Molecular dynamics simulation, synthesis and topoisomerase inhibitory actions of vanillin derivatives: a systematic computational structural integument

Design and synthesis of tetrahydrochromeno[3,4-e]isoindole-1,3(2H,3aH)-dione derivatives via the Diels-Alder reaction: molecular docking, antibacterial activity, ADMET analysis and photophysical properties

A series of fused tetrahydrochromeno[3,4-e]isoindole-1,3(2H,3aH)-dione derivatives was successfully synthesized via the Diels-Alder reaction. Molecular docking studies were conducted to understand the interaction modes between the synthesized hybrid compounds and the receptor bacterial strains of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). Notably, the in silico results demonstrated that compound 19l (-8.7 kcal mol-1 with E. coli and -8.4 kcal mol-1 with S. aureus) and 19p (-8.7 kcal mol-1 with E. coli and -9.1 kcal mol-1 with S. aureus) exhibited good binding values. Additionally, the in vitro antibacterial studies showed that compounds 19l and 19p demonstrated excellent antibacterial activities, with a zone of inhibition (ZI) of 17 mm and a minimum inhibitory concentration (MIC) of 12.5 μg mL-1 against both E. coli and S. aureus, which were comparable to the performance of the standard antibiotic ciprofloxacin. Further, the bioavailability was assessed through virtual ADMET parameters, which suggested that most of the compounds possessed favorable pharmacokinetic profiles. To further enrich the study, photophysical properties of all the synthesized molecules were also examined using UV-visible and fluorescent spectroscopies.

Molecular Insights on Coffee Components as Chemical Antioxidants

Coffee is not only a delicious beverage but also an important dietary source of natural antioxidants. We live in a world where it is impossible to avoid pollution, stress, food additives, radiation, and other sources of oxidants that eventually lead to severe health disorders. Fortunately, there are chemicals in our diet that counteract the hazards posed by the reactive species that trigger oxidative stress. They are usually referred to as antioxidants; some of them can be versatile compounds that exert such a role in many ways. This review summarizes, from a chemical point of view, the antioxidant effects of relevant molecules found in coffee. Their mechanisms of action, trends in activity, and the influence of media and pH in aqueous solutions, are analyzed. Structure-activity relationships are discussed, and the protective roles of these compounds are examined. A particular section is devoted to derivatives of some coffee components, and another one to their bioactivity. The data used in the analysis come from theoretical and computational protocols, which have been proven to be very useful in this context. Hopefully, the information provided here will pro-mote further investigations into the amazing chemistry contained in our morning coffee cup.   Resumen. El café no solo es una bebida deliciosa, sino también una importante fuente dietética de antioxidantes naturales. Vivimos en un mundo donde es imposible evitar la contaminación, el estrés, los aditivos alimentarios, la radiación y otras fuentes de oxidantes que eventualmente conducen a trastornos de salud graves. Afortunadamente, existen sustancias químicas en nuestra dieta que contrarrestan los peligros planteados por las especies reactivas que desencadenan el estrés oxidativo. Por lo general, se les denomina antioxidantes; algunos de ellos pueden ser compuestos versátiles que ejercen dicho papel de muchas maneras. Este artículo de revisión resume, desde un punto de vista químico, los efectos antioxidantes de moléculas relevantes encontradas en el café. Se analizan sus mecanismos de acción, tendencias en la actividad y la influencia del medio y el pH en soluciones acuosas. Se discuten las relaciones estructura-actividad, y se examinan los roles protectores de estos compuestos. Se dedica una sección particular a los derivados de algunos componentes del café, y otra a su bioactividad. Los datos utilizados en el análisis provienen de protocolos teóricos y computacionales, que han demostrado ser muy útiles en este contexto. Se espera que la información proporcionada aquí promueva investigaciones futuras sobre la química contenida en nuestra taza de café matutina.

