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With the aim of finding the plant-derived allosteric inhibitors of caspase-3/-7, we conducted computational investigations of bioactive compounds present in various berry fruits. In a molecular docking study, perulactone demonstrated excellent binding affinity scores of −12.1 kcal/mol and −9.1 kcal/mol for caspase 7 and 3, respectively, whereas FDA-approved allosteric inhibitors (DICA and FICA) were found to show lower docking scores (−5.6 and −6.1 kcal/mol) against caspase 7 while (−5.0 and −5.1 kcal/mol) for caspase 3, respectively. MD simulations were used to validate the binding stability of perulactone in the active sites of caspase-7/-3, and the results showed outstanding stability with lower ligand RMSDs of 1.270–3.088 Å and 2.426–9.850 Å against the targeted receptor. Furthermore, we performed MMGBSA free binding energy, where the perulactone values of ΔGBind were determined to be −63.98 kcal/mol and −66.32 kcal/mol for both receptors (3IBF and 1NME), which are significantly better than the −45.16 kcal/mol and −39.51 kcal/mol for DICA as well as −26.37 kcal/mol and −15.50 kcal/mol for FICA, respectively. The drug resemblance of perulactone was effectively evaluated by ADMET. Thus, our findings indicated that perulactone could be an orally administered therapeutic candidate for regulating apoptosis in a variety of disorders. However, there may be an urgent need to study using in vitro and in vivo experiments. [ABSTRACT FROM AUTHOR]

A wide range of bioactive compounds have been created using the versatile pharmacophore pyrimidine. In order to improve biological applications, we, therefore, envisioned adding these privileged moieties. In this work, we developed an efficient 2-aminopyrimidine derivatives. We further investigated the anticancer activity of all the compounds against colon cancer cell lines COLO-205 and HT-29. Out of several compounds synthesized, two compounds SD2 and SD4 have shown comparable potent anticancer activity when compared to standard Cabozantinib. The most potent cytotoxic compound against colon cancer cells in our study was found to be SD2 with an IC50 value of 9.57 μM. The investigation from molecular docking showed the best binding affinity. The complex stability within an enzyme’s pocket was demonstrated by the molecular dynamic simulation running for 100 ns. [ABSTRACT FROM AUTHOR]

InhA is an enoyl acyl carrier reductase that catalyzes the chemo-selective reduction of its 2-trans-enoyl-ACP substrate. The pharmacological effects of the frontline medications used in the treatment of tuberculosis are elicited by inhibiting the enzyme InhA, which disrupts the mycolic acid biosynthesis pathway. The present study involves development of ligand-based pharmacophore model, docking studies, generation of 3D-QSAR model, and molecular dynamic simulation studies of virtually screened putative InhA inhibitors. The best field-based 3D-QSAR model was validated using partial least-square regression (PLS) method with high regression coefficient for training set (R2) = 0.9256 and test set (R2) = 0.7542, cross-validated coefficient (rcv2) = 0.72 and R2pred = 0.9764. Also, virtual screening yielded compounds 4, 25, 1, and 30 exhibiting appreciable interactions (docking scores −5.972, −3.819, −3.801, and −3.701, respectively with InhA synthetase; PDB ID: 1BVR). Further, ADMET studies supported drug-like potential of compounds 25, 1, and 30 whereas compound 4 showed negligible human oral absorption. The molecular dynamic simulation studies of the top scored molecule 25 suggested stability of 25-1BVR complex over the course of simulation run. Therefore, this work can be helpful for future discovery of novel InhA inhibitors against drug-resistant tuberculosis. [ABSTRACT FROM AUTHOR]

Several computational methods have been developed to identify neutralizing antibodies (NAbs) covering four dengue virus serotypes (DENV-1 to DENV-4); however, limitations of the dataset and the resulting performance remain. Here, we developed a new computational framework to predict potent and stable NAbs against DENV-1 to DENV-4 using only antibody (CDR-H3) and epitope sequences as input. Specifically, our proposed computational framework employed sequence-based ML and molecular dynamic simulation (MD) methods to achieve more accurate identification. First, we built a novel dataset (n = 1108) by compiling the interactions of CDR-H3 and epitope sequences with the half maximum inhibitory concentration (IC50) values, which represent neutralizing activities. Second, we achieved an accurately predictive ML model that showed high AUC values of 0.879 and 0.885 by tenfold cross-validation and independent tests, respectively. Finally, our computational framework could be applied to filter approximately 2.5 million unseen antibodies into two final candidates that showed strong and stable binding to all four serotypes. In addition, the most potent and stable candidate (1B3B9_V21) was evaluated for its development potential as a therapeutic agent by molecular docking and MD simulations. This study provides an antibody computational approach to facilitate the high-throughput identification of NAbs and accelerate the development of therapeutic antibodies. [ABSTRACT FROM AUTHOR]

One of the most challenging issues scientists face is finding a suitable non-invasive treatment for cancer, as it is widespread around the world. The efficacy of phytochemicals that target oncogenic pathways appears to be quite promising and has gained attention over the past few years. We investigated the effect of docking phytochemicals isolated from the rhizomes of the Cimicifuga foetida plant on different domains of the IκB kinase alpha (IKK1/alpha) protein. The Cimicifugoside H-2 phytochemical registered a high docking score on the activation loop of IKK1/alpha amongst the other phytochemicals compared to the positive control. The interaction of the protein with Cimicifugoside H-2 was mostly stabilized by hydrogen bonds and hydrophobic interactions. A dynamic simulation was then performed with the Cimicifugoside H-2 phytochemical on the activation loop of IKK1/alpha, revealing that Cimicifugoside H-2 is a possible inhibitor of this protein. The pharmacokinetic properties of the drug were also examined to assess the safety of administering the drug. Therefore, in this in silico study, we discovered that the Cimicifugoside H-2 phytochemical inhibits the actively mutated conformation of IKK1/alpha, potentially suppressing the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway. [ABSTRACT FROM AUTHOR]

Flemingia macrophylla has traditionally been applied to relieve inflammation, diabetes, and circulatory complications. The leaf extract of F. macrophylla and its fractions were investigated for their in-vitro antioxidant and anti-diabetic properties. The phytochemical screening showed valuable phytochemicals, including glycosides, flavonoids, saponins, etc. GC-MS analysis of the phytochemicals in the methanol extract detected 19 bioactive compounds. Among the diverse fractions, the ethyl acetate fraction (EFM) exhibited the highest phenol and flavonoid contents of 557 mg GAE/g and 326 mg QCE/g, respectively. The total antioxidant content of EFM was found to be 292.41±19.16 mg AAE/g, while its antidiabetic study showed the greatest level of α -glucosidase (IC50: 11.27±1.25 µg/mL) and α -amylase (IC50: 10.04±0.63 µg/mL) inhibitory effects. The docking results showed that C6 had the highest binding scores of -9.0, -7.4, and -7.6 kcal/mol against antioxidant (6NGJ), α-glucosidase (5NN5), and α-amylase (4GQR) proteins, respectively. The dynamics simulation disclosed that C6-receptor protein complexes remained stable at the binding pocket under human body conditions and retained their stiff morphology for 100 nanoseconds (ns). ADMET results demonstrated their noncarcinogenic and well-absorbed properties, where PASS prediction data confirmed their efficacy as an antioxidant, antiulcerative, thrombolytic, and antidiabetic. Therefore, F. macrophylla has potential health benefits. [ABSTRACT FROM AUTHOR]

Quercetin is a flavonoid with notable pharmacological effects and promising therapeutic potential. Quercetin plays a significant role in neuroinflammation, which helps reduce Alzheimer's disease (AD) severity. Quercetin (Q) and quercetin 3-O-glucuronide (Q3OG) are some of the most potent antioxidants available from natural sources. However, the natural form of quercetin converted into Q3OG when reacted with intestinal microbes. The study aims to ensure the therapeutic potential of Q and Q3OG. In this study, potential molecular targets of Q and Q3OG were first identified using the Swiss Target Prediction platform and pathogenic targets of AD were identified using the DisGeNET database. Followed by compound and disease target overlapping, 77 targets were placed in that AKT1, EGFR, MMP9, TNF, PTGS2, MMP2, IGF1R, MCL1, MET and PARP1 was the top-ranked target, which was estimated by CytoHubba plug-in. The Molecular docking was performed for Q and Q3OG towards the PDB:1UNQ target. The binding score of Q and Q3OG was − 6.2 kcal/mol and − 6.58 kcal/mol respectively. Molecular dynamics simulation was conducted for Q and Q3OG towards the PDB:1UNQ target at 200 ns. This study's results help identify the multiple target sites for the bioactive compounds. Thus, synthesizing new chemical entity-based quercetin on structural modification may aid in eradicating AD complications. [ABSTRACT FROM AUTHOR]

