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168 articles for “protein-protein docking”
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In Silico Screening of Terminalia chebula Phytocompounds as Potential Inhibitors of NTCP and DDB1 in Hepatitis B Virus Infection
Abstract: Hepatitis B virus (HBV) infection is a major global health concern, and chronic carriers are at risk of developing cirrhosis, hepatocellular carcinoma (HCC), and even death. Existing treatments can effectively inhibit viral replication, but they achieve little eradication of the virus because of covalently closed circular DNA (cccDNA) retention. In this investigation, bioactive compounds of Terminalia chebula, a plant known for its hepatoprotective and antiviral properties in traditional medicine, were …
Published in Research & Reviews: A Journal of Drug Formulation, Development and Production · Vol. 13, Issue 1, 2026 · pp. 33–44 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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Molecular Docking Analysis of Berberis aristata Phytocompounds as Potential Growth Factor Receptor Blockers in Cancer Therapy
Abstract: Middle-aged and older women are susceptible to breast cancer (BC), a potentially fatal condition. When breast cancer is diagnosed, the median age is 62. Breast cancer diagnoses in women under 45 are comparatively uncommon, whereas the bulk of breast cancer diagnoses occur in women 62 and older. Growth factor receptors are interesting therapeutic targets because of their critical role in the pathophysiology of cancer. Vascular endothelial growth factor receptors (VEGFR-2) …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 3, Issue 2, 2025 · pp. 1–10 Read article
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Screening Phytocompounds of Tinospora cordifolia to Find Potential Drug Targets for Cystic Fibrosis
Abstract: This study aimed to evaluate the therapeutic potential of phytocompounds derived from Tinospora cordifolia in treating cystic fibrosis (CF), a genetic disorder caused by mutations in the CFTR gene that lead to severe respiratory and digestive complications. Phytocompounds were retrieved from the IMPPAT database and subjected to molecular docking simulations using PyRx to assess their binding affinity to the CFTR protein. The top-scoring compounds – sterol, magnoflorine, tembetarine, kaempferol, and …
Published in International Journal of Genetic Modifications and Recombinations · Vol. 3, Issue 1, 2025 · pp. 16–24 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 · Vol. 1, Issue 3, 2023 · pp. 10–27 Read article
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Emerging Therapeutic Discovery Against Escherichia coli Infection by Rational Inhibition of Fatty Acid Responsive Transcription Factor: Theoretical Molecular Investigations of Some Metabolites as Inhibitors of Fatty Acid Metabolism Protein
Abstract: For the discovery of effective agent for overcoming resistance against Escherichia coli (E. coli) bacteria by modulating Fatty Acid Metabolism Protein (FadR)—a Fatty Acid Responsive Transcription Factor. The present study involved discovery of some metabolites of furan, furan-2-yl, macrolactin, and chromene scaffold via in silico structure-based drug design (SBDD) technique by utilizing the Maestro 9.1 software. The study will provide clues, motivate, and throw light on imperative aspects for the …
Published in Research and Reviews : Journal of Computational Biology · Vol. 7, Issue 3, 2018 · pp. 1–7 Read article
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Neuro-Symbolic Agentic AI for Autonomous Scientific Discovery: Integrating Deep Reinforcement Learning, Quantum Simulation, and XAI-Audited LLM Hypothesis Generation in Drug Target Identification
Abstract: The exponential growth of multi-omics data and the increasing complexity of disease-associated protein interactomes have rendered conventional drug target identification pipelines computationally and epistemologically inadequate. This paper presents the Neuro-Symbolic Agentic AI for Scientific Discovery (NS-AASD) framework, a unified architecture that cohesively integrates deep reinforcement learning (DRL) exploration strategies, variational quantum simulation (VQS) of protein conformational dynamics, and XAI-audited large language model (LLM) hypothesis generation within an autonomous scientific discovery …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 · pp. 15–24 Read article
