Target identification, screening and in vivo evaluation of pyrrolone-fused benzosuberene compounds against human epilepsy using Zebrafish model of pentylenetetrazol-induced seizures

Acute and sub-chronic toxicity study of novel polyherbal formulation in non-alcoholic fatty liver using Wistar rats

Aim: This study assessed the acute and sub-chronic toxicity of a novel polyherbal formulation tablet in Wistar rats Materials & methods: Acute toxicity and sub-chronic toxicity was assessed following OECD (Organisation for the Economic Co-operation and Development) guidelines based on 423 and 408. Results & conclusion: No mortality and toxicity showed in rats during acute toxicity. The LD50 of the extract was at 2000 mg/kg. In sub-chronic study, both sex rats were orally administered at 250, 500,1000 and 2000 mg/kg for 90 days and revealed no significant difference (p < 0.05) in hematological and other parameters compared with the control. Histopathology study did not reveal morphological alteration. The No observed adverse effect level of the tablet was observed until 2000 mg/kg.

Integration of ligand and structure-based pharmacophore screening for the identification of novel natural leads against Euchromatic histone lysine methyltransferase 2 (EHMT2/G9a)

Herein, we report a blended ligand and structure-based pharmacophore screening approach to identify new natural leads against the Protein Lysine Methyltransferase 2 (EHMT2/G9a). The EHMT2/G9a has been associated with Cancer, Alzheimer's, and aging and is considered an emerging drug target having no clinically passed inhibitor. Purposefully, we developed the ligand-based pharmacophore (Pharmacophore-L) based on the common features of known inhibitors and the structure-based pharmacophore (Pharmacophore-S) based on the interaction profile of available crystal structures. The Pharmacophore-L and Pharmacophore-S were subjected to multiple tiers of validations and utilized in combination for the screening of total 741543 compounds coming from multiple databases. Additional layers of stringency were applied in the screening process to test drug-likeness (using Lipinski's rule, Veber's rule, SMARTS and ADMET filtration), to rule out any toxicity (TOPKAT analysis). The interaction profiles, stabilities, and comparative analysis against the reference were carried out by flexible docking, MD simulation, and MM-GBSA analysis, which finally led to three leads as potential inhibitors of G9a.Communicated by Ramaswamy H. Sarma.

Exosomes derived from human umbilical cord mesenchymal stem cells decrease neuroinflammation and facilitate the restoration of nerve function in rats suffering from intracerebral hemorrhage

Exosomes derived from human umbilical cord mesenchymal stem cells (hUCMSC-ex) have become a hopeful substitute for whole-cell therapy due to their minimal immunogenicity and tumorigenicity. The present study aimed to investigate the hypothesis that hUCMSC-ex can alleviate excessive inflammation resulting from intracerebral hemorrhage (ICH) and facilitate the rehabilitation of the nervous system in rats. In vivo, hemorrhagic stroke was induced by injecting collagenase IV into the striatum of rats using stereotactic techniques. hUCMSC-ex were injected via the tail vein at 6 h after ICH model establishment at a dosage of 200 µg. In vitro, astrocytes were pretreated with hUCMSC-ex and then stimulated with hemin (20 μmol/mL) to establish an ICH cell model. The expression of TLR4/NF-κB signaling pathway proteins and inflammatory factors, including TNF-α, IL-1β, and IL-10, was assessed both in vivo and in vitro to investigate the impact of hUCMSC-ex on inflammation. The neurological function of the ICH rats was evaluated using the corner turn test, forelimb placement test, Longa score, and Bederson score on the 1st, 3rd, and 5th day. Additionally, RT-PCR was employed to examine the mRNA expression of TLR4 following hUCMSC-ex treatment. The findings demonstrated that hUCMSC-ex downregulated the protein expression of TLR4, NF-κB/P65, and p-P65, reduced the levels of pro-inflammatory cytokines TNF-α and IL-1β, and increased the expression of the anti-inflammatory cytokine IL-10. Ultimately, the administration of hUCMSC-ex improved the behavioral performance of the ICH rats. However, the results of PT-PCR indicated that hUCMSC-ex did not affect the expression of TLR4 mRNA induced by ICH, suggesting that hUCMSCs-ex may inhibit TLR4 translation rather than transcription, thereby suppressing the TLR4/NF-κB signaling pathway. We can conclude that hUCMSC-ex mitigates hyperinflammation following ICH by inhibiting the TLR4/NF-κB signaling pathway. This study provides preclinical evidence for the potential future application of hUCMSC-ex in the treatment of cerebral injury.

A discovery of potent kaempferol derivatives as multi-target medicines against diabetes as well as bacterial infections: an in silico approach

Flavonoids demonstrate beneficial effects on human health because flavonoids contain important biological properties. Kaempferol is a flavonol, type of flavonoid found in eatable plants and in plants usually employed in ancient drugs (Moringa oleifera, Tilia spp., fern genus spp. and gingko etc.). Some medicinal studies have shown that the use of foods full of kaempferol decreases the risk of many (cancer, vascular) diseases. All the data of 50 kaempferol derivatives were collected from PubChem database. Through Schrödinger software, 3D-QSAR study was performed for 50 compounds by using method of field base. Conformer of kaempferol derivatives was docked against anti-diabetic, anti-microbial co-crystal structures and protein. To monitor the best anti-diabetic and antibacterial agent, particular kaempferol derivatives were downloaded from PubChem database. Virtual screening by molecular docking provided four lead compounds with four different proteins. These hit compounds were found to be potent inhibitor for diabetic enzymes alpha-amylase and DPP IV and had the potential to suppress DNA gyrase and dihydrofolate reductase synthesis. Molecular dynamic simulation of docked complexes evaluates the value of root mean square fluctuation by iMOD server. Kaempferol 3-O-alpha-L-(2, 3-di-Z-p-coumaroyl) rhamnoside (42) compound used as anti-diabetic and kaempferol 3-O-gentiobioside (3) as antibacterial with good results can be used for drug discovery.Communicated by Ramaswamy H. Sarma.

Genes adaptability and NOL6 protein inhibition studies of fabricated flavan-3-ols lead skeleton intended to treat breast carcinoma

Breast cancer invasive 2.3 million women worldly and second prominent factor of cancer-related mortality. Finding a new site-specific and safe small molecule is a current need in this field. With the aid of deep learning Algorithms, we analyzed the published big database from cancer CBioportal to find the best target protein. Further, Multi-omics analysis such as enrichment analysis, scores of molecular, RNA biological function at a cellular level, and protein domain were obtained and matched to find the better hit molecules. The gene analysis output shows nucleolar protein 6 plays a significant responsibility in breast carcinoma and 354 natural and synthetic lead molecules are docked inside the active site. Docking result gave the output hit molecule falavan-3-ols with a binding score of -5.325 (Kcal/mol) and interaction analysis illustrates, 13 active amino acids favoring the binding interaction with functional groups of the hit molecule compared to the standard molecule Abemacilib (-2.857 (Kcal/mol)). Best docked complex of flavan-3-ols and NOL6 protein subjected to dynamic simulation 100 ns to study the stability. The results proved that π-π stacked, carbon‑hydrogen and electrostatic interactions are stable throughout the 100 ns simulation. The overall results conclude the hit molecule flavan-3-ol will be a safe and potent lead molecule to generate and treat breast carcinoma patients.

