![conference banner](/images/conference-banner.jpeg)
Abstract
Biological systems rely on the establishment of interactions between biomolecules, which take place in the aqueous environment of the cell. It was already demonstrated that a small set of residues at the interface, Hot-Spots(HS), contributes significantly to the binding free energy. However, these energetic determinants of affinity and specificity are still not fully understood. Moreover, the contribution of water to their HS character is also poorly characterized. In this review, we have focused on the structural data available that support the occlusion of HS from solvent, and therefore the “Oring theory”not only on protein-protein but also on protein-DNA complexes. We also emphasized the use of Solvent Accessible Surface Area (SASA) features in a variety of machine-learning approaches that aim to detect binding HS.
Keywords: Feature-based methods, Hot-spots, O-ring, Solvent accessible surface area, Water, Wet-spots.
Current Topics in Medicinal Chemistry
Title:The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot
Volume: 15 Issue: 20
Author(s): Irina S. Moreira
Affiliation:
Keywords: Feature-based methods, Hot-spots, O-ring, Solvent accessible surface area, Water, Wet-spots.
Abstract: Biological systems rely on the establishment of interactions between biomolecules, which take place in the aqueous environment of the cell. It was already demonstrated that a small set of residues at the interface, Hot-Spots(HS), contributes significantly to the binding free energy. However, these energetic determinants of affinity and specificity are still not fully understood. Moreover, the contribution of water to their HS character is also poorly characterized. In this review, we have focused on the structural data available that support the occlusion of HS from solvent, and therefore the “Oring theory”not only on protein-protein but also on protein-DNA complexes. We also emphasized the use of Solvent Accessible Surface Area (SASA) features in a variety of machine-learning approaches that aim to detect binding HS.
Export Options
About this article
Cite this article as:
Moreira S. Irina, The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot, Current Topics in Medicinal Chemistry 2015; 15 (20) . https://dx.doi.org/10.2174/1568026615666150519103733
DOI https://dx.doi.org/10.2174/1568026615666150519103733 |
Print ISSN 1568-0266 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4294 |
Call for Papers in Thematic Issues
Adaptogens—History and Future Perspectives
Adaptogens are pharmacologically active compounds or plant extracts that are associated with the ability to enhance the body’s stability against stress. The intake of adaptogens is associated not only with a better ability to adapt to stress and maintain or normalise metabolic functions but also with better mental and physical ...read more
AlphaFold in Medicinal Chemistry: Opportunities and Challenges
AlphaFold, a groundbreaking AI tool for protein structure prediction, is revolutionizing drug discovery. Its near-atomic accuracy unlocks new avenues for designing targeted drugs and performing efficient virtual screening. However, AlphaFold's static predictions lack the dynamic nature of proteins, crucial for understanding drug action. This is especially true for multi-domain proteins, ...read more
Artificial intelligence for Natural Products Discovery and Development
Our approach involves using computational methods to predict the potential therapeutic benefits of natural products by considering factors such as drug structure, targets, and interactions. We also employ multitarget analysis to understand the role of drug targets in disease pathways. We advocate for the use of artificial intelligence in predicting ...read more
Chemistry Based on Natural Products for Therapeutic Purposes
The development of new pharmaceuticals for a wide range of medical conditions has long relied on the identification of promising natural products (NPs). There are over sixty percent of cancer, infectious illness, and CNS disease medications that include an NP pharmacophore, according to the Food and Drug Administration. Since NP ...read more
![Wayfinder Image](/images/wayfinder.jpg)
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements