Computational Methods for Drug Repurposing

1. Front Matter

   Pages i-xi

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2. Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing

   • E. Sila Ozdemir, Farideh Halakou, Ruth Nussinov, Attila Gursoy, Ozlem Keskin

   Pages 1-21

3. Performing an In Silico Repurposing of Existing Drugs by Combining Virtual Screening and Molecular Dynamics Simulation

   • Farzin Sohraby, Milad Bagheri, Hassan Aryapour

   Pages 23-43

4. Repurposing Drugs Based on Evolutionary Relationships Between Targets of Approved Drugs and Proteins of Interest

   • Sohini Chakraborti, Gayatri Ramakrishnan, Narayanaswamy Srinivasan

   Pages 45-59

5. Drug Repositioning by Mining Adverse Event Data in ClinicalTrials.gov

   • Eric Wen Su

   Pages 61-72

6. Transcriptomic Data Mining and Repurposing for Computational Drug Discovery

   • Yunguan Wang, Jaswanth Yella, Anil G. Jegga

   Pages 73-95

7. Network-Based Drug Repositioning: Approaches, Resources, and Research Directions

   • Salvatore Alaimo, Alfredo Pulvirenti

   Pages 97-113

8. A Computational Bipartite Graph-Based Drug Repurposing Method

   • Si Zheng, Hetong Ma, Jiayang Wang, Jiao Li

   Pages 115-127

9. Implementation of a Pipeline Using Disease-Disease Associations for Computational Drug Repurposing

   • Preethi Balasundaram, Rohini Kanagavelu, Nivya James, Sayoni Maiti, Shanthi Veerappapillai, Ramanathan Karuppaswamy

   Pages 129-148

10. An Application of Computational Drug Repurposing Based on Transcriptomic Signatures

    • Evangelos Karatzas, George Kolios, George M. Spyrou

    Pages 149-177

11. Drug-Induced Expression-Based Computational Repurposing of Small Molecules Affecting Transcription Factor Activity

    • Kaitlyn Gayvert, Olivier Elemento

    Pages 179-184

12. A Drug Repurposing Method Based on Drug-Drug Interaction Networks and Using Energy Model Layouts

    • Mihai Udrescu, Lucreţia Udrescu

    Pages 185-201

13. Integrating Biological Networks for Drug Target Prediction and Prioritization

    • Xiao Ji, Johannes M. Freudenberg, Pankaj Agarwal

    Pages 203-218

14. Using Drug Expression Profiles and Machine Learning Approach for Drug Repurposing

    • Kai Zhao, Hon-Cheong So

    Pages 219-237

15. Computational Prediction of Drug-Target Interactions via Ensemble Learning

    • Ali Ezzat, Min Wu, Xiaoli Li, Chee-Keong Kwoh

    Pages 239-254

16. A Machine-Learning-Based Drug Repurposing Approach Using Baseline Regularization

    • Zhaobin Kuang, Yujia Bao, James Thomson, Michael Caldwell, Peggy Peissig, Ron Stewart et al.

    Pages 255-267

17. Machine Learning Approach for Predicting New Uses of Existing Drugs and Evaluation of Their Reliabilities

    • Yutaka Fukuoka

    Pages 269-279

18. A Drug-Target Network-Based Supervised Machine Learning Repurposing Method Allowing the Use of Multiple Heterogeneous Information Sources

    • André C. A. Nascimento, Ricardo B. C. Prudêncio, Ivan G. Costa

    Pages 281-289

19. Heter-LP: A Heterogeneous Label Propagation Method for Drug Repositioning

    • Maryam Lotfi Shahreza, Nasser Ghadiri, James R. Green

    Pages 291-316

20. Tripartite Network-Based Repurposing Method Using Deep Learning to Compute Similarities for Drug-Target Prediction

    • Nansu Zong, Rachael Sze Nga Wong, Victoria Ngo

    Pages 317-328

This detailed book explores techniques commonly used for research into drug repurposing, a well-known strategy to find alternative indications for drugs which have already undergone toxicology and pharma-kinetic studies but have failed later stages during the development, via computational methods. Thereby, it addresses the intense challenges of identifying the appropriate type of algorithm and relevant technical information for computational repurposing. Written for the highly successful Methods in Molecular Biology series, the authors of each chapter use their experience in the field to describe the implementation and successful use of a specific repurposing method thus providing lab-ready instruction. 

Authoritative and practical, Computational Methods for Drug Repurposing serves as an ideal guide to researchers interested in this vital area of drug development.

• Drug discovery
• Alternative indications for drugs
• Algorithm adaptation
• In silico methods
• Pharmaceutical development

• Insilico Medicine, Inc., Rockville, USA

  Quentin Vanhaelen

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