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Lu J, Rahman MI, Kazan IC, Halloran NR, Bobkov AA, Ozkan SB, Ghirlanda G. Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis. Protein Sci 2023; 32:e4759. [PMID: 37574787 PMCID: PMC10464296 DOI: 10.1002/pro.4759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/17/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Proteins gain optimal fitness such as foldability and function through evolutionary selection. However, classical studies have found that evolutionarily designed protein sequences alone cannot guarantee foldability, or at least not without considering local contacts associated with the initial folding steps. We previously showed that foldability and function can be restored by removing frustration in the folding energy landscape of a model WW domain protein, CC16, which was designed based on Statistical Coupling Analysis (SCA). Substitutions ensuring the formation of five local contacts identified as "on-path" were selected using the closest homolog native folded sequence, N21. Surprisingly, the resulting sequence, CC16-N21, bound to Group I peptides, while N21 did not. Here, we identified single-point mutations that enable N21 to bind a Group I peptide ligand through structure and dynamic-based computational design. Comparison of the docked position of the CC16-N21/ligand complex with the N21 structure showed that residues at positions 9 and 19 are important for peptide binding, whereas the dynamic profiles identified position 10 as allosterically coupled to the binding site and exhibiting different dynamics between N21 and CC16-N21. We found that swapping these positions in N21 with matched residues from CC16-N21 recovers nature-like binding affinity to N21. This study validates the use of dynamic profiles as guiding principles for affecting the binding affinity of small proteins.
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Affiliation(s)
- Jin Lu
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - I. Can Kazan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | | | - Andrey A. Bobkov
- Conrad Prebys Center for Chemical GenomicsSanford Burnham Prebys Medical Discovery InstituteCaliforniaUSA
| | - S. Banu Ozkan
- Department of Physics and Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
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2
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Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO. Sci Rep 2022; 12:17984. [PMID: 36289271 PMCID: PMC9606277 DOI: 10.1038/s41598-022-22703-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Parallel cascade selection molecular dynamics-based ligand binding-path sampling (LB-PaCS-MD) was combined with fragment molecular orbital (FMO) calculations to reveal the ligand path from an aqueous solution to the SARS-CoV-2 main protease (Mpro) active site and to customise a ligand-binding pocket suitable for delivering a potent inhibitor. Rubraxanthone exhibited mixed-inhibition antiviral activity against SARS-CoV-2 Mpro, relatively low cytotoxicity, and high cellular inhibition. However, the atomic inhibition mechanism remains ambiguous. LB-PaCS-MD/FMO is a hybrid ligand-binding evaluation method elucidating how rubraxanthone interacts with SARS-CoV-2 Mpro. In the first step, LB-PaCS-MD, which is regarded as a flexible docking, efficiently samples a set of ligand-binding pathways. After that, a reasonable docking pose of LB-PaCS-MD is evaluated by the FMO calculation to elucidate a set of protein-ligand interactions, enabling one to know the binding affinity of a specified ligand with respect to a target protein. A possible conformation was proposed for rubraxanthone binding to the SARS-CoV-2 Mpro active site, and allosteric inhibition was elucidated by combining blind docking with k-means clustering. The interaction profile, key binding residues, and considerable interaction were elucidated for rubraxanthone binding to both Mpro sites. Integrated LB-PaCS-MD/FMO provided a more reasonable complex structure for ligand binding at the SARS-CoV-2 Mpro active site, which is vital for discovering and designing antiviral drugs.
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3
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Kazan IC, Sharma P, Rahman MI, Bobkov A, Fromme R, Ghirlanda G, Ozkan SB. Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations. eLife 2022; 11:67474. [PMID: 36472898 PMCID: PMC9725752 DOI: 10.7554/elife.67474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 β-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.
