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Life Sciences

Elsevier BV

All preprints, ranked by how well they match Life Sciences's content profile, based on 25 papers previously published here. The average preprint has a 0.04% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

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Virtaul screening of MAP-Tau protein inhibitors from Semecarpus anacardium Linn. leaf extract for cancer prevention

Singh, R. K.; Ranjan, A.; Tripathi, R.; Srivastava, A. K.; Singh, M.; Kumar, A.; Singh, A. K.; Dwivedi, K. N.; Atri, N.; Singh, S. K.

2020-01-09 bioinformatics 10.1101/2020.01.08.899708 medRxiv
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Semecarpus anacardium is a well known Indian medicinal plant with various medicinal properties like hypoglycemic, antioxidant, anticancer, anti-inflammatory, anti-geriatric, antimicrobial and hair growth promoter, etc. The molecular mechanism of metabolites from fruiting bodies of S. anacardium against cancer has been described but anticancerous properties in its leaves are still unknown. The leaves were extracted in petroleum ether, ethyl acetate and methanol and assayed for anticancer activity using MTT assay. The active extract was evaluated for mode of cell death induction using EtBr-AO double staining and analyzed for phytochemical constituents using GC-MS, followed by molecular docking studies for exploration of possibility for anticancer agents and Drugability. In this study, ethyl acetate extract of leaf was found potent cytotoxic in MCF-7 cells and also induced apoptosis. It has also found the SLE is safe for normal cells. The molecular docking studies were done to explore the probable mechanism of action of the extract which showed 9 compounds are targeting the microtubule-associated protein tau (MAPT). MAPT promotes assembling and prevents disassembling to arrest the cell cycle. The overexpression of MAPT induces chemoresistance to cancerous cells against conventional drugs like paclitaxel. We have identified 17 compounds from ethyl acetate extract of S. anacardium leaves and drawn its chemical structure by using chembiodraw software to transform into pdb format. Further, the compounds have been subjected for molecular docking study to investigate its interactive efficiency with MAPT protein. The compound 13 had higher interactive potential to MAPT with binding energy -31.75 kcal/mol and lowest binding energy (-15.44 kcal/mol) was observed in compound 6. The present study suggested that the compounds from leaves of S. anacardium could be alternative approach of conventional drug for cancer treatment with cost effective and less side effect.

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Investigation of biological activities of Colocasia gigantea Hook.f. leaves and PASS prediction, in silico molecular docking with ADME/T analysis of its isolated bioactive compounds

Alam, S.; Emon, N. U.; A. Rashid, M.; Arman, M.; Rashedul Haque, M.

2020-05-19 bioinformatics 10.1101/2020.05.18.101113 medRxiv
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BackgroundColocasia gigantea is locally named as kochu and also better known due to its various healing power. This research is to investigate the antidiarrheal, antimicrobial, and antioxidant possibilities of the methanol soluble extract of Colocasia gigantea. MethodsAntidiarrheal investigation was performed by using in vivo castor oil induced diarrheal method where as in vitro antimicrobial and antioxidant investigation have been implemented by disc diffusion and DPPH scavenging method respectively. Moreover, in silico studies were followed by molecular docking analysis of several secondary metabolites were appraised with Schrodinger-Maestro v 11.1. ResultsThe induction of plant extract (200 and 400 mg/kg, b.w, p.o), the castor oil mediated diarrhea has been minimized 19.05 % (p < 0.05) and 42.86 % (p < 0.001) respectively. The methanolic extract of C. gigantea showed mild sensitivity against almost all the tested strains but it shows high consistency of phenolic content and furthermore yielded 67.68 g/mL of IC50 value in the DPPH test. The higher and lower binding affinity was shown in beta-amyrin and monoglyceryl stearic acid against the kappa-opioid receptor (PDB ID: 4DJH) with a docking score of -3.28 kcal/mol and -6.64 kcal/mol respectively. In the antimicrobial investigation, Penduletin and Beta-Amyrin showed the highest and lowest binding affinity against the selected receptors with the docking score of -8.27 kcal/mol and -1.66 kcal/mol respectively. ConclusionThe results of our scientific research reflect that the methanol soluble extract of C. gigantea is safe which may provide possibilities of alleviation of diarrhea and as a potential wellspring of antioxidants which can be considered as an alternate source for exploration of new medicinal products.

