Highest Docking Score Research Articles

Investigation of Novel Quinoline Derivatives Targeting Epidermal Growth Factor Receptors as Anticancer Agents a Computational Approach

Background: Newer chemical entities are created and synthesis has been made feasible by a variety of computer-aided drug design (CAAD) techniques. In addition to facilitating the visualisation of the ligand-target binding process, the application of in silico methodologies and structure-based drug design (SBDD) allows for the prediction of receptor affinities and significant binding pocket locations. Objective: The goal of the current study was to identify new quinoline derivatives by computational methods specially designed to bind the EGFR receptor in the treatment of breast cancer. Materials and Methods: ChemAxon Marvin Sketch 5.11.5 was used to create derivatives of quinolines. The admetSAR online web tools and SwissADME were utilised to forecast the toxicity and pharmacokinetic characteristics of several substances. A multitude of software programmes, such as Autodock 1.1.2, MGL Tools 1.5.6, Procheck, Protparam ExPasy tool, PyMOL, and Biovia Discovery Studio Visualizer v20.1.0.19295 were also employed to ascertain the ligand-receptor interactions between quinoline derivatives and the target receptor (PDB -5GNK). Result: Almost all components were shown to be less hazardous, orally consumable and to have the appropriate pharmacokinetic characteristics based on in silico study. All newly generated derivative compounds have higher docking scores when compared to the widely used medication sorafenib. Conclusion: Interactions with quinoline analogues boost binding energy and the number of Hbonds produced, making them a suitable place to start when creating compounds for further exploration. The quinoline moiety increases its potential as a novel therapy alternative for breast cancer and could facilitate more comprehensive in vivo, in vitro, chemical-based, and pharma studies by medicinal chemists.

Unveiling Novel Hybrids Quinazoline/Phenylsulfonylfuroxan Derivatives with Potent Multi‐Anticancer Inhibition: DFT and In Silico Approach Combining 2D‐QSAR, Molecular Docking, Dynamics Simulations, and ADMET Properties

AbstractIn this work, the biological activities of 29 novel quinazoline/phenylsulfonylfuroxan derivatives (1a–z, 1aa, 1ab, 2a, 2b, 2d, and 2f) were computationally investigated as potential anti‐cancer inhibitors against five cell lines, i.e., H1975, MCF‐7, Eca‐109, MGC‐803, and A549, which are involved in various diseases, including lung, breast, esophageal squamous carcinoma, and gastric cancer. The 2D‐QSAR predictive approach, exploiting multiple linear regression (MLR) models and rigorous internal and external cross‐validation, showed a correlation factor R2 of range: 0.68−0.82. Moreover, the MLR‐derived R2test and Y randomization (R2rand) values for the five cell lines are higher than 0.60 and less than 0.3, respectively, indicating a strong alignment with the internal and external validation data. New 70 quinazoline hybrids based on the most effective in vivo 1q inhibitor were designed, and their pIC50 activity was predicted. The best‐scoring 15 (N1–N15) compounds were further evaluated using molecular docking and dynamics simulations (100 ns) with the VEGFR‐2 kinase target (PDB code: 3U6J). All the data sets accurately predict the strongest binding affinity for the selected (N6, N7, N9, and N11) molecules, as evidenced by the highest docking score, hydrogen bond energy, and significant amino acid steric interactions. Furthermore, the RMS/RMSF/Rg dynamics parameters show that the formed complexes are satisfactorily stable. The ADMET properties indicate that the selected new ligands have shown a promising drug‐like profile and can be considered potential candidates for future anti‐cancer therapies, with perspective validating their anticancer activity by in vitro and in vivo studies.

Deciphering the 4',7-Dihydroxy-3'-Methylflavone from Boerhavia, Agonist/Antagonist Interactions Against 5-HT2 Receptors using Homology Modeling, Molecular Docking, and Dynamic Simulation Studies.