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Affiliation(s)
- I Can Kazan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States,School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Prerna Sharma
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | | | - Andrey Bobkov
- Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State UniversityTempeUnited States
| | - S Banu Ozkan
- Center for Biological Physics and Department of Physics, Arizona State UniversityTempeUnited States
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4
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Computer-Aided Drug Designing. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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5
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Abdizadeh H, Jalalypour F, Atilgan AR, Atilgan C. A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs. Front Mol Biosci 2020; 7:210. [PMID: 33195399 PMCID: PMC7477071 DOI: 10.3389/fmolb.2020.00210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/03/2020] [Indexed: 11/13/2022] Open
Abstract
We address the problem of triggering dissociation events between proteins that have formed a complex. We have collected a set of 25 non-redundant, functionally diverse protein complexes having high-resolution three-dimensional structures in both the unbound and bound forms. We unify elastic network models with perturbation response scanning (PRS) methodology as an efficient approach for predicting residues that have the propensity to trigger dissociation of an interacting protein pair, using the three-dimensional structures of the bound and unbound proteins as input. PRS reveals that while for a group of protein pairs, residues involved in the conformational shifts are confined to regions with large motions, there are others where they originate from parts of the protein unaffected structurally by binding. Strikingly, only a few of the complexes have interface residues responsible for dissociation. We find two main modes of response: In one mode, remote control of dissociation in which disruption of the electrostatic potential distribution along protein surfaces play the major role; in the alternative mode, mechanical control of dissociation by remote residues prevail. In the former, dissociation is triggered by changes in the local environment of the protein, e.g., pH or ionic strength, while in the latter, specific perturbations arriving at the controlling residues, e.g., via binding to a third interacting partner is required for decomplexation. We resolve the observations by relying on an electromechanical coupling model which reduces to the usual elastic network result in the limit of the lack of coupling. We validate the approach by illustrating the biological significance of top residues selected by PRS on select cases where we show that the residues whose perturbation leads to the observed conformational changes correspond to either functionally important or highly conserved residues in the complex.
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Affiliation(s)
- Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
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6
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Prabhu R, Sitharam M, Ozkan A, Wu R. Atlasing of Assembly Landscapes using Distance Geometry and Graph Rigidity. J Chem Inf Model 2020; 60:4924-4957. [PMID: 32786706 DOI: 10.1021/acs.jcim.0c00763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This Article describes a novel geometric methodology for analyzing free energy and kinetics of assembly driven by short-range pair-potentials in an implicit solvent and provides a proof-of-concept illustration of its unique capabilities. An atlas is a labeled partition of the assembly landscape into a roadmap of maximal, contiguous, nearly-equipotential-energy conformational regions or macrostates, together with their neighborhood relationships. The new methodology decouples the roadmap generation from sampling and produces: (1) a queryable atlas of local potential energy minima, their basin structure, energy barriers, and neighboring basins; (2) paths between a specified pair of basins, each path being a sequence of conformational regions or macrostates below a desired energy threshold; and (3) approximations of relative path lengths, basin volumes (configurational entropy), and path probabilities. Results demonstrating the core algorithm's capabilities and high computational efficiency have been generated by a resource-light, curated open source software implementation EASAL (Efficient Atlasing and Search of Assembly Landscapes, ACM Trans. Math. Softw. 2018 44, 1-48. 10.1145/3204472; see software, Efficient Atlasing and Search of Assembly Landscapes, 2016. https://bitbucket.org/geoplexity/easal; video, Video Illustrating the opensource software EASAL, 2016. https://cise.ufl.edu/~sitharam/EASALvideo.mpeg; and user guide, EASAL software user guide, 2016. https://bitbucket.org/geoplexity/easal/src/master/CompleteUserGuide.pdf). Running on a laptop with Intel(R) Core(TM) i7-7700@3.60 GHz CPU with 16GB of RAM, EASAL atlases several hundred thousand conformational regions or macrostates in minutes using a single compute core. Subsequent path and basin computations each take seconds. A parallelized EASAL version running on the same laptop with 4 cores gives a 3× speedup for atlas generation. The core algorithm's correctness, time complexity, and efficiency-accuracy trade-offs are formally guaranteed using modern distance geometry, geometric constraint systems and combinatorial rigidity. The methodology further links the shape of the input assembling units to a type of intuitive and queryable bar-code of the output atlas, which in turn determine stable assembled structures and kinetics. This succinct input-output relationship facilitates reverse analysis and control toward design. A novel feature that is crucial to both the high sampling efficiency and decoupling of roadmap generation from sampling is a recently developed theory of convex Cayley (distance-based) custom parametrizations specific to assembly, as opposed to folding. Representing microstates with macrostate-specific Cayley parameters, to generate microstate samples, avoids gradient-descent search used by all prevailing methods. Further, these parametrizations convexify conformational regions or macrostates. This ratchets up sampling efficiency, significantly reducing number of repeated and discarded samples. These features of the new stand-alone methodology can also be used to complement the strengths of prevailing methodologies including Molecular Dynamics, Monte Carlo, and Fast Fourier Transform based methods.
