Molecular Operating Environment Software Research Articles

In-silico Molecular Docking of Two Bioactive Constituents (Quercetin 3-Glucuronide and Quercitrin) from Polygonum minus Leaves into Monoamine Oxidase-A Crystal Structure

The aim of the current research was to dock the two abundant bioactive constituents of Polygonum minus leaf extract, in1cluding Quercetin 3-Glucuronide (Miquelianin) and Quercitrin (Quercetin-3-rhamnoside). In-silico Molecular modelling technique was used to predict about a protein (enzyme) interacts with molecules (ligands). Monoamine oxidase-A (MAO-A) is the key enzyme that is involved in the breakdown of neurotransmitters like serotonin and noradrenaline. Drugs that are involved in its inhibition, are considered to be antidepressant agents. This molecular docking study observed the binding energy of selected ligands and their interactions with amino acid residue along with bond types in the MAO-A structure. Molecular docking was done using Molecular Operating Environment (MOE) software, whereas visualization and expression of results were carried out using Discovery Studio (DS) visualizer. Clorgyline was used in this study as a co-crystal ligand, whereas moclobemide was used as a standard MAO-A inhibitor, and Amitriptyline was used as a common antidepressant which also has some MAO-A inhibitory effect. Quercetin 3-glucuronide (Miquelianin) and Quercitrin (Quercetin-3-rhamnoside) have more binding affinities with MAO-A structure as compared to all other drugs. Its interaction pattern was most likely moclobemide and Clorgyline, which are considered standard MAO-A inhibitors in this study. Based on these results, it is concluded that Quercetin 3-Glucuronide (Miquelianin) and Quercitrin (Quercetin-3-rhamnoside) have the potential to become potent MAO-A inhibitors in future.

Search for potential Alzheimer’s disease therapeutics: Identification of inhibitors of amyloid oligomerization with high affinity for the zinc-binding site

The progression of Aβ peptide aggregation in the brain has been suggested to play a significant role in the pathogenesis and development of Alzheimer’s disease. This study is intended to provide insight into the interactions between the zinc-binding site of beta-amyloids and the zinc ion itself. The absence of zinc bonded to the beta-amyloid has been shown to potentially slow down the progression of Alzheimer's disease, so the goal is to provide an analysis of available drugs that can be repurposed and could profoundly impact Alzheimer's disease treatment. We address how and with what strength the existing compounds bind with beta-amyloid, potentially replacing or blocking zinc and preventing it from attaching to the amyloid. The analysis was performed using molecular operating environment software, which, starting from a filtered database, identified the drugs most likely to bind to the zinc-binding site on beta-amyloid.

Synthesis, application and molecular docking of modified cellulose with diaminoguanidine as complexing agent for selective separation of Cu (II), Cd (II) and Hg (II) ions from alum sample

A new modified cellulose with diaminoguanidine (Cel-Gua) synthesized for specific recovery of Cu (II), Cd (II), and Hg (II) from the alum sample. Cellulose was silanized by 3-chloropropyltrimethoxysilane and then was modified with diaminoguanidine to obtain N-donor chelating fibers. Fourier transform-infrared spectroscopy, scanning electron microscopy, X-ray diffraction, zeta potential, electrons disperse X-ray analysis, elemental analyses (C, H and N), and thermogravimetric analysis were used for characterization. Factors influencing the adsorption were thoroughly examined. Under the optimal conditions, the Cel-Gua sorbent displayed maximum adsorption capacities of 94.33, 112.10 and 95.78 mg/g for Cu (II), Cd (II), and Hg (II), respectively. The sorption process of metal ions is equipped by kinetic model PSO and Langmuir adsorption isotherm. The calculated thermodynamic variables confirmed that the adsorption of Cu (II), Cd (II) and Hg (II) by Cel-Gua sorbent is a spontaneous and exothermic process. In our study, we used the molecular operating environment software to conduct molecular docking simulations on the Cel-Gua compound. The results of the docking simulations showed that the Cel-Gua compound displayed greater potency and a stronger affinity for the Avr2 effector protein derived from Fusarium oxysporum, a fungal plant pathogen (code 5OD4). The adsorbent was stable for 7 cycles, thus allowing its safe reutilization.

