OpenTox 2022 - Virtual Conference

SPILLOproject contribution:

TITLE OF THE TALK:   SPILLO-PBSS: discovering target proteins of xenobiotics through 3D identification of their (hidden) binding sites and experimental validations

Authors: Alessandro Di Domizio^1,* (Speaker),  Alessandro Contini²

Affiliations: 1. SPILLOproject, 20037 Paderno Dugnano, MI, Italy;  2. Dipartimento Di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milano, Italy

* E-mail address: alessandro.didomizio@spilloproject.com

The property of a drug to interact with multiple molecular targets is usually a major drawback both in the drug development process, where off-target interactions often lead to safety-related failures, and in medicine, where therapeutic agents often lead to side effects that can cause dose limitation or even treatment discontinuation. SPILLOproject [1] developed innovative in silico technologies focused on the identification of target and off-target proteins of any small molecule on a proteome-wide scale. Among them, the SPILLO potential binding sites searcher (SPILLO-PBSS) software [2] is based on an innovative structure-based approach with unique capabilities in identifying (often previously unknown) binding sites, which can be detected even when hidden or completely closed, and therefore not identifiable by traditional approaches (e.g., molecular docking simulations, QSAR, etc.). SPILLO-PBSS has been successfully applied to many challenging pharmacological problems, such as providing biomolecular interpretations of some serious adverse effects of drugs (e.g., bortezomib, finasteride, paroxetine) on the market for many years. The top-ranked off-targets emerged from the systematic and unbiased analysis of the whole available (from the RCSB Protein Data bank) structural proteome of Homo sapiens and other organisms (i.e., Mus musculus and Rattus norvegicus) were well consistent with the reported adverse effects of such drugs. Furthermore, the direct knowledge of the binding sites provided by the software has also allowed further in-depth in silico studies through molecular dynamics (MD) simulations associated with Nwat-MMGBSA analyses [3][4], to get more accurate and precise information on both stability of the interactions and binding modes of the drugs within the newly discovered off-target proteins. The results obtained so far have been experimentally confirmed in vitro, in vivo and/or by NMR binding studies [5][6][7], highlighting the great potential of SPILLO-PBSS and its manifold applications in the drug R&D, including (among others): i) identification of main targets; ii) identification of off-targets responsible for adverse effects; iii) drug rescue/repositioning/repurposing; iv) rational design of animal testing, in compliance with the guidelines provided by the 3R principles.

 

References:

[1] SPILLOproject website: https://www.spilloproject.com/

[2] SPILLO-PBSS: Detecting Hidden Binding Sites within Protein 3D-Structures Through a Flexible Structure-Based Approach. J. Comput. Chem. (2014); DOI: 10.1002/jcc.23714

[3] Improved Computation of Protein–Protein Relative Binding Energies with the Nwat-MMGBSA Method. J. Chem. Inf. Model. (2016); DOI: 10.1021/acs.jcim.6b00196

[4] An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings. Front. Chem. (2018); DOI: 10.3389/fchem.2018.00043

[5] Tubulin binding potentially clears up Bortezomib and Carfilzomib differential neurotoxic effect. Sci. Rep. (2021); DOI: 10.1038/s41598-021-89856-3

[6] Three-Dimensional Proteome-Wide Scale Screening for the 5-Alpha Reductase Inhibitor Finasteride: Identification of a Novel Off-Target. J. Med. Chem. (2021); DOI: 10.1021/acs.jmedchem.0c02039

[7] Identification of a novel off-target of paroxetine: Possible role in sexual dysfunction induced by this SSRI antidepressant drug. J. Mol. Struct. (2022); DOI: 10.1016/j.molstruc.2022.133690