1
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Castellani B, Eleuteri M, Di Bona S, Cruciani G, Desantis J, Goracci L. VHL-Modified PROteolysis TArgeting Chimeras (PROTACs) as a Strategy to Evade Metabolic Degradation in In Vitro Applications. J Med Chem 2023; 66:13148-13171. [PMID: 37699425 DOI: 10.1021/acs.jmedchem.3c01144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are tripartite molecules consisting of a linker connecting a ligand for a protein of interest to an E3 ligase recruiter, whose rationale relies on proteasome-based protein degradation. PROTACs have expanded as a therapeutic strategy to open new avenues for unmet medical needs. Leveraging our expertise, we undertook a series of in vitro experiments aimed at elucidating PROTAC metabolism. In particular, we focused on PROTACs recruiting the von Hippel-Lindau (VHL) E3 ligase. After high-resolution mass spectrometry measurements, a characteristic metabolite with mass reduction of 200 units was detected and successively confirmed as a product deriving from the cleavage of the VHL ligand moiety. Subsequently, we identified hepatic and extrahepatic prolyl endopeptidases as the main putative metabolic enzymes involved. Finally, we designed and synthesized analogs of the VHL ligands that we further exploited for the synthesis of novel VHL-directed PROTACs with an improved metabolic stability in in vitro applications.
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Affiliation(s)
| | - Michela Eleuteri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | | | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
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2
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Biolatti M, Blangetti M, Baggieri M, Marchi A, Gioacchini S, Bajetto G, Arnodo D, Bucci P, Fioravanti R, Kojouri M, Bersani M, D'Arrigo G, Siragusa L, Ghinato S, De Andrea M, Gugliesi F, Albano C, Pasquero S, Visentin I, D'Ugo E, Esposito F, Malune P, Tramontano E, Prandi C, Spyrakis F, Magurano F, Dell'Oste V. Strigolactones as Broad-Spectrum Antivirals against β-Coronaviruses through Targeting the Main Protease M pro. ACS Infect Dis 2023; 9:1310-1318. [PMID: 37358826 DOI: 10.1021/acsinfecdis.3c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
The current SARS-CoV-2 pandemic and the likelihood that new coronavirus strains will emerge in the immediate future point out the urgent need to identify new pan-coronavirus inhibitors. Strigolactones (SLs) are a class of plant hormones with multifaceted activities whose roles in plant-related fields have been extensively explored. Recently, we proved that SLs also exert antiviral activity toward herpesviruses, such as human cytomegalovirus (HCMV). Here we show that the synthetic SLs TH-EGO and EDOT-EGO impair β-coronavirus replication including SARS-CoV-2 and the common cold human coronavirus HCoV-OC43. Interestingly, in silico simulations suggest the binding of SLs in the SARS-CoV-2 main protease (Mpro) active site, and this was further confirmed by an in vitro activity assay. Overall, our results highlight the potential efficacy of SLs as broad-spectrum antivirals against β-coronaviruses, which may provide the rationale for repurposing this class of hormones for the treatment of COVID-19 patients.