Seizures, depression, and anxiety are neurological disorders that affected innumerable people worldwide. Recent research has revealed that targeting 5-hydroxytryptamine 2 (5-HT2) receptors can help suppress these conditions. An in-depth literature study has identified that phytocompounds from the Boerhavia genus could reduce seizures. Therefore, homology models of 5-HT2 receptors were generated and validated using techniques such as the alignment of amino acid sequences and the Ramachandran plot. Later, a comparison of modeled structures was made with a non-redundant set of PDB structures. The pharmacokinetics, drug-likeness, blood-brain barrier (BBB) permeability, and Lipinski's rule of five shed light on 22 phytocompounds, which are the potential candidates for molecular docking among 127 Boerhavia's bioactive. Notably, molecular docking analysis revealed 4',7-dihydroxy-3'-methylflavone as the most potent lead compound, which has a strong binding affinity to all modeled receptors. Additionally, with a remarkably high docking score of -9.1 kcal/mol, 4',7-dihydroxy-3'-methylflavone showed promising interactions, particularly with 5-HT2A receptor, as seen from the RMSD, SASA, Rg, and number of hydrogen bonds during 100 ns molecular dynamic (MD) simulation. Principal component analysis (PCA) and Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) further confirmed that 4',7-dihydroxy-3'-methylflavone is the best novel phytocompound in Boerhavia genus for 5-HT2 receptor as agonist/antagonist activity against seizures.

In Silico Discovery of a Novel PI3Kδ Inhibitor Incorporating 3,5,7-Trihydroxychroman-4-one Targeting Diffuse Large B-Cell Lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma, and it is highly aggressive and heterogeneous. Targeted therapy is still the main treatment method used in clinic due to its lower risk of side effects and personalized medication. Excessive activation of PI3Kδ in DLBCL leads to abnormal activation of the PI3K/Akt pathway, promoting the occurrence and development of DLBCL. The side effects of existing PI3Kδ inhibitors limit their clinical application. The discovery of PI3Kδ inhibitors with novel structures and minimal side effects is urgently needed. This study constructed a PI3Kδ inhibitor screening model to screen natural product libraries. Revealing the mechanism of natural product therapy for DLBCL through network pharmacology, kinase assays, and molecular dynamics. The results of molecular docking indicated that Silibinin had a high docking score and a good binding mode with PI3Kδ. The results of network pharmacology indicated that Silibinin could exert therapeutic effects on DLBCL by inhibiting PI3Kδ activity and affecting the PI3K/Akt pathway. The kinase assays indicated that Silibinin concentration dependently inhibited the activity of PI3Kδ. The results of molecular dynamics indicated that Silibinin could stably bind to PI3Kδ. Silibinin was a structurally novel 3,5,7-trihydroxychroman-4-one PI3Kδ inhibitor, providing valuable information for the subsequent discovery of PI3Kδ inhibitors.

In silico investigation of therapeutic potential of phytosteroids against SARS-CoV2 infection via inhibition of viral multiplication and attenuation of host cytokine storm

SARS-CoV2 infection overcomes host cell membrane barrier, followed by utilization of host cellular processes for viral multiplication. Simultaneously, it triggers a cytokine storm within and around infected cells and tissues. Anti-inflammatory agents that can potentially inhibit viral penetration and multiplication within the host cells may be ideal drug candidates against COVID-19. Dietary phytosteroids have significant anti-inflammatory potential. Hence, the present study intends to investigate anti-viral potential of three dietary phytosteroids, namely, brassinolide, 28-homocastasterone and 24-epibrassinolide against SARS-CoV2 proteins, S1 spike protein, nucleocapsid protein and main protease enzyme, in addition to host pro-inflammatory proteins, interleukin-1, tumour necrosis factor-α, cyclooxygenase-2 and prostaglandin synthase, as drug targets. Molecular docking studies by AutoDock version 4.0 was performed. Brassinolide, 28-homocastasterone and 24-epibrassinolide exhibits high docking score against all the seven proteins, as compared to hydroxychloroquine. Brassinolide and 28- homocastasterone has maximum binding affinity for pro-inflammatory proteins and SARS-CoV2 proteins.Dietary phytosteroids may potentially attenuate cytokine storm with simultaneous inhibition of host entry and multiplication of SARS-CoV2. In-vitro and in-vivo anti-viral studies of plant steroids may provide a clear path for the identification and development of novel drug candidates against COVID-19, that also provides evidence for the concept of reverse pharmacognosy.

