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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5440_Библиотеки_им_академика_М_И_Перельмана.pdf
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- •Computational Methods for Rational Drug Design
- •Contents
- •1.1.2.2 GROMACS
- •1.1.2.3 Amber
- •1.1.2.4 CHARMM
- •1.1.2.5 AutoDock
- •1.1.2.6 VMD
- •1.1.2.7 PyMOL
- •1.1.2.8 Open Babel
- •List of Contributors
- •Preface
- •1. Molecular Modeling and Drug Design
- •1.1 Introduction
- •1.1.1 What Is Molecular Modeling?
- •1.1.2 Software Used for Molecular Modeling
- •1.1.2.1 Schrodinger
- •1.1.2.9 Avogadro
- •1.1.2.10 Discovery Studio
- •1.1.3 Molecular Mechanics
- •1.1.3.1 Prediction of Binding Affinity
- •1.1.3.2 Conformational Analysis
- •1.1.3.3 Virtual Screening
- •1.1.3.4 Lead Discovery
- •1.1.3.5 Mechanism of Action
- •1.2 Types of Molecular Models
- •1.2.1 Ball-and-Spoke Model
- •1.2.1.1 Future Directions
- •1.2.2 Space-filling Models
- •1.2.2.1 Future Directions
- •1.2.3 Crystal Lattice Models
- •1.2.3.1 Future Directions
- •1.3 Computational Methods in Drug Discovery
- •1.3.1 What Is Drug Discovery?
- •1.3.2 Computational Platforms for Drug Discovery
- •1.3.2.1 NCBI
- •1.3.2.2 Chemical Databases
- •1.3.2.3 PDB
- •1.3.2.5 UniProt
- •1.3.2.6 QSAR
- •1.3.2.8 Desmond
- •1.3.2.9 OpenBabel
- •1.3.2.10 DeepChem and Cheminformatics for Python (RDKit)
- •1.3.2.11 SBML
- •1.3.2.12 Virtual Screening
- •1.3.3 Applications of Computer-Based Methods in Steps of Drug Discovery
- •1.4 Potential Use and Application of AI in Drug Designing
- •1.4.1 Target Identification and Validation
- •1.4.2 Drug Screening and Lead Optimization
- •1.4.3 De Novo Drug Design
- •1.4.4 Predictive Toxicology and ADMET
- •1.4.5 Clinical Trial Optimization
- •1.4.6 Drug Repurposing
- •1.4.7 Concept of Personalized Medicine
- •1.4.8 Drug Combination Optimization
- •1.5 Limitations of Current Methods
- •1.5.1 Data Restrictions
- •1.5.2 Interpretability
- •1.5.3 Generalization
- •1.5.4 Resources and Computation
- •1.5.5 Ethical Considerations
- •1.5.6 Validation and Experimentation
- •1.5.7 Regulatory Obstacles
- •1.6 Case Studies
- •1.7 Molecular Docking
- •1.7.1 What Is Molecular Docking?
- •1.7.1.1 Procedure
- •1.7.1.2 Biophysical Laws
- •1.7.1.3 Rigid and Flexible Docking
- •1.7.1.4 Types of Docking
- •1.7.1.5 Challenges and Future Perspectives
- •1.7.2 Applications of Molecular Docking in Drug Designing
- •1.7.3 Success of Molecular Docking Cases in Drug Designing
- •1.8 Conclusion and Future Works
- •References
- •2. Bioactive Small Molecules and Drug Discovery
- •2.1 Introduction
- •2.1.1 Introduction to Drug Design and Discovery
- •2.1.2 Brief History of Small-Molecule Drug Discovery
- •2.1.3 Importance of Bioactive Small Molecules in Drug Discovery
- •2.2.1 Structure-Based Methods
- •2.2.2 Ligand-Based Methods
- •2.2.3 Network-Based Methods
- •2.3 Natural Products in Bioactive Small-Molecule Discovery
- •2.3.1 Plant Primary and Secondary Molecules as Bioactive Molecules
- •2.3.2 Anticancer Agents as Bioactive Molecules
- •2.3.3 Antiviral Agents as Bioactive Molecules
- •2.3.4 Antimalarial Agents as Bioactive Molecules
- •2.6.6 Toxicity and Side Effects
- •2.6.7 Cost-Effectiveness, Synthetic Feasibility, and Scalability
- •2.6.8 Structural Diversity and Novelty
- •2.6.9 Patentability and Intellectual Property
- •2.3.5 Marine Bioactive Products
- •2.4.1 Importance of DFT in Small-Molecule Drug Discovery
- •2.5 Application of DFT to Bioactive Small Molecules
- •2.5.1 HOMO–LUMO Calculation
- •2.5.1.1 Molecular Electrostatic Potential (MEP) Map
- •2.5.1.3 Natural Bond Orbital (NBO) Analysis
- •2.5.1.4 Implementations and Tools
- •2.6.1 Target Identification and Validation
- •2.6.2 Target Specificity
- •2.6.3 Bioavailability and Pharmacokinetics
- •2.6.4 Chemical Structure and Drug-likeness
- •2.6.5 Safety and Toxicity
- •2.7 Conclusion
- •References
- •3. Novel Drug Targets for Small Molecule-based Drug Discovery
- •3.1 Introduction
- •3.2 Drug Target Identification
- •3.3 Classification of Novel Drug Targets
- •3.3.1 Transcription Factors
- •3.3.2 Cytokines
- •3.3.3 Chaperones
- •3.3.4 Viral Targets
- •3.3.5 G Protein-coupled Receptors
- •3.3.6 Transporters
- •3.3.7 Enzymes
- •3.3.8 RNA Targets
- •3.4 Small Molecules as Drugs
- •3.5 Conclusion
- •References
- •4.1 Introduction
- •4.2 Structure-Based Drug Discovery Concept
- •4.2.1 Structure Generation of the Target
- •4.2.1.1 The Detailed Description of Each Tool
- •4.2.2 Active Binding Site Within the Target
- •4.2.2.1 The Detailed Description of Each Tool
- •4.2.2.2 Molecular Docking Analysis
- •4.2.2.3 The Detailed Description of Each Tool
- •4.2.3 Molecular Dynamic Simulations
- •4.2.3.1 The Detailed Description of Each Tool
- •4.3 Ligand-Based Drug Discovery Concept
- •4.3.1.1 The Detailed Description of Each Tool
- •4.4 Structure- and Ligand-Based Assisted Studies
- •4.4.1 The Detailed Description of Each Tool
- •4.4.2 The Detailed Description of Each Tool
- •4.5 Advancement and Challenges in SBDD and LBDD
- •4.6 Conclusion
- •References
- •5. Virtual Screening and Lead Discovery
- •5.1 Introduction to Virtual Screening and Lead Discovery
- •5.1.1 Overview of Drug Discovery Process
- •5.1.2 Role of Virtual Screening
- •5.1.3 Importance of Lead Discovery
- •5.2 Molecular Targets and Biomolecular Structures
- •5.3 Virtual Screening Approaches
- •5.3.1 Structure-based Virtual Screening
- •5.3.2 Ligand-based Virtual Screening
- •5.3.3 Hybrid Approaches
- •5.4 Databases and Compound Collections
- •5.4.1 Overview of Chemical Databases
- •5.4.2 Compound Filtering and Preparation
- •5.4.3 Diversity and Size of Compound Collections
- •5.5 Molecular Docking
- •5.5.1 Principles of Molecular Docking
- •5.5.2 Docking Algorithms and Scoring Functions
- •5.5.3 Validation of Docking Results
- •5.6 Pharmacophore Modeling
- •5.6.1 Concept of Pharmacophores
- •5.6.2 Generating Pharmacophore Models
- •5.6.3 Applications in Lead Discovery
- •5.7 Quantitative Structure–Activity Relationship (QSAR)
- •5.7.1 Basics of QSAR
- •5.7.2 Model Development and Validation
- •5.7.3 QSAR in Virtual Screening
- •5.8 Machine Learning and AI in Virtual Screening
- •5.8.1 Introduction to Machine Learning and AI
- •5.8.2 Feature Selection and Model Training
- •5.8.3 Applications in Virtual Screening
- •5.9 Hit-to-Lead Optimization
- •5.9.1 Prioritizing Hits from Virtual Screening
- •5.9.2 SAR Analysis and Iterative Design
- •5.9.2.1 SAR Analysis (Structure–Activity Relationship)
- •5.9.2.2 Iterative Design
- •5.9.3 ADME/Tox Considerations
- •5.9.3.1 ADME (Absorption, Distribution, Metabolism, Excretion)
- •5.9.3.2 Toxicity Considerations
