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Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers. J Phys Chem Lett 2019; 10:7333-7339. [PMID: 31714784 DOI: 10.1021/acs.jpclett.9b02861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Due to the poor aqueous solubility of retinoids, evolution has tuned their binding to cellular proteins to address specialized physiological roles by modulating uptake, storage, and delivery to specific targets. With the aim to disentangle the structure-function relationships in these proteins and disclose clues for engineering selective carriers, the binding mechanism of the two most abundant retinol-binding isoforms was explored by using enhanced sampling molecular dynamics simulations and surface plasmon resonance. The distinctive dynamics of the entry portal site in the holo species was crucial to modulate retinol dissociation. Remarkably, this process is controlled to a large extent by the replacement of Ile by Leu in the two isoforms, thus suggesting that fine control of ligand release can be achieved through a rigorous selection of conservative mutations in accessory sites.
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2
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Abstract
Drug-target binding kinetics has recently emerged as a sometimes critical determinant of in vivo efficacy and toxicity. Its rational optimization to improve potency or reduce side effects of drugs is, however, extremely difficult. Molecular simulations can play a crucial role in identifying features and properties of small ligands and their protein targets affecting the binding kinetics, but significant challenges include the long time scales involved in (un)binding events and the limited accuracy of empirical atomistic force fields (lacking, e.g., changes in electronic polarization). In an effort to overcome these hurdles, we propose a method that combines state-of-the-art enhanced sampling simulations and quantum mechanics/molecular mechanics (QM/MM) calculations at the BLYP/VDZ level to compute association free energy profiles and characterize the binding kinetics in terms of structure and dynamics of the transition state ensemble. We test our combined approach on the binding of the anticancer drug Imatinib to Src kinase, a well-characterized target for cancer therapy with a complex binding mechanism involving significant conformational changes. The results indicate significant changes in polarization along the binding pathways, which affect the predicted binding kinetics. This is likely to be of widespread importance in binding of ligands to protein targets.
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3
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Small compounds modulating bi‐directional allostery in protein kinases: a new grip with an old trick. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.797.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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Assessment of the model refinement category in CASP12. Proteins 2017; 86 Suppl 1:152-167. [PMID: 29071750 DOI: 10.1002/prot.25409] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/03/2017] [Accepted: 10/24/2017] [Indexed: 01/07/2023]
Abstract
We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the previous experiments, the predictors were invited to refine selected server models received in the regular (nonrefinement) stage of the CASP experiment. We assessed the submitted models using a combination of standard CASP measures. The coefficients for the linear combination of Z-scores (the CASP12 score) have been obtained by a machine learning algorithm trained on the results of visual inspection. We identified eight groups that improve both the backbone conformation and the side chain positioning for the majority of targets. Albeit the top methods adopted distinctively different approaches, their overall performance was almost indistinguishable, with each of them excelling in different scores or target subsets. What is more, there were a few novel approaches that, while doing worse than average in most cases, provided the best refinements for a few targets, showing significant latitude for further innovation in the field.
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5
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An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. J Chem Inf Model 2017; 57:1210-1217. [PMID: 28453271 DOI: 10.1021/acs.jcim.6b00772] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A generally applicable metadynamics scheme for predicting the free energy profile of ligand binding to G-protein-coupled receptors (GPCRs) is described. A common and effective collective variable (CV) has been defined using the ideally placed and highly conserved Trp6.48 as a reference point for ligand-GPCR distance measurement and the common orientation of GPCRs in the cell membrane. Using this single CV together with well-tempered multiple-walker metadynamics with a funnel-like boundary allows an efficient exploration of the entire ligand binding path from the extracellular medium to the orthosteric binding site, including vestibule and intermediate sites. The protocol can be used with X-ray structures or high-quality homology models (based on a high-quality template and after thorough refinement) for the receptor and is universally applicable to agonists, antagonists, and partial and reverse agonists. The root-mean-square error (RMSE) in predicted binding free energies for 12 diverse ligands in five receptors (a total of 23 data points) is surprisingly small (less than 1 kcal mol-1). The RMSEs for simulations that use receptor X-ray structures and homology models are very similar.
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6
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Investigating allosteric effects on the functional dynamics of β2-adrenergic ternary complexes with enhanced-sampling simulations. Chem Sci 2017; 8:4019-4026. [PMID: 30155211 PMCID: PMC6094175 DOI: 10.1039/c6sc04647a] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/24/2017] [Indexed: 12/27/2022] Open
Abstract
Signalling by G-protein coupled receptors usually occurs via ternary complexes formed under cooperative binding between the receptor, a ligand and an intracellular binding partner (a G-protein or β-arrestin). While a global rational for allosteric effects in ternary complexes would be of great help in designing ligands with specific effects, the paucity of structural data for ternary complexes with β-arrestin, together with the intrinsic difficulty of characterizing the dynamics involved in the allosteric coupling, have hindered the efforts to devise such a model. Here we have used enhanced-sampling atomistic molecular-dynamics simulations to investigate the dynamics and complex formation mechanisms of both β-arrestin- and Gs-complexes with the β2-adrenergic receptor (ADRB2) in its apo-form and in the presence of four small ligands that exert different allosteric effects. Our results suggest that the structure and dynamics of arrestin-ADRB2 complexes depend strongly on the nature of the small ligands. The complexes exhibit a variety of different coupling orientations in terms of the depth of the finger loop in the receptor and activation states of ADRB2. The simulations also allow us to characterize the cooperativity between the ligand and intracellular binding partner (IBP). Based on the complete and consistent results, we propose an experimentally testable extended ternary complex model, where direction of the cooperative effect between ligand and IBP (positive or negative) and its magnitude are predicted to be a characteristic of the ligand signaling bias. This paves the avenue to the rational design of ligands with specific functional effects.
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7
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Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations. eLife 2017; 6. [PMID: 28445123 PMCID: PMC5406204 DOI: 10.7554/elife.22175] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/06/2017] [Indexed: 01/03/2023] Open
Abstract
p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its molecular mechanism of activation remains largely unexplained, even after decades of research. By using state-of-the-art molecular dynamics simulations, we decipher the key elements of the complex molecular mechanism refined by evolution to allow for a fine tuning of p38α kinase activity. Our study describes for the first time the molecular effects of different regulators of the enzymatic activity, and provides an integrative picture of the activation mechanism that explains the seemingly contradictory X-ray and NMR data. DOI:http://dx.doi.org/10.7554/eLife.22175.001
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8
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Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET. Sci Rep 2017; 7:39841. [PMID: 28045057 PMCID: PMC5206623 DOI: 10.1038/srep39841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.
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9
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Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations. J Am Chem Soc 2016; 138:14257-14263. [PMID: 27726386 DOI: 10.1021/jacs.6b05425] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cryptic pockets, that is, sites on protein targets that only become apparent when drugs bind, provide a promising alternative to classical binding sites for drug development. Here, we investigate the nature and dynamical properties of cryptic sites in four pharmacologically relevant targets, while comparing the efficacy of various simulation-based approaches in discovering them. We find that the studied cryptic sites do not correspond to local minima in the computed conformational free energy landscape of the unliganded proteins. They thus promptly close in all of the molecular dynamics simulations performed, irrespective of the force-field used. Temperature-based enhanced sampling approaches, such as Parallel Tempering, do not improve the situation, as the entropic term does not help in the opening of the sites. The use of fragment probes helps, as in long simulations occasionally it leads to the opening and binding to the cryptic sites. Our observed mechanism of cryptic site formation is suggestive of an interplay between two classical mechanisms: induced-fit and conformational selection. Employing this insight, we developed a novel Hamiltonian Replica Exchange-based method "SWISH" (Sampling Water Interfaces through Scaled Hamiltonians), which combined with probes resulted in a promising general approach for cryptic site discovery. We also addressed the issue of "false-positives" and propose a simple approach to distinguish them from druggable cryptic pockets. Our simulations, whose cumulative sampling time was more than 200 μs, help in clarifying the molecular mechanism of pocket formation, providing a solid basis for the choice of an efficient computational method.
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Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol 2016; 23:1193-1205. [PMID: 27693059 DOI: 10.1016/j.chembiol.2016.06.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/06/2016] [Accepted: 06/30/2016] [Indexed: 01/10/2023]
Abstract
Allostery is a phenomenon observed in many proteins where binding of a macromolecular partner or a small-molecule ligand at one location leads to specific perturbations at a site not in direct contact with the region where the binding occurs. The list of proteins under allosteric regulation includes AGC protein kinases. AGC kinases have a conserved allosteric site, the phosphoinositide-dependent protein kinase 1 (PDK1)-interacting fragment (PIF) pocket, which regulates protein ATP-binding, activity, and interaction with substrates. In this study, we identify small molecules that bind to the ATP-binding site and affect the PIF pocket of AGC kinase family members, PDK1 and Aurora kinase. We describe the mechanistic details and show that although PDK1 and Aurora kinase inhibitors bind to the conserved ATP-binding site, they differentially modulate physiological interactions at the PIF-pocket site. Our work outlines a strategy for developing bidirectional small-molecule allosteric modulators of protein kinases and other signaling proteins.
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11
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Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome. Sci Rep 2016; 6:30293. [PMID: 27456546 PMCID: PMC4960638 DOI: 10.1038/srep30293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/01/2016] [Indexed: 10/25/2022] Open
Abstract
WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function.
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12
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Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling. Cancer Cell 2016; 30:176-178. [PMID: 27479031 DOI: 10.1016/j.ccell.2016.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors. Angew Chem Int Ed Engl 2016; 55:8008-12. [DOI: 10.1002/anie.201602729] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/06/2016] [Indexed: 01/26/2023]
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14
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A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. J Cheminform 2016; 8:18. [PMID: 29270804 PMCID: PMC4896257 DOI: 10.1186/s13321-016-0119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase. Sci Rep 2016; 6:24439. [PMID: 27087366 PMCID: PMC4834493 DOI: 10.1038/srep24439] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/29/2016] [Indexed: 01/06/2023] Open
Abstract
Understanding the conformational changes associated with the binding of small ligands to their biological targets is a fascinating and meaningful question in chemistry, biology and drug discovery. One of the most studied and important is the so-called "DFG-flip" of tyrosine kinases. The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind. Despite many studies, the details of this prototypical conformational change are still debated. Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src. We find that both conformational selection and induced fit play a role in the binding mechanism, reconciling opposing views held in the literature. Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.
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17
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An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase. Sci Rep 2016; 6:24235. [PMID: 27063862 PMCID: PMC4827121 DOI: 10.1038/srep24235] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/22/2016] [Indexed: 11/09/2022] Open
Abstract
Phosphorylation of the activation loop is a fundamental step in the activation of most protein kinases. In the case of the Src tyrosine kinase, a prototypical kinase due to its role in cancer and its historic importance, phosphorylation of tyrosine 416 in the activation loop is known to rigidify the structure and contribute to the switch from the inactive to a fully active form. However, whether or not phosphorylation is able per-se to induce a fully active conformation, that efficiently binds ATP and phosphorylates the substrate, is less clear. Here we employ a combination of solution NMR and enhanced-sampling molecular dynamics simulations to fully map the effects of phosphorylation and ATP/ADP cofactor loading on the conformational landscape of Src tyrosine kinase. We find that both phosphorylation and cofactor binding are needed to induce a fully active conformation. What is more, we find a complex interplay between the A-loop and the hinge motion where the phosphorylation of the activation-loop has a significant allosteric effect on the dynamics of the C-lobe.