Cystatin C alleviates unconjugated bilirubin-induced neurotoxicity by promoting bilirubin clearance from neurocytes via exosomes, dependent on hepatocyte UGT1A1 activity.

There is an urgent need to identify effective drugs for the treatment of nerve injury caused by unconjugated bilirubin (UCB). Our previous research found that cystatin C (CST3) alleviates UCB-induced neurotoxicity by promoting autophagy in nerve cells, but that autophagy inhibitors did not completely inhibit the effects of CST3. This study investigated whether CST3 could alleviate the neurotoxicity of UCB by promoting the secretion and transport of exosomes containing UCB to the liver for metabolism. It demonstrated that hyperbilirubinemia mice treated with CST3 had a higher number of serum exosomes than those in hyperbilirubinemia mice treated with phosphate-buffered saline. CST3-mediated protection against UCB-induced damage was abolished when autophagy and extracellular vesicle inhibitors were used in combination. The number of exosomes in the CST3 overexpression group was higher than that in the control group. Molecular docking experiments showed that UCB and CST3 had high docking score (-8.2). These results suggest that UCB may be excreted from cells by exosomes, and CST3 may promote this process by binding to UCB and entering the exosomes. We demonstrated that the effect of CST3 relied on liver cells with normal UDP-glucuronyl transferase1A1 (UGT1A1) activity in a coculture system of HT22 and L02 cells. CST3 levels were lower in exosomes secreted by L02 cells than in those secreted by human umbilical vein endothelial cells (HUVECs), whereas CST3 levels were higher in the culture supernatants of L02 cells than in the culture supernatants of HUVECs. This suggests that UCB exosomes in L02 cells may be released and internalized by CST3 and that UCB is then processed by UGT1A1 to conjugate UCB, thus reducing its toxicity. These results suggest that CST3 might alleviate UCB-induced neurotoxicity by promoting the clearance of UCB from cells via exosomes and that these effects are dependent on UGT1A1 activity in liver cells.

De novo Drug Design and Repurposing to suppress Liver Cancer via VEGF-R1 Mechanism: Comprehensive Molecular Docking, MolecularDynamics Simulations and ADME Estimation

Aims: The aim is to halt the progression of liver cancer [Hepatocellular carcinoma] by suppressing the VEGF-R1 receptor using Myricetin and its de novo-designed analogues. Background: VEGF/VEGFR autocrine signalling promotes the growth, progression, and metastasis of Hepatocellular carcinoma, making the development of molecularly targeted therapies highly feasible. Invasive and metastatic behaviours in various cancers, including hepatocellular carcinoma [HCC], are closely monitored through the use of VEGF signalling pathway inhibitors. Specifically in HCC, VEGFR-1 facilitates the invasive capabilities of cancer cells primarily by triggering the epithelial-mesenchymal transition [EMT] process. VEGFR-1 significantly influences the activity of proteolytic enzymes that are critical for the invasive behaviour of HCC cells. Notably, a novel mechanism has been discovered where VEGFR-1 activation leads to the upregulation of MMP-9, thereby enhancing the invasiveness of HCC cells. The scientists, in their study, have elaborated on the various antiangiogenic agents developed for the treatment of HCC. They have highlighted clinical trials that explore the efficacy of these treatments, which include the application of monoclonal antibodies and small-molecule kinase inhibitors designed to target specific pathways involved in tumour angiogenesis and growth. Objective: Creating a pharmaceutical chemistry table regarding ‘’Structure-Activity Relationship of New Compounds on anticancer’’. To do so, Myricetin and its de novo designed structured variants were used in molecular docking, molecular dynamics, cluster analyses, and 1H NMR estimation to specifically understand and enhance the mechanism of suppressing the VEGF-R1 receptor. Method: Proper ligand [Myricetin and its analogues] and receptor [VEGF-R1] preparations, and optimizations were done using the density functional theory [DFT]/B3LYP function along with the 6-31G[d,p] basis set principle in the latest software programs such as Gaussian 09, Gauss View 6.0 and Avogadro. Then using PyRx and Autodock Vina 1.1.2., many molecular docking trials were achieved with 100 posed simulations in each run. An extensive cluster analysis was performed to identify the most optimal docking poses with the highest accumulation and most favourable binding interactions, ensuring the accuracy of the study. The docking configurations that exhibited the most precise and advantageous binding energies were chosen as initial structured data for subsequent Molecular Dynamics [MD] simulations for each drug candidate. To verify the molecular docking results, MD runs were achieved in our supercomputers and the trajectory analyses were made. The data confirmed what was found in molecular docking results, verifying the high efficiency of the druggable molecules’ inhibition towards VEGF-R1. Result: Amine-derivatized Myricetin has a significantly high docking score [-10.56 kcal/mol] and great inhibition constant compared to pristine Myricetin [-4.77 kcal/mol] itself while Fluorinederivatized Myricetin [-6.45 kcal/mol] has an affinity towards VEGF-R1 between the first two molecules. Thus, the structure-activity relationship concerning pharmaceutical chemistry aspects of all the molecules studied, yielded us a great insight into what Myricetin’s organic structure possesses towards inhibiting the progression of Liver Cancer. Also, ADME studies showed that both Amine and Fluorined-derivatized Myricetin molecules are good drug candidates. Conclusion: This study highlighted the significant potential of Myricetin as an anti-cancer drug when modified with specific functional groups. Through comprehensive in silico computational analyses, our research group enhanced Myricetin's inhibitory capabilities by derivatizing its Hydroxyl group with Amine and Fluorine, resulting in improved docking scores and inhibition constants. The findings from molecular docking and molecular dynamics simulations provide a promising foundation for future in vitro and in vivo investigations of this molecule as a potential drug in cancer research.