- •5.10 Case Studies and Examples
- •5.10.1 Exploration Protocol for Mutant-targeted PI3K Inhibitors
- •5.11 Challenges and Future Directions
- •5.11.1 Limitations of Virtual Screening
- •5.11.2 Emerging Technologies and Trends
- •5.11.3 Integration with High-throughput Experimentation
- •5.12 Ethical and Regulatory Considerations
- •5.12.1 Intellectual Property and Patents
- •5.12.2 Ethical Use of Computational Tools
- •5.12.3 Regulatory Approval Process
- •5.13 Conclusion
- •5.13.1 Future Prospects in Virtual Screening and Lead Discovery
- •5.13.2 Summary of Key Points
- •References
- •6. ADMET and Physicochemical Assessments in Drug Design
- •6.1 ADMET
- •6.1.1 Absorption
- •6.1.1.1 Solubility and Dissolution
- •6.1.1.2 Lipophilicity
- •6.1.1.3 Permeability
- •6.1.2 Distribution
- •6.1.3 Metabolism
- •6.1.4 Excretion
- •6.1.5 Toxicity
- •6.2 Physicochemical Assessments
- •6.2.1 Partition Coefficient
- •6.2.2 Log D: Ionizable Compound Lipophilicity
- •6.2.2.1 Methods for Calculating Lipophilicity
- •6.2.2.2 Direct Experimental Determination of Lipophilicity
- •6.2.2.3 Indirect Experimental Determination of Lipophilicity
- •6.2.3 Acid–Base Properties and Ionization
- •6.2.4 Solubility
- •6.2.5 Polymorphism
- •6.2.6 Molecular Weight
- •6.2.7 Number of Hydrogen Bond Donors (HDB) and Acceptors (HDA)
- •References
- •7. In Silico Modeling and Drug Design
- •7.1 Introduction
- •7.2 Target Identification
- •7.2.1 Experimental Approaches
- •7.2.2 Computational Target Identification
- •7.2.3 Target Validation
- •7.3 Computer-Aided Drug Design
- •7.3.1 Ligand-based CADD
- •7.3.2 Structure-Based CADD
- •7.4 ADMET Assessment
- •7.5 Conclusion
- •References
- •8. Pharmacophore Modeling in Drug Design
- •8.1 Introduction
- •8.1.1 The Role of Pharmacophore Modeling in Drug Design
- •8.1.2 Historical Perspective and Evolution of Pharmacophore Concepts
- •8.2 Essential Concepts in Pharmacophore Hypothesis Generation
- •8.2.1.1 Partitioning Initial Data into Distinctive Datasets
- •8.3 Diverse Approaches to Pharmacophore Modeling
- •8.3.1 Ligand-Based Pharmacophore Modeling
- •8.3.2 Structure-Based Pharmacophore Modeling
- •8.4 Application of Pharmacophore Modeling
- •8.4.1 Applications of Pharmacophore-Based Virtual Screening
- •8.4.1.1 Drug Discovery
- •8.4.2 Applications in Drug Target Fishing
- •8.4.3 Applications in Ligand Profiling
- •8.4.4 Applications in Docking
- •8.4.5 Applications in ADMET
- •8.4.6 Modulation of the Immune System
- •8.5 Emerging Trends in Pharmacophore Model Development
- •8.5.1 Involvement of Machine Learning
- •8.5.2 Prediction of Pharmacokinetic Properties
- •8.5.3 Structural Biology and Protein Functionality Studies
- •8.5.4 Integration with MDs Simulations
- •8.6 Case Studies
- •8.6.1 Case 1
- •8.6.2 Case 2
- •8.7 Challenges in Pharmacophore Modeling
- •8.8 Conclusion
- •Acknowledgments
- •References
- •9. Scaffold Hopping and De Novo Drug Design
- •9.1 Introduction
- •9.2 Scaffold Hopping
- •9.2.1 Classification of Scaffold Hopping
- •9.2.1.1 1° Hop: Heterocycle Replacement
- •9.2.1.2 2° Hop: Ring Opening and Closure: Pseudo Ring Structures
- •9.2.1.3 3° Hop: Pseudopeptides and Peptidomimetics
- •9.2.1.4 4° Hop: Topology/Shape-Based Scaffold Hopping
- •9.2.2 Advantages of Scaffold Hopping
- •9.2.3 Disadvantages of Scaffold Hopping
- •9.2.4 Reasons for Scaffold Hopping
- •9.2.5 Properties and Key Methods of Scaffold Hopping
- •9.3 De Novo Drug Design
- •9.3.1 Classification of De Novo Drug Design
- •9.3.1.1 Structure-based Drug Design
- •9.3.1.2 Ligand-based Drug Design
- •9.3.1.3 De Novo Design Strategies
- •9.3.1.4 Artificial Intelligence (AI) and Machine Learning-based Design
- •9.3.1.5 Hybrid Approaches
- •9.3.2 Basic Principle of De Novo Drug Design
- •9.3.3 Application of De Novo Drug Design
- •9.3.4 Historical Overview of Scaffold Hoping and De Novo Drug Design
- •9.3.5 Methodological Approaches in De Novo Drug Design
- •9.3.5.1 Structure-based De Novo Drug Design
- •9.3.5.2 Ligand-based De Novo Drug Design
- •9.3.5.3 Generation of Drug-Like Molecular Fragments
- •9.3.5.4 Similarity Searching
- •9.3.5.5 Selection of Target Reference Structure
- •9.3.5.6 Similarity Analysis of De Novo-generated Compounds
- •9.3.5.7 Evaluation of Scaffold Diversity
- •9.4 Results and Discussion
- •9.4.1 Generation of Drug-Like Molecular Fragments
- •9.4.2 De Novo Design with a Single Reference Structure
- •9.4.3 De Novo Design with a Focused Set of Five Similar Templates
- •9.4.4 De Novo Design with a Diverse Set of Five Templates
- •9.6 Case Study
- •9.6.1 De Novo Drug Design
- •9.6.2 Scaffold Hopping
- •9.7 Conclusion
- •References
- •10. Fragment-based Drug Design and Drug Discovery
- •10.1 Introduction
- •10.2 The Process of Finding Fragments
- •10.3 FBDD Strategies
- •10.4 Case Studies
- •10.5 Conclusion and Future Perspectives
- •References
- •11. AI/ML Approaches in Drug Design
- •11.1 Introduction
- •11.2 Traditional Drug Design Methods
- •11.2.1 The Rise of Computational Methods
- •11.2.2 The Importance of AI/ML in Modern Drug Design
- •11.3 AI/ML Landscape in Drug Design
- •11.3.1 AI/ML Algorithms and Methods
- •11.3.1.1 Machine Learning Models
- •11.3.1.2 Neural Networks
- •11.3.2 Applications in Drug Design
- •11.3.2.1 Peptide Synthesis
- •11.3.2.2 Molecular Design
- •11.3.2.3 Virtual Screening (VS)
- •11.3.2.4 Quantitative Structure–Activity Relationship Models
- •11.3.2.5 Drug Repurposing
- •11.3.3 Challenges and Failures
- •11.4 Ethics, Reliability, and Regulatory Issues
- •11.5 Future Directions
- •11.6 Conclusion
- •References
- •12. Network-based Methods in Drug Discovery
- •12.1 Introduction
- •12.1.1 Background of Drug Discovery Future Challenges
- •12.1.2 Single Target Approach Limitations
- •12.1.3 Emergence of Network Biology and Polypharmacology
- •12.2 Network Pharmacology: Practical Guide
- •12.2.1 Common Network Pharmacology Databases
- •12.2.1.1 Network Pharmacology-Related Databases and Data Analysis Tools
- •12.2.1.2 Exploring IMPPAT Network Pharmacology Databases
- •12.2.1.3 Target Genes of Phytoconstituents
- •12.2.2 Network Analysis and Visualization
- •12.2.3 Applications of Network Pharmacology in Drug Discovery
- •12.3 Ayurveda and Traditional Indian Medicine
- •12.3.1 Overview of Ayurveda and Its Complex Formulations
- •12.3.2 Diversity of Ingredients and Bioactive Compounds in Ayurvedic Medicines
- •12.4 Network Pharmacology in Herbal Remedies
- •12.4.1 Application of Network Pharmacology in Herbal Drug Discovery
- •12.4.1.1 Cancer
- •12.4.1.2 Cardiovascular Diseases (CVDs)
- •12.4.1.3 Diabetes Mellitus (DM)
- •12.4.2 Screening Pharmacological Efficacy of Herbal Remedies
