molecular docking
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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
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In Silico Molecular Docking Studies of Phytocompounds from Melissa officinalis Against MPXV Poxin Target
Abstract: Objectives: This study aimed to evaluate the inhibitory potential of phytocompounds of Melissa officinalis against the MPXV poxin protein target, a key virulence factor in monkeypox infection. Methods: Molecular docking performed using PyRx, a virtual screening software, was conducted to predict the binding affinities of the compounds to MPXV poxin. Prior to docking, the compounds were subjected to comprehensive analysis, including Lipinski's rule of five, evaluation of physicochemical properties, pharmacological …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 2, 2024 · pp. 25–38 Read article
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An Insilico Study of Isobutrin and Phosphorylase Kinase - A Ray of Hope for Psoriasis Patients – Clinical Hypothesis
Abstract: Psoriasis is a chronic, hyper-proliferative and inflammatory skin disease. Increased levels of the calmodulin-containing enzyme, namely, phosphorylase kinase (PhK), were observed in the human epidermis of the active psoriasis cases. Thus PhK is a potential biomarker for the diagnosis and progression of the skin disease, namely, psoriasis. The search for the potential molecules that could supress the over expression of PhK is underway and any break-through in this direction leads …
Published in International Journal of Cheminformatics · Vol. 2, Issue 1, 2024 · pp. 1–8 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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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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Modern Computer-aided Drug Design Methods: A Review
Abstract: Computer-aided drug design (CADD) has emerged as a crucial tool in the drug discovery process, offering a time-efficient and cost-effective approach to identifying potential drug candidates. This review aims to provide an overview of modern CADD methods, including high-throughput screening (HTS), structure-based drug design (SBDD), ligand-based drug design (LBDD), structure-based virtual screening (SBVS), and ligand-based virtual screening (LBVS). We discuss the basic principles, applicability, and limitations of each method, highlighting …
Published in Research and Reviews: A Journal of Dentistry · Vol. 15, Issue 2, 2024 · pp. 14–20 Read article
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Quantitative Structure-activity Relationship in Computer-aided Drug Design: A Review
Abstract: Quantitative Structure-Activity Relationship stands at the forefront of Computer-Aided Drug Design, providing a systematic framework for understanding the relationship between the chemical structure of molecules and their biological activity. The present review delves into the multifaceted realm of quantitative structure-activity relationship methodologies within the landscape of drug discovery. Through an exploration of diverse quantitative structure-activity relationship models, molecular descriptors, validation techniques, and recent advancements, the present article aims to elucidate …
Published in Research and Reviews: A Journal of Pharmaceutical Science · Vol. 15, Issue 2, 2024 · pp. 55–63 Read article
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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
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A Review on Anesthetic Drug Discovery with Computer Aided Drug Design
Abstract: In contemporary medicine, anaesthesia is essential for enabling surgical procedures, pain control, and patient comfort. Finding and creating safe and efficient anaesthetics is crucial to enhancing patient outcomes and developing the medical field. In this review, we provide a comprehensive overview of anesthetic drug discovery with a focus on the integration of computer-aided drug design (CADD) methodologies. Beginning with an exploration of anesthesia mechanisms and targets, we delve into the …
Published in International Journal of Antibiotics Read article
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Characterization of Synthesized Heterocyclic Oxadiazole Derivatives Using Mass, UV, IR, and NMR Spectroscopy, Among other Spectroscopic Techniques: Review
Abstract: The current study synthesized and assessed 3-heteroarylazo 4-hydroxy coumarin derivatives' initial antibacterial activities in vitro against four distinct pathogenic bacterial strains, including Pseudomonas aeruginosa, Bacillus subtilis, Escherichia coli, and Staphylococcus aureus. Ampicillin, a common medication, was used to compare each compound's antibacterial properties. UV, IR, 1H NMR, mass spectroscopy, and X-ray diffraction examinations were used to analyze the compounds. By using UV–vis spectra, the solute-chromic behavior of these compounds was …
Published in International Journal of Photochemistry and Photochemical Research · Vol. 1, Issue 1, 2023 · pp. 28–33 Read article
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Analysis of Bioinformatics Software Applied in Computer-Aided Drug Design