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Role of selective Bioactive Compounds as an Angiotensin Converting Enzyme Inhibitor

Khan, H.; Hussain, T.; Kataria, M.; SETH, A.; Malik, M. Z.; Dash, A.; Chand, S.; KHAN, M. A.

2020-08-19 bioinformatics 10.1101/2020.08.17.254359 medRxiv
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Hypertension is one of a major reason of mortality and morbidity and it is associated with heart and renal disease. The aim of this study is to find out the antihypertensive role of bioactive compounds from selected medicinal plants targeting ACE molecule which so far is not known. The plants taken in this study were Moringa oleifera, Azadirachta indica, and Hibiscus sabdariffa. The nitric oxide and superoxide scavenging property vary from 39.50% to 68% and 37.67 % to 75.50 %. respectively. The inhibition of ACE activity was found maximally in methanolic extract of A. indica (74 %), followed by H. sabdariffa (73.4%), and least in M. oleifera (71.8 %). The bioactive chloroform fraction was characterized for the presence of compound using standard techniques such as LCMS and NMR (13C-NMR 1H-NMR). The results revealed the presence of beta-sitosterol in M. oleifera, azadiradionolide in A. indica and hibiscitrin in H. sabdariffa. The compounds have shown significant low binding energy for hibiscitrin (-12.3kcal/mol), beta-sitosterol (-11.2kcal/mol) and azadiradionolide (-11.3kcal/mol) indicating the high efficacy of binding on the enzyme. While, binding energy of drug captopril was -5.6kcal/mol & enalpril - 8.1kcal/mol in the same pocket of the ACE molecule. Upon subjecting molecular dynamic simulation results indicated that beta sitosterol complex provided more compactness than the hibiscitrin and azadiradionolide compounds. The current study delivers a new perspective for the drug development against systolic blood pressure regulation and also opens new horizons for considering alternate highly potent drug target for hypertension.

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A preliminary study on the reproductive toxicity of GS-5734 on male mice

Fan, J.; Zhao, D.; Li, X.; Deng, T.; Sun, Y.; Luo, J.; Weng, Y.

2020-04-23 developmental biology 10.1101/2020.04.21.050104 medRxiv
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BackgroundGS-5734 as a novel and promising medicine for COVID-2019, its biological impact on the mammalian reproductive system has not been systematically studied. The aim of this study was to evaluate the effects of GS-5734 on sperm parameters and spermatogenesis in mice. Materials and MethodsIn this study, GS-5734 was synthesized according to the report. 28 adult male mice were randomly segregated into four groups (n=7 for each group). The group 1 was set as the control group, the group 1, 2, 3 and 4 were administered with GS-5734 at a daily dose of 0, 10, 50, 150 g/mouse respectively, by intraperitoneal injection for 10 days. On the 7th day after the last injection, the testes and cauda epididymides were collected for HE staining and sperm concentration, motility, morphology analysis. ResultsThe results indicated that after treated with GS-5734, the total sperm count and motile sperm rate showed downward trends, the abnormal sperm rate showed an increasing trend. As compared with the control group, GS-5734 at a daily dose of 150 g/mouse caused a significant decrease in sperm concentration and motility, and a significant increased of abnormal sperm rate; the 50 g/mouse drug treatment lead to a significant decrease in sperm motility and an increase in abnormal sperm rate. The HE staining of testicular and epididymal tissues showed that the spermatogenesis of mice was significantly deteriorated with the increasing dosage of GS-5734, especially in the 150 g/mouse group. ConclusionOur findings suggest that a high dosage of GS-5734 may induce testicular toxicity and result in deterioration of sperm parameters in mice. More investigation on the reproductive toxicity of GS-5734 is required.

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Network Pharmacology Integrated Molecular Docking Based Prediction of Active Compounds and Potential Targets in Tinospora crispa Linn. as Insulin Sensitizer

Zuhri, U. M.; Purwaningsih, E. H.; Fadilah, F.; Yuliana, N. D.