Docking of Drugs-Protein for COVID-19 and Prediction of pKa Using Quantum Calculations

For the computations of the compounds, the Gaussian 03 software has been applied utilizing (AM1), (HF), and density functional theory (DFT). Four medications have been theoretically assessed to anticipate the pKa values based on the calculations of HOMO, LUMO, DG, DH, and DS parameters. The prediction of the protein-drugs has been carried out using the docking studies. The docking simulations for the drugs with the receptor and parameterization were carried out using the molecular operating environment (MOE) software program. Theoretically, four medications were docked with the COVID-19 protein on a receptor (PDB ID: 6wtt). Four medications have been looked into virtually in an effort to find a possible anti-COVID molecule. The drugs have been molecularly docked with the covid-19 protein (6wtt).

Design, Synthesis, and the Biological Evaluation of Some New Fused Thiazolotriazine Derivatives

Thiazolotriazine is an essential medicinal chemistry molecule due to its biological properties, particularly antifungalactivity. Antifungal drug resistance is rising worldwide, necessitating the development of innovative, safer, and more effectiveantifungals. This study intended to uncover safer and more effective thiazolotriazine antifungals. ProTox II software was employedto forecast the toxicity of the designed thiazolotriazines. The pharmacokinetic parameters were calculated using the Swiss-ADMEdatabase. The Molecular Operating Environment software (2019.0102 version) was employed for the docking studies utilizing 14-α-demethylase protein (PDB ID: 3LD6). Compounds 4c, 4d, and 4e were prepared and evaluated for in vitro antifungal activity.The computational studies revealed compounds 4a, 4b, 5b, 5c, 6b, 6c and 6d as carcinogenic; 4a, 4b, 4c, 4d and 4e demonstratedbetter pharmacokinetic behaviour; and docking results of 4c, 4d, and 4e were superior than fluconazole (FLU). The moleculardocking studies establish 4c, 4d, and 4e as SDM inhibitors, suggesting a mechanism similar to FLU and ketoconazole (KET). Theantifungal activity evaluation revealed 4d (MIC = 6.25 μg/ml) as a more potent antifungal agent than KET (MIC = 12.5 μg/ml) andFLU (MIC = 12.5 μg/ml). Compounds 4c and 4e showed equal antifungal activity to KET (MIC = 12.5 μg/ml) and FLU (MIC = 12.5μg/ml). Compounds 4c, 4d, and 4e displayed encouraging antifungal activity with a favorable safety profile. Assessing the broadspectrum of 4c, 4d, and 4e against various pathogenic fungi, including resistant forms, is recommended.

Exploring active ingredients and mechanisms of Coptidis Rhizoma-ginger against colon cancer using network pharmacology and molecular docking.