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Affiliation(s)
- Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Marco Blangetti
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Melissa Baggieri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Marchi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Silvia Gioacchini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Greta Bajetto
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, 28100 Novara, Italy
| | - Davide Arnodo
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Paola Bucci
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Raoul Fioravanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Maedeh Kojouri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Matteo Bersani
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy
| | - Giulia D'Arrigo
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy
| | - Lydia Siragusa
- Molecular Discovery Ltd., Kinetic Business Centre, Elstree, Borehamwood, WD6 4PJ Hertfordshire, United Kingdom
- Molecular Horizon s.r.l., 06084 Bettona (PG), Italy
| | - Simone Ghinato
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Center for Translational Research on Autoimmune and Allergic Disease-CAAD, 28100 Novara, Italy
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Camilla Albano
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Ivan Visentin
- Department of Agricultural, Forestry, and Food Sciences, University of Turin, 10095 Grugliasco, Turin, Italy
| | - Emilio D'Ugo
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Paolo Malune
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Cristina Prandi
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy
| | - Fabio Magurano
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
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3
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Luque-Navarro PM, Carrasco-Jiménez MP, Goracci L, Paredes JM, Espinar-Barranco L, Valverde-Pozo J, Torretta A, Parisini E, Mariotto E, Marchioro C, Laso A, Marco C, Viola G, Lanari D, López Cara LC. New bioisosteric sulphur-containing choline kinase inhibitors with a tracked mode of action. Eur J Med Chem 2023; 246:115003. [PMID: 36493617 DOI: 10.1016/j.ejmech.2022.115003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Since the identification of human choline kinase as a protein target against cancer progression, many compounds have been designed to inhibit its function and reduce the biosynthesis of phosphatidylcholine. Herein, we propose a series of bioisosteric inhibitors that are based on the introduction of sulphur and feature improved activity and lipophilic/hydrophilic balance. The evaluation of the inhibitory and of the antiproliferative properties of the PL (dithioethane) and FP (disulphide) libraries led to the identification of PL 48, PL 55 and PL 69 as the most active compounds of the series. Docking analysis using FLAP suggests that for hits to leads, binding mostly involves an interaction with the Mg2+ cofactor, or its destabilization. The most active compounds of the two series are capable of inducing apoptosis following the mitochondrial pathway and to significantly reduce the expression of anti-apoptotic proteins such as the Mcl-1. The fluorescence properties of the compounds of the PL library allowed the tracking of their mode of action, while PAINS (Pan Assays Interference Structures) filtration databases suggest the lack of any unspecific biological response.
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Affiliation(s)
- Pilar M Luque-Navarro
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain; Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy
| | - M Paz Carrasco-Jiménez
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain.
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, 06123, Italy
| | - Jose M Paredes
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Laura Espinar-Barranco
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Javier Valverde-Pozo
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Archimede Torretta
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy; Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV, 1006, Latvia; Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, Bologna, 40126, Italy
| | - Elena Mariotto
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Chiara Marchioro
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Alejandro Laso
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Carmen Marco
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Giampietro Viola
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy; Istituto di Ricerca Pediatrica (IRP) Fondazione Città della Speranza, Corso Stati Uniti 4, Padova, 35128, Italy.
| | - Daniela Lanari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy.
| | - Luisa Carlota López Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain.
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4
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Palomba T, Baroni M, Cross S, Cruciani G, Siragusa L. ELIOT: A platform to navigate the E3 pocketome and aid the design of new PROTACs. Chem Biol Drug Des 2023; 101:69-86. [PMID: 35857806 DOI: 10.1111/cbdd.14123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 12/15/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) are novel therapeutics for the treatment of human disease. They exploit the enormous potential of the E3 ligases, a class of proteins that mark a target protein for degradation via the ubiquitin-proteasome system. Despite the existence of several E3 ligase-related databases, the choice of the functioning ligase is limited to only 1.6% of those available, probably due to the fragmentary understanding of their structures and their known ligands; in fact, none of the existing databases report detailed studies covering their 3D structure or their pockets. Here, we report ELIOT (E3 LIgase pocketOme navigaTor), an accurate and complete platform containing the E3 ligase pocketome to enable navigation and selection of new E3 ligases and new ligands for the design of new PROTACs. All E3 ligase pockets were characterized with innovative 3D descriptors including their PROTAC-ability score, and similarity analyses between E3 pockets are presented. Tissue specificity and their degree of involvement in patients with specific cancer types are also annotated for each E3 ligase, enabling appropriate selection for the design of a PROTAC with improved specificity. All data are available at https://eliot.moldiscovery.com.
