Review on the use of Molecular Docking as the First Line Tool in Drug Discovery and Development

Real-Time Bacterial Monitoring and Drug Screening Using the Interdigitated Wave-Shaped Biosensor (IWE), Combined with FEM and Molecular Docking Studies

Rapid and accurate detection of bacteria in water, food, and air is essential for protecting public health, especially amid rising antimicrobial resistance and outbreaks. Traditional detection methods, while reliable, are time-consuming, resource-intensive, and unsuitable for real-time monitoring. Similarly, antibiotic efficacy assessment requires laborious culturing, delaying treatment. This study presents an interdigitated wave-shaped electrode (IWE) capacitance biosensor for real-time bacterial monitoring and drug evaluation. The IWE, optimized via COMSOL simulations addresses edge effects and enhances electric field uniformity and capacitance sensitivity. Simulated capacitance in PBS (5.21 × 10-7 F at 1 Hz) closely matched the experimental value (3.19 × 10-7 F at 1 Hz), validating the optimized IWE design. Integrated with a 16-channel multiplexer, the biosensor enabled high-throughput, real-time detection of Staphylococcus aureus, Bacillus cereus, and Escherichia coli over a range of 10 to 104 CFU/mL, with a detection limit of 10 CFU/mL. Molecular docking simulations were employed to assess antibiotics, which were subsequently tested through real-time capacitance measurements. A decrease in the capacitance indicated effective bacterial inhibition at concentrations exceeding the minimum inhibitory concentration. Results were further validated through disk diffusion assays and scanning electron microscopy, confirming the accuracy. This integrated approach demonstrates the biosensor's potential for real-time pathogen detection and antimicrobial susceptibility assessment.

Enzyme immobilization with plant-based polysaccharides through complex coacervation

Plant-based polysaccharides (PSs) were used to immobilize phytase in a coacervate system. Molecular docking predicted the intermolecular interactions and conformations between the phytase and the polysaccharide and correlated them to the activity recovery of phytase in the coacervate complex. PSs with two different functional groups, sulfate (iota (IC), lambda (LC), and kappa (KC) carrageenan) and carboxylate (low methoxyl pectin (LMP) and sodium alginate (SA)) were investigated. The optimized conditions for coacervation and activity recovery were pH 4 with a phytase-to-polysaccharide volume ratio of 12:1. Zeta potential measurements, FTIR spectroscopy, and molecular docking confirmed that electrostatic interactions and hydrogen bonding were the main driving forces for coacervate formation. Coacervate complexes of phytase formed with LMP, SA, or KC showed a high activity retention after immobilization, with approximately 30% yield of complex and 75% immobilization efficiency of the phytase. The lower enzyme activity retention observed for IC and LC complexes is attributed to these PSs binding to the enzyme's active site. Overall, this work contributes to the body of knowledge about intermolecular interactions between phytase and polysaccharides and can serve as a guide to formulating stable, functional ingredients for a plant-based diet.

Exploring anticancer potential of betanin in DMBA-induced oral squamous cell carcinoma: an in silico and experimental study

In addition to being able to fight cancer, betanin (BTN) has amazing natural antioxidant and peroxy-radical scavenging properties. 7,12-Dimethylbenz[a]anthracene (DMBA) can impair the activities of enzymes accountable for breaking down xenobiotics and can also cause lipid peroxidation. The study's goal was to find out if betanin could protect against these problems. We determined 100% tumor incidence, abnormal tumor volume, inclined tumor burden, and deduced body weight in DMBA-induced hamsters. We observed diminished lipid peroxidation and enzymatic and nonenzymatic antioxidant activities in DMBA-induced hamsters. The histological study showed that the hamster that receives only DMBA undergoes hyperkeratosis, epithelial hyperplasia, dysplasia, and well-differentiated oral squamous cell carcinoma (OSCC). The hamsters received three different dosages of BTN (10, 20, and 40 mg/kg b.w.) via intragastric intubation for 14 weeks, on alternate days of DMBA painting. The levels of antioxidants, xenobiotic enzymes, and lipid peroxidation (LPO) were significantly restored and inhibited tumor development in a dose-dependent manner. The molecular docking study found high levels of binding affinity in Bax (PDB ID: 2K7W), Caspase-3 (PDB ID: 4JJ8), Caspase-9 (PDB ID: 2AR9), PI3K (PDB ID: 5XGI), AKT (PDB ID: 6BUU), p53 (PDB ID: 1YCS), SMAD-2 (PDB ID: 1DEV), SMAD-4 (PDB ID: 1YGS), SMAD-7 (PDB ID: 2DJY), TGFβ-I (PDB ID: 1PY5), and TGFβ-II (PDB ID: 1M9Z). So, therefore, in vivo and in silico studies were providing prominent anticancer activity of betanin against DMBA-induced oral cancer.

Novel drug design and repurposing: An opportunity to improve translational research in cardiovascular diseases?

Drug repurposing is defined as the use of approved therapeutic drugs for indications different from those for which they were originally designed. Repositioning diminishes both the time and cost for drug development by omitting the discovery stage, the analysis of absorption, distribution, metabolism, and excretion routes, as well as the studies of the biochemical and physiological effects of a new compound. Besides, drug repurposing takes advantage of the increased bioinformatics knowledge and availability of big data biology. There are many examples of drugs with repurposed indications evaluated in in vitro studies, and in pharmacological, preclinical, or retrospective clinical analyses. Here, we briefly review some of the experimental strategies and technical advances that may improve translational research in cardiovascular diseases. We also describe exhaustive research from basic science to clinical studies that culminated in the final approval of new drugs and provide examples of successful drug repurposing in the field of cardiology.