Promising Novel Heterocyclic Drug Candidates: Synthesis, Characterization, DFT Calculations and In Silico Investigations of Anticancer Behaviors

In recent years, the inadequacy and high costs of current cancer treatment drugs have led to an increase in research focused on the design and synthesis of new compounds with potential applications in this field and the evaluation of their anticancer properties using in silico methods. For this purpose, four novel heterocyclic compounds (6–9) were synthesized and characterized using spectroscopic techniques. The DFT approach and B3LYP/6-311G(d,p) basis set were used to compare theoretical data with experimental ones and to obtain optimized geometries. It was observed that experimental and theoretical data were in harmony. In silico techniques were used to investigate the potential of synthesized compounds as drug candidates. ADMEt results have shown that all synthesized compounds have Lipinski’s rule of five which has searched criteria in drug candidates. Molecular docking studies were also performed against cancer-related proteins. The highest docking score between 2XIR protein and compound 8 was found to be −11.7 kcal/mol, while the lowest was −8.2 kcal/mol between 1MP8 protein and compound 9. To do meaningful comparisons standard drugs were also used in Molecular Docking studies. It was observed that all synthesized molecules had higher docking scores than standard drugs except ifebemtinib. It can be suggested that based on ADMET and molecular docking studies compound 8 has the potential to be a drug candidate after further investigations such as in vitro, in silico, etc., have been performed in this area.

In-silico Investigation of Ginseng Phytoconstituents as Novel Therapeutics Against MAO-A.

Ginseng (Panax ginseng) is a herb of medicinal and nutritional importance. Ginseng has been used since ancient times for the treatment of numerous ailments as it has many therapeutic properties. Several phytoconstituents are present in Panax ginseng that possess a variety of beneficial pharmacological properties. To explore the potential of phytoconstituents of Panax ginseng in the treatment of depression, a molecular modeling technique was utilized targeting monoamine oxidase-A (MAO-A). A total of sixty-one phytoconstituents of ginseng were drawn with the help of ChemBioDraw Ultra 12.0 software and PDBs for MAO-A enzyme were retrieved from the RCSB PDB database. The prepared ligands were screened for MAO-A properties using the software Molegro Virtual Docker (MVD 2010.4.1.0). All the prepared ligands were evaluated for drug-likeliness properties using Swiss ADME. Among the docking studies of 60 Ginseng phytochemicals including one standard, 15 phytoconstituents with the highest dock score and better binding interactions were selected further for absorption, distribution, metabolism and excretion (ADME) studies. Stachyose (-227.287, 17 interactions), Raffinose (-222.157, 14 interactions), and Ginsenoside Rg1 (-216.593, 10 interactions) were found to possess better interactions as compared to Clorgyline taken as a standard drug. Stachyose was found to be the most potent inhibitor of MAO-A enzyme under investigation and can be a potential lead molecule for the development of newer phytochemical-based treatment of depression.