- •12.4.3 Utilizing Network Pharmacology to Understand Complex Diseases
- •12.5 Conclusion and Future Prospects
- •References
- •13. Rational Design of Natural Products for Drug Discovery
- •13.1 Introduction
- •13.2 Natural Products for the Development of New Drugs
- •13.3 Criteria for Selecting Natural Products for Drug Design
- •13.4 Importance of Biodiversity in Sourcing Natural Products
- •13.5 Structural Elucidation of Natural Products
- •13.6.3 High-Throughput Screening Methods for Efficient Compound Selection
- •13.6.4 Molecular Dynamics Simulations for Predicting Solubility and Stability
- •13.6.5 ADMET Attributes Predicted In Silico
- •13.7 Formulation Challenges with Natural Products
- •13.8 Quality by Design (QbD) Approaches
- •13.8.1 Use of Computational Models for Formulation Optimization
- •13.9 Conclusion
- •References
- •14. Design of Enzyme Inhibitors in Drug Discovery
- •14.1 Introduction
- •14.3 Classification of Enzyme Inhibitors
- •14.3.1 Reversible Inhibitors
- •14.3.2 Irreversible Inhibitors
- •14.3.3 Competitive Inhibitors
- •14.3.4 Noncompetitive Inhibitors
- •14.3.5 Allosteric Modulators
- •14.4.1 Structure-Based Design
- •14.4.2 Computer-Aided Design
- •14.4.3 Fragment-Based Design
- •14.4.4 Virtual Screening Method
- •14.4.4.1 Ligand Based
- •14.4.4.2 Receptor Based
- •14.4.5 Natural Product-Based Discovery
- •14.4.6 Using Iterative Protein Crystallographic Analysis
- •14.4.7 Utilization of Covalent Inhibitors
- •14.4.8 Encapsulation Techniques
- •14.4.9 Based on Active-Site Specificity
- •14.4.10 Machine Learning Inhibitor Design
- •14.4.11 Enzyme-Templated Dynamic Combinatorial Chemistry
- •14.5 Limitations and Challenges
- •14.6 Future Directions
- •14.7 Conclusion
- •References
- •15.1 Introduction
- •15.2 Peptides as Therapeutics
- •15.2.1 Peptide Antibiotics
- •15.2.1.1 Peptides in Bone Diseases
- •15.2.1.2 Peptides in Cancer
- •15.2.1.3 Peptides in Metabolic Diseases
- •15.2.1.4 Peptides in Gastrointestinal Diseases
- •15.2.2 Advantages and Limitations of Peptide Therapeutics
- •15.2.3 FDA-Approved Peptide Therapeutics
- •15.2.4 Peptide-Based Entities in Clinical Trials
- •15.2.5 Peptide Synthesis and Diversification
- •15.2.5.1 Chemical Synthesis of Peptides
- •15.2.5.2 Chemical Modification of Peptide and Peptidomimetics
- •15.2.5.3 Backbone Modification of Peptides
- •15.2.5.4 Side-Chain Modification of Peptides
- •15.2.5.5 Peptide Cyclization
- •15.2.5.6 Peptide Mimicking of α-Helices and Stabilization
- •15.2.5.7 Peptide Mimicking of β-Strands and β-Sheets
- •15.2.5.8 Peptide Production by Recombinant Technology
- •15.2.5.9 Peptides Modification by Genetic Code Expansion
- •15.2.5.10 PEGylation of Peptides and Proteins
- •15.3 New Technologies for Peptide-Based Drug Discovery
- •15.3.1 Phage Display
- •15.3.2 mRNA Display
- •15.3.3 DNA-Encoded Libraries
- •15.3.4 Cell-Penetrating Peptides
- •15.3.5 Macrocyclic Peptides
- •15.4 Computational Approaches in Peptide Drug Discovery
- •15.5 Conclusion
- •References
- •16. Rational Design of Drugs for Neurodegenerative Disorders
- •16.1 Introduction
- •16.2 Common Mechanism of Neurodegeneration
- •16.3 Brief Overview of Computational Methods in Drug Design
- •16.4 Parkinson’s Disease as Prevalent Neurodegenerative Disorder
- •16.4.1 Epidemiology of Parkinson’s Disease
- •16.4.2 Pathogenesis of PD
- •1) Accumulation of Lewy bodies in substantia nigra
- •2) Mitochondrial dysfunction
- •3) Genetic factors
- •4) Neuroinflammation
- •5) Impaired protein handling
- •6) Oxidative stress
- •7) Environmental toxins
- •16.4.3 Signaling Pathway of Parkinson’s Disease
- •1) DA signaling
- •2) MAPK/ERK pathway
- •3) PI3K/Akt/mTOR pathway
- •4) Wnt/β-catenin pathway
- •5) NF-κB (nuclear factor-κB) pathway
- •6) Autophagy-lysosomal pathway
- •7) JNK (c-Jun N-terminal kinase) pathway
- •8) AMPK (AMP-activated protein kinase) pathway
- •9) Nrf2 (nuclear factor erythroid 2-related factor 2) pathway
- •16.4.4 Enzymatic Targets in Parkinson’s Disease
- •1) MAO-B (monoamine oxidase B)
- •2) COMT (catechol-O-methyltransferase)
- •3) LRRK2
- •4) GCase (glucocerebrosidase)
- •5) PARP-1 [poly(ADP-ribose) polymerase-1]
- •6) PINK1
- •7) DJ-1 (Parkinson protein 7)
- •8) Nrf2
- •16.4.5 Current Therapeutic Approaches to Treat PD
- •1) Drugs to treat motor symptoms of PD
- •2) Drugs to treat non-motor symptoms of PD
- •3) Disease-modifying therapies to treat PD
- •16.4.6 Current Therapeutic Challenges to Treat Parkinson’s disease
- •1) Symptomatic relief only
- •2) Motor fluctuations and dyskinesias
- •3) Limited efficacy in nonmotor symptoms
- •4) Disease progression
- •5) Side effects
- •6) Limited treatment options for advanced PD
- •7) Individual variability
- •16.4.7 Unmet Needs in Parkinson’s Disease Therapeutics
- •16.4.8 Significance of Computational Approaches in Parkinson’s Disease
- •16.4.9 Use of Computational Tools in Identifying Biomarkers
- •16.4.10 Neuroprotective Strategies Through Computational Insights
- •16.4.10.1 Computational Models for Neuroprotection
- •1) Target identification and validation
- •2) Drug repurposing
- •3) Alpha-synuclein aggregation inhibitors
- •4) Deep learning in biomarker discovery
- •5) Personalized medicine
- •6) Drug-induced neuroprotection
- •7) Optimizing clinical trials
- •1) ML and AI-based diagnostics
- •2) Wearable technology integration
- •3) Multimodal data fusion
- •4) Predictive modeling of disease progression
- •5) Network analysis of brain connectivity
- •6) Personalized treatment optimization
- •7) Data sharing and collaboration platforms
- •16.5 Conclusion
- •References
- •17. Rational Design of Anti-inflammatory Therapeutics
- •17.1 Introduction
- •17.2 Navigating Inflammation and its Microenvironment
- •17.2.1 Inflammatory Cell Infiltration and Vascular Permeability
- •17.2.2 Acidosis
- •17.2.3 Increased Oxidative Stress in Tissues
- •17.3 The Demand for Advanced Anti-inflammatory Medications
- •17.5 Rational Design of Anti-inflammatory Agents
- •17.5.2 New Anti-inflammatory Agent with Indoyl-imidazole Hybrids
- •17.5.3 Rational Design of Novel Aminopiperidinyl Amide
- •17.5.4 Lipid Nanoparticles (LNPs) as Anti-inflammatory Agents
- •17.6 Conclusion and Future Perspectives
- •Authors’ Contribution
- •References
- •18.1 Introduction
- •18.2 Treatment
- •18.3 Antibacterial Resistance
- •18.3.1 Mutation
- •18.3.2 Horizontal Gene Transfer (HGT)
- •18.3.3 Enzymatic Modification or Degradation
- •18.3.4 Target Site Modification
- •18.3.5 Decreased Permeability
- •18.3.6 Efflux Pumps
- •18.3.7 Plasmids
- •18.3.8 Transposons
- •18.3.9 Gene Amplification
- •18.3.10 Formation of Biofilms
- •18.3.11 Modified Metabolic Pathways
- •18.3.12 Adaptive Evolution