Colon cancer is the most prevalent and rapidly increasing malignancy globally. It has been suggested that some of the ingredients in the herb pair of Coptidis Rhizoma and ginger (Zingiber officinale), a traditional Chinese medicine, have potential anti-colon cancer properties. This study aimed to investigate the molecular mechanisms underlying the effects of the Coptidis Rhizoma-ginger herb pair in treating colon cancer, using an integrated approach combining network pharmacology and molecular docking. The ingredients of the herb pair Coptidis Rhizoma-ginger, along with their corresponding protein targets, were obtained from the Traditional Chinese Medicine System Pharmacology and Swiss Target Prediction databases. Target genes associated with colon cancer were retrieved from the GeneCards and OMIM databases. Then, the protein targets of the active ingredients in the herb pair were identified, and the disease-related overlapping targets were determined using the Venn online tool. The protein-protein interaction (PPI) network was constructed using STRING database and analyzed using Cytoscape 3.9.1 to identify key targets. Then, a compound-target-disease-pathway network map was constructed. The intersecting target genes were subjected to Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for colon cancer treatment. Molecular docking was performed using the Molecular Operating Environment (MOE) software to predict the binding affinity between the key targets and active compounds. Besides 1922 disease-related targets, 630 targets associated with 20 potential active compounds of the herb pair Coptidis Rhizoma-ginger were collected. Of these, 229 intersection targets were obtained. Forty key targets, including STAT3, Akt1, SRC, and HSP90AA1, were further analyzed using the ClueGO plugin in Cytoscape. These targets are involved in biological processes such as miRNA-mediated gene silencing, phosphatidylinositol 3-kinase (PI3K) signaling, and telomerase activity. KEGG enrichment analysis showed that PI3K-Akt and hypoxia-inducible factor 1 (HIF-1) signaling pathways were closely related to colon cancer prevention by the herb pair Coptidis Rhizoma-ginger. Ten genes (Akt1, TP53, STAT3, SRC, HSP90AA1, JAK2, CASP3, PTGS2, BCl2, and ESR1) were identified as key genes for validation through molecular docking simulation. This study demonstrated that the herb pair Coptidis Rhizoma-ginger exerted preventive effects against colon cancer by targeting multiple genes, utilizing various active compounds, and modulating multiple pathways. These findings might provide the basis for further investigations into the molecular mechanisms underlying the therapeutic effects of Coptidis Rhizoma-ginger in colon cancer treatment, potentially leading to the development of novel drugs for combating this disease.

Biological evaluation of levofloxacin and its thionated derivatives: antioxidant activity, aldehyde dehydrogenase enzyme inhibition, and cytotoxicity on A549 cell line.

Levofloxacin (LVX) is among the fluoroquinolones antibiotics that has also been studied in vitro and in vivo for its anticancer effects. In this study, we used LVX and novel LVX thionated derivatives; compounds 2 and 3, to evaluate their antioxidant activity, aldehyde dehydrogenase (ALDH) enzymes activity inhibition, and anticancer activity. Combination treatments with doxorubicin (DOX) were investigated as well. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay was used to determine the antioxidant activity. The NADH fluorescence spectrophotometric activity assay was used to determine the ALDH inhibitory effects. Resazurin dye method was applied for cell viability assays. Molecular Operating Environment software was used for the molecular docking experiments. Compared to ascorbic acid, DPPH assay showed that compound 3 had the highest antioxidant activity among the tested compounds with approximately 35% scavenging activity. On ALDH enzymes, compound 3 showed a significant ALDH activity inhibition compared to compound 2 at 200 µM. The IC50 values for the tested compounds were approximately 100 µM on A549 cell line, a non-small cell lung cancer (NSCLC) cell line. However, significant enhancement of cytotoxicity and reduction of IC50 values were observed by combining DOX and synergism was achieved with LVX with a combination index value of 0.4. The molecular docking test showed a minimum binding energy with a good affinity for compound 3 towards ALDH enzymes. Thionated LVX derivatives, may be repurposed for NSCLC therapy in combination with DOX, taking into account the antioxidant activity, ALDH activity inhibition, and the molecular docking results of compound 3.

In Silico Investigation of Novel Compounds as Inhibitors of Acetylcholinesterase Enzyme for the Treatment of Alzheimer's Diseases.

