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83 articles for “ligand docking”
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INVESTIGATING PHYTOCHEMICAL INHIBITORS OF PSEUDOMONAS AERUGINOSA'S AHL SYNTHASE LASI: A PATH TOWARD NOVEL THERAPEUTIC AGENTS
Abstract: Objectives: This study intended to explore the potential of phytochemicals from Allium sativum to inhibit AHL synthase LasI, a critical protein of the Quorum Sensing (QS) pathway in Pseudomonas aeruginosa, with the ultimate objective of developing therapeutic agents for managing P. aeruginosa infections. Methods: The physicochemical properties, toxicity, aggregation ability and binding potential of phytochemicals from Allium sativum to the protein AHL synthase LasI were determined. Physicochemical properties, toxicity and …
Published in Research and Reviews : Journal of Computational Biology · Vol. 12, Issue 3, 2023 · pp. 40–54 Read article
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Network Pharmacology and Molecular Docking Approach to Reveal the Underlying Mechanisms of Isorhamnetin in the Treatment of Lymphangitis Carcinomatosis
Abstract: Objective: Lymphangitic carcinomatosis (LC) is a tumor that spreads through lung lymphatics and is most commonly seen secondary to adenocarcinoma. In the majority of cases, LC is a result of tumor cells spreading through the lymphatic system. However, approximately 20% of LC cases can be attributed to lymphangitis caused by tumors obstructing lymphatic drainage. This blockage commonly occurs near the lung hilum, where a centrally located mass can cause inflammation …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 1, Issue 1, 2023 · pp. 28–45 Read article
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Grid based docking study of some 2-(4-methylsulfonyl phenyl) pyrimidine derivatives (designed after QSAR studies) with Cyclooxygenase
Abstract: Molecular docking helps in studying drug/ligand or receptor/ protein interactions by identifying the suitable active sites in protein, obtaining the best geometry of ligand-receptor complex and calculating the energy of interaction for different ligands to design more effective ligands. In Grid based docking, after unique conformers of the ligand are generated, the receptor cavity of interest is chosen and a grid is generated around the cavity. Cavity points are found …
Published in International Journal of Antibiotics · Vol. 1, Issue 1, 2024 · pp. 23–41 Read article
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Pharmacokinetic Profiling and Molecular Docking of Carvacrol and Structural Analogs: Targeting Quorum Sensing Proteins to Disrupt Biofilm-Mediated Antimicrobial Resistance in Multidrug-Resistant Bacterial Pathogen
Abstract: Antibiotic resistance, particularly in Pseudomonas aeruginosa, has become a major global health threat, exacerbated by the organism's ability to form biofilms and regulate virulence through quorum sensing (QS). The LuxR and LasR receptors are key regulators in this process, influencing both pathogenicity and antibiotic resistance. This study investigates potential QS inhibitors targeting these receptors as a strategy to mitigate antibiotic resistance. The primary objective was to identify novel ligands that …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 3, Issue 2, 2025 · pp. 43–61 Read article
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A Novel Genetic Algorithm For Biomolecular Interaction Studies
Abstract: The examination of recent developments in genetic algorithms is covered in this work. The genetic algorithms chosen for analysis are those that the scientific community finds to be of considerable interest. The fresh and demanding researchers will benefit from this review's ability to provide a broader perspective on genetic algorithms. The popular algorithms' benefits and drawbacks, as well as how they are implemented, are presented. In order to aid novice …
Published in Journal of Microelectronics and Solid State Devices · Vol. 9, Issue 2, 2022 · pp. 22–28 Read article
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Pharmacophore mapping, 3D QSAR, docking, and ADME prediction studies of novel Benzothiazinone derivatives
Abstract: Background Tuberculosis is a major public health concern worldwide which is caused by Mycobacterium tuberculosis. DprE1 (Decaprenyl Phosphoryl Ribose 2’- Epimerase) is the most challenging target for development of novel anti- tubercular agents because it is a small protein and located into cytoplasmic membrane. So, novel anti-TB drugs did not bound effectively with it. DprE1 catalyzes the oxidation of the 2’ hydroxyl group of DPR (Decaprenyl Phosphoryl D- Ribose) …
Published in International Journal of Antibiotics · Vol. 1, Issue 1, 2024 · pp. 59–82 Read article
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Targeting Homogentisate Dioxygenase Dysfunction in Alkaptonuria: Investigating Curcuma longa’s Therapeutic Potential
