Modelling the structural and reactivity landscapes of tucatinib with special reference to its wavefunction-dependent properties and screening for potential antiviral activity

Long COVID as a disease of accelerated biological aging: An opportunity to translate geroscience interventions

It has been four years since long COVID-the protracted consequences that survivors of COVID-19 face-was first described. Yet, this entity continues to devastate the quality of life of an increasing number of COVID-19 survivors without any approved therapy and a paucity of clinical trials addressing its biological root causes. Notably, many of the symptoms of long COVID are typically seen with advancing age. Leveraging this similarity, we posit that Geroscience-which aims to target the biological drivers of aging to prevent age-associated conditions as a group-could offer promising therapeutic avenues for long COVID. Bearing this in mind, this review presents a translational framework for studying long COVID as a state of effectively accelerated biological aging, identifying research gaps and offering recommendations for future preclinical and clinical studies.

Antioxidant Properties of Curcumin Analogues to Inhibit Thermal Degradation of Low-Density Polyethylene: Experimental and DFT Study

Curcumin can be isolated from plants (Curcuma longa) and it belongs to the ginger family. It exhibits many useful properties and acts as an antioxidant. The aim of the current study was to prepare eight curcumin analogues and investigate their antioxidant activities to inhibit the thermal degradation of low-density polyethylene (LDPE). The carbonyl index (CI) was measured to test the effectiveness of the curcumin analogues. Various doses (0.5, 1, 2, 4, and 6% wt/wt) of a mixture containing LDPE and curcumin analogues were prepared, and the CI was measured. The eight curcumin analogues were found to have good to excellent antioxidant activity against the degradation of LDPE. It was clear that the curcumin analogue derived from vanillin and acetone has the highest antioxidant activity. The density functional theory study was conducted for the eight curcumin analogues to test their reactivity and stability. Again, the global reactivity descriptors analysis showed that compound derived from vanillin and acetone was the most reactive compound to inhibit thermal degradation of LDPE.

Evaluation of bioactive compounds from Boswellia serrata against SARS-CoV-2

With the COVID-19 pandemic still wreaking havoc worldwide, new variants being discovered every month in some parts of the globe due to the mutating nature of the virus. There is no specific solution for this highly transmissible disease. In search of a lead molecule for the discovery and development of drug, extensive research is being conducted throughout the world. Many synthetic drugs are already in clinical trials and some are utilized for the treatment of this viral infection. Apart from synthetic drugs, phytocompounds from plants act as a potential drug candidate which can inhibit the growth of virus and thus able to prevent the viral infection. In this study, 26 ligands (bioactive compounds) from Boswellia serrata (an important medicinal plant) were tested against SARS-CoV-2 by using computational method. Selected ligands were shortlisted using Lipinski's rule and then subjected to molecular docking against one of the main proteins of SARS-CoV-2, i.e., Mpro. Out of these compounds, Euphane, Ursane, α-Amyrin, Phytosterols, and 2,3-Dihydroxyurs-12-en-28-oic acid were potential to inhibit the Mpro activity with binding energies of - 10.47 kcal/mol, - 10.41 kcal/mol, - 9.99 kcal/mol, - 9.94 kcal/mol and - 9.72 kcal/mol respectively. A comparative study was performed using the best five ligands against four possible drug targets of SARS-CoV-2. It was found that Euphane showed highest negative binding energy against all the four crucial targets of SARS-CoV-2. Further, in-vitro experimentation is required to validate the use of Euphane as a potent drug against SARS-CoV-2.

Energy and reactivity profile and proton affinity analysis of rimegepant with special reference to its potential activity against SARS-CoV-2 virus proteins using molecular dynamics

Rimegepant is a new medicine developed for the management of chronic headache due to migraine. This manuscript is an attempt to study the various structural, physical, and chemical properties of the molecules. The molecule was optimized using B3LYP functional with 6-311G + (2d,p) basis set. Excited state properties of the compound were studied using CAM-B3LYP functional with same basis sets using IEFPCM model in methanol for the implicit solvent atmosphere. The various electronic descriptors helped to identify the reactivity behavior and stability. The compound is found to possess good nonlinear optical properties in the gas phase. The various intramolecular electronic delocalizations and non-covalent interactions were analyzed and explained. As the compound contain several heterocyclic nitrogen atoms, they have potential proton abstraction features, which was analyzed energetically. The most important result from this study is from the molecular docking analysis which indicates that rimegepant binds irreversibly with three established SARS-CoV-2 proteins with ID 6LU7, 6M03, and 6W63 with docking scores − 9.2988, − 8.3629, and − 9.5421 kcal/mol respectively. Further assessment of docked complexes with molecular dynamics simulations revealed that hydrophobic interactions, water bridges, and π–π interactions play a significant role in stabilizing the ligand within the binding region of respective proteins. MMGBSA-free energies further demonstrated that rimegepant is more stable when complexed with 6LU7 among the selected PDB models. As the pharmacology and pharmacokinetics of this molecule are already established, rimegepant can be considered as an ideal candidate with potential for use in the treatment of COVID patients after clinical studies.