Alzheimer's disease (AD) is a "progressive, neurodegenerative disease that occurs when nerve cells in the brain die." There are only 4 drugs approved by the United States Food and Drug Administration (FDA). Three (donepezil, rivastigmine, and galantamine) out of these four drugs are anticholinesterase inhibitors, while the fourth one memantine is an N-methyl-D-aspartate (NMDA) receptor inhibitor. Currently, two immunotherapy drugs that target amyloid protein (donanemab and lecanemab) are being considered for the treatment of Alzheimer's disease at an early stage. All these drug molecules are still not the complete answer to the treatment of Alzheimer's disease. A recent report from the Office of National Statistics showed that AD is the leading cause of death in 2022. Therefore, there is an urgency to develop more drugs that can treat AD. Based on this urgency, we aim to investigate how bioactive and already approved drugs could be repurposed for inhibiting the anticholinesterase enzyme using computational studies. To achieve this, the data science tool-Python coding was compiled on Jupyter Notebook to mine bioactive compounds from the ChEMBL database. The most bioactive compounds obtained were further investigated using Molecular Operating Environment (MOE) software to carry out molecular docking and ligand analysis, and this was followed by molecular dynamics simulation production at 35 ns using GROMACS 2022.4 on Archer 2 machine. The molecular dynamic analysis was carried out using HeroMDanalysis software. Data mining of the ChEMBL database was carried out for lipase inhibitors, and this gave CHEMBL-ID 1240685, a peptide molecule, the most active compound at the time of data mining. Further literature studies gave Zoladex an FDA-approved drug for the treatment of breast cancer as another compound of interest. The in silico studies were carried out against the anticholinesterase enzyme using two FDA-approved drugs donepezil and galantamine as a template for comparing the in silico activities of the repurposed drugs. A very useful receptor for this study was PDB-1DX6, a cocrystallized galantamine inhibitor of acetylcholinesterase enzyme. The molecular docking analysis (using ligand interactions) and molecular dynamic analysis (root mean square deviation (RMSD) and root mean square fluctuation (RMSF)) showed that the two peptide molecules CHEMBL-1240685 and Zoladex gave the best binding energy and stability when compared to the FDA-approved drugs (donepezil and galantamine). Finally, further literature studies revealed that Zoladex affects memory reduction; therefore, it was dropped as a possible repurposed drug. Our research showed that CHEMBL-1240685 is a potential compound that could be investigated for the inhibition of anticholinesterase enzyme and might be another drug molecule that could be used to treat Alzheimer's disease.

A novel isatin Schiff based cerium complex: synthesis, characterization, antimicrobial activity and molecular docking studies

In this work, a novel isatin-Schiff base L2 had been synthesized through a simple reaction between isatin and 2-amino-5-methylthio-1,3,4-thiadiazole. The produced Schiff base L2 was then subjected to a hydrothermal reaction with cerium chloride to produce the cerium (III)-Schiff base complex C2. Several spectroscopic methods, including mass spectra, FT-IR, elemental analysis, UV–vis, 13C-NMR, 1H-NMR, Thermogravimetric Analysis, HR-TEM, and FE-SEM/EDX, were used to completely characterize the produced L2 and C2. A computer simulation was performed using the MOE software program to find out the probable biological resistance of studied compounds against the proteins in some types of bacteria or fungi. To investigate the interaction between the ligand and its complex, we conducted molecular docking simulations using the molecular operating environment (MOE). The docking simulation findings revealed that the complex displayed greater efficacy and demonstrated a stronger affinity for Avr2 effector protein from the fungal plant pathogen Fusarium oxysporum (code 5OD4) than the original ligand. The antibacterial activity of the ligand and its Ce3+ complex were applied in vitro tests against different microorganism. The study showed that the complex was found to be more effective than the ligand.

Chemical profile and radical scavenging of the Psidium guajava flower’s essential oil: Molecular docking study on the human cytochrome P450 CYP2C9