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Affiliation(s)
- Tommaso Palomba
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK
| | - Simon Cross
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK
| | - Gabriele Cruciani
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy
| | - Lydia Siragusa
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK.,Molecular Horizon Srl, Bettona, Italy
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5
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Trisciuzzi D, Siragusa L, Baroni M, Cruciani G, Nicolotti O. An Integrated Machine Learning Model To Spot Peptide Binding Pockets in 3D Protein Screening. J Chem Inf Model 2022; 62:6812-6824. [PMID: 36320100 DOI: 10.1021/acs.jcim.2c00583] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The prediction of peptide-protein binding sites is of utmost importance to tackle the onset of severe neurodegenerative diseases and cancer. In this work, we detail a novel machine learning model based on Linear Discriminant Analysis (LDA) demonstrating to be highly predictive in detecting the putative protein binding regions of small peptides. Starting from 439 high-quality pockets derived from peptide-protein crystallographic complexes, three sets of well-established peptide-binding regions were first selected through a Partitioning Around Medoids (PAM) clustering algorithm based on morphological and energetic 3D GRID-MIF molecular descriptors. Next, the best combination between all the putative interacting peptide pockets and related GRID-MIF scores was automatically explored by using the LDA-based protocol implemented in BioGPS. This approach proved successful to recognize the actual interacting peptide regions (that is, AUC = 0.86 and partial ROC enrichment at 5% of 0.48) from all the other pockets of the protein. Validated on two external collections sets, including 445 and 347 crystallographic peptide-protein complexes, our LDA-based model could be effective to further run peptide-protein virtual screening campaigns.
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Affiliation(s)
- Daniela Trisciuzzi
- Department of Pharmacy-Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125Bari, Italy.,Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, HertfordshireWD6 4PJ, United Kingdom
| | - Lydia Siragusa
- Molecular Horizon s.r.l., Via Montelino, 30, 06084Bettona (PG), Italy.,Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, HertfordshireWD6 4PJ, United Kingdom
| | - Massimo Baroni
- Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, HertfordshireWD6 4PJ, United Kingdom
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, via Elce di Sotto, 8, 06123Perugia (PG), Italy
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125Bari, Italy
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6
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Scott O, Gu J, Chan AE. Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network. J Chem Inf Model 2022; 62:5383-5396. [PMID: 36341715 PMCID: PMC9709917 DOI: 10.1021/acs.jcim.2c00832] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The analysis and comparison of protein-binding sites aid various applications in the drug discovery process, e.g., hit finding, drug repurposing, and polypharmacology. Classification of binding sites has been a hot topic for the past 30 years, and many different methods have been published. The rapid development of machine learning computational algorithms, coupled with the large volume of publicly available protein-ligand 3D structures, makes it possible to apply deep learning techniques in binding site comparison. Our method uses a cutting-edge spherical convolutional neural network based on the DeepSphere architecture to learn global representations of protein-binding sites. The model was trained on TOUGH-C1 and TOUGH-M1 data and validated with the ProSPECCTs datasets. Our results show that our model can (1) perform well in protein-binding site similarity and classification tasks and (2) learn and separate the physicochemical properties of binding sites. Lastly, we tested the model on a set of kinases, where the results show that it is able to cluster the different kinase subfamilies effectively. This example demonstrates the method's promise for lead hopping within or outside a protein target, directly based on binding site information.
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7
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Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design. Int J Mol Sci 2022; 23:ijms232214218. [PMID: 36430693 PMCID: PMC9698485 DOI: 10.3390/ijms232214218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
The field of targeted protein degradation, through the control of the ubiquitin-proteasome system (UPS), is progressing considerably; to exploit this new therapeutic modality, the proteolysis targeting chimera (PROTAC) technology was born. The opportunity to use PROTACs engaging of new E3 ligases that can hijack and control the UPS system could greatly extend the applicability of degrading molecules. To this end, here we show a potential application of the ELIOT (E3 LIgase pocketOme navigaTor) platform, previously published by this group, for a scaffold-repurposing strategy to identify new ligands for a novel E3 ligase, such as TRIM33. Starting from ELIOT, a case study of the cross-relationship using GRID Molecular Interaction Field (MIF) similarities between TRIM24 and TRIM33 binding sites was selected. Based on the assumption that similar pockets could bind similar ligands and considering that TRIM24 has 12 known co-crystalised ligands, we applied a scaffold-repurposing strategy for the identification of TRIM33 ligands exploiting the scaffold of TRIM24 ligands. We performed a deeper computational analysis to identify pocket similarities and differences, followed by docking and water analysis; selected ligands were synthesised and subsequently tested against TRIM33 via HTRF binding assay, and we obtained the first-ever X-ray crystallographic complexes of TRIM33α with three of the selected compounds.