Discovery of Palbociclib as a potent c-Myc G4 stabilizer for lung cancer treatment using molecular docking, molecular dynamics simulation, and in vitro activity evaluation

Despite significant progress in lung cancer treatment, this disease remains a prevalent and serious global malignancy, leading to high rates of illness and death. Urgent research is needed to discover new or alternative therapies that can improve clinical outcomes for lung cancer patients. In our study, we successfully demonstrated the effectiveness of Palbociclib, a CDK4/6 inhibitor, in suppressing the growth of lung cancer cells. The IC50 values obtained were 11.00 μM and 11.74 μM for H1299 and A549 cells, respectively. Furthermore, our findings indicate that Palbociclib may possess strong c-Myc G4 stabilizing properties by significantly reducing both protein and mRNA expression levels of c-Myc. Additionally, Palbociclib induces apoptosis and causes cell cycle arrest at the G2/M phase in two cells. Through circular dichroism (CD), molecular docking, and molecular dynamics (MD) simulation, we have provided evidence that Palbociclib enhances the structural stability of c-Myc G4 while exhibiting a high binding affinity to its ligand's binding site on c-Myc G4. These results suggest that Palbociclib holds promise as a novel c-Myc G4 stabilizer for treating cancers associated with abnormal c-Myc activity; further optimization and development are warranted.

Cuproptosis gene-related, neural network-based prognosis prediction and drug-target prediction for KIRC

BACKGROUND

Kidney renal clear cell carcinoma (KIRC), as a common case in renal cell carcinoma (RCC), has the risk of postoperative recurrence, thus its prognosis is poor and its prognostic markers are usually based on imaging methods, which have the problem of low specificity. In addition, cuproptosis, as a novel mode of cell death, has been used as a biomarker to predict disease in many cancers in recent years, which also provides an important basis for prognostic prediction in KIRC. For postoperative patients with KIRC, an important means of preventing disease recurrence is pharmacological treatment, and thus matching the appropriate drug to the specific patient's target is also particularly important. With the development of neural networks, their predictive performance in the field of medical big data has surpassed that of traditional methods, and this also applies to the field of prognosis prediction and drug-target prediction.

OBJECTIVE

The purpose of this study is to screen for cuproptosis genes related to the prognosis of KIRC and to establish a deep neural network (DNN) model for patient risk prediction, while also developing a personalized nomogram model for predicting patient survival. In addition, sensitivity drugs for KIRC were screened, and a graph neural network (GNN) model was established to predict the targets of the drugs, in order to discover potential drug action sites and provide new treatment ideas for KIRC.

METHODS

We used the Cancer Genome Atlas (TCGA) database, International Cancer Genome Consortium (ICGC) database, and DrugBank database for our study. Differentially expressed genes (DEGs) were screened using TCGA data, and then a DNN-based risk prediction model was built and validated using ICGC data. Subsequently, the differences between high- and low-risk groups were analyzed and KIRC-sensitive drugs were screened, and finally a GNN model was trained using DrugBank data to predict the relevant targets of these drugs.

RESULTS

A prognostic model was built by screening 10 significantly different cuproptosis-related genes, the model had an AUC of 0.739 on the training set (TCGA data) and an AUC of 0.707 on the validation set (ICGC data), which demonstrated a good predictive performance. Based on the prognostic model in this paper, patients were also classified into high- and low-risk groups, and functional analyses were performed. In addition, 251 drugs were screened for sensitivity, and four drugs were ultimately found to have high sensitivity, with 5-Fluorouracil having the best inhibitory effect, and subsequently their corresponding targets were also predicted by GraphSAGE, with the most prominent targets including Cytochrome P450 2D6, UDP-glucuronosyltransferase 1A, and Proto-oncogene tyrosine-protein kinase receptor Ret. Notably, the average accuracy of GraphSAGE was 0.817 ± 0.013, which was higher than that of GAT and GTN.

CONCLUSION

Our KIRC risk prediction model, constructed using 10 cuproptosis-related genes, had good independent prognostic ability. In addition, we screened four highly sensitive drugs and predicted relevant targets for these four drugs that might treat KIRC. Finally, literature research revealed that four drug-target interactions have been demonstrated in previous studies and the remaining targets are potential sites of drug action for future research.

Computational insights into NIMA-related kinase 6: unraveling mutational effects on structure and function

The NEK6 (NIMA-related kinase 6) serine/threonine kinase is a pivotal player in a multitude of cellular processes, including the regulation of the cell cycle and the response to DNA damage. Its significance extends to disease pathogenesis, as changes in NEK6 activity have been linked to the development of cancer. Non-synonymous single nucleotide polymorphisms (nsSNPs) in NEK6 have been linked to cancer as they alter the protein's native structure and function. The association between NEK6 activity and cancer development has prompted researchers to explore the effects of genetic variations within the NEK6 gene. Therefore, we utilized advanced computational tools to analyze 155 high-confidence nsSNPs in the NEK6 gene. From this analysis, 21 nsSNPs were identified as potentially harmful, raising concerns about their impact on NEK6 activity and cancer risk. These 21 mutations were then examined for structural alterations, and eight of nsSNPs (I51M, V76A, I134N, Y152D, R171Q, V186G, L237R, and C285S) were found to destabilize the protein. Among the destabilizing mutations screened, a specific mutation, R171Q, stood out due to its conserved nature. To understand its impact on the protein and conformation, all-atom molecular dynamics simulations (MDS) for 100 ns were performed for both Wildtype NEK6 (WT-NEK6) and R171Q. The simulations revealed that the R171Q variant was unstable and led to significant conformational changes in NEK6. This study provides valuable insights into NEK6 dysfunction caused by single amino acid alterations, offering a novel understanding of the molecular mechanisms underlying NEK6-related cancer progression.

In Vitro Antioxidant and In Vivo Hepatoprotective Properties of Wissadula periplocifolia Extract

Wissadula periplocifolia (L.) Thwaites is a traditional medicinal plant belonging to the family Malvaceae, used in folk medicine for inflamed snake bites and bee stings. The current study was designed to investigate the in vitro antioxidant and in vivo anti-inflammatory and hepatoprotective activities of 80% ethanol extract of W. periplocifolia and its different fractions. The crude ethanolic extract (CEE) was then serially fractionated with petroleum ether fraction (PEF), chloroform fraction (CHF), and aqueous fraction (AQF). The antioxidant activity was assessed using 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical assay, anti-inflammatory activity was determined in the xylene-induced ear edema model, and hepatoprotective activity was measured in the paracetamol-induced hepatic injury model. PEF showed a significant scavenging effect with an IC50 value of 33.5 μg/mL, followed by CEE (IC50 = 42.2 μg/mL), CHF (IC50 = 77 μg/mL), and AQF (IC50 = 80 μg/mL), compared to standard butylated hydroxytoluene (IC50 = 14.8 μg/mL). Both doses of CEE (250 and 500 mg/kg) could reduce ear edema by 41.3 and 50%, respectively, compared to standard diclofenac sodium (76.09%). Moreover, CEE significantly reduces the elevated liver enzymes (ALT, AST, and ALP), compared to control. Nevertheless, it elevated blood protein and reduced the blood bilirubin level (p < 0.01), compared to control. Histopathological studies also indicated significant protection of the liver from paracetamol-induced liver damage. In conclusion, W. periplocifolia could be a good source of antioxidant and hepatoprotective phytochemicals; meanwhile, toxicological and pharmacokinetic studies are recommended.

High-throughput virtual screening of potential inhibitors of GPR52 using docking and biased sampling method for Huntington's disease therapy

Huntington's disease (HD) is a rare and progressive neurodegenerative disorder caused by polyglutamine (poly-Q) mutations of the huntingtin (HTT) gene resulting in chorea, cognitive, and psychiatric dysfunctions. Being a monogenic condition, reducing the levels of the mutated huntingtin protein (mHTT) holds promise as an effective therapeutic approach. GPR52, an orphan G-protein coupled receptor (GPCR), enriched in the striatum, is a novel target for slowing down the progression of HD by lowering the mHTT levels. Therefore, the study focuses on identifying potent small-molecule inhibitors for GPR52 using a combination of robust high-throughput virtual screening (HTVS) and pharmacokinetics profiling followed by fast pulling of ligand (FPL) and umbrella sampling (US) simulations. Initially, screening a library of 2,36,545 compounds was done against the binding pocket of GPR52. Based on binding affinity, stereochemical and non-bonded interactions, and pharmacokinetic profiling, 50 compounds were shortlisted. Selected hit compounds 1, 2, and 3 were subjected to FPL simulations with applied external bias potential to investigate their unique dissociation pathways and intermolecular interactions over time. Subsequently, the US simulations were performed on the selected hit compounds to estimate their binding free energy (ΔG). The analysis of the trajectories obtained from simulations revealed that the residues TYR34, TYR185, GLY187, ASP188, ILE189, SER299, PHE300, and THR303 within the active site of GPR52 were significant for efficient ligand binding through the formation of various hydrogen bond interactions and hydrophobic contacts. Out of the three hit compounds, compound 3 had the lowest ΔG of - 20.82 ± 0.44 kcal/mol. The study identified compounds 1, 2, and 3 as potential molecules that can be developed as GPR52 inhibitors holding promise for lowering mHTT levels.