- •18.4.1 Structure- Based Drug Design
- •18.4.2 Modification of Existing Antibiotics
- •18.4.3 Bioisosterism
- •18.4.4 Prodrug Strategies
- •18.4.5 Similar Bacterial Components Target
- •18.4.6 Combine or Combination Therapy
- •18.4.7 Drug Repurposing
- •18.4.8 Resistant Mechanism Blocking
- •18.4.9 Improving Drug Delivery by Nanotechnology
- •18.4.10 Phage Intervention
- •18.4.11 Host Targeting
- •18.4.12 CRISPR-Cas Technique
- •18.4.13 Peptides as Antibacterials
- •18.4.14 Immunizations and Immunotherapy
- •18.4.15 Natural Product Derivatives
- •18.4.16 Fragment- Based Drug Discovery (FBDD)
- •18.4.17 Metabolomics and Genetics
- •18.4.18 Cheminformatics
- •18.5 Summary and Conclusion
- •References
- •19. Rational Design of Antiviral Therapeutics
- •19.1 Introduction to Antiviral Therapeutics
- •19.1.1 Overview
- •19.1.2 Blueprints for Antiviral Drug Interventions
- •19.1.2.1 Protein Folding and Binding Sites
- •19.1.2.2 Conformational Changes
- •19.1.2.3 Protein–Protein Interactions (PPIs)
- •19.1.2.4 Capsid and Envelope Structures
- •19.1.2.5 Structural Vulnerabilities
- •19.1.2.6 Enzymatic Activities
- •19.1.2.7 Viral Attachment
- •19.1.2.8 Viral Assembly and Replication Machinery
- •19.1.2.9 The Host’s Immune Response
- •19.2 Targets for Antiviral Therapeutics and Inhibition Strategies
- •19.2.1 Enzyme Inhibitors
- •19.2.2 Antiviral Peptides
- •19.2.3 Antiviral Antibodies
- •19.2.4 Lipid-Mimicking Compounds
- •19.2.5 Vaccines
- •19.2.6 Immunomodulation
- •19.3 Rational Strategies for Antiviral Therapeutics
- •19.3.1 CADD and QSAR (Quantitative Structure–Activity Relationship)
- •19.3.2 AI and ML
- •19.3.3 Systems Biology and Network Pharmacology
- •19.3.4 CRISPR Systems
- •19.3.5 Nanotechnology-Based Design and Delivery Systems
- •19.3.6 Reverse Vaccinology
- •19.4 Conclusion
- •References
- •20. Rational Design of Anticancer Therapeutics
- •20.1 Introduction
- •20.2 Rational Design of Nanomedicine for Cancer Treatment
- •20.4.1 Particle Size
- •20.4.2 Shape
- •20.4.3 Surface Modification
- •20.6 Artificial Intelligence’s Progress in Anticancer Drug Development
- •20.6.1 Identification of Anticancer Drug Targets Using Artificial Intelligence
- •20.6.3 Artificial Intelligence-Based De Novo Anticancer Drug Design
- •20.6.4 Artificial Intelligence for Repurposing Anticancer Drugs
- •20.7 Conclusion
- •References
- •21. PROTAC and ProTide Strategies in Drug Design
- •21.1 Introduction
- •21.2 Drug Design: Past to Present
- •21.3 PROTAC Strategy in Drug Design
- •21.3.1 Ubiquitin Proteasome System and PROTACs
- •21.3.2 Chemical Formulations of PROTACs
- •21.3.3 Advent of PROTACs as Antiviral
- •21.3.4 NS3/4A-Targeting PROTACs Against HCV
- •21.3.4.1 Neuraminidase-Targeting PROTACs
- •21.4 Emergence of ProTide Technology in Drug Design
- •21.5 Approaches of ProTides in Drug Development
- •21.6 Implementation of ProTides as Nucleoside Analogs
- •21.6.1 Antiviral Applications of ProTides
- •21.7 Conclusion
- •References

12.4 Network Pharmacology in erbal Remedies 273
Table 12.5 (Continued)
Photoactive compounds Subclass/Type Role in treating diseases
Cyanogenic glycosides Hydrocyanic acid aglycone Cytotoxic, anticancer
Flavonoid glycosides Phenolic aglycone 2 phenylbenzopyrenes Antioxidant, anti-
inflammatory, cardiovascular
health
Resinous glycosides Resin aglycone Anti-inflammatory, wound
healing
Volatile oils
Terpenoids in association with alcohols,
phenols, aldehydes, esters
Respiratory health,
antimicrobial, aromatherapy
Gums Amorphous polysaccharides Gastrointestinal health, wound
healing
Resins Complex organic compounds Anti-inflammatory, wound
healing
monoterpenoids to carotenoids, provide anti-inflammatory, antibacterial, and immunological
support properties [88–90]. Glycosides, volatile oils, gums, and resins are essential components
that have significant impacts in several fields, ranging from promoting cardiovascular well-being
to facilitating the process of wound healing. The incorporation of ancestral wisdom into modern
medicine demonstrates the capacity for comprehensive healing and tackles a wide range of ill-
nesses, representing notable progress in the discipline. Nature is widely acknowledged as a reser-
voir of innovative chemical compounds [91, 92]. It is critical to improve traditional medicine
procedures, particularly the preservation of historical knowledge and the optimization of herbal
medicine’s use in human healthcare, to guarantee the efficacy, safety, and quality of traditional
medicine. The following must be prioritized: postmarketing surveillance, consumer awareness,
clinical risk assessment, validation methods, standardization, authentication, quality control, and
regulatory elements of herbal medical products to guarantee their safe and effective usage [42, 93].
12.4 Network Pharmacology in Herbal Remedies
12.4.1 Application of Network Pharmacology in Herbal Drug Discovery
12.4.1.1 Cancer
Cancer is a major cause of illness and death worldwide. Multiple targets and carcinogenic signal-
ing cascades must be regulated to effectively treat cancer. Similar to cancer, single-targeted drug
discovery fails for severe systemic disorders with complex biological systems. Network pharmacol-
ogy approaches, in contrast to more conventional drug discovery strategies, aim to inhibit disease
progression by interacting with several protein or network components. When conducting clinical
trials, network pharmacology is useful for addressing issues such as patient heterogeneity and
disease [94, 95]. Cancers differ depending on whether therapeutic targets are present or not.
Therapy choices are limited for heterogeneous populations with various malignancies. Therefore,
in order to alter drug development and enhance our understanding of mechanisms of action,
approaches based on network pharmacology are required. Cancer treatment therapy and

12 Network-based Methods in Drug Discovery274
medication development can both be accelerated by network pharmacology [96, 97]. There are
genes that have been uncovered using network analysis that could be therapeutic targets for the
reduction and treatment of cancer. Receptor 2 for human epidermal growth factor is present in
HER2-positive breast cancers. Cancer cell proliferation is enhanced by protein. Amplified HER2
genes are found in 20% of breast cancer cases. To investigate the impact of Yanghe decoction on
HER2-positive breast cancer, Zeng et al. employed network pharmacology [98]. Anticancer com-
ponents like quercetin, luteolin, and naringenin may be present in Yanghe decoction. It was proven
that Yanghe decoction works in tandem with other molecules to treat HER2-positive breast cancer.