In this study, the enantioselectivity of β‐cyclodextrin and its derivatives towards propranolol enantiomers are investigated by molecular dynamic (MD) simulations. β‐cyclodextrin (β‐CD) have previously been shown to be able to recognize propranolol (PRP) enantiomers. To improve upon the enantioselectivity of β‐cyclodextrin, we propose the use of an ionic‐liquid‐modified‐β‐cyclodextrin (β‐CD‐IL). β‐CD‐IL was found to be able to complex R and S propranolol enantiomers with differing binding energies. The molecular docking study reveals that the ionic liquid chain attached to the β‐CD molecule has significant interaction with propranolol. The formation of the most stable complex occurred between (S)‐β‐CD‐IL and (S)‐propranolol with an energy of −5.80 kcal/mol. This is attributed to the formation of a hydrogen bond between the oxygen of the propranolol and the hydrogen on the primary rim of the (S)‐β‐CD‐IL cavity. This interaction is not detected in other complexes. The root mean‐squared fluctuation (RMSF) value indicates that the NH group is the most flexible molecular fragment, followed by the aromatic group. Also of note, the formation of a complex between pristine β‐CD and (S)‐propranolol is the least favorable. [ABSTRACT FROM AUTHOR]

The primary aim of the current investigation is to contribute to SARS-CoV-2 research by identifying potential lead compounds for clinical applications, with a specific focus on inhibitors targeting the main protease (Mpro). In this research, molecular docking analysis was conducted using the software molecular operating environmental (MOE) to evaluate the potency of bioactive compounds sourced from medicinal plants as inhibitors of SARS--CoV-2 Mpro. Among 118 natural compounds with anti-HIV characteristics, the top seven candidates (h3, h84, h85, h87, h90, h108 and h110), were identified based on their superior binding energies with comparison to the reference ligand N3. These selected compounds exhibited binding affinities of -33.996, -35.336, -32.615, -32.154, -33.452, -31.903 and -40.360 kJ mol-1, respectively. To further refine our shortlist of potential candidates for human application, we examined the drug-likeness, and the pharmaceutical attributes of these compounds using the SwissADME web server. Among them, only two compounds, namely h85 and h87, demonstrated favorable pharmacological properties suitable for human administration. These two compounds were subsequently shortlisted for further investigation. To explore the conformational stability of ligands within the Mpro active site, we performed molecular dynamics (MD) simulations. These simulations showed reliable and steady trajectories, supported by analyses of root-mean-square-fluctuation (RMSF) and root--mean-square deviation (RMSD). These findings and favorable molecular properties as well as interaction profiles suggest that these two lead compounds may be promising SARS-CoV-2 therapeutic candidates. They present exciting starting points for further drug design. [ABSTRACT FROM AUTHOR]

Type 2 diabetes mellitus (T2DM) has become a serious public health problem both in our country and worldwide, being the most prevalent type of diabetes. The combined use of drugs in the treatment of T2DM leads to serious side effects, including gastrointestinal problems, liver toxicity, hypoglycemia, and treatment costs. Hence, there has been a growing emphasis on drugs that demonstrate dual interactions. Several studies have suggested that dual-target agents for peroxisome proliferator-activated receptor-γ (PPAR-γ) and alpha-glucosidase (α-glucosidase) could be a potent approach for treating patients with diabetes. We aim to develop new antidiabetic agents that target PPAR-γ and α-glucosidase enzymes using molecular modeling techniques. These compounds show dual interactions, are more effective, and have fewer side effects. The molecular docking method was employed to investigate the enzyme-ligand interaction mechanisms of 159 newly designed compounds with target enzymes. Additionally, we evaluated the ADME properties and pharmacokinetic suitability of these compounds based on Lipinski and Veber's rules. Compound 70, which exhibited favorable ADME properties, demonstrated more effective binding energy with both PPAR-γ and α-glucosidase enzymes (-12,16 kcal/mol, -10.07 kcal/mol) compared to the reference compounds of Acetohexamide (-9.31 kcal/mol, -7.48 kcal/mol) and Glibenclamide (-11.12 kcal/mol, -8.66 kcal/mol). Further, analyses of MM/PBSA binding free energy and molecular dynamics (MD) simulations were conducted for target enzymes with compound 70, which exhibited the most favorable binding affinities with both enzymes. Based on this information, our study aims to contribute to the development of new dual-target antidiabetic agents with improved efficacy, reduced side effects, and enhanced reliability for diabetes treatment. [ABSTRACT FROM AUTHOR]

Objective: The tandem Knoevenagel-cyclocondensation reaction of aromatic aldehydes, malonitrile, and phenylhydrazine in water and ethanol at room temperature is described as an effective, one-pot, threecomponent synthesis of many scientifically relevant heterocyclic compounds. Methods: As a part of our efforts, we have synthesized pyrazole-4-carbonitriles and characterized using various spectroscopic methods and subjected for antimicrobial analysis. Results and Discussion: From our analysis, we observed best in vitro candidate as 5-amino-3-(2,5-difluorophenyl)-1-phenyl-1H-pyrazole-4-carbonitrile. The molecular docking analysis on common bacterial target suggested the involvement of 2,2-dialkylglycine decarboxylase (PDB ID: 1D7U) as a target for compound (IVi) (docking score: –9.32 kcal/mol). Furthermore, a molecular dynamic simulation of 100 ns resulted in the stability of best docked candidate, (IVi): 1D7U. Conclusions: We propose that best docked candidate, (IVi) as potential antimicrobial agents. [ABSTRACT FROM AUTHOR]

Arteriovenous fistula (AVF) failure poses a significant prognostic challenge for patients undergoing hemodialysis. This study aimed to elucidate the mechanisms underlying the potential therapeutic effects of Taohong Siwu Decoction (TSD) in addressing AVF failure. A comprehensive approach integrating network pharmacology, molecular docking, and dynamic simulation was employed to validate it. The active constituents and putative targets of TSD were acquired from the Traditional Chinese Medicine Systems Pharmacology (TCMSP), Traditional Chinese Medicine Integrative Platform (TCMIP), and SwissTargetPrediction databases. Targets relevant to AVF failure were retrieved from the Online Mendelian Inheritance in Man (OMIM), DisGeNET, and GeneCards databases. The construction of the herb-ingredient-target network and protein-protein interaction (PPI) network was carried out using Cytoscape. Furthermore, we performed GO and KEGG enrichment analyses using the Metascape database. Molecular docking was executed with AutoDock, and results were visualized via PyMOL software. Additionally, molecular dynamics simulations were conducted using GROMACS. In this comprehensive analysis, we identified a total of 66 active ingredients and 769 potential targets, which subsequently led us to identify 87 targets closely associated with AVF failure. Notably, 10 key ingredients and 15 core targets were singled out. Among the pivotal constituents were gibberellin A120, gibberellin A30, kaempferol, and paeoniflorin, while core targets included TNF-α, IL-6, VEGFA and MMP9. Enrichment analyses, encompassing GO and KEGG, illuminated that TSD's potential therapeutic effects in addressing AVF failure might hinge on the modulation of inflammation, shear stress, and extracellular matrix remodeling. Furthermore, molecular docking investigations and dynamic simulations corroborated strong binding interactions between the key active constituents and the core targets. Consequently, it is plausible that TSD may enhance AVF patency primarily by regulating processes related to inflammation, shear stress, and extracellular matrix remodeling. These findings constitute a solid molecular rationale for the application of TSD in the context of AVF failure. [ABSTRACT FROM AUTHOR]

Phytophthora infestans (Mont.) de Bary, the oomycotic pathogen responsible for potato late blight, is the most devastating disease of potato production. The primary pesticides used to control oomycosis are phenyl amide fungicides, which cause environmental pollution and toxic residues harmful to both human and animal health. To address this, an antimicrobial peptide, NoPv1, has been screened to target Plasmopara viticola cellulose synthase 2 (PvCesA2) to inhibit the growth of Phytophthora infestans (P. infestans). In this study, we employed AlphaFold2 to predict the three-dimensional structure of PvCesA2 along with NoPv peptides. Subsequently, utilizing computational methods, we dissected the interaction mechanism between PvCesA2 and these peptides. Based on this analysis, we performed a saturation mutation of NoPv1 and successfully obtained the double mutants DP1 and DP2 with a higher affinity for PvCesA2. Meanwhile, dynamics simulations revealed that both DP1 and DP2 utilize a mechanism akin to the barrel-stave model for penetrating the cell membrane. Furthermore, the predicted results showed that the antimicrobial activity of DP1 was superior to that of NoPv1 without being toxic to human cells. These findings may offer insights for advancing the development of eco-friendly pesticides targeting various oomycete diseases, including late blight. [ABSTRACT FROM AUTHOR]

