Design, synthesis of pyridine coupled pyrimidinone/pyrimidinthione as anti-MRSA agent: Validation by molecular docking and dynamics simulation

Methicillin Resistant Staphylococcus aureus (MRSA) is a major cause of severe hospital and infections acquired by the population and related morbidity and mortality. In this unique situation, there is a need of dynamic strong drug candidates to control MRSA diseases. Thus, the present work focuses on the synthesis and characterization of pyrimidinones and pyrimidinthiones coupled pyridine derivatives as anti-MRSA agent. The synthesized compounds were characterized by different spectroscopic techniques and evaluated against MRSA strain. Among them, 4e and 4 g possessed better antibacterial activity with MIC values of 10 μg and 8 μg respectively. The key determinant of the wide range beta-lactam resistance in MRSA strains is the Penicillin-Binding Protein 2a (PBP2a) but the gene encodes PBP2a which has a low affinity towards β-lactam antibiotics. Because of this, the present investigation focused on the mechanism of PBP2a protein binding studies by in-silico studies. The synthesized compounds showed very good interactions with PBP2A compared with standard drug Vancomycin, among them compound 4 g showed better interaction with the binding score of -9.8 kcal/mol. Antibacterial activity was validated with molecular docking and molecular dynamic simulation. Simulation results revealed that protein-ligand interactions of 4 g compound stably sustained up to 20,000ps.Communicated by Ramaswamy H. Sarma.

Unprecedented 2D GNR-CoB nanocomposite for detection and degradation of malachite green - A computational prediction of degradation pathway and toxicity

In the present work, we have synthesized a novel 2D GNR-CoB composite and was applied it for electrochemical sensing and photocatalytic degradation of the malachite green (MG). The physicochemical properties of the 2D GNR-CoB were analyzed using X-ray diffraction, Transmission electron microscopy, Energy dispersive X-ray diffraction which depicts the morphological and crystalline nature of the prepared composite. The pencil graphite electrode modified with 2D GNR-CoB composite showed excellent electrochemical response for MG detection with a LOD of 1.92 nM, linear range of 25-350 nM with a high sensitivity of 1.714 μA μM^-1 cm^-2. Besides, the 2D GNR-CoB modified PGE exhibited good recovery for the detection of MG in real samples such as green peas and lady's fingers. Furthermore, the 2D GNR-CoB modified electrode showed excellent photocatalytic activity for the degradation of MG. It suggests that under visible light, GNR-CoB material generates superoxide (·O₂^-) and hydroxyl (·OH) radicals for MG degradation. The prepared composite showed an efficiency of 91.28% towards the degradation of MG. Based on the experimental analysis and density functional theory calculations, a photocatalytic degradation mechanism pathway for MG is proposed. A quantitative structure-activity relationship study was used to examine the toxicity of the degradation intermediates.

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.

Post-synthetic modification of supramolecular assemblies of β-diketonato Cu(ii) complexes: comparing and contrasting the molecular topology by crystal structure and quantum computational studies

Solvent-induced structural transformations on the metal coordination sphere in homoleptic (1 and 2) and heteroleptic (3 and 4) Cu(ii) complexes were analyzed and investigated by crystallographic and quantum computational studies.

Solvent induced mononuclear and dinuclear mixed ligand Cu(ii) complex: structural diversity, supramolecular packing polymorphism and molecular docking studies

Phenolate bridged dinuclear and solvent induced mononuclear supramolecular isomers of Cu(ii) complex have been reported to explore the structural diversity and their antibacterial activity supported by molecular docking studies.

