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28 articles for “protein-ligand interaction”
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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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In-Silico Docking of Rubia cordifolia Phytocompounds as Potential MMP-2 Inhibitors for Varicose Vein Management
Abstract: Varicose veins are one of the most common disorders, affecting the vein structure and function of lower limbs, yet there has been no absolute cure found yet. One of the underlying causes for worsening of the condition is the proteolytic activity of MMPs which are a group of enzymes that affect the extracellular matrix (ECM) surrounding the affected veins. Phytocompounds of Rubia cordifolia (Manjishta) were docked against the MMP-2 protein …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 3, Issue 2, 2025 · pp. 31–42 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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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
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Exploring Oroxylum indicum Phytochemicals as VEGFR-2 Inhibitors: A Molecular Docking Approach for Cancer Management
Abstract: Cancer is still a major health problem around the world and is one of the top causes of death. A protein called VEGFR-2 (vascular endothelial growth factor receptor 2) is important because it helps blood vessels grow by supporting the survival, movement, and growth of certain cells. This process is essential for tumors to grow and spread to other parts of the body. This study focused on evaluating the binding …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 3, Issue 2, 2025 · pp. 48–62 Read article
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Multitarget Molecular Docking Using Curcuma longa Phytocompounds for Polycystic Ovary Syndrome Treatment
Abstract: Objective: The primary goal of this research is to understand and describe specific aspects of molecular interaction, it includes studying various aspects such as binding affinity, binding mode, and stability of the ligand-protein complex. Molecular docking is a computational technique used to predict the preferred orientation of one molecule to a second when bound together to form a stable complex. In this study, molecular docking will be employed to stimulate …
Published in International Journal of Molecular Biotechnological Research · Vol. 2, Issue 1, 2024 · pp. 15–28 Read article
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Molecular Docking Studies of Wildtype P53 with Damnacanthal and Scopoletin- Phytochemicals Derived from Morinda Citrifolia
Abstract: Cancer is a prominent cause of mortality globally, and it has the potential to impact any region of the body. The tumor suppressor protein P53 plays a significant role in inhibiting tumor growth by regulating DNA repair, inducing cell cycle arrest, promoting senescence, and triggering apoptosis when confronted with genotoxic stress. P53 is found mutated in 50% of cancers where it loses its tumor suppressive properties and gains oncogenic properties …
Published in International Journal of Molecular Biotechnological Research · Vol. 1, Issue 2, 2023 · pp. 20–31 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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Molecular Pharmacokinetics and Structural Docking of Phenolic Acids for Targeting NF-κB Pathway Components in Inflammation and Fibrosis: A Computational Approach Toward Therapeutic Discovery
Abstract: Inflammation and Fibrosis are critical pathological processes associated with various chronic diseases, often mediated by the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway. This study investigates the therapeutic potential of phenolic acids as modulators of the NF-κB pathway, aiming to identify novel ligands that can effectively interact with key components of this signaling cascade. A comprehensive computational approach was employed, utilizing molecular docking, pharmacological screening, and post-docking …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 3, Issue 1, 2025 · pp. 14–31 Read article
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Drugs for Alzheimer’s Disease from Salix Alba Discovered Computationally Utilizing Virtual Screening and Docking against 1b41 Protein
Abstract: Objective : The of this research is to evaluate the feasibility of using molecular docking techniques to identify novel acetylcholinesterase, a key enzyme implicated in the pathogenesis of Alzheimer’s disease, a neurodegenerative disorder with a gradual but steady progression to death, due to the gradual accumulation of beta-plaques and neurofibrillary tangles, as well as a decline in acetylcholine levels. Due to its function in converting acetylcholine into acyl and choline …
Published in International Journal of Genetic Modifications and Recombinations · Vol. 1, Issue 2, 2023 · pp. 07–19 Read article
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Investigating The Alkalizing Potential of Chandanasava For Restoring Acid-Base Homeostasis in Renal Tubular Acidosis: A Computational and In Silico Pharmacological Study
Abstract: Chandanasava, a traditional Ayurvedic formulation, is recognized for its potential alkalizing properties, which may help restore acid-base homeostasis in conditions such as renal tubular acidosis (RTA). This study aims to investigate the active components of Chandanasava and their interactions with key renal target proteins, Pendrin and Carbonic Anhydrase II, which are essential for maintaining acid-base balance. An in silico approach was utilized to explore the pharmacological potential of the phytochemicals …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 3, Issue 2, 2025 · pp. 28–52 Read article
