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183 articles for “Binding proteins”
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Anthrax Toxin Time-Resolved Absorption and Resonance FT-IR and Raman Biospectroscopy and Density Functional Theory (DFT) Investigation of Vibronic-Mode Coupling Structure in Vibrational Spectra Analysis
Abstract: Anthrax toxin is a three-protein exotoxin that is secreted by the bacterium's virulent strains, the anthrax causative agent Bacillus anthracis. Harry Smith first found the toxin in 1954. Anthrax toxin consists of a protein called a protective antigen (PA) binding cell protein and two enzyme parts called an edema factor (EF) and a deadly factor (LF). These three protein components act together to impart their physiological effects. Assembled complexes containing …
Published in Research and Reviews : Journal of Computational Biology · Vol. 8, Issue 2, 2019 · pp. 23–51 Read article
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Molecular Docking of Nigella Sativa Phytocompound as Inhibitors of Transcription Factors NF-KB Implicated in Rheumatoid Arthritis
Abstract: Objectives: Nigella sativa, a plant considered around the world as the most treasured nutrient-rich herb for centuries together in different civilizations, is exceptionally known for its high levels of antioxidant properties. Free radical intensification due to oxidative stress plays a key role in the pathogenesis of rheumatoid arthritis by activating the NF-KB protein that regulates the expression of the genes involved in inflammation. Methods: This study involves in-silico approach to …
Published in International Journal of Molecular Biotechnological Research · Vol. 2, Issue 2, 2024 · pp. 42–55 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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Stilbenes: A Molecular Docking and ADMET Analysis Approach on an Emerging Resource for Scavenging Reactive Oxygen Species in the Field of Colon Malignancy
Abstract: Objective: Colon malignancy, also referred to as colon cancer, originates as precancerous polyps in the colon or rectum, which have the potential to thrive and progress into cancerous tumors over time. This study delves into various bioactive compounds (from natural sources like plants) to assess their potential efficacy in inhibiting colon malignancy as compared to conventional methods. Methods: The objective of this study was to employ computational methodologies to evaluate …
Published in Research and Reviews : A Journal of Biotechnology · Vol. 14, Issue 3, 2024 · pp. 29–38 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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Exploring The Therapeutical Potential Of Pongamia Pinnata For Herpes Simplex Virus Type 1 (HSV-1)
Abstract: Objective: Pongamia pinnata (L.), commonly known as Indian beech or pongam tree, is a tropical plant renowned for its medicinal properties in traditional medicine systems. Extracts derived from various parts of Pongamia pinnata have demonstrated antimicrobial, anti-inflammatory, and immunomodulatory activities. Such attributes make it a compelling candidate for exploring its therapeutic potential against HSV infections. Thymidine kinase is the target protein mostly used in the treatment of HSV1 infections. In …
Published in Research and Reviews: A Journal of Microbiology and Virology · Vol. 15, Issue 1, 2025 · pp. 1–9 Read article
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Interaction of Bioactive Component of Aframomum melegueta on Molecular Docking
Abstract: Computational mimicry of the structure of large complexes created by di- and poly-interaction of molecules has been termed molecular docking. The purpose of molecular docking is the prediction of the three-dimensional structures of interest, this is due to that docking only produces plausible candidate structures. The docking was carried out between the bioactive compounds against 5α-reductase, 3β-hydroxy-steroid dehydrogenase, and 17β-hydroxy-steroid dehydrogenase of returned binding energy, BE (kcal/mol) between -5.9 and …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 2, Issue 1, 2024 · pp. 51–60 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 · Vol. 1, Issue 3, 2023 · pp. 46–61 Read article
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A Structure-based Design Approach to Catharanthus roseus Phytoconstituents as Potential Inhibitors of B-Cell Lymphoma 6 Protein
Abstract: Objectives: Lymphoma is a cancerous disease. It develops into millions of people worldwide. Identify the naturally active compounds from Catharanthus roseus, they have multiple values in the medicinal field of Siddha, and Indian Ayurveda are used as a disease-preventing agent. Drug illness prediction, toxicity prediction, statistical information, molecular docking, as well as absorption, distribution, metabolism, and excretion (ADME) analysis are used to predict the fit ligand as a drug. Methods: …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 1, Issue 2, 2023 · pp. 14–34 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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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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Computational Investigation of Withania somnifera Compounds Targeting S. pombe SMN YG-Dimerin Spinal Muscular Atrophy: Insights from Molecular Docking Analysis