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Molecular Docking Approach on Thiazolidinedione Analogs as HIV-1-RT Inhibitors
Abstract: Potentially life threatening condition due to chronic syndrome caused by human immunodeficiency virus (HIV) is known as Acquired immunodeficiency syndrome(AIDS).Virus weakens the immune system of human being and body’s ability to fight against the organism, thereby causing the disease. When a person becomes infected with HIV, the virus attacks and weakens the immune system. In the given study, molecular docking study was performed on 30polysubstitutedThiazolidinedione (TZD) analogs as HIV-1 reverse …
Published in Research & Reviews: A Journal of Bioinformatics · Vol. 7, Issue 1, 2020 · pp. 1–6 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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Computational Analysis of Tinospora Cordifolia Phytochemicals as Potential Inhibitors of BRCA1-BRCT Domain Interaction in Breast Cancer
Abstract: Breast cancer is a leading cause of cancer-related deaths worldwide, accounting for a significant proportion of mortality rates among women. Despite current therapeutic approaches, the disease remains characterized by molecular heterogeneity, making it challenging to develop effective treatments. This study explores the potential of Tinospora cordifolia, a medicinal plant, in breast cancer therapy. Guduchi, scientifically known as Tinospora cordifolia, boasts a centuries-long history of use in traditional medicine, with a …
Published in International Journal of Molecular Biotechnological Research · Vol. 3, Issue 1, 2025 · pp. 27–37 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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Network Pharmacological Studies in Biological Interactions of Thymoquinone
Abstract: Thymoquinone, a bioactive phytochemical compound belonging to the class of benzoquinones, is prominently present in the plant Nigella sativa. Despite its widespread use, the precise molecular mechanisms underlying its beneficial effects remain elusive. To address this gap, we employed network pharmacology to investigate the actions of Thymoquinone (TQ). Our methodology encompassed the utilization of diverse bioinformatic tools to scrutinize this molecule of interest comprehensively. Initially, we retrieved the chemical structure, …
Published in Research and Reviews : Journal of Crop science and Technology · Vol. 12, Issue 3, 2023 · pp. 18–25 Read article
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Molecular Docking of Compounds against Dengue Virus Serotype 2 and Prediction of ADME Properties Using Computational Approaches.
Abstract: Objective: Human lives are now seriously threatened by dengue fever, which is brought on by the dengue virus (DENV). It is well known that phytochemicals have a great deal of promise for curing human viral, bacterial, and fungal diseases. The purpose of this research was to develop drugs against the nonstructural protein (NS5) of dengue virus 2 (DENV2).Methods: Five phytochemicals from various medicinal plants were chosen for this research. The …
Published in Research and Reviews : Journal of Computational Biology · Vol. 12, Issue 1, 2023 · pp. 1–11 Read article
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Computational Identification of Protein Tyrosine Phospatase-1B (PTP-1B) Inhibitors for Checking Type II Diabetes
Abstract: Protein tyrosine phosphatases (PTPs) are a family of enzyme that comprises of about 100 proteins which catalyze dephosphorylation of phosphotyrosine residues in protein substrates. Phosphotyrosine is a central element in cell signaling, and its activity is essential for cellular homeostasis and for appropriate responses to extracellular signals. PTP-1B antagonizes insulin signaling by reducing the activation state of the insulin receptor kinase, thereby inhibiting post-receptor signaling in insulin responsive tissue. The …
Published in Research and Reviews : A Journal of Medical Science and Technology · Vol. 6, Issue 3, 2017 · pp. 21–25 Read article
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Exploring Phytochemicals from Ricinus Communis for Potential Therapeutic Applications in Rheumatoid Arthritis: An in-Silico Approach