Psidium guajava L. plant is frequently utilized as therapeutic plant due to its nutritional benefits and bioactive metabolites. The current study intends to identify the chemical characterization and antioxidant activity of essential oil (EO) of freshly harvested P. guajava flowers. The EO was analyzed using GC with flame-ionization detection (FID), gas chromatography-mass spectrometry (GC-MS) along with chemometric analysis. With 98.87% of overall oil mass, 37 volatile constituents were assigned. All identified compounds were categorized into two classes including mono-(30.34%) and sesquiterpenes (68.53%). The d-limonene (26.10%), trans-β-caryophyllene (17.24%), trans-nerolidol (11.01%), and ledol (5.12%) served as predominant compounds. Using three separate methods, DPPH, ABTS, and reducing power, the free radical scavenging activity of P. guajava flower oil was assessed in comparison with ascorbic acid as a reference antioxidant. The net results revealed that EO has considerable activities with respective IC50 values of 224.53, 125.78, and 231.78 mg L−1. All main compounds (> 3.00%) were in silico studied by Molecular Operating Environment (MOE) software on human cytochrome P450 CYP2C9. The net findings showed that the tested compounds have good binding affinity ranging from ΔG at −4.43 to −5.65 kcal/mol, while ascorbic acid exhibits binding affinity with ΔG = −4.58 kcal/mol. Cubenol revealed the best binding affinity with ΔG = −5.65 kcal/ mol. The present findings verified the guava flower EO’s powerful functions. For a better knowledge of the action pathways both in vitro and in vivo, more scientific studies on this oil’s antioxidant and/or its main components in pure form were advised.

Exploring Substituted Tetrazoloquinazoline: Biological Activities, Molecular Docking Analysis, and Anti-Breast Cancer MCF7/HER2 Effects.

Breast cancer is a condition where breast tissue cells grow uncontrollably. Various natural and synthesized compounds, such as quinazoline, have been studied for their potential as anticancer agents. Quinazoline derivatives have shown diverse bioactivities, including antimalarial, antifungal, antimicrobial, and anticancer properties. This research aims to synthesize substituted tetrazoloquinazoline and evaluate its potential as an anticancer agent using molecular docking studies with the Molecular Operating Environment (MOE) software. Furthermore, molecular dynamic was also performed to analyze the binding stability of this protein-ligand complex. Additionally, the physicochemical and pharmacokinetic properties of quinazoline compounds were assessed using the website https://www.swissadme.ch. The cytotoxic activity of the compounds was evaluated using the MTT assay. The docking results revealed that substituted tetrazoloquinazoline exhibited a significantly different range of binding free energy compared to the positive control. Moreover, the substituted tetrazoloquinazoline compounds comply with Lipinski's Rule of Five (Ro5), indicating that they are easily absorbable and have good permeability. The cytotoxic activity of the compounds was found to have an IC50 value of >1000 ppm, classifying them as noncytotoxic. It therefore paved the way for the discovery of promising next-generation drugs against breast cancer.

An In Silico Investigation of the Molecular Interactions between Volatile Anesthetics and Actin.

Volatile anesthetics (VAs) are medicinal chemistry compounds commonly used to enable surgical procedures for patients who undergo painful treatments and can be partially or fully sedated, remaining in an unconscious state during the operation. The specific molecular mechanism of anesthesia is still an open issue, but scientific evidence supports the hypothesis of the involvement of both putative hydrophobic cavities in membrane receptors as binding pockets and interactions between anesthetics and cytoplasmic proteins. Previous studies demonstrated the binding of VAs to tubulin. Since actin is the other major component of the cytoskeleton, this study involves an investigation of its interactions with four major anesthetics: halothane, isoflurane, sevoflurane, and desflurane. Molecular docking was implemented using the Molecular Operating Environment (MOE) software (version 2022.02) and applied to a G-actin monomer, extrapolating the relative binding affinities and root-mean-square deviation (RMSD) values. A comparison with the F-actin was also made to assess if the generally accepted idea about the enhanced F-to-G-actin transformation during anesthesia is warranted. Overall, our results confirm the solvent-like behavior of anesthetics, as evidenced by Van der Waals interactions as well as the relevant hydrogen bonds formed in the case of isoflurane and sevoflurane. Also, a comparison of the interactions of anesthetics with tubulin was made. Finally, the short- and long-term effects of anesthetics are discussed for their possible impact on the occurrence of mental disorders.