Abstract: Objectives: Alkaptonuria is known to have a faulty gene HGO in the metabolic process. In the present research work, the focus is towards investigating the therapeutic capabilities of the Curcuma longa upon the faulty Homogentisate dioxygenase gene using ligand-protein binding, which would assist in the corrective tyrosine metabolism. Methods: This study is based on the computational approach using different phytochemicals for evaluation of the potency against the abnormal Homogentisate dioxygenase …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 2, Issue 2, 2024 · pp. 1–11 Read article
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Identification of Secondary Metabolites from Zingiber officinale as Inhibitors for Keap 1-Nrf2 small Molecules through Molecular Docking Techniques
Abstract: Objective: Therapeutic plants aid in treating cancer-based cell signaling pathways and preventing certain risk factors. Zingiber officinale has a variety of anti-inflammatory characteristics also contributing to enhanced immunity, reducing cancer risk and used to target the KEAP NRF2. When overexpressed in response to oxidative stress and DNA damage, elevates the risk of developing multiple cancers. NRF2 cellular sensors, which also control and coordinate their expression aid in defending healthy cells …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 1, Issue 2, 2023 · pp. 35–48 Read article
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Molecular Docking Analysis of Punica granatum Compounds as Potential Inhibitors for Colorectal Cancer-Associated Molecular Targets
Abstract: Objective: Cancer is one of the most common worldwide disease which threat the life of a person. Colorectal cancer is one of the common cause of death nowadays. As computation approach is now employed for new drug discovery, target protiens like CDK-2, matrix metalloproteinase 2 (MMP-2), cyclin A, poly (ADP- ribose) polymerase (PARP-1) and Cox2 were chosen to perform molecular docking against the derivatives of Punica granatum phtyochemicals and Food …
Published in Research and Reviews : Journal of Computational Biology · Vol. 11, Issue 03, 2022 · pp. 28–42 Read article
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Inhibition of PI3K/Akt/mTOR Signaling Pathway by Vitis Vinifera Phytocompounds: A Promising Strategy for Supressing Colorectal Cancer Growth and Metastasis
Abstract: Objectives: Colorectal cancer was not typically identified a few decades ago. Today, with almost 900 000 fatalities each year, it is the fourth most dangerous cancer in the world. Colorectal cancer is responsible for about 10% of all cancer diagnoses annually and cancer-related deaths worldwide. It is the second most common type of cancer in women and the third most common type in men. Incidence and death are roughly 25% …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 1, Issue 2, 2023 · pp. 64–75 Read article
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Experimental Studies and in silico Analysis on Quarum Sensing and System Simulation in Pseudomonas aeruginosa
Abstract: Pseudomonas aeruginosa is the most common pathogenic bacterium present in human microbial flora, biofilms, soil and water associated and support self microbial communications and survilance. The present study shows estimated protein concentration present in two days grown in Mullar hinton broth was resulted around 32.5 mg/ml. The studies in protein interaction on X-ray film with aqueous fruit and vegetable extracts showed good results with apple, straw berry, cucumber, grape, orrange, …
Published in Research and Reviews : Journal of Computational Biology · Vol. 7, Issue 1, 2018 · pp. 1–8 Read article
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An Integrated Study to Extrapolate the Interaction of NMDAR with Potential Ligands for the Treatment of Alzheimer’s Disease Symptoms
Abstract: Objective: Alzheimer’s disease (AD) is the most common neurodegenerative disease affecting the health status of older adults especially those above the age of 60 years. As an outcome, two types of medications have been developed for the treatment of its symptoms which are acetylcholinesterase (AChE) and N-methyl-D-aspartate receptor (NMDAR) antagonist. This paper uses the computational approach to understand the interaction of NMDAR with four major phytocompounds (curcumin, L-epicatechin, ginsenosides, and …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 1, Issue 1, 2023 · pp. 15–27 Read article
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Pharmacological Management of Parkinson’s Disease: Current Therapies and Emerging Treatments
Abstract: Objective: Parkinson's disease, behind Alzheimer's, is the second most common neurodegenerative ailment and a major cause of neurological morbidity worldwide. Clinical diagnosis is made, and current management is limited to symptomatic treatments, with levodopa remaining the cornerstone of pharmaceutical therapy. In certain patient groups, deep brain stimulation of specific basal ganglia targets can provide significant clinical relief. There are currently no proven disease-modifying medicines in clinical use that can halt …
Published in International Journal of Genetic Modifications and Recombinations · Vol. 1, Issue 1, 2023 · pp. 27–39 Read article
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Melanogenic Inhibitory Effects of Sesamum indicum Phytocompounds Towards CDK 2, c-KIT, and BRAF.