2021-05-05 bioinformatics 10.1101/2021.05.05.442728 medRxiv
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Insulin resistance is a metabolic disorder characterized by the decreased response to insulin in muscle, liver, and adipose cells. The normal insulin levels are unable to control glucose, lipids, and energy homeostasis. This condition remains a complex phenomenon that involves several genetic defects and environmental stresses, such as obesity. A full understanding is required to understand the entire itinerary and functional consequences of the occurrence of insulin resistance to develop a potent drug in diabetes management. In the present study, we investigated the mechanism of known phytochemical constituents of Tinospora crispa and its interaction with insulin resistant target proteins by using network pharmacology and molecular docking. The insulin sensitizer activities of Tinospora crispa may be associated with the inhibition of the activation of the inflammatory pathway and the activation of insulin signaling. Tinoscorside A, Makisterone C, Borapetoside A and B, and {beta} sitosterol consider the main phytoconstituents of Tinospora crispa by its binding with active sites of main protein targets of insulin resistance potential therapy. In conclusion, Tinospora crispa was one of the promising therapeutic agent in type 2 diabetes mellitus management. Regulation in glucose homeostasis, adipolysis, cell proliferation, and antiapoptosis may be the critical mechanism of Tinospora crispa as an insulin sensitizer.

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Discovery of Novel Inhibitors of HMG-CoA Reductase using Bioactive Compounds isolated from Cochlospermum Species through Computational Methods

Olatoye, T. I.

2025-01-22 bioinformatics Community evaluation 10.1101/2025.01.19.633828 medRxiv
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Cholesterol biosynthesis is a critical pathway in cellular metabolism, with 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR) catalyzing its committed step. The inhibition of HMGR has been widely explored as a therapeutic target for managing hypercholesterolemia, and statins are the most commonly used competitive inhibitors. However, the search for novel, natural inhibitors of HMGR is still a vital area of research, especially in light of the adverse effects of the prolonged use of statins. In this study, the potential of 84 phytochemicals isolated from two species of Cochlospermum (C. planchonii and C. tinctorium) reported in the literature, was investigated as novel inhibitors of human HMGR using molecular docking techniques. The phytochemicals were screened for their drug-likeness and ADMET properties in accordance with Lipinskis rule of five, and 32 of them were docked against the HMG-binding portion of the enzymes active site, together with its native ligand and 6 known statins serving as control ligands. The docking results revealed that 10 of the compounds exhibited strong binding affinities and interactions with the HMG-binding pocket of the enzyme, comparable to or exceeding those of the control ligands. This evidence strongly suggests their potential as effective inhibitors of HMGR. For the first time, the findings from this research identify and directly implicate the specific bioactive compounds of C. planchonii and C. tinctorium capable of exerting cholesterol-lowering effects in humans, while validating previously reported studies on the efficacy of these plants extracts used in West African traditional medicine to manage dyslipidemia, among a host of other ailments. The compounds identified may serve as promising drug candidates which can be further optimized and developed as novel, natural inhibitors of HMGR.

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Transcriptome Network Biology Reveals the Neuroprotective Potential of Rosmarinic Acid Against Frontotemporal Dementia

Arif, A.; Garg, P.; Srivastava, P.

2025-09-10 bioinformatics 10.1101/2025.09.05.674389 medRxiv
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Frontotemporal dementia (FTD) is a neurodegenerative disorder characterised by impaired behaviour and language. It affects individuals between 45 and 65 years of age. The present study aims to identify potential phytochemicals against target receptor of FTD. Transcriptome data analysis guided computer-aided drug design (CADD) was conducted to investigate molecular interactions between active phytochemicals present in Indian spices and differentially expressed genes. In present study, samples for patients with FTD were obtained from GEO dataset [GSE92340]. The samples were pre-processed followed by differential gene expression analysis using DESeq2. The patient sample was analyzed for 1882 upregulated genes. Hub gene out of DEGs was identified using CytoHubba Plugin of Cytoscape based on eleven parameters (Degree, Edge Percolated Component (EPC), Maximum Neighbourhood Component (MNC), Density of Maximum Neighbourhood Component (DMNC), Maximal Clique Centrality (MCC), Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress). HDAC1 gene was identified as hub gene and key target in case of FTD. CADD pipeline was used to identify phytochemicals against HDAC1 gene. A list of eighty-one phytochemicals found in Indian spices was analyzed for their drug likeness abilities using molinspiration and toxicity prediction using ProTox-II, which identified twenty-three phytochemicals as safe drug-like compounds. PatchDock was employed to examine interactions between phytochemical compounds and HDAC1. Molecular interactions revealed rosmarinic acid derived from rosemary (Salvia rosmarinus) as the most effective drug for FTD having lowest ACE value of -395 kcal/mol. In conclusion, this study demonstrates essential role of HDAC1 in pathogenesis of FTD and demonstrates the neuroprotective potential of rosmarinic acid against FTD.