FormulationAI: a novel web-based platform for drug formulation design driven by artificial intelligence

Today, pharmaceutical industry faces great pressure to employ more efficient and systematic ways in drug discovery and development process. However, conventional formulation studies still strongly rely on personal experiences by trial-and-error experiments, resulting in a labor-consuming, tedious and costly pipeline. Thus, it is highly required to develop intelligent and efficient methods for formulation development to keep pace with the progress of the pharmaceutical industry. Here, we developed a comprehensive web-based platform (FormulationAI) for in silico formulation design. First, the most comprehensive datasets of six widely used drug formulation systems in the pharmaceutical industry were collected over 10 years, including cyclodextrin formulation, solid dispersion, phospholipid complex, nanocrystals, self-emulsifying and liposome systems. Then, intelligent prediction and evaluation of 16 important properties from the six systems were investigated and implemented by systematic study and comparison of different AI algorithms and molecular representations. Finally, an efficient prediction platform was established and validated, which enables the formulation design just by inputting basic information of drugs and excipients. FormulationAI is the first freely available comprehensive web-based platform, which provides a powerful solution to assist the formulation design in pharmaceutical industry. It is available at https://formulationai.computpharm.org/.

Decoding the deactivation mechanism of R192W mutation of ZAP-70 using molecular dynamics simulations and binding free energy calculations

CONTEXT

ZAP-70 (zeta-chain-associated protein of 70 kDa), serving as a critical regulator for T cell antigen receptor signaling, represents an attractive therapeutic target for autoimmunity disease. How the mechanistical mechanism of ZAP-70 to a human autoimmune syndrome-associated R192W mutation remains unclear. The results indicated that the R192W mutation of ZAP-70 clearly affected the conformational flexibility of the N-terminal ITAM-Y2P. Structural analysis unveiled that the R192W mutation of ZAP-70 caused the exposure of the N-terminal ITAM-Y2P to the solvent. MM-GBSA binding free energy calculations exhibited that the R192W mutation decreased the binding affinity of ITAM-Y2P to the ZAP-70 mutant. Residue-based free energy decomposition further revealed that the protein-peptide interaction networks involving electrostatic interactions provide significant contributions for complex formation. The energy unfavorable residues include Arg43, Arg192, Tyr240, and Lys244 from ZAP-70 and Asn301, Leu303, pY304, and pY315 from ITAM-Y2P in the R192W mutant. Our obtained results may help the understanding of the deactivation mechanism of ZAP-70 induced by the R192W mutation.

METHODS

In the work, multiple replica molecular dynamics simulations and molecular mechanics-generalized Born surface area (MM-GBSA) method were performed to reveal the doubly phosphorylated ITAMs (ITAM-Y2P)-mediated deactivation mechanism of ZAP-70 induced by the R192W mutation.

Chemically-induced epileptic seizures in zebrafish: A systematic review

The use of zebrafish as a model organism is gaining evidence in the field of epilepsy as it may help to understand the mechanisms underlying epileptic seizures. As zebrafish assays became popular, the heterogeneity between protocols increased, making it hard to choose a standard protocol to conduct research while also impairing the comparison of results between studies. We conducted a systematic review to comprehensively profile the chemically-induced seizure models in zebrafish. Literature searches were performed in PubMed, Scopus, and Web of Science, followed by a two-step screening process based on inclusion/exclusion criteria. Qualitative data were extracted, and a sample of 100 studies was randomly selected for risk of bias assessment. Out of the 1058 studies identified after removing duplicates, 201 met the inclusion criteria. We found that the most common chemoconvulsants used in the reviewed studies were pentylenetetrazole (n = 180), kainic acid (n = 11), and pilocarpine (n = 10), which increase seizure severity in a dose-dependent manner. The main outcomes assessed were seizure scores and locomotion. Significant variability between the protocols was observed for administration route, duration of exposure, and dose/concentration. Of the studies subjected to risk of bias assessment, most were rated as low risk of bias for selective reporting (94%), baseline characteristics of the animals (67%), and blinded outcome assessment (54%). Randomization procedures and incomplete data were rated unclear in 81% and 68% of the studies, respectively. None of the studies reported the sample size calculation. Overall, these findings underscore the need for improved methodological and reporting practices to enhance the reproducibility and reliability of zebrafish models for studying epilepsy. Our study offers a comprehensive overview of the current state of chemically-induced seizure models in zebrafish, highlighting the common chemoconvulsants used and the variability in protocol parameters. This may be particularly valuable to researchers interested in understanding the underlying mechanisms of epileptic seizures and screening potential drug candidates in zebrafish models.

Free energy landscape and thermodynamics properties of novel mutations in PncA of pyrazinamide resistance isolates of Mycobacterium tuberculosis

Pyrazinamide (PZA) is one of the first-line antituberculosis therapy, active against non-replicating Mycobacterium tuberculosis (Mtb). The conversion of PZA into pyrazinoic acid (POA), the active form, required the activity of pncA gene product pyrazinamidase (PZase) activity. Mutations occurred in pncA are the primary cause behind the PZA resistance. However, the resistance mechanism is important to explore using high throughput computational approaches. Here we aimed to explore the mechanism of PZA resistance behind novel P62T, L120R, and V130M mutations in PZase using 200 ns molecular dynamics (MD) simulations. MD simulations were performed to observe the structural changes for these three mutants (MTs) compared to the wild types (WT). Root means square fluctuation, the radius of gyration, free energy landscape, root means square deviation, dynamic cross-correlation motion, and pocket volume were found in variation between WT and MTs, revealing the effects of P62T, L120R, and V130M. The free energy conformational landscape of MTs differs significantly from the WT system, lowering the binding of PZA. The geometric shape complementarity of the drug (PZA) and target protein (PZase) further confirmed that P62T, L120R, and V130M affect the protein structure. These effects on PZase may cause vulnerability to convert PZA into POA.Communicated by Ramaswamy H. Sarma.

Design of siRNA Bioconjugates for Efficient Control of Cancer-Associated Membrane Receptors

Research on siRNA delivery has seen tremendous growth over the past few decades. As one of the major delivery strategies, siRNA bioconjugates offer the potential to enhance and extend the pharmacological properties of siRNAs while minimizing toxicity. In this paper, we suggest the development of a siRNA conjugate platform with peptides and proteins that are ligands of target receptors for cancer treatment. The siRNA bioconjugates target and block the receptor membrane proteins, enter the cells through receptor-mediated endocytosis, and inhibit the expression of that same target membrane receptor, thereby doubly controlling the function of the membrane proteins. The three kinds of bioconjugates targeting CD47, PD-L1, and EGFR were synthesized via two different copper-free click chemistry reactions. Results showed the cellular uptake of each conjugate, reduction of target gene expression, and efficient functional control of receptor proteins. This platform provides an effective approach for regulating membrane proteins in various diseases beyond cancer.

