Davide Provasi
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View article: Structural and dynamic studies uncover a distinct allosteric modulatory site at the μ-opioid receptor
Structural and dynamic studies uncover a distinct allosteric modulatory site at the μ-opioid receptor Open
Positive allosteric modulators (PAMs) of the μ opioid receptor (MOR) offer a promising path toward safer opioid therapeutics, yet their mechanisms of action remain poorly understood. Here, we uncover the structural and mechanistic basis of…
View article: BOLD-GPCRs: A Transformer-Powered App for Predicting Ligand Bioactivity and Mutational Effects Across Class A GPCRs
BOLD-GPCRs: A Transformer-Powered App for Predicting Ligand Bioactivity and Mutational Effects Across Class A GPCRs Open
G protein-coupled receptors (GPCRs) are important targets for drug discovery owing to their ability to respond to a broad range of stimuli and their involvement in numerous pathologies. Although traditional ligand-based and structure-based…
View article: Synthesis and Characterization of Photoswitchable Covalent Ligands for the β<sub>2</sub>‐Adrenoceptor
Synthesis and Characterization of Photoswitchable Covalent Ligands for the β<sub>2</sub>‐Adrenoceptor Open
The β 2 ‐adrenergic receptor (β 2 AR) is a critical target for the treatment of airway diseases such as asthma or chronic obstructive pulmonary disease (COPD). To better understand its mechanism of action and study its dynamics, photoswitc…
View article: Synthesis and Characterization of Photoswitchable Covalent Ligands for the β<sub>2</sub>‐Adrenoceptor
Synthesis and Characterization of Photoswitchable Covalent Ligands for the β<sub>2</sub>‐Adrenoceptor Open
The β 2 ‐adrenergic receptor (β 2 AR) is a critical target for the treatment of airway diseases such as asthma or chronic obstructive pulmonary disease (COPD). To better understand its mechanism of action and study its dynamics, photoswitc…
View article: Fine-Tuned Deep Transfer Learning Models for Large Screenings of Safer Drugs Targeting Class A GPCRs
Fine-Tuned Deep Transfer Learning Models for Large Screenings of Safer Drugs Targeting Class A GPCRs Open
G protein-coupled receptors (GPCRs) remain a focal point of research due to their critical roles in cell signaling and their prominence as drug targets. However, directly linking drug efficacy to the receptor-mediated activation of specifi…
View article: Fine-Tuned Deep Transfer Learning Models for Large Screenings of Safer Drugs Targeting Class A GPCRs
Fine-Tuned Deep Transfer Learning Models for Large Screenings of Safer Drugs Targeting Class A GPCRs Open
G protein-coupled receptors (GPCRs) remain a focal point of research due to their critical roles in cell signaling and their prominence as drug targets. However, directly linking drug efficacy to receptor-mediated activation of specific in…
View article: De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework Open
Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown t…
View article: A Novel Mitragynine Analog with Low-Efficacy Mu Opioid Receptor Agonism Displays Antinociception with Attenuated Adverse Effects
A Novel Mitragynine Analog with Low-Efficacy Mu Opioid Receptor Agonism Displays Antinociception with Attenuated Adverse Effects Open
Mitragynine and 7-hydroxymitragynine (7OH) are the major alkaloids mediating the biological actions of the psychoactive plant kratom. To investigate the structure-activity relationships of mitragynine/7OH templates, we diversified the arom…
View article: Structural insights into the unexpected agonism of tetracyclic antidepressants at serotonin receptors 5-HT <sub>1e</sub> R and 5-HT <sub>1F</sub> R
Structural insights into the unexpected agonism of tetracyclic antidepressants at serotonin receptors 5-HT <sub>1e</sub> R and 5-HT <sub>1F</sub> R Open
Serotonin [5-hydroxytryptamine (5-HT)] acts via 13 different receptors in humans. Of these receptor subtypes, all but 5-HT 1e R have confirmed roles in native tissue and are validated drug targets. Despite 5-HT 1e R’s therapeutic potential…
View article: Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques
Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques Open
The opioid epidemic has cast a shadow over public health, necessitating immediate action to address its devastating consequences. To effectively combat this crisis, it is crucial to discover better opioid drugs with reduced addiction poten…
View article: Opioid classifiers: dataset sharing for submission Cot 31, 2023
Opioid classifiers: dataset sharing for submission Cot 31, 2023 Open
