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Exscalate contributes to publications and journals

Based on the research we undertake at Exscalate, we have co-authored a number of articles published in a range of scientific and computer science journals and publications. These cover topics from high performance computing and virtual screening through to small molecules and drug discovery.

Drug Repurposing
High Performance Computing
Drug Discovery
Small Molecules
In Silico
9th June 2023

ProfhEX: AI-based platform for small molecules liability profiling

Authors: Filippo Lunghini, Anna Fava, Vincenzo Pisapia, Francesco Sacco, Daniela Iaconis, Andrea Rosario Beccari
Off-target drug interactions are a major reason for candidate failure in the drug discovery process. Anticipating potential drug’s adverse effects in the early stages is necessary to minimize health risks to patients, animal testing, and economical costs. With the constantly increasing size of virtual screening libraries, AI-driven methods can be exploited as first-tier screening tools to provide liability estimation for drug candidates. In this work we present ProfhEX, an AI-driven suite of 46 OECD-compliant machine learning models that can profile small molecules on 7 relevant liability groups: cardiovascular, central nervous system, gastrointestinal, endocrine, renal, pulmonary and immune system toxicities. Experimental affinity data was collected from public and commercial data sources. The entire chemical space comprised 289′202 activity data for a total of 210′116 unique compounds, spanning over 46 targets with dataset sizes ranging from 819 to 18896. Gradient boosting and random forest algorithms were initially employed and ensembled for the selection of a champion model. Models were validated according to the OECD principles, including robust internal (cross validation, bootstrap, y-scrambling) and external validation. Champion models achieved an average Pearson correlation coefficient of 0.84 (SD of 0.05), an R2 determination coefficient of 0.68 (SD = 0.1) and a root mean squared error of 0.69 (SD of 0.08). All liability groups showed good hit-detection power with an average enrichment factor at 5% of 13.1 (SD of 4.5) and AUC of 0.92 (SD of 0.05). Benchmarking against already existing tools demonstrated the predictive power of ProfhEX models for large-scale liability profiling. This platform will be further expanded with the inclusion of new targets and through complementary modelling approaches, such as structure and pharmacophore-based models. ProfhEX is freely accessible at the following address: https://profhex.exscalate.eu/.
High Performance Computing
Drug Discovery
Small Molecules
30th May 2023

MEDIATE - Molecular Docking at home: Turning collaborative simulations into therapeutic solutions

Authors: Giulio Vistolia, Candida Manelfib, Carmine Talaricob, Anna Favab, Arieh Warshelc, Igor V. Tetkod,p, Rossen Apostolove, Yang Yef, Chiara Latinig, Federico Ficarellig, Gianluca Palermoh, Davide Gadiolih, Emanuele Vitalih, Gaetano Varrialei, Vincenzo Pisapiai, Marco Scaturroj, Silvano Colettik, Daniele Gregoril, Daniel Gruffatm, Edgardo Leijam, Sam Hessenauerm, Alberto Delbiancon, Marcello Allegrettio, Andrea R. Beccari
Collaborative computing has attracted great interest in the possibility of joining the efforts of researchers worldwide. Its relevance has further increased during the pandemic crisis since it allows for the strengthening of scientific collaborations while avoiding physical interactions. Thus, the E4C consortium presents the MEDIATE initiative which invited researchers to contribute via their virtual screening simulations that will be combined with AI-based consensus approaches to provide robust and method-independent predictions. The best compounds will be tested, and the biological results will be shared with the scientific community.Areas covered: In this paper, the MEDIATE initiative is described. This shares compounds’ libraries and protein structures prepared to perform standardized virtual screenings. Preliminary analyses are also reported which provide encouraging results emphasizing the MEDIATE initiative’s capacity to identify active compounds.Expert opinion: Structure-based virtual screening is well-suited for collaborative projects provided that the participating researchers work on the same input file. Until now, such a strategy was rarely pursued and most initiatives in the field were organized as challenges. The MEDIATE platform is focused on SARS-CoV-2 targets but can be seen as a prototype which can be utilized to perform collaborative virtual screening campaigns in any therapeutic field by sharing the appropriate input files.
Drug Repurposing
High performance Computing
19th May 2023

Relevance of Spike/Estrogen Receptor-α interaction for endothelial-based coagulopathy induced by SARS-CoV-2

