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Molecules 2018, 23(9), 2256; https://doi.org/10.3390/molecules23092256

Targeting Difficult Protein-Protein Interactions with Plain and General Computational Approaches

1
Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
2
Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy
*
Author to whom correspondence should be addressed.
Received: 4 July 2018 / Revised: 27 August 2018 / Accepted: 31 August 2018 / Published: 4 September 2018
(This article belongs to the Special Issue Molecular Modeling in Drug Design)
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Abstract

Investigating protein-protein interactions (PPIs) holds great potential for therapeutic applications, since they mediate intricate cell signaling networks in physiological and disease states. However, their complex and multifaceted nature poses a major challenge for biochemistry and medicinal chemistry, thereby limiting the druggability of biological partners participating in PPIs. Molecular Dynamics (MD) provides a solid framework to study the reciprocal shaping of proteins’ interacting surfaces. Here, we review successful applications of MD-based methods developed in our group to predict interfacial areas involved in PPIs of pharmaceutical interest. We report two interesting examples of how structural, dynamic and energetic information can be combined into efficient strategies which, complemented by experiments, can lead to the design of new small molecules with promising activities against cancer and infections. Our advances in targeting key PPIs in angiogenic pathways and antigen-antibody recognition events will be discussed for their role in drug discovery and chemical biology. View Full-Text
Keywords: molecular dynamics; proteins; molecular recognition; protein protein interactions molecular dynamics; proteins; molecular recognition; protein protein interactions
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Ferraro, M.; Colombo, G. Targeting Difficult Protein-Protein Interactions with Plain and General Computational Approaches. Molecules 2018, 23, 2256.

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