Pharmacokinetic and molecular docking studies to pyrimidine drug using Mn3O4 nanoparticles to explore potential anti-Alzheimer activity

Alzheimer disease (AD) is the cause of dementia and accounts for 60-80% cases. Tumor Necrosis Factor-alpha (TNF-α) is a multifunctional cytokine that provides resistance to infections, inflammation, and cancer. It developed as a prospective therapeutic target against multiple autoimmune and inflammatory disorders. Cholinergic insufficiency is linked to Alzheimer's disease, and several cholinesterase inhibitors have been created to treat it, including naturally produced inhibitors, synthetic analogs, and hybrids. In the current study, we tried to prepared compounds may also support the discovery and development of novel therapeutic and preventative drugs for Alzheimer's using manganese tetroxide nanoparticles (Mn3O4-NPs) as a catalyst to generate compounds with excellent reaction conditions. The Biginelli synthesis yields 4-(4-cyanophenyl)-6-oxo-2-thioxohexahydropyrimidine-5-carbonitrile when the 4-cyanobenzaldehyde, ethyl cyanoacetate, and thiourea were coupled with Mn3O4-NPs to produce compound 1. This multi-component method is non-toxic, safe, and environmentally friendly. The new approach reduced the amount of chemicals used and preserved time. Compound 1 underwent reactions with methyl iodide, acrylonitrile, chloroacetone, ethyl chloroacetate, and chloroacetic acid/benzaldehyde, each of the synthetized compounds was docked with TNF-α converting enzyme. These compounds may also support the discovery and development of novel therapeutic and preventative drugs for Alzheimer's disease. The majority of the produced compounds demonstrated pharmacokinetic features, making them potentially attractive therapeutic candidates for Alzheimer's disease treatment.

From desert flora to cancer therapy: systematic exploration of multi-pathway mechanisms using network pharmacology and molecular modeling approaches

Ovarian cancer, often labeled a "silent killer," remains one of the most compelling and challenging areas of cancer research. In 2019 alone, a staggering 222,240 new cases of ovarian cancer were reported, with nearly 14,170 lives tragically lost to this relentless disease. The absence of effective diagnostic methods, increased resistance to chemotherapy, and the heterogeneous nature of ovarian cancer collectively contribute to the unfavorable prognosis observed in the majority of cases. Thus, there is a pressing need to explore therapeutic interventions that offer superior efficacy and safety, thereby enhancing the survival prospects for ovarian cancer patients. Recognizing this potential, our research synergizes bioinformatics with a network pharmacology approach to investigate the underlying molecular interactions of Saudi Arabian flora (Onopordum heteracanthum, Acacia ehrenbergiana, Osteospermum vaillantii, Cyperus rotundus, Carissa carandas, Carissa spinarum, and Camellia sinensis) in ovarian cancer treatment. At first, phytoconstituents of indigenous flora and their associated gene targets, particularly those pertinent to ovarian cancer, were obtained from open-access databases. Later, the shared targets of plants and diseases were compared to identify common targets. A protein-protein interaction (PPI) network of predicted targets was then constructed for the identification of key genes having the highest degree of connectivity among networks. Following that, a compound-target protein-pathway network was constructed, which uncovered that, namely, hispidulin, stigmasterol, ascorbic acid, octopamine, cyperene, kaempferol, pungenin, citric acid, d-tartaric acid, beta-sitosterol, (-)-epicatechin gallate, and (+)-catechin demonstrably influence cell proliferation and growth by impacting the AKT1 and VEGFA proteins. Molecular docking, complemented by a 20-ns molecular dynamic (MD) simulation, was used, and the binding affinity of the compound was further validated. Molecular docking, complemented by a 20-ns MD simulation, confirmed the binding affinity of these compounds. Specifically, for AKT1, ascorbic acid showed a docking score of -11.1227 kcal/mol, interacting with residues Ser A:240, Leu A:239, Arg A:243, Arg C:2, and Glu A:341. For VEGFA, hispidulin exhibited a docking score of -17.3714 kcal/mol, interacting with Asn A:158, Val A:190, Gln B:160, Ser A:179, and Ser B:176. To sum up, both a theoretical and empirical framework were established by this study, directing more comprehensive research and laying out a roadmap for the potential utilization of active compounds in the formulation of anti-cancer treatments.