The shikimate pathway is crucial for the biosynthesis of aromatic amino acids in plants and represents a promising target for developing new herbicides. This work aimed to identify inhibitors of shikimate dehydrogenase (SDH), a key enzyme of the shikimate pathway that catalyzes the conversion of 3-dehydroshikimate to shikimate. Virtual screening and molecular dynamic simulations were performed on the SDH active site of Arabidopsis thaliana (AtSDH), and 6-nitroquinazoline-2,4-diol (NQD) was identified as a potential inhibitor. In vitro assays showed that NQD decreased the activity of AtSDH by reducing Vmax while keeping KM unchanged, indicating non-competitive inhibition. In vivo, hydroponic experiments revealed that NQD reduced the root length of soybean and maize. Additionally, NQD increased the total protein content and certain amino acids. Soybean roots uptake NQD more efficiently than maize roots. Furthermore, NQD reduced shikimate accumulation in glyphosate-treated soybean roots, suggesting its potential to restrict the flow of metabolites along the shikimate pathway in soybean. The simultaneous treatment of maize seedlings with glyphosate and NQD accumulated gallic acid in the roots, indicating that NQD inhibits SDH in vivo. Overall, the data indicate that NQD inhibits SDH both in vitro and in vivo, providing valuable insights into the potential development of herbicides targeting SDH. [ABSTRACT FROM AUTHOR]

Single-point mutations in the Kirsten rat sarcoma (KRAS) viral proto-oncogene are the most common cause of human cancer. In humans, oncogenic KRAS mutations are responsible for about 30% of lung, pancreatic, and colon cancers. One of the predominant mutant KRAS G12D variants is responsible for pancreatic cancer and is an attractive drug target. At the time of writing, no Food and Drug Administration (FDA) approved drugs are available for the KRAS G12D mutant. So, there is a need to develop an effective drug for KRAS G12D. The process of finding new drugs is expensive and time-consuming. On the other hand, in silico drug designing methodologies are cost-effective and less time-consuming. Herein, we employed machine learning algorithms such as K-nearest neighbor (KNN), support vector machine (SVM), and random forest (RF) for the identification of new inhibitors against the KRAS G12D mutant. A total of 82 hits were predicted as active against the KRAS G12D mutant. The active hits were docked into the active site of the KRAS G12D mutant. Furthermore, to evaluate the stability of the compounds with a good docking score, the top two complexes and the standard complex (MRTX-1133) were subjected to 200 ns MD simulation. The top two hits revealed high stability as compared to the standard compound. The binding energy of the top two hits was good as compared to the standard compound. Our identified hits have the potential to inhibit the KRAS G12D mutation and can help combat cancer. To the best of our knowledge, this is the first study in which machine-learning-based virtual screening, molecular docking, and molecular dynamics simulation were carried out for the identification of new promising inhibitors for the KRAS G12D mutant. [ABSTRACT FROM AUTHOR]

Context: SHP2 is a non-receptor protein tyrosine phosphatase to remove tyrosine phosphorylation. Functionally, SHP2 is an essential bridge to connect numerous oncogenic cell-signaling cascades including RAS-ERK, PI3K-AKT, JAK-STAT, and PD-1/PD-L1 pathways. This study aims to discover novel and potent SHP2 inhibitors using a hierarchical structure-based virtual screening strategy that combines molecular docking and the fragment molecular orbital method (FMO) for calculating binding affinity (referred to as the Dock-FMO protocol). For the SHP2 target, the FMO method prediction has a high correlation between the binding affinity of the protein–ligand interaction and experimental values (R2 = 0.55), demonstrating a significant advantage over the MM/PBSA (R2 = 0.02) and MM/GBSA (R2 = 0.15) methods. Therefore, we employed Dock-FMO virtual screening of ChemDiv database of ∼2,990,000 compounds to identify a novel SHP2 allosteric inhibitor bearing hydroxyimino acetamide scaffold. Experimental validation demonstrated that the new compound (E)-2-(hydroxyimino)-2-phenyl-N-(piperidin-4-ylmethyl)acetamide (7188–0011) effectively inhibited SHP2 in a dose-dependent manner. Molecular dynamics (MD) simulation analysis revealed the binding stability of compound 7188–0011 and the SHP2 protein, along with the key interacting residues in the allosteric binding site. Overall, our work has identified a novel and promising allosteric inhibitor that targets SHP2, providing a new starting point for further optimization to develop more potent inhibitors. Methods: All the molecular docking studies were employed to identify potential leads with Maestro v10.1. The protein–ligand binding affinities of potential leads were further predicted by FMO calculations at MP2/6-31G* level using GAMESS v2020 system. MD simulations were carried out with AmberTools18 by applying the FF14SB force field. MD trajectories were analyzed using VMD v1.9.3. MM/GB(PB)SA binding free energy analysis was carried out with the mmpbsa.py tool of AmberTools18. The docking and MD simulation results were visualized through PyMOL v2.5.0. [ABSTRACT FROM AUTHOR]

Cancer is a serious threat to human life and social development and the use of scientific methods for cancer prevention and control is necessary. In this study, HQSAR, CoMFA, CoMSIA and TopomerCoMFA methods are used to establish models of 65 imidazo[4,5-b]pyridine derivatives to explore the quantitative structure-activity relationship between their anticancer activities and molecular conformations. The results show that the cross-validation coefficients q2 of HQSAR, CoMFA, CoMSIA and TopomerCoMFA are 0.892, 0.866, 0.877 and 0.905, respectively. The non-cross-validation coefficients r2 are 0.948, 0.983, 0.995 and 0.971, respectively. The externally validated complex correlation coefficients r2pred of external validation are 0.814, 0.829, 0.758 and 0.855, respectively. The PLS analysis verifies that the QSAR models have the highest prediction ability and stability. Based on these statistics, virtual screening based on R group is performed using the ZINC database by the Topomer search technology. Finally, 10 new compounds with higher activity are designed with the screened new fragments. In order to explore the binding modes and targets between ligands and protein receptors, these newly designed compounds are conjugated with macromolecular protein (PDB ID: 1MQ4) by molecular docking technology. Furthermore, to study the nature of the newly designed compound in dynamic states and the stability of the protein-ligand complex, molecular dynamics simulation is carried out for N3, N4, N5 and N7 docked with 1MQ4 protease structure for 50 ns. A free energy landscape is computed to search for the most stable conformation. These results prove the efficient and stability of the newly designed compounds. Finally, ADMET is used to predict the pharmacology and toxicity of the 10 designed drug molecules. [ABSTRACT FROM AUTHOR]

The diterpene 7α-acetoxy-6β-hydroxyroyleanone isolated from Plectranthus grandidentatus demonstrates promising antibacterial, anti-inflammatory and anticancer properties. However, its bioactivity may be enhanced via strategic structural modifications of such natural products through semisynthesis. The anticancer potential of 7α-acetoxy-6β-hydroxyroyleanone and five derivatives was analyzed in silico via the prediction of chemicals absorption, distribution, metabolism, excretion, and toxicity (ADMET), quantum mechanical calculations, molecular docking and molecular dynamic simulation. The protein targets included regulators of apoptosis and cell proliferation. Additionally, network pharmacology was used to identify potential targets and signaling pathways. Derivatives 7α-acetoxy-6β-hydroxy-12-O-(2-fluoryl)royleanone and 7α-acetoxy-6β-(4-fluoro)benzoxy-12-O-(4-fluoro)benzoylroyleanone achieved high predicted binding affinities towards their respective protein panels, with stable molecular dynamics trajectories. Both compounds demonstrated favorable ADMET parameters and toxicity profiles. Their stability and reactivity were confirmed via geometry optimization. Network analysis revealed their involvement in cancer-related pathways. Our findings justify the inclusion of 7α-acetoxy-6β-hydroxy-12-O-(2-fluoryl)royleanone and 7α-acetoxy-6β-(4-fluoro)benzoxy-12-O-(4-fluoro)benzoylroyleanone in in vitro analyses as prospective anticancer agents. Our binding mode analysis and stability simulations indicate their potential as selective inhibitors. The data will guide studies into their structure optimization, enhancing efficacy and drug-likeness. [ABSTRACT FROM AUTHOR]