3D based generative PROTAC linker design with reinforcement learning

Proteolysis targeting chimera (PROTAC), has emerged as an effective modality to selectively degrade disease-related proteins by harnessing the ubiquitin-proteasome system. Due to PROTACs' hetero-bifunctional characteristics, in which a linker joins a warhead binding to a protein of interest (POI), conferring specificity and a E3-ligand binding to an E3 ubiquitin ligase, this could trigger the ubiquitination and transportation of POI to the proteasome, followed by degradation. The rational PROTAC linker design is challenging due to its relatively large molecular weight and the complexity of maintaining the binding mode of warhead and E3-ligand in the binding pockets of counterpart. Conventional linker generation method can only generate linkers in either 1D SMILES or 2D graph, without taking into account the information of ternary structures. Here we propose a novel 3D linker generative model PROTAC-INVENT which can not only generate SMILES of PROTAC but also its 3D putative binding conformation coupled with the target protein and the E3 ligase. The model is trained jointly with the RL approach to bias the generation of PROTAC structures toward pre-defined 2D and 3D based properties. Examples were provided to demonstrate the utility of the model for generating reasonable 3D conformation of PROTACs. On the other hand, our results show that the associated workflow for 3D PROTAC conformation generation can also be used as an efficient docking protocol for PROTACs.

In silico identification of potential protein kinase C alpha inhibitors from phytochemicals from IMPPAT database for anticancer therapeutics: a virtual screening approach

Protein Kinase C alpha (PKCα) is a critical signaling molecule that plays a crucial role in various physiological processes, including cell growth, differentiation, and survival. Over the years, there has been a growing interest in targeting PKCα as a promising drug target for the treatment of various diseases, including cancer. Targeting PKCα can, therefore, serve as a potential strategy to prevent cancer progression and enhance the efficacy of conventional anticancer therapies. We conducted a systematic search for promising compounds for their anticancer potential that target PKCα using natural compounds from the IMPPAT database. The initial compounds were screened through various tests, including analysis of their physical and chemical properties, PAINS filter, ADMET analysis, PASS analysis, and specific interaction analysis. We selected those that showed high binding affinity and specificity to PKCα from the screened compounds, and we further analyzed them using molecular dynamics simulations (MDS) and principal component analysis (PCA). Various systematic parameters from the MDS analyses suggested that the protein-ligand complexes were stabilized throughout the simulation trajectories of 100 nanoseconds (ns). Our findings indicated that compounds Nicandrenone and Withaphysalin D bind to PKCα with high stability and affinity, making them potential candidates for further research in cancer therapeutics innovation in clinical contexts.Communicated by Ramaswamy H. Sarma.

mPGES-1 Inhibitor Discovery Based on Computer-Aided Screening: Pharmacophore Models, Molecular Docking, ADMET, and MD Simulations

mPGES-1 is an enzyme, which, when activated by inflammatory factors, can cause prostaglandin E synthesis. Traditional non-steroidal anti-inflammatory drugs are capable of inhibiting prostaglandin production, yet they can also cause gastrointestinal reactions and coagulation disorders. mPGES-1, the enzyme at the conclusion of prostaglandin production, does not cause any adverse reactions when inhibited. Numerous studies have demonstrated that mPGES-1 is more abundant in cancerous cells than in healthy cells, indicating that decreasing the expression of mPGES-1 could be a potential therapeutic strategy for cancer. Consequently, the invention of mPGES-1 inhibitors presents a fresh avenue for the treatment of inflammation and cancer. Incorporating a database of TCM compounds, we collected a batch of compounds that had an inhibitory effect on mPGES-1 and possessed IC50 value. Firstly, a pharmacophore model was constructed, and the TCM database was screened, and the compounds with score cut-off values of more than 1 were retained. Then, the compounds retained after being screened via the pharmacodynamic model were screened for docking at the mPGES-1 binding site, followed by high-throughput virtual screening [HTVS] and standard precision [SP] and super-precision [XP] docking, and the compounds in the top 20% of the XP docking score were selected to calculate the total free binding energy of MM-GBSA. The best ten compounds were chosen by comparing their score against the reference ligand 4U9 and the MM-GBSA_dG_Bind score. ADMET analysis resulted in the selection of ten compounds, three of which had desirable medicinal properties. Finally, the binding energy of the target protein mPGES-1 and the candidate ligand compound was analyzed using a 100 ns molecular dynamics simulation of the reference ligand 4U9 and three selected compounds. After a gradual screening study and analysis, we identified a structure that is superior to the reference ligand 4U9 in all aspects, namely compound 15643. Taken together, the results of this study reveal a structure that can be used to inhibit mPGES-1 compound 15643, thereby providing a new option for anti-inflammatory and anti-tumor drugs.

Elucidation of Pharmacological Mechanism Underlying the Anti-Alzheimer's Disease Effects of Evodia rutaecarpa and Discovery of Novel Lead Molecules: An In Silico Study

Alzheimer's disease (AD) is a brain disease with a peculiarity of multiformity and an insidious onset. Multiple-target drugs, especially Chinese traditional medicine, have achieved a measure of success in AD treatment. Evodia rutaecarpa (Juss.) Benth. (Wuzhuyu, WZY, i.e., E. rutaecarpa), a traditional Chinese herb, has been identified as an effective drug to cure migraines. To our surprise, our in silico study showed that rather than migraines, Alzheimer's disease was the primary disease to which the E. rutaecarpa active compounds were targeted. Correspondingly, a behavioral experiment showed that E. rutaecarpa extract could improve impairments in learning and memory in AD model mice. However, the mechanism underlying the way that E. rutaecarpa compounds target AD is still not clear. For this purpose, we employed methods of pharmacology networking and molecular docking to explore this mechanism. We found that E. rutaecarpa showed significant AD-targeting characteristics, and alkaloids of E. rutaecarpa played the main role in binding to the key nodes of AD. Our research detected that E. rutaecarpa affects the pathologic development of AD through the serotonergic synapse signaling pathway (SLC6A4), hormones (PTGS2, ESR1, AR), anti-neuroinflammation (SRC, TNF, NOS3), transcription regulation (NR3C1), and molecular chaperones (HSP90AA1), especially in the key nodes of PTGS2, AR, SLCA64, and SRC. Graveoline, 5-methoxy-N, N-dimethyltryptamine, dehydroevodiamine, and goshuyuamide II in E. rutaecarpa show stronger binding affinities to these key proteins than currently known preclinical and clinical drugs, showing a great potential to be developed as lead molecules for treating AD.

Juvenile hormone mimics with phenyl ether and amide functionality to be insect growth regulators (IGRs): synthesis, characterization, computational and biological study

A series of substituted phenyl ethers derivatives as juvenile hormone (JH) mimics (V₁-V₈) have been synthesized. Substituted phenoxyacetic acid and amino acid ethyl ester hydrochloride were prepared using NaOH, SOCl₂. DCC method has been used for amide linkage. The structure of prepared compounds has been confirmed by Fourier Transform Infra-Red (FT-IR), Electrospray ionization-Mass spectrometry (ESI-MS), Proton and Carbon-13 nuclear magnetic resonance (¹H-NMR, ¹³C-NMR) spectroscopic techniques. Biological efficacy of synthesized analogs has been carried out under laboratory conditions. Galleria mellonella (honey bee pest) has been chosen as testing insect. Juvenile hormone (JH) activity of synthesized compounds has been tested at different concentrations and compared with the standard juvenile hormone analogs (JHAs) pyriproxyfen (M₁) and fenoxycarb (M₂) against the fifth larval instar of G. mellonella. Compound ethyl 2-[2-(4-methylphenoxy)aminoacetyl]-3-phenyl-propanoate (V₆) exhibited better activity among all the synthesized compounds (V₁-V₈) with LC₅₀ and LC₉₀ values of 0.11 mg/mL and 0.56 mg/mL respectively. Compounds showed insect growth regulating (IGR) activity at lower concentrations. In silico screening of all synthesized compounds with the W-cavity of juvenile hormone-binding protein (JHBP) of insect G. mellonella has been carried out. Chemical reactivity of synthesized series has been studied using DFT/B3LYP/6-311 + G(d,2p) method. Non-toxic behavior of molecules has also been observed from ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) study using discovery studio client 3.0.Communicated by Ramaswamy H. Sarma.