Computational study on Schiff base derived salicylaldehyde and furfuraldehyde derivatives as potent anti-tubercular agents: prospect to dihydropteroate synthase inhibitors

Nowadays, bacterial multidrug resistance has become a commonplace problem in clinics due to several intrinsic factors mediated through resistance to antibacterials obtained via bacterial consortia and extrinsic factors, such as non-uniform antibacterial policy and migration of resistant bacteria through human and other routes. The development of newer, effective anti-mycobacterial candidate(s) is coveted by clinics. Hybrid molecules would be comparatively more emulating against invasive bacterial strains; nevertheless, newer antibiotics are continually added. Herein, designing and developments of two series of Schiff-based salicylaldehyde S1-S7 and furfuraldehyde F1-F7 molecules individually bearing sulfonamide group are described; and those were synthesized and their structures by spectral characterization were confirmed. Concomitantly, molecule dynamic simulations of all atoms had been performed to fathom the mechanism of the action with these leading complexes. These data imply that the synthesized Schiff-based salicylaldehyde hybrids would be promising anti-tubercular compounds, which further need potent pharmacological evaluations.Communicated by Ramaswamy H. Sarma.

An immunoinformatic approach towards development of a potent and effective multi-epitope vaccine against monkeypox virus (MPXV)

Monkeypox is a viral zoonotic disease, often transmitted to humans from animals. While the whole world is haggling with the COVID-19 pandemic, the emergence of the monkeypox virus (MPXV) arose as a new challenge to mankind. Till date, numerous cases related to the MPXV have been reported in several countries across the globe, but, its momentary distribution in the current time has left everyone in fright with increasing mortality and limited clinically approved treatments. Therefore, it is of immense importance to develop a potent and highly effective vaccine capable of inducing desired immunogenic responses against the highly contagious MPXV. Herein, using various immunoinformatic and computational biology tools, we made an attempt to develop a multi-epitope vaccine construct against the MPXV which is antigenic, non-allergen and non-toxic in nature and capable of exhibiting immunogenic behavior. The sequence of vaccine construct was designed using the proposed 4 MHC-I, 3 MHC-II and 4 B-cell epitopes linked with suitable adjuvant and linkers. The modeled structure of the vaccine construct was used to assess its interaction with the Toll-like Receptor 4 (TLR4) using ClusPro and HADDOCK. All-atoms molecular dynamics simulation of the MPXV vaccine construct-TLR4 complex followed by a high level of gene expression of the construct within the bacterial system affirmed its stability along with induction of immunogenic response within the host cell. Altogether, our immunoinformatic approach aid in the development of a stable chimeric vaccine construct against MPXV and needs further experimental validation for its immunological relevance and usefulness as a vaccine candidate.Communicated by Ramaswamy H. Sarma.

Structure-Based In Silico Investigation of Agonists for Proteins Involved in Breast Cancer

Cancer is recognized as one of the main causes of mortality worldwide by the World Health Organization. The high cost of currently available cancer therapy and certain limitations of current treatment make it necessary to search for novel, cost-effective, and efficient methods of cancer treatment. Therefore, in the current investigation, sixty-two compounds from five medicinal plants (Tinospora cordifolia, Ocimum tenuiflorum, Podophyllum hexandrum, Andrographis paniculata, and Beta vulgaris) and two proteins that are associated with breast cancer, i.e., HER4/ErbB4 kinase and ERα were selected. Selected compounds were screened using Lipinski's rule, which resulted in eighteen molecules being ruled out. The remaining forty-four compounds were then taken forward for docking studies followed by molecular dynamics studies of the best screened complexes. Results showed that isocolumbin, isopropylideneandrographolide, and 14-acetylandrographolide were potential lead compounds against the selected breast cancer receptors. Furthermore, in vitro studies are required to confirm the efficacy of the lead compounds.