Introduction: The CXCR4 chemokine receptor is a G protein-coupled receptor that plays a role in many physiological processes and diseases, such as cancer metastasis, HIV infection, and immune response. Because of this, it may be possible to target it therapeutically. In addition, the active ingredient of Phaseolus vulgaris L (PVL) has been reported to have anti-inflammatory, antioxidant, and anticancer properties. Novel CXCR4 antagonists from natural resources can be a promising drug development product using a computational approach. This study aims to explore the active compound in PVL that has the responsibility to inhibit CXCR4 using molecular docking and dynamics simulation. Materials and methods: Pharmacokinetic analysis were performed using the pkCSM, OSIRIS for toxicity risk analysis, and the PerMM for membrane permeability assessment. Molecular docking was performed using PyRx software to determine the interaction between the CXCR4 target protein from the PDB database and the active component of PVL from the PubChem database. A molecular dynamics (MD) simulation was performed to determine the stability of the interaction using the WEBGRO Macromolecular Simulations online server. The analysis were performed by comparing the results with plerixafor as a control ligand. Results and discussion: The pharmacokinetic analysis of quercetin, kaempferol, myricetin, catechin, 3,4-dihydroxybenzoic acid, and daidzin in PVL showed that they met the drug-like criteria. These chemicals were expected to have medium-risk effects on mutagenesis and tumorigenesis, with the exception of catechin, which has no risk of toxicity, and daidzin, which has high-risk effects on mutagenesis and reproduction. Molecular docking identified that quercetin (− 6.6 kcal/mol), myricetin (− 6.6 kcal/mol), catechin (− 6.5 kcal/mol), and 3,4-dihydroxybenzoic acid (− 5.4 kcal/mol) bind to CXCR4 with the highest affinity compared to plerixafor (− 5.0 kcal/mol) and can bind to the same binding pocket with key residues Asp187, Asp97, and Glu288. The MD simulation analysis showed that quercetin has a similar stability interaction compared to the control. Conclusions: Considering the pharmacokinetic analysis, molecular docking, and MD simulations, quercetin, myricetin, and 3,4-dihydroxybenzoic acid have the potential to become CXCR4 agonists with their good oral bioavailability and safety properties for the novel drug candidates. Future studies are needed to consider the molecular docking result. [ABSTRACT FROM AUTHOR]

Objective: This article is focused on synthesis and characterisation of 1,1-(((5-(3,4,5triethoxybenzyl)pyrimidine-2,4-diyl))bis(azanediyl))bis(substituted phenyl methylene))bis(naphthalen-2-ol) moieties and evaluated for antibacterial and antioxidant activities as well as molecular docking and molecular dynamic simulation investigations. Methods: In this article we conducted one-pot three component reactions through Betti type reaction. Agar diffusion method was used to evaluate anti-bacterial properties. The DPPH method was used to determine antioxidant activity results. Results: A series of 1,1-(((5-(3,4,5triethoxybenzyl)-pyrimidine-2,4-diyl))bis(azanediyl))bis(substituted phenyl methylene))bis(naphthalen-2-ol) were synthesized via Betti type reaction and evaluated for their antibacterial and antioxidant activities. Further, all the synthesized compounds were characterized by FT-IR, 1H, and 13C NMR, and mass spectral analysis. Discussion: Molecular docking was carried out to study possible potential binding interaction of synthesized Betti base derivatives with 1NC6 PDB as receptor. The molecular dynamic (MD) was performed to investigate stability of binding interaction of drug-target (protein–ligand) complex. All the synthesized compounds were investigated for their antibacterial and antioxidant activity. Conclusions: Betti base derivatives were synthesized and studied on the basis of computer aided drug design including docking and molecular dynamic (MD) simulations and pharmacologically assessed for antioxidant and antibacterial activity. Molecular docking investigation revealed that compounds showed better binding energies in the range –4.1 to –7.3 kcal/mol suggests that the binding occurs efficiently in the receptor–ligand complex. These Betti base derivatives were synthesized via Betti base protocol at 70oC through one-pot three component reaction with acceptable yields, as cost efficient, high yield, easy workup and environmental friendliness. Afterwards, obtained molecules have characterized by FT-IR, NMR, and Mass spectra which confirms the chemical structure of the synthesized compounds. [ABSTRACT FROM AUTHOR]

Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and − 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder. [ABSTRACT FROM AUTHOR]

The present study was based on an exploration of NCI database for searching specific CDK-7 kinase inhibitor by HTVS, SP, XP, molecular docking, molecular dynamic simulation, and ADMET evaluation. The best CDK-7 kinase inhibitors (NCI613391, NCI169676, NCI281246, NCI339580) were identified via NCI database screening. The stability of binding interaction between receptor protein and protein-ligand complex of potent finding compounds (NCI613391) was further confirmed by dynamics simulations and MM--GBSA. The RMSD value of receptor and receptor-ligand complexes was analysed, and it revealed the stability of binding interactions and remained stable throughout the simulation. The RMSF values and gyration radius of the unbound receptor and backbone atoms of the complex were found to be equal, which indicates that the drug molecule inside the CDK7 receptor is also stable. The study of MM-GBSA data also revealed stronger binding interactions of ligands to CDK7 receptors. With the exception of NCI169676, all compounds were shown to be substrates for CYP450 2D6, CYP450 3A4, inhibitors of CYP450 2C9, and non-inhibitors of p-glycoprotein. All compounds were qualified and found suitable to be as drug-likeness according to the Lipinski rule, Ghose filter, MDDR like rule and CMC-like rule. The compound (NCI613391) exhibited human intestinal absorption (76.08%), displayed negative AMES and T.E.S.T (US-EPA) toxicity with OSIRIS property and found to be a promising CDK-7 kinase inhibitor and its efficacy may be further explored in clinical trials. [ABSTRACT FROM AUTHOR]

Tuberculosis, also known as TB, is a widespread bacterial infection that remains a significant global health issue. This study focuses on conducting a thorough investigation into the synthesis, evaluation of anti-Tb activity, molecular docking, and molecular dynamic simulation of substituted benzimidazole derivatives. A series of twelve substituted benzimidazole derivatives (1–12) were successfully synthesized, employing a scaffold consisting of electron-withdrawing and electron-donating groups. The newly synthesized compounds were defined by their FTIR, 1H NMR, and mass spectra. The microplate Alamar blue assay (MABA) was used to evaluate the antimycobacterial activity of the synthesized compound against Mycobacterium tuberculosis (Mtb). Compounds 7 (MIC = 0.8 g/mL) and 8 (MIC = 0.8 g/mL) demonstrated exceptional potential to inhibit M. tuberculosis compared to the standard drug (isoniazid). In addition, the synthesized compounds were docked with the Mtb KasA protein (PDB ID: 6P9K), and the results of molecular docking and molecular dynamic simulation confirmed the experimental results, as compounds 7 and 8 exhibited the highest binding energy of −7.36 and −7.17 kcal/mol, respectively. The simulation results such as the RMSD value, RMSF value, radius of gyration, and hydrogen bond analysis illustrated the optimum potential of compounds 7 and 8 to inhibit the M. tuberculosis strain. Hydrogen bond analysis suggested that compound 7 has greater stability and affinity towards the KasA protein compared to compound 8. Moreover, both compounds (7 and 8) were safe for acute inhalation and cutaneous sensitization. These two compounds have the potential to be potent M. tuberculosis​ inhibitors. [ABSTRACT FROM AUTHOR]

Background: Obesity is a precursor for many co-morbid diseases. One of the main triggering factors for obesity is the abnormal expansion of white adipose tissue characterized by high rates of genesis and differentiation of precursor cells into mature adipocytes. As a result, targeting adipogenesis and adipogenic transcription factors opens new roadmaps for developing novel antiobesity pharmacotherapies. The present study was intended to rationally develop topiramate–phenolic acid conjugate for targeting obesity via inhibition of PPARγ which is often considered as the master regulator of adipogenesis. Results: 2D QSAR models were built to foretell PPARγ inhibitory activity of designed conjugates. The models presented excellent robustness, goodness of fit, and predictive capability compounds. The highest PPARγ inhibitory activity was predicted for T3 (topiramate–caffeic acid conjugate) with a pIC50 value of 7.08 µM. Molecular docking was performed for all the designed conjugates against PPARγ (PDB ID: 3VSO). The highest binding affinity was exhibited by T3 (− 11.27 kcal/mol) and displayed strong and stable interactions with the receptor within the allosteric pocket in comparison to the irreversible PPARγ antagonist, GW9662 (binding affinity, − 9.0 kcal/mol). These results were confirmed by subjecting the best-docked molecules to molecular dynamic simulations. The PPARγ–T3 complex was observed to be most stable with maximum number of hydrogen bonds (maximum observed RMSD = 0.57 Å at 100 ns) in comparison to PPARγ–topiramate and PPARγ–caffeic acid complexes. Consequently, T3 was synthesized and further subjected to in vitro screening. The TR-FRET assay established T3 as a PPARγ antagonist (IC50 = 6.78 µM). T3 also significantly reduced the lipid buildup in the 3T3-L1 adipocytes in a dose-dependent manner. In addition, T3 also reduced the protein expression levels of PPARγ as evidenced from western blot results. Conclusions: Studies clearly indicated that T3 reduces adipose tissue cell differentiation by downstreaming PPARγ expression at protein levels, thereby emerging as a novel scaffold for antiobesity pharmacotherapy. [ABSTRACT FROM AUTHOR]