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The Quercetin And Quercetin Derivatives Interaction With Cyclooxygenase-1 And Cyclooxygenase-2

Manukyan, A.

2020-12-07 bioinformatics 10.1101/2020.12.05.413088 medRxiv
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The cyclooxygenase (COX) enzymes are tumor markers, the inhibition of which can be used in the prevention and therapy of carcinogenesis. It was found that COX-1 and COX-2 are considered as targets for tumor inhibition. In anticancer therapy, plant compounds are considered that can inhibit their activity. Modeling of the COX-1 and COX-2 enzymes was carried out on the basis of molecular models of three-dimensional structures from the PDB database [PDB ID: 3KK6, 5f19] RCSB. For docking analysis, 3D ligand models were created using MarvinSketch based on the PubChem database [CID: 5280343, 5281654]. In silico experiments, for the first time, revealed the possible interaction and inhibition of COX-1 and COX-2 by quercetin and quercetin derivatives. Aspirin and Celecoxib [CID: 2244, 2662] were taken to compare the results. Possible biological activities and possible side effects of the ligands have been identified. It is noteworthy that Celecoxib is not active on the studied cell lines, while quercetin and quercetin derivatives are more active than Aspirin.

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Computational prediction of gamma-oryzanol as potential agonist of human peroxisome proliferator-activated receptor gamma (ppar-γ)

Biswal, P. K.; Behera, S.; Mohapatra, S.; Kar, D. M.; Samanta, L.; Behera, P. M.; Kar, R. K.

2023-06-11 bioinformatics 10.1101/2023.06.10.542647 medRxiv
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Diabetes mellitus is one of the complex metabolic disorders associated with individuals leading sedentary lifestyles. It leads to several complications rendering the normal function of vital organs like heart, liver, kidney, eye and brain. Scientists and doctors across the globe are involved in research for understanding the complex genetics of this disorder and formulating newer therapeutics accordingly. The finding of potential chemical entities and their underlying agonists or antagonist activities significantly controls the disorder but with some consequences. Thus there is demand for natural compounds and indigenous treatment methods for controlling the disorder with least or no adverse consequences. In the current work we present computational prediction of gamma-oryzanol as potential agonist of human peroxisome proliferator-activated receptor gamma (PPAR-{gamma}). A group of four gamma-oryzanol compound structures reported in PubChem database were downloaded and docked in the ligand binding site of five different human PPAR-{gamma} structures reported in PDB database. It was observed that most of the gamma-oryzanol compounds occupied themselves in the ligand binding P1, P2, P3, P4 sites with similar orientations as that of co-crystal agonists. Their binding conformations were assisted by some reasonable docking scores (-7 to -11 kcal/mol) and hydrogen bond interactions with some important conserved amino acid residues lining the ligand binding site. Additionally we have done a comparative molecular dynamics studies to reveal the flexibility of gamma-oryzanol in the ligand binding site in comparison to the co-crystal agonist and a scaffold analysis using the structure of six agonists and gamma-oryzanol for fetching potential scaffolds which may helpful in designing of new chemical entities.

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Mechanisms underlying the therapeutic effects of Semen Cuscutae in treating Recurrent Spontaneous Abortion based on Network Pharmacology and Molecular Docking

zheng, w.; Lei, M.; Yao, Y.; Zhan, J.; Zhang, Y.; Huang, F.