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19
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Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics. PLoS Comput Biol 2015; 11:e1004578. [PMID: 26606374 PMCID: PMC4659586 DOI: 10.1371/journal.pcbi.1004578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/01/2015] [Indexed: 11/18/2022] Open
Abstract
Due to its inhibition of the Abl kinase domain in the BCR-ABL fusion protein, imatinib is strikingly effective in the initial stage of chronic myeloid leukemia with more than 90% of the patients showing complete remission. However, as in the case of most targeted anti-cancer therapies, the emergence of drug resistance is a serious concern. Several drug-resistant mutations affecting the catalytic domain of Abl and other tyrosine kinases are now known. But, despite their importance and the adverse effect that they have on the prognosis of the cancer patients harboring them, the molecular mechanism of these mutations is still debated. Here by using long molecular dynamics simulations and large-scale free energy calculations complemented by in vitro mutagenesis and microcalorimetry experiments, we model the effect of several widespread drug-resistant mutations of Abl. By comparing the conformational free energy landscape of the mutants with those of the wild-type tyrosine kinases we clarify their mode of action. It involves significant and complex changes in the inactive-to-active dynamics and entropy/enthalpy balance of two functional elements: the activation-loop and the conserved DFG motif. What is more the T315I gatekeeper mutant has a significant impact on the binding mechanism itself and on the binding kinetics.
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MESH Headings
- Computational Biology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Imatinib Mesylate/chemistry
- Imatinib Mesylate/metabolism
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive
- Molecular Dynamics Simulation
- Mutagenesis, Site-Directed
- Thermodynamics
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20
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New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations. J Chem Theory Comput 2015; 11:1354-9. [PMID: 26574347 DOI: 10.1021/ct5010164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Three-dimensional domain swapping is an important mode of protein association leading to the formation of stable dimers. Monomers associating via this mechanism mutually exchange a domain to form a homodimer. Classical cadherins, an increasingly important target for anticancer therapy, use domain swapping to mediate cell adhesion. However, despite its importance, the molecular mechanism of domain swapping is still debated. Here, we study the conformational changes that lead to activation and dimerization via domain swapping of E-cadherin. Using state-of-the-art enhanced sampling atomistic simulations, we reconstruct its conformational free energy landscape, obtaining the free energy profile connecting the inactive and active form. Our simulations predict that the E-cadherin monomer populates the open and closed forms almost equally, which is in agreement with the proposed "selected fit" mechanism in which monomers in an active conformational state bind to form a homodimer, analogous to the conformational selection mechanism often observed in ligand-target binding. Moreover, we find that the open state population is increased in the presence of calcium ions at the extracellular boundary, suggesting their possible role as allosteric activators of the conformational change.
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21
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Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms. Acc Chem Res 2015; 48:277-85. [PMID: 25496113 DOI: 10.1021/ar500356n] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
CONSPECTUS: This Account highlights recent advances and discusses major challenges in the field of drug-target recognition, binding, and unbinding studied using metadynamics-based approaches, with particular emphasis on their role in structure-based design. Computational chemistry has significantly contributed to drug design and optimization in an extremely broad range of areas, including prediction of target druggability and drug likeness, de novo design, fragment screening, ligand docking, estimation of binding affinity, and modulation of ADMET (absorption, distribution, metabolism, excretion, toxicity) properties. Computationally driven drug discovery must continuously adapt to keep pace with the evolving knowledge of the factors that modulate the pharmacological action of drugs. There is thus an urgent need for novel computational approaches that integrate the vast amount of complex information currently available for small (bio)organic compounds, biologically relevant targets and their complexes, while also accounting accurately for the thermodynamics and kinetics of drug-target association, the intrinsic dynamical behavior of biomolecular systems, and the complexity of protein-protein networks. Understanding the mechanism of drug binding to and unbinding from biological targets is fundamental for optimizing lead compounds and designing novel biologically active ones. One major challenge is the accurate description of the conformational complexity prior to and upon formation of drug-target complexes. Recently, enhanced sampling methods, including metadynamics and related approaches, have been successfully applied to investigate complex mechanisms of drugs binding to flexible targets. Metadynamics is a family of enhanced sampling techniques aimed at enhancing the rare events and reconstructing the underlying free energy landscape as a function of a set of order parameters, usually referred to as collective variables. Studies of drug binding mechanisms have predicted the most probable association and dissociation pathways and the related binding free energy profile. In addition, the availability of an efficient open-source implementation, running on cost-effective GPU (i.e., graphical processor unit) architectures, has considerably decreased the learning curve and the computational costs of the methods, and increased their adoption by the community. Here, we review the recent contributions of metadynamics and other enhanced sampling methods to the field of drug-target recognition and binding. We discuss how metadynamics has been used to search for transition states, to predict binding and unbinding paths, to treat conformational flexibility, and to compute free energy profiles. We highlight the importance of such predictions in drug discovery. Major challenges in the field and possible solutions will finally be discussed.
