Druggability Assessment in TRAPP using Machine Learning Approaches

AbstractAccurate protein druggability predictions are important for the selection of drug targets in the early stages of drug discovery. Due to the flexible nature of proteins, the druggability of a binding pocket may vary due to conformational changes. We have therefore developed two statistical models, a logistic regression model (TRAPP-LR) and a convolutional neural network model (TRAPP-CNN), for predicting druggability and how it varies with changes in the spatial and physicochemical properties of a binding pocket. These models are integrated into TRAPP (TRAnsient Pockets in Proteins), a tool for the analysis of binding pocket variations along a protein motion trajectory. The models, which were trained on publicly available and self-augmented data sets, show equivalent or superior performance to existing methods on test sets of protein crystal structures, and have sufficient sensitivity to identify potentially druggable protein conformations in trajectories from molecular dynamics simulations. Visualization of the evidence for the decisions of the models in TRAPP facilitates identification of the factors affecting the druggability of protein binding pockets.

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Structural basis for ligand modulation of the CCR2 conformational landscape

10.1101/392068 ◽

2018 ◽

Author(s):

Bryn C. Taylor ◽

Christopher T. Lee ◽

Rommie E. Amaro

Keyword(s):

Chemokine Receptor ◽

Chemokine Receptors ◽

Drug Targets ◽

Control Cell ◽

Binding Pocket ◽

Drug Binding ◽

Structural Basis ◽

Cc Chemokine ◽

Wide Range ◽

Dynamics Simulations

AbstractCC Chemokine Receptor 2 (CCR2) is a part of the chemokine receptor family, an important class of therapeutic targets. These class A G-protein coupled receptors (GPCRs) are involved in mammalian signaling pathways and control cell migration toward endogenous CC chemokine ligands. Chemokine receptors and their associated ligands are involved in a wide range of diseases and thus have become important drug targets. Of particular interest is CCR2, which has been implicated in cancer, autoimmunity driven type-1 diabetes, diabetic nephropathy, multiple sclerosis, asthma, atherosclerosis, neuropathic pain, and rheumatoid arthritis. Although promising, CCR2 antagonists have been largely unsuccessful to date. Here, we investigate the effect of an orthosteric and an allosteric antagonist on CCR2 dynamics by coupling long timescale molecular dynamics simulations with Markov-state model theory. We find that the antagonists shift CCR2 into several stable inactive conformations that are distinct from the crystal structure conformation, and that they disrupt a continuous internal water and sodium ion pathway preventing transitions to an active-like state. Several of these stable conformations contain a putative drug binding pocket that may be amenable to targeting with another small molecule antagonist. In the absence of antagonists, the apo dynamics reveal intermediate conformations along the activation pathway that provide insight into the basal dynamics of CCR2, and may also be useful for future drug design.

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In vitro study of Hesperetin and Hesperidin as inhibitors of zika and chikungunya virus proteases

PLoS ONE ◽

10.1371/journal.pone.0246319 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0246319

Author(s):

Raphael J. Eberle ◽

Danilo S. Olivier ◽

Carolina C. Pacca ◽

Clarita M. S. Avilla ◽

Mauricio L. Nogueira ◽

...

Keyword(s):