Design, Synthesis, and Quantum Chemical Calculations of Triazole-Based Aroylhydrazone Molecules: Dual Assessment of Antioxidant Properties via in vitro and in silico Approaches

In this study, five novel Triazole-Based Aroylhydrazone compounds (6a-e) were synthesized in high yields (87-79%), starting from deferasirox which has known iron chelator, and characterized with NMR, FTIR, Mass, and UV-vis spectroscopic methods. Quantum chemical calculations of all synthesized molecules were performed at the DFT/B3LYP/6,311G(d,p) level. It was observed that both theoretical and experimental spectral values were compatible. Optimized molecular geometries were acquired from DFT calculations and used in molecular docking studies. Tyrosinase (PDB ID: 3NM8) protein, which is a related antioxidant, was utilized in molecular docking studies. 6d-3NM8 complex had the highest docking score with the -10.1 kcal/mol. Stabilization of the 6d-3NM8 complex during 100 ns was determined via molecular dynamics simulations. Intramolecular interactions of all molecules were also analyzed by NCI-RDG analysis. The frequently used cupric ion reducing antioxidant capacity method (CUPRAC) was used to determine the antioxidant activity of synthesized compounds and Trolox which is unknown in the literature on its activity in DMSO. The highest TEAC value was 1.76 (6d) while the lowest one was 1.34 (6e). It is possible to say that the synthesized substance 6d has the potential to be an antioxidant reagent based on the results of in vitro and in silico antioxidant activity. An explanation of the reason for using the CUPRAC method was added to the manuscript.

Key role of PPAR-γ-mediated suppression of the NFκB signaling pathway in rutin's antidepressant effect

BackgroundDepression is a chronic and recurrent disorder with an unknown etiology. Efficacious antidepressant treatments with minimal side effects are urgently needed. Neuroinflammation may contribute to depression, as anti-inflammatory drugs have been shown to alleviate depressive symptoms in clinical practice. Rutin, a naturally occurring flavonoid derived from plants, is abundant in many antidepressant herbs, including Hemerocallis citrina Baroni. Historical Chinese medical texts, including the renowned Compendium of Materia Medica, document H. citrina Baroni as possessing antidepressant properties. Rutin, one of its primary active constituents, is recognized for its anti-inflammatory effects. Despite this, little is known about its specific target and mechanism. MethodsIn the present study, molecular docking, and surface plasmon resonance imaging (SPRi) analysis were used to identify the special targets of rutin. Meanwhile, the potential antidepressant effects were evaluated in the chronic social defeat stress (CSDS) paradigm, an animal model of depression. Then, Western blotting, quantitative real-time polymerase chain reaction (qRT-PCR), Co-immunoprecipitation (Co-IP) as well as antagonists of PPAR-γ were utilized to investigate the mechanism underlying the antidepressant effect of rutin. ResultsBoth molecular docking and SPRi analysis showed high docking scores and interactions between rutin and PPAR-γ. In vivo, rutin promoted the nuclear translocation of PPAR-γ in the hippocampus of mice, inhibited NFκB-mediated inflammatory pathways, and subsequently reduced the expression of pro-inflammatory factors (e.g., iNOS, IL-6), aligning with an antidepressant effect. However, this therapeutic effect was attenuated by GW9662, a specific antagonist of PPAR-γ. ConclusionAs a result of activating PPAR-γ and inhibiting NFκB pathway activation, rutin reduces neuroinflammation and exhibits an antidepressant effect. These findings shed light on the antidepressant mechanism of rutin and could be valuable for the development of new antidepressants.

