Search
54 articles for “drug-target affinity”
-
Ligand Based Drug Virtual Screening in Computer Aided Drug Design: A Review
Abstract: Computer-Aided Drug Design (CADD) has revolutionized the drug discovery process by providing efficient and cost-effective methods for identifying potential drug candidates. Within CADD, ligandbased virtual screening techniques play a pivotal role in the early stages of drug discovery. This review provides a comprehensive overview of ligand-based drug virtual screening, focusing on its principles, applications, challenges, and future directions. Fundamentals of ligand-based virtual screening, including pharmacophore-based methods, similarity searching, and machine …
Published in Research & Reviews: A Journal of Drug Formulation, Development and Production · Vol. 11, Issue 2, 2024 · pp. 1–8 Read article
-
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
-
Computational Exploration of Bhrijraj-derived Phytochemicals as Potential Anti-inflammatory Agents: A Molecular Docking Study with Cyclooxygenase-II Complex
Abstract: The molecular docking analysis was meticulously conducted using state-of-the-art computational tools, notably Chimera and Python. These tools were employed to unravel the complex interactions between the identified phytochemicals from Bhrijraj and the target protein, COX-II. The 3D structures of the phytochemicals were prepared with precision using ChemSketch, ensuring accuracy in the subsequent molecular docking simulations. This rigorous approach enhances the reliability and validity of the findings. This research aims to …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 1, 2024 · pp. 31–37 Read article
-
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
-
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
-
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
-
Computational Investigation of Withania somnifera Compounds Targeting S. pombe SMN YG-Dimer in 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
-
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
-
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
-
In Silico Exploration of Podophyllum Hexandrum-Derived Phytocompounds as Potential Therapeutics Against Small Cell Lung Cancer (SCLC): A Molecular Docking Approach
Abstract: Small Cell Lung Cancer (SCLC) is a fast-growing and aggressive type of lung cancer that spreads quickly strongly associated with smoking. It is characterized by symptoms, such as persistent cough, breathing difficulties, or hoarseness, though it can sometimes be asymptomatic which makes early detection challenging. The tumor suppressor gene TP53 is critical in regulating the cell cycle and preventing uncontrolled cell division. Mutations in TP53 result in the loss of …
Published in International Journal of Molecular Biotechnological Research · Vol. 3, Issue 1, 2025 · pp. 1–11 Read article
-
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
-
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
-
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
-
Computational Simulations in Drug Discovery: Modeling Protein Folding and Drug Binding
Abstract: Computational simulations have become essential tools in drug discovery, offering unprecedented insights into molecular behavior at the atomic level. These simulations, particularly in the domains of protein folding and drug binding, allow for the exploration of complex biological systems that are often difficult to study experimentally. Protein folding, a critical aspect of drug discovery, involves the transition of a polypeptide chain from an unfolded to a biologically active structure. Understanding …
Published in Research and Reviews : Journal of Computational Biology · Vol. 14, Issue 1, 2025 · pp. 23–29 Read article
-
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
-
Targeting Dystrophin Restoration and Neuroprotection in Duchenne Muscular Dystrophy: Insights from Withania somnifera
Abstract: Duchenne muscular dystrophy is a genetic disorder. This disease affects men more common than women. Main objective of the present study was to identify the naturally active phytocompounds from Withania somnifera (Ashwagandha). Ashwagandha has a great value in the field of Ayurveda and Indian medicine and is used for treating muscular and neurological disorders. Toxicity prediction, molecular docking, statistical information, drug illness prediction, and Absorption, distribution, metabolism, excretion, and toxicity …
Published in Research and Reviews: A Journal of Pharmaceutical Science · Vol. 15, Issue 2, 2024 · pp. 64–84 Read article
-
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
-
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
-
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
-
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 Read article