Molecular Modeling Approach Research Articles

Unveiling the multi-target compounds of Rhazya stricta: Discovery and inhibition of novel target genes for the treatment of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is a prevalent kidney malignancy with a pressing need for innovative therapeutic strategies. In this context, emerging research has focused on exploring the medicinal potential of plants such as Rhazya stricta. Nevertheless, the complex molecular mechanisms underlying its potential therapeutic efficacy remain largely elusive. Our study employed an integrative approach comprising data mining,network pharmacology,tissue cell type analysis, and molecular modelling approaches to identify potent phytochemicals from R. stricta, with potential relevance for ccRCC treatments. Initially, we collected data on R. stricta's phytochemical from public databases. Subsequently, we integrated this information with differentially expressed genes (DEGs) in ccRCC, which were derived from microarray datasets(GSE16441,GSE66270, and GSE76351). We identified potential intersections between R. stricta and ccRCC targets, which enabled us to construct a compound-genes-pathway network using Cytoscape software. This helped illuminate R. stricta's multi-target pharmacological effects on ccRCC. Moreover, tissue cell type analysis added another layer of insight into the cellular specificity of potential therapeutic targets in the kidney. Through further Kaplan–Meier survival analysis, we pinpointed MMP9,ACE,ERBB2, and HSP90AA1 as prospective diagnostic and prognostic biomarkers for ccRCC. Notably, our study underscores the potential of R. stricta derived compounds-namely quebrachamine,corynan-17-ol, stemmadenine,strictanol,rhazinilam, and rhazimolare-to impede ccRCC progression by modulating the activity of MMP9,ACE,ERBB2, and HSP90AA1 genes. Further, molecular docking and dynamic simulations confirmed the plausible binding affinities of these compounds. Despite these promising findings, we recognize the need for comprehensive in vivo and in vitro studies to further investigate the pharmacokinetics and biosafety profiles of these compounds.

Deciphering conformational changes in human serum albumin induced by bile salts using spectroscopic and molecular modeling approaches

Bile salts are physiologically-important natural amphiphilic biosurfactants synthesized in the liver and play a vital role in the solubilization and digestion of dietary lipids, cholesterol, and other fat-soluble compounds in the body. Bile salts also exhibit pharmacological and biological uses as carriers for transporting scarce water-soluble drugs and other chemicals owing to their unique emulsifying, solubilizing capacities and micelle forming ability. In this context, we present an endeavor towards the possibilities underlying the interaction and binding between the most abundant plasma protein namely, human serum albumin (HSA) and bile salts to demonstrate an intriguing interplay of hydrophobic, electrostatic and hydrogen bonding effects using steady state absorption, fluorescence emission, anisotropy, time-resolved emission, and molecular modelling approaches. The outcome illuminates how amphiphilic interfaces of bile salts under various physico-chemical conditions trigger the conformational changes and binding affinities of native and molten-globule forms of HSA. To elucidate non-covalent interactions during HSA-bile salt supramolecular host–guest complex formation, changes in intrinsic (tryptophan) and extrinsic (ANS) fluorescence have been investigated. The results reveal upon binding of bile salts in subdomain IIA of HSA, the protein undergoes conformational changes mediated primarily by hydrophobic interactions. Furthermore, time-resolved fluorescence measurements provide important structural and dynamical insights into the protein-bile salt supramolecular complexes. Additionally, molecular docking studies on these complexes clearly reveal spontaneous binding of bile salts into subdomain IIA of HSA while suggesting that the binding affinity decreases with the decreasing order of hydrophobicity of the bile salts (NaDC > NaC > NaTC) (ΔGdock = −29.64 kJ mol−1, −26.15 kJ mol−1, −14.35 kJ mol−1), respectively. This study exclusively highlights the molecular mechanism of conformational perturbation in the native (pH 7) and molten-globule (pH 3) forms of HSA, induced by bile salts. We believe that the results reported herein will be helpful in the design and formulation of protein-bile salt-based pharmacological carriers suitable for drug delivery.