The active components and critical pathways of the Shenqi-Yi-zhu decoction were investigated by
Zhen et al. for the purpose of treating stomach cancer. Network pharmacology and in vitro tests
demonstrate the effective and advantageous molecular mechanism of Shen-qi-Yi-zhu decoc-
tion [99]. The study found that Shen-qi-Yi-zhu decoction inhibits the PI3K/AKT/mTOR pathway,
which may prevent cancer. The PI3K/AKT/mTOR pathway is present in most cancers and affects
cancer biology. Thus, herb/herbal formulations were crucial to antitumor research [100]. The most
common cancer killer is colorectal cancer, which is quiet and lethal. Liu et al. used network phar-
macology to determine how Hedyotis diffusa fights colorectal cancer. Hedyotis diffusa may cure
colorectal cancer by targeting tumor growth signaling pathways, according to network analysis.
This explains Hedyotis diffusa’s anti-colorectal cancer properties [101]. Hedyotis diffusa was used
by Song et al. to uncover prostate cancer’s multi-target pharmacological mechanism. To find the
medicinal properties of herbs and herbal combinations, network pharmacology is a great tool.
Bing et al. investigated the efficacy of Fuzheng Kangai’s lung cancer treatment using bioinformat-
ics and network pharmacology. The molecular mechanisms of the Kushen injection’s effects on
lung cancer treatment were studied by Meng et al. using molecular docking and network pharma-
cology. Finally, results from network pharmacology provide fresh insight into the efficacy of herb/
herbal combinations in cancer treatment [102].
12.4.1.2 Cardiovascular Diseases (CVDs)
Cardiovascular and cerebral vascular diseases are significant worldwide health issues. Botanical
drugs derived from traditional medicinal plants provide multiple advantages for the treatment of
cardiovascular and cerebrovascular diseases (CCVDs). Nevertheless, the molecular mechanisms
underlying the therapeutic effects of medicinal plants on CCVDs remain elusive. An innovative
approach in systems pharmacology, network pharmacology helps us understand the pharmaco-
logical mechanisms of medicinal plants for CCVDs treatment by integrating pharmacokinetic
screening, target identification, and network analysis [103]. This approach introduces an innova-
tive methodology for investigating the mechanism by which herb/herbal formulations act against
CCVDs. Yang et al. conducted a study on network pharmacology, focusing on the active com-
pounds found in Ginkgo biloba leaf. They explored the potential targets and pathways that may be
used to treat CCVD. This study provides a foundation for future research in this field. Studies sug-
gest that Ginkgo biloba leaves have the potential to safeguard against CCVDs by modulating sev-
eral biological pathways and targeting specific processes. Ginkgo biloba leaves are effective in
treating CCVDs, according to this study, which also introduces a new way to find therapeutic pos-
sibilities derived from plants. To combat stroke, Ren et al. used herbal treatments [104]. Their
investigation unveiled bioactive compounds that efficiently addressed stroke by specifically target-
ing genes associated with the condition. Tao et al. employed network pharmacology to predict the
active components and possible targets of the Radix Curcumae recipe for the treatment of CCVDs.
The study provides a thorough explanation of how the Radix Curcumae recipe works to treat
CCVD and finds areas where herbal medicine could be improved in the future [105]. For the

12.4 Network Pharmacology in erbal Remedies 275
purpose of treating CCVD, Wang et al. investigated the active components of Salvia miltiorrhiza
Burge and Carthamus tinctorius L. Salvia miltiorrhiza Burge and Carthamus tinctorius L. may
increase blood flow to the brain by widening blood vessels, which in turn decreases neurotoxic
damage and protects brain tissue from free radical damage, according to the study [106]. Academics
can better understand the Yangxinshi tablet’s complex mechanism with the use of network-based
analysis. Finding the chemical and pharmacological components of other herbal compositions can
also benefit from this method [107].
12.4.1.3 Diabetes Mellitus (DM)
Global DM is spreading quickly. Diabetics are more susceptible to acute diseases. Network
pharmacology using natural compounds may treat DM and address the difficulties stated above.
Wang et al. used network pharmacology to find the most powerful Astragaloside IV active compo-
nents for type 2 diabetes [108]. Docking and network analysis can reduce screening costs and
provide a complete understanding of drug development and discovery processes, according to
recent research. Gu et al. used network pharmacology and molecular docking to explain
Tangminling pills’ T2DM therapy mechanism. The compound–compound network and com-
pound target network showed that over 100 of the 667 compounds in the formula can target 37
T2DM proteins. Tangminling tablets include essential components, some of which have been pub-
lished [109]. Procyanidin C1, Rheidin A, Rheidin C, Sennoside C, and Dihydrobaicalin have been
studied as diabetes treatments. Sorghum bicolor is a prospective source of antidiabetic compounds
due to its bioactive components. Oh et al. used network pharmacology to find diabetes treating
Sorghum bicolor active chemicals. Sorghum bicolor activates PPAR signaling pathways to lower
T2DM severity, according to the study [110, 111]. Four chemicals in Sorghum bicolor – alpha-
sitosterol, 25-oxo-27-norcholesterol, campesterol, and propyleneglycol monoleate – are associated
with the plant’s antidiabetic effects. Zhou et al. investigate the mechanism of action of Xiao Ke Yin
Shui’s T2DM treatment using network pharmacology. Xiao Ke Yin Shui’s formula significantly
impacts tumor necrosis factor, phosphatidylinositol 3-kinase, and protein kinase B, according to
the study. Reduced insulin resistance and antidiabetic properties are two of the Xiao Ke Yin Shui
chemical’s synergistic therapeutic benefits [107].
12.4.2 Screening Pharmacological Efficacy of Herbal Remedies
In developing nations, people often turn to herbal remedies, which are mixtures of plants that
contain a number of different pharmacologically active chemicals. Because of advantageous “syn-
ergistic” interactions, complex combinations are more effective than individual drugs at modulat-
ing the activity of target networks linked with disease characteristics. The methods that produce
their synergistic or antagonistic combinations and interactions are discovered and explained in
this chapter through the application of systematic, systems pharmacology, network analysis, and
machine learning methodologies. Here we take a look at a variety of studies that have investigated
synergistic interactions, all using various approaches that stem from the network pharmacology
paradigm [89, 90, 112]. The chapter provides a thorough analysis of evaluation mechanisms that
expedite innovation in botanical research. Evaluating the pharmacological effectiveness of herbal
treatments is an essential procedure in contemporary medicine. Given the increasing interest in
natural remedies, it is imperative to conduct thorough scientific evaluations. Scientists utilize
many techniques, including in vitro and in vivo investigations, to evaluate the bioactivity of herbal
substances. In vitro investigations investigate molecular interactions, enzyme activity, and cellular
responses, offering valuable insights into potential treatment pathways [112]. In vivo studies utilize

12 Network-based Methods in Drug Discovery276
animal models to enable researchers to directly evaluate the comprehensive physiological impacts
and potential harm. In addition, clinical trials evaluate the effectiveness of herbal treatments in
humans, establishing their safety, dose, and efficacy. Advanced methodologies such as chromatog-
raphy and mass spectrometry facilitate the identification and quantification of active sub-
stances [113]. Pharmacological screening encompasses multiple factors, such as anti-inflammatory,
antioxidant, antimicrobial, and immunomodulatory properties. By combining ancient knowledge
with modern pharmacology, herbal therapy is able to be grounded in evidence-based practices. The
rigorous screening process is essential for ensuring the safety and effectiveness of herbal treat-
ments, enabling their incorporation into mainstream healthcare, and providing a scientific basis
for their utilization in the treatment of different medical diseases [114].
