Pascal Bonnet
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View article: Spatio-temporal learning from molecular dynamics simulations for protein–ligand binding affinity prediction
Spatio-temporal learning from molecular dynamics simulations for protein–ligand binding affinity prediction Open
Motivation The field of protein–ligand binding affinity prediction continues to face significant challenges. While deep learning (DL) models can leverage 3D structural information of protein–ligand complexes, they perform well only on heav…
View article: Virtual screening of natural products to enhance melanogenosis
Virtual screening of natural products to enhance melanogenosis Open
Natural products have long been an important source of inspiration for medicinal chemistry and drug discovery. In the cosmetic field, they remain the major elements of the composition and serve as marketing asset. Recent research showed th…
View article: Highlighting the Major Role of Cyclin C in Cyclin-Dependent Kinase 8 Activity through Molecular Dynamics Simulations
Highlighting the Major Role of Cyclin C in Cyclin-Dependent Kinase 8 Activity through Molecular Dynamics Simulations Open
Dysregulation of cyclin-dependent kinase 8 (CDK8) activity has been associated with many diseases, including colorectal and breast cancer. As usual in the CDK family, the activity of CDK8 is controlled by a regulatory protein called cyclin…
View article: Highlighting the Major Role of Cyclin C on Cyclin-Dependent Kinase 8 Activity by Molecular Dynamics Simulations
Highlighting the Major Role of Cyclin C on Cyclin-Dependent Kinase 8 Activity by Molecular Dynamics Simulations Open
Dysregulation of the Cyclin-dependent kinase 8 (CDK8) activity has been associated to many diseases including the colorectal and breast cancer. As usual in the CDK family, the activity of CDK8 is controlled by a regulatory protein called c…
View article: Oral anticoagulant safety in family practice: prognostic accuracy of Bleeding Risk Scores (from the CACAO study)
Oral anticoagulant safety in family practice: prognostic accuracy of Bleeding Risk Scores (from the CACAO study) Open
Background To assess bleeding risk of patients treated by oral anticoagulants, several scores have been constructed to assist physicians in the evaluation of the benefit risk. Most of these scores lack a strong enough level of evidence for…
View article: The Identification of New c-FLIP Inhibitors for Restoring Apoptosis in TRAIL-Resistant Cancer Cells
The Identification of New c-FLIP Inhibitors for Restoring Apoptosis in TRAIL-Resistant Cancer Cells Open
The catalytically inactive caspase-8-homologous protein, c-FLIP, is a potent antiapoptotic protein highly expressed in various types of cancers. c-FLIP competes with caspase-8 for binding to the adaptor protein FADD (Fas-Associated Death D…
View article: Identification of New c-FLIP Inhibitors to Restore Apoptosis in TRAIL-Resistant Cancer Cells
Identification of New c-FLIP Inhibitors to Restore Apoptosis in TRAIL-Resistant Cancer Cells Open
The catalytically inactive caspase-8-homologous protein, c-FLIP, is a potent antiapoptotic protein highly expressed in various types of cancers. c-FLIP competes with caspase-8 for binding to the adaptor protein FADD (Fas-Associated Death D…
View article: The Impact of Data on Structure-Based Binding Affinity Predictions Using Deep Neural Networks
The Impact of Data on Structure-Based Binding Affinity Predictions Using Deep Neural Networks Open
Artificial intelligence (AI) has gained significant traction in the field of drug discovery, with deep learning (DL) algorithms playing a crucial role in predicting protein–ligand binding affinities. Despite advancements in neural network …
View article: Research Activities at the University of Orléans
Research Activities at the University of Orléans Open
Evropska univerza ATHENA je zveza devetih visokošolskih ustanov z misijo spodbujanja odličnosti v raziskavah in inovacijah z omogočanjem mednarodnega sodelovanja. Akronim ATHENA pomeni združenje naprednih tehnologij v visokošolskem izobraž…
View article: Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations
Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations Open
Drug-target residence time has emerged as a key selection factor in drug discovery since the binding duration of a drug molecule to its protein target can significantly impact its in vivo efficacy. The challenge in studying the residence t…
View article: Data FAIRification in a cross-institutional governance framework : recommendations from the ANR-BRIDGE project
Data FAIRification in a cross-institutional governance framework : recommendations from the ANR-BRIDGE project Open
Abstract Open science is a priority for the European Commission, fostering research data management policies and infrastructures. In France, the Second National Plan for Open Science aims to ensure that open science becomes a common and sh…