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8
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Discovery of novel SARS-CoV-2 inhibitors targeting the main protease M pro by virtual screenings and hit optimization. Antiviral Res 2022; 204:105350. [PMID: 35688349 PMCID: PMC9172283 DOI: 10.1016/j.antiviral.2022.105350] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Two years after its emergence, SARS-CoV-2 still represents a serious and global threat to human health. Antiviral drug development usually takes a long time and, to increase the chances of success, chemical variability of hit compounds represents a valuable source for the discovery of new antivirals. In this work, we applied a platform of variably oriented virtual screening campaigns to seek for novel chemical scaffolds for SARS-CoV-2 main protease (Mpro) inhibitors. The study on the resulting 30 best hits led to the identification of a series of structurally unrelated Mpro inhibitors. Some of them exhibited antiviral activity in the low micromolar range against SARS-CoV-2 and other human coronaviruses (HCoVs) in different cell lines. Time-of-addition experiments demonstrated an antiviral effect during the viral replication cycle at a time frame consistent with the inhibition of SARS-CoV-2 Mpro activity. As a proof-of-concept, to validate the pharmaceutical potential of the selected hits against SARS-CoV-2, we rationally optimized one of the hit compounds and obtained two potent SARS-CoV-2 inhibitors with increased activity against Mpro both in vitro and in a cellular context, as well as against SARS-CoV-2 replication in infected cells. This study significantly contributes to the expansion of the chemical variability of SARS-CoV-2 Mpro inhibitors and provides new scaffolds to be exploited for pan-coronavirus antiviral drug development.
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9
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ZHANG BY, ZHENG YF, ZHAO J, KANG D, WANG Z, XU LJ, LIU AL, DU GH. Identification of multi-target anti-cancer agents from TCM formula by in silico prediction and in vitro validation. Chin J Nat Med 2022; 20:332-351. [DOI: 10.1016/s1875-5364(22)60180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/03/2022]
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10
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Trisciuzzi D, Siragusa L, Baroni M, Autiero I, Nicolotti O, Cruciani G. Getting Insights into Structural and Energetic Properties of Reciprocal Peptide-Protein Interactions. J Chem Inf Model 2022; 62:1113-1125. [PMID: 35148095 DOI: 10.1021/acs.jcim.1c01343] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptide-protein interactions play a key role for many cellular and metabolic processes involved in the onset of largely spread diseases such as cancer and neurodegenerative pathologies. Despite the progress in the structural characterization of peptide-protein interfaces, the in-depth knowledge of the molecular details behind their interactions is still a daunting task. Here, we present the first comprehensive in silico morphological and energetic study of peptide binding sites by focusing on both peptide and protein standpoints. Starting from the PixelDB database, a nonredundant benchmark collection of high-quality 3D crystallographic structures of peptide-protein complexes, a classification analysis of the most representative categories based on the nature of each cocrystallized peptide has been carried out. Several interpretable geometrical and energetic descriptors have been computed both from peptide and target protein sides in the attempt to unveil physicochemical and structural causative correlations. Finally, we investigated the most frequent peptide-protein residue pairs at the binding interface and made extensive energetic analyses, based on GRID MIFs, with the aim to study the peptide affinity-enhancing interactions to be further exploited in rational drug design strategies.