12.4.3 Utilizing Network Pharmacology to Understand Complex Diseases
Network pharmacology is an advanced interdisciplinary field that has become a strong method for
understanding the complicated mechanisms behind complex disorders. This novel approach inte-
grates concepts from network science, pharmacology, bioinformatics, and systems biology to
provide a comprehensive comprehension of the relationships among medications, targets, and
diseases. Traditionally, drug development mostly concentrated on specific molecular targets within
the traditional paradigm. Nevertheless, numerous diseases, particularly those that are intricate,
encompass a multitude of interrelated pathways. Network pharmacology acknowledges the com-
plex nature of biological systems and highlights the importance of investigating the comprehen-
sive interactions between medications and the various networks within the body. An essential
component of network pharmacology is in its capacity to elucidate the polypharmacology of medi-
cines. Instead of acting on a single target, numerous therapies exert their effects on multiple tar-
gets [115]. Network pharmacology utilizes the integration of extensive omics data, including
genomes, proteomics, and metabolomics, to identify prospective drug targets within intricate net-
works. The process entails the construction of biological networks that depict the associations
among genes, proteins, and metabolites that are involved in illnesses. These networks might focus
either on diseases or on drugs. Condition networks facilitate the integration of molecular data
linked to a particular condition, aiding in the identification of crucial pathways and prospective
targets for therapeutic intervention. Conversely, drug networks depict the connections between
medications and the specific proteins they target [114]. Examining these networks yields valuable
understanding of the biological underpinnings of diseases and the effects of drugs. By identifying
network hubs, which are nodes with high connectivity, and essential pathways, researchers can
prioritize prospective treatment targets. Moreover, network pharmacology assists in forecasting
the adverse effects and possible off-target impacts of therapies, hence facilitating the advancement
of more secure medications. The incorporation of traditional medicine into network pharmacol-
ogy is remarkable. Conventional medical systems frequently include herbal treatments that consist
of multiple components (Figure 12.6). Network pharmacology enables researchers to comprehend
the combined effects of different chemicals inside these formulations. Through the creation of
herb–drug networks, researchers can uncover the intricate connections between herbal compo-
nents and pathways related to diseases. Furthermore, network pharmacology enables the investi-
gation of the idea of “network target” [116, 117]. Instead of exclusively concentrating on particular
targets, this strategy takes into account the entire network linked to a disease. Network-targeted
medicines, which modulate several targets simultaneously, have the potential to be more effica-
cious and demonstrate reduced side effects in comparison to interventions that target a single
entity. Thus, network pharmacology signifies a fundamental change in the approach to drug

12.5 onclusion and uture Prospects 277
discovery and comprehension of diseases. The holistic approach takes into account the complex
interconnections within biological systems, which allows for the creation of therapies that are both
more effective and safer. Network pharmacology, via the integration of various data sources and
the acceptance of the intricacies of diseases, provides a complete framework for understanding
complex diseases and expedites the identification of new medicines [106, 116].
12.5 Conclusion and Future Prospects
To summarize, the incorporation of Indian traditional medicines into the process of drug development
via network pharmacology represents a notable advancement toward comprehensive and efficient
healthcare remedies. Ancient pharmaceutical systems, firmly grounded in traditional wisdom,
provide a rich collection of varied substances with therapeutic potential. Network pharmacology
offers a powerful framework for comprehending the intricate relationships inside biological sys-
tems, enabling a thorough knowledge of the diverse characteristics of traditional medicines.
Network pharmacology has shed light on the multitarget effects and synergistic interactions of
plant-derived chemicals, including polyphenols, terpenoids, and glycosides, through a thorough
investigation. This technique not only confirms the practical information contained in traditional
medications but also reveals new ways to treat complicated conditions. The integration of old and
new knowledge systems facilitates a fundamental change in the approach to drug discovery,
placing emphasis on a comprehensive comprehension of diseases and therapies. By developing
extensive networks that capture the interactions between medications, targets, and diseases,
network pharmacology aids researchers in finding critical pathways, possible drug targets, and
forecasting side effects. This understanding facilitates the creation of safer and more effective drugs.
Multiple
targets
Enhanced
bioavailability
Reduces
side
effects
Target proteins
Charaka samhita
Disease pathway
KCNH2
CYPIA2
PON1
ESR2
PLAU
EGFR
NCF1
HSPB1
ILI0
NOS3
ACHE
ABCG1
CYP3A4
H6
IL1B
Network and pathways
Figure 12.6 Developing the current in silico methods by integrating it with ancient texts of Indian
traditional medicines to treat various deadly diseases.

12 Network-based Methods in Drug Discovery278
The future potential of Indian traditional remedies in drug development through network phar-
macology is highly exciting and diverse. Realizing these opportunities necessitates cooperative
endeavors among indigenous healers, scientists, and pharmaceutical investigators. Here are some
crucial paths for investigation: Omics data integration: The progress in genomes, proteomics, and
metabolomics will improve the accuracy of network pharmacology. By combining omics data with
traditional pharmaceutical expertise, a more intricate comprehension of the molecular mecha-
nisms involved can be achieved. Standardization and quality control are essential for guaranteeing
consistency and dependability in drug research. It involves establishing uniformity in traditional
formulations and implementing strict mechanisms to monitor and evaluate the quality of the
drugs. Utilizing contemporary analytical methods can enhance the uniformity and security of con-
ventional medications. Clinical validation is crucial for confirming the effectiveness and safety of
traditional drugs revealed using network pharmacology. Although in silico and in vitro researches
offer useful insights, thorough clinical trials are necessary for this validation. This shift will be
facilitated by collaborations between traditional medicine practitioners and modern healthcare
experts. Ethnopharmacological research, which concentrates on the traditional knowledge present
in diverse cultures throughout India, has the potential to reveal exceptional medicinal substances.
Network pharmacology can be used to analyze the molecular pathways that are responsible for the
effects of these traditional treatments.
Personalized Medicine: The customized approach of conventional medicine is well suited to
the emerging concept of personalized medicine. Customizing therapies according to an individu-
al’s genetic composition and lifestyle variables, under the guidance of network pharmacology, has
significant promise for improving treatment results. The interaction between Indian traditional
medicines and network pharmacology gives potentially exciting prospects in drug discovery. This
multidisciplinary approach not only acknowledges and values historic healing traditions but also
advances them to the forefront of modern medicine, facilitating a seamless blending of the tradi-
tional and contemporary practices for the betterment of world healthcare.
References
1 Ellingson, S.R., Smith, J.C., and Baudry, J. (2014). Polypharmacology and supercomputer-based
docking: opportunities and challenges. Molecular Simulation 40 (10–11): 848–854.
2 Hopkins, A.L. (2007). Network pharmacology. Nature Biotechnology 25 (10): 1110–1111. 3
Hopkins, A.L. (2008). Network pharmacology: the next paradigm in drug discovery. Nature
Chemical Biology 4 (11): 682–690.
4 Patwardhan, B., Warude, D., Pushpangadan, P., and Bhatt, N. (2005). Ayurveda and traditional
Chinese medicine: a comparative overview. Evidence-based Complementary and Alternative Medicine
2: 465–473.
5 Mukheriee, P.K. and Wahile, A. (2006). Integrated approaches towards drug development from
Ayurveda and other Indian system of medicines. Journal of Ethnopharmacology 103 (1): 25–35.
6 Atanasov, A.G., Zotchev, S.B., Dirsch, V.M. et al. (2021). Natural products in drug discovery:
advances and opportunities. Nature Reviews Drug Discovery 20 (3): 200–216.
7 Choo, M.Z.Y. and Chai, C.L.L. (2023). Chapter Two—The polypharmacology of natural products in
drug discovery and development. In: Annual Reports in Medicinal Chemistry (ed. K.-H. Altmann),
55–100. 61: Academic Press.
8 Mohs, R.C. and Greig, N.H. (2017). Drug discovery and development: role of basic biological
research. Alzheimer’s & Dementia (New York, NY) 3 (4): 651–657.

eferences 279
9 Kiriiri, G.K., Njogu, P.M., and Mwangi, A.N. (2020). Exploring different approaches to improve the
success of drug discovery and development projects: a review. Future Journal of Pharmaceutical
Sciences 6 (1): 27.
10 Vora, L.K., Gholap, A.D., Jetha, K. et al. (2023). Artificial intelligence in pharmaceutical
technology and drug delivery design. Pharmaceutics 15 (7): 1916.
11 Seyhan, A.A. (2019). Lost in translation: the valley of death across preclinical and clinical divide –
identification of problems and overcoming obstacles. Translational Medicine Communications
4 (1): 18.
12 de Vrueh, R.L.A. and Crommelin, D.J.A. (2017). Reflections on the future of pharmaceutical
public-private partnerships: from input to impact. Pharmaceutical Research 34 (10): 1985–1999.
13 Glicksberg, B.S., Li, L., Chen, R. et al. (2019). Leveraging big data to transform drug discovery.
Methods in Molecular Biology (Clifton, NJ) 1939: 91–118.
14 Takebe, T., Imai, R., and Ono, S. (2018). The current status of drug discovery and development as
originated in United States Academia: the influence of industrial and academic collaboration on
drug discovery and development. Clinical and Translational Science 11 (6): 597–606.
15 Cheng, F., Ma, Y., Uzzi, B., and Loscalzo, J. (2020). Importance of scientific collaboration in
contemporary drug discovery and development: a detailed network analysis. BMC Biology
18 (1): 138.
16 Anderson, M. (2021). How the COVID-19 pandemic is changing clinical trial conduct and driving
innovation in bioanalysis. Bioanalysis 13 (15): 1195–1203.
17 Li, G., Hilgenfeld, R., Whitley, R., and De Clercq, E. (2023). Therapeutic strategies for COVID-19:
progress and lessons learned. Nature Reviews Drug Discovery 22 (6): 449–475.
18 Nogales, C., Mamdouh, Z.M., List, M. et al. (2022). Network pharmacology: curing causal
mechanisms instead of treating symptoms. Trends in Pharmacological Sciences 43 (2): 136–150.
19 Baryakova, T.H., Pogostin, B.H., Langer, R., and McHugh, K.J. (2023). Overcoming barriers to
patient adherence: the case for developing innovative drug delivery systems. Nature Reviews Drug
Discovery 22 (5): 387–409.
20 Wang, X., Hu, Y., Zhou, X., and Li, S. (2022). Network pharmacology and traditional medicine:
setting the new standards by combining in silico and experimental work. Frontiers in Pharmacology
13: 1002537.
21 Nguyen, C., Naunton, M., Thomas, J. etal. (2021). Availability and use of number needed to treat
(NNT) based decision aids for pharmaceutical interventions. Exploratory Research in Clinical and
Social Pharmacy 2: 100039.
22 Ingber, D.E. (2022). Human organs-on-chips for disease modelling, drug development and
personalized medicine. Nature Reviews Genetics 23 (8): 467–491.
23 Klein, J. (2022). Improving the reproducibility of findings by updating research methodology.
Quality & Quantity 56 (3): 1597–1609.
24 Gao, Q., Xu, L., and Cai, J. (2021). New drug targets for hypertension: a literature review.
Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1867 (3): 166037.
25 Noor, F., Rehman, A., Ashfaq, U.A. et al. (2022). Integrating network pharmacology and molecular
docking approaches to decipher the multi-target pharmacological mechanism of Abrus precatorius
L. acting on diabetes. Pharmaceuticals 15 (4): 414.
26 Zaman, M.A., Awais, N., Satnarine, T. et al. (2023). Comparing triple combination drug therapy
and traditional monotherapy for better survival in patients with high-risk hypertension: a
systematic review. Cureus 15 (7): e41398.
27 Kondej, M., Stępnicki, P., and Kaczor, A.A. (2018). Multi-target approach for drug discovery against
schizophrenia. International Journal of Molecular Sciences 19 (10): 3105.

12 Network-based Methods in Drug Discovery280
28 Talevi, A. (2015). Multi-target pharmacology: possibilities and limitations of the “skeleton key
approach” from a medicinal chemist perspective. Frontiers in Pharmacology 6: 205.
29 Löscher, W. (2021). Single-target versus multi-target drugs versus combinations of drugs with multiple
targets: preclinical and clinical evidence for the treatment or prevention of epilepsy. Frontiers in
Pharmacology 12: 730257.
30 Parmar, G. (2022). Nanotechnology in health care. Medknow 10 (2): 51–52. 31
Parmar, G., Chudasama, J.M., Aundhia, C. et al. (2024). A comprehensive review on eco-friendly
synthesized gold nanoparticles and its advantages. Nanotechnology and In Silico Tools 169–182.
32 Valcourt, D.M., Harris, J., Riley, R.S. et al. (2018). Advances in targeted nanotherapeutics: from
bioconjugation to biomimicry. Nano Research 11: 4999–5016.
33 Church, D.L. (2004). Major factors affecting the emergence and re-emergence of infectious
diseases. Clinics in Laboratory Medicine 24 (3): 559–586. v.
34 Zhou, Z., Chen, B., Chen, S. et al. (2020). Applications of network pharmacology in traditional
Chinese medicine research. Evidence-based Complementary and Alternative Medicine 2020:
1646905.
35 Vitali, F., Mulas, F., Marini, P., and Bellazzi, R. (2013). Network-based target ranking for
polypharmacological therapies. Journal of Biomedical Informatics 46 (5): 876–881.
36 Naik, B., Mattaparthi, V.S.K., Gupta, N. et al. (2022). Chemical system biology approach to identify
multi-targeting FDA inhibitors for treating COVID-19 and associated health complications.
Journal of Biomolecular Structure & Dynamics 40 (19): 9543–9567.
37 Zhao, Y., Gericke, O., Li, T. et al. (2023). Polypharmacology-labeled molecular networking: an
analytical technology workflow for accelerated identification of multiple bioactive constituents in
complex extracts. Analytical Chemistry 95 (9): 4381–4389.
38 Lee, J.H. (2003). Methicillin (Oxacillin)-resistant Staphylococcus aureus strains isolated from major
food animals and their potential transmission to humans. Applied and Environmental Microbiology
69 (11): 6489–6494.
39 Barnes, E.C., Kavanagh, A.M., Ramu, S. et al. (2013). Antibacterial serrulatane diterpenes from the
Australian native plant Eremophila microtheca. Phytochemistry 93: 162–169.
40 Cho, D.Y., Kim, Y.A., and Przytycka, T.M. (2012). Chapter 5: Network biology approach to complex
diseases. PLoS Computational Biology 8 (12): e1002820.
41 Turnbull, L., Hütt, M.-T., Ioannides, A.A. et al. (2018). Connectivity and complex systems: learning
from a multi-disciplinary perspective. Applied Network Science 3 (1): 11.
42 Fokunang, C.N., Ndikum, V., Tabi, O.Y. et al. (2011). Traditional medicine: past, present and future
research and development prospects and integration in the National Health System of Cameroon.
African Journal of Traditional, Complementary, and Alternative Medicines: AJTCAM 8 (3): 284–295.
43 Petrovska, B.B. (2012). Historical review of medicinal plants’ usage. Pharmacognosy Reviews
6 (11): 1–5.
44 Eshete, M.A. and Molla, E.L. (2021). Cultural significance of medicinal plants in healing human
ailments among Guji semi-pastoralist people, Suro Barguda District, Ethiopia. Journal of
Ethnobiology and Ethnomedicine 17 (1): 61.
45 Harakeh, S., Niyazi, H.A., Niyazi, H.A. et al. (2024). Integrated network pharmacology approach to
evaluate bioactive phytochemicals of Acalypha indica and their mechanistic actions to suppress
target genes of tuberculosis. ACS Omega 9 (2): 2204–2219.
46 Noor, F., Tahir ul Qamar, M., Ashfaq, U.A. et al. (2022). Network pharmacology approach for
medicinal plants: review and assessment. Pharmaceuticals 15 (5): 572.
47 Mohanraj, K., Karthikeyan, B.S., Vivek-Ananth, R.P. et al. (2018). IMPPAT: a curated database of
Indian medicinal plants, phytochemistry and therapeutics. Scientific Reports 8 (1): 4329.

eferences 281
48 Rai, M.K. (1995). A review on some antidiabetic plants of India. Ancient Science of Life
14 (3): 168.
49 Dash, V.B. and Kashyap, V.L. (1999). Ayurveda Materia Medica, 711. Concept Publishing
Company.
50 Lagunin, A.A., Goel, R.K., Gawande, D.Y. et al. (2014). Chemo- and bioinformatics resources for in
silico drug discovery from medicinal plants beyond their traditional use: a critical review. Natural
Product Reports 31 (11): 1585–1611.