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Affiliation(s)
- Rahul Prabhu
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, United States of America
| | - Meera Sitharam
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, United States of America
| | - Aysegul Ozkan
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, United States of America
| | - Ruijin Wu
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, United States of America
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7
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Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Curr Opin Struct Biol 2020; 64:34-41. [PMID: 32622329 DOI: 10.1016/j.sbi.2020.05.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022]
Abstract
With the explosion of normal mode analyses (NMAs) based on elastic network models (ENMs) in the last decade, and the proven precision of MD simulations for visualizing interactions at atomic scale, many hybrid methods have been proposed in recent years. These aim at exploiting the best of both worlds: the atomic precision of MD that often fall short of exploring time and length scales of biological interest, and the capability of ENM-NMA to predict the cooperative and often functional rearrangements of large structures and assemblies, albeit at low resolution. We present an overview of recent progress in the field with examples of successful applications highlighting the utility of such hybrid methods and pointing to emerging future directions guided by advances in experimental characterization of biomolecular systems structure and dynamics.
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Affiliation(s)
- James M Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA
| | - Ana Ligia Scott
- Laboratory of Bioinformatics and Computational Biology, Federal University of ABC, Santo André, SP, Brazil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Superieure Paris-Saclay, UMR 8113, CNRS, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Suite 3064 BST3, Pittsburgh, PA 15260, USA.
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8
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Gattani S, Mishra A, Hoque MT. StackCBPred: A stacking based prediction of protein-carbohydrate binding sites from sequence. Carbohydr Res 2019; 486:107857. [DOI: 10.1016/j.carres.2019.107857] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/05/2019] [Accepted: 10/23/2019] [Indexed: 11/26/2022]
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9
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Gilburt JAH, Girvan P, Blagg J, Ying L, Dodson CA. Ligand discrimination between active and inactive activation loop conformations of Aurora-A kinase is unmodified by phosphorylation. Chem Sci 2019; 10:4069-4076. [PMID: 31015948 PMCID: PMC6461105 DOI: 10.1039/c8sc03669a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/01/2019] [Indexed: 01/14/2023] Open
Abstract
Activation loop phosphorylation changes the position of equilibrium between DFG-in-like and DFG-out-like conformations but not the conformational preference of inhibitors.
Structure-based drug design is commonly used to guide the development of potent and specific enzyme inhibitors. Many enzymes – such as protein kinases – adopt multiple conformations, and conformational interconversion is expected to impact on the design of small molecule inhibitors. We measured the dynamic equilibrium between DFG-in-like active and DFG-out-like inactive conformations of the activation loop of unphosphorylated Aurora-A alone, in the presence of the activator TPX2, and in the presence of kinase inhibitors. The unphosphorylated kinase had a shorter residence time of the activation loop in the active conformation and a shift in the position of equilibrium towards the inactive conformation compared with phosphorylated kinase for all conditions measured. Ligand binding was associated with a change in the position of conformational equilibrium which was specific to each ligand and independent of the kinase phosphorylation state. As a consequence of this, the ability of a ligand to discriminate between active and inactive activation loop conformations was also independent of phosphorylation. Importantly, we discovered that the presence of multiple enzyme conformations can lead to a plateau in the overall ligand Kd, despite increasing affinity for the chosen target conformation, and modelled the conformational discrimination necessary for a conformation-promoting ligand.
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Affiliation(s)
- James A H Gilburt
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Paul Girvan
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit , The Institute of Cancer Research , 15 Cotswold Road , Sutton , Surrey SM2 5NG , UK
| | - Liming Ying
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK
| | - Charlotte A Dodson
- Molecular Medicine , National Heart & Lung Institute , Imperial College London , SAF Building , London SW7 2AZ , UK.,Department of Pharmacy and Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK .
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10
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Computational Methods for Efficient Sampling of Protein Landscapes and Disclosing Allosteric Regions. COMPUTATIONAL MOLECULAR MODELLING IN STRUCTURAL BIOLOGY 2018; 113:33-63. [DOI: 10.1016/bs.apcsb.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A. Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Sci Rep 2017; 7:7180. [PMID: 28775330 PMCID: PMC5543104 DOI: 10.1038/s41598-017-07351-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/27/2017] [Indexed: 12/19/2022] Open
Abstract
Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies.