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In Silico Drug Design for Mycobacterium tuberculosis and Development of Host–Pathogen Interaction Network and Molecular Docking Procedures
Abstract: Objective: A leading cause of illness is the contagious disease tuberculosis (TB), this infection with Mycobacterium tuberculosis complex (MTBC) particularly M. tuberculosis and M. africanum, is what causes tuberculosis. Diverse receptor proteins (mycobacterial proteins) with various 3D structures and functions were evaluated to access the multi-domain antimycobacterial action of ligands. The specific receptor proteins PDB ID: 3PTY, PDB ID: 4OW8, PDB ID: 5KWA, and PDB ID: 3ZXR, were opted for …
Published in International Journal of Molecular Biotechnological Research · Vol. 1, Issue 1, 2023 · pp. 1–19 Read article
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Prediction of Molecular Targets for Anthraquinone and Its Analogs for Treatment of Good Pasteur Syndrome
Abstract: Objective: In order to find prospective molecular targets for the treatment of Good Pasteur Syndrome (GPS), a rare autoimmune disease that affects the kidneys and other organs, computational methods and network pharmacology were applied in this work. The goal of the study is to identify particular human proteins that might interact with anthraquinone and its analogues as well as to uncover potential mechanisms of action by which these drugs might …
Published in International Journal of Bioinformatics and Computational Biology Read article
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A Computational Study to Elucidate the Phytochemicals as An Antagonist Against Pruritis in Psoriasis
Abstract: Objective: Psoriasis is a chronic, non-contagious, auto-immune skin disorder that causes inflammation, pain, and itching in the affected areas. The etiology of this condition is not entirely understood, and while there are treatments available to manage the symptoms, there is currently no cure. The Transient receptor potential cation channel, subfamily Vanillin, member 3 (TRPV3), present in keratinocytes, allegedly had a part in the development of psoriasis-related pain and itching. Specifically, …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 1, Issue 2, 2023 · pp. 49–61 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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Molecular Dynamics and Therapeutic Architectures of Cannabinoid Receptors: A Comprehensive Review
Abstract: Expanding on these foundations, recent structural biology studies using cryo-electron microscopy have provided high-resolution insights into the conformational dynamics of CB₁ and CB₂ receptors. These findings have enabled a more precise understanding of ligand–receptor interactions, particularly how agonists, antagonists, and reverse agonists stabilize distinct receptor states. Such knowledge is critical for rational drug design, allowing researchers to selectively modulate downstream signaling pathways. For instance, CB₁ receptors primarily couple to Gi/o …
Published in International Journal of Cheminformatics · Vol. 4, Issue 1, 2026 · pp. 36–40 Read article
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A Molecular Docking Study: Targetting HIV-1 Integrase Protein Against Selected Phytocompounds from Calophyllum Lanigerum
Abstract: Objectives: The most common form of HIV that causes AIDS is HIV-1. The World Health Organization has estimated roughly 75 million plus HIV-1 infections till date and roughly 40 million deaths (as of 2021). Thus, this study was done to identify natural compounds from Calophyllum lanigerum, a medicinal plant largely endemic to South-East Asia, to inhibit the spread of this disease. It did so by using molecular docking methods, Lipinski …
Published in International Journal of Molecular Biotechnological Research · Vol. 1, Issue 2, 2023 · pp. 43–55 Read article
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Molecular Docking Studies of Nyctanthes arbor-tristis Phytochemicals for Targeting TNF Receptor in Arthritis
Abstract: Rheumatoid Arthritis is an autoimmune disorder which results in inflammation. Tumor necrosis factor-alpha (TNF-α) is responsible for the progression of inflammatory arthritis by promoting immune cell activation and cytokine release. The present study explores the potential of bioactive compounds derived from Nyctanthes arbor-tristis (Parijat) in modulating TNF receptor activity through molecular docking. Computational methods were employed to evaluate the binding affinity of selected phytocompounds from N. arbor-tristis against the extracellular …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 3, Issue 2, 2025 · pp. 11–21 Read article
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Drug Repurposing of Anticancer Agents JP-8g and REDX05358 Against the Target Protein Plectin 1a in Epidemolysis Bullosa Simplex with Muscular Dystrophy (EBS-MD)
Abstract: Epidermolysis Bullosa Simplex with Muscle Dystrophy is a genetic disease affecting the skin and muscles which can be seen at birth or start at adulthood due to the mutation in the protein Plectin 1a (PLEC gene) causing skin blisters and muscle weakness. This protein is seen in sarcolemma, Z disks in skeletal muscles, hemidesmosomes in skin and cardiac muscles giving stability to cytoskeleton, playing a crucial role in neuromuscular transmission …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 3, Issue 2, 2025 · pp. 22–34 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