2023-05-30 bioinformatics 10.1101/2023.05.28.542653 medRxiv
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BackgroundThis paper aims to analyze the active components of SC by network pharmacology and screen the most stable compounds with TNF-a by molecular docking, to explore the mechanism of SC treatment of RSA and provide theoretical basis for drug development. MethodsActive compounds of SC and the potential inflammatory targets of RSA were obtained from the Traditional Chinese Medicine Systematic Pharmacology Database and GeneCard, respectively. The interaction network of RSA-SC-target gene was accomplished and Visualizing by STRING database and Cytoscape software.GO and KEGG pathway enrichment analyses were obtained from DAVID to further explore the RSA mechanism and therapeutic effects of SC. Interactions between TNF- and active compounds were analyzed by molecular docking. Results10 active ingredients and 128 target genes were screened from SC, and 79 of them intersected with RSA target inflammatory genes,which were considered to be potential therapeutic targets. Network pharmacological analysis showed that Sesamin, matrine, matrol and other SC active components had good correlation with the inflammatory target genes of RSA.Related genes include PGR, PTGS1, PTGS2, TGFB1 and CHRNA7. Multiple signaling pathways are involved in RSA pathogenesis,sunh as TNF- signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway, proteoglycans in cancer, FoxO signaling pathway, etc. Molecular docking results suggested that sesamin was the most appropriate natural TNFis. ConclusionOur findings provide an important role and basis for further research on the molecular mechanism of SC treatment of RSA and drug development of TNFis.

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Evaluation of the efficacy of a full-spectrum medicinal cannabis plant extract with less than 0.3% Delta9-tetrahydrocannabinol in in vitro models of inflammation and excitotoxicity

Ross-Munro, E.; Isikgel, E.; Fleiss, B.

2024-01-11 cell biology 10.1101/2024.01.10.575133 medRxiv
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The rapid development of research on the therapeutic benefits of medicinal cannabis, in parallel with an increased understanding of the endocannabinoid system, has driven research of Cannabis sativa constituents for managing neurological conditions. While most studies have focused on the therapeutic potential of the major components of cannabis plant extract isolated or combined, limited research has explored the pharmacological benefits of whole cannabis plant extract. In this study, we investigated the potential anti-inflammatory and neuroprotective effects of NTI-164, a novel full-spectrum cannabis extract with negligible {Delta}9-tetrahydrocannabinol (THC), compared with cannabidiol (CBD) alone in BV-2 microglial and SHSY-5Y neuronal cells. The inflammation-induced upregulation of microglial inflammatory mediators, being tumour necrosis factor (TNF), granulocyte-macrophage colony-stimulating factor (GM-CSF), inducible nitric oxide synthase (iNOS), and Arginase-1 (Arg-1), were significantly attenuated by NTI-164. This immunomodulatory effect was not observed upon treatment with isolated CBD. Compared to CBD alone, NTI-164 prevented elevated mitochondrial activity while normalising cell numbers in immune-activated microglia cells. NTI-164 also promoted the proliferation of undifferentiated neurons and the survival of differentiated neurons under excitotoxic conditions. Overall, our work shows that the anti-inflammatory and neuroprotective effects of NTI-164 as a full-spectrum cannabis extract are enhanced relative to that of CBD alone, highlighting the potential therapeutic efficacy of NTI-164 for the treatment of neuropathologies such as autism spectrum disorder (ASD) and related neuropathologies. This study has further shown that understanding the synergistic effect of phytocannabinoids is integral to realising the therapeutic potential of full-spectrum cannabis extract to inform the design of botanical-derived treatments for managing neurological disorders.

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Phomoarcherin B as a novel HIV-1 reverse transcriptase RNase H activity inhibitor: conclusions from comprehensive computational analysis

Abdul Ghafoor, N.; Baysal, O.; Süzek, B. E.; Silme, R. S.