Molecular Iodine-Catalyzed Synthesis of Imidazo[1,2-a]Pyridines: Screening of Their In Silico Selectivity, Binding Affinity to Biological Targets, and Density Functional Theory Studies Insight

The present paper discloses an ultrasonication strategy assisted by molecular iodine as an environmentally benign catalyst leading to the synthesis of pharmacologically significant imidazo[1,2-a]pyridine scaffolds. The molecular-iodine-catalyzed approach for the synthesis of biologically active synthetic equivalents was achieved through three-component coupling embracing 2-aminopyridine derivatives, pertinent acetophenones, and dimedone in water medium under aerobic conditions. The higher product yield (up to 96%) with a miniature reaction time and modest catalyst loading as demonstrated by higher ecological compatibility and sustainability factors are fascinating features of this protocol. The structures of synthesized compounds were accomplished through FT-IR, ¹H NMR,¹³C NMR, mass, and elemental analysis data. The virtual screening of synthetic moieties was performed to ascertain the in silico selectivity and binding affinities against several biological targets. Lipinski's rules of five, ADMET, and TOPKAT descriptors were used to evaluate the drug-likeness assets. Furthermore, a quantum computational study was computed at the B3LYP/6-311G++(d,p) level of theory to investigate the density functional theory-based chemical reactivity parameters and HOMO-LUMO energy gap of the synthesized derivatives. The present studies open the way for in vitro and in vivo testing of synthesized derivatives as potent inhibitors with an improved pharmacological profile against farnesyl diphosphate synthase, phosphodiesterase III, CXCR4, and GABAa receptor agonists.

Inhibition of Mammalian Target of Rapamycin Attenuates Recurrent Seizures Associated Cardiac Damage in a Zebrafish Kindling Model of Chronic Epilepsy

Sudden Unexpected Death in Epilepsy (SUDEP) is primarily linked with the cardiac irregularities that occur due to recurrent seizures. Our previous studies found a role of mTOR pathway activation in seizures-linked cardiac damage in a rat model. In continuation to the earlier work, the present study was devised to explore the role of rapamycin (mTOR inhibitor and clinically used immunosuppressive agent) in a zebrafish kindling model and associated cardiac damage. Adult zebrafish were incubated with increasing concentrations of rapamycin (1, 2 and, 4 μM), followed by pentylenetetrazole (PTZ) exposure to record seizure latency and severity. In another experiment, zebrafish were subjected to a standardized PTZ kindling protocol. The kindled fish were treated daily with rapamycin for up to 25 days, along with PTZ to record seizure severity. At the end, zebrafish heart was excised for carbonylation assay, gene expression, and protein quantification studies. In the acute PTZ convulsion test, treatment with rapamycin showed a significant increase in seizure latency and decreased seizure severity without any change in seizure incidence. Treatment with rapamycin also reduced the severity of seizures in kindled fish. The cardiac expressions of gpx, nppb, kcnh2, scn5a, mapk8, stat3, rps6 and ddit were decreased, whereas the levels of trxr2 and beclin 1 were increased following rapamycin treatment in kindled fish. Furthermore, rapamycin treatment also decreased p-mTOR expression and protein carbonyls level in the fish cardiac tissue. The present study concluded that rapamycin reduces seizures and associated cardiac damage by inhibiting mTOR activation in the zebrafish kindling model.

Elucidating the anti-aging mechanism of Si Jun Zi Tang by integrating network pharmacology and experimental validation in vivo

Si Jun Zi Tang (SJZT) is a classic Traditional Chinese Medicine (TCM) prescription used to treat aging-related diseases. However, the potential molecular mechanisms of the anti-aging effects of the bioactive compounds and their targets remain elusive. In this study, we combined network pharmacology and molecular docking with in vivo experiments to elucidate the anti-aging molecular mechanism of SJZT. A series of network pharmacology strategies were used to predict potential targets and therapeutic mechanisms of SJZT, including compound screening, pathway enrichment analysis and molecular docking studies. Based on the network pharmacology predictions and observation of outward signs of aging, the expression levels of selected genes and proteins and possible key targets were subsequently validated and analysed using qRT-PCR and immunoblotting. Using a data mining approach, 235 effective targets of SJZT and aging were obtained. AKT1, STAT3, JUN, MAPK3, TP53, MAPK1, TNF, RELA, MAPK14 and IL6 were identified as core genes in the Protein-Protein Interaction Networks (PPI) analysis. The results of the effective target Gene Ontology (Go) functional enrichment analysis suggested that SJZT may be involved aging and antiapoptotic biological processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the anti-aging mechanism of SJZT may be associated with the PI3K-AKT and P38 MAPK signalling pathways. Molecular docking analysis suggested that kaempferol and quercetin could fit in the binding pockets of the core targets. In addition, SJZT alleviated the aging symptoms of mice such as osteoporosis and hair loss. In conclusion, the anti-aging effect of SJZT was associated with the inhibition of the PI3K-AKT and P38 MAPK signalling pathways, and these findings were consistent with the network pharmacology prediction.

Elaborate the Mechanism of Ancient Classic Prescriptions (Erzhi Formula) in Reversing GIOP by Network Pharmacology Coupled with Zebrafish Verification

Osteoporosis is a degenerative disease that endangers human health. At present, chemical drugs used for osteoporosis have serious side effects. Therefore, it is valuable to search herbs with high safety and good curative effect in antiosteoporosis. Erzhi formula (EZF), an ancient classic compound, has been reported to have a beneficial effect in antiosteoporosis, but its mechanism is unclear. In this paper, the active compounds of EZF were found in Systems Pharmacology Database, and gene targets related to osteoporosis were obtained in GeneCards. The GO functional and KEGG pathway enrichment analysis were performed by Metascape. The network of “components-targets-signal pathway” was constructed by Cytoscape. Next, molecular docking between the active components and hub genes related to the PI3K-Akt signaling pathway was conducted by Autodock. In the verification experiment, the zebrafish induced by prednisolone (PNSL) was used to reproduce glucocorticoid-induced osteoporosis (GIOP) model, and then the reversal effects of EZF were systematically evaluated according to the behavior, skull staining area, bone mineralization area (BMA), average optical density (AOD), and cumulative optical density (COD). Finally, it was shown that 24 components in EZF could regulate 39 common gene targets to exert antiosteoporosis effect. Besides, the main regulatory mechanisms of EZF were 4 signaling pathways: PI3K-Akt, JAK-STAT, AGE-RAGE, and cancer pathway. In PI3K-Akt signaling pathway, wedelolactone, dimethyl wedelolactone, specnuezhenide, ursolic acid, acacetin, beta-sitosterol, apigenin, and kaempferol can bind tightly with EGF, IL-2, and IL-4 genes. Compared with the model group, the moving distance, swimming speed, and cumulative swimming time of zebrafish in EZF group were significantly increased (P < 0.05). Meanwhile, the BMA and COD of zebrafish were significantly improved after the intervention of EZF (P < 0.05). In summary, the 24 components of EZF exert their antiosteoporosis effects by regulating 39 related gene targets, among which the PI3K signaling pathway is crucial. EZF can promote bone formation and reversed GIOP through “multicomponent/multitarget/multipathway” and the medium dose of EZF may be the most suitable concentration for the treatment of GIOP in zebrafish model.