Conformational Changes ◽

Chikungunya Virus ◽

In Vitro Study ◽

3D Models ◽

Binding Pocket ◽

Starting Point ◽

Low Cytotoxicity ◽

Inhibitory Potential ◽

Dynamics Simulations

The potential outcome of flavivirus and alphavirus co-infections is worrisome due to the development of severe diseases. Hundreds of millions of people worldwide live under the risk of infections caused by viruses like chikungunya virus (CHIKV, genus Alphavirus), dengue virus (DENV, genus Flavivirus), and zika virus (ZIKV, genus Flavivirus). So far, neither any drug exists against the infection by a single virus, nor against co-infection. The results described in our study demonstrate the inhibitory potential of two flavonoids derived from citrus plants: Hesperetin (HST) against NS2B/NS3pro of ZIKV and nsP2pro of CHIKV and, Hesperidin (HSD) against nsP2pro of CHIKV. The flavonoids are noncompetitive inhibitors and the determined IC50 values are in low µM range for HST against ZIKV NS2B/NS3pro (12.6 ± 1.3 µM) and against CHIKV nsP2pro (2.5 ± 0.4 µM). The IC50 for HSD against CHIKV nsP2pro was 7.1 ± 1.1 µM. The calculated ligand efficiencies for HST were > 0.3, which reflect its potential to be used as a lead compound. Docking and molecular dynamics simulations display the effect of HST and HSD on the protease 3D models of CHIKV and ZIKV. Conformational changes after ligand binding and their effect on the substrate-binding pocket of the proteases were investigated. Additionally, MTT assays demonstrated a very low cytotoxicity of both the molecules. Based on our results, we assume that HST comprise a chemical structure that serves as a starting point molecule to develop a potent inhibitor to combat CHIKV and ZIKV co-infections by inhibiting the virus proteases.

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Dynamic Control of Ca2+ Binding in the C2 Domains of Synaptotagmin 1

10.1101/412031 ◽

2018 ◽

Author(s):

Patrick J. Rock ◽

Austin G. Meyer ◽

Chantell S. Evans ◽

Edwin R. Chapman ◽

R. Bryan Sutton

Keyword(s):

Structural Changes ◽

Dynamic Control ◽

Point Mutations ◽

Binding Pocket ◽

Snare Complex ◽

C2 Domains ◽

Domain Interactions ◽

Synaptotagmin 1 ◽

Binding Pockets ◽

Dynamics Simulations

AbstractSynaptotagmin senses fluctuations in the Ca2+ environment of neurons near active zones and transduces a signal to the SNARE complex to initiate exocytosis at the presynaptic terminus. The 3D structures of the two tandem C2 domains of synaptotagmin have been determined to high resolution; however, it is currently unclear how each domain dynamically interacts with Ca2+ at the atomic level. To study the mechanistic consequences of the lethal mutations at the AD3 locus, we introduced tyrosine to asparagine point mutations in both the C2A and C2B domains of synaptotagmin 1, and we have constructed a model that describes the relationship between Ca2+ -binding and the structural changes within each C2 domain. We show that the mobility of loop 3 in the Ca2+ binding pocket increases markedly in C2A, while the mobility of loop 1 changes in C2B with the AD3 mutation. This increase in loop mobility results in an increase in the average volume and variance of the Ca2+ -binding pockets of C2A and C2B. The volume of the unbound Ca2+ -binding pocket in C2A is usually restrained by intra-domain interactions between the tyrosine residue at the AD3 locus and residues on loop 3; however, the AD3 mutation decouples the restraint and results in a larger, more variable Ca2+ -binding pocket in C2A. C2B maintains a more compact Ca2+ -binding pocket; however, its volume also fluctuates significantly with the AD3 mutation. Changes in binding pocket volume that involve more variable Ca2+ binding loops would likely affect Ca2+ affinity in the neurons of the affected organism. Using molecular-dynamics simulations, we show that mutations at the AD3 locus alter the mobility of the Ca2+ -binding loops by removing a key stabilization mechanism that is normally present in C2 domains. The lack of loop stabilization results in a net increase in the volume of the Ca2+ -binding pocket and provides an explanation for the observed lethal phenotype.

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Homology Modeling and Protein-Protein Molecular Docking analyses elucidate the Potential Binding Pockets of ATP7B: A Candidate Wilson’s disease

Biomedical Letters ◽

10.47262/bl/7.1.20210409 ◽

2021 ◽

Vol 7 (1) ◽

pp. 42-47

Keyword(s):

