Comprehensive resource covering computational tools and techniques for the development of cost-effective drugs to combat diseases, with specific disease examples Computational Methods for Rational Drug Design covers the tools and techniques of drug design with applications to the discovery of small molecule-based therapeutics, detailing methodologies and practical applications and addressing the challenges of techniques like AI/ML and drug design for unknown receptor structures. Divided into 23 chapters, the contributors address various cutting-edge areas of therapeutic importance such as neurodegenerative disorders, cancer, multi-drug resistant bacterial infections, inflammatory diseases, and viral infections. Edited by a highly qualified academic with significant research contributions to the field, Computational Methods for Rational Drug Design explores topics including: Computer-assisted methods and tools for structure- and ligand-based drug design, virtual screening and lead discovery, and ADMET and physicochemical assessments In silico and pharmacophore modeling, fragment-based design, de novo drug design and scaffold hopping, network-based methods and drug discovery Rational design of natural products, peptides, enzyme inhibitors, drugs for neurodegenerative disorders, anti-inflammatory therapeutics, antibacterials for multi-drug resistant infections, and antiviral and anticancer therapeutics Protac and protide strategies in drug design, intrinsically disordered proteins (IDPs) in drug discovery and lung cancer treatment through ALK receptor-targeted drug metabolism and pharmacokinetics Helping readers seamlessly navigate the challenges of drug design, Computational Methods for Rational Drug Design is an essential reference for pharmaceutical and medicinal chemists, biochemists, pharmacologists, and phytochemists, along with molecular modeling and computational drug discovery professionals.

Table of Contents:
List of Contributors xxi Preface xxvii 1 Molecular Modeling and Drug Design 1 Monalisa Kesh, Abhirup Ghosh, and Diptanil Biswas 1.1 Introduction 1 1.2 Types of Molecular Models 4 1.3 Computational Methods in Drug Discovery 7 1.4 Potential Use and Application of AI in Drug Designing 12 1.5 Limitations of Current Methods 14 1.6 Case Studies 16 1.7 Molecular Docking 17 1.8 Conclusion and Future Works 19 References 20 2 Bioactive Small Molecules and Drug Discovery 25 Ashish Shah, Vaishali Patel, Sathiaseelan Perumal, Riddhi Dave, Neha Zachariah, Ghanshyam Parmar, and Jay Mukesh Chudasama 2.1 Introduction 25 2.2 Importance of Computational Methods in Bioactive Small-Molecules Discovery 26 2.3 Natural Products in Bioactive Small-Molecule Discovery 30 2.4 Role of Density Functional Theory (DFT) Studies in Bioactive Small-Molecule Discovery 33 2.5 Application of DFT to Bioactive Small Molecules 34 2.6 Factors Affecting the Choice of Bioactive Molecules in Drug Discovery 36 2.7 Conclusion 43 References 43 3 Novel Drug Targets for Small Molecule-based Drug Discovery 49 Raghu Ram Achar, Ipsita Panigrahi, Aditi Singh, N. Chandana, and Shivananju Nanjunda Swamy 3.1 Introduction 49 3.2 Drug Target Identification 51 3.3 Classification of Novel Drug Targets 53 3.4 Small Molecules as Drugs 57 3.5 Conclusion 60 References 65 4 Computer-assisted Methods and Tools for Structure- and Ligand-based Drug Design 69 Saurav Kumar Mishra, Sneha Roy, Tabsum Chhetri, and John J. Georrge 4.1 Introduction 69 4.2 Structure-Based Drug Discovery Concept 69 4.3 Ligand-Based Drug Discovery Concept 81 4.4 Structure- and Ligand-Based Assisted Studies 84 4.5 Advancement and Challenges in SBDD and LBDD 90 4.6 Conclusion 90 References 91 5 Virtual Screening and Lead Discovery 97 Nisha Kumari Singh, Nigam Jyoti Maiti, Manshi Mishra, Shantanu Raj, Gourav Rakshit, Rahul Ghosh, and