Application and advantages of zebrafish model in the study of neurovascular unit

The concept of "Neurovascular Unit" (NVU) was put forward, so that the research goal of Central Nervous System (CNS) diseases gradually transitioned from a single neuron to the structural and functional integrity of the NVU. Zebrafish has the advantages of high homology with human genes, strong reproductive capacity and visualization of neural circuits, so it has become an emerging model organism for NVU research and has been applied to a variety of CNS diseases. Based on CNKI (https://www.cnki.net/) and PubMed (https://pubmed.ncbi.nlm.nih.gov/about/) databases, the author of this article sorted out the relevant literature, analyzed the construction of a zebrafish model of various CNS diseases，and the use of diagrams showed the application of zebrafish in the NVU, revealed its relationship, which would provide new methods and references for the treatment and research of CNS diseases.

Dendrobium catenatum Lindl. Water Extracts Attenuate Atherosclerosis

Objectives

Dendrobium catenatum Lindl. (DH) is a Chinese herbal medicine, which is often used to make tea to improve immunity in China. Rumor has it that DH has a protective effect against cardiovascular disease. However, it is not clear how DH can prevent cardiovascular disease, such as atherosclerosis (AS). Therefore, the purpose of this study is to study whether DH can prevent AS and the underlying mechanisms.

Methods

Zebrafish larvae were fed with high-cholesterol diet (HCD) to establish a zebrafish AS model. Then, we used DH water extracts (DHWE) to pretreat AS zebrafish. The plaque formation was detected by HE, EVG, and oil red O staining. Neutrophil and macrophage counts were calculated to evaluate the inflammation level. Reactive oxygen species (ROS) activity, malondialdehyde (MDA) content, and superoxide dismutase (SOD) activity in zebrafish were measured to reflect oxidative stress. The cholesterol accumulation and the levels of lipid, triglyceride (TG), and total cholesterol (TC) were measured to reflect lipid metabolism disorder. Then, parallel flow chamber was utilized to establish a low shear stress- (LSS-) induced endothelial cell (EC) dysfunction model. EA.hy926 cells were exposed to LSS (3 dyn/cm²) for 30 min and treated with DHWE. The levels of ROS, SOD, MDA, glutathione (GSH), and glutathiol (GSSG) in EA.hy926 cells were analysed to determine oxidative stress. The release of nitric oxide (NO), endothelin-1 (ET-1), and epoprostenol (PGI₂) in EA.hy926 cells was measured to reflect EC dysfunction. The mRNA expression of intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) in EA.hy926 cells was detected to reflect EC dysfunction inflammation.

Results

The results showed that DHWE significantly reduced cholesterol accumulation and macrophage infiltration in early AS. Finally, DHWE significantly alleviate the lipid metabolism disorder, oxidative stress, and inflammation to reduce the plaque formation of AS zebrafish larval model. Meanwhile, we also found that DHWE significantly improved LSS-induced EC dysfunction and oxidative stress in vitro.

Conclusion

Our results indicate that DHWE could be used as a prevention method to prevent AS.

A zebrafish-centric approach to antiepileptic drug development

Danio rerio (zebrafish) are a powerful experimental model for genetic and developmental studies. Adaptation of zebrafish to study seizures was initially established using the common convulsant agent pentylenetetrazole (PTZ). Larval PTZ-exposed zebrafish exhibit clear behavioral convulsions and abnormal electrographic activity, reminiscent of interictal and ictal epileptiform discharge. By using this model, our laboratory developed simple locomotion-based and electrophysiological assays to monitor and quantify seizures in larval zebrafish. Zebrafish also offer multiple advantages for rapid genetic manipulation and high-throughput phenotype-based drug screening. Combining these seizure assays with genetically modified zebrafish that represent Dravet syndrome, a rare genetic epilepsy, ultimately contributed to a phenotype-based screen of over 3500 drugs. Several drugs identified in these zebrafish screens are currently in clinical or compassionate-use trials. The emergence of this 'aquarium-to-bedside' approach suggests that broader efforts to adapt and improve upon this zebrafish-centric strategy can drive a variety of exciting new discoveries.

Schaftoside Suppresses Pentylenetetrazol-Induced Seizures in Zebrafish via Suppressing Apoptosis, Modulating Inflammation, and Oxidative Stress

The lack of disease-modifying therapeutic strategies against epileptic seizures has caused a surge in preclinical research focused on exploring and developing novel therapeutic candidates for epilepsy. Compounds from traditional Chinese medicines (TCMs) have gained much attention for a plethora of neurological diseases, including epilepsy. Herein, for the first time, we evaluated the anticonvulsive effects of schaftoside (SS), a TCM, on pentylenetetrazol (PTZ)-induced epileptic seizures in zebrafish and examined the underlying mechanisms. We observed that SS pretreatments significantly suppressed seizure-like behavior and prolonged the onset of seizures. Zebrafish larvae pretreated with SS demonstrated downregulation of c-fos expression during seizures. PTZ-induced upregulation of apoptotic cells was decreased upon pretreatment with SS. Inflammatory phenomena during seizure progression including the upregulation of interleukin 6 (IL-6), interleukin 1 beta (IL-1β), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) were downregulated upon pretreatment with SS. The PTZ-induced recruitment of immunocytes was in turn reduced upon SS pretreatment. Moreover, SS pretreatment modulated oxidative stress, as demonstrated by decreased levels of catalase (CAT) and increased levels of glutathione peroxidase-1a (GPx1a) and manganese superoxide dismutase (Mn-SOD). However, pretreatment with SS modulated the PTZ-induced downregulation of the relative enzyme activity of CAT, GPx, and SOD. Hence, our findings suggest that SS pretreatment ameliorates PTZ-induced seizures, suppresses apoptosis, and downregulates the inflammatory response and oxidative stress, which potentially protect against further seizures in zebrafish.

Structure-based investigation of MARK4 inhibitory potential of Naringenin for therapeutic management of cancer and neurodegenerative diseases

MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of serine/threonine kinase family and considered an attractive drug target for many diseases. Screening of Indian Medicinal Plants, Phytochemistry, and Therapeutics (IMPPAT) using virtual high-throughput screening coupled with enzyme assay suggested that Naringenin (NAG) could be a potent inhibitor of MARK4. Structure-based molecular docking analysis showed that NAG binds to the critical residues found in the active site pocket of MARK4. Furthermore, molecular dynamics (MD) simulation studies for 100 ns have delineated the binding mechanism of NAG to MARK4. Results of MD simulation suggested that binding of NAG further stabilizes the structure of MARK4 by forming a stable complex. In addition, no significant conformational change in the MARK4 structure was observed. Fluorescence binding and isothermal titration calorimetric measurements revealed an excellent binding affinity of NAG to MARK4 with a binding constant (K) = 0.13 × 10⁶ M^-1 obtained from fluorescence binding studies. Further, enzyme inhibition studies showed that NAG has an admirable IC₅₀ value of 4.11 µM for MARK4. Together, these findings suggest that NAG could be an effective MARK4 inhibitor that can potentially be used to treat cancer and neurodegenerative diseases.

Plant-based analogues identified as potential inhibitor against tobacco mosaic virus: A biosimulation approach

Benzosuberene compounds with a pyrrolone group adhered to it are compounds extracted from the oils of Cedrus deodara plant, that bear inhibitory capabilities. Tobacco mosaic virus is known to affect crop production every year. The currently known inhibitors against TMV have a weak inhibition effect and also tend to be toxic towards non-target living organisms as well as the environment. Thus, the requirement of non-toxic potent inhibitors is the need of the hour, which led us to test our benzosuberene molecules on the binding site of TMV and check their affinity as well as stability. The non-toxic nature of these molecules has already been experimentally established. Through in-silico analysis involving docking and simulation experiments, we compared the interaction pattern of these ligand molecules with the already present inhibitors. Our investigation proved that the reported ligands (ligands 3, 7, 9, and 17 obtained -177.103, -228.632, -184.134, and - 188.075 kJ/mol binding energies, respectively) interacted with the binding site of TMV much efficiently than the known inhibitors (Ribavirin and Zhao et al. 2020 obtained 121.561 and - 221.393 kJ/mol binding energies, respectively). Moreover, they acquired a stable conformation inside the binding pocket, where a higher number of binding site residues contributed towards interaction. Thus, their structural framework can be optimized for the exploration of their antiviral properties to develop potent botanical viricides against plant virus infection.