Adsorption behavior, different green solvent effect and surface enhanced Raman spectra (SERS) investigation on inhibition of SARS-CoV-2 by antineoplastic drug Carmofur with silver/gold/platinum loaded silica nanocomposites: A combined computational analysis and molecular modelling approach

In recent times, extensive research has been carried out to uncover effective drug treatments for coronavirus disease (COVID-19). The Carmofur (HCFU) molecule is primarily known for its antineoplastic properties and its use in cancer treatment. Nowadays, the antineoplastic drug Carmofur has shown its effectiveness in inhibiting the SARS-CoV-2 virus. The primary objective of this article is to utilize theoretical knowledge to explore the absorption mechanism and interaction between the HCFU molecule and the noble metal (Ag/Au/Pt)-loaded silica nanocomposites (HCFU + Ag/Au/Pt…SiO2). The optimized geometry, frequency, and intensity of the vibrational bands of the HCFU molecule and its complexes were obtained from the DFT method with the LANL2DZ basis set. The SERS technique was carried out to explore the adsorption of HCFU molecule with metal (Ag/Au/Pt)-loaded silica nanocomposites. The chemical reactivity and the charge distribution within the molecule were analysed with the help of HOMO-LUMO, Molecular Electrostatic Potential (MEP), Electron Localized Function (ELF), and Localized Orbital Locator (LOL) studies. The polar protic (ethanol, methanol, and water) and polar aprotic (DMSO) solvents were used to analyse the UV–Visible spectra of the molecules using the TD-DFT method. The drug-likeness properties of the molecules were calculated utilizing Lipinski’s rule, and finally, the molecular docking prediction was carried out for the Carmofur (HCFU) and its complexes with the selected proteins.

Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein.

The entry of SARS-CoV-2 into the host cell is mediated by its S-glycoprotein (SGP). Sulfated glycans bind to the SGP receptor-binding domain (RBD), which forms a ternary complex with its receptor angiotensin converting enzyme 2. Here, we have conducted a thorough and systematic computational study of the binding of four oligosaccharide building blocks from novel marine sulfated glycans (isolated from Pentacta pygmaea and Isostichopus badionotus) to the non-glycosylated and glycosylated RBD. Blind docking studies using three docking programs identified five potential cryptic binding sites. Extensive site-targeted docking and molecular dynamics simulations using two force fields confirmed only two binding sites (Sites 1 and 5) for these novel, highly charged sulfated glycans, which were also confirmed by previously published reports. This work showed the structural features and key interactions driving ligand binding. A previous study predicted Site 2 to be a potential binding site, which was not observed here. The use of several molecular modeling approaches gave a comprehensive assessment. The detailed comparative study utilizing multiple modeling approaches is the first of its kind for novel glycan-SGP interaction characterization. This study provided insights into the key structural features of these novel glycans as they are considered for development as potential therapeutics.

Correlation between Molecular Docking Score and Ligand Molar Mass: Statistical Approach

In recent days, pharmacology researchers have studied secondary metabolic compounds because they are naturally produced by plants, bacteria, fungi, and marine sponges, leading to increased worldwide use of the computational technique of molecular modelling approaches to drug discovery. Flavonoids, which belong to secondary metabolic compounds, play a role in biological activity. In the present study, the flavonoids subclass of secondary metabolic compounds molecular docking binding energy was dependent on the compound's molecular weight on binding interaction with antioxidant proteins using the statistical approaches of correlation coefficient and cluster statistical analysis. To evaluate a strong negative relationship, higher molecular mass flavonoids compounds had high active properties and lower molecular mass flavonoids compounds had low active properties, as reported on antioxidant proteins in correlation (r = -0.76 to -0.91 for a strong relationship) and cluster analysis. Flavonoids subclass compounds molecular docking binding scores were based on ligand molecular mass and depended on a similarly strong negative relationship in molecular mass vs 1HD2, 1MFM, 2F8A, and 2HCK antioxidant proteins. In this study, statistical analysis concluded that molecular docking binding energy depends on ligand molecular mass. Overall, the higher molecular mass compounds have higher active properties may be used in biological activity.