2021-09-10 bioinformatics 10.1101/2021.09.09.459559 medRxiv
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The HIV epidemic has claimed more than 32.7 million live since its emergence in 1981, while many ART and HAART therapies are available and provide relief and control for patients, most of these therapeutics come with long-term side effects, resistance, socio-economical barriers, and other obstacles. In this study, genomic analysis was performed on 98 HIV-1 genomes to determine the most coherent target that could be utilized to restrict and cease the viral replication, the reverse transcriptase enzyme. Following the identification of the target protein, the RNase H activity of the reverse transcriptase was nominated as the potent target given the limited research associated with it. A library of 94 thousand small molecule inhibitors was generated and virtual screening was performed to identify hits, based on the reproducibility of the screening results, 4 compounds with the best scores were considered and their interaction within the active site was analyzed. Subsequently, all-atom molecular dynamics simulations and MM-PBSA was performed to validate the stability and binding free energy of the hits within the RNase H active. In silico ADMET assays were performed on the hit compounds to analyze their drug-likeness, physicochemical and pharmacological properties. Phomoarcherin B, a pentacyclic aromatic sesquiterpene naturally found in the endophytic fungus Phomopsis archeri, known for its anticancer properties scored the best in all the experiments and was nominated as a potential inhibitor of the HIV-1 reverse transcriptase RNase H activity. Author SummaryThe Human immunodeficiency virus 1 (HIV-1) has remained a global public health issue for the past 4 decades with millions of patients around the globe affected. Long years of research in the field of anti-viral therapies had introduced several drugs to combat the viral infection, however, most of these drugs come with their shortcomings. In this study, computational drug discovery approaches were utilized to research novel drugs that could be used as anti-viral agents against the former virus, the results had revealed Phomoarcherin B, a natural compound from an endophytic fungus to hold promising therapeutic potentials.

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Molecular docking and molecular dynamics simulation of the anticancer active ligand from Mimosa pudica to the Fibronectin Extra Domain A (EDA).

kohli, M.; Bole, S. B.; C, K.; Kimar, K.

2021-08-01 bioinformatics 10.1101/2021.07.30.454465 medRxiv
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Mimosa pudica was observed to have many useful characters the main aim of the experiment is to strengthen the multiple potential value of M. Pudica L. To study its secondary metabolites antioxidant, anti-cancerous, GCMS and in-silico studies. In general, the methanol method is employed for obtaining leaf extracts. The preliminary phytochemical screening of the M. pudica leaf extract showed the presence of bioactive components such as terpenoids, flavonoids, glycosides, alkaloids, quinines, phenols, tannins, saponins, and coumarins. An attempt is made to check the anticancer activity towards the cancer cell line A549 (Lung cancer cells) by MTT assay. For the identification of the compounds and to obtain its structure the crude extract is analyzed by GC-MS technique. The result of the GC-MS is analyzed using bioinformatics tool for in-silico docking to find out its targets against lung cancer receptors and PDB ID is obtained from the RCBS PDB database. The affinity of the identified ligand molecules to bind to the active site of the protein was studied through docking. And the effectiveness of the ligand molecules was obtained through molecular dynamics for longer simulation. The RMSD, RMSF and RG interaction were studied to the screened compounds. Further, MMPBSA analysis was carried out for the selected and standard drug like irigenin compounds. These selected lead molecules shown the better binding energy compare to irigenin drug in MMPBSA. The lead derivatives have shown potential results against lung cancer cell lines.

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Exploring Harmala Alkaloids as Novel Antimalarial Agents against Plasmodium falciparum through Bioinformatics Approaches

Dipto, K. Z.; Shariar, R.; Saha, C. K.; Huzaifa, A.; Robin, T. B.; Patil, R. B.; Alam, M. T.; Rafi, M. I. H.; Faruk, A. Z.; Moin, A. T.; Zinnah, K. M. A.; Hasanuzzaman, M.; Islam, T.

2024-07-18 bioinformatics 10.1101/2024.07.17.603828 medRxiv
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Malaria, caused by the Plasmodium falciparum, remains a significant global health challenge, with Plasmodium falciparum accounting for approximately 50% of cases and posing a considerable threat. Despite advances in control measures, malaria continues to cause an estimated one million deaths annually. The complex lifecycle of P. falciparum, involving both vertebrate hosts and Anopheles mosquitoes, complicates eradication efforts. The parasites resistance to existing antimalarial drugs, along with medication toxicity, necessitates innovative therapeutic approaches. Recent research has revealed that harmine, an alkaloid produced by an endophytic gut bacterium of Anopheles mosquitoes, can impede the transmission of the malarial parasite to humans by inhibiting a crucial life stage. This study investigates harmala alkaloids, sourced from plants and bacteria such as Peganum harmala, as potential alternatives to conventional antimalarial drugs. Notably, harmine and harmaline have shown promising antimalarial activity by inhibiting the essential enzyme protein kinase 4 (PK4), which is vital for the parasites survival. These compounds exhibit lower toxicity, effectively inhibiting both the blood stage growth and transmission of the parasite. Using in silico methodologies, including ADME analysis, molecular docking, MD simulation, and toxicity analysis, this study identifies harmala alkaloids as potential inhibitors against crucial P. falciparum proteins. Targeting proteins essential for the parasites survival, similar to established drugs like pfCRT protein, lays the foundation for developing effective antimalarial treatments. The comprehensive screening of harmala alkaloid molecules opens avenues for the pharmaceutical industry to tackle challenges related to drug resistance and toxicity, offering a promising route for the biorational management of malaria.