Authors: Silvia Stella Barbieri, Franca Cattani, Leonardo Sandrini, Magda Maria Grillo, Alessandra Amendola, Carmen Valente, Carmine Talarico, Daniela Iaconis, Gabriele Turacchio, Miriam Lucariello, Lucia Lione, Erika Salvatori, Patrizia Amadio, Gloria Garoffolo, Mariano Maffei, Francesca Galli, Andrea Rosario Beccari, Giuseppe Sberna, Emanuele Marra, Marica Zoppi, Michael Michaelides, Giuseppe Roscilli, Luigi Aurisicchio, Riccardo Bertini, Maurizio Pesce
In summary, also corroborated by mounting evidences from clinical and in vitro studies showing the potential effectiveness of SERMs (e.g., Raloxifene) as an anti-viral agent in COVID-19,10 our results suggest a new non-infective pathologic action of the S-protein at the vascular level enhancing the endothelial pro-coagulation activity. Given the residual risk of coagulopathy observed in subjects treated with COVID-19 vaccines, our study indicates two variants of the original Spike sequence that could be employed to design new versions of COVID-19 vaccines lacking any residual risk of VITT in the still ongoing vaccination and boosting campaign.
20th October 2022

Structure of human TRPM8 channel

Authors: Sergii Palchevskyi, Mariusz Czarnocki-Cieciura, Giulio Vistoli, Silvia Gervasoni, Elżbieta Nowak, Andrea R. Beccari, Marcin Nowotny, Carmine Talarico
TRPM8 is a calcium ion channel that is activated by multiple factors, such as temperature, voltage, pressure, and osmolality. It is a therapeutic target for anticancer drug development, and its modulators can be utilized for several pathological conditions. Here, we present a cryo-electron microscopy structure of a human TRPM8 channel in the closed state that was solved at 2.7 Å resolution. Based on our reconstruction, we built the most complete model of the N-terminal pre-melastatin homology region. We also visualized several ligands that are bound by the protein and modeled how the human channel interacts with icilin. Analyses of pore helices showed that all available TRPM8 structures can be grouped into closed and desensitized states based on the register of pore helix S6 and the resulting positioning of particular amino acid residues at the channel constriction.
Drug Discovery
6th September 2022

Computational Insights into the Sequence-Activity Relationships of the NGF(1–14) Peptide by Molecular Dynamics Simulations

Authors: Serena Vittorio, Candida Manelfi, Silvia Gervasoni, Andrea R. Beccari, Alessandro Pedretti, Giulio Vistoli, Carmine Talarico
The Nerve Growth Factor (NGF) belongs to the neurothrophins protein family involved in the survival of neurons in the nervous system. The interaction of NGF with its high-affinity receptor TrkA mediates different cellular pathways related to Alzheimer’s disease, pain, ocular dysfunction, and cancer. Therefore, targeting NGF-TrkA interaction represents a valuable strategy for the development of new therapeutic agents. In recent years, experimental studies have revealed that peptides belonging to the N-terminal domain of NGF are able to partly mimic the biological activity of the whole protein paving the way towards the development of small peptides that can selectively target specific signaling pathways. Hence, understanding the molecular basis of the interaction between the N-terminal segment of NGF and TrkA is fundamental for the rational design of new peptides mimicking the NGF N-terminal domain. In this study, molecular dynamics simulation, binding free energy calculations and per-residue energy decomposition analysis were combined in order to explore the molecular recognition pattern between the experimentally active NGF(1–14) peptide and TrkA. The results highlighted the importance of His4, Arg9 and Glu11 as crucial residues for the stabilization of NGF(1–14)-TrkA interaction, thus suggesting useful insights for the structure-based design of new therapeutic peptides able to modulate NGF-TrkA interaction.
Drug Discovery
High Performance Computing
4th August 2022

Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins

Authors: Ingrid Guarnetti Prandi, Carla Mavian, Emanuela Giombini, Cesare E. M. Gruber, Daniele Pietrucci, Stefano Borocci, Nabil Abid, Andrea R. Beccari, Carmine Talarico, Giovanni Chillemi
The vast amount of epidemiologic and genomic data that were gathered as a global response to the COVID-19 pandemic that was caused by SARS-CoV-2 offer a unique opportunity to shed light on the structural evolution of coronaviruses and in particular on the spike (S) glycoprotein, which mediates virus entry into the host cell by binding to the human ACE2 receptor. Herein, we carry out an investigation into the dynamic properties of the S glycoprotein, focusing on the much more transmissible Delta and Omicron variants. Notwithstanding the great number of mutations that have accumulated, particularly in the Omicron S glycoprotein, our data clearly showed the conservation of some structural and dynamic elements, such as the global motion of the receptor binding domain (RBD). However, our studies also revealed structural and dynamic alterations that were concentrated in the aa 627–635 region, on a small region of the receptor binding motif (aa 483–485), and the so-called “fusion-peptide proximal region”. In particular, these last two S regions are known to be involved in the human receptor ACE2 recognition and membrane fusion. Our structural evidence, therefore, is likely involved in the observed different transmissibility of these S mutants. Finally, we highlighted the role of glycans in the increased RBD flexibility of the monomer in the up conformation of Omicron.
Drug Discovery
High Performance Computing
13th July 2022

Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort

Authors: Andrea Zaliani, Laura Vangeel, Jeanette Reinshagen, Daniela Iaconis, Maria Kuzikov, Oliver Keminer, Markus Wolf, Bernhard Ellinger, Francesca Esposito, Angela Corona, Enzo Tramontano, Candida Manelfi, Katja Herzog, Dirk Jochmans, Steven De Jonghe, Winston Chiu, Thibault Francken, Joost Schepers, Caroline Collard, Kayvan Abbasi, Carsten Claussen, Vincenzo Summa, Andrea R. Beccari, Johan Neyts, Philip Gribbon & Pieter Leyssen
Worldwide, there are intensive efforts to identify repurposed drugs as potential therapies against SARS-CoV-2 infection and the associated COVID-19 disease. To date, the anti-inflammatory drug dexamethasone and (to a lesser extent) the RNA-polymerase inhibitor remdesivir have been shown to be effective in reducing mortality and patient time to recovery, respectively, in patients. Here, we report the results of a phenotypic screening campaign within an EU-funded project (H2020-EXSCALATE4COV) aimed at extending the repertoire of anti-COVID therapeutics through repurposing of available compounds and highlighting compounds with new mechanisms of action against viral infection. We screened 8702 molecules from different repurposing libraries, to reveal 110 compounds with an anti-cytopathic IC50 < 20 µM. From this group, 18 with a safety index greater than 2 are also marketed drugs, making them suitable for further study as potential therapies against COVID-19. Our result supports the idea that a systematic approach to repurposing is a valid strategy to accelerate the necessary drug discovery process.
Drug Discovery
8th July 2022

Extensive Sampling of Molecular Dynamics Simulations to Identify Reliable Protein Structures for Optimized Virtual Screening Studies: The Case of the hTRPM8 Channel

Authors: Silvia Gervasoni, Carmine Talarico, Candida Manelfi, Alessandro Pedretti, Giulio Vistoli and Andrea R. Beccari
Virtual screening campaigns require target structures in which the pockets are properly arranged for binding. Without these, MD simulations can be used to relax the available target structures, optimizing the fine architecture of their binding sites. Among the generated frames, the best structures can be selected based on available experimental data. Without experimental templates, the MD trajectories can be filtered by energy-based criteria or sampled by systematic analyses. (2) Methods: A blind and methodical analysis was performed on the already reported MD run of the hTRPM8 tetrameric structures; a total of 50 frames underwent docking simulations by using a set of 1000 ligands including 20 known hTRPM8 modulators. Docking runs were performed by LiGen program and involved the frames as they are and after optimization by SCRWL4.0. For each frame, all four monomers were considered. Predictive models were developed by the EFO algorithm based on the sole primary LiGen scores. (3) Results: On average, the MD simulation progressively enhances the performance of the extracted frames, and the optimized structures perform better than the non-optimized frames (EF1% mean: 21.38 vs. 23.29). There is an overall correlation between performances and volumes of the explored pockets and the combination of the best performing frames allows to develop highly performing consensus models (EF1% = 49.83). (4) Conclusions: The systematic sampling of the entire MD run provides performances roughly comparable with those previously reached by using rationally selected frames. The proposed strategy appears to be helpful when the lack of experimental data does not allow an easy selection of the optimal structures for docking simulations. Overall, the reported docking results confirm the relevance of simulating all the monomers of an oligomer structure and emphasize the efficacy of the SCRWL4.0 method to optimize the protein structures for docking calculations.
6th July 2022