Exploring the molecular structural requirements of 3, 4, 5-trisubstituted triazoles and imidazotriazole analogues as angiotensin II receptor using molecular modeling approach

Exploring the molecular structural requirements of 3, 4, 5-trisubstituted triazoles and imidazotriazole analogues as angiotensin II receptor using molecular modeling approach

Systematic elucidation of the multi-target pharmacological mechanism of Terminalia arjuna against congestive cardiac failure via network pharmacology and molecular modelling approaches

Congestive cardiac failure (CCF) is a pathophysiologic state when the heart is not able to maintain its cardiac output to meet the demand of metabolising tissues. CCF is responsible for approximately 2.9 million deaths worldwide. The heterogeneous nature of CCF draws the attention of researchers to find more enthralling and promising diagnostic and treatment options. Terminalia arjuna (Arjuna) is an evergreen, deciduous tree exhibited various astringent, anti-bacterial, and anti-microbial properties. T. arjuna is being used in various regions for anginal pain, hypertension, congestive heart failure, and dyslipidemia. Although previous in vitro studies have demonstrated the therapeutic potential of T. arjuna, the exact molecular mechanism underlying its protective effect on the heart remains unclear. In this study, a network pharmacology technique was used to explore the active ingredients, potential targets in T. arjuna for the treatment of CCF. In the framework of this study, we explored the active ingredient–target–pathway network and figured out that oleanolic acid, arjunolic acid, luteolin, kaempferol, cholesterol, ellagic acid 4-O-xylopyranoside 3,3’-dimethyl ether, and cyclohexyl (2,4-dimethyl phenyl) methanone contributed significantly to the development of CCF by affecting AKT1, MAPK14, TNF, IL6, ESR1, and HSP90AA1 genes. Molecular docking analysis further validated the activities of these compounds against potential targets. To sum up, integrated network pharmacology and docking analysis revealed that T. arjuna exerts its cardioprotective effect by acting on various signalling pathways, including the thyroid hormone, VEGF signalling pathway, AGE-RAGE signalling pathway in diabetic complications, HIF signalling pathway, sphingolipid signalling pathway, and oestrogen signalling pathways. Overall, this study provides valuable insights into the molecular mechanism of T. arjuna in CCF and highlights its potential as a promising preventive treatment for this condition.

Targeting Spike‐ACE2 Interface of SARS‐CoV‐2 and its Omicron Variant: A Comparative Screening of Potential Inhibitors for Existing and Anticipating Variants Using Molecular Modelling Approach

AbstractThe recent COVID pandemic has shown major impact on public health and economic crisis. Despite the development of many vaccines and drugs against the severe acute respiratory syndrome (SARS) coronavirus 2, the pandemic still persists. The continued spread of the virus is largely driven by the emergence of viral variants such as α, β, γ, delta, epsilon spike, omicron and its subvariants (BA.1,2,3) which can evade the current vaccines through mutations in the spike protein.[1] For instance, spike to omicron has modifications at different mutations (D405N, K417N, S477N, E484A, Q493R, N501Y, Y505H).[1b] These mutations will affect functional properties and hence may alter the specificity towards potential drug candidates. Therefore, it is important to understand the role of these mutations on interactions with existing drug candidates. In this study, we focus on the two forms of SARS‐CoV‐2, such as wild‐type spike and omicron and unveil their interactions with different drugs. For this purpose, we have taken about hundred drugs categorised in twelve groups of anticancer, natural products, enzyme inhibitors, antivirals, antioxidants, anti‐bacterials, anti‐malarials, antidiabetics, antimicrobials, anti‐inflammatory, antifungals and other drugs. We used in‐silico methods to understand the effect of these drug molecules on wild type and omicron spike RBD at the interface of ACE2 enzyme. Based on molecular docking results, we have chosen 7 best docked compounds and studied their interaction patterns in detail by molecular dynamics simulation.

Exploring the chemical composition, in vitro and in silico study of the anticandidal properties of annonaceae species essential oils from the Amazon.