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Exploring phytoconstituents of Juglans regia to treat cervical cancer using integrative Bioinformatics

Dua, R.; Ahmad, I.; Bhardwaj, T.; Somvanshi, P.

2023-06-15 bioinformatics 10.1101/2023.06.15.545164 medRxiv
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Cervical cancer is the fourth most common malignancy among women, which also turns out to be the most common cause of death in women worldwide. Medicinal plants have traditionally been used to treat various diseases and disorders. The current study utilizes the molecular docking technique to investigate the anticancer potential of Juglans regia phytoconstituents against cervical cancer target proteins. This study includes the microarray dataset analysis of GSE63678 from the NCBI Gene Expression Omnibus database to identify differentially expressed genes. Furthermore, network biology approaches were employed to construct protein-protein interaction of differentially expressed genes. Next, the computation of topological parameters utilizing Cytohubba renders the top five hub genes (IGF1, FGF2, ESR1, MYL9, and MYH11). In addition, Juglans regia phytocompounds mined from the IMPPAT database were subjected to molecular docking analysis against identified hub genes. The application of molecular dynamics simulation validated the stability of prioritized docked complexes with minimum binding energy.

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Phytochemical Analysis and Cytotoxic Effects of Phyllanthus polygonoides Leaf Extracts on Hepatocellular Carcinoma: A Combined In-Vitro and In-Silico Approach

Khalid, A.; Akram, A.; Afzal, A.; Khalid, M. N.; Masroor, A.; Hameed, A.; Ali, H.

2024-08-19 bioinformatics 10.1101/2024.08.16.608215 medRxiv
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The authors have withdrawn their manuscript owing to the Paper was mistakenly uploaded by the students and the paper was having a lots of mistake and fake data. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

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Anti-inflammatory and neuroprotective activity of Viphyllin a standardized extract of β-caryophyllene from black pepper (Piper Nigrum L) and its associated mechanisms in mouse macrophage cells and Human Neuroblastoma SH-SY5Y cells

K, G.; Heggar Venkataramana, S.; Sathish, A.; raj, A.; H B, L.; Puttaswamy, N.; Kodimule, S. P.

2021-12-16 cell biology 10.1101/2021.12.16.472916 medRxiv
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Oxidative stress breeds various chronic lifestyle ailments including inflammatory conditions and neurodegenerative diseases. {beta}-caryophyllene natural bicyclic sesquiterpene, obtained from various plants sources found to be effective against inflammation and neuroprotection. In this study, we have evaluated the protective effect of Viphyllin, a standardized extract of {beta}-caryophyllene from black pepper against inflammation induced by lipopolysaccharide in RAW264.7 macrophage cells and mechanisms involved in hydrogen peroxide (H2O2)-challenged oxidative stress in human neuroblastoma SH-SY5Y cells. Viphyllin demonstrated the anti-inflammatory activity by subsiding the release of the pro-inflammatory intermediaries like NO, cytokines, interleukins, and protein expression levels of cyclooxygenase (COX-2) and inducible nitric oxide synthase (iNOS). In addition, Viphyllin suppressed the extracellular signal-regulated kinase (ERK). c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK) phosphorylation. On the other hand, Viphyllin showed neuroprotective effect against neuronal oxidative damage caused by H2O2. Viphyllin lessened the expression B-cell lymphoma-2 (Bcl-2), B-cell lymphoma-2-associated X protein (BAX), cleaved caspase-9, and PARP-1 proteins associated with apoptosis. Our results indicate that Viphyllin ameliorated LPS-mediated inflammation in macrophages by regulating inflammation and Viphyllin exerted remarkable anti apoptotic effect against neuronal damage challenged by H2O2. Altogether, Viphyllin could be potential functional food ingredient for inflammation and neurodegenerative diseases.