Molecular Docking ◽

Drug Targets ◽

Wilson’S Disease ◽

3D Structure ◽

Binding Pocket ◽

Wilson's Disease ◽

Therapeutic Drug ◽

Hepatic Cells ◽

Research Article ◽

Binding Pockets

There has been progressive improvement in computational drug design from last decade. Numerous computer aided compounds have been reported against neurodegenerative disorders. Wilson’s disease is a common neurodegenerative disease in humans associated with ATP7B that encodes a transmembrane copper-transporting ATPase which induces the copper export from hepatic cells into bile and supplies copper for the functional synthesis of Ceruloplasmin. Almost, 150 mutations of ATP7B have been identified lead to cause Wilson's disease having symptoms of cancers, loss of memory and postural instability. In this research article, 3D structure of ATP7B was predicted by using comparative modelling approaches. The predicted structures were evaluated by utilizing numerous evaluation tools and 98.50% of overall quality factor was observed for the final selected structure. ATOX1 was predicted as the interacting partner of ATP7B and molecular docking analyses of ATP7B and ATOX1 were conducted by using PatchDock. The least global energy of -35.45 Kcal/mol was observed having the interacting residues in the binding pocket. The reported interacting residues may help to target the specific drug development against ATP7B. This research article can be a major initiative to predict the therapeutic drug targets against Wilson’s disease.

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Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798318003479 ◽

2018 ◽

Vol 74 (5) ◽

pp. 411-421 ◽

Cited By ~ 4

Author(s):

Michael C. Thompson ◽

Duilio Cascio ◽

Todd O. Yeates

Keyword(s):

Principal Component ◽

Unit Cell ◽

Protein Crystal ◽

Data Sets ◽

Structural Variations ◽

Data Set ◽

X Ray ◽

Unit Cells ◽

Factor Data ◽

Dynamics Simulations

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

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ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer

Scientific Reports ◽

10.1038/s41598-021-89556-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bárbara Abreu ◽

Carlos Cruz ◽

A. Sofia F. Oliveira ◽

Cláudio M. Soares

Keyword(s):

Conformational Changes ◽

Abc Transporters ◽

Atp Hydrolysis ◽

Binding Pocket ◽

Potential Of Mean Force ◽

Type I ◽

Concomitant Increase ◽

Transport Cycle ◽

Dynamics Simulations ◽

Key Residues

AbstractATP binding cassette (ABC) transporters employ ATP hydrolysis to harness substrate translocation across membranes. The Escherichia coli MalFGK2E maltose importer is an example of a type I ABC importer and a model system for this class of ABC transporters. The MalFGK2E importer is responsible for the intake of malto-oligossacharides in E.coli. Despite being extensively studied, little is known about the effect of ATP hydrolysis and nucleotide exit on substrate transport. In this work, we studied this phenomenon using extensive molecular dynamics simulations (MD) along with potential of mean force calculations of maltose transport across the pore, in the pre-hydrolysis, post-hydrolysis and nucleotide-free states. We concluded that ATP hydrolysis and nucleotide exit trigger conformational changes that result in the decrease of energetic barriers to maltose translocation towards the cytoplasm, with a concomitant increase of the energy barrier in the periplasmic side of the pore, contributing for the irreversibility of the process. We also identified key residues that aid in positioning and orientation of maltose, as well as a novel binding pocket for maltose in MalG. Additionally, ATP hydrolysis leads to conformations similar to the nucleotide-free state. This study shows the contribution of ATP hydrolysis and nucleotide exit in the transport cycle, shedding light on ABC type I importer mechanisms.

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Binding of Azobenzene and p-Diaminoazobenzene to the Human Voltage-Gated Sodium Channel NaV1.4

10.26434/chemrxiv.13311692.v1 ◽

2020 ◽

Author(s):

Vito F. Palmisano ◽

Carlos Gómez-Rodellar ◽

Hannah Pollak ◽

Gustavo Cárdenas ◽

Ben Corry ◽

...