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Affiliation(s)
- Farideh Halakou
- Department of Computer Engineering, Koc University, Istanbul, 34450, Turkey
| | - Emel Sen Kilic
- Department of Chemical and Biological Engineering, Koc University, Istanbul, 34450, Turkey.,Microbiology, Immunology and Cell Biology Department, West Virginia University, Morgantown, 26505, WV, USA
| | - Engin Cukuroglu
- Computational Sciences and Engineering, Graduate School of Sciences and Engineering, Koc University, Istanbul, 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, 34450, Turkey
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul, 34450, Turkey.
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12
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Motta S, Bonati L. Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches. J Chem Inf Model 2017; 57:1563-1578. [DOI: 10.1021/acs.jcim.7b00125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental
Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Laura Bonati
- Department of Earth and Environmental
Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
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13
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Xia J, Hsieh JH, Hu H, Wu S, Wang XS. The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening. J Chem Inf Model 2017; 57:1414-1425. [PMID: 28511009 DOI: 10.1021/acs.jcim.6b00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based virtual screening (SBVS) has become an indispensable technique for hit identification at the early stage of drug discovery. However, the accuracy of current scoring functions is not high enough to confer success to every target and thus remains to be improved. Previously, we had developed binary pose filters (PFs) using knowledge derived from the protein-ligand interface of a single X-ray structure of a specific target. This novel approach had been validated as an effective way to improve ligand enrichment. Continuing from it, in the present work we attempted to incorporate knowledge collected from diverse protein-ligand interfaces of multiple crystal structures of the same target to build PF ensembles (PFEs). Toward this end, we first constructed a comprehensive data set to meet the requirements of ensemble modeling and validation. This set contains 10 diverse targets, 118 well-prepared X-ray structures of protein-ligand complexes, and large benchmarking actives/decoys sets. Notably, we designed a unique workflow of two-layer classifiers based on the concept of ensemble learning and applied it to the construction of PFEs for all of the targets. Through extensive benchmarking studies, we demonstrated that (1) coupling PFE with Chemgauss4 significantly improves the early enrichment of Chemgauss4 itself and (2) PFEs show greater consistency in boosting early enrichment and larger overall enrichment than our prior PFs. In addition, we analyzed the pairwise topological similarities among cognate ligands used to construct PFEs and found that it is the higher chemical diversity of the cognate ligands that leads to the improved performance of PFEs. Taken together, the results so far prove that the incorporation of knowledge from diverse protein-ligand interfaces by ensemble modeling is able to enhance the screening competence of SBVS scoring functions.
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Affiliation(s)
- Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Jui-Hua Hsieh
- Kelly Government Solutions , Research Triangle Park, North Carolina 27709, United States
| | - Huabin Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, China
| | - Xiang Simon Wang
- Molecular Modeling and Drug Discovery Core Laboratory for District of Columbia Center for AIDS Research (DC CFAR), Department of Pharmaceutical Sciences, College of Pharmacy, Howard University , Washington, D.C. 20059, United States
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14
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Toussi CA, Soheilifard R. A better prediction of conformational changes of proteins using minimally connected network models. Phys Biol 2017; 13:066013. [PMID: 28112101 DOI: 10.1088/1478-3975/13/6/066013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Elastic network models have recently been used for studying low-frequency collective motions of proteins. These models simplify the complexity that arises from normal mode analysis by considering a simplified potential involving a few parameters. Two common parameters in most of the elastic network models are cutoff radius and force constant. Although the latter has been studied extensively and even elaborate new models were introduced, for the former usually an ad-hoc cutoff radius is considered. Moreover, the quality of the network models is usually assessed by evaluating their prediction against experimental B-factors. In this work, we consider various common elastic network models with different cutoff radii and assess them by their ability to predict conformational changes of proteins in complexes from unbound to bound state. This prediction is performed by perturbing the unbound structure using a number of low-frequency normal modes of its network model to optimally fit the bound structure. We evaluated a dataset of 30 proteins with distinct unbound and bound structures using this criterion. The results showed that, opposed to the common calibration process based on B-factors, a meaningful relationship exists between the quality of the prediction and model parameters. It was shown that the cutoff radius has a major role in this prediction and minimally connected network models, which use the shortest cutoff radius for which the network is stable, give the best results. It was also shown that by considering the first ten normal modes, the conformational changes can be predicted by about 25 percent. Hence, the evaluation process was extended to the case of considering the contribution of all normal modes in the prediction. The results indicated that minimally connected network models are superior, despite their simplicity, when any number of modes are considered in the prediction.