Molecular Docking Studies and Antibacterial Evaluation of Urtica massaica Leaves

Bacterial resistance is at its peak challenging humankind and researchers dealing with microorganisms. To prevent further risk due to microbial infections, there is an emergency to solve this problem. The practice of using herbs in treating diseases is from ancient years, especially in African countries with rich natural remedies resources. Urtica Massaica from the Urticaceae family is abundantly found in Africa. Methanolic extract of leaf powder was tested against resistant microorganisms (Acinetobacter baumannii and MRSA (Methicillin-resistant Staphylococcus aureus). Ciprofloxacin was used as the standard antibacterial drug. Molecular docking studies were performed for the selected flavonoids of the plant from literature against penicillin-binding protein 2a and DNA gyrase subunit B. The results from the antimicrobial studies indicated the zone of inhibitions ranging from 6±0.00 mm to 11.67±0.33 mm. Molecular docking studies revealed the ability of Urtica flavonoids to bind with the selected target receptors. Kaempferol was found to have a higher docking score with a less binding energy of -11.25kCal/Mol and 9.83Kcal/Mol against PBP2a and DNA gyrase respectively. The results of the current study strongly indicate the need for further studies involving the isolation of pure compounds and their use against resistant bacteria.

A network pharmacology approach-based decoding of Resveratrol's anti-fibrotic mechanisms

BackgroundInhalation of crystalline silica (CS) frequently leads to chronic lung inflammation and pulmonary fibrosis (PF), a condition with limited effective treatments. Resveratrol (Res) has demonstrated potential in PF treatment; however, its underlying mechanisms remain incompletely elucidated. PurposeThis study represents the first comprehensive attempt to uncover the novel mechanisms underlying Res's anti-fibrotic effects against PF through an innovative, integrated approach combining network pharmacology and experimental validation. MethodsWe employed network pharmacology to investigate the holistic pharmacological mechanism of Res, then validated the predicted pharmacological effects using in vivo and in vitro studies. ResultsIn total, 216 genes were identified to be simultaneously associated with PF and Res. An integrated bioinformatics analysis implicated a crucial role of the autophagy signaling pathway in dominating PF, with AMPK and mTOR showing high docking scores. Animal studies revealed that Res significantly alleviated silica-induced lung damage in silicotic mice, with decreased collagen I (Col-I) levels and reduced expression of vimentin and α-SMA. In-depth investigation demonstrated that Res modulated CS-dysregulated autophagy by targeting the AMPK/mTOR pathway. in vitro, Res treatment significantly reduced lactate dehydrogenase (LDH), TNF-α, and TGF-β levels and improved cell viability of Raw264.7 cells post-CS exposure. Notably, Res was demonstrated to suppress fibroblast-to-myofibroblast transition via mediating macrophage autophagy through the AMPK/mTOR pathway. ConclusionRes can alleviate CS-induced PF by targeting AMPK in the autophagy signaling pathway, which sheds light on Res' therapeutic potential in treating PF.

Synthesis and functional mechanism evaluation of novel polymer-graphene oxide-biochar nanocomposite for efficient removal of diethyl phthalate

Phthalates, categorized as a main constituent of endocrine-disrupting chemicals (EDCs), are present in polymeric products. These substances can enter the environment through several pathways, including improper handling, which leads to their presence in toilet water, floor washings, surface runoff, and landfill leachate. This study focuses on the performance analysis of nanocomposite materials made of polymer (polypyrrole), quasi-metal (graphene oxide), and biochar (from palmyra seed) for the elimination of diethyl phthalates (DEP) from aqueous environments. Scanning electron microscope (SEM), X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FTIR) were used to describe the nanocomposite characteristics. The experimental results supported a chemisorption process by agreeing well with the pseudo-second order. The Langmuir isotherm explained the DEP sorption data, which aligned to monolayer DEP adsorption on the nanocomposite surface. With a binding affinity of −13.36 (kcal/mol) and the highest docking score, Diethyl phthalates and graphene oxide interaction is validated. The produced nanocomposite is suggested as a possible alternative for the sorption of DEP. Future applications could benefit from the higher adsorption capacity, and environmental friendliness of nanocomposites.

Phytochemicals of Different Medicinal Herbs as Potential Inhibitors Against Dengue Serotype 2 Virus: A Computational Approach.