Benzosuberene-sulfone analogues synthesis from Cedrus deodara oil and their therapeutic evaluation by computational analysis to treat type 2 diabetes

Benzosuberene-sulfone (BSS) analogues have been semi-synthesized following green approaches from himachalenes, which has been extracted from essential oil of Cedrus deodara. In this process, benzosuberene in presence of different aryl or alkyl sodium sulfinates, I₂ and potassium persulfate (K₂S₂O₈) in acetonitrile-water solvent conditions gave BSS-analogues at room temperature. Under this reaction, a facile endocyclic β-H elimination has been noticed for BSS-analogues synthesis instead of vinyl sulfones and the reason may be due to its specific structure and electronic environment. The BSS-compounds were obtained with moderate to excellent yields under mild conditions. All the compounds were computationally subjected to drug likeliness and toxicity prediction studies. Further, the synthesized molecules were evaluated under in-silico studies for their binding affinity towards the native Peroxisome Proliferator-Activated Receptor Gamma (PPARG), and two PPARG mutants (R357A and V290M). Both the mutant forms of PPARG are deficient in eliciting a response to treatment with full and partial agonists. Our computational studies suggested that the molecule 3q performed better than the standard drug (Rosiglitazone) in all three protein structures. This implies that our suggested molecule could act as a more potent antagonist to native PPARG and could also be developed to treat type-2 diabetes patients with R357A and V290M mutations, which didn't elicit any response to currently available drugs in the market.

Hesperidin Interacts With CREB-BDNF Signaling Pathway to Suppress Pentylenetetrazole-Induced Convulsions in Zebrafish

Hesperidin (3,5,7-trihydroxyflavanone 7-rhamnoglucoside) is a β-7-rutinoside of hesperetin (4'-methoxy-3',5,7-trihydroxyflavanone), abundantly found in citrus fruits and known to interact with various cellular pathways to show a variety of pharmacological effects. The present study was envisaged to understand the anticonvulsant effect of hesperidin in a zebrafish model of pentylenetetrazole (PTZ)-induced convulsions, with the support of in silico docking. Healthy zebrafish larvae were preincubated with hesperidin (1, 5, and 10 µM) for 1 h, before PTZ exposure. Hesperidin treatment significantly increased the seizure latency and minimized PTZ-induced hyperactive responses. A significant reduction in c-fos expression further supported the suppression of neuronal excitation following hesperidin incubation in the larvae exposed to PTZ. The treatment also modulated larval bdnf expression and reduced the expression of il-10. The results of in vivo studies were further supported by in silico docking analysis, which showed the affinity of hesperidin for the N-methyl-d-aspartate receptor, the gamma-aminobutyric acid receptor, Interleukin 10 and the TrkB receptor of brain-derived neurotrophic factor. The results concluded that hesperidin suppresses PTZ-mediated seizure in zebrafish larvae through interaction with the central CREB-BDNF pathway.

In-silico prediction of potential inhibitors against phosphatidylinositol 3-kinase catalytic subunit alpha involved in head and neck squamous cell carcinomas

Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers, globally. Its high mortality rates remained unaltered in the last three decades, therefore, there is an enormous need for novel therapeutics. The most frequent somatically mutated oncogenic pathway in HNSCC tumors is the Phosphatidylinositol-3-kinases (PI3K) pathway. PI3Ks are lipid kinases involved in the regulation of cell survival, growth and metabolism. PI3Ks phosphorylates PI (4,5) P2 (PIP2) converting it to PI (3, 4, 5) P3 (PIP3). Alterations such as mutation, gene amplification and overexpression in PIK3CA, encoding the catalytic subunit p110α of PI3K pathway were found to be prevalent. The aberrant activation leads to irregulated cell growth due to improper p110α enzymatic activity. p110α is therefore, considered a potential oncogenic target for cancer therapy. The only FDA approved specific inhibitor of p110α is Alpelisib (BYL719). Therefore, designing more effective and specific p110α inhibitors could be a promising strategy in the treatment of HNSCC. The present study aims to find out the potent and novel inhibitors of p110α using High Throughput Screening (HTS) of huge databases (National Cancer Institute (NCI), Life Chemicals, ChemDiv and ChEMBL) and Molecular Dynamic Simulations. As a result, from more than 400,000 compounds, a total of 3 best candidate compounds (Echinacoside, Isoacteoside, K284-4402) were selected and validated for their binding to catalytic site of p110α and stability during Molecular Dynamics (MD) simulations. The binding free energy (calculated from MM-PBSA) of the selected compounds, Echinacoside, Isoacteoside, K284-4402 were -23.43 kcal/mol, -33.02 kcal/mol and -30.57 kcal/mol, respectively, which suggested these compounds bind to p110α with higher affinity than Alpelisib which has binding free energy -20.9 kcal/mol. This study provides a significant in-depth understanding of p110α inhibitors that can be used in the development of potential therapeutics against HNSCC.Communicated by Ramaswamy H. Sarma.

Development and validation of chemical kindling in adult zebrafish: A simple and improved chronic model for screening of antiepileptic agents

BACKGROUND

Zebrafish has emerged as a potential animal model of acute convulsion for early screening of antiepileptic agents. There is a need for alternative chronic zebrafish models of epilepsy with more correlation to the clinical condition.

NEW METHOD

Adult zebrafish were repeatedly exposed to subeffective concentrations of pentylenetetrazole (PTZ), until appearance to tonic-clonic seizures, considered as kindled. Valproic acid (VPA) exposure was given during kindling and in kindled fish in 2 different groups. The neurotransmitters level and expression of the genes associated with kindling were studied in the fish brain.

RESULTS

There was an increase in seizure severity score at 1.25 mM concentration of PTZ, and 66.66 % of fish achieved kindling after 22 days' exposure. A marked increase in c-fos, crebbpa and crebbpbexpression, and glutamate/GABA level was observed in the brain of kindled fish. VPA inhibited the induction of PTZ-mediated kindling and reduced seizure severity in kindled fish.

COMPARISON WITH EXISTING METHOD

In contrast to an existing adult zebrafish kindling method, the present protocol is of longer duration, with more similarity to clinical epilepsy. Moreover, the induction of kindling involves a simple non-invasive technique without the use of anesthesia. The protocol can be used for evaluation of both antiepileptic and antiepileptogenic agents.

CONCLUSION

Repeated exposure of 1.25 mM PTZ induced kindling in zebrafish, altering the brain neurotransmitter levels and gene expression. Inhibition of kindling induction and decrease in seizures in normal and kindled fish, respectively by VPA validated application of the model for preclinical testing of agents against epilepsy.

Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs

Background

The main protease (Mpro) of SARS-CoV-2 is involved in the processing of vital polypeptides required for viral genome replication and transcription and is one of the best-characterized targets to inhibit the progression of SARS-CoV-2 in infected individuals.

Methods

We screened a set of novel classes of acridinediones molecules to efficiently bind and inhibit the activity of the SARS-CoV-2 by targeting the Mpro. The repurposed FDA-approved antivirals were taken as standard molecules for this study. Long term (1.1 μs) MD simulations were performed to analyze the conformational space of the binding pocket of Mpro bound to the selected molecules.

Results

The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated more deeply inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). Moreover, DSPD-5 also exhibited comparable binding energy to Saquinavir. The analysis of per residue contribution energy and SASA studies indicated that the molecules showed efficient binding by targeting the S1 subsite of the Mpro binding pocket.

Conclusion

The DSPD-2, DSPD-6, and DSPD-5 could be developed as potential inhibitors of SARS-CoV-2. Moreover, we suggest that targeting molecules to bind effectively to the S1 subsite could potentially increase the binding of molecules to the SARS-CoV-2 Mpro.

•

A robust computational strategy applied to identify the potential lead for COVID-19.