51 Polur, H., Joshi, T., Workman, C.T. et al. (2011). Back to the roots: prediction of biologically active
natural products from ayurveda traditional medicine. Molecular Informatics 30 (2–3): 181–187.
52 Chen, C.Y.-C. (2011). TCM Database@ Taiwan: the world’s largest traditional Chinese medicine
database for drug screening in silico. PLoS One 6 (1): e15939.
53 Vainio, M.J. and Johnson, M.S. (2007). Generating conformer ensembles using a multiobjective
genetic algorithm. Journal of Chemical Information and Modeling 47 (6): 2462–2474.
54 O’Boyle, N.M., Banck, M., James, C.A. et al. (2011). Open Babel: an open chemical toolbox. Journal
of Cheminformatics 3 (1): 1–14.
55 Cheng, F., Li, W., Zhou, Y. et al. (2012). admetSAR: A Comprehensive Source and Free Tool for
Assessment of Chemical ADMET Properties. ACS Publications.
56 Lipinski, C.A., Lombardo, F., Dominy, B.W., and Feeney, P.J. (2012). Experimental and
computational approaches to estimate solubility and permeability in drug discovery and
development settings. Advanced Drug Delivery Reviews 64: 4–17.
57 Lobell, M., Hendrix, M., Hinzen, B. et al. (2006). In silico ADMET traffic lights as a tool for the
prioritization of HTS hits. ChemMedChem: Chemistry Enabling Drug Discovery 1 (11): 1229–1236.
58 Hughes, J.D., Blagg, J., Price, D.A. et al. (2008). Physiochemical drug properties associated with in
vivo toxicological outcomes. Bioorganic & Medicinal Chemistry Letters 18 (17): 4872–4875.
59 Gleeson, M.P. (2008). Generation of a set of simple, interpretable ADMET rules of thumb. Journal
of Medicinal Chemistry 51 (4): 817–834.
60 Veber, D.F., Johnson, S.R., Cheng, H.-Y. et al. (2002). Molecular properties that influence the oral
bioavailability of drug candidates. Journal of Medicinal Chemistry 45 (12): 2615–2623.
61 Egan, W.J., Merz, K.M., and Baldwin, J.J. (2000). Prediction of drug absorption using multivariate
statistics. Journal of Medicinal Chemistry 43 (21): 3867–3877.
62 Szklarczyk, D., Santos, A., Von Mering, C. et al. (2016). STITCH 5: augmenting protein–chemical
interaction networks with tissue and affinity data. Nucleic Acids Research 44 (D1): D380–D384.
63 Olsson, T. and Oprea, T.I. (2001). Cheminformatics: a tool for decision-makers in drug discovery.
Current Opinion in Drug Discovery & Development 4 (3): 308–313.
64 Law, V., Knox, C., Djoumbou, Y. et al. (2014). DrugBank 4.0: shedding new light on drug
metabolism. Nucleic Acids Research 42 (D1): D1091–D1097.
65 Hamosh, A., Scott, A.F., Amberger, J.S. et al. (2005). Online Mendelian Inheritance in Man
(OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research
33 (suppl_1): D514–D517.
66 Bodenreider, O. (2004). The unified medical language system (UMLS): integrating biomedical
terminology. Nucleic Acids Research 32 (suppl_1): D267–D270.
67 Vivek-Ananth, R.P., Mohanraj, K., Sahoo, A.K., and Samal, A. (2023). IMPPAT 2.0: an enhanced
and expanded phytochemical atlas of Indian medicinal plants. ACS Omega 8 (9): 8827–8845.
68 Doncheva, N.T., Morris, J.H., Gorodkin, J., and Jensen, L.J. (2019). Cytoscape StringApp: network
analysis and visualization of proteomics data. Journal of Proteome Research 18 (2): 623–632.
69 Ebrahimi, S.B. and Samanta, D. (2023). Engineering protein-based therapeutics through structural
and chemical design. Nature Communications 14 (1): 2411.

12 Network-based Methods in Drug Discovery282
70 Tang, J. and Aittokallio, T. (2014). Network pharmacology strategies toward multi-target anticancer
therapies: from computational models to experimental design principles. Current Pharmaceutical
Design 20 (1): 23–36.
71 Zheng, S., Xue, T., Wang, B. et al. (2022). Application of network pharmacology in the study of
mechanism of Chinese medicine in the treatment of ulcerative colitis: a review. Frontiers in
Bioinformatics 2: 928116.
72 Askr, H., Elgeldawi, E., Aboul Ella, H. et al. (2023). Deep learning in drug discovery: an integrative
review and future challenges. Artificial Intelligence Review 56 (7): 5975–6037.
73 Ekor, M. (2014). The growing use of herbal medicines: issues relating to adverse reactions and
challenges in monitoring safety. Frontiers in Pharmacology 4: 177.
74 Pandey, M.M., Rastogi, S., and Rawat, A.K. (2013). Indian traditional ayurvedic system of medicine
and nutritional supplementation. Evidence-based Complementary and Alternative Medicine: Ecam
2013: 376327.
75 Sharma, R., Bedarkar, P., Timalsina, D. et al. (2022). [Retracted] Bhavana, an ayurvedic
pharmaceutical method and a versatile drug delivery platform to prepare potentiated micro-nano
sized drugs: core concept and its current relevance. Bioinorganic Chemistry and Applications 2022:
1685393.
76 Das, C., Ghosh, G., and Das, D. (2017). Ayurvedic liquid dosage form Asava and Arista: an
overview. Indian Journal Of Pharmaceutical Education And Research 51: 169–176.
77 Savrikar, S.S. and Ravishankar, B. (2011). Introduction to ‘Rasashaastra’ the Iatrochemistry of
Ayurveda. African Journal of Traditional, Complementary, and Alternative Medicines: AJTCAM
8 (5 Suppl): 66–82.
78 Gokarn, R.A., Gokarn, S.R., and Hiremath, S.G. (2014). Process standardization and
characterization of Rajata Sindura. AY U 35 (1): 63–70.
79 Mishra, A., Mishra, A.K., Ghosh, A.K., and Jha, S. (2013). Standardization of a traditional
polyherbo-mineral formulation – Brahmi vati. African Journal of Traditional, Complementary, and
Alternative Medicines: AJTCAM 10 (3): 390–396.
80 Maurya, S.K., Seth, A., Laloo, D. et al. (2015). Śodhana: an ayurvedic process for detoxification and
modification of therapeutic activities of poisonous medicinal plants. Ancient Science of Life 34 (4):
188–197.
81 Kaur, J., Baghel, D., Singh, S., and Mittal, A. (2019). Avaleha kalpana (medicated semisolid preparation):
an synoptic overview. International Journal of Research and Analytical Reviews 6: 591–599.
82 Banothe, G.D., Mahanta, V., Gupta, S.K., and Dudhamal, T.S. (2018). A clinical evaluation of
Kanchanara Guggulu and Bala Taila Matra Basti in the management of Mutraghata with special
reference to benign prostatic hyperplasia. AYU 39 (2): 65–71.
83 Yuan, H., Ma, Q., Ye, L., and Piao, G. (2016). The traditional medicine and modern medicine from
natural products. Molecules (Basel, Switzerland) 21 (5): 559.
84 Parmar, G.R., Shah, A.P., Sailor, G.U., and Seth, A.K. (2021). In silico discovery of novel
phytoconstituents of Amyris pinnata as mitotic spindle kinase inhibitor. Current Drug Research
Reviews 12 (2): 175–182.
85 Dias, D.A., Urban, S., and Roessner, U. (2012). A historical overview of natural products in drug
discovery. Metabolites 2 (2): 303–336.
86 Riaz, M., Khalid, R., Afzal, M. et al. (2023). Phytobioactive compounds as therapeutic agents for
human diseases: a review. Food Science & Nutrition 11 (6): 2500–2529.
87 Parmar, G. and Baile, S. (2020). A review: pharmacognosy, phytochemistry, ethnopharmacology
and biological activity of inula racemose. International Journal of Pharmaceutical Research
12 (Spl 1): 412–417.
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