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Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling. Cancer Cell 2013; 23:489-501. [PMID: 23597563 DOI: 10.1016/j.ccr.2013.02.018] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 12/12/2012] [Accepted: 02/19/2013] [Indexed: 01/12/2023]
Abstract
The fibroblast growth factor (FGF)/fibroblast growth factor receptor (FGFR) signaling network plays an important role in cell growth, survival, differentiation, and angiogenesis. Deregulation of FGFR signaling can lead to cancer development. Here, we report an FGFR inhibitor, SSR128129E (SSR), that binds to the extracellular part of the receptor. SSR does not compete with FGF for binding to FGFR but inhibits FGF-induced signaling linked to FGFR internalization in an allosteric manner, as shown by crystallography studies, nuclear magnetic resonance, Fourier transform infrared spectroscopy, molecular dynamics simulations, free energy calculations, structure-activity relationship analysis, and FGFR mutagenesis. Overall, SSR is a small molecule allosteric inhibitor of FGF/FGFR signaling, acting via binding to the extracellular part of the FGFR.
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23
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Intrarticular treatment of osteoartropaty knee with polynucleotides: a pilot study with medium-term follow-up. J BIOL REG HOMEOS AG 2013; 27:543-549. [PMID: 23830403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Knee osteoarthritis is a major cause of disability in the elderly. Many therapies are nowadays available, ranging from non-pharmacologic to pharmacological approaches like visco-supplementation, oral supplements or topical treatments, but a flawless treatment is still to be found. Visco-supplementation represents a valid treatment option for reducing pain associated with knee osteoarthritis and improving function in the affected joint. Many literature data report on the efficacy and safety profiles of hyaluronic acid in knee osteoarthritis, however the efficacy of intra-articular hyaluronic acid remains controversial, in fact while several clinical trials claimed a disease-modifying effect for hyaluronic acid, subsequent meta-analyses have cast doubts on this fact. The ideal intra-articular treatment for osteoarthritis should not only provide a mechanical protection of the cartilage surface, but also restore condrocytes homeostasis by restoring the physiological articular micro-environment and supplying nutrients. In this perspective an innovative medical product made up of polynucleotides (Condrotide) has been developed. The aim of this study is to test the 2-months efficacy in pain relief and improving function of intra-articular injections of Condrotide in patients with knee osteoarthritis or with grade III or IV chondropathy. Ninety-five subjects (33 men, 62 women), aged between 53 and 80, were included between May 2011 to July 2012. All subjects received intra-articular injections of Condrotide and were evaluated with the Knee injury and Osteoarthritis Outcome Score (KOOS), the NRS scale for pain assessment, the measurement of the range of motion (R.O.M.). In all subjects a significant improvement was found in KOOS score after 60 days. The mean global NRS pain decreased in both groups and there was also a R.O.M. improvement. These results show that the intra-articular administration of nucleotides in subjects with both severe knee arthritis and chondropathy can be recommended since is able to reverse in the short and medium term symptoms and function with a significant improvement in quality of life.
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Efficient numerical reconstruction of protein folding kinetics with partial path sampling and pathlike variables. PHYSICAL REVIEW LETTERS 2013; 110:108106. [PMID: 23521305 DOI: 10.1103/physrevlett.110.108106] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Indexed: 06/01/2023]
Abstract
Numerically predicting rate constants of protein folding and other relevant biological events is still a significant challenge. We show that the combination of partial path transition interface sampling with the optimal interfaces and free-energy profiles provided by path collective variables makes the rate calculation for practical biological applications feasible and efficient. This methodology can reproduce the experimental rate constant of Trp-cage miniprotein folding with the same level of accuracy as transition path sampling at a fraction of the cost.