Dengue is one of the major mosquito-borne infectious diseases of the present century, reported to affect about 100-400 million people globally. The lack of effective therapeutic options has inspired several in vitro and in silico studies for the search of antivirals. Our previous study revealed the anti-dengue activity of different plant extracts from Plumeria alba, Bacopa monnieri, Vitex negundo, and Ancistrocladus heyneanus. Therefore, the current in silico study was designed to identify the phytochemicals present in the aforementioned plants, which are possibly responsible for the anti-dengue activity. Different plant databases as well as relevant literature were explored to find out the major compounds present in the above-stated plants followed by screening of the retrieved phytochemicals for the assessment of their binding affinity against different dengue viral proteins via molecular docking. The best poses of protein-ligand complexes obtained after molecular docking were selected for the calculation of binding free energy via MM-GBSA method. Based on the highest docking score and binding energy, six complexes were considered for further analysis. To analyze the stability of the complex, 100ns molecular dynamics (MD) simulations were carried out using Desmond module in the Schrodinger suite. The MD simulation analysis showed that four compounds viz. liriodendrin, bacopaside VII, isoorientin, and cynaroside exhibited stability with viral targets including the RdRp, NS3 helicase, and E protein indicating their potential as novel anti-dengue antivirals.

Identification of different extracts and phytoconstituents of Callistemon viminalis Cheel for their anti-anxiety effects based on pharmacognostic, toxicological, and pharmacological strategies

BackgroundPsychiatric disorders like depression and anxiety are global challenges, exacerbated by the limitations of synthetic medications, including addiction and toxic side effects. MethodsThis study meticulously investigated the pharmacognostic, phytochemical, toxicological, and pharmacological properties of Callistemon viminalis Cheel. Toxicological assessments, including hemocompatibility assays, LD50 studies, FOB analysis, biochemical parameters, and structural integrity of vital organs, were conducted on aqueous, methanolic, chloroform, and petroleum ether extracts of leaves and stems. Phytochemical profiling via qualitative tests and GC-MS screened extracts for molecular docking against key receptors. Categorically screened extracts were evaluated for therapeutic potential against LPS-induced anxiety in mice. ResultsToxicological evaluations on experimental animals demonstrated the safety of various extracts, evidenced by no in vitro and in vivo toxicity. GC-MS identified numerous phytochemicals that passed “Lipinski's Rule of Five.” These compounds were screened for molecular docking, revealing significant binding affinities with CB1, SERT, α2A-AR, and GABAβ2 receptors, suggesting potential therapeutic effects against anxiety. The phytoconstituents with the highest docking scores, particularly in aqueous and methanolic extracts, were further validated for their therapeutic efficacy. Preliminary analysis based on the EPM test and serum cortisol levels confirmed these extracts' superior therapeutic effectiveness. ConclusionIn conclusion, aqueous and methanolic extracts of Callistemon viminalis Cheel’s leaf and stem showed promising potential as therapeutic interventions for anxiety disorders.

Design, Molecular Docking and Molecular Dynamic Simulation of New Heterocyclic Derivatives as Potential Anticancer Agents

Background: Despite significant progress in the development of anticancer medications, obstacles such as drug resistance, poor efficacy, and excessive toxicity have significantly impacted the daily lives of cancer patients. Consequently, the search for highly selective, effective, and non-toxic molecules remains a major challenge for cancer researchers. Objective: To utilize a computer program for evaluating new benzothiophene derivatives to investigate how they influence the estrogen-related receptor-gamma (ERRγ) active sites as anticancer agents. Methods: The molecular docking method used the Cambridge Crystallographic Data Centre's (CCDC) Genetic Optimization for Ligand Docking (GOLD) tool. We used the Desmond modules of the Schrodinger 2023 to perform MDS on the derivative with the highest docking score. The Swiss ADME server then assessed our drugs' pharmacokinetic profile, which included how well they crossed the blood-brain barrier (BBB), bound to P-gp, and were bioavailable. Results: The compounds were docked with the ERRγ crystal structure (2GPV) to assess their binding affinity to active sites. One of them earned a high score (102.62), and six compounds had a higher binding energy than the gold standard medication, tamoxifen. The molecular dynamic simulation analysis found that compound 1 closely matched the ERRγ based on RMSD and RMSF data. After examining the ADME study of practically active substances, they follow Lipinski's laws and other pharmacokinetic features. Conclusions: These chemicals have the potential to act as precursors in the development of new anticancer medicines.