Advancing vaccine development against Opisthorchis viverrini: A synergistic integration of omics technologies and advanced computational tools

The liver fluke O. viverrini (Opisthorchis viverrini), a neglected tropical disease (NTD), endemic to the Great Mekong Subregion (GMS), mainly afflicts the northeastern region of Thailand. It is a leading cause of cholangiocarcinoma (CCA) in humans. Presently, the treatment modalities for opisthorchiasis incorporate the use of the antihelminthic drug praziquantel, the rapid occurrence of reinfection, and the looming threat of drug resistance highlight the urgent need for vaccine development. Recent advances in "omics" technologies have proven to be a powerful tool for such studies. Utilizing candidate proteins identified through proteomics and refined via immunoproteomics, reverse vaccinology (RV) offers promising prospects for designing vaccines targeting essential antibody responses to eliminate parasite. Machine learning-based computational tools can predict epitopes of candidate protein/antigens exhibiting high binding affinities for B cells, MHC classes I and II, indicating strong potential for triggering both humoral and cell-mediated immune responses. Subsequently, these vaccine designs can undergo population-specific testing and docking/dynamics studies to assess efficacy and synergistic immunogenicity. Hence, refining proteomics data through immunoinformatics and employing computational tools to generate antigen-specific targets for trials offers a targeted and efficient approach to vaccine development that applies to all domains of parasite infections. In this review, we delve into the strategic antigen selection process using omics modalities for the O. viverrini parasite and propose an innovative framework for vaccine design. We harness omics technologies to revolutionize vaccine development, promising accelerated discoveries and streamlined preclinical and clinical evaluations.

Impacts of Biosynthesized Manganese Dioxide Nanoparticles on Antioxidant Capacity, Hematological Parameters, and Antioxidant Protein Docking in Broilers

Using green tomato extract, a green approach was used to synthesize manganese oxide nanoparticles (MnO2NPs). The synthesis of MnO2NPs was (20.93-36.85 nm) confirmed by energy-dispersive X-ray (EDX), scanning and transmission electron microscopy (SEM and TEM), Fourier transform infrared spectroscopy (FTIR), and UV-visible spectroscopy (UV-vis) analyses. One hundred fifty-day-old Arbor Acres broiler chicks were randomly divided into five groups. The control group received a diet containing 60 mg Mn/kg (100% NRC broiler recommendation). The other four groups received different levels of Mn from both bulk MnO2 and green synthesized MnO2NPs, ranging from 66 to 72 mg/kg (110% and 120% of the standard level). Each group comprised 30 birds, in three replicates of 10 birds each. Generally, the study's results indicate that incorporating MnO2NPs as a feed additive had no negative effects on broiler chick growth, antioxidant status, and overall physiological responses. The addition of MnO2NPs, whether at 66 or 72 mg/kg, led to enhanced superoxide dismutase (SOD) activity in both serum and liver tissues of the broiler chicks. Notably, the 72 mg MnO2NPs group displayed significantly higher SOD activity compared to the other groups. The study was further justified through docking. High throughput targeted docking was performed for proteins GHS, GST, and SOD with MnO2. SOD showed an effective binding affinity of -2.3 kcal/mol. This research sheds light on the potential of MnO2NPs as a safe and effective feed additive for broiler chicks. Further studies are required to explore the underlying mechanisms and long-term effects of incorporating MnO2NPs into broiler feed, to optimize broiler production and promote its welfare.

Docking Studies on Biomolecules from Marine Microalga Skeletonema costatum Against Hemolysin Protein of Bioluminescence Disease-Causing Vibrio harveyi

Grow-out and hatchery units of shrimps are being impacted by disease-causing bacterial pathogens and predominantly marine Vibrios. The use of chemicals for governing bacterial pathogens in the aquaculture practices is developing resistance to bacteria. Henceforth, the application of bio-therapeutic agents from marine resources for controlling pathogens is most vital to be considered. Molecular docking is computer-assisted drug design tool to detect and counteract for drug-receptor interaction for known target protein of diseases. Therefore, an effort was made with the extract of the marine micro alga Skeletonema costatum against hemolysin protein of pathogenic bacteria Vibrio harveyi. The extract of S. costatum was tested against growth and virulence produced by V. harveyi during larviculture of Penaeus monodon. The extract was analyzed for phyto-constituents through GC-MS and used them as ligand molecule in docking. S. costatum extract at 200 µg mL-1 was found to decrease 35.20% of cumulative percentage mortality (CPM) in postlarvae of P. monodon against V. harveyi infections. The biomolecule Docasane, an alkane from the extract of S. costatum, exposed highest binding interaction than other compounds during docking analysis. The level of significance (P < 0.05) was found in CPM, growth, and virulence factors of V. harveyi studies. Thus, the present finding predicts that extract of S. costatum containing biomolecules can be recommended for use in the shrimp culture-based grow-out and hatchery units for eliminating bioluminescent V. harveyi.