBA was predicted using pkCSM online software. Based on the molecular docking analysis, we introduce here a potent drug molecule that binds to the COVID-19 proteins.Communicated by Ramaswamy H. Sarma.

Screening possible drug molecules for Covid-19. The example of vanadium (III/IV/V) complex molecules with computational chemistry and molecular docking

We are still facing a Covid-19 pandemic these days and after the aggressively infection control measures taken by the governments in the whole world, there is a need of a rapid pharmaceutical solution in order to control this crisis. The computer aided chemistry and molecular docking is a rapid tool for drug screening and investigation. Moreover, more metal-based drugs are tested daily by research institutes for their antiviral activity. Here, we make use of theoretical studies on previously published biological active complex molecules of vanadium as an example of evaluating possible drug candidates before entering the laboratory. We used DFT calculation studies for structural elucidation and optimization of the molecules and molecular docking studies on several Covid-19 related proteins. Our findings suggest that drug discovery should always be computer -aided. Additionally, it is found that Vtocdea and VXn molecules are seem to be good candidates for further studies as antiviral agents.

Oral Bioavailability Comparison of Artemisinin, Deoxyartemisinin, and 10-Deoxoartemisinin Based on Computer Simulations and Pharmacokinetics in Rats

Deoxyartemisinin, a compound separated from Artemisinin annua L., shows anti-inflammatory and antiulcer activities. 10-Deoxoartemisinin is a novel compound with a strong antimalarial effect derivatized from artemisinin. Compared to the famous antimalarial natural compound artemisinin, deoxyartemisinin lacks the peroxide bridge structure, while 10-deoxoartemisinin remains this special peroxide bridge group but loses the 10-position keto group. To clarify their pharmacological differences, the absorption, distribution, metabolism, excretion (ADME) properties of artemisinin, deoxyartemisinin, and 10-deoxoartemisinin were first predicted using QikProp software. Also, their pharmacokinetic behaviors in rats were further evaluated by a rapid, sensitive, and specific liquid chromatography-tandem mass spectrometry (LC-MS/MS) method after oral and intravenous administration of each compound, in which deoxyartemisinin and 10-deoxoartemisinin were first evaluated for their pharmacokinetics. All parameters about ADME properties calculated by software met the criteria and the ADME performance order was 10-deoxoartemisinin > deoxyartemisinin > artemisinin. The oral bioavailability of artemisinin was calculated to be 12.2 ± 0.832%, which was about 7 times higher than that of deoxyartemisinin (1.60 ± 0.317%). For 10-deoxoartemisinin, its bioavailability (26.1 ± 7.04%) was superior to artemisinin at a degree of more than twice. Considering their chemical structures, losing the peroxide bridge might decrease the absorption rate of deoxyartemisinin in the gastrointestinal tract, while retaining the peroxide bridge but losing the 10-position ketone might improve the bioavailability of 10-deoxoartemisinin.