Contains datasets for submission of manuscript "Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques" Davide Provasi and Marta…
View article: Opioid classifiers: dataset sharing for submission Cot 31, 2023
Opioid classifiers: dataset sharing for submission Cot 31, 2023 Open
Contains datasets for submission of manuscript "Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques" Davide Provasi and Marta…
View article: Structural Insights into the Unexpected Agonism of Tetracyclic Antidepressants at Serotonin Receptors 5-HT<sub>1e</sub>R and 5-HT<sub>1F</sub>R
Structural Insights into the Unexpected Agonism of Tetracyclic Antidepressants at Serotonin Receptors 5-HT<sub>1e</sub>R and 5-HT<sub>1F</sub>R Open
Serotonin (5-hydroxytryptamine, 5-HT) acts via 13 different receptors in humans. Of these receptor subtypes, all but 5-HT 1e R have confirmed roles in native tissue and are validated drug targets. Despite 5-HT 1e R’s therapeutic potential …
View article: De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework Open
Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown t…
View article: Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques
Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques Open
The opioid epidemic has cast a shadow over public health, necessitating immediate action to address its devastating consequences. To effectively combat this crisis, it is crucial to discover better opioid drugs with reduced addiction poten…
View article: De Novo KOR Antagonists Datasets
De Novo KOR Antagonists Datasets Open
Datasets used as input, generated or analyzed in the manuscript De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework: 1. Pre-training Dataset #1 (4.6 million compounds from ZINC 20): zinc20_train.csv (…
View article: De Novo KOR Antagonists Datasets
De Novo KOR Antagonists Datasets Open
Datasets used as input, generated or analyzed in the manuscript De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework: 1. Pre-training Dataset #1 (4.6 million compounds from ZINC 20): zinc20_train.csv (…
View article: De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework Open
Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown t…
View article: Decision letter: Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase
Decision letter: Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase Open
Article Figures and data Abstract Editor's evaluation Introduction Results and discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract β-Lactam antibioti…
View article: Gαs slow conformational transition upon GTP binding and a novel Gαs regulator
Gαs slow conformational transition upon GTP binding and a novel Gαs regulator Open
SUMMARY G proteins are major signaling partners for G protein-coupled receptors (GPCRs). Although stepwise structural changes during GPCR–G protein complex formation and guanosine diphosphate (GDP) release have been reported, no informatio…
View article: A Novel Mitragynine Analog with Low-Efficacy Mu Opioid Receptor Agonism Displays Antinociception with Attenuated Adverse Effects
A Novel Mitragynine Analog with Low-Efficacy Mu Opioid Receptor Agonism Displays Antinociception with Attenuated Adverse Effects Open
Mitragynine and 7-hydroxymitragynine (7OH) are the major alkaloids mediating the biological actions of the psychoactive plant kratom. To investigate the structure-activity relationships of mitragynine/7OH templates, we diversified the arom…
View article: A novel mitragynine analog with low efficacy mu-opioid receptor agonism displays antinociception with attenuated adverse effects
A novel mitragynine analog with low efficacy mu-opioid receptor agonism displays antinociception with attenuated adverse effects Open
Dried kratom leaves are anecdotally used for the treatment of pain, opioid dependence, and alcohol use disorder. We have previously shown that kratom’s natural products (mitragynine) and semi-synthetic analogs (7-hydroxy mitragynine (7OH) …
View article: Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors
Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors Open
The metabotropic glutamate receptors (mGluRs) form a family of neuromodulatory G-protein-coupled receptors that contain both a seven-helix transmembrane domain (TMD) and a large extracellular ligand-binding domain (LBD) which enables stabl…
View article: Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors
Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors Open
The metabotropic glutamate receptors (mGluRs) form a family of neuromodulatory G protein-coupled receptors that contain both a seven-helix transmembrane domain (TMD) and a large extracellular ligand-binding domain (LBD) which enables stabl…