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Identification of potential human pancreatic α-amylase inhibitors from natural products by molecular docking, MM/GBSA calculations, MD simulations, and ADMET analysis

Basnet, S.; Ghimire, M. P.; Lamichhane, T. R.; Adhikari, R.; Adhikari, A.

2022-09-27 bioinformatics 10.1101/2022.09.26.509544 medRxiv
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Human pancreatic -amylase (HPA), which works as a catalyst for carbohydrate hydrolysis, is one of the viable targets to control type 2 diabetes. The inhibition of -amylase lowers blood glucose levels and helps to alleviate hyperglycemia complications. Herein, we systematically screened the potential HPA inhibitors from an in-house library of natural products by molecular modeling. The modeling encompasses molecular docking, MM/GBSA binding energy calculations, MD simulations, and ADMET analysis. This research identified newboulaside B, newboulaside A, quercetin-3-O-{beta}-glucoside, and sasastilboside A as the top four potential HPA inhibitors from the library of natural products, whose Glide docking scores and MM/GBSA binding energies range from -9.191 to -11.366 kcal/mol and -19.38 to -50.29 kcal/mol, respectively. Based on the simulation, among them, newboulaside B was found as the best HPA inhibitor. Throughout the simulation, with the deviation of 3[A] (acarbose = 3[A]), it interacted with ASP356, ASP300, ASP197, THR163, ARG161, ASP147, ALA106, and GLN63 via hydrogen bonding. Additionally, the comprehensive ADMET analysis revealed that it has good pharmacokinetic properties having not acutely toxic, moderately bioavailable, and non-inhibitor nature toward cytochrome P450. All the results suggest that newboulaside B might be a promising candidate for drug discovery against type 2 diabetes. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

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Molecular Docking of Glycyrrhiza glabra against the Conserved Target M1, NA andNS1 Proteins of Influenza A Viral Strains Identified through Pangenome Analysis

S, A.; Shantha, E.; Devi, N.; Jansi, S.

2019-11-05 bioinformatics 10.1101/831461 medRxiv
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Influenza viruses that infect humans are known to swiftly evolve over time. Influenza A virus has a negative single-stranded RNA genome in eight segments. Pangenome analysis of twelve strains of Influenza A viruses H1N1, H1N2, H2N2, H3N2, H5N1, H5N6, H7N2, H7N3, H7N7, H7N9, H9N2, and H10N8 gave insight on the core genes that are conserved and accessory genes that are specific for the strains. The proteins Neuraminidase, Matrix M1 and Nonstructural protein 1 were encoded by the core genes of segments 6, 7, and 8 respectively which proves that they are conserved in almost all the strains of influenza. The 3Dimensional structures of the core genes were interpreted by homology modeling and compared with corresponding Protein Data Bank structures (4MWQ, IEA3, 2GX9). Among several anti-viral phytocompounds that were virtually screened against the modeled and PDB target proteins, three molecules of Indian plant Glycyrrhiza glabra had high scores and interactions. Compounds 2,4,4 Trihydrochalcone, Davidigenin and Licoflavone B docked well with the Neuraminidase, Matrix protein M1 and Nonstructural Protein NS1 respectively with good scores, minimized energy and interacted with the active sites. The compounds obeyed Lipinskis Rule of five and exhibited drugability as well. Thus the present study focused on the drugable lead compounds from glabra that has inhibitory activities against the viral attachment, replication and matrix structure.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC=\"FIGDIR/small/831461v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (24K):\norg.highwire.dtl.DTLVardef@de27deorg.highwire.dtl.DTLVardef@10b9cc9org.highwire.dtl.DTLVardef@1628b20org.highwire.dtl.DTLVardef@9c2336_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Cardioprotective Activities of Artemisia lactiflora Extract in Rat Cardiomyoblast (H9c2) Under Inflmmatory Sepsis

Kooltheat, N.; Chaiissarapap, A.; Jeanthaisong, O.; Molek, N.; Kawinwanalai, W.; Nokkaew, N.

2023-04-29 cell biology 10.1101/2023.04.29.538793 medRxiv
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Withdrawal StatementThe authors have withdrawn their manuscript owing to add more results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.