In silico Molecular Docking and Dynamic Study of MDM2-p53 Inhibitor Alkaloids Extracted from Withania somnifera Against Tumor Growth

In today’s world, human tumor growth has become a critical health issue. Many patients experience ineffective chemotherapeutic treatments, prompting the need for alternative methods. Our recent research has explored active alkaloid extracts from Withania somnifera as potential inhibitors of the MDM2-p53 interaction, a key factor in tumor growth. Using in silico molecular docking and dynamic approaches, we identified eight effective alkaloids with high docking score are WithanolideD (–10.0Kcal/mol), Withanolide (–10.0Kcal/mol), WithaferinA ( ̶ 9.9Kcal/mol), WithanolideB ( ̶ 9.5Kcal/mol), WithalongolideA ( –9.4Kcal/mol), WithanolideE ( ̶ 9.4Kcal/mol), WithanolideA ( ̶ 9.0Kcal/mol), Withanone ( ̶ 8.9Kcal/mol). Among them, WithaferinA, WithanolideA, WithanolideD, WithanolideE, and Withanone demonstrated the most stable hydrogen bonding, stable RMSD, and RMSF. Lipinski’s rule of five, which assesses drug-like qualities, confirmed their potential through canonical SMILES verification. Molecular dynamics of the protein-ligand complex revealed that these docked complexes remain thermally stable, with consistent bond energy, dihedral angles, and stereochemical conformation over a 100 ns time frame. Our findings suggest that these alkaloids from Withania somnifera hold promise as effective treatments against tumor growth. Further investigation and exploration are necessary to confirm their efficacy in clinical settings.

A Structure-Based Design Strategy with Pyrazole-Pyridine Derivatives Targeting TNFα as Anti-Inflammatory Agents: E-Pharmacophore, Dynamic Simulation, Synthesis and In Vitro Evaluation.

Any pathogenic attack, infection, or disease can initiate inflammation. It results in significant adverse consequences like inflammatory bowel disease, rheumatoid arthritis, etc. TNFα is one of the major pro-inflammatory cytokines for the progression of inflammation-the present study designed a series of hybrid compounds consisting of the pyrazole-pyridine moiety. Virtual screening was performed utilizing the e-pharmacophore hypothesis with the co-ligand of TNFα, screening, docking, and ADMET study. Induced fit docking, DFT analysis, and molecular dynamic simulation showed that the four best molecules - Dh1- Dh4-showed crucial interaction with Tyrosine, higher dock scores, and better stability than Diclofenac. Following the synthesis of hit molecules, an in vitro albumin denaturation IC50 of Dh1 was found to be 118.01 μM. Further in-depth in vitro and in vivo analyses of these pyrazole-pyridine small compounds may serve as potential space for creating new anti-inflammatory leads.

Disrupting protease and deubiquitinase activities of SARS-CoV-2 papain-like protease by natural and synthetic products discovered through multiple computational and biochemical approaches

The single-stranded RNA genome of SARS-CoV-2 encodes several structural and non-structural proteins, among which the papain-like protease (PLpro) is crucial for viral replication and immune evasion and has emerged as a promising therapeutic target. The current study aims to discover new inhibitors of PLpro that can simultaneously disrupt its protease and deubiquitinase activities. Using multiple computational approaches, six compounds (CP1-CP6) were selected from our in-house compounds database, with higher docking scores (−7.97 kcal/mol to −8.14 kcal/mol) and fitted well in the active pocket of PLpro. Furthermore, utilizing microscale molecular dynamics simulations (MD), the dynamic behavior of selected compounds was studied. Those molecules strongly binds at the PLpro active site and forms stable complexes. The dynamic motions suggest that the binding of CP1-CP6 brought the protein to a closed conformational state, thereby altering its normal function. In an in vitro evaluation, CP2 showed the most significant inhibitory potential for PLpro (protease activity = 2.71 ± 0.33 μM and deubiquitinase activity = 3.11 ± 0.75 μM), followed by CP1, CP5, CP4 and CP6. Additionally, CP1-CP6 showed no cytotoxicity at a concentration of 30 μM in the human BJ cell line.