Identification of new small molecule allosteric SHP2 inhibitor through pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation studies, synthesis and in vitro evaluation

Src homology-2 (SH2) domain-containing phosphatase-2 (SHP2) is the first identified protooncogene and is a promising target for developing small molecule inhibitors as cancer chemotherapeutic agents. Pharmacophore-based virtual screening (PBVS) is a pharmacoinformatics methodology that employs physicochemical knowhow of the chemical space into the dynamic environs of computational technology to extract virtual molecular hits that are precise and promising for a drug target. In the current study, PBVS has been applied on EnamineTM Advanced Collection of 551,907 molecules by using a pharmacophore model developed upon SHP099 by Molecular Operating Environment (MOE) software to identify potential small molecule allosteric SHP2 inhibitors. Obtained 37 hits were further filtered through DruLiTo software for drug-likeness and PAINS remover which yielded 35 hits. These were subjected to molecular docking studies against the tunnel allosteric site of SHP2 (PDB ID: 5EHR) to screen them according to their binding affinity for the enzyme. Top 5 molecules having highest binding affinity for 5EHR were passed through an ADMET prediction screening and the top 2 hits (ligands 111675 and 546656) with the most favourable ADMET profile were taken for post screening molecular docking and MD simulation studies. From the protein-ligand interaction pattern, conformational stability and energy parameters, ligand 111675 (SHP2 Ki = 0.118 µM) resulted as the most active molecule. Further, the synthesis and in vitro evaluation of the lead compound 111675 unveiled its potent inhibitory activity (IC50 = 0.878 ± 0.008 µM) against SHP2. Communicated by Ramaswamy H. Sarma

In silico study, synthesis, and antineoplastic evaluation of thiazole-based sulfonamide derivatives and their silver complexes with expected carbonic anhydrase inhibitory activity.

This study aimed to design, synthesize, and evaluate the cytotoxic activity of novel thiazole-sulfanilamide derivatives, specifically compounds M3, M4, and M5, through molecular docking and biological assays. The synthesis utilized essential chemical compounds, including sulfanilamide, chloro-acetyl chloride, thiourea, derivatives of benzaldehyde, and silver nitrate. The docking study was carried out using Molecular Operating Environment (MOE) software, and cytotoxic activity was predicted by MTT assay. The synthesized compounds demonstrated a reduction in the viability of cancer cells. Compound M5 had an IC50 of 18.53 µg/ml against MCF-7 cells, comparable to the IC50 of cisplatin. Additionally, compounds M3 and M4 had higher S scores than acetazolamide, indicating greater binding affinity to the active pocket of the receptor. Incorporating the thiazole ring in the synthesized compound augmented their flexibility and affinity for binding to the receptor. The inclusion of the metal complex additionally heightened the compounds' capacity to impede cellular growth.

In silico study of new carbonic anhydrase inhibitor derivatives bearing 1, 3, 4-Oxadiazole moiety with promising anti-cancer activity.

Objectives: Molecular docking simulations were performed to assess the theoretical binding affinities of six (6) compounds created where they are derivatives having 1,3,4, oxadiazole moiety, and their target was cancer and Human carbonic anhydrase IX (PDB code: 6U4T). Using ChemDraw Ultra 12.0, the molecular structure was meticulously sketched. Molecular Operating environment software was used to verify the developed compounds by looking at their S. score and Rmsd values. Promising activity was seen with these proteins from the theoretically generated compounds, which exhibited strong binding contacts with the receptor active pocket.
 
 Methods: Chemically by joining together several oxadiazole derivatives, sulfanilamide analogues (IVa-IVd) may be created in the lab. Molecular docking and ligand/receptor priming by MOE software.
 Results: Acetazolamide was selected because it had the same pharmacophore as the sulfanilamide group, and cisplatin was used in clinical trials for cancer therapy. IVc and IVa yielded max score and irrevocable relationship compared with acetazolamide and cisplatin.
 Conclusion: The MOE docking results validated the potent anticancer activity, the identified compounds showing good binding affinity with target proteins relative to the reference drugs (Acetazolamide and cisplatin). The most effective anticancer compounds were IVc and IVa, which yielded a maximum score with a Rmsd of less than 2, the MOE docking results were able prove this.
 Compounds IVc and IVa exhibited the greatest cytotoxic impact of the synthetic compounds against MCF7, and all four synthesized compounds showed a superior safety profile than the standards in MCF10a.

