Davide Provasi

Davide Provasi
Icahn School of Medicine at Mount Sinai | MSSM · Department of Pharmacological Sciences

PhD

About

172
Publications
11,393
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3,981
Citations
Citations since 2017
44 Research Items
2064 Citations
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20172018201920202021202220230100200300
20172018201920202021202220230100200300
Additional affiliations
January 2009 - December 2013
Icahn School of Medicine at Mount Sinai
January 2001 - present
Mario Negri Institute for Pharmacological Research
January 2000 - December 2008
University of Milan

Publications

Publications (172)
Preprint
Full-text available
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 information is available with regard to guanosine triphosphate (GTP) binding. Here, we used a novel Bayesian integrative modeling...
Article
Full-text available
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 aromatic ring of the indole at the C9, C10, and C12 positions and investigated their G-protein and arrestin signali...
Preprint
Full-text available
Dried kratom leaves are anecdotally used for the treatment of pain, opioid dependence, and alcohol use disorder. We have previously shown that kratom and its natural products (mitragynine) and semi-synthetic analogs (7-hydroxy mitragynine (7OH) and mitragynine pseudoindoxyl) are mu opioid receptor (MOR) agonists that show minimal beta-arrestin2 rec...
Article
Full-text available
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 stable dimerization. While numerous studies have revealed variability across subtypes in the initial activation step...
Preprint
Full-text available
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 stable dimerization. While numerous studies have revealed variability across subtypes in the initial activation step...
Article
Pain management devoid of serious opioid adverse effects is still far from reach despite vigorous research and development efforts. Alternatives to classical opioids have been sought for years, and mounting reports of individuals finding pain relief with kratom have recently intensified research on this natural product. Although the composition of...
Article
Full-text available
Determining the drug-target residence time (RT) is of major interest in drug discovery given that this kinetic parameter often represents a better indicator of in vivo drug efficacy than binding affinity. However, obtaining drug-target unbinding rates poses significant challenges, both computationally and experimentally. This is particularly palpab...
Article
Full-text available
G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Methadone is a synthetic opioid agonist with notoriously unique properties, such as lower abuse liability and induced relief of withdrawal symptoms and drug cravings, despite acting on the same opioid receptors triggered by classical opioids, in particular the µ-opioid receptor (MOR). Its distinct pharmacologic properties, which have recently been...
Article
Objective The αIIbβ3 antagonist antiplatelet drug abciximab is the chimeric antigen-binding fragment comprising the variable regions of murine monoclonal antibody 7E3 and the constant domains of human IgG1 and light chain κ. Previous mutagenesis studies suggested that abciximab binds to the β3 C177-C184 specificity-determining loop (SDL) and Trp129...
Article
DN, YZ, AS, & JL contributed equally, as did MF, TW, & BSC The αIIbβ3 antagonist antiplatelet drug abciximab, approved in 1994, is the chimeric antigen-binding fragment (Fab) comprising the variable regions of murine mAb 7E3 and human IgG1 and light chain κ constant domains. In studies involving thousands of patients undergoing percutaneous coronar...
Article
In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the μ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, ar...
Chapter
All-atom molecular dynamics simulations can capture the dynamic degrees of freedom that characterize molecular recognition, the knowledge of which constitutes the cornerstone of rational approaches to drug design and optimization. In particular, enhanced sampling algorithms, such as metadynamics, are powerful tools to dramatically reduce the comput...
Preprint
In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the µ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, ar...
Article
Full-text available
The differential modulation of agonist and antagonist binding to opioid receptors (ORs) by sodium (Na⁺) has been known for decades. To shed light on the molecular determinants, thermodynamics, and kinetics of Na⁺ translocation through the μ-OR (MOR), we used a multi-ensemble Markov model framework combining equilibrium and non-equilibrium atomistic...
Data
List of mouse MOR residues selected for tICA analysis. (DOCX)
Data
List of MOR residue pairs whose minimum heavy atom distance fluctuation has a correlation larger than 0.6 to the most dominant tICA0 and tICA1 components in the simulated active or inactive MOR systems. (DOCX)
Data
Transition times (in μs) between metastable states obtained from the MSM constructed for the simulated active MOR system with a protonated D2.50. The label “Inf” indicates the absence of transitions between two states. (DOCX)
Data
Spatial location of the 105 residues listed in S1 Table in a representative active MOR state from molecular dynamics simulations shown in vertical and horizontal views. The Cα atoms of these residues are shown as spheres. (TIFF)
Data
Summary of number, type, and length of simulations. (DOCX)
Data
Transition times (in μs) between metastable states obtained from the MSM constructed for the simulated inactive MOR system. The label “Inf” indicates the absence of transitions between two states. (DOCX)
Data
Transition times (in μs) between metastable states obtained from the MSM constructed for the simulated active MOR system with a charged D2.50. The label “Inf” indicates the absence of transitions between two states. (DOCX)
Data
The MSM implied time scales as a function of lag-time for the first 10 eigenvalues obtained for each simulated MOR system. The data points correspond to the median estimated from all bootstraps samples and the full sample. The upper and lower error bars represent the differences between the median and 1st and 3rd quantiles, respectively. (TIFF)
Data
Saturation of 3H-DAMGO binding in the absence and presence of NaCl. Binding of 3H-DAMGO was carried out with for increasing ligand concentrations in the absence (red) and presence (blue) of NaCl (25 nM). Results are the means ± s.e.m. of three independent replications. Nonlinear regression analysis of the curves is indicated by the solid lines. KD...