A novel copper (II) PAmPiCaT complex (cPAmPiCaTc) as a biologically potent candidate: A contraption evidence against methicillin-resistant Staphylococcus aureus (MRSA) and a molecular docking proof

Increasing in the alarm against the resistant bacteria due to the failure of antibiotics, thereby the need of more efficiency/potent molecule to treat infections. In the present investigation, series of piperazine derivatives 5(a-l) compounds were synthesized and they were characterised by different spectral techniques such as ¹H NMR, ¹³C NMR, IR and LCMS. A novel copper complex (cPAmPiCaTc) was developed for the first time by using potent analog 5e and characterized by IR and LCMS. The cPAmPiCaTc evaluated for antibacterial activity and showed excellent antimicrobial effect (12 ± 0.08 mm, ZOI) at MIC 20 µg/mL against MRSA compared to standard antibiotics streptomycin and bacitracin at MIC 10 µg/mL. The results show promising anti-staphylococcal action against MRSA which confirmed by membrane damage, bioelectrochemistry, gene regulation (SarA and DHFR), and in silico molecular docking studies. Further, the cPAmPiCaTc also showed excellent blood compatibility and this result pave the way for interesting metallodrug therapeutics in future against MRSA infections.

New approach to address antibiotic resistance: Miss loading of functional membrane microdomains (FMM) of methicillin-resistant Staphylococcus aureus (MRSA)

The synthesized potent piperazine analog ChDiPiCa was characterised by various spectroscopic techniques and for the first time evaluated functional membrane microdomain (FMM) disassembly in methicillin-resistant Staphylococcus aureus (MRSA). The ChDiPiCa showed excellent in vitro biocidal activity against MRSA at 26 μg/mL compared to the antibiotic streptomycin and bacitracin 14 μg/mL and 13 μg/mL at 10 μg concentration respectively. The membrane damaging property was confirmed by the SEM analysis. Further, we addressed the new approach for the first time to overcome antibiotic resistance of MRSA through membrane microdomain miss loading to lipids. By which, the ChDiPiCa confirms the significant activity in miss loading of FMM of MRSA which is validated by the fatty acid profile and lipid analysis. The result shows that, altered saturated (Lauric acid and Myristic acid), mono unsaturated (Oleic acid), and poly unsaturated (Linoleic acid and Linolenic acid) fatty acids and hypothesises, altered the membrane functional lipids. For the better understanding of miss loading of FMM by the ChDiPiCa, the in-silico molecular docking studies was analyzed and confirmed the predicted role. This suggests the way to develop ChDiPiCa in medicinal chemistry as anti-MRSA candidates and also this report opens up new window to treat microbial pathogens and infections.

Development of piperazine-1-carbothioamide chitosan silver nanoparticles (P1C-Tit*CAgNPs) as a promising anti-inflammatory candidate: a molecular docking validation

Natural products are important leads in drug discovery. The search for effective plant-derived agents or their synthetic analogues has continued to be of interest to biologists and chemists for a long time. Herein, we have synthesized a novel compound, P1C, and P1C-Tit*CAgNPs from chitosan; P1C is a precursor and an anti-inflammatory candidate, which has been validated by molecular docking studies. The synthesized P1C-Tit*CAgNPs showed monodisperse, spherical, and cationic nature and antioxidant properties, protecting destabilization of the erythrocyte membrane by the azo compound 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH); the involvement of NPs as a protective agent for biomolecules, such as DNA and protein, followed by the treatment of NPs with AAPH was confirmed. The inhibition of cellular damage and leakage of cellular inflammatory agents was confirmed by AFM, SEM, TEM, SDS-PAGE, LDH, and PLA2 enzyme inhibition via in vitro studies. The anti-inflammatory property of P1C was further validated by in silico molecular docking studies and showed that, the P1C best pose aligned to PLA2 compared to standard drug. The significant anticancer property of P1C-Tit*CAgNPs was confirmed against MCF7, U373, and C6 cancer cell lines. Thus, the present study highlights the synthesized P1C in P1C-Tit*CAgNPs as a target PLA2-specific anti-inflammatory candidate, and further tuning of small and development-functionalized nanoparticles has a great future in medicine; hence, their clinical applications are warranted.