Abstract: Aim: Rheumatoid arthritis (RA) is a long-term autoimmune condition characterized by the immune system mistakenly attacking the joints, leading to swelling, discomfort, and joint deformities. Current management strategies include anti-rheumatic drugs and biologics, which have limitations. This study aims to explore the therapeutic potential of Ricinus communis (castor bean plant) phytochemicals as plant-based therapies for autoimmune conditions, like RA. Methods: Phytochemicals from Ricinus communis were retrieved using the IMPPAT database, …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 3, Issue 1, 2025 · pp. 32–41 Read article
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In Silico Prediction of Multitarget Mechanism of Quinoline and Its Analogs on Phosphoinositide-3-Kinase Pathway Proteins
Abstract: Objective: Phosphoinositide 3-kinases (PI3Ks), the target of rapamycin (PI3K/Akt/mTOR, PAM), are a family of enzymes that play a role in the growth, proliferation, differentiation, motility, survival, and intracellular trafficking of cells, all of which are essential for healthy cellular function and are also connected to cancer. In this study, quinoline and its derivatives were employed to analyze its inhibition activity on the phosphoinositide-3-kinase pathway. Methods: In this work, eight phytocompounds …
Published in International Journal of Molecular Biotechnological Research · Vol. 1, Issue 1, 2023 · pp. 57–76 Read article
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Epitope-Based Peptide Vaccine Design Against Nuclear Protein EBNA3C of Epstein-Barr Virus: An Approach to Treat Multiple Sclerosis
Abstract: Almost 95% of the world’s population is affected by the Epstein-Barr virus (EBV); it is an oncogenic virus of herpes virus family. The nuclear protein Epstein-Barr nuclear antigens (EBNA)-3C of EBV are related to multiple sclerosis (MS) which is an inflammatory disease of the nervous system. Regardless of multiple occurrences of infections due to EBV and shortage of licensed antiviral drugs, there is not much advancement on vaccine designed for …
Published in Research and Reviews : A Journal of Life Sciences · Vol. 9, Issue 1, 2019 · pp. 62–72 Read article
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In Silico Analysis and Molecular Docking Studies of COX-2 Inhibitors for Anti-Inflammatory Activity
Abstract: Although nonsteroidal anti-inflammatory drugs (NSAIDs) are frequently used to treat pain, lower fevers, and control inflammation, they frequently cause gastrointestinal side effects because they inhibit the COX-1 and COX-2 enzymes. Despite their effectiveness and lack of gastrointestinal side effects, selective COX-2 inhibitors have been linked to cardiovascular risks. To find new COX-2 inhibitors that are safer and more effective, this study uses in silico techniques, such as molecular docking and …
Published in International Journal of Molecular Biotechnological Research · Vol. 3, Issue 1, 2025 · pp. 38–55 Read article
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Advancements in Drug Design Technology and Its Impact on COVID-19 Treatment
Abstract: The deadly coronavirus disease 19 (COVID-19) pandemic has recently spread, raising concerns about global health. The search for novel therapeutic compounds is made more necessary by the persistent problem of the absence of licensed medications or vaccinations. By saving money and time, computer-aided drug design has sped up the process of finding and developing new drugs. The structured-based and ligand-based drug discovery subcategories of computer-aided drug design (CADD) are the …
Published in International Journal of Virus Studies · Vol. 1, Issue 1, 2024 · pp. 1–15 Read article
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Multifarious Pharmacotherapeutic Perspectives of Some Natural Bromophenol Compounds: In silico Enzyme Inhibitory Potentials
Abstract: The process of drug discovery, design, and development often designated as 3Ds has played enormous role in modern era. The present research investigation includes in silico exploration of possible pharmacological potentials of bromophenol compounds by the aid of Schrodinger Maestro 9.1 software against six pharmacotherapeutic targets; Dipeptidyl peptidase (anti-diabetic), Angiotensin-1-Converting Enzyme (anti-hypertensive), Cyclin-Dependent Kinase-5 (anti-cancer), Protein kinase C (anti-cancer), Lipoxygenase-5 (anti-inflammatory), and Cycloxygenase-2 (anti-inflammatory). The docking scores, referred to as …
Published in Research & Reviews: A Journal of Drug Design & Discovery · Vol. 6, Issue 2, 2019 · pp. 24–29 Read article