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Affiliation(s)
- Daniela Trisciuzzi
- Department of Pharmacy, Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy.,Molecular Horizon s.r.l., Via Montelino, 30, 06084 Bettona (PG), Italy
| | - Lydia Siragusa
- Molecular Horizon s.r.l., Via Montelino, 30, 06084 Bettona (PG), Italy.,Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Massimo Baroni
- Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Ida Autiero
- Molecular Horizon s.r.l., Via Montelino, 30, 06084 Bettona (PG), Italy.,National Research Council, Institute of Biostructures and Bioimaging, 80138 Naples, Italy
| | - Orazio Nicolotti
- Department of Pharmacy, Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, via Elce di Sotto, 8, 06123 Perugia (PG), Italy
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11
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Apigenin enhances apoptosis induction by 5-fluorouracil through regulation of thymidylate synthase in colorectal cancer cells. Redox Biol 2021; 47:102144. [PMID: 34562873 PMCID: PMC8476449 DOI: 10.1016/j.redox.2021.102144] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/05/2021] [Accepted: 09/19/2021] [Indexed: 12/18/2022] Open
Abstract
Although effective drugs have been developed, including 5-fluorouracil (5-FU), advanced colorectal cancer (CRC) shows low therapeutic sensitivity resulting from the development of 5-FU resistance. Thymidylate synthase (TS) is a target protein of 5-FU, and elevated TS lowers the 5-FU sensitivity of CRC cells. Here, we tested the efficacy of several candidate phytochemicals against human CRC-derived HCT116 cells expressing wild-type tumor suppressor protein P53 and HT29 cells expressing mutant P53. Among them, we found that apigenin enhanced the inhibitory effect of 5-FU on cell viability. In addition, apigenin inhibited the upregulation of TS induced by 5-FU. Apigenin also potentiated 5-FU-induced apoptosis of HCT116 cells and enhanced cell cycle disruption. Furthermore, apigenin increased reactive oxygen species production, intracellular and intramitochondrial Ca2+ concentrations, and mitochondrial membrane potential upon cotreatment with 5-FU. Knockdown of forkhead box protein M, a transcription factor modulating 5-FU sensitivity, enhanced the potentiation of apoptosis by apigenin in HCT116 cells. Moreover, apigenin suppressed TS expression and inhibited the viability of 5-FU-resistant HCT116 cells. Therefore, apigenin may improve the therapeutic efficacy of 5-FU against CRC by suppressing TS, but apoptosis induction is mainly dependent on functional P53. Apigenin inhibits the upregulation of TS induced by 5-FU for apoptosis of CRC. FOXM1 silencing enhances the potentiation of apoptosis by apigenin. Suppressing TS and promoting P53 activity by apigenin reduce acquired 5-FU resistance.
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12
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Roleira FMF, Varela C, Amaral C, Costa SC, Correia-da-Silva G, Moraca F, Costa G, Alcaro S, Teixeira NAA, Tavares da Silva EJ. C-6α- vs C-7α-Substituted Steroidal Aromatase Inhibitors: Which Is Better? Synthesis, Biochemical Evaluation, Docking Studies, and Structure–Activity Relationships. J Med Chem 2019; 62:3636-3657. [DOI: 10.1021/acs.jmedchem.9b00157] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fernanda M. F. Roleira
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- CIEPQPF Centre for Chemical Processes Engineering and Forest Products, University of Coimbra, 3030-790 Coimbra, Portugal
| | - Carla Varela
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- CIEPQPF Centre for Chemical Processes Engineering and Forest Products, University of Coimbra, 3030-790 Coimbra, Portugal
| | - Cristina Amaral
- UCIBIO.REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Saul C. Costa
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Georgina Correia-da-Silva
- UCIBIO.REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Federica Moraca
- Laboratorio di Chimica Farmaceutica, Dipartimento di Scienze della Salute, Università Magna Græcia di Catanzaro, 88100 Catanzaro, Italy
- Department of Pharmacy, University of Naples “Federico II”, via D. Montesano 49, 80131, Naples, Italy
- Net4Science Academic Spin-Off, “Magna Græcia” University of Catanzaro, “S. Venuta”, Catanzaro, Italy
| | - Giosuè Costa
- Laboratorio di Chimica Farmaceutica, Dipartimento di Scienze della Salute, Università Magna Græcia di Catanzaro, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, “Magna Græcia” University of Catanzaro, “S. Venuta”, Catanzaro, Italy
| | - Stefano Alcaro
- Laboratorio di Chimica Farmaceutica, Dipartimento di Scienze della Salute, Università Magna Græcia di Catanzaro, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, “Magna Græcia” University of Catanzaro, “S. Venuta”, Catanzaro, Italy
| | - Natércia A. A. Teixeira
- UCIBIO.REQUIMTE, Laboratory of Biochemistry, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Elisiário J. Tavares da Silva
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- CIEPQPF Centre for Chemical Processes Engineering and Forest Products, University of Coimbra, 3030-790 Coimbra, Portugal
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13
