Rational Drug Design: Methods and Protocols

ISBN-13: 9781493959006 / Angielski / Miękka / 2016 / 230 str.

Yi Zheng

Opis

This Methods in Molecular Biology(TM) book details rational drug design, including virtual screening of chemical hits, lead discovery by high throughput screening, combinatorial and fragment based lead generation, peptide based drug discovery and animal models.

Recenzje

From the reviews:

"This book covers some of the tools and techniques involved in rational drug design with a series of case studies designed to act as a compendium of methods and protocols intended for readers to adopt or modify. ... The book would therefore make interesting reading to any student or investigator looking to gain a wider appreciation of strategies and activities across different disciplines or unfamiliar projects in the early drug discovery phase as well as the primary target audience of organic/medicinal chemists and molecular biologists." (Stefan Kavanagh, BTS Newsletter - The British Toxicology Society, Issue 43, Winter, 2013)

Spis treści

1. On Setting up and Assessing Docking Simulations for Virtual Screening

Jacek Biesiada, Aleksey Porollo, Jaroslaw Meller

 

2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt Signaling

Jufang Shan and Jie J. Zheng

 

3. Rational Design of Rho GTPase Targeting Inhibitors

Xun Shang and Yi Zheng

 4. Rational Design of Peptide Ligands Against a Glycolipid by NMR Studies

Wenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi

 

5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase Inhibitors

Sheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang

 

6. Identification of Allosteric Inhibitors of p21-Activated Kinase

Julien Viaud and Jeffrey R. Peterson

 7. Using a Modified Yeast Two-hybrid System to Screen for Chemical GEF InhibitorsAnne Blangy and Philippe Fort .

 

8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor Screening

Nathalie Bouquier, Sylvie Fromont, Anne Debant and Susanne Schmidt

 

9. A Screening Strategy for Trapping the Inactive Conformer of a Dimeric Enzyme with a Small Molecule Inhibitor

Tina Shahian and Charles S. Craik

 

10. Use of a Fluorescent ATP Analog to Probe the Allosteric Conformational Change in the Active Site of the Protein Kinase PDK1

Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi

 11. Affinity Purification of Protein Kinases that Adopt a Specific Inactive ConformationPratistha Ranjitkar and Dustin J. Maly 12. Determination of the Kinetics and Thermodynamics of Ligand Binding to a Specific Inactive Conformation in Protein KinasesSanjay B. Hari, Pratistha Ranjitkar and Dustin J. Maly

 

13. Purification and Specific Assays for Measuring APE-1 Endonuclease Activity

Adrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati

 

14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic Agents

Mohammad Azam

 

15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow Cells

Chinavenmeni S. Velu and H. Leighton Grimes

 

16. Synthesis, Conjugation, and Labeling of Multifunctional pRNA Nanoparticles for Specific Delivery of siRNA, Drugs and Other Therapeutics to Target Cells

Mathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo

 

17. Mouse Models for Tumor Metastasis

Shengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang

1. On Setting up and Assessing Docking simulations for Virtual Screening

Jacek Biesiada, Aleksey Porollo, Jaroslaw Meller

 

2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt Signaling

Jufang Shan and Jie J. Zheng

 

3. Rational Design of Rho GTPase Targeting Inhibitors

Xun Shang and Yi Zheng

 4. Rational Design of Peptide Ligands Against a Glycolipid by NMR Studies

Wenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi

 

5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase Inhibitors

Sheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang

 

6. Identification of Allosteric Inhibitors of p21-Activated Kinase

Julien Viaud and Jeffrey R. Peterson

 7. Using a Modified Yeast Two-hybrid System to Screen for Chemical GEF InhibitorsAnne Blangy and Philippe Fort .

 

8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor Screening

Nathalie Bouquier, Sylvie Fromont, Anne Debant and Susanne Schmidt

 

9. A Screening Strategy for Trapping the Inactive Conformer of a Dimeric Enzyme with a Small Molecule Inhibitor

Tina Shahian and Charles S. Craik

 

10. Use of a Fluorescent ATP Analog to Probe the Allosteric Conformational Change in the Active Site of the Protein Kinase PDK1

Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi

 11. Affinity Purification of Protein Kinases that Adopt a Specific Inactive ConformationPratistha Ranjitkar and Dustin J. Maly 12. Determination of the Kinetics and Thermodynamics of Ligand Binding to a Specific Inactive Conformation in Protein KinasesSanjay B. Hari, Pratistha Ranjitkar and Dustin J. Maly

 

13. Purification and Specific Assays for Measuring APE-1 Endonuclease Activity

Adrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati

 

14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic Agents

Mohammad Azam

 

15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow Cells

Chinavenmeni S. Velu and H. Leighton Grimes

 

16. Synthesis, Conjugation, and Labeling of Multifunctional pRNA Nanoparticles for Specific Delivery of siRNA, Drugs and Other Therapeutics to Target Cells

Mathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo

 

17. Mouse Models for Tumor Metastasis

Shengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang

1. On Setting up and Assessing Docking simulations for Virtual Screening

Jacek Biesiada, Aleksey Porollo, Jaroslaw Meller

 

2. Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ Domain Inhibitors Targeting the Wnt Signaling

Jufang Shan and Jie J. Zheng

 

3. Rational Design of Rho GTPase Targeting Inhibitors

Xun Shang and Yi Zheng

 4. Rational Design of Peptide Ligands Against a Glycolipid by NMR Studies

Wenyong Tong, Tara Sprules, Kalle Gehring, H. Uri Saragovi

 

5. A Combinatorial Strategy for the Acquisition of Potent and Specific Protein Tyrosine Phosphatase Inhibitors

Sheng Zhang, Lan Chen, David S. Lawrence and Zhong-Yin Zhang

 

6. Identification of Allosteric Inhibitors of p21-Activated Kinase

Julien Viaud and Jeffrey R. Peterson

 7. Using a Modified Yeast Two-hybrid System to Screen for Chemical GEF InhibitorsAnne Blangy and Philippe Fort .

 

8. Random Mutagenesis of Peptide Aptamers As An Optimization Strategy for Inhibitor Screening

Nathalie Bouquier, Sylvie Fromont, Anne Debant and Susanne Schmidt

 

9. A Screening Strategy for Trapping the Inactive Conformer of a Dimeric Enzyme with a Small Molecule Inhibitor

Tina Shahian and Charles S. Craik

 

10. Use of a Fluorescent ATP Analog to Probe the Allosteric Conformational Change in the Active Site of the Protein Kinase PDK1

Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi

 11. Affinity Purification of Protein Kinases that Adopt a Specific Inactive ConformationPratistha Ranjitkar and Dustin J. Maly 12. Determination of the Kinetics and Thermodynamics of Ligand Binding to a Specific Inactive Conformation in Protein KinasesSanjay B. Hari, Pratistha Ranjitkar and Dustin J. Maly

 

13. Purification and Specific Assays for Measuring APE-1 Endonuclease Activity

Adrian Esqueda, Mohammed Z Mohammed, Srinivasan Madhusudan, and Nouri Neamati

 

14. An in vitro Screening to Identify Drug Resistant Mutations for Target-directed Chemotherapeutic Agents

Mohammad Azam

 

15. Utilizing AntagomiR (anti-sense microRNA) to Knock Down microRNA in Murine Bone Marrow Cells

Chinavenmeni S. Velu and H. Leighton Grimes

 

16. Synthesis, Conjugation, and Labeling of Multifunctional pRNA Nanoparticles for Specific Delivery of siRNA, Drugs and Other Therapeutics to Target Cells

Mathieu Cinier, Yi Shu, Daniel Binzel, and Peixuan Guo

 

17. Mouse Models for Tumor Metastasis

Shengyu Yang,  J. Jillian Zhang, and Xin-Yun Huang

Blurb

Over the past  three decades there have been new developments in therapeutic drug design. In Rational Drug Design: Methods and Protocols,  expert researchers in the field detail many of the methodologies used to study rational drug design. These include methods such as virtual screening of chemical hits, rational lead discovery by high throughput screening, combinatorial and fragment based lead generation, peptide based drug discovery, and animal models of lead validation. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and practical, Rational Drug Design: Methods and Protocols seeks to aid scientists in the further study of rational drug design and future drug discovery.