Rational Drug Design Methods and Protocols By Zheng, Yi (Ed.)

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Rational Drug Design

Methods and Protocols

SeriesMethods in Molecular Biology, Vol. 928

Zheng, Yi (Ed.)

2012, XI, 230 p. 58 illus., 22 illus. in color

 

  • Aids scientists in further study of rational drug design
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Over the past  three decades there have been new developments in therapeutic drug design. InRational 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.

Content Level » Professional/practitioner

Keywords » ATP binding GTPases Structure based virtual screening anti-sense microRNA -drug discovery drug resistance molecular biology phosphotases rational designed wnt pathway targets

 

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
 1 On Setting Up and Assessing Docking Simulations for Virtual Screening. . . . . 1
Jacek Biesiada, Aleksey Porollo, and Jaroslaw Meller
 2 Virtual Ligand Screening Combined with NMR to Identify Dvl PDZ 
Domain Inhibitors Targeting the Wnt Signaling . . . . . . . . . . . . . . . . . . . . . . . 17
Jufang Shan and Jie J. Zheng
 3 Rational Design of Rho GTPase-Targeting Inhibitors . . . . . . . . . . . . . . . . . . . 29
Xun Shang and Yi Zheng
 
4 Rational Design of Peptide Ligands Against a Glycolipid by NMR Studies. . . . 39
Wenyong Tong, Tara Sprules, Kalle Gehring, and H. Uri Saragovi
 5 A Combinatorial Strategy for the Acquisition of Potent and Specific 
Protein Tyrosine Phosphatase Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Sheng Zhang, Lan Chen, David S. Lawrence, and Zhong-Yin Zhang
 
6 Identification of Allosteric Inhibitors of p21-Activated Kinase . . . . . . . . . . . . . 67
Julien Viaud and Jeffrey R. Peterson
 7 Using a Modified Yeast Two-Hybrid System to Screen 
for Chemical GEF Inhibitors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Anne Blangy and Philippe Fort
 8 Random Mutagenesis of Peptide Aptamers as an Optimization Strategy 
for Inhibitor Screening . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
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. . . . . . . . . . . . . . . . . . . 119
Charles S. Craik and Tina Shahian
10 Use of a Fluorescent ATP Analog to Probe the Allosteric Conformational 
Change in the Active Site of the Protein Kinase PDK1 . . . . . . . . . . . . . . . . . . 133
Valerie Hindie, Laura A. Lopez-Garcia, and Ricardo M. Biondi
11 Affinity Purification of Protein Kinases that Adopt a Specific 
Inactive Conformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Pratistha Ranjitkar and Dustin J. Maly
12 Determination of the Kinetics and Thermodynamics of Ligand Binding 
to a Specific Inactive Conformation in Protein Kinases . . . . . . . . . . . . . . . . . . 153
Sanjay B. Hari, Pratistha Ranjitkar, and Dustin J. Maly
13 Purification and Specific Assays for Measuring APE-1 Endonuclease Activity . . 161
Adrian Esqueda, Mohammed Z. Mohammed, Srinivasan Madhusudan, 
and Nouri Neamativiii Contents
14 An In Vitro Screening to Identify Drug-Resistant Mutations 
for Target-Directed Chemotherapeutic Agents . . . . . . . . . . . . . . . . . . . . . . . . 175
Mohammad Azam
15 Utilizing AntagomiR (Antisense microRNA) to Knock Down 
microRNA in Murine Bone Marrow Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Peixuan Guo, Yi Shu, Daniel Binzel, and Mathieu Cinier
17 Mouse Models for Tumor Metastasis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Shengyu Yang, J. Jillian Zhang, and Xin-Yun Huang
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229

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