Huperzine A (HUP) plays a crucial role in Alzheimer's therapy by enhancing cognitive function through increased cholinergic activity as a reversible acetylcholinesterase (AChE) inhibitor. Despite some limitations being seen in AChE inhibitors, ongoing research remains dedicated to finding innovative and more effective treatments for Alzheimer's disease. To achieve the goal of the discovery of potential HUP analogues with improved physicochemical properties, less toxic properties, and high biological activity, many in silico methods were applied. Based on the acetylcholinesterase–ligand complex, an e-pharmacophore model was developed. Subsequently, a virtual screening involving a collection of 1762 natural compounds, sourced from the PubChem database, was performed. This screening yielded 131 compounds that exhibited compatibility with the established pharmacophoric hypothesis. These selected ligands were then subjected to molecular docking within the active site of the 4EY5 receptor. As a result, we identified four compounds that displayed remarkable docking scores and exhibited low free binding energy to the target. These top four compounds, CID_162895946, CID_44461278, CID_44285285, and CID_81108419, were submitted to ADMET prediction and molecular dynamic simulations, yielding encouraging findings in terms of their pharmacokinetic characteristics and stability. Finally, the molecular dynamic simulation, cross-dynamic correlation matrix, free energy landscape, and MM-PBSA calculations demonstrated that two ligands from the selected ligands formed very resilient complexes with the enzyme acetylcholinesterase, with significant binding affinity. Therefore, these two compounds are recommended for further experimental research as possible (AChE) inhibitors. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 virus and its mutations have affected human health globally and created significant danger for the health of people all around the world. To cure this virus, the human Angiotensin Converting Enzyme-2 (ACE2) receptor, the SARS-CoV-2 main protease (Mpro), and spike proteins were found to be likely candidates for the synthesis of novel therapeutic drug. In the past, proteins were capable of engaging in interaction with a wide variety of ligands, including both manmade and plant-derived small molecules. Pyrus communis L., Ginko bibola, Carica papaya, Syrian rue, and Pimenta dioica were some of the plant species that were studied for their tendency to interact with SARS-CoV-2 main protease (Mpro) in this research project (6LU7). This scenario investigates the geometry, electronic, and thermodynamic properties computationally. Assessing the intermolecular forces of phytochemicals with the targets of the SARS-CoV-2 Mpro spike protein (SP) resulted in the recognition of a compound, kaempferol, as the most potent binding ligand, −7.7 kcal mol−1. Kaempferol interacted with ASP-187, CYS-145, SER-144, LEU 141, MET-165, and GLU-166 residues. Through additional molecular dynamic simulations, the stability of ligand–protein interactions was assessed for 100 ns. GLU-166 remained intact with 33% contact strength with phenolic OH group. We noted a change in torsional conformation, and the molecular dynamics simulation showed a potential variation in the range from 3.36 to 7.44 against a 45–50-degree angle rotation. SAR, pharmacokinetics, and drug-likeness characteristic investigations showed that kaempferol may be the suitable candidate to serve as a model for designing and developing new anti-COVID-19 medicines. [ABSTRACT FROM AUTHOR]

We provide promising computational (in silico) data on phytochemicals (compounds 1–10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1–10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1–10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests. [ABSTRACT FROM AUTHOR]

Simple Summary: One of the most destructive pests of cruciferous plants that quickly develops resistance to most pesticide groups is Plutella xylostella. Investigating the resistant strain of P. xylostella revealed the molecular mechanisms underlying resistance to chlorpyrifos, concentrating specifically on the ace1 gene. The sequencing results revealed amino acid substitutions in ace1 of the resistant strain. The structures of the wild-type and mutant ace1 strains were compared via molecular dynamics (MDs) simulations and docking investigations. The results showed that the mutant ace1 has different substrate entry points and structural modifications that affect the enzyme inhibitor affinity. Significant differences in ace1 gene expression between the mutant and wild-type strains were revealed by real-time quantitative PCR, which raises the possibility of a relationship between ace1 mutations and changes in mRNA transcription levels. Plutella xylostella, a destructive crucifer pest, can rapidly develop resistance to most classes of pesticides. This study investigated the molecular resistance mechanisms to chlorpyrifos, an organophosphate pesticide. Two P. xylostella genes, ace1 and ace2, were described. The nucleotide sequence results revealed no variation in ace2, while the resistant strain (Kar-R) had four amino acid alterations in ace1, two of which (A298S and G324A) were previously shown to confer organophosphate resistance in P. xylostella. In the present study, the 3D model structures of both the wild-type (Gu-S) and mutant (Kar-R) of P. xylostella ace1 strains were studied through molecular dynamics (MDs) simulations and molecular docking. Molecular dynamics simulations of RMSD revealed less structural deviation in the ace1 mutant than in its wild-type counterpart. Higher flexibility in the 425–440 amino acid region in the mutant active site (Glu422 and Acyl pocket) increased the active site's entropy, reducing the enzyme's affinity for the inhibitors. Gene expression analysis revealed that the relative transcription levels of ace1 were significantly different in the Kar-R strain compared with the Gu-S strain. This study enhances the understanding of the mechanisms governing ace1′s resistance to insecticide and provides essential insights for new insecticides as well as valuable insights into environmentally conscious pest management techniques. [ABSTRACT FROM AUTHOR]

In this study, (z)-5-((3-(2,3-dihydroxyphenyl) acryloyl) oxy)- 1,3,4-trihydroxycyclohexa-2,4-diene-1-carboxylic acid (chlorogenic acid) was isolated and characterized using UV-Visible, 1H NMR and 13C NMR, FT-IR, along with detailed investigation using density functional theory (DFT), in-silico molecular docking, and molecular dynamics (MD) simulation. Results from DFT calculation indicates that the titled compound is very stable with energy gap of 3.7–7.8 for variable functionals, and similarly, the structural parameters show very close agreement with X-ray data for bond lengths and angles. The FT-IR spectrum results revealed stretching vibration O–H (3366 cm−1), C=O (1689 cm−1), C–H (1636, 1606, 1522, and 1442 cm−1), C–O (1192 and 1122 cm−1). The drug-likeness analyses and ADME studies showed drug-likeness ability and good oral behavior of the investigated compound as it obeys Lipinski, Ghose, Veber and Egan rules. Hepatotoxic and immunotoxic activities were indicated for the toxicity/toxicological endpoints of the studied compound. The molecular docking indicates a binding affinity of −8.30 and 9.5 kcal/mol for the titled compound, which is higher than the standard drug. From the molecular dynamic simulation results, chlorogenic-2H14 (complex B) revealed variations in RMSD values of less than 3Å, indicating that the protein structure underwent minor conformational changes throughout the simulation. Chlorogenic-protein complexes had average RGyr values of 3.704 − 4.907Å, which indicates compaction during the simulation. Therefore, it can be said that the titled compound has potential to be effective as an agent for cholera management, and the results obtained can be platform further in-vitro, vivo and clinical trials. [ABSTRACT FROM AUTHOR]

The study is focused on examining 2,5‐Substituted 4‐Pyrone based compounds through quantum chemical and topological analysis techniques, evaluating the properties of these compounds, including their geometrical structure, intermolecular interactions and assess their possible applications. Additionally, the molecular stability, charge delocalization and UV‐Visible data was investigated and compared with the calculated energy and oscillator strength using the TD‐DFT approach. The researchers observed that charge transfer occurred within the molecule, indicated by the HOMO and LUMO energies. It was also found that the compound exhibited planarity and higher chemical reactivity. The calculated Mulliken charges and molecular electrostatic potential were used to interpret the Fukui index data that help predict reactive sites and understand the reactivity patterns of specific atoms in a compound. The study is aimed to understand the role of NCI in the molecule under investigation using electron localization functions and localized orbit locator methods. Molecular docking and ADMET studies were conducting involving a detailed MD simulation of a protein‐ligand complex using the OPLS3e force field and the SPC water model. These findings could prove to be beneficial in developing new therapeutic agents with various pharmacological effects and potential toxicities. [ABSTRACT FROM AUTHOR]