Abstract: The integration of bioinformatic tools with computational methods has revolutionized the field of Computer-aided Drug Design (CADD), enabling researchers to expedite the discovery and optimization of new therapeutics. This review provides an in-depth analysis of the bioinformatic tools utilized in CADD, encompassing molecular docking, molecular dynamics simulation, virtual screening, homology modelling, and molecular visualization. We go over the tenets, approaches, and uses of these instruments, emphasizing their value in expediting …
Published in Research & Reviews: A Journal of Drug Design & Discovery · Vol. 11, Issue 2, 2024 · pp. 1–10 Read article
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Computer Aided Drug Designing for Targeted Drug Delivery Systems
Abstract: The discovery and development of a contemporary sedate is widely acknowledged as an extremely difficult task that requires significant resources and effort. Therefore, computer-aided medication design techniques are widely utilized today to increase the productivity of the drug discovery and development process. Among structure-based and ligand-based drug design approaches, both recognized for their efficiency in drug discovery and development, various CADD (Computer-Aided Drug Design) techniques are evaluated based on specific …
Published in Trends in Drug Delivery · Vol. 11, Issue 2, 2024 · pp. 34–41 Read article
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Unveiling Nature’s Potential: In Silico Exploration and Identification of Herbal Remedies for Major Depressive Disorder Through Molecular Interaction Studies
Abstract: Major depressive disorder (MDD), a globally discussed mental health condition, has drawn significant attention because of its unique and intricate nature. This is marked by the enduring presence of negative emotions stemming from a lack of interest, diminished self-esteem, and excessive rumination. Despite the widespread availability of various antidepressant medications, their effectiveness is hindered by low response rates, prolonged treatment durations, and the prevalence of side effects, such as headaches, …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 1, 2024 · pp. 54–62 Read article
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Exploring Glucagon-like peptide-1 as a Target Protein for Diabetes Mellitus Treatment: Molecular Docking and Pharmacokinetic Analysis of Phytocompounds from Momordica charantia
Abstract: Objective: This study aimed to use molecular docking techniques to explore the potential of GLP-1 (glucagon-like peptide-1) as a target protein for the treatment of diabetes mellitus, a chronic metabolic disease marked by elevated blood glucose levels. Given its crucial role in maintaining insulin secretion and glucose homeostasis, GLP-1 may serve as a future target for diabetes therapy. Method: The study employed a multi-phase method. Initially, protein extraction was carried …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 2, Issue 1, 2024 · pp. 8–20 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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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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Computational Screening of Vitex negundo Compounds for Potential Arthritis Therapies in India
Abstract: Objective: Arthritis is a pervasive medical condition that manifests as inflammation and discomfort within the joints. As of September 2021, arthritis has affected an estimated 180 million people in India, making it a substantial public health concern with a considerable impact on individuals' quality of life and healthcare systems. Therefore, using molecular docking, drug-likeness prediction, and ADME analysis, an effort was made to identify natural compounds from Vitex negundo, which …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 1, 2024 · pp. 01–18 Read article
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In Silico Assessment of Demethoxycurcumin: Molecular Docking and Computational Insights into its various therapeutic Potential
Abstract: Natural compounds are increasingly explored for their therapeutic potential in medical research. Here, we focused on demethoxycurcumin (DMC), a polyphenolic bioactive compound extracted from Curcuma longa, commonly found in turmeric. DMC, with a chemical formula of C20H18O5 and a molecular weight of 340 g/mol, possesses two aromatic ring systems, each featuring a β-diketone moiety connected by a seven-carbon chain. This unique structure allows DMC to engage in tautomerism, which is …
Published in Research & Reviews: A Journal of Drug Design & Discovery · Vol. 11, Issue 1, 2024 · pp. 9–15 Read article
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In Silico Investigation of 2,3-Dihydrobenzofuran from Centella asiatica: A Possible Pioneer in the Management of Tetanus
Abstract: Objective: Tetanus toxin (TeNT) is a neuroprotein toxin, the most toxic known. They have three functional domains and are structurally similar. They possess an N-terminal catalytic section (light chain), an internal domain for heavy-chain translocation (HN domain), and a C-terminal receptor binding domain for the heavy chain (Hc domain or RBD). Tetanus, an acute nerve-affecting disease, is provoked by a toxin-producing bacterium called Clostridium tetani. This bacterium is environmental, Gram-positive, …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 1, 2024 · pp. 19–30 Read article
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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