Chemical composition of the essential oils (EOs) from the leaves of five Annonaceae species found in the amazon region was analyzed by Gas chromatography coupled to mass spectrometry. The antifungal activity of theses EOs was tested against Candida albicans, Candida auris, Candida famata, Candida krusei and Candida tropicalis. In addition, an in silico study of the molecular interactions was performed using molecular modeling approaches. Spathulenol (29.88%), α-pinene (15.73%), germacra-4(15),5,10(14)-trien-1-α-ol (6.65%), and caryophylene oxide (6.28%) where the major constitents from the EO of Anaxagorea dolichocarpa. The EO of Duguetia echinophora was characterized by β-phellanderene (24.55%), cryptone (12.43%), spathulenol (12.30%), and sabinene (7.54%). The major compounds of the EO of Guatteria scandens where β-pinene (46.71%), α-pinene (9.14%), bicyclogermacrene (9.33%), and E-caryophyllene (8.98%). The EO of Xylopia frutescens was characterized by α-pinene (40.12%) and β-pinene (36.46%). Spathulenol (13.8%), allo-aromadendrene epoxide (8.99%), thujopsan-2-α-ol (7.74%), and muurola-4,10(14)-dien-1-β-ol (7.14%) were the main chemical constituents reported in Xylopia emarginata EO. All EOs were active against the strains tested and the lowest inhibitory concentrations were observed for the EOs of D. echinophora, X. emarginata, and X. frutescens against C. famata the Minimum Inhibitory Concentration values of 0.07, 0.019 and 0.62 μL.mL-1, respectively. The fungicidal action was based on results of minimum fungicidal concentration and showed that the EOs showed fungicide activity against C. tropicalis (2.5 μL.mL-1), C. krusei (2.5 μL.mL-1) and C. auris (5 μL.mL-1), respectively. The computer simulation results indicated that the major compounds of the EOs can interact with molecular targets of Candida spp.

Combining molecular modelling and experimental approaches to gain mechanistic insights into the LuxP drug target in Streptococcus pyogens

Autoinducer-2 can mediate inter- and intra-species communication signal between bacteria and these signals from AI-2 is noted from limited species of bacteria. In humans, S. pyogenes is a pathogen that causes a wide range of illnesses and can survive in the host system and transmit infection. The process by which S. pyogenes acquires the competence to live and disseminate infection remains unknown. We hypothesized that AI-2 and their receptors would play a significant role during infection, and for that present investigation provides the experimental and molecular insights. In the absence of details about the receptor LuxP and LuxQ, the screening approach provides supporting insights. The evolutionary relationship and similarities of the PBP domain (Spy 1535) and the signal transmission PDZ domain (Spy 1536) were studied in relation to their counterparts in other bacteria. Molecular docking and modeling confirmed the domain-enhanced specificity for AI-2 binding. In vitro studies showed that AI-2, which is present in the cell-free supernatant of S. pyogenes, regulates luminescence in P. luminous and biofilm development in E. coli using the LuxS reporter genes. Examination of S. pyogenes gene expression revealed modulation of virulence genes when the pathogen was exposed to V. harveyi HSL and AI-2. Therefore, S. pyogenes pathogenicity is sequentially regulated by AI-2 it acquires from other commensal bacteria. Overall, this study lays the groundwork for understanding the signalling mechanism from AI-2, which are critical to the pathogenic mechanism of S. pyogenes. Communicated by Ramaswamy H. Sarma

A novel molecular modeling approach for simulating asphalt-aggregate debonding: Considering interfacial moisture migration

The asphalt-aggregate debonding behavior in moisture environments is a fundamental but unresolved issue in pavement engineering. In this study, a novel molecular dynamics (MD) modeling method was developed to address this challenge. Compared with previous layered modeling methods, the new method considers the moisture diffusion and migration at the interface, which better reflects the real debonding process. Based on the results, we found a layered diffusion phenomenon at the interface, which significantly affects the efficiency of moisture migration and interfacial debonding. The strong interactions between water molecules and alkaline aggregates (represented by calcite) restrict the interfacial moisture diffusion and migration, making it more resistant to moisture damage than acidic aggregates (represented by quartz). This study highlights the limitations of energy-based parameters obtained from the layered modeling method and resolves a long-standing controversy over whether calcite or quartz is more susceptible to water damage. Findings from this research contribute to comprehending the fundamental debonding mechanisms and provide an atomic-level perspective to investigate moisture damage in pavement engineering.