Computational investigation, comparative approaches, molecular structural, vibrational spectral, non-covalent interaction (NCI), and electron excitations analysis of benzodiazepine derivatives

The present work explores the structural parameters and vibrational frequencies as well as molecular interactions of benzodiazepine derivatives, such as clothiapine (CT), clozapine (CZ), and loxapine (LX). Employing fitting experimental data to theoretical results is used to assess the structural parameters of heading composites. The main assignment is passed out according to the overall distribution of energy of the vibrational modes. From the hyper-conjugative interaction, the permanency of the structure had been predicted through natural bond orbital analysis; it is also used to identify the bonding and antibonding regions of the molecules. Moreover, electrostatic potential (ESP), density of states (DOS), and charge transfer occurring of the molecule among HOMO as well as LUMO energy were calculated and presented; utilizing electron localized field (ELF), localized orbital locator (LOL), and reduced density gradient (RDG), the chemical interactive regions are found. Additionally, mean polarizability (α_tot), the first-order hyperpolarizability (β_tot), and softness and hardness of the entitled compounds were also performed. The interaction between protein-ligand was also predicted by docking studies.

Potential activity of Linezolid against SARS-CoV-2 using electronic and molecular docking study

The crescent evolution of a global pandemic COVID-19 and its respiratory syndrome (SARS-Cov-2) has been a constant concern (Ghosh 2021; Khan et al. 2021; Alazmi and Motwalli 2020; Vargas et al. 2020). The absence of a proven and effective medication has compelled all the scientific community to search for a new drug. The use of known drugs is a faster way to develop new therapies. Molecular docking is a powerful tool (Gao et al. J Mol Model 10: 44-54, 2004; Singh et al. J Mol Model 18: 39-51, 2012; Schulz-Gasch and Stahl J Mol Model 9:47-57, 2003) to study the interaction of potential drugs with SARS-CoV-2, Alsalme et al. (2020) and Sanders et al. (2020) spike protein as a consequence the main goal of this article is to present the result of the study of an interaction between (R and S)-Linezolid with receptor-binding domain (RBD) of SARS-Cov-2 spike protein complexed with human Angiostensin-converting enzyme 2 (ACE2) (6vW1 - from PDB). The Linezolid enantiomers were optimized at B3LYP/6-311++G(2d,p) level of theory. Molecular docking of the system (S)-Linezolid⋯RBD⋯ACE2 and (R)-Linezolid⋯RBD⋯ACE2 was performed, the analysis was made using LigPlot+ and NCIplot software packages, to understand the intermolecular interactions. The UV-Vis and ECD of the complexes - (R and S)-Linezolid⋯RBD⋯ACE2 were performed in two layers with DFT/6-311++G(3df,2p) and DFT/6-31G(d), respectively. The results showed that only the (S)-Linezolid had a stable interaction with - 8.05 kcal.mol- 1, whereas all the R-enantiomeric configurations had positive values of binding energy. The (S)-Linezolid had the same interactions as in the (S)-Linezolid ⋯ Haluarcula morismortui Ribosomal system, where it is well-known the fact that the latter has biological activity. A specific interaction on the fluorine ring justified an attenuation on the ECD signal, in comparison to isolated species. Therefore, some biological activity of (S)-Linezolid with SARS-CoV-2 RBD was expected, indicated by the modification of its ECD signal and justified by a similar interaction in the S-Linezolid⋯Haluarcula marismortui Ribosomal system.

Excited-state electronic properties, structural studies, noncovalent interactions, and inhibition of the novel severe acute respiratory syndrome coronavirus 2 proteins in Ripretinib by first-principle simulations

Ripretinib is a recently developed drug for the treatment of adults with advanced gastrointestinal stromal tumors. This paper reports an attempt to study this molecule by electronic modeling and molecular mechanics to determine its composition and other specific chemical features via the density-functional theory (DFT), thereby affording sufficient information on the electronic properties and descriptors that can enable the estimation of its molecular bioactivity. We explored most of the physico-chemical properties of the molecule, as well as its stabilization, via the studies of the natural bond orbitals and noncovalent interactions. The electronic excitation, which is a time-dependent process, was examined by the time-dependent DFT with a CAM-B3LYP functional. The molecular docking study indicated that Ripretinib strongly docks with three known novel severe acute respiratory syndrome coronavirus 2 (SARS-n-CoV-2) proteins with a reasonably good docking score.