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25
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The mechanism of allosteric coupling in choline kinase α1 revealed by the action of a rationally designed inhibitor. Angew Chem Int Ed Engl 2013; 52:4582-6. [PMID: 23441033 DOI: 10.1002/anie.201209660] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/16/2013] [Indexed: 01/21/2023]
Abstract
Applying a CHOK hold: Combined experimental and computational studies of the binding mode of a rationally designed inhibitor of the dimeric choline kinase α1 (CHOKα1) explain the molecular mechanism of negative cooperativity (see scheme) and how the monomers are connected. The results give insight into how the symmetry of the dimer can be partially conserved despite a lack of conservation in the static crystal structures.
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The Mechanism of Allosteric Coupling in Choline Kinase α1 Revealed by the Action of a Rationally Designed Inhibitor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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New Insights in Protein Kinase Conformational Dynamics. Curr Top Med Chem 2012; 12:1889-95. [DOI: 10.2174/156802612804547407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 09/27/2012] [Accepted: 09/29/2012] [Indexed: 11/22/2022]
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Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors. J Chem Theory Comput 2012; 8:1165-70. [DOI: 10.1021/ct3001377] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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29
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A Simple Mechanism Underlying the Effect of Protecting Osmolytes on Protein Folding. J Chem Theory Comput 2011; 7:3846-52. [PMID: 26598273 DOI: 10.1021/ct200471w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Osmolytes are small organic compounds that confer to the cell an enhanced adaptability to external conditions. Many osmolytes not only protect the cell from osmotic stress but also stabilize the native structure of proteins. While simplified models able to predict changes to protein stability are available, a general physicochemical explanation of the underlying microscopic mechanism is still missing. Here, we address this issue by performing very long all-atom MD simulations, free energy calculations, and experiments on a well-characterized mini-protein, the villin headpiece. Comparisons between the folding free energy landscapes in pure water and osmolyte solutions, together with experimental validation by means of circular dichroism, unfolding experiments, and NMR, led us to formulate a simple hypothesis for the protecting mechanism. Taken together, our results support a novel mechanistic explanation according to which the main driving force behind native state protection is a change in the solvent rotational diffusion.
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Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece. J Chem Theory Comput 2011; 7:2675-80. [PMID: 26605458 DOI: 10.1021/ct2002489] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The increasing accuracy of molecular dynamics force fields parameters and the increasing resolution of experimental results allow one to carefully compare and complement in silico data with experimental observations. Here, we study the human villin headpiece C-terminal helical subdomain (HP35) with the recent highly optimized Amber99SB*-ILDN force field and compare the results with recent high resolution triplet-triplet energy transfer (TTET) experiments. The correct reproduction of the main structural features reveals a good agreement between experimental data and simulations.