Computer screening of peptidomimetics and small-molecule ligands of B-cell membrane proteins for therapy of Burkitt lymphoma

The capabilities of molecular modelling and docking allow for the discovery of new potential drug agents to improve the treatment of diseases, which is a current concern. The objective of this study was to conduct in silico screening for antibody mimetics to B-cell membrane proteins for the treatment of Burkitt lymphoma through virtual screening. In this work, a standard protocol for structure-based virtual screening was employed, with the distinction that pharmacophores for screening were built not based on small-molecule ligands but on selected amino acid residues of antibodies. Based on literature data and the presence of a mechanism of direct cytotoxic action, as well as the availability of 3D structures of complexes, three monoclonal antibodies were selected: obinutuzumab, epratuzumab, and atezolizumab. The identification of biological targets was carried out by searching for 3D structures of selected complexes with target proteins in the Protein Data Bank. For virtual screening, the web service Pharmit was chosen. Using the Molecular Operating Environment program, pharmacophore models were constructed for three complexes: CD20 and obinutuzumab, CD22 and epratuzumab, and PD-L1 and atezolizumab. Docking with the CD20, CD22, and PD-L1 proteins was conducted at the binding sites recognised by the original antibody. Through in silico virtual screening using the Molecular Operating Environment software, a search for antibody mimetics to B-cell membrane proteins for Burkitt lymphoma treatment was conducted, resulting in the selection of 5 potential anti-lymphoma agents: CHEMBL505179 for the CD20 receptor, an antagonist of the melanocortin receptor for CD20 (PubChem-44406884), an inhibitor of blood clotting Factor Xa for CD22 (PubChem-136510605), and a blocker of epithelial Na+ channels for CD22 (PubChem-126761430), and an agonist of the melanocortin receptor for PD-L1 (PubChem-25078192). The obtained results can be applied in the pharmaceutical industry and oncological practice to enhance therapeutic outcomes in the treatment of patients with Burkitt lymphoma

Molecular Docking of Several Medicines with Covid-19 Protein

The docking studies have been used to predict the protein drugs. Utilizing the molecular operating environment (MOE) software,parameterization and docking simulations for medicines with receptors were performed. Thirty drugs might theoretically bind with the COVID- 19 protein on a receptor (PDB ID: 6wzo). To identify a potential anti- COVID molecule, several drugs have been virtually examined. The medicines have bound with the covid-19 protein at the molecular level (6wzo).

Rumex vesicarius L. boosts the effectiveness of sorafenib in triple-negative breast cancer by downregulating BCl2, mTOR, and JNK, and upregulating p21 expression