•

Repurposed FDA approved antiviral drugs were compared with a set of acridinedione analogs against Mpro of SARS-CoV-2.

•

The acridinedione analogs have acceptable ADMET values and low toxicity profile.

•

In-house synthesized acridinedione analogs showed good amount of interaction with Mpro of SARS-CoV-2.

Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation- regulated kinase

Background and Objectives The Dual-specificity tyrosine-phosphorylation regulated kinase-1A (DYRK1A) a serine/threonine kinase that has freshly gained recognition as an essential drug target due to the discovery of its involvement in pathological diseases. The development of new potent inhibitors of DYRK1A would contribute to clarify the molecular mechanisms of associated diseases. It would administer a new lead compound for molecular-targeted protein, which was the primary focus of our study. Methods The library of in-house synthesized pyrrolone-fused benzosuberene (PBS) compounds was docked with DYRK1A receptor. Further, molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) estimations were conducted to confirm our docking outcomes and compared the stability of chosen complexes with the 2C3 (standard molecule) complex. Results This study reports Ligand15, Ligand14, and Ligand11 as potent inhibitors which showed higher ligand efficiency, binding affinity, lipophilic ligand efficiency, and favorable torsion values as compared to 2C3. Conclusion The stated methodologies revealed a unique mechanism of active site binding. The binding interactions within the active site showed that the chosen molecules had notable interactions than the standard molecule, which led to the generation of potential compounds to inhibit DYRK1A.

Discovery of Lonafarnib-Like Compounds: Pharmacophore Modeling and Molecular Dynamics Studies

Progeria is a globally noticed rare genetic disorder manifested by premature aging with no effective treatment. Under these circumstances, farnesyltransferase inhibitors (FTIs) are marked as promising drug candidates. Correspondingly, a pharmacophore model was generated exploiting the features of lonafarnib. The selected pharmacophore model was allowed to screen the InterBioScreen natural compound database to retrieve the potential lead candidates. A series of filtering steps were applied to assess the drug-likeness of the compounds. The obtained compounds were advanced to molecular docking employing the CDOCKER module available with Discovery Studio (DS). Subsequently, three compounds (Hits) have displayed a higher dock score and demonstrated key residue interactions with stable molecular dynamics simulation results compared to the reference compound. Taken together, we therefore put forth three identified Hits as FTIs that may further serve as chemical spaces in designing new compounds.

Natural analogues inhibiting selective cyclin-dependent kinase protein isoforms: a computational perspective

Cyclin-dependent kinases (CDKs) are known for their vital role in regulating cell cycle progression through protein-kinase interactions. CDKs also help in regulating transcription and development of the central nervous system. Inhibition of CDKs is a very fundamental approach for drug discovery in areas of different types of cancers, Alzheimer's, and HIV infections. The present research focuses on finding a novel, potent, and specific natural inhibitors of CDK isoforms (CDK2, CDK5, CDK7, CDK9). Molecular docking, molecular dynamics (MD) simulations, and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) were carried out to get an in-depth understanding of protein-ligand interactions. Based on our molecular docking results, Ligands-3, 5, 14, and 16 were screened among 17 different Pyrrolone-fused benzosuberene compounds as potent and specific inhibitors without any cross-reactivity against different CDK isoforms. Analysis of MD simulations and MM-PBSA studies, revealed the binding energy profiles of all the selected complexes. Our selected ligands performed better than the standard inhibitor (Roscovitine). Ligands-3 and 14 show specificity for CDK7 and Ligands-5 and 16 were specific against CDK9. These ligands are expected to possess lower risk of side effects due to their natural origin. Moreover, the backbone structure of these ligands could also be exploited to develop specific inhibitors against other CDK isoforms.Communicated by Ramaswamy H. Sarma.

Structural Perturbations due to Mutation (H1047R) in Phosphoinositide-3-kinase (PI3Kα) and Its Involvement in Oncogenesis: An in Silico Insight

PI3Kα is a heterodimer protein consisting of two subunits (p110α and p85α) which promotes various signaling pathways. Oncogenic mutation in the catalytic subunit p110α of PI3Kα at the 1047 position in the kinase domain substitutes the histidine with arginine. This mutation brings about conformational transitions in the protein complex. These transitions expose the membrane binding region of PI3Kα, and then it independently binds to the cell membrane through its kinase domain without the involvement of the membrane-bound protein RAS. We observed notable changes between the protein complexes (p110α-p85α) of native and mutant structures at the atomic level using molecular dynamics simulations. Simulation results revealed formation of a less number of hydrogen bonds between the two subunits in the mutant protein complex which led the two subunits to move away from each other. This increase in distance between the subunits led to an expanded structure, thereby increasing the flexibility of the protein complex. Furthermore, a study of secondary structure elements and the electrostatic potential of the protein also gave a molecular insight into the change in interaction patterns of the protein with the plasma membrane. Our finding clearly indicates the role of mutation in oncogenesis and provides an insight into considering the structural aspects to handle this mutation.

Structure-based drug target prioritisation and rational drug design for targeting Chlamydia trachomatis eye infections

Chlamydia trachomatis (C.t) is a major causative of infectious blindness in world. It is a real challenge to combat Chlamydial infection as it is an intracellular pathogen. Hence, it is essential to determine the most potential targets of C.t in order to inhibit or suppress its virulence during its infectious phase. Thus, in this study, the highly expressed-cum-most essential genes reported through our earlier study were reprioritized by structure-based comparative binding site analysis with host proteome. Therefore, computational approaches involving molecular modelling, large-scale binding site prediction and comparison, molecular dynamics simulation studies were performed to narrow down the most potential targets. Furthermore, high-throughput virtual screening and ADMETox were also performed to identify potential hits that shall efficiently inhibit the prioritised targets. Hence, by this study we report Pyruvoyl-dependent arginine decarboxylase (PvlArgDC), DNA-repair protein (RecO) and porin (outer membrane protein) as the most viable targets of C.t which can be potentially targeted by compounds, NSC_13086, MFCD00276409, MFCD05662003, respectively. AbbreviationsC.tChlamydia trachomatisSTDSexually transmitted diseaseHTVSHigh-throughput virtual screeningADMEToxAbsorption, Distribution, Metabolism, Excretion and ToxicityPMPocketMatchMDMolecular Dynamics simulationSPStandard precisionXPExtra precisionMMGBSAMolecular mechanics energies combined with generalised Born and surface area continuum solvationOMPOuter membrane proteinPvlArgDCPyruvoyl-dependent arginine decarboxylaseRecORecombination protein O.Communicated by Ramaswamy H. Sarma.

Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway

From bacteria to mammals, DNA mismatch repair (MMR) pathway plays an essential role in eliminating mismatched nucleotides and insertion-deletion mismatches during the process of DNA replication. Among many of the proteins which participate in the mismatch repair process, proliferating cell nuclear antigen (PCNA) remains the principal conductor at the replication fork. The pol30-201 and pol30-204 are the two mutated alleles which encode for C22Y and C81R mutant forms of PCNA proteins. We performed long term molecular dynamics (MD) simulations analysis (0.8 μs) to understand the dynamic behavior and alterations in the structure of wild type and mutated forms of PCNA at the atomic level. We observed changes in the structural characteristics like length, radius, rise per residue of alpha helices in both the mutated forms of PCNA. Apart from it, disfigurement of the charge distribution which effects binding with the dsDNA due to mutant C22Y and other structural perturbations were also seen in regions significant for the formation of a biologically active trimeric form of PCNA due to mutant C81R. Our analysis of native and mutated forms of PCNA provides an insight into the essential structural and functional features required for proper and well-coordinated DNA mismatch repair process and consequences of the mutation leading to an impaired process of MMR. These structural characteristics are fundamental for the MMR process and hence our analysis likely contributes to or presents the novel mechanism involved in the process of MMR.Communicated by Ramaswamy H. Sarma.