Data
Graphical illustration of MOR residue pairs whose minimum heavy atom distance fluctuations have a correlation larger than 0.6 to the most dominant tIC0 and tIC1 components. (TIFF)
Data
Fraction of Na+-bound receptor as a function of the extracellular sodium concentration for the inactive MOR (green), active MOR with charged D1142.50 (red), active MOR with protonated D1142.50 (brown), and active MOR at constant pH = 7 (orange). A dashed black line indicates 50% occupation probability that intersects the curves at the corresponding...
Article
Full-text available
Computational strategies aimed at unveiling the thermodynamic and kinetic properties of G Protein-Coupled Receptor (GPCR) activation require extensive molecular dynamics simulations of the receptor embedded in an explicit lipid-water environment. A possible method for efficiently sampling the conformational space of such a complex system is metadyn...
Article
G-protein-coupled receptors (GPCRs) control vital cellular signaling pathways. GPCR oligomerization is proposed to increase signaling diversity. However, many reports have arrived at disparate conclusions regarding the existence, stability, and stoichiometry of GPCR oligomers, partly because of cellular complexity and ensemble averaging of intrarec...
Preprint
Computational strategies aimed at unveiling the thermodynamic and kinetic properties of G Protein-Coupled Receptor (GPCR) activation require extensive molecular dynamics simulations of the receptor embedded in an explicit lipid-water environment. A possible method for efficiently sampling the conformational space of such a complex system is metadyn...
Article
Full-text available
Various experimental and computational techniques have been employed over the past decade to provide structural and thermodynamic insights into G Protein-Coupled Receptor (GPCR) dimerization. Here, we use multiple microsecond-long, coarse-grained, biased and unbiased molecular dynamics simulations (a total of ~4 milliseconds) combined with multi-en...
Article
Full-text available
While the therapeutic effect of opioids analgesics is mainly attributed to µ-opioid receptor (MOR) activation leading to G protein signaling, their side effects have mostly been linked to β-arrestin signaling. To shed light on the dynamic and kinetic elements underlying MOR functional selectivity, we carried out close to half millisecond high-throu...
Article
Full-text available
Gαs (Gs) and Gαolf (Golf) are highly homologous G protein α; subunits that activate adenylate cyclase, thereby serving as crucial mediators of intracellular signaling. Owing to their dramatically different brain expression patterns, we studied similarities and differences between their activation processes with the aim of comparing their receptor c...
Article
Full-text available
The lipid composition of cell membranes has increasingly been recognized as playing an important role in the function of various membrane proteins, including G Protein-Coupled Receptors (GPCRs). For instance, experimental and computational evidence has pointed to lipids influencing receptor oligomerization directly, by physically interacting with t...
Data
Lipid distributions of A) PA, B) PI, C) PIP1-3, D) PS, and E) GM around individual protomers during the final 2 μs of the low receptor density simulations with the BB beads of the receptors fixed. The dots indicate the centers of mass of the BB beads of the receptor helices. (PDF)
Data
Plots showing the average lipid order (left) and bilayer thickness (right) for one high receptor density simulation run of a mixed array of inactive and active MOR during which time the BB beads of the receptors were fixed. The data is averaged over all lipids, excluding the ones that flip-flop across the membrane (i.e. CHOL, CER, and DAG). For the...
Data
Structure of A) a cholesterol, B) a PC/SM lipid, and C) a GM lipid with the ROH, GL1, and AM1 beads used in the lipid analysis colored in cyan. The headgroup beads are in pink and the remaining tail beads in grey. (PDF)
Data
The fraction of lipids with each headgroup in the plasma membrane at the start of all of the simulations. ‘Other’ in the upper leaflet includes: CER (0.7%), LPC (1.0%), and DAG (0.4%). ‘Other’ in the lower leaflet includes: PA (1.5%), PIP1-3 (1.6%), CER (0.1%), and DAG (0.5%). The total number of lipids in the upper and lower leaflets was approxima...