View article: Design and biological evaluation of substituted 5,7-dihydro-6 <i>H</i> -indolo[2,3- <i>c</i> ]quinolin-6-one as novel selective Haspin inhibitors
Design and biological evaluation of substituted 5,7-dihydro-6 <i>H</i> -indolo[2,3- <i>c</i> ]quinolin-6-one as novel selective Haspin inhibitors Open
A library of substituted indolo[2,3-c]quinolone-6-ones was developed as simplified Lamellarin isosters. Synthesis was achieved from indole after a four-step pathway sequence involving iodination, a Suzuki-Miyaura cross-coupling reaction, a…
View article: Equipping Coiled-Coil Peptide Dimers With Furan Warheads Reveals Novel Cross-Link Partners
Equipping Coiled-Coil Peptide Dimers With Furan Warheads Reveals Novel Cross-Link Partners Open
Using a coiled-coil peptide dimer as a model system to explore furan reactivity, we describe novel cross-link partners of furan warheads for site-specific cross-linking. We demonstrate that replacement of weak interhelical ionic contacts w…
View article: Design, Synthesis and SAR in 2,4,7-Trisubstituted Pyrido[3,2-d]Pyrimidine Series as Novel PI3K/mTOR Inhibitors
Design, Synthesis and SAR in 2,4,7-Trisubstituted Pyrido[3,2-d]Pyrimidine Series as Novel PI3K/mTOR Inhibitors Open
This work describes the synthesis, enzymatic activities on PI3K and mTOR, in silico docking and cellular activities of various uncommon 2,4,7 trisubstituted pyrido[3,2-d]pyrimidines. The series synthesized offers a chemical diversity in C-…
View article: Developing a data collection application for following up the small-scale dairy farms’ performance in rural areas
Developing a data collection application for following up the small-scale dairy farms’ performance in rural areas Open
The mobile application is an effective tool for data collection of performance in agriculture, particularly for small and geographically scattered farms. This study aimed to develop an economical and straightforward application to monitor …
View article: Palladium‐Catalyzed Regioselective C−H Arylation of 4‐Azaindazole at C3, C5 and C7 Positions
Palladium‐Catalyzed Regioselective C−H Arylation of 4‐Azaindazole at C3, C5 and C7 Positions Open
Direct and site‐selective C5 and C7 palladium‐catalyzed C−H arylations of 4‐azaindazole N ‐oxide have been achieved. A bidentate ligand and Pd(OAc) 2 catalyst in toluene promoted the activation of C5 position, while a phosphine ligand and …
View article: Comparative Assessment of Protein Kinase Inhibitors in Public Databases and in PKIDB
Comparative Assessment of Protein Kinase Inhibitors in Public Databases and in PKIDB Open
Since the first approval of a protein kinase inhibitor (PKI) by the Food and Drug Administration (FDA) in 2001, 55 new PKIs have reached the market, and many inhibitors are currently being evaluated in clinical trials. This is a clear indi…
View article: Fr-PPIChem: An Academic Compound Library Dedicated to Protein–Protein Interactions
Fr-PPIChem: An Academic Compound Library Dedicated to Protein–Protein Interactions Open
Protein-protein interactions (PPIs) mediate nearly every cellular process and represent attractive targets for modulating disease states but are challenging to target with small molecules. Despite this, several PPI inhibitors (iPPIs) have …
View article: Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites
Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites Open
Allosteric effect can modulate the biological activity of a protein. Thus, the discovery of new allosteric sites is very attractive for designing new modulators or inhibitors. Here, we propose an innovative way to identify allosteric sites…
View article: OneARK: Strengthening the links between animal production science and animal ecology
OneARK: Strengthening the links between animal production science and animal ecology Open
1. Wild and farmed animals are key elements of natural and managed ecosystems that deliver functions such as pollination, pest control and nutrient cycling. They are submitted to global changes with a profound impact on natural range and v…
View article: Design of new disubstituted imidazo[1,2-<i>b</i>]pyridazine derivatives as selective Haspin inhibitors. Synthesis, binding mode and anticancer biological evaluation
Design of new disubstituted imidazo[1,2-<i>b</i>]pyridazine derivatives as selective Haspin inhibitors. Synthesis, binding mode and anticancer biological evaluation Open
Haspin is a mitotic protein kinase required for proper cell division by modulating Aurora B kinase localisation and activity as well as histone phosphorylation. Here a series of imidazopyridazines based on the CHR-6494 and Structure Activi…
View article: Declaration for the Sharing and Opening of Research Data for Sustainable Development
Declaration for the Sharing and Opening of Research Data for Sustainable Development Open
This declaration has been produced by the participants in the “Open Science in the South: Challenges and Perspectives for a New Dynamic” symposium, held in Dakar from 23 to 25 October 2019, by African and European organizations i. These pa…