Phytochemical profiling and evaluation of the antidiabetic potential of Ichnocarpus frutescens (Krishna Sariva): kinetic study, molecular modelling, and free energy approach

This research explored novel antidiabetic drugs from natural sources using the Ayurvedic Rasayana herb Ichnocarpus frutescens through invitro enzyme assay, kinetics study, and computational approaches. Invitro enzyme inhibition assay demonstrated the promising inhibitory activity of root extract against alpha-amylase (α-A) and alpha-glucosidase (α-G) enzyme with IC50 value 7.34 ± 0.22 mg/ml and 4.40 ± 0.25 mg/ml respectively. Enzyme kinetic study revealed the competitive inhibition of both proteins by Ichnocarpus frutescens extract. High-Resolution Liquid Chromatography Mass Spectrometer and Docking study revealed the better binding energy of phytoconstituents 23-Acetoxysoladulcidine, Atrovirinone, Bismurrayaquinone A, Lamprolobine, Zygadenine, and Gambiriin A3 than standard drug acarbose. Molecular modelling showed stable protein-ligands binding interaction during the 100 ns simulation. It revealed comparable Root Mean Square Deviation, Radius of Gyration, and Solvent Accessible Surface Area of these compounds with acarbose. The active site residues of both proteins remained stable and showed significantly less Root Mean Square Fluctuation. Molecular Mechanics with Generalised Bonn Surface Area analysis has illustrated the similar inhibitory activity of Zygadenine for α-A, 23-Acetoxysoladulcidine, and Gambiriin A3 for α-G protein, compared to the FDA-approved drug acarbose. Thus, the study suggested that the root of Ichnocarpus frutescens can be used as α-A and α-G inhibitors and be considered a compelling lead for the medication of type 2 diabetes. Communicated by Ramaswamy H. Sarma

Resistance profiles for the investigational neuraminidase inhibitor AV5080 in influenza A and B viruses

Neuraminidase inhibitors (NAIs) are recommended for influenza treatment and prevention worldwide. The most widely prescribed NAI is oral oseltamivir, while inhaled zanamivir is less commonly used. Using phenotypic neuraminidase (NA) enzymatic assays and molecular modeling approaches, we examined the ability of the investigational orally-dosed NAI AV5080 to inhibit viruses of the influenza A(H1N1)pdm09, A(H3N2), A(H5N1), and A(H7N9) subtypes and the influenza B/Victoria- and B/Yamagata-lineages containing NA substitutions conferring oseltamivir or zanamivir resistance including: NA-R292K, NA-E119G/V, NA-H274Y, NA-I122L/N, and NA-R150K. Broadly, AV5080 showed enhanced in vitro efficacy when compared with oseltamivir and/or zanamivir. Reduced AV5080 inhibition was determined for influenza A viruses with NA-E119G and NA-R292K, and for B/Victoria-lineage viruses with NA-I122N/L and B/Yamagata-lineage virus with NA-R150K. Molecular modeling suggested loss of the short hydrogen bond to the carboxyl group of AV5080 affected inhibition of NA-R292K viruses, whereas loss of the salt bridge with the guanidine group of AV5080 affected inhibition of NA-E119G. The resistance profiles and predicted binding modes of AV5080 and zanamivir are most similar, but dissimilar to those of oseltamivir, in part because of a guanidine moiety compensatory binding effect. Overall, our data suggests that AV5080 is a promising orally-dosed NAI that exhibited similar or superior in vitro efficacy against viruses with reduced or highly reduced inhibition phenotypes with respect to currently approved NAIs.