Data
The bilayer thickness (nm, top row) and lipid order (bottom row) of the non-flipping lipids within 3.125 nm of the protein center of mass calculated as a function of the helix index during the last 2 μs of membrane equilibration of the high receptor density simulations with the BB beads of the receptors kept fixed. For the thickness, the average an...
Data
The residues on helices involved in dimer interfaces with which CHOL is in contact for more than 50% of the final microsecond of the high receptor density simulations with the receptors free to move. Residues in contact with CHOL for more than 75% of the simulation time are in bold. (PDF)
Data
Plots showing the average lipid order (left column) and bilayer thickness (nm, right column) during the final 2 μs of membrane equilibration for one high receptor density simulation run of inactive (top row) or active (bottom row) receptors with fixed BB beads. The data is averaged over all lipids, excluding the ones that flip-flop across the membr...
Data
The correlation between the bilayer thickness and the lipid order for the high receptor density simulations of inactive (left) or activated (right) MOR with the BB beads of the receptors fixed. For each bin, the average order is plotted vs. the average thickness. (PDF)
Data
Tilting of the principal axis of the active or inactive MOR in the low receptor density simulations with either restrained BB beads or freely moving receptors. The angle θ (radial coordinate, measuring the amount of tilting) is the angle between the protein principal axis and the normal to the membrane, while φ (polar angle, representing the direct...
Data
Normalized distribution of lipid order during the final 2 μs of membrane equilibration for lipids near inactive MOR (blue) or active MOR (red) in the high receptor density simulations with the BB beads of the receptors kept fixed. The thick lines are the average of the five individual runs which are shown as thin lines. The individual runs are an a...
Data
Plots showing the average the lipid order as a function of time for one of the runs in the high receptor density simulations of inactive (top row) or active (bottom row) MORs. The data is averaged over all lipids, excluding the ones that flip-flop across the membrane (i.e. CHOL, CER, and DAG). A value of 0 (orange color) indicates a fully ordered l...
Data
Residence time of PC (left) or cholesterol (right) during the production runs of the membrane with high receptor density. The error bars represent the deviation over the five runs. (PDF)
Data
Average of the number of isolated receptors calculated as a function of time during the production runs of the membrane with high receptor density. Values for the simulations with inactive or active receptors are reported in blue and red, respectively. (PDF)
Data
Model structures of the A) inactive/inactive MORs interacting at the TM1,2,H8/TM4 interface and B) active/active MORs interacting at the TM1,2,H8/TM1,2,H8 interface during the final μs of the high density simulations in which the BB beads of the receptors were kept fixed. Helices involved in the interface are colored by frequency of interaction wit...
Data
The fraction of the final 2 μs of the low receptor density simulation with fixed receptor backbone (BB) beads during which the BB beads of the residues are in contact with the GL1 bead of a PIP1-3 lipid. All residues listed are in contact with either the inactive or active receptor at least 10% of the simulation time. Residues exhibiting the greate...
Data
Fraction of interfaces formed between inactive, active, and inactive/active MOR determined by clustering the conformations observed during the final microsecond of the high receptor density trajectories in which the receptors were free to move. The mean fraction of dimers belonging to each specific interface is reported along with its 97.5% credibl...
Data
Probability distribution of CHOL order in the headgroup region of the membrane (dashed line) and the hydrophobic part of the membrane (solid lines) during the low receptor density simulations in which the BB beads of the receptors were kept fixed. (PDF)
Data
The z-coordinate of the AM1 or GL1 beads as a function of lipid order for the DAG (top row) or CER (bottom row) lipids in the plasma membrane with inactive MOR, active MOR, or no receptors. The data in the plots for the membranes with receptors are from the final 2 μs membrane equilibration in the simulations with high receptor density and the BB b...
Data
Kinetic network of the cholesterol movement in the z-direction as a function of the distance from the protein for the A) inactive and B) active MORs generated with the plot_network routine of pyemma using the final 2 μs of membrane equilibration of the simulations with high receptor density and the BB beads of the receptors fixed. The initial geome...
Data
Snapshot of the production runs of the simulations with high receptor density at 0, 5, 10, and 20 μs for the A) inactive, B) active, and C) mixed arrays of MOR. The lipids are in grey, the inactive proteins in blue, and the active proteins are red. (PDF)
Data
Movie showing the average of the lipid order as a function of time for one run with inactive receptors in the membrane with high receptor density. The snapshots in S11 Fig were taken from this trajectory. The data is averaged over all lipids, excluding the ones that flip-flop across the membrane (i.e. CHOL, CER, and DAG). A value of 0 (orange color...
