Intrinsically Disordered Proteins: From Sequence and Conformational Properties toward Drug Discovery

ChemBioChem ◽  
2012 ◽  
Vol 13 (7) ◽  
pp. 930-950 ◽  
Author(s):  
Nasrollah Rezaei-Ghaleh ◽  
Martin Blackledge ◽  
Markus Zweckstetter
Keyword(s):  
Drug Discovery ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Conformational Properties

Mathematical and Computational Techniques for Drug Discovery: Promises and Developments

2019 ◽  
Vol 18 (32) ◽  
pp. 2774-2799 ◽  
Author(s):  
Krishnan Balasubramanian
Keyword(s):  
Drug Discovery ◽  
Protein Interactions ◽  
Quantum Chemical ◽  
Intrinsically Disordered Proteins ◽  
Hepatitis Virus ◽  
Disordered Proteins ◽  
Computational Techniques ◽  
Large Set ◽  
Structural Protein ◽  
Intrinsically Disordered

We review various mathematical and computational techniques for drug discovery exemplifying some recent works pertinent to group theory of nested structures of relevance to phylogeny, topological, computational and combinatorial methods for drug discovery for multiple viral infections. We have reviewed techniques from topology, combinatorics, graph theory and knot theory that facilitate topological and mathematical characterizations of protein-protein interactions, molecular-target interactions, proteomics, genomics and statistical data reduction procedures for a large set of starting chemicals in drug discovery. We have provided an overview of group theoretical techniques pertinent to phylogeny, protein dynamics especially in intrinsically disordered proteins, DNA base permutations and related algorithms. We consider computational techniques derived from high level quantum chemical computations such as QM/MM ONIOM methods, quantum chemical optimization of geometries complexes, and molecular dynamics methods for providing insights into protein-drug interactions. We have considered complexes pertinent to Hepatitis Virus C non-structural protein 5B polymerase receptor binding of C5-Arylidebne rhodanines, complexes of synthetic potential vaccine molecules with dengue virus (DENV) and HIV-1 virus as examples of various simulation studies that exemplify the utility of computational tools. It is demonstrated that these combinatorial and computational techniques in conjunction with experiments can provide promising new insights into drug discovery. These techniques also demonstrate the need to consider a new multiple site or allosteric binding approach to drug discovery, as these studies reveal the existence of multiple binding sites.

scholarly journals Quantitative Determination of the Conformational Properties of Partially Folded and Intrinsically Disordered Proteins Using NMR Dipolar Couplings

Structure ◽  
2009 ◽  
Vol 17 (9) ◽  
pp. 1169-1185 ◽  
Author(s):  
Malene Ringkjøbing Jensen ◽  
Phineus R.L. Markwick ◽  
Sebastian Meier ◽  
Christian Griesinger ◽  
Markus Zweckstetter ◽  
...  
Keyword(s):  
Quantitative Determination ◽  
Intrinsically Disordered Proteins ◽  
Dipolar Couplings ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Conformational Properties

Conformational properties of intrinsically disordered proteins bound to the surface of silica nanoparticles

2018 ◽  
Vol 1862 (7) ◽  
pp. 1556-1564 ◽  
Author(s):  
Michele Vitali ◽  
Valentina Rigamonti ◽  
Antonino Natalello ◽  
Barbara Colzani ◽  
Svetlana Avvakumova ◽  
...  
Keyword(s):  
Silica Nanoparticles ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Conformational Properties

Influence of macromolecular crowding on the charge regulation of intrinsically disordered proteins

Soft Matter ◽  
2021 ◽  
Author(s):  
Pablo M. Blanco ◽  
Sergio Madurga ◽  
Josep L. Garcés ◽  
Francesc Mas ◽  
Rita S. Dias
Keyword(s):  
Monte Carlo ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Grand Canonical Monte Carlo ◽  
Histatin 5 ◽  
Charge Regulation ◽  
Intrinsically Disordered ◽  
Conformational Properties ◽  
Β Amyloid ◽  
Grand Canonical

The coupling between the ionization and conformational properties of two IDPs, histatin-5 and β-amyloid 42, in the presence of neutral and charged crowders is studied by performing semi-grand canonical Monte Carlo simulations.

ChemInform Abstract: Intrinsically Disordered Proteins: From Sequence and Conformational Toward Drug Discovery

ChemInform ◽  
2012 ◽  
Vol 43 (29) ◽  
pp. no-no
Author(s):  
Nasrollah Rezaei-Ghaleh ◽  
Martin Blackledge ◽  
Markus Zweckstetter
Keyword(s):  
Drug Discovery ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered
Sign in / Sign up

Export Citation Format

Share Document