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Application of Computational and Bioinformatics Techniques in Drug Repurposing for Effective Development of Potential Drug Candidate for the Management of COVID-19
Published in Hajiya Mairo Inuwa, Ifeoma Maureen Ezeonu, Charles Oluwaseun Adetunji, Emmanuel Olufemi Ekundayo, Abubakar Gidado, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Medical Biotechnology, Biopharmaceutics, Forensic Science and Bioinformatics, 2022
Charles Oluwaseun Adetunji, Olaniyan Tope Olugbemi, Muhammad Akram, Umme Laila, Michael Olugbenga Samuel, Ayomide Michael Oshinjo, Juliana Bunmi Adetunji, Gloria E. Okotie, Nwadiuto (Diuto) Esiobu, Omotayo Opemipo Oyedara, Folasade Muibat Adeyemi
Molecular docking is an approach in drug repurposing which is used to study and analyze different interactions of various amino acids in the proteins and ligands. This technique is thus applied in order to anticipate the confirmation and accurate orientation of a molecule interacting and binding to another molecule resulting in a stable adduct. There are several programs to carry out molecular docking and these include Glide, Autodock Vina, and Gold, among others (Pagadala et al., 2017). In Glide Standard Precision protocol, for instance, the binding affinity of the ligand and predicting activity of a drug suitable against an infection can be carried out flexibly. At the end of docking analysis, the final free energy assessment is concluded by calculating what is known as the dock score, and the lower the dock scores, the better and efficient is the drug to fight against the infection. The docked ligands can also be visualized using applications such as Maestro interface, PyMOL, and Discovery studio (Kannadasan et al., 2016).
Macromolecular Architecture and Molecular Modelling of Dendrimers
Published in Neelesh Kumar Mehra, Keerti Jain, Dendrimers in Nanomedicine, 2021
Rahul Gauro, Keerti Jain, Vineet Kumar Jain, Neelesh Kumar Mehra, Harvinder Popli
In the field of molecular modelling, docking is a technique that predicts the preferred orientation of one molecule to another when bound together to form a stable complex. Knowledge of the desired orientation, in effect, can be used to predict the strength of the interaction or binding affinity between the two molecules by using, for example, the role of score. Associations between biologically related molecules, such as proteins, carbohydrates, nucleic acids and lipids, play a central role in the transmission of signals. In addition, the relative orientation of the two interactive partners can influence the type of signal produced (e.g. agonism vs. antagonism). Docking is therefore useful for predicting both the intensity and the form of signal generated. Docking is often used to predict the binding orientation of small molecule drug candidates to their protein targets in order to predict the affinity and behaviour of small molecules. Docking therefore plays a significant role in the ethical production of drugs. Considering the biological and pharmaceutical importance of molecular docking, significant efforts have been made to develop the methods used to predict docking (Joseph-mccarthy et al. 2003).
Computer-Aided Drug Design for the Identification of Multi-Target Directed Ligands (MTDLs) in Complex Diseases: An Overview
Published in Peter Grunwald, Pharmaceutical Biocatalysis, 2019
Molecular docking is a computational technique to find and measure the inter-molecular interactions between the ligand and the binding site of the target protein. Additionally, it helps in predicting the bioactive conformation as well as the probable binding energy (or docking score) that is computed using several available scoring functions (Ambure and Roy, 2016). Molecular docking technique is extensively used to screen big chemical databases to identify a set of ligands that can bind aptly to the target of interest and thus such study involves several ligands, but one target protein. However, a MTDD study usually involves a few or more ligands against multiple target proteins and since this approach is opposite to the usual molecular docking, thus it is termed as “inverse docking.” Initially inverse docking was employed to understand or find the side effects of known drugs by finding the “off-targets,” but the same approach can be successfully employed to find off-targets that will improve the desired pharmacological response (Rognan, 2010). Although inverse docking is a powerful technique to identify MTDLs, it should be noted that inverse docking is considerably time-consuming technique as it requires exhaustive protein structure preparation and usually the target flexibility issue is not addressed. Further, results can be affected based on the poor performance of scoring functions, so selection of appropriate scoring function (Perola et al., 2004) is important.