Data
The bilayer thickness (nm, top row) and lipid order (bottom row) of the non-flipping lipids within 3.125 nm of the protein center of mass calculated as a function of the helix index during the last 2 μs of membrane equilibration of the low receptor density simulations with the BB beads of the receptors kept fixed. For the thickness, the average and...
Data
Average lipid thickness (upper triangle) and order (lower triangle) calculated as a function of the protein-protein distance r and the lipid position d for the following interfaces: TM5/TM5 and TM1,2,H8/TM1,2,H8 for the active MOR (panels A and B, respectively), and TM1,2,H8/TM5 for the inactive or active MOR (panels C and D, respectively). Traject...
Data
The z-coordinate of the CHOL’s ROH or CER/DAG’s AM1 or GL1 beads as a function of the minimum distance to the BB beads of the protein for inactive MORs (top row) or active MORs (bottom row) during the final 2 μs membrane equilibration in the simulations with high receptor density and the BB beads of the receptors kept fixed. (PDF)
Article
Opioids are widely used to treat millions suffering from pain, but their analgesic utility is limited due to associated side effects. Herein we report the development and evaluation of a chemical probe exhibiting analgesia and reduced opioid-induced side effects. This compound, kurkinorin (5), is a potent and selective µ-opioid receptor (MOR) agoni...
Article
Substantial attention has recently been devoted to G protein-biased agonism of the µ-opioid receptor (MOR) as an ideal new mechanism for the design of analgesics devoid of serious side effects. However, designing opioids with appropriate efficacy and bias is challenging because it requires an understanding of the ligand binding process and of the a...
Article
Available crystal structures of opioid receptors provide a high-resolution picture of ligand binding at the primary ("orthosteric") site, that is, the site targeted by endogenous ligands. Recently, positive allosteric modulators of opioid receptors have also been discovered, but their modes of binding and action remain unknown. Here, we use a metad...
Poster
The ability of certain μ-opioid receptor agonists to preferentially activate G protein-dependent over β-arrestin-dependent signaling pathways holds great potential for the design of improved therapeutic agents. In fact, some opioid molecules that exhibit limited arrestin recruitment have been shown to display effective analgesia with reduced advers...
Poster
While oligomerization of several G Protein-Coupled Receptor systems, including the μ-opioid receptor (MOR), is an accepted phenomenon, its role in receptor signaling is the subject of much debate as are the specific interfaces formed and the time-scales of their formation and disruption. Crystallographic information of the antagonist-bound, inactiv...
Poster
Classical opioid receptor drugs, like morphine and its derivatives, have been used for centuries to manage chronic pain despite frequent occurrence of adverse effects, including addiction, respiratory depression, vomiting, constipation, and severe sedation. A recent campaign to identify μ-opioid receptor agonists that are effective as analgesics bu...
Chapter
The publication of high-resolution structures for all of the opioid receptor subfamilies has unveiled exciting opportunities for mechanistic insight into the molecular mechanisms underlying the biology of nociception, reward, and higher cognitive functions, as well as promises for progress in several clinical areas such as pain management, physiolo...
Article
Full-text available
Major advances in G Protein-Coupled Receptor (GPCR) structural biology over the past few years have yielded a significant number of high-resolution crystal structures for several different receptor subtypes. This dramatic increase in GPCR structural information has underscored the use of automated docking algorithms for the discovery of novel ligan...
Article
Full-text available
Substantial evidence in support of the formation of opioid receptor (OR) di-/oligomers suggests previously unknown mechanisms used by these proteins to exert their biological functions. In an attempt to guide experimental assessment of the identity of the minimal signaling unit for ORs, we conducted extensive coarse-grained (CG) molecular dynamics...
Article
G protein-coupled receptors (GPCRs) continue to hold leading positions as drug targets. However, many GPCR drug candidates fail in clinical trials because of limited in vivo efficacy. While binding affinity, i.e. the strength of association of a drug to its receptor, has traditionally been viewed as an appropriate surrogate for in vivo efficacy, re...
Article
Platelet aggregation is the consequence of the binding of extracellular bivalent ligands such as fibrinogen and von Willebrand factor to the high affinity, active state of integrin αIIbβ3. This state is achieved through a so-called "inside-out" mechanism characterized by the membrane-assisted formation of a complex between the F2 and F3 subdomains...
Article
Delta-opioid (DOP) receptors are members of the G protein-coupled receptor (GPCR) sub-family of opioid receptors, and are evolutionarily related, with homology exceeding 70%, to cognate mu-opioid (MOP), kappa-opioid (KOP), and nociceptin opioid (NOP) receptors. DOP receptors are considered attractive drug targets for pain management because agonist...