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- 1. IN-SILICO DRUG DESIGN computational Biology – YBT303 Submitted to presented by Ms p Mala M.Muthulakshmi Assistant professor II M.sc Biotech Department of biotechnology 123011356013 pmist
- 2. CONTENTS • Introduction • In- silico drug design • Methods • Structure based drug design methods • Applications • Conclusion • MCQ • Reference
- 3. INTRODUCTON • Drug discovery and development is an intense, lengthy and an interdisciplinary endeavor. • Drug discovery is mostly portrayed as a linear, consecutive process that starts with target and lead discovery, followed by lead optimization and pre-clinical in vitro and in vivo studies. • To determine if such compounds satisfy a number of pre-set criteria for initiating clinical development.
- 4. IN-SILICO DRUG DESIGN • In silico methods can help in identifying drug targets via bioinformatics tools. • It can also be used to analyze the target structures for possible binding/ active sites. • Generate candidate molecules, check for their drug likeness , dock these molecules with the target. • IN SILICO DRUG DESIGN METHODS a) Structure-based drug design (SBDD) b) ligand-based drug design (LBDD)
- 5. STRUCTURE BASED DRUG DESIGN • SBDD is a method used in drug design to develop new drugs based on the three-dimensional (3D) structure of a target protein that is associated with a specific disease. • The process involves several steps, including the identification of a therapeutic target and active ligands, determination of the 3D structure of the target protein. • The methods used in SBDD are described below.
- 6. TARGET DETERMINATION AND STRUCTURE GENERATION • Drug target identification is a crucial step in the drug design process, where a specific biomolecule is targeted for the treatment of a particular disease. • SBDD starts determining and validating the target protein’s 3D structure. • Target protein can be determined using both experimental techniques (NMR or X-ray crystallography) and computational techniques (homology modeling and protein folding).
- 7. BINDING SITE PREDICTION • To identify the binding site. • A binding site is a specific region on a protein surface where a ligand molecule binds and interacts with the protein to produce a specific biological effect.
- 8. LIGAND SEARCH • Ligand search is the process of identifying potential ligands that can bind to a specific target protein or receptor. • Ligand search is virtual screening (VS), which is a computational approach used to identify potential ligands for drug discovery from large databases of compounds.
- 9. MOLECULAR DOCKING • Molecular docking is a computational technique used in drug design and screening to predict the interactions between ligands and target proteins. • The goal of molecular docking is to identify potential drug candidates by predicting their ability to form a stable complex with the target biomolecule. • It determines the correct binding conformation of ligands and proteins.
- 10. FRAGMENT-BASED DOCKING • In this approach, molecules are broken down into smaller fragments, and these fragments are screened for binding affinity with the target receptor. • They can provide important information about the key interactions that occur between the molecule and the receptor.
- 11. MOLECCULAR DYNAMICS SIMULATIONS • Molecular dynamics (MD) simulation is a computational technique used to study the physical behavior of atoms and molecules in a system, such as protein-ligand complexes. • MD simulations use mathematical algorithms to calculate the movements of atoms and molecules • These simulations can provide insights into the structure and function of proteins, drug-target interactions, and the behavior of molecules
- 12. APPLICATIONS • In silico drug design can be used to screen large databases of compounds and identify potential drug candidates. • It can be used to optimize the structure of potential drug candidates to improve their binding affinity, safety, efficacy, and other pharmacological properties • In silico methods can be used to predict the binding mode of a drug candidate to a target protein • In this design and identification of drug compounds to treat various diseases, including cancer, diabetes, and viral and bacterial infections
- 13. CONCLUSION • In silico drug design, also known as computer- aided drug design (CADD), is a crucial part of the drug discovery process. It uses computational methods to identify, develop, and optimize new drugs.
- 14. MCQ 1) What is the primary goal of in silico drug design? A)To synthesize new compounds B)To predict protein-ligand interactions C) To analyze clinical trial data D)To identify new targets for existing drugs 2) Which of the following software tools is commonly used for molecular docking? A) AutoDock B) BLAST C) ClustalW D) FASTA 3) Which of the following is a type of scoring function used in molecular docking? A) Force field B) Knowledge-based C) Empirical D) All of the above
- 15. 4) What is the difference between ligand-based and structure-based drug design? A) Ligand-based focuses on protein structure, while structure-based focuses on ligand properties B) Ligand-based focuses on ligand properties, while structure-based focuses on protein structure C) Ligand-based is experimental, while structure-based is computational D) Ligand-based is faster, while structure-based is more accurate 5) What is the purpose of molecular dynamics simulation in drug design? A) To predict protein-ligand interactions B) To analyze protein flexibility C) To optimize lead compounds D) To identify new targets
- 16. ANSWERS 1. B 2. A 3. D 4. B 5. B
- 17. REFERENCE 1) Jabalia, N., Kumar, A., Kumar, V., Rani, R. (2021). In Silico Approach in Drug Design and Drug Discovery: An Update. In: Singh, S.K. (eds) Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design. Springer, Singapore. https://doi.org/10.1007/978-981-15-8936-2_10 2) Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021). In silico methods and tools for drug discovery. Computers in biology and medicine, 137, 104851. https://doi.org/10.1016/j.compbiomed.2021.104851 3) Singh, S. K. (Ed.). (2021). Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design. doi:10.1007/978-981-15-8936-2 4) Yu, W. (2017). Computer-Aided Drug Design Methods. Methods in molecular biology (Clifton, N.J.), 1520, 85. https://doi.org/10.1007/978-1- 4939-6634-9_5
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