Phytochemical and biological characterization of aqueous extract of Vassobia breviflora on proliferation and viability of melanoma cells: involvement of purinergic pathway
Published in Journal of Toxicology and Environmental Health, Part A, 2023
Altevir Rossato Viana, Nathieli Bianchin Bottari, Vinícius Rodrigues Oviedo, Daniel Santos, James Eduardo Lago Londero, Maria Rosa Chitolina Schetinger, Erico Marlon Moraes Flores, Aline Pigatto, André Passaglia Schuch, Alexandre Krause, Luciana Maria Fontanari Krause
Molecular docking is a computational tool to predict and understand the interaction of a biologic macromolecule (e.g., a protein) with a small ligand (Silakari and Singh 2021). Thus, molecular docking may be used during virtual screening of new drugs (Menchaca, Juárez-Portilla, and Zepeda 2020), such as novel antioxidant agents. As mentioned previously, N-methyl-(2S,4 R)-trans-4-hydroxy-L-proline and calystegine B are two main components detected in V. breviflora extract. Thus, the interaction of such bioactive compounds against P2X7 and P2Y1 purinergic receptor was evaluated with molecular docking. The quantitative results obtained by molecular docking are presented in Table 3. ATP is the endogenous ligand that has the highest affinity for P2 receptors such as purinergic P2X7. According to the docking results, evidence indicates that bioactive compounds from V. breviflora as N-methyl-(2S,4 R)-trans-4-hydroxy-L-proline and calystegine B play a important role in the P2×7and P2Y receptors functions. These structures transformed our understanding of the conformational changes induced by bioactive compounds present in V. breviflora binding. The mechanism of ligand specificity, in P2 receptors for ligand docking suggesting that bio-compounds act as agonist molecules of P2 receptors.
Antibacterial and anticancer activity (PANC-1) of green synthesized copper oxide nanoparticles from Catharanthus roseus
Published in Inorganic and Nano-Metal Chemistry, 2023
S. Karthika, P. Kanchana, B. Prabha Devi, S. Shanmuga Sundari
Molecular docking is a significant tool for better understanding of binding interactions taking place between ligand and targeted proteins.[27] The crystal structures of Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and pancreatic ductal cell lines (PANC-1) proteins (PDB codes- 3T88, 5WZE, 5TW8 and 1 HNY, respectively) were obtained from the RCSB - PDB (Protein Databank). The proteins were initially stabilized by removing the water molecules using Autodock-4 software. The synthesized metal oxide ligands were built as pdb file using Open Bable software. Gasteigeric and Kollman united atomic charges were added to the metal oxide ligands and the receptors. Grid spacing was set using Autogrid-4. The created grid box permits the nanoparticles to rotate freely inside the protein to confirm the best binding energy. LGA is used as a global optimizer for energy minimization for docking simulation studies. The Cygwin software if finally used for the creating the autodock (dlg) and autogrid (glg) files. The docked conformers were visualized using Chimera software.
A facile and practical p-toluenesulfonic acid catalyzed route to dicoumarols and their biological evaluation
Published in Green Chemistry Letters and Reviews, 2023
Sadeq M. Al-Hazmy, Donia Bensalah, Najet Aouled Dlala, Younes Bouazizi, Houcine Ghalla, Naceur Hamdi
Molecular docking is a very valuable and popular tool used for drug discovery and design to create new therapies for diseases. This technique is used to predict and examine the conformations and binding interactions of a ligand in the active site of a target enzyme. Herein, molecular docking calculations were carried out to evaluate in silico the antimicrobial and antifungal activities of the synthesized compounds 2a–g and 3a–g. DNA gyrase and Mycobacterium tuberculosis-CYP51 are selected to explore the antimicrobial and antifungal activities, respectively. DNA gyrase protein has long been known as an efficient target for antibacterial drugs evaluation such as nalidixicacid and ciprofloxacin, and its inhibition results in the disruption of DNA synthesis and, subsequently, cell death (35,43).