scholarly journals Thermodynamics-based drug design: strategies for inhibiting protein–protein interactions

2011 ◽  
Vol 3 (9) ◽  
pp. 1129-1137 ◽  
Author(s):  
Arne Schön ◽  
Sonia Y Lam ◽  
Ernesto Freire
Keyword(s):  
Drug Design ◽  
Protein Interactions ◽  
Design Strategies ◽  
Protein Protein Interactions ◽  
Inhibiting Protein

CHAPTER 8. Double-click Stapled Peptides for Inhibiting Protein–Protein Interactions

2017 ◽  
pp. 164-187 ◽  
Author(s):  
K. Sharma ◽  
D. L. Kunciw ◽  
W. Xu ◽  
M. M. Wiedmann ◽  
Y. Wu ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Stapled Peptides ◽  
Inhibiting Protein

scholarly journals Structure-Based Stabilization of Non-native Protein–Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design

2020 ◽  
Vol 63 (6) ◽  
pp. 3131-3141 ◽  
Author(s):  
Shan-Meng Lin ◽  
Shih-Chao Lin ◽  
Jia-Ning Hsu ◽  
Chung-ke Chang ◽  
Ching-Ming Chien ◽  
...  
Keyword(s):  
Drug Design ◽  
Protein Interactions ◽  
Antiviral Drug ◽  
Native Protein ◽  
Protein Protein Interactions ◽  
Nucleocapsid Proteins

scholarly journals Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis

2016 ◽  
Vol 113 (50) ◽  
pp. E8051-E8058 ◽  
Author(s):  
Fang Bai ◽  
Faruck Morcos ◽  
Ryan R. Cheng ◽  
Hualiang Jiang ◽  
José N. Onuchic
Keyword(s):  
Drug Design ◽  
Protein Interactions ◽  
Binding Sites ◽  
Hot Spots ◽  
Therapeutic Agents ◽  
Molecular Probes ◽  
Therapeutic Drug ◽  
Protein Protein Interactions ◽  
Protein Surface ◽  
Fragment Docking

Protein−protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein−protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

scholarly journals 26th Annual GP2A Medicinal Chemistry Conference & 32nd Journées Franco-Belges de Pharmacochimie

2019 ◽  
Vol 12 (2) ◽  
pp. 73
Author(s):  
Patrick Dallemagne ◽  
Christophe Rochais ◽  
Pascal Marchand ◽  
Thierry Besson
Keyword(s):  
Drug Design ◽  
Natural Product ◽  
Protein Interactions ◽  
Medicinal Chemistry ◽  
Young Researcher ◽  
Protein Protein Interactions ◽  
Computer Aided Drug Design ◽  
Computer Aided ◽  
Wide Group ◽  
New Strategies

As a joint meeting, the 26th Medicinal Chemistry Conference of GP2A and 32nd Journées Franco-Belges de Pharmacochimie took place between 13th and 15th June at Asnelles sur Mer (Normandie, France), providing a unique opportunity for a wide group of European medicinal chemists to engage. Topics included chemical tools for medicinal chemistry, protein-protein interactions, epigenetics, natural product-inspired molecules, computer-aided drug design, and new strategies for the design and development of drugs. Abstracts of invited lectures, proffered young researcher communications, flash communications and posters presented during the meeting are collected in this report.

Divide-and-Link Peptide Docking: A Fragment-Based Peptide Docking Protocol

2021 ◽  
Author(s):  
Lu Sun ◽  
Tingting Fu ◽  
Dan Zhao ◽  
Hongjun Fan ◽  
Shijun Zhong
Keyword(s):  
Protein Folding ◽  
Drug Design ◽  
Protein Interactions ◽  
Structural Data ◽  
Peptide Drug ◽  
Protein Protein Interactions ◽  
Peptide Docking ◽  
Docking Protocol ◽  
Peptide Interaction

Protein-peptide interaction is crucial for various important cellular regulations, and also a basis for understanding protein-protein interactions, protein folding and peptide drug design. Due to the limited structural data obtained...

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