An integrative computational approach for the identification of dual inhibitors of isocitrate dehydrogenase 1 and 2 from phytocompounds of Phyllantus amarus

Genetic alterations of the genes encoding the isocitrate dehydrogenase (IDH) enzymes have been identified in about 20% of acute myeloid leukemia (AML) cases as well as many other forms of cancers. Notable among these alterations are the neomorphic IDH1_R132H and IDH2_R140Q mutations which lead to the production of an oncometabolite. Hence, their inhibition is widely considered a therapeutic strategy in the treatment of many cancers. While many inhibitors of the mutant enzymes have been developed, an inhibitor that is capable of co-inhibiting both enzymes are currently lacking while drug resistance has also limited the clinical usage of previously identified mono inhibitors. Consequently, this study employed molecular modeling approaches, such as molecular docking, molecular mechanics generalized Born Surface area (MM/GBSA), molecular dynamics (MD) simulation, and density functional theory (DFT) analysis to identify potential dual inhibitors of the previously mentioned mutant IDH1/2 from the phytocompounds of Phyllantus amarus. Of the 31 phytocompounds identified, 20 showed good binding affinities for both IDH1 _R132H and IDH2 _R140Q (ranging from −5.2 Kca/mol to −9.6 Kcal/mol) and had desirable pharmacokinetic properties. However, ellagic acid and pinoresinol possessed better pharmacokinetic properties, rendering suitable hits. Investigation of the behavior of the IDH1_R132H and IDH2_R140Q complexes with ellagic acid and pinoresinol via the RMSD, RMSF, and contact map analyses showed that all the complexes-maintained stability throughout the simulation time. Ultimately, ellagic acid and pinoresinol were identified as promising hits for the development of IDH1_R132H and IDH2_R140Q dual inhibitors. However, further experimental studies are needed to confirm their potential as therapies. Communicated by Ramaswamy H. Sarma

Change in thermal stability and molecular structure characteristics of whey protein beta-lactoglobulin upon the interaction with levamisole hydrochloride

The interaction between beta-lactoglobulin (BLG) and anthelmintic compounds including levamisole (LEV) is a matter of great concern as it not only poses potential health and environmental risks but also has significant implications for food processing and production. The mechanisms of LEV-BLG interaction were investigated through spectral and molecular modeling approaches. Fluorescence and UV–Visible investigations indicated the formation of a spontaneous and stable LEV-BLG complex. Structural changes of BLG were revealed by circular dichroism and Fourier transform infrared studies. The thermal stability of BLG increased in the presence of LEV. Molecular docking studies indicated the best mode of LEV-BLG interaction and molecular dynamics simulation confirmed the stability of the LEV-BLG complex. In conclusion, our study sheds light on the potential of BLG to interact with deleterious substances such as anthelmintic agents, thus highlighting the necessity of further research in this field to assure food safety and prevent any health hazards.

In silico design, docking simulation, and ANN-QSAR model for predicting the anticoagulant activity of thiourea isosteviol compounds as FXa inhibitors

AbstractNovel oral anticoagulants are frequently used for the pharmacotherapy of thromboembolic disorders but still have drawbacks and side effects. While numerous synthetic and semisynthetic derivatives of nontoxic isosteviol possess potential therapeutic properties, including anticoagulant activity. Besides, thiourea is recognized in medicinal chemistry research as a component of a common framework of many drugs or bioactive compounds. The present work combines molecular modeling and docking approach for searching and designing novel thiourea isosteviol-based compounds as potential FXa inhibitors. Elaborated regression model well reflects the relationships between experimentally determined anticoagulant activity and molecular descriptors and may be used for the prediction of FXa inhibitory activity of novel thiourea isosteviol compounds. Among 20 descriptors incorporated into the ANN model, 60% are 2D topological descriptors, 25% describe three-dimensional molecular structure, and remaining 15% belong to constitutional descriptors. Additionally, docking simulation confirms the prominent binding of the newly in silico designed molecules with the active sites of the protein, which may be the lead molecules and can be further optimized for the efficient pharmacodynamic and pharmacokinetic profiles. Based on the results obtained, thiourea derivatives of isosteviol with 3-chloro-4-fluorophenyl, 3-fluoro-4-chlorophenyl or 4-(oxazol-5-yl)phenyl substituent may be promising FXa inhibitors. Findings reported in the present work can be used as valuable information for the development of anticoagulants.

