Journal of Computational Biophysics and Chemistry

This study explores the interactions between hexanal Schiff bases and a B12N12 nanocage, employing density functional theory (DFT) calculations to deepen our understanding of noncovalent bonds. Hexanal, a key component in tea, plays a vital role in prolonging the shelf-life of various plant-based products by inhibiting phospholipase-D. Our research initially focused on synthesizing Schiff bases through the condensation of hexanal with nucleobases and an amino acid. We then conducted a series of DFT calculations, including geometry optimizations, frontier molecular orbital (FMO), natural bond orbital (NBO) and noncovalent interactions (NCI) assays, using Gaussian 16 and ORCA 5.0.2 software packages. This study reveals that hexanal Schiff bases form stable complexes with the B12N12 nanocage, exhibiting notable dative coordinate bonding. The FMO analysis indicates a significant energy gap variation among the complexes, with CSB2 showing the lowest energy gap, hinting at its high reactivity. In the LED assay, CSB2 demonstrates the lowest decomposition energy, highlighting its potential stability. The AIMD simulations provide insights into the electronic motions of these complexes, underscoring their dynamic nature. Our NBO analysis offers a comprehensive view of the electron distribution within these complexes, emphasizing the significance of nitrogen and boron atoms in the bonding process. The NCI assay sheds light on the predominant van der Waals and steric interactions contributing to the stability of the complexes. This investigation provides a detailed account of the NCI between hexanal Schiff bases and the B12N12 nanocage. The findings not only contribute to the field of noncovalent bonding in inorganic-fullerene structures but also open avenues for future applications in material science and molecular engineering.

In this study, we focus on exploring the medicinal potential of Olea Europaea L., a commonly used plant with diverse indigenous medicinal applications. The main aim is to identify promising phytoconstituents from Olea Europaea L. leaves that can act as inhibitors for the PTP-1B target, utilizing an in silico approach. The phytoconstituents were sourced from the IMMPAT database, and molecular docking was employed to assess their binding affinities. The docking results revealed that rutin (−10.05 kcal/mol) and quercetin (−8.28 kcal/mol) displayed the highest binding scores against PTP-1B, outperforming reference compounds. Furthermore, MM-GBSA calculations indicated favorable free binding energy. To ensure stability, 200 ns Molecular Dynamics simulations were conducted on the 2QBS-Rutin complex. The results revealed that the 2QBS-Rutin complex showed stable conformation throughout the simulation, maintaining consistency with RMSD values below 1 Å. This study highlights rutin and quercetin as promising phytoconstituents from Olea Europaea L. leaves, demonstrating potent-binding affinities against PTP-1B inhibitors.

The aim of the study is to design and synthesize thiazolidinone derivatives having therapeutic potential using PABA as a core component. The characterization of thiazolidinones MS1–MS6 was carried out using different spectroscopic techniques before being subjected to DFT studies to calculate various parameters such as HOMO/LUMO energy gaps and global chemical properties. Thiazolidinones MS1–MS6 were screened to evaluate their in vitro enzyme inhibition potential. In addition to experimental work, theoretical approaches were used as supporting components to design the enzyme inhibitors. In-silico ADMET and docking studies were performed to check the therapeutic properties of thiazolidinone derivatives. The enzyme inhibition potential predicted that MS1–MS6 have potential to inhibit AChE and BChE. The highest activity was depicted by MS4 with a percentage inhibition of 81.7 ± 1.1% against AChE. The molecular dynamic simulation was run for MS4 showing a similar activity on enzyme compared to the standard inhibitor. Both experimental and theoretical assessments suggested the therapeutic importance of the thiazolidinone derivatives MS1–MS6. In-depth studies are ongoing to complete therapeutic probing in terms of toxicity and chemical uses.

Alzheimer’s disease (AD) is a common factor contributing to cognitive decline in aged people. The etiology of AD involves several mechanisms, including the breakdown of acetylcholine, the accumulation of amyloid beta, the formation of neurofibrillary tangles and inflammation. Several targets have been discovered in the study that are useful in reducing the cognitive decline associated with AD. By employing network pharmacology, molecular docking and MD simulations, we have ascertained that Roemerine can specifically interact with MAO-A. Network pharmacology identified a set of genes with a higher degree of interactions. MAO-A was identified as the gene with the highest interaction level with 37 other genes. MAO-A gene was interconnected with other top 10 genes with overall higher degrees of interactions. Roemerine molecule showed a binding energy of −5.27 kcal/mol, which was better than the reference ligand found to be −4.43 kcal/mol. MD simulations demonstrated that the average RMSD for Roemerine was 4.67 Å, whereas the average RMSF was 1.06 Å. Conversely, the unbound protein and the reference chemical exhibited average RMSD values of 5.57 Å and 5.74 Å, respectively. In addition, the average RMSF values for them were 1.30 Å and 1.00 Å, respectively. Based on these results, it may be inferred that Roemerine can inhibit MAO-A and potentially be used as a lead for AD.