Abstract: Objective: Melanoma is thought to be the fifth most frequent cancer in the US population, despite cancer being the most common cause of death in the globe. BRAF, CDK2, and c-KIT proteins are regarded as potential therapeutic agents since mutations in these proteins are the primary cause of melanoma. For the investigation of their pharmacological properties and therapeutic activities against the target proteins, Sesamum indicum L. and its phytocompounds were …
Published in International Journal of Bioinformatics and Computational Biology Read article
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Exploring Pharmacological Mechanism Of Pteridines And Its Derivatives Against Neurodegenerative Disorders Using Network Pharmacology And Molecular Docking Techniques
Abstract: Objectives: Pteridines have been identified via various research and shown therapeutic efficacy in Neurodegenerative disorders(ND) preclinical models. In the current study, a network pharmacology technique was applied to determine the underlying mechanism of the pteridines' protective effects on ND. Network pharmacology was utilised in order to reveal the interactions between medications and the targets of illnesses, and it is capable of completely articulating the complexity between diseases and medications. The …
Published in Research and Reviews : Journal of Computational Biology · Vol. 11, Issue 03, 2022 · pp. 1–13 Read article
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In Silico Analysis and Docking Study of the Active Phyto Compounds of Ginkgo Biloba Against Alzheimer's Amyloid-Beta Protein
Abstract: Objective: Alzheimer's disease, an age-related progressive neurological condition, arises due to the accumulation of amyloid-beta protein within the brain. In this study, an attempt was made to explore the potential of natural compounds derived from Ginkgo, known for their diverse medicinal properties, in the prevention of the disorder by employing molecular docking techniques, conducting drug-likeness prediction assessments, and performing ADME analysis. Methods: Amyloid beta protein was retrieved from the PDB …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 1, Issue 2, 2023 Read article
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Hydroxybowdichione Flavonoids As Inhibitors of Dengue Virus Ns5 RNA-Dependent RNA Polymerase Using Molecular Docking Approach
Abstract: Objectives: Human lives are now seriously threatened by dengue fever, which is brought on by the dengue virus (DENV). Aedes aegypti mosquitoes, which reproduce in still water, are the primary vectors of the arboviral virus known as dengue. It is well-recognized that phytochemicals have a high potential to eliminate bacterial, viral, and fungal infections in people. Thus, it demonstrates its inhibitory effects on the dengue virus. This study identifies some …
Published in International Journal of Genetic Modifications and Recombinations · Vol. 1, Issue 1, 2023 · pp. 1–16 Read article
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In Silico Drug Designing of Breast Cancer in Homo sapiens
Abstract: Breast cancer is a severe health concern in India, with the highest mortality rate among women. It is brought on by uncontrolled cell division and has the potential to spread to other body regions. As a transcription factor, interactions with estrogen receptor (ER) alpha are primarily responsible for malignant tumors through regulating the transcription of numerous genes. Because most of the medications now used to treat breast cancer have significant …
Published in Research and Reviews : Journal of Computational Biology · Vol. 11, Issue 2, 2022 · pp. 12–27 Read article
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In Silico Molecular Docking of Indigofera tinctoria Phytocompounds to Target EGFR/ERK and FGFR/FGF Pathway Proteins Involved in Prostate Cancer
Abstract: Objective: Prostate cancer being the second major cause of cancer-related deaths in males, affects the small walnut-shaped gland below the bladder called the prostate gland. The epidermal growth factor protein (EGFR), cascade protein (ERK), and fibroblast growth factor proteins (FGFR and FGF) are involved in the different signaling pathways that lead to the formation of different products, that are responsible for the progression of cancer and thus can be considered …
Published in International Journal of Molecular Biotechnological Research · Vol. 1, Issue 1, 2023 · pp. 34–56 Read article
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Anticancer Activity of Calotropis procera by Molecular Docking Analysis
Abstract: Cyclin-dependent kinase 2 (CDK2) is a protein synthesized by Calotropis procera. It is known to be responsible for causing cancer in the human body. Studies have presented the significance of the phytochemicals to inhibit the CDK2 protein. Adsorption, distribution, metabolism, and excretion (Swiss ADME) and PubChem were the pharmacological tools which were used to check molecular weight, which should be less than 500D, acceptors less than 10, and donors less …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 2, Issue 1, 2024 · pp. 01–07 Read article