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Ehrt C, Brinkjost T, Koch O. A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs). PLoS Comput Biol 2018; 14:e1006483. [PMID: 30408032 PMCID: PMC6224041 DOI: 10.1371/journal.pcbi.1006483] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 09/02/2018] [Indexed: 11/24/2022] Open
Abstract
The automated comparison of protein-ligand binding sites provides useful insights into yet unexplored site similarities. Various stages of computational and chemical biology research can benefit from this knowledge. The search for putative off-targets and the establishment of polypharmacological effects by comparing binding sites led to promising results for numerous projects. Although many cavity comparison methods are available, a comprehensive analysis to guide the choice of a tool for a specific application is wanting. Moreover, the broad variety of binding site modeling approaches, comparison algorithms, and scoring metrics impedes this choice. Herein, we aim to elucidate strengths and weaknesses of binding site comparison methodologies. A detailed benchmark study is the only possibility to rationalize the selection of appropriate tools for different scenarios. Specific evaluation data sets were developed to shed light on multiple aspects of binding site comparison. An assembly of all applied benchmark sets (ProSPECCTs–Protein Site Pairs for the Evaluation of Cavity Comparison Tools) is made available for the evaluation and optimization of further and still emerging methods. The results indicate the importance of such analyses to facilitate the choice of a methodology that complies with the requirements of a specific scientific challenge. Binding site similarities are useful in the context of promiscuity prediction, drug repurposing, the analysis of protein-ligand and protein-protein complexes, function prediction, and further fields of general interest in chemical biology and biochemistry. Many years of research have led to the development of a multitude of methods for binding site analysis and comparison. On the one hand, their availability supports research. On the other hand, the huge number of methods hampers the efficient selection of a specific tool. Our research is dedicated to the analysis of different cavity comparison tools. We use several binding site data sets to establish guidelines which can be applied to ensure a successful application of comparison methods by circumventing potential pitfalls.
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Affiliation(s)
- Christiane Ehrt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Tobias Brinkjost
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Computer Science, TU Dortmund University, Dortmund, Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- * E-mail: ,
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14
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Grammer AC, Lipsky PE. Drug Repositioning Strategies for the Identification of Novel Therapies for Rheumatic Autoimmune Inflammatory Diseases. Rheum Dis Clin North Am 2017; 43:467-480. [DOI: 10.1016/j.rdc.2017.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Duran-Frigola M, Siragusa L, Ruppin E, Barril X, Cruciani G, Aloy P. Detecting similar binding pockets to enable systems polypharmacology. PLoS Comput Biol 2017; 13:e1005522. [PMID: 28662117 PMCID: PMC5490940 DOI: 10.1371/journal.pcbi.1005522] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 04/15/2017] [Indexed: 01/19/2023] Open
Abstract
In the era of systems biology, multi-target pharmacological strategies hold promise for tackling disease-related networks. In this regard, drug promiscuity may be leveraged to interfere with multiple receptors: the so-called polypharmacology of drugs can be anticipated by analyzing the similarity of binding sites across the proteome. Here, we perform a pairwise comparison of 90,000 putative binding pockets detected in 3,700 proteins, and find that 23,000 pairs of proteins have at least one similar cavity that could, in principle, accommodate similar ligands. By inspecting these pairs, we demonstrate how the detection of similar binding sites expands the space of opportunities for the rational design of drug polypharmacology. Finally, we illustrate how to leverage these opportunities in protein-protein interaction networks related to several therapeutic classes and tumor types, and in a genome-scale metabolic model of leukemia. Traditionally, the fact that most drugs are promiscuous binders has been a major concern in pharmacology, due to the occurrence of undesired off-target clinical events. In the recent years, however, the realization that many diseases are the result of complex biological processes has encouraged rethinking of drug promiscuity as a promising feature, since it is sometimes necessary to interfere with multiple receptors in order to overcome the robustness of disease-related networks. One way to identify groups of proteins that could be targeted simultaneously is to look for similar binding sites. We have massively done so for all human proteins with a known high-resolution three-dimensional structure, unveiling a vast space of ‘polypharmacology’ opportunities. Of these, we know, a great majority is not of therapeutic interest. To pinpoint promising multi-target combinations, we advocate for the use of computational tools that are able to rapidly simulate the effect of drug-target interactions on biological networks.
