Syllabus

Principles of Target Identification – Disease mechanisms, target validation, and druggability assessments, Predicting Novel Targets via Whole Transcriptome Sequencing, Mass Spectrometry Based Proteomics in Target Discovery, Chemoproteomics, Mechanism-Centric Proteomics for Target Validation. 3D Structure Prediction – Experimental Structure Prediction, Biological Databases, Homology Modeling, Ab Initio and Threading Methods, AI in Structure Prediction.

Molecular Docking – Binding Site Analysis, Fundamentals of Molecular Docking, Scoring Functions, Search Algorithms, Protein-Ligand Docking, Antigen-Antibody Docking, Protein-Protein Docking, Preparing Protein and Ligand for Docking, Virtual Screening (HTVS), Advanced Docking Techniques, Post-Docking Analysis, Docking Software.

Molecular Dynamics Simulation - Fundamentals of Molecular Dynamics, Computational Requirement, System Preparation, Force Fields, Energy Minimization, Heating, and Equilibration Steps, Trajectory Analysis, Free Energy Calculations (MM-PBSA and MM-GBSA), Advanced MD Applications

Computational Design of Small RNA Therapeutics - Introduction to RNA Therapeutics, Sequence Design and Target Accessibility, Off-Target Prediction, Thermodynamic Profiling, Ensuring Internal RNA Duplex Stability, RNA-Protein Docking (Structural Biology), In Silico Chemical Modifications, Delivery System Design.

The first module enables students to identify and validate novel drug targets using whole transcriptome sequencing, mass spectrometry-based proteomics, bioinformatics, and AI-driven 3D structure prediction tools.

The second module aims to equip students with computational virtual screening skills to simulate, optimize, and analyze protein-ligand interactions utilizing advanced docking algorithms and scoring functions.

In the third module, students will apply molecular mechanics principles to evaluate the thermodynamic stability and conformational flexibility of targeted protein-ligand complexes using advanced molecular dynamics simulations.

In the fourth module, learners will master computational tools to design and optimize small RNA therapeutics, focusing on sequence bioinformatics, structural RNA-protein docking, and lipid nanoparticle delivery system simulations.

Students will identify and validate drug targets utilizing transcriptomics and chemoproteomics and predict three-dimensional protein structures using advanced bioinformatics tools and artificial intelligence modeling algorithms.

Students will execute comprehensive virtual screening workflows, applying diverse scoring functions and search algorithms to accurately model, simulate, and analyze complex molecular docking interaction profiles.

Students will implement molecular mechanics principles and force fields to prepare, simulate, and analyze molecular dynamics trajectories, computing the thermodynamic stability of target biomolecular complexes.

Students will master computational strategies to optimize small RNA therapeutics, focusing on sequence design, structural RNA-protein docking, chemical modifications, and simulating lipid nanoparticle delivery systems.

Andrew R. Leach, Molecular Modelling: Principles and Applications, Prentice Hall , Target Modules: Module 2 (Molecular Docking) & Module 3 (Molecular Dynamics Simulation).

John Parrington and Kevin Coward, Comparative Genomics and Proteomics in Drug Discovery, Taylor & Francis Group , Target Module: Module 1 (Target Identification & 3D Structure Prediction).

Irina Vlasova-St. Louis, RNA Therapeutics: History, Design, Manufacturing, and Applications , IntechOpen , Target Module: Module 4 (Computational Design of Small RNA Therapeutics).

Kunal Roy, Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development, Elsevier , Target Modules: Module 2 (Molecular Docking) and Module 3 (Molecular Dynamics Simulation)

Dinh-Toi Chu and Van Thai Than, RNA Therapeutics Part A & B (Volumes 203 & 204), Academic Press , Target Module: Module 4 (Computational Design of Small RNA Therapeutics).

Mithun Rudrapal and Chukwuebuka Egbuna, Computer Aided Drug Design (CADD): From Ligand-Based Methods to Structure-Based Approaches, Elsevier , Target Modules: Module 1, Module 2, and Module 3.