EXSCALATE: An Extreme-Scale Virtual Screening Platform for Drug Discovery Targeting Polypharmacology to Fight SARS-CoV-2

Authors: Laura Brandolini, Michele d’Angelo, Rubina Novelli, Vanessa Castelli, Cristina Giorgio, Anna Sirico, Pasquale Cocchiaro, Francesco D’Egidio, Elisabetta Benedetti, Claudia Cristiano, Antonella Bugatti, Anna Ruocco, Pier Giorgio Amendola, Carmine Talarico, Candida Manelfi, Daniela Iaconis, Andrea Beccari, Andreza U. Quadros, Thiago M. Cunha, Arnaldo Caruso, Roberto Russo, Annamaria Cimini, Andrea Aramini & Marcello Allegretti
The social and economic impact of the COVID-19 pandemic demands a reduction of the time required to find a therapeutic cure. In this paper, we describe the EXSCALATE molecular docking platform capable to scale on an entire modern supercomputer for supporting extreme-scale virtual screening campaigns. Such virtual experiments can provide in short time information on which molecules to consider in the next stages of the drug discovery pipeline, and it is a key asset in case of a pandemic. The EXSCALATE platform has been designed to benefit from heterogeneous computation nodes and to reduce scaling issues. In particular, we maximized the accelerators’ usage, minimized the communications between nodes, and aggregated the I/O requests to serve them more efficiently. Moreover, we balanced the computation across the nodes by designing an ad-hoc workflow based on the execution time prediction of each molecule. We deployed the platform on two HPC supercomputers, with a combined computational power of 81 PFLOPS, to evaluate the interaction between 70 billion of small molecules and 15 binding-sites of 12 viral proteins of SARS-CoV-2. The experiment lasted 60 hours and it performed more than one trillion ligand-pocket evaluations, setting a new record on the virtual screening scale.
25th May 2022

Paclitaxel binds and activates C5aR1: A new potential therapeutic target for the prevention of chemotherapy-induced peripheral neuropathy and hypersensitivity reactions

Authors: Laura Brandolini, Michele d’Angelo, Rubina Novelli, Vanessa Castelli, Cristina Giorgio, Anna Sirico, Pasquale Cocchiaro, Francesco D’Egidio, Elisabetta Benedetti, Claudia Cristiano, Antonella Bugatti, Anna Ruocco, Pier Giorgio Amendola, Carmine Talarico, Candida Manelfi, Daniela Iaconis, Andrea Beccari, Andreza U. Quadros, Thiago M. Cunha, Arnaldo Caruso, Roberto Russo, Annamaria Cimini, Andrea Aramini & Marcello Allegretti
Chemotherapy-induced peripheral neuropathy (CIPN) and hypersensitivity reactions (HSRs) are among the most frequent and impairing side effects of the antineoplastic agent paclitaxel. Here, we demonstrated that paclitaxel can bind and activate complement component 5a receptor 1 (C5aR1) and that this binding is crucial in the etiology of paclitaxel-induced CIPN and anaphylaxis. Starting from our previous data demonstrating the role of interleukin (IL)-8 in paclitaxel-induced neuronal toxicity, we searched for proteins that activate IL-8 expression and, by using the Exscalate platform for molecular docking simulations, we predicted the high affinity of C5aR1 with paclitaxel. By in vitro studies, we confirmed the specific and competitive nature of the C5aR1-paclitaxel binding and found that it triggers intracellularly the NFkB/P38 pathway and c-Fos. In F11 neuronal cells and rat dorsal root ganglia, C5aR1 inhibition protected from paclitaxel-induced neuropathological effects, while in paclitaxel-treated mice, the absence (knock-out mice) or the inhibition of C5aR1 significantly ameliorated CIPN symptoms—in terms of cold and mechanical allodynia—and reduced the chronic pathological state in the paw. Finally, we found that C5aR1 inhibition can counteract paclitaxel-induced anaphylactic cytokine release in macrophages in vitro, as well as the onset of HSRs in mice. Altogether these data identified C5aR1 as a key mediator and a new potential pharmacological target for the prevention and treatment of CIPN and HSRs induced by paclitaxel.


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