Therapeutic targeting of Sp1 transcription factor and survivin, are studied in various cancers due to their consistent overexpression. These markers result in poorer cancer prognoses and their downregulation has been investigated as an effective treatment approach. Mithramycin-A and Tolfenamic acid are two drugs with innate anti-cancer properties and are suggested to be able to target Sp1 through GC/GT DNA binding interference, however in-depth binding and mechanistic studies are lacking. Through docking analysis, we investigated Mithramycin-A and Tolfenamic acid in terms of their specific binding interactions with Sp1 and survivin. Through further molecular dynamics simulations including Root Mean Square (RMS) Fluctuation and RMS Deviation, rGYr, and H-bond analysis, we identified critical residues involved in drug interactions with each protein in question. We show Mithramycin-A as the superior binding candidate to each protein and found that it exhibited stronger binding with Sp1, and then survivin. Subsequent molecular dynamics simulations followed the same trend as initial binding energy calculations and showed crucial amino acids involved in each Mithramycin-A-protein complex. Our findings warrant further investigation into Mithramycin-A and its specific interaction with Sp1 and their downstream targets giving a better understanding of Mithramycin-A and its potential as an effective cancer treatment. [Display omitted] • Docking studies showed binding affinity for both Mithramycin and tolfenamic acid with Sp1 and BIRC5. • Docking analysis confirmed that Mithramycin exhibits higher binding affinity in compared to Tolfenamic acid. • Molecular Docking/Dynamic Simulation studies are consistent with in vitro results using Ewing sarcoma cells. • Intermolecular H-bonds revealed novel bonds and interactions forming post Molecular Dynamic simulations. [ABSTRACT FROM AUTHOR]

Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer's randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, − 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein–ligand complexes, yielding five promising novel UPPS inhibitors. [ABSTRACT FROM AUTHOR]

Isoxazolidine derivatives were designed, synthesized, and characterized using different spectroscopic techniques and elemental analysis and then evaluated for their ability to inhibit both α-amylase and α-glucosidase enzymes to treat diabetes. All synthesized derivatives demonstrated a varying range of activity, with IC50 values ranging from 53.03 ± 0.106 to 232.8 ± 0.517 μM (α-amylase) and from 94.33 ± 0.282 to 258.7 ± 0.521 μM (α-glucosidase), revealing their high potency compared to the reference drug, acarbose (IC50 = 296.6 ± 0.825 µM and 780.4 ± 0.346 µM), respectively. Specifically, in vitro results revealed that compound 5d achieved the most inhibitory activity with IC50 values of 5.59-fold and 8.27-fold, respectively, toward both enzymes, followed by 5b. Kinetic studies revealed that compound 5d inhibits both enzymes in a competitive mode. Based on the structure–activity relationship (SAR) study, it was concluded that various substitution patterns of the substituent(s) influenced the inhibitory activities of both enzymes. The server pkCSM was used to predict the pharmacokinetics and drug-likeness properties for 5d, which afforded good oral bioavailability. Additionally, compound 5d was subjected to molecular docking to gain insights into its binding mode interactions with the target enzymes. Moreover, via molecular dynamics (MD) simulation analysis, it maintained stability throughout 100 ns. This suggests that 5d possesses the potential to simultaneously target both enzymes effectively, making it advantageous for the development of antidiabetic medications. [ABSTRACT FROM AUTHOR]

Potentilla nepalensis belongs to the Rosaceae family and has numerous therapeutic applications as potent plant-based medicine. Forty phytoconstituents (PCs) from the root and stem through n-hexane (NR and NS) and methanolic (MR and MS) extracts were identified in earlier studies. However, the PCs affecting human genes and their roles in the body have not previously been disclosed. In this study, we employed network pharmacology, molecular docking, molecular dynamics simulations (MDSs), and MMGBSA methodologies. The SMILES format of PCs from the PubChem was used as input to DIGEP-Pred, with 764 identified as the inducing genes. Their enrichment studies have shown inducing genes' gene ontology descriptions, involved pathways, associated diseases, and drugs. PPI networks constructed in String DB and network topological analyzing parameters performed in Cytoscape v3.10 revealed three therapeutic targets: TP53 from MS-, NR-, and NS-induced genes; HSPCB and Nf-kB1 from MR-induced genes. From 40 PCs, two PCs, 1b (MR) and 2a (MS), showed better binding scores (kcal/mol) with p53 protein of −8.6 and −8.0, and three PCs, 3a, (NR) 4a, and 4c (NS), with HSP protein of −9.6, −8.7, and −8.2. MDS and MMGBSA revealed these complexes are stable without higher deviations with better free energy values. Therapeutic targets identified in this study have a prominent role in numerous cancers. Thus, further investigations such as in vivo and in vitro studies should be carried out to find the molecular functions and interlaying mechanism of the identified therapeutic targets on numerous cancer cell lines in considering the PCs of P. nepalensis. [ABSTRACT FROM AUTHOR]

Depression, along with grief and anxiety, is currently one of the most common mental illnesses. It was placed 25th among the major diseases. QSAR (CoMFA) of 37 compounds with MAO-A inhibitory activity yielded the most significant QSAR model, m.3, with r²= 0.963, SDEC= 0.129, q² = 0.742, SDEP= 0.34. Using the lead likeness matrix, thirty-seven 1,5-disubstituted MAO-A inhibitors were developed and tested based on the QSAR models. The top 13 compounds were identified. Furthermore, compound 2B (ΔG: -10.3 kcal mol-1, RMSD: 0.151 Å) was selected among the top 13 hits obtained from molecular docking experiments. Significant interactions were also observed, including π-π contacts with Phe208, Tyr444, Trp407, and hydrogen bond interactions with Ala68 and Tyr69. Furthermore, dynamic modelling demonstrated that compound 2B (0.11 nm) has higher overall stability than clorgyline, with a lower RMSD value, and may reach equilibrium in the final 20-25 ns. In terms of RMSF, 2B produced around 0.34 nm with less variation than clorgyline. Throughout the simulation, 2B (No. of H-bond: 6) had more hydrogen bonding than clorgyline (No. of H-bond: 3) with the highest occupancy, i.e. 117.39% for GLU216, 29% for TYR444, and 49% for PRO72, and so on. Compound 2B was proven to be the most essential throughout the experiments. These new chemicals will be optimized in vitro and in vivo in the future. This study will surely contribute to the development of novel MAO-A inhibitors for the treatment of depression. [ABSTRACT FROM AUTHOR]

Context: Electronic sustainable behavior on the material surface and in situ metal configuration were accompted with some metal atoms like Li, Na, and K elements. Metal-doped ZrO2 crystal exported modified characteristics related to electronic conduction and exhibited some dynamic modification around the surface of the metal oxide. Computational perturbations were considered to discuss the modification behavior in addition to the studied Li, Na, and K metals. Optimization of the three doping systems was achieved followed by generating DOS and electronic band structure maps. A dynamic simulation was performed with temperature over 2000 k: the presence of the metal on the surface and prediction of its ZrO2 inclusion leading to access adsorption behavior, besides generating predictive designed models described the adsorption affinity on the solid-state surface. It cannot be neglected the importance of various metals as a main role in chemotherapy. Molecular docking investigation was considered to predict the binding behavior of the studied metal ZrO2 carrier system as an anticancer agent. Also, docking affinity was helpful in comparing the active sites binding for the studied metals, resulting in a notable binding affinity for both Li- and Na-zirconia incorporation. Methods: The program PWSCF, which is a component of the quantum ESPRESSO suite for quantum simulation of materials, was used to construct geometric systems. The generalized gradient approximation in the Perdew-Burke-Ernzerhof (GGA/PBE) function with D3 correction (Becke-Jonson damping) was applied to the exchange-correlation energy. As the last step in the DFT postulation and design, adsorption locator annealing was carried out on the convergent models using the Materials Studio simulation package. The main roles played by metal atoms are in protein binding and the suppression of bio-active regions. For the docking process, the protein was produced using AutoDock 4.2 and Discovery Studio software in accordance with the usual methodology. Chimera and Discovery Studio were used to examine the docking data that was processed after generating specific grid box dimensions for 7BTN. [ABSTRACT FROM AUTHOR]

Significant advancements have been made in the domain of targeted anticancer therapy for the management of malignancies in recent times. VEGFR-2 is characterised by its pivotal involvement in angiogenesis and subsequent mechanisms that promote tumour cells survival. Herein, novel N-arylmethyl-aniline/chalcone hybrids 5a–5n were designed and synthesised as potential anticancer and VEGFR-2 inhibitors. The anticancer activity was evaluated at the NCI-USA, resulting in the identification of 10 remarkably potent molecules 5a–5j that were further subjected to the five-dose assays. Thereafter, they were explored for their VEGFR-2 inhibitory activity where 5e and 5h emerged as the most potent inhibitors. 5e and 5h induced apoptosis with cell cycle arrest at the SubG0-G1 phase within HCT-116 cells. Moreover, their impact on some key apoptotic genes was assessed, suggesting caspase-dependent apoptosis. Furthermore, molecular docking and molecular dynamics simulations were conducted to explore the binding modes and stability of the protein–ligand complexes. [ABSTRACT FROM AUTHOR]