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Affiliation(s)
- Miquel Duran-Frigola
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | | | - Eytan Ruppin
- Department of Computer Science & Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- School of Computer Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Xavier Barril
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Gabriele Cruciani
- Molecular Discovery Limited, London, United Kingdom
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- * E-mail:
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16
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Di Pisa F, Landi G, Dello Iacono L, Pozzi C, Borsari C, Ferrari S, Santucci M, Santarem N, Cordeiro-da-Silva A, Moraes CB, Alcantara LM, Fontana V, Freitas-Junior LH, Gul S, Kuzikov M, Behrens B, Pöhner I, Wade RC, Costi MP, Mangani S. Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity. Molecules 2017; 22:molecules22030426. [PMID: 28282886 PMCID: PMC6155272 DOI: 10.3390/molecules22030426] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 01/28/2023] Open
Abstract
Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues (1–3) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes (Trypanosoma brucei PTR1–TbPTR1 and Leishmania major–LmPTR1) and parasites (Trypanosoma brucei and Leishmania infantum). A crystal structure of TbPTR1 in complex with compound 1 and the first crystal structures of LmPTR1-flavanone complexes (compounds 1 and 3) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.
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Affiliation(s)
- Flavio Di Pisa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Lucia Dello Iacono
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Chiara Borsari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Nuno Santarem
- Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal.
| | - Anabela Cordeiro-da-Silva
- Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal.
| | - Carolina B Moraes
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Laura M Alcantara
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Vanessa Fontana
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Lucio H Freitas-Junior
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
- GARDE, Instituto Butantan, São Paulo SP05503-900, Brazil.
| | - Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Birte Behrens
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Ina Pöhner
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino (FI), Italy.
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17
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Vanhaelen Q, Mamoshina P, Aliper AM, Artemov A, Lezhnina K, Ozerov I, Labat I, Zhavoronkov A. Design of efficient computational workflows for in silico drug repurposing. Drug Discov Today 2016; 22:210-222. [PMID: 27693712 DOI: 10.1016/j.drudis.2016.09.019] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/26/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022]
Abstract
Here, we provide a comprehensive overview of the current status of in silico repurposing methods by establishing links between current technological trends, data availability and characteristics of the algorithms used in these methods. Using the case of the computational repurposing of fasudil as an alternative autophagy enhancer, we suggest a generic modular organization of a repurposing workflow. We also review 3D structure-based, similarity-based, inference-based and machine learning (ML)-based methods. We summarize the advantages and disadvantages of these methods to emphasize three current technical challenges. We finish by discussing current directions of research, including possibilities offered by new methods, such as deep learning.
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Affiliation(s)
- Quentin Vanhaelen
- Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA.
| | - Polina Mamoshina
- Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA
| | - Alexander M Aliper
- Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA
| | - Artem Artemov
- Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA
| | - Ksenia Lezhnina
- Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA
| | - Ivan Ozerov
- Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA
| | - Ivan Labat
- BioTime Inc., 1010 Atlantic Avenue, 102, Alameda, CA 94501, USA
| | - Alex Zhavoronkov
- Insilico Medicine Inc., Johns Hopkins University, ETC, B301, MD 21218, USA
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