Background/AimTriple-negative breast cancer (TNBC) is characterized by poor prognosis, rapid progression, serious clinical behavior, an elevated risk of metastasis, and resistance to standard treatments. Traditional medicine practitioners value Rumex vesicarius L. (RMV) for a variety of reasons, including the plant's antioxidant capabilities. Our study's goals were to ascertain the efficacy of RMV alone and in combination with sorafenib (SOR) against the aggressive TNBC cell line (MDA-MB-231) and use in vitro and in silico analysis to deduce the fundamental mechanism of action. MethodsIn the current study, molecular operating environment (MOE, 2019.0102) software was used for performing molecular docking. The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay was used to determine the cytotoxicity of RMV, SOR or RMV/SOR combination against the TNBC cell line MDA-MB-231 cells. The effects of RMV, SOR, and RMV and SOR combining on mRNAs expressions of the target genes including mTOR, p21, JNK, and BCl2 were evaluated. In TNBC cells, the relative expressions of mRNAs of the genes were examined by using real-time quantitative polymerase chain reaction (RT-qPCR). ResultsIn our experiments, we discovered that both RMV extracts alone and in combination with SOR considerably reduced cancer cell proliferation (IC50 = 0.83 and 0.19 μM, respectively). Additionally, the expression of the tumor suppressor gene p21 was elevated whereas the expression of the invasion and anti-apoptosis genes BCl2, mTOR, and JNK were significantly decreased after treatment with RMV and SOR. Based on in silico analysis, it was found that RMV extract contains bioactive chemicals with a high affinity for inhibiting JNK and VEGFR-2. ConclusionIn conclusion, in vitro and in silico investigations show that the RMV extract improves the anticancer efficiency of SOR through molecular processes involving the downregulation of mTOR, BCl2, and JNK1 and overexpression of p21 tumor suppressor gene. Finally, we suggest conducting additional in vivo investigations on RMV and its bioactive components to verify their potential in cancer therapy.

A molecular dynamics simulations analysis of repurposing drugs for COVID-19 using bioinformatics methods

A number of multidisciplinary methods have piqued the interest of researchers as means to accelerate and lower the cost of medication creation. The goal of this research was to find target proteins and then select a lead drug against SARS-CoV-2. The three-dimensional structure is taken from the RCSB PDB using its specific PDB ID 6lu7. Virtual screening based on pharmacophores is performed using Molecular Operating Environment software. We looked for a potent inhibitor in the FDA-approved database. For docking, AutoDock Vina uses Pyrx. The compound-target protein binding interactions were tested using BIOVIA Discovery Studio. The stability of protein and inhibitor complexes in a physiological setting was investigated using Desmond’s Molecular Dynamics Simulation (MD simulation). According to our findings, we repurpose the FDA-approved drugs ZINC000169677008 and ZINC000169289767, which inhibit the activity of the virus’s main protease (6lu7). The scientific community will gain from this finding, which might create new medicine. The novel repurposed chemicals were promising inhibitors with increased efficacy and fewer side effects. Communicated by Ramaswamy H. Sarma

Analysis of the Interaction of UBE2Q1 with B4GALT1 and P53: Experimental and Molecular Modeling Study.

UBE2Q1-dependent ubiquitination of key proteins including β 1,4- galactosyltransferase (GalT1), and P53 might play a pivotal role in cancer development. The present study aimed to evaluate the molecular analysis of possible interactions between UBE2Q1 with B4GALT1 and P53 proteins. We established SW1116 colorectal cancer cell line stably transfected with UBE2Q1. To verify the overexpression of UBE2Q1, we performed western blot and fluorescent microscopy analysis. Using the immunoprecipitation (IP) product of the over-expressed protein on the silver staining gel, we observed the potential interacting partners of UBE2Q1. The Molecular Operating Environment (MOE) software was also used to perform the molecular docking of the UBC domain of UBE2Q1 (2QGX) with B4GALT1 (2AGD), and P53 (tetramerization (1AIE) and DNA binding domains (1GZH)) proteins. Western blot and IP analysis detected a UBE2Q1-GFP band in transfected cells, while no band was detected for mock-transfected cells. Moreover, the overexpression of UBE2Q1 tagged with GFP was observed under fluorescent microscopy as well with about 60-70% shining. Silver staining of IP gel revealed several bands in colorectal cancer (CRC) with UBE2Q1 overexpression. Protein- Protein interaction (PPI) analysis also depicted a high affinity of the UBC domain of UBE2Q1 to the B4GALT1 and P53 (tetramerization and DNA binding domains). Molecular docking also revealed hot-spot regions for all poses. Our data suggest that UBE2Q1 as an E2 enzyme of ubiquitination system can interact with B4GALT1 and P53, and may contribute to the accumulation of misfolded important proteins and colorectal tumor development.