γ-Aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that degrades γ-aminobutyric (GABA) in the brain. GABA is an important inhibitory neurotransmitter that plays important neurological roles in the brain. Therefore, GABA-AT is an important drug target that regulates GABA levels. Novel and potent drug development to inhibit GABA-AT is still a very challenging task. In this study, we aimed to devise novel and potent inhibitors against GABA-AT using computer-aided drug design (CADD) tools. Since the crystal structure of human GABA-AT was not yet available, we utilized a homologous structure derived from our previously published paper. To identify highly potent compounds relative to vigabatrin, an FDA-approved drug against human GABA-AT, we developed a pharmacophore analysis protocol for 530,000 Korea Chemical Bank (KCB) compounds and selected the top 50 compounds for further screening. Preliminary biological analysis was carried out for these 50 compounds and 16 compounds were further assessed. Subsequently, molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations were carried out. In the results, four predicted compounds, A07, B07, D08, and H08, were found to be highly potent and were further evaluated by a biological activity assay to confirm the results of the GABA-AT activity inhibition assay. [ABSTRACT FROM AUTHOR]

Synthesis of phenyl/benzothiazole functionalized C−C linked pyrazolyl‐thiazoles has been achieved from non‐lachrymatory α‐tosyloxy pyrazolylketones with different thioamides. The pyrazolyl‐thiazoles were characterized by spectroscopic studies and evaluated for antimicrobial activity and phytotoxicity. Compound 6 n displayed better activity with MIC value of 0.0045 μmol/mL against Gram‐positive bacteria B. cereus in comparison to the standard drug Ciprofloxacin (0.0047 μmol/mL). Compound 6 i displayed better activity against fungal strain C. albicans (MIC=0.0152 μmol/mL) in comparison to the standard drug Fluconazole (0.0204 μmol/mL). Compound 6 o diplayed 95 % cell viability against Mouse Fibroblast cell line and 100 % plant seed germination. Docking studies at the topoisomerase II DNA gyrase B (PDB ID: 1KZN) and C. albicans (PDB ID: 1IYL) were used to investigate potential interactions between the most active compound and the receptor protein. The stability of the compounds with 1KZN and 1IYL by molecular dynamic simulations showed that 6 r, 6 n and 6 i present leading structures for next drug development because of their simple synthesis and useful bioactivity. [ABSTRACT FROM AUTHOR]

In this study, six analogs of 2-arylquinoline were synthesized and evaluated for their in vitro and in vivo antiplasmodial and leishmanicidal activity. At a later stage, hemolytic activity and druggability were tested in vitro and in silico, respectively, observing as a result: firstly, compounds showed half-maximal effective concentration (EC50) values between 3.6 and 19.3 µM. Likewise, a treatment using the compounds 4a–f caused improvement in most of the treated hamsters and cured some of them. Regarding the antiplasmodial activity, the compounds showed moderate to high activity, although they did not show hemolytic activity. Furthermore, 4e and 4f compounds were not able to control P. berghei infection when administered to animal models. Molecular dynamic simulations, molecular docking and ligand binding affinity indicate good characteristics of the studied compounds, which are expected to be active. And lastly, the compounds are absorbable at the hematoencephalic barrier but not in the gastrointestinal tract. In summary, ADMET properties suggest that these molecules may be used as a safe treatment against Leishmania. [ABSTRACT FROM AUTHOR]

Neurodegenerative disorders, such as Alzheimer's disease (AD), negatively affect the economic and psychological system. For AD, there is still a lack of disease-altering treatments and promising cures due to its complex pathophysiology. In this study, we computationally screened the natural database of fungal metabolites against three known therapeutic target proteins of AD. Initially, a pharmacophore-based, drug-likeness category was employed for screening, and it filtered the 14 (A–N) best hits out of 17,544 fungal metabolites. The 14 best hits were docked individually against GSK-3β, the NMDA receptor, and BACE-1 to investigate the potential of finding a multitarget inhibitor. We found that compounds B, F, and L were immuno-toxic, whereas E, H, I, and J had a higher LD50 dose (5000 mg/kg). Among the examined metabolites, the Bisacremine-C (compound I) was found to be the most active molecule against GSK-3β (ΔG: −8.7 ± 0.2 Kcal/mol, Ki: 2.4 × 106 M−1), NMDA (ΔG: −9.5 ± 0.1 Kcal/mol, Ki: 9.2 × 106 M−1), and BACE-1 (ΔG: −9.1 ± 0.2 Kcal/mol, Ki: 4.7 × 106 M−1). It showed a 25-fold higher affinity with GSK-3β, 6.3-fold higher affinity with NMDA, and 9.04-fold higher affinity with BACE-1 than their native ligands, respectively. Molecular dynamic simulation parameters, such as RMSD, RMSF, Rg, and SASA, all confirmed that the overall structures of the targeted enzymes did not change significantly after binding with Bisacremine-C, and the ligand remained inside the binding cavity in a stable conformation for most of the simulation time. The most significant hydrophobic contacts for the GSK-3β-Bisacremine-C complex are with ILE62, VAL70, ALA83, and LEU188, whereas GLN185 is significant for H-bonds. In terms of hydrophobic contacts, TYR184 and PHE246 are the most important, while SER180 is vital for H-bonds in NMDA-Bisacremine-C. THR232 is the most crucial for H-bonds in BACE-1-Bisacremine-C and ILE110-produced hydrophobic contacts. This study laid a foundation for further experimental validation and clinical trials regarding the biopotency of Bisacremine-C. [ABSTRACT FROM AUTHOR]

Traumatic brain injury (TBI) is the primary injury to the brain caused by mechanical forces. It is one of the leading causes of mortality in mid-life. Increased levels of inflammation and oxidation, and decreased levels of neuro-trophic factor lead to a worsening of the condition. In previous studies, the authors demonstrated that the ethanol extract of Citrus sinensis peel (CSPE) functioned as an antioxidant using molecular docking and dynamic simulations. In the present study, in order to confirm these findings, a Marmarou weight drop model which included rats with TBI. Molecular docking against c-Jun N-terminal kinase 3 (JNK3) was also performed. The rats were divided into the sham-operated, control and treatment groups. The treatment groups received CSPE at 50, 250 and 500 mg/kg body weight (groups 1, 2 and 3, respectively) orally once a day for 7 days following the induction of TBI. Superoxide dismutase (SOD)1, SOD2, and brain-derived neurotrophic factor (BDNF) expression levels were analyzed using immunohistochemistry. Surviving neurons were analyzed using hematoxylin and eosin staining. Barnes' maze and wire grip tests were performed on the 1st, 3rd and 7th days following TBI. The results revealed a significant increase in the numbers of surviving neurons and in BDNF expression in groups 2 and 3, a higher expression of SOD1 in group 3, and a higher expression of SOD2 in all the treatment groups. Wire grip duration was significantly longer on the 7th day following TBI in group 3, and Barnes maze latency was significantly shorter on the 3rd and 7th days following TBI compared to the previous time in all treatment groups. Molecular docking analysis also revealed that CSPE compounds, particularly chanoclavine and nootkatone, interacted with JNK3 in the same binding pocket. On the whole, the present study demonstrates that CSPE helps protect the brain from damage by functioning as an antioxidant, increasing neurotrophic activities and inhibiting apoptosis. This reduces the overall neurological issues that are associated with TBI. However, further studies on the efficacy and safety of CSPE are required in order to determine its full potential in improving motor and cognitive functions following TBI. [ABSTRACT FROM AUTHOR]

In this study, six analogs of 2-arylquinoline were synthesized and evaluated for their in vitro and in vivo antiplasmodial and leishmanicidal activity. At a later stage, hemolytic activity and druggability were tested in vitro and in silico, respectively, observing as a result: firstly, compounds showed half-maximal effective concentration (EC50) values between 3.6 and 19.3 µM. Likewise, a treatment using the compounds 4a–f caused improvement in most of the treated hamsters and cured some of them. Regarding the antiplasmodial activity, the compounds showed moderate to high activity, although they did not show hemolytic activity. Furthermore, 4e and 4f compounds were not able to control P. berghei infection when administered to animal models. Molecular dynamic simulations, molecular docking and ligand binding affinity indicate good characteristics of the studied compounds, which are expected to be active. And lastly, the compounds are absorbable at the hematoencephalic barrier but not in the gastrointestinal tract. In summary, ADMET properties suggest that these molecules may be used as a safe treatment against Leishmania. [ABSTRACT FROM AUTHOR]

