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168 articles for “protein-protein docking”
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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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A molecular docking study and in silico analysis: targeting the marburg virus protein vp35 using active phytocompounds from alchemilla vulgaris
Abstract: Objective: The Marburg Virus Disease (MVD) is an infectious viral disease originating from African Fruit Bats (Rousettus aegyptiacus) that has become the root cause of a fatal hemorrhaging viral fever. As per reports from the WHO, MVD has claimed the lives of millions of people worldwide, with a disease fatality rate ranging from 24% in initial outbreaks to 88% in recent times owing to a difference in viral strains and …
Published in Research and Reviews : Journal of Computational Biology · Vol. 12, Issue 2, 2023 · pp. 39–62 Read article
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Molecular Docking-Based Analysis of Rauvolfia serpentina Alkaloids Targeting HPV E1 and L1 Proteins for Antiviral Therapeutic Potential
Abstract: Human papillomavirus (HPV) is a major cause of cervical cancer and other epithelial cancers. E1 and L1 proteins are crucial to the virus's lifespan. E1 is a viral helicase that is needed for HPV DNA replication, and L1 is the main structural capsid protein that builds the virion and infects target cells. Going after these proteins is a good way to stop viruses from spreading. In this case, Rauvolfia serpentina, …
Published in Research and Reviews: A Journal of Pharmaceutical Science · Vol. 17, Issue 1, 2026 · pp. 100–113 Read article
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Effectiveness of Temporins for the Treatment of HPV Infections
Abstract: Objectives: Human papillomavirus (HPV), especially high-risk variants like type-16 have been linked to the formation of malignant tumors. HPV-16 has been implicated in most cases of cervical cancer in women. This study aims to assess the effectiveness of three types of temporin molecules, i.e., antiviral peptides secreted by certain frog species, for the inhibition of the viral L1 protein. Methods: In the present study, various computational tools were used to …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 2, Issue 1, 2024 · pp. 41–53 Read article
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Molecular Docking: A Powerful Approach for Structure based Drug Discovery
Abstract: Molecular Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a central …
Published in Research & Reviews: A Journal of Bioinformatics · Vol. 3, Issue 2, 2016 · pp. 15–19 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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Investigating Curcumin Phytocompounds as Prospective Parkinson's Disease Therapeutic Agents: A Computational Method that Targets LRRK2 Protein
Abstract: Objective: Parkinson’s Disease is the second stage predominant neurodegenerative illness. Primary aetiology is still unknown. One of the biggest battlegrounds in modern medicine is discovering the cause of Parkinson’s disease (PD), as well as the hunt for palliative treatments and, if feasible, a cure. The objective of this work is to identify the phytocompounds from curcumin (curcuma longa) for the treatment of PD. Curcumin, a well-researched phytochemical, has been suggested …
Published in Research and Reviews : Journal of Computational Biology · Vol. 12, Issue 3, 2023 · pp. 55–67 Read article
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A Combined Molecular Docking Analysis of The Phytochemicals of Ginkgo biloba against The Parkin Protein Target (Autoinhibited Parkin Catalytic Domain)
Abstract: This study's goal is to evaluate the specific therapeutic targets for Parkinson's disease (PDB ID: 4BM9) using molecular docking simulation and ADME analysis against bilobalide, quercetin, ginkgolide B, and protocatechuic acid (3,4-Dihydroxybenzoic acid). The Protein Data Base was used to extract theprotein's three-dimensional structure, and the PubChem database was used to retrieve the ligands. Using Auto-Dock Tools-1.5.7, a molecular docking simulation of the compounds was carried out. Since none of …
Published in Journal of Catalyst & Catalysis · Vol. 10, Issue 1, 2023 · pp. 1–9 Read article
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Exploring the Potential of Allium sativum Phytocompounds as B-Cell Leukemia 2 Inhibitors in Acute Lymphoblastic Leukemia: Molecular Docking Study
Abstract: Objective: Acute lymphoblastic leukemia (ALL) is a lymphoid progenitor cell malignancy that could be treated with plant-based drugs, thus alleviating the off-target effects caused by conventional chemotherapy. Since ancient days, Allium sativum has been an integral part of traditional medicine and an excellent antimicrobial, antioxidant, and antiproliferative agent. Hence, this study aims to assess the anti-leukemic potential of A. sativum phytoconstituents as the B-cell leukemia 2 protein (Bcl-2) natural inhibitor …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 2, 2024 · pp. 53–80 Read article
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Protein-Tyrosine Phosphatase-1B (PTP-1B) Inhibitory Perspectives of Hydroxylated Chalcones: Exploration through Docking Studies
Abstract: The current research emphasized on exploring the Protein-Tyrosine Phosphatase-1 B (PTP-1B) inhibitory potentials of hydroxylated chalcone derivatives against PDB ID: 4I8N (PTP-1B in complex with an inhibitor [(4-{(2s)-2-(1,3-benzoxazol-2-yl)-2-[(4-fluorophenyl)sulfamoyl]ethyl}phenyl)amino](oxo)acetic acid) by molecular docking approach using the iGEMDOCK (Genetic Evolutionary Method for Molecular Docking) software. The current molecular docking analysis of some hydroxylated chalcone derivatives have presented a profound inhibition of the antidiabetic target PTP-1B by interacting with the amino acid residues …
Published in Research & Reviews: A Journal of Bioinformatics · Vol. 6, Issue 1, 2019 · pp. 4–8 Read article
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In Silico Stability Analysis and Phosphorylation Induced Structural Simulation of Alpha-synuclein in Parkinson’s disease
Abstract: Alpha-synuclein (α-syn) is the major component of pathologic inclusions that characterizes neurodegenerative disorders such as Parkinson’s disease (PD), dementia with Lewy body disease, and multiple system atrophy. Mutations and phosphorylation of α-syn causes familial PD. Phosphorylation of α-syn at TYR125 and SER129 plays an important role in PD and enhances its partial digestion by calpains leading to its aggregation; however, the exact mechanism is unknown. The present study uses in …