Structural and functional fine mapping of cysteines in mammalian glutaredoxin reveal their differential oxidation susceptibility

Protein-S-glutathionylation is a post-translational modification involving the conjugation of glutathione to protein thiols, which can modulate the activity and structure of key cellular proteins. Glutaredoxins (GLRX) are oxidoreductases that regulate this process by performing deglutathionylation. However, GLRX has five cysteines that are potentially vulnerable to oxidative modification, which is associated with GLRX aggregation and loss of activity. To date, GLRX cysteines that are oxidatively modified and their relative susceptibilities remain unknown. We utilized molecular modeling approaches, activity assays using recombinant GLRX, coupled with site-directed mutagenesis of each cysteine both individually and in combination to address the oxidizibility of GLRX cysteines. These approaches reveal that C8 and C83 are targets for S-glutathionylation and oxidation by hydrogen peroxide in vitro. In silico modeling and experimental validation confirm a prominent role of C8 for dimer formation and aggregation. Lastly, combinatorial mutation of C8, C26, and C83 results in increased activity of GLRX and resistance to oxidative inactivation and aggregation. Results from these integrated computational and experimental studies provide insights into the relative oxidizability of GLRX’s cysteines and have implications for the use of GLRX as a therapeutic in settings of dysregulated protein glutathionylation.

Evaluation of the Stereochemical Lability of Benzo‐Cycloheptene‐Based Drugs Endowed with Potentially Modulable Planar Chirality

AbstractAn experimental and theoretical study was carried out to analyze the configurational lability possessed by some of the most common drugs endowed with a central non‐planar seven‐membered cycloheptadiene ring, which confers chirality to these compounds. In fact, the absence of planarity allows the existence of two enantiomeric species that can interconvert thanks to a ring overturning mechanism. The energy barrier that opposes the inversion of the chiral tricyclic scaffold characterizing such species, which is strongly dependent on the presence of appropriate substituents on the two external cycles, has been investigated through Dynamic‐HPLC and off‐column racemization techniques, as well as through assessments based on molecular modelling approaches. Interesting indications were obtained by making targeted structural changes to allow accurate control of the stereolability characterizing the tricyclic framework.

Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study.

CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst's functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.

Discovery of imidazopyridine derived oxadiazole-based thiourea derivatives as potential anti-diabetic agents: Synthesis, in vitro antioxidant screening and in silico molecular modeling approaches

A series of new imidazopyridine based oxadiazole derivatives (5a-l) were designed and synthesized. Their structures were confirmed by spectral data and then subjected to in vitro assessment including α-glucosidase, α-amylase inhibitory, and 2- diphenyl-1-picrylhydrazyl (DDPH) and 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activities. The inhibitory activity results revealed that all the synthesized analogs displayed significant α-glucosidase and α-amylase inhibition with IC50 values of 0.90 ± 0.10 to 18.10 ± 0.20 µM (for α-glucosidase) and 1.10 ± 0.10 to 19.70 ± 0.20 µM (for α-amylase) respectively as compared to standard acarbose with IC50 values of 11.50 ± 0.30 µM (α-glucosidase) and 12.20 ± 0.30 µM (for α-amylase).The synthesized analogs also showed significant DPPH and ABTS radical scavenging activities with IC50 values in the range of 1.05 ± 0.05 to 4.56 ± 3.12 µM (for DDPH) and 1.15 ± 0.05 to 4.89 ± 2.89 µM (for ABTS) respectively, incomparison to standard ascorbic acid with IC50 = 1.83 ± 1.32 µM (for DDPH) and 1.84 ± 1.16 µM (for ABTS) respectively. After crucial analysis of varying substitution effects on inhibitory (α-glucosidase &α-amylase) and radical scavenging (DPPH & ABTS) potentials respectively, the structure-activity relationship (SAR) was established. Through the in silico molecular docking analysis, the ability of the synthesized analogs to inhibit α-glucosidase and α -amylase was also examined.There was a good correlation between in vitro and in silico studies for synthesized analogs 5i and 5d Further studies are required to determine whether these potent analogs could be a potential treatment for diabetes disease.