Ubiquitin-specific protease-7 (USP7) is a potential target for cancer therapy. In this work, the evaluation and design of USP7 inhibitors are conducted employing a comprehensive computational approach. Initially, a large database of compounds undergoes preliminary screening via similarity and pharmacophore analyses. Subsequently, a secondary selection process is executed based on both quantitative structure–activity relationship modeling and molecular docking. The final selection is refined through rescoring treatments via consensus scores and MM/GBSA binding free energy. A total of 138 experimental USP7 inhibitors were collected for the construction of random forest regression models using four different feature selection methods. 17 top experimentally active inhibitors were used as models in similarity searching, and eight representative USP7-ligand binding models were used in pharmacophore screening, performed over a database of 14 million compounds. The rescoring approach applied in this study offers an alternative and beneficial method for the ranking and selection of desired molecules. Based on the molecular scaffolds of the highly active inhibitors, some new derivatives have been designed and received high predicted scores for inhibition.

The primary aim of this investigation is to shed light on potential targets within the main protease Mpro, spike protein of SARS-CoV-2, and Angiotensine converting enzyme 2 (ACE2) for the exploration of novel inhibitors derived from therapeutic natural compounds originating from Atriplex halimus (AH). Many constituents were discerned within AH extracts through comprehensive gas chromatography/mass spectrometry (GC/MS). Notably, compounds, such as oleocanthal and methyl stearate, exhibited promising attributes across various biological activities, including inhibition of key proteins associated with SARS-CoV-2. Furthermore, absorption, distribution, metabolism, excretion, and toxicity (ADMET) settings were evaluated to explore the potential safety and viability of these compounds for pharmaceutical application, affirming their non-interference with human physiology and thus suggesting their suitability for pharmaceutical use. Catechin, epigallocatechin, and methyl stearate were discovered to be the compounds with the highest affinity to the studied protein showing a great potential to be inhibitors to COVID-19. Consequently, this discovery highlights Atriplex halimus as a promising candidate for utilization in combating the virus.

Organic solar cells (OSCs) have made remarkable progress due to developing novel materials and device architectures. Herein, we designed six new non-fullerene acceptors (QM1–QM6) having a quinoxalineimide (QI) as the central-building-block. We aimed to explore the potential of QI-containing structures for developing high-performance acceptors for OSCs. These designed molecules possess a fusion of the QI unit with a thienylthiophene backbone and are equipped with various efficient end-capping groups. Extensive theoretical calculations were carried out to evaluate the structural and charge distribution characteristics, including the optical, optoelectronics, density of states, transition density matrix, molecular electrostatic potential (ESP), reorganization energies, and photovoltaic properties. The results revealed that the designed series exhibited improved electron–hole pair coherences, efficient charge transportation, and favorable ESP patterns, suggesting their suitability for enhanced optical and electronic characteristics. Furthermore, the hole and electron overlap analyses demonstrated significant overlap in QM1–QM6, indicating efficient charge transfer and higher charge mobilities. Additionally, the analysis of reorganization energies showed low reorganization energy values, indicating favorable charge mobility rates and potential for high-efficiency solar cell devices. This research establishes a strong foundation for utilizing QI-containing fused units as central building blocks for designing high-performance acceptors, opening up new avenues for advancements in OSCs technology.

During thermal utilization of biomass, a complex array of reactions ensues in the oxidative environment between fragments of the biomass and reactive species. In the low-temperature window, hydroperoxyl (HO${}_2)$ radicals assume a central role prior to the establishment of the O/H radical pool. Anisole, cresol, guaiacol and vanillin are often utilized as representative model compounds to comprehend the combustion chemistry of the phenolic entities in biomass and oxygen-containing derived bio-oil. This paper reports thermo-kinetic parameters for the reactions of HO₂ radicals with anisole, cresol, guaiacol and vanillin. Computed activation enthalpies entail facile values for H abstraction from the side-chain functional groups in the investigated compounds. H abstraction from the hydroxyl groups incurs lower activation energies in reference to methyl sites in cresol and guaiacol. Hence, H abstraction from the OH sites in these two molecules proceeds at a faster reaction rate constant when compared to abstraction from the methyl site. In the vanillin molecule, abstraction from the aldehydic and hydroxyl sites portrays comparable importance. The effect of scaling vibrational frequencies and the type of applied quantum tunneling on the computed reaction rate constants were thoroughly explored. Analysis of entropies of activation indicates that the transition states exhibit a product-like character. While ignition delay times of fuels often exhibit a profound sensitivity towards initial H abstraction reactions by HO₂, we found that ignition delay times of the four title molecules remain almost unchanged when updating literature kinetics models with new reaction rate constants calculated herein. It is anticipated that reported outcomes from this study aid in formulating a better understanding of the complex chemical reactions that dictate oxidative decomposition of oxygenated bio-oil model compounds.