Keyword(s):

Electrostatic Interactions ◽

Hydrophobic Interactions ◽

Binding Pocket ◽

Internal Cavity ◽

Amino Groups ◽

Voltage Gated ◽

Accelerated Molecular Dynamics ◽

Binding Pockets ◽

Voltage Gated Ion Channels ◽

Dynamics Simulations

The activity of voltage-gated ion channels can be controlled by the binding of photoswitches inside their internal cavity and subsequent light irradiation. We investigated the binding of azobenzene and p-diaminoazobenzene to the human Na<sub>V</sub>1.4 channel in the inactivated state by means of Gaussian accelerated molecular dynamics simulations and free-energy computations. Three stable binding pockets were identified for each of the two photoswitches. In all the cases, the binding is controlled by the balance between the favorable hydrophobic interactions of the ligands with the nonpolar residues of the protein and the unfavorable polar solvation energy. In addition, electrostatic interactions between the ligand and the polar aminoacids are also relevant for p-diaminoazobenzene due to the presence of the amino groups on the benzene moieties. These groups participate in hydrogen bonding in the most favorable binding pocket and in long-range electrostatic interactions in the other pockets. The thermodinamically preferred binding sites found for both photoswitches are close to the selectivity filter of the channel. Therefore, it is very likely that the binding of these ligands will induce alterations in the ion conduction through the channel.

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A mechanism for the activation of the mechanosensitive Piezo1 channel by the small molecule Yoda1

Nature Communications ◽

10.1038/s41467-019-12501-1 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 13

Author(s):

Wesley M. Botello-Smith ◽

Wenjuan Jiang ◽

Han Zhang ◽

Alper D. Ozkan ◽

Yi-Chun Lin ◽

...

Keyword(s):

Small Molecule ◽

Conformational Changes ◽

Calcium Imaging ◽

Rational Design ◽

Binding Pocket ◽

Mechanical Forces ◽

Biological Processes ◽

Clinical Value ◽

Mechanical Threshold ◽

Dynamics Simulations

Abstract Mechanosensitive Piezo1 and Piezo2 channels transduce various forms of mechanical forces into cellular signals that play vital roles in many important biological processes in vertebrate organisms. Besides mechanical forces, Piezo1 is selectively activated by micromolar concentrations of the small molecule Yoda1 through an unknown mechanism. Here, using a combination of all-atom molecular dynamics simulations, calcium imaging and electrophysiology, we identify an allosteric Yoda1 binding pocket located in the putative mechanosensory domain, approximately 40 Å away from the central pore. Our simulations further indicate that the presence of the agonist correlates with increased tension-induced motions of the Yoda1-bound subunit. Our results suggest a model wherein Yoda1 acts as a molecular wedge, facilitating force-induced conformational changes, effectively lowering the channel’s mechanical threshold for activation. The identification of an allosteric agonist binding site in Piezo1 channels will pave the way for the rational design of future Piezo modulators with clinical value.

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Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors

International Journal of Molecular Sciences ◽

10.3390/ijms22010187 ◽

2020 ◽

Vol 22 (1) ◽

pp. 187

Author(s):

Pedro Renault ◽

Jesús Giraldo

Keyword(s):

G Protein ◽

Conformational Changes ◽

Drug Targets ◽

Normal Mode Analysis ◽

G Protein Coupled Receptors ◽

Mode Analysis ◽

Allosteric Sites ◽

Basic Hypothesis ◽

Dynamics Simulations ◽

G Protein Coupled

G protein-coupled Receptors (GPCRs) play a central role in many physiological processes and, consequently, constitute important drug targets. In particular, the search for allosteric drugs has recently drawn attention, since they could be more selective and lead to fewer side effects. Accordingly, computational tools have been used to estimate the druggability of allosteric sites in these receptors. In spite of many successful results, the problem is still challenging, particularly the prediction of hydrophobic sites in the interface between the protein and the membrane. In this work, we propose a complementary approach, based on dynamical correlations. Our basic hypothesis was that allosteric sites are strongly coupled to regions of the receptor that undergo important conformational changes upon activation. Therefore, using ensembles of experimental structures, normal mode analysis and molecular dynamics simulations we calculated correlations between internal fluctuations of different sites and a collective variable describing the activation state of the receptor. Then, we ranked the sites based on the strength of their coupling to the collective dynamics. In the β2 adrenergic (β2AR), glucagon (GCGR) and M2 muscarinic receptors, this procedure allowed us to correctly identify known allosteric sites, suggesting it has predictive value. Our results indicate that this dynamics-based approach can be a complementary tool to the existing toolbox to characterize allosteric sites in GPCRs.

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