Cocaine use disorder is a psychiatric condition affecting millions of people worldwide. Up till now, there are no FDA approved medications reported against this disorder. Previous pharmacological studies suggested that, simultaneously targeting all types of opioid receptors, some agonistically while others antagonistically have been proven a much useful strategy for the treatment of cocaine addiction. Recent evidence indicated that a novel agonist cebranopadol has a high binding affinity towards Nociceptin opioid receptor (NOP) and Mu opioid receptor (MOP), and partial affinity with Kappa opioid receptor (KOP) and Delta opioid receptor (DOP). Interestingly, in vivo studies revealed that cebranopadol blocked the cocaine seeking in animal models. In the present study, quantum chemical calculations were performed to calculate various thermodynamic parameters of cebranopadol using density functional theory. Flexible docking was performed to rationalize the molecular basis of cis and trans isomers of cebranopadol. Further, the atomistic description of activation mechanism of MOP receptor by cebranopadol investigated by sub‐microsecond timescale molecular dynamic (MD) simulation. Our results revealed that the operating mode of the activation switch composed of Trp2936.48 and Asn3287.45 residues, was accountable for down‐ and up‐regulation, respectively, of the β‐arrestin signaling. This particular conformational change in turn affected the G‐protein‐biased activation of MOP receptor. Cebranopadol stabilized the Asn3287.45 by mediating halogen bond formation. According to best of our knowledge, this is the first mechanistic study of cebranopadol with MOP receptor using the quantum mechanical calculations and MD simulations to explain the inhibition of cocaine addiction. [ABSTRACT FROM AUTHOR]

The chaotic proliferation of immature immune cells in the bone marrow, blood, and spleen is a hallmark of leukemia, a leukocyte malignancy. There are various types of leukemia, and the optimal treatment and a patient's likelihood of survival depend on the condition. Natural products have vast chemical diversity and it has ability to act on various biological systems. Plants and its products are the important elements in the plant medicine system. Many of the plant extracts currently used in the treatment of cancer therapy and those agents were also isolated from plants. The burden of disease is still great despite tremendous advancements in our understanding of epidemiology, pathology, molecular causes, therapy alternatives, and strategies. Tinospora cordifolia is an invasive plant that is present throughout the entire state of Tamil Nadu. This endeavor involves the creation of potential anti-cancer drugs from its bioactive components. Tinospora cordifolia extract are done with GC-MS, in which 19 components were obtained. The compounds were examined for ADMET characteristics and docked against the CSKN2A1 protein. Biphenyl was selected as potential component as it has lowest binding affinity in all 19 components. For simulation experiments, the Biphenyl-8P06 complex with the lowest binding affinity that resulted from molecular docking is chosen. Biphenyl-8P06 complex hardness and stability are modelled via dynamics simulation. For the sake of this paper, dynamic simulation studies utilise the CHARM-GUI and NAMD tools. Additionally already existing commercial drug ibrutinib is taken as reference and docked then processed with dynamic simulation and compared with biphenyl complex. The Biphenyl has slightly high binding affinity then ibrutinib complex which can be used as potential for leukemia which has low side effects than existing commercial drug ibrutinib. [ABSTRACT FROM AUTHOR]

The synthesis of eleven new and previously undescribed benzamides was designed. These compounds were specifically projected as potential inhibitors of the enzymes acetylcholinesterase (AChE) and β-secretase (BACE1). N,N′-(1,4-phenylene)bis(3-methoxybenzamide) was most active against AChE, with an inhibitory concentration of AChE IC50 = 0.056 µM, while the IC50 for donepezil was 0.046 µM. This compound was also the most active against the BACE1 enzyme. The IC50 value was 9.01 µM compared to that for quercetin, with IC50 = 4.89 µM. Quantitative results identified this derivative to be the most promising. Molecular modeling was performed to elucidate the potential mechanism of action of this compound. Dynamic simulations showed that new ligands only had a limited stabilizing effect on AChE, but all clearly reduced the flexibility of the enzyme. It can, therefore, be concluded that a possible mechanism of inhibition increases the stiffness and decreases the flexibility of the enzyme, which obviously impedes its proper function. An analysis of the H-bonding patterns suggests a different mechanism (from other ligands) when interacting the most active derivative with the enzyme. [ABSTRACT FROM AUTHOR]

The prospective compound pencycuron (PNC) was probed using FT-IR, FT-Raman, NMR, and UV-Vis spectra and quantum chemical computation. Vibrational assignment pertaining to different modes of vibration with potential energy distribution has been augmented by normal coordinate analysis (NCA). The most stable minimum energy conformer was identified by performing potential energy surface scan (PES) along the rotational bonds at the B3LYP/6-311++G(d,p) level of theory. The chemical reactivity and stability of PNC were estimated based on the HOMO-LUMO energy gap and NBO approach. The overall picture of accumulation of charges on individual atoms of the molecule was predicted by molecular electrostatic potential (MEP) surface map which in turn identifies the nucleophilic and electrophilic region or sites. The intermolecular interaction in the PNC was confirmed by using Hirshfeld surfaces. Antifungal activity of the compound with different bacterial strains was validated by the agar well diffusion method. Ligand-protein interaction was explored by using molecular docking studies, while the pharmacokinetic aspects of the compound were probed using drug likeness and Absorption, Distribution, Metabolism, Excretion, and Toxicity properties. The stability of the title compound has been investigated via molecular dynamics simulation (MDS). [ABSTRACT FROM AUTHOR]

TAK1 (transforming growth factor-beta-activated kinase 1) is a crucial therapeutic target in inflammation-related diseases. This study investigated the inhibitory potential of cannflavin A, a flavonoid found in Cannabis sativa, against TAK1. Through in silico approaches, including drug-likeness analysis, ADMET assessment, molecular docking, and molecular dynamics simulation, the binding affinity and stability of cannflavin A were evaluated. The results demonstrate that cannflavin A exhibits excellent ADMET properties and displays superior binding affinity and stability at the ATP binding site of TAK1 when compared to the known inhibitor takinib. Notably, the decomposition of binding free energy unveils critical amino acid residues involved in TAK1 binding, underscoring the inhibitory effect of cannflavin A through TAK1 inhibition. These findings highlight the potential of cannflavin A as a TAK1 inhibitor and its significant implications for the development of targeted therapies in inflammation-related diseases. Through modulating inflammatory signaling pathways, cannflavin A holds promise for more effective and tailored treatment strategies, particularly in rheumatoid arthritis. This study contributes to the current understanding of cannflavin A's application and provides a foundation for further research and innovative approaches in targeted therapies for inflammatory conditions. [ABSTRACT FROM AUTHOR]

Oleanolic acid (OA), as a ubiquitous compound in the plant kingdom, is studied for both its neuroprotective and neurotoxic properties. The mechanism of acetylcholinesterase (AChE) inhibitory potential of OA is investigated using molecular dynamic simulations (MD) and docking as well as biomimetic tests. Moreover, the in vitro SH-SY5Y human neuroblastoma cells and the in vivo zebrafish model were used. The inhibitory potential towards the AChE enzyme is examined using the TLC-bioautography assay (the IC50 value is 9.22 μM). The CH-π interactions between the central fragment of the ligand molecule and the aromatic cluster created by the His440, Phe288, Phe290, Phe330, Phe331, Tyr121, Tyr334, Trp84, and Trp279 side chains are observed. The results of the in vitro tests using the SH-SY5Y cells indicate that the viability rate is reduced to 71.5%, 61%, and 43% at the concentrations of 100 µg/mL, 300 µg/mL, and 1000 µg/mL, respectively, after 48 h of incubation, whereas cytotoxicity against the tested cell line with the IC50 value is 714.32 ± 32.40 µg/mL. The in vivo tests on the zebrafish prove that there is no difference between the control and experimental groups regarding the mortality rate and morphology (p > 0.05). [ABSTRACT FROM AUTHOR]

Nature has always been a source of drug candidates. Since ancient times, people have been using plants and their metabolites for various medicinal purposes. Glaucarubinone is a quassinoid present in the family Simaroubaceae. Simarouba glauca, also known as Laxmitaru or Paradise tree is grouped under the family Simaroubaceae, Glaucarubinone present in S. glauca is known for its medicinal property. Molecular docking methods are widely used to investigate the interactions between a drug candidate and its target, and to discern the therapeutic action to design new drug candidate with enhanced activities. The information generated from docking studies helps to obtain an insight into interactions of drug candidate with amino acid in the active site of the target proteins, and to predict the binding energy of ligands to the target. By Molecular Dynamic Simulation, the flexibility and the conformational stability of target proteins-glaucarubinone complex is confirmed. [ABSTRACT FROM AUTHOR]