Published in Research & Reviews: A Journal of Bioinformatics · Vol. 2, Issue 1, 2015 · pp. 15–21 Read article
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Integrating Network Pharmacology and Molecular Docking to Investigate Boerhavia diffusa for Pancreatic Cancer Treatment
Abstract: Objective: In this study, network pharmacology was applied to determine the therapeutic effects of the bioactive compounds of Boerhavia diffusa. Network pharmacology can unearth the underlying mechanisms between drugs and the disease targets and aids in the discovery of novel medications for complex conditions such as cancer. Methods: To predict the molecular mechanisms of action of Boerhavia diffusa in the treatment of was screened using the GeneCards database. The Venn …
Published in International Journal of Molecular Biotechnological Research · Vol. 2, Issue 1, 2024 · pp. 29–49 Read article
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Using Multitarget Molecular Docking to Examine the Antiviral Potential of Clerodendrum Phlomidis against Measles
Abstract: Objective: Measles, a viral disease caused by a member of the Paramyxoviridae virus family, is highly contagious and characterized by a respiratory illness and a maculopapular rash on the skin. Children are the main victims of the illness. In the context of drug development, this study investigates the efficacy of phytocompounds derived from Clerodendrum phlomidis against the target protein of the measles virus. Methods: The 7SKS protein was retrieved from …
Published in International Journal of Molecular Biotechnological Research · Vol. 1, Issue 2, 2023 · pp. 32–42 Read article
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Molecular Docking Evaluation of Cedrus deodara Secondary Metabolites as a Potent Anti-ovarian Cancer Agent
Abstract: Objective: According to the statistics for the year 2022 it was seen that cancer total cases is 14,61,427. After breast cancer, ovarian cancer is the second most frequent cancer among women. The estrogen receptor (PDB ID: 1X7E), progesterone receptor (PDB ID: 1A28), and Phosphoinositide 3-kinases (PDB ID: 4FJY) can be considered as target protein for ovarian cancer. The plant Cedrus deodara and its phytochemicals were chosen in this study to …
Published in International Journal of Molecular Biotechnological Research · Vol. 1, Issue 1, 2023 · pp. 77–93 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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Deciphering Th-Related Gene Interactions in Chronic Spontaneous Urticaria: Bioinformatics Insights and Drug Affinity Exploration
Abstract: Objective: There has been a great deal of interest in how inflammatory dermatosis and The cell interact, but the etiopathogenesis of chronic spontaneous urticaria (CSU) is still inadequately comprehended. Through bioinformatics techniques, the purpose of this work is to elucdate the molecular mechanism underlying Th-related genes in CSU and seeks to find the highest affinity drug. Methods: The CSU RNA expression profiling dataset provided the basis for the investigation. The …
Published in International Journal of Genetic Modifications and Recombinations · Vol. 2, Issue 1, 2024 · pp. 1–15 Read article
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Exploring The Multitarget Pharmacological Mechanism of Diabex for T2dm by Combining Network Pharmacology and Molecular Docking Techniques
Abstract: Objective: Hyperglycemia brought on by an absolute or relative absence of insulin synthesis or action characterises a set of illnesses known as diabetes mellitus. Chronic hyperglycemia in diabetes mellitus has been linked to organ damage, heart, and blood vessels. The persistent metabolic condition Diabetes is a severe global issue with negative social, health, and economic effects. It is a type of metabolism disorder that interferes with food digestion in the …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 1, Issue 3, 2023 · pp. 62–73 Read article
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Extrapolations of Periwinkle Secondary Metabolites as Multitarget Inhibitor of Breast Cancer Proteins
Abstract: Objective: Breast cancer is considered one of the most common and dangerous forms of cancer. It is a significant public health issue on a global scale. The study estimates that 10.0 million people will die from cancer this year, and 19.3 million people will develop the disease overall (BC). In this computation approach, nowadays emphasizes new drug discovery, the target protein epidermal growth factor receptor (EGFR) (5UGB), estrogen receptor (ER) …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 1, Issue 1, 2023 · pp. 36–49 Read article
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Precision Medicine for Neurofibromatosis Type 1: Progress and Prospects in Drug Discovery
Abstract: Objective: The development of neurofibromas, café-au-lait spots, and other neurological problems are the hallmarks of neurofibromatosis type 1 (NF1), a hereditary disorder. The dearth of efficacious pharmaceutical therapies underscores the need for novel therapeutic approaches, even in the face of clinical variability. Through very accurate prediction of the binding affinity of possible therapeutic drugs with the target protein, the computational technique known as “molecular docking” has become a potent tool …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 2, Issue 1, 2024 · pp. 01–15 Read article
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Anti-hyperglycemia Effects of Plant Secondary Metabolites Towards PKA/CREB Pathway Activation in Diabesity
Abstract: Objective: Diabesity, the amalgamation of diabetes and obesity, presents a significant global health challenge. This research carefully examines how plant secondary metabolites influence glucose regulation in diabetes using the PKA/CREB pathway, paying particular attention to diabesity—the combination of diabetes and obesity. Understanding the complex ways in which these metabolites affect metabolic health will help to identify new treatment approaches for managing diabetes and its associated problems. By conducting a thorough …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 2, Issue 1, 2024 · pp. 33–50 Read article