Sharanya Roy 5.1 Introduction to Virtual Screening and Lead Discovery 97 5.2 Molecular Targets and Biomolecular Structures 99 5.3 Virtual Screening Approaches 99 5.4 Databases and Compound Collections 101 5.5 Molecular Docking 102 5.6 Pharmacophore Modeling 104 5.7 Quantitative Structure–Activity Relationship (QSAR) 105 5.8 Machine Learning and AI in Virtual Screening 107 5.9 Hit-to-Lead Optimization 109 5.10 Case Studies and Examples 112 5.11 Challenges and Future Directions 114 5.12 Ethical and Regulatory Considerations 116 5.13 Conclusion 116 References 117 6 ADMET and Physicochemical Assessments in Drug Design 123 Ulviye Acar Çevik, Ayşen Işik, and Abdüllatif Karakaya 6.1 ADMET 123 6.2 Physicochemical Assessments 135 References 144 7 In Silico Modeling and Drug Design 153 Sonali S. Shinde, Sanket S. Rathod, and Sohan S. Chitlange 7.1 Introduction 153 7.2 Target Identification 154 7.3 Computer-Aided Drug Design 156 7.4 ADMET Assessment 160 7.5 Conclusion 160 References 161 8 Pharmacophore Modeling in Drug Design 167 Rahul Ghosh, Sharanya Roy, Gourav Rakshit, Nisha Kumari Singh, and Nigam Jyoti Maiti 8.1 Introduction 167 8.2 Essential Concepts in Pharmacophore Hypothesis Generation 170 8.3 Diverse Approaches to Pharmacophore Modeling 173 8.4 Application of Pharmacophore Modeling 176 8.5 Emerging Trends in Pharmacophore Model Development 180 8.6 Case Studies 183 8.7 Challenges in Pharmacophore Modeling 186 8.8 Conclusion 187 Acknowledgments 188 References 188 9 Scaffold Hopping and De Novo Drug Design 195 Shrimanti Chakraborty, Soumi Chakraborty, Biprajit Sarkar, Rahul Ghosh, Sharanya Roy, Nisha Kumari Singh, and Gourav Rakshit 9.1 Introduction 195 9.2 Scaffold Hopping 196 9.3 De Novo Drug Design 201 9.4 Results and Discussion 211 9.5 Software Tools for SH (Scaffold Hopping) and De Novo Design Selection 214 9.6 Case Study 214 9.7 Conclusion 215 References 216 10 Fragment-based Drug Design and Drug Discovery 221 André M. Oliveira and Mithun Rudrapal 10.1 Introduction 221 10.2 The Process of Finding Fragments 222 10.3 FBDD Strategies 227 10.4 Case Studies 228 10.5 Conclusion and Future Perspectives 230 References 232 11 AI/ML Approaches in Drug Design 237 Kevser Kübra Kırboğa 11.1 Introduction 237 11.2 Traditional Drug Design Methods 237 11.3 AI/ML Landscape in Drug Design 239 11.4 Ethics, Reliability, and Regulatory Issues 244 11.5 Future Directions 246 11.6 Conclusion 247 References 247 12 Network-based Methods in Drug Discovery 255 Ghanshyam Parmar, Ashish Shah, Jay Mukesh Chudasama, Priya Kashav, and Vanesa James 12.1 Introduction 255 12.2 Network Pharmacology: Practical Guide 260 12.3 Ayurveda and Traditional Indian Medicine 269 12.4 Network Pharmacology in Herbal Remedies 273 12.5 Conclusion and Future Prospects 277 References 278 13 Rational Design of Natural Products for Drug Discovery 285 Ankita Kashyap, Anupam Sarma, Bhrigu Kumar Das, and Ashis Kumar Goswami 13.1 Introduction 285 13.2 Natural Products for the Development of New Drugs 286 13.3 Criteria for Selecting Natural Products for Drug Design 288 13.4 Importance of Biodiversity in Sourcing Natural Products 288 13.5 Structural Elucidation of Natural Products 289 13.6 In Silico Computational Tools for Rational Drug Discovery from Natural Sources 290 13.7 Formulation Challenges with Natural Products 298 13.8 Quality by Design (QbD) Approaches 300 13.9 Conclusion 303 References 304 14 Design of Enzyme Inhibitors in Drug Discovery 311 Koyel Kar 14.1 Introduction 311 14.2 Importance of Enzyme Inhibition as a Strategy for Modulating Enzyme Activity 312 14.3 Classification of Enzyme Inhibitors 312 14.4 Strategies Employed in the Design and Development of Enzyme Inhibitors 314 14.5 Limitations and Challenges 321 14.6 Future Directions 321 14.7 Conclusion 322 References 322 15 Rational Design of Peptides