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Treatment of lesions of the rotator cuff. J BIOL REG HOMEOS AG 2010; 24:453-459. [PMID: 21122285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The impingement syndrome and tendinopathy of the rotator cuff are the most common causes (complaints) of pain and disability of the shoulder. The aim of this study is to evaluate the efficacy of a specific rehabilitative protocol, integrated with the administration of a nutritional supplement, in the conservative rehabilitative treatment, as well as in post-surgery, of patients with lesions of the rotator cuff. Two groups with syndrome of the rotator cuff were formed to follow different therapeutic courses, in relation to the choice of each subject to undergo the conservative treatment (Arm A) or the surgical one (Arm B). In Arm A the study included the association of therapy with ESWT (shock waves) with the proprioceptive Multi Joint System, for rehabilitating joint movement and muscle strength of the shoulder, and a specific nutritional supplement to reduce the pain and conserve the cartilage tissue. Between February 2009 and June 2009, we enrolled 30 subjects (randomized into three homogenous groups A1, A2, A3), average age 45±10 years, with rotator cuff syndrome with calcification of the shoulder, diagnosed through clinical examination and investigative instruments (X-ray, echography or NMR). In Arm B, from September 2009 to January 2010, we enrolled 50 patients (randomized into two groups, B1 and B2), 24 male (average age 58.4: min 28 and max 78) and 26 females (average age 59.5: min 30 and max 80), who had undergone rotator cuff operations and acromionplasty for non-massive lesions without important gleno-humeral instability, with either open or arthroscopic procedures. The analysis of the results of Arm A highlights that in terms of reducing pain the main benefits were found in Group A1 where the supplement was given. From the analysis of the data of Arm B, in both groups an improvement of the first 4 items evaluated was evident. In Group B1, 84 percent of the patients declared to be satisfied and improved and 16 percent were dissatisfied; in Group B2, where the nutritional supplement was given, 92 percent were satisfied and 8 percent were dissatisfied. In conclusion, we retain that in cases of rotator cuff syndrome, an integrated rehabilitative approach, whether conservative or post-surgical, directed at taking total control of the patient, must observe particular attention to the optimization of the articular tissular metabolic balance in order to favour better functional recovery.
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In silico design of tubulin-targeted antimitotic peptides. Nat Chem 2009; 1:642-8. [DOI: 10.1038/nchem.401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 09/08/2009] [Indexed: 11/09/2022]
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DENPOL: A new program to determine electron densities of polypeptides using extremely localized molecular orbitals. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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A molecular dynamics study of an endostatin-derived peptide with antiangiogenic activity and of its mutants. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.02.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
A cross-sectional epidemiological study was carried out on 2932 farmers (response rate 92%) living in Northern Italy. A questionnaire on respiratory symptoms was supplied, chest X-ray taken and simple spirometry tests made. Thirty-nine subjects reported attacks of breathlessness associated with fever after exposure to mouldy hay; thirty-six had a clinical history of farmer's lung and X-ray and/or respiratory function changes indicative of chronic farmer's lung; 113 were classified as having bronchial asthma. These 118 subjects and a random sample of 131 non-symptomatic subjects were examined by intracutaneous skin tests and double diffusion precipitation tests with antigens associated with farmer's lung. All sera positive by precipitation were examined by immunoelectrophoresis, counterimmunoelectrophoresis, and C1q binding test, and Bovine conglutinin test in solid phase for the detection of circulating immunocomplexes. 27.8% cases of chronic farmer's lung, 4.4% of cases of bronchial asthma and 2.3% of non-symptomatic subjects showed precipitating antibodies against farmer's lung antigens. Of the precipitin-positive subjects, the majority had precipitating antibodies against Micropolyspora faeni. No differences in immunoelectrophoregrams in number and pattern of precipitation arcs for M. faeni were found between chronic farmer's lung and bronchial asthma subjects. Circulating immune complexes were present in 50% of chronic farmer's lung patients, 40% of those with bronchial asthma and 33.3% of non-symptomatic subjects. Three farmer's lung subjects (9.3%) showed immediate skin-test reactions to rural environmental allergens.
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Polyvinyl chloride pneumoconiosis: epidemiological study of exposed workers. JOURNAL OF OCCUPATIONAL MEDICINE. : OFFICIAL PUBLICATION OF THE INDUSTRIAL MEDICAL ASSOCIATION 1979; 21:540-2. [PMID: 469619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Among 1216 workers who were employed in a polyvinyl chloride production factory and who had had no previous dust exposure elsewhere, 20 cases of pneumoconiosis were found. Chest x-ray abnormalities were characterized by limited profusion, irregular type and low gravity. All 20 workers had been exposed to high PVC dust levels. The chest x-ray changes were observed after a minimum exposure of five years and, in a small percentage of cases, were associated with slight restrictive respiratory function impairments. Moreover, in the whole group of workers 388 cases (31.9%) were found with non-specific x-ray abnormalities mainly related to age and smoking.
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