Abstract: Objectives: The primary objective of this study is to determine the potential of phytochemical constituents of Withania somnifera in treating spinal muscular atrophy, an autosomal recessive genetic neurodegenerative disorder, through computational techniques. To investigate the binding affinity of phytocompound to the target protein S. pombe SMN YG-Dimer through molecular docking. Besides, evaluating the pharmacological attributes of phytochemical constituents to assess their ability as an ideal prospect for developing therapeutic medication. …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 2, 2024 · pp. 39–52 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
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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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Drug Discovery and Design: Focus on computational approaches used in the discovery and design of new drugs
Abstract: Computational approaches have revolutionized the field of drug discovery and design, offering efficient and cost-effective strategies for identifying and developing new therapeutics. This review article explores the application of computational methods in drug discovery, with a focus on virtual screening techniques, molecular docking, molecular dynamics simulations, and quantitative structure-activity relationship (QSAR) models. Virtual screening plays a crucial role in narrowing down large chemical libraries by utilizing ligand-based and structure-based approaches. …
Published in Research and Reviews : Journal of Computational Biology · Vol. 12, Issue 1, 2023 · pp. 26–30 Read article
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Targeting Vasopressin 2 Receptor (V2R) in Renal Cystogenesis by Exploring the Nephroprotective Potential of “Terminalia arjuna”
Abstract: Objectives: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder, leading to the formation of multiple cysts in the kidneys. It is a major cause of end-stage renal disease (ESRD), which often requires dialysis or a kidney transplant for survival. This research focuses on identifying potential bioactive compounds derived from natural sources that show promise for drug development targeting the V2R gene. Methods: The naturally occurred …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 2, 2024 · pp. 14–24 Read article
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Exploring Potential Phytochemicals for Myasthenia Gravis Treatment: A Molecular Docking and ADME Analysis Approach
Abstract: Objective: Muscle feebleness and exhaustion derived from a disruption in neuromuscular transference are hallmarks of the crippling autoimmune disease myasthenia gravis (MG). The drawbacks of the current MG therapy options are frequently partial efficacy and adverse effects. To investigate the potential of phytochemicals in MG control, in this work we integrated molecular docking with ADME (absorption, distribution, metabolism, and excretion) analysis using a computer method. We identified molecules exhibiting favorable …
Published in International Journal of Molecular Biotechnological Research · Vol. 2, Issue 2, 2024 · pp. 1–13 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 Role of MAPK3 in Major Depressive Disorder: Molecular Docking, Dynamics, and Binding Free Energy Analysis of Natural Compounds as Alternatives to Conventional Drugs
Abstract: Major Depressive Disorder (MDD) is a prevalent neuropsychiatric disorder with limited treatment efficacy and significant side effects associated with conventional antidepressants. Recent studies have highlighted the role of mitogen-activated protein kinase 3 (MAPK3) in the mechanisms underlying MDD, positioning it as a potential target for the development of novel therapeutic drugs. In this study, we employed various computational approaches to explore natural compounds as viable alternatives to synthetic antidepressants. Researchers …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 3, Issue 2, 2025 · pp. 53–68 Read article
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Advanced Computational Models for Predicting Molecular Interactions
Abstract: Understanding molecular interactions is essential for a number of disciplines, including biochemistry, materials science, and medication development. Traditional experimental methods, while accurate, are often time-consuming and expensive. Advanced computational models have emerged as powerful tools to predict molecular interactions efficiently. In order to predict the behavior and interactions of molecules at the atomic and subatomic levels, this paper reviews the most recent developments in computational techniques, such as machine learning …
Published in International Journal of Advance in Molecular Engineering · Vol. 2, Issue 1, 2024 · pp. 8–13 Read article