and Protein Molecules in Drug Discovery 327 Ipsa Padhy, Abanish Biswas, Chandan Nayak, and Tripti Sharma 15.1 Introduction 327 15.2 Peptides as Therapeutics 328 15.3 New Technologies for Peptide-Based Drug Discovery 344 15.4 Computational Approaches in Peptide Drug Discovery 347 15.5 Conclusion 350 References 351 16 Rational Design of Drugs for Neurodegenerative Disorders 363 Priyanka Kamaria 16.1 Introduction 363 16.2 Common Mechanism of Neurodegeneration 364 16.3 Brief Overview of Computational Methods in Drug Design 365 16.4 Parkinson’s Disease as Prevalent Neurodegenerative Disorder 367 16.5 Conclusion 382 References 382 17 Rational Design of Anti-inflammatory Therapeutics 389 Kratika Singh, Anmol Gupta, Irum Siddiqui, Ashapurna Sinha, Mukesh Kumar Patwa, and Urmila Singh 17.1 Introduction 389 17.2 Navigating Inflammation and its Microenvironment 390 17.3 The Demand for Advanced Anti-inflammatory Medications 393 17.4 Natural Products Used for Anti-inflammatory Drug Development: Systematic Approach in Use of Different Animal Models for Evaluations 394 17.5 Rational Design of Anti-inflammatory Agents 394 17.6 Conclusion and Future Perspectives 397 Authors’ Contribution 397 References 397 18 Rational Design of Antibacterial Agents for Multidrug-Resistant Infections 403 Sathish Kumar Konidala, Podila Naresh, Risy Namratha Jamullamudi, Kamma Harsha Sri, Richie Rashmin Bhandare, and Afzal Basha Shaik 18.1 Introduction 403 18.2 Treatment 404 18.3 Antibacterial Resistance 405 18.4 Medicinal Chemistry Strategies for the Design of Antibacterials Combating Multidrug-Resistant Bacterial Infections 408 18.5 Summary and Conclusion 418 References 418 19 Rational Design of Antiviral Therapeutics 423 Sneha Dokhale, Samiksha Garse, Shine Devarajan, Vaishnavi Thakur, and Shaunak Kolhapure 19.1 Introduction to Antiviral Therapeutics 423 19.2 Targets for Antiviral Therapeutics and Inhibition Strategies 427 19.3 Rational Strategies for Antiviral Therapeutics 431 19.4 Conclusion 437 References 438 20 Rational Design of Anticancer Therapeutics 445 Debarupa Dutta Chakraborty and Prithviraj Chakraborty 20.1 Introduction 445 20.2 Rational Design of Nanomedicine for Cancer Treatment 446 20.3 The CAPIR Cascade: A Nanomedicine Strategy for Administering Cancer Medications 447 20.4 Rational Regulation of Nanoparticle’s Physicochemical Characteristics 447 20.5 Some Approaches of Rational Drug Design in Anticancer Theranostics 448 20.6 Artificial Intelligence’s Progress in Anticancer Drug Development 450 20.7 Conclusion 452 References 452 21 PROTAC and ProTide Strategies in Drug Design 457 Maitreyee Mukherjee 21.1 Introduction 457 21.2 Drug Design: Past to Present 458 21.3 PROTAC Strategy in Drug Design 459 21.4 Emergence of ProTide Technology in Drug Design 465 21.5 Approaches of ProTides in Drug Development 466 21.6 Implementation of ProTides as Nucleoside Analogs 470 21.7 Conclusion 471 References 471 22 Advancing Lung Cancer Treatment Through ALK Receptor-targeted Drug Metabolism and Pharmacokinetics 477 Vivek Yadav, Shikha Goswami, Rajiv Kumar Tonk, and Mithun Rudrapal 22.1 Introduction 477 22.2 ALK Receptor and Its Role 478 22.3 Diagnostic Methods for ALK Rearranged NSCLC 479 22.4 ALK Inhibitors Drug Development 481 22.5 Drug Metabolism of Reported ALK Inhibitor 484 22.6 Resistance and Mutations 487 22.7 Conclusion 488 Conflict of Interest 488 References 489 23 Targeting Intrinsically Disordered Proteins (IDPs) in Drug Discovery: Opportunities and Challenges 493 Sridhar Vemulapalli 23.1 Introduction 493 23.2 Properties and Significance of IDPs 493 23.3 Challenges in Targeting IDPs 496 23.4 Computational Tools for IDP Analysis 499 23.5 Rational Design Approaches for IDP Inhibition 500 23.6 Case Studies 505 23.7 Future Directions 508 23.8 Conclusions 509 References 510 Index 519