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Affiliation(s)
- Cyrus Ahmadi Toussi
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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15
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Incorporation of side chain flexibility into protein binding pockets using MTflex. Bioorg Med Chem 2016; 24:4978-4987. [DOI: 10.1016/j.bmc.2016.08.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 01/15/2023]
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16
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Taherzadeh G, Zhou Y, Liew AWC, Yang Y. Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. J Chem Inf Model 2016; 56:2115-2122. [PMID: 27623166 DOI: 10.1021/acs.jcim.6b00320] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Carbohydrate-binding proteins play significant roles in many diseases including cancer. Here, we established a machine-learning-based method (called sequence-based prediction of residue-level interaction sites of carbohydrates, SPRINT-CBH) to predict carbohydrate-binding sites in proteins using support vector machines (SVMs). We found that integrating evolution-derived sequence profiles with additional information on sequence and predicted solvent accessible surface area leads to a reasonably accurate, robust, and predictive method, with area under receiver operating characteristic curve (AUC) of 0.78 and 0.77 and Matthew's correlation coefficient of 0.34 and 0.29, respectively for 10-fold cross validation and independent test without balancing binding and nonbinding residues. The quality of the method is further demonstrated by having statistically significantly more binding residues predicted for carbohydrate-binding proteins than presumptive nonbinding proteins in the human proteome, and by the bias of rare alleles toward predicted carbohydrate-binding sites for nonsynonymous mutations from the 1000 genome project. SPRINT-CBH is available as an online server at http://sparks-lab.org/server/SPRINT-CBH .
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Affiliation(s)
- Ghazaleh Taherzadeh
- School of Information and Communication Technology and ‡Institute for Glycomics, Griffith University , Parklands Drive, Southport, Queensland 4215, Australia
| | - Yaoqi Zhou
- School of Information and Communication Technology and ‡Institute for Glycomics, Griffith University , Parklands Drive, Southport, Queensland 4215, Australia
| | - Alan Wee-Chung Liew
- School of Information and Communication Technology and ‡Institute for Glycomics, Griffith University , Parklands Drive, Southport, Queensland 4215, Australia
| | - Yuedong Yang
- School of Information and Communication Technology and ‡Institute for Glycomics, Griffith University , Parklands Drive, Southport, Queensland 4215, Australia
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17
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Anselmi M, Pisabarro MT. Exploring Multiple Binding Modes Using Confined Replica Exchange Molecular Dynamics. J Chem Theory Comput 2016; 11:3906-18. [PMID: 26574471 DOI: 10.1021/acs.jctc.5b00253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular docking is extensively applied to determine the position of a ligand on its receptor despite the rather poor correspondence between docking scores and experimental binding affinities found in several studies, especially for systems structurally unrelated with those used in the scoring functions' training sets. Here, we present a method for the prediction of binding modes and binding free energies, which uses replica exchange molecular dynamics in combination with a receptor-shaped piecewise potential, confining the ligand in the proximity of the receptor surface and limiting the accessible conformational space of interest. We assess our methodology with a set of protein receptor-ligand test cases. In every case studied, the method is able to locate the ligand on the experimentally known receptor binding site, and it gives as output the binding free energy. The added value of our approach with respect to other available methods is that it quickly performs a conformational space search, providing a set of bound (or unbound) configurations, which can be used to determine phenomenological structural and energetic properties of an experimental binding state as a result of contributions provided by diversified multiple binding poses.
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Affiliation(s)
- Massimiliano Anselmi
- Structural Bioinformatics, BIOTEC TU Dresden , Tatzberg 47-51, 01307 Dresden, Germany.,Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - M Teresa Pisabarro
- Structural Bioinformatics, BIOTEC TU Dresden , Tatzberg 47-51, 01307 Dresden, Germany
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Mangiatordi GF, Alberga D, Trisciuzzi D, Lattanzi G, Nicolotti O. Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future. Int J Mol Sci 2016; 17:ijms17071119. [PMID: 27420052 PMCID: PMC4964494 DOI: 10.3390/ijms17071119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/30/2016] [Accepted: 07/02/2016] [Indexed: 12/26/2022] Open
Abstract
Among the different aquaporins (AQPs), human aquaporin-4 (hAQP4) has attracted the greatest interest in recent years as a new promising therapeutic target. Such a membrane protein is, in fact, involved in a multiple sclerosis-like immunopathology called Neuromyelitis Optica (NMO) and in several disorders resulting from imbalanced water homeostasis such as deafness and cerebral edema. The gap of knowledge in its functioning and dynamics at the atomistic level of detail has hindered the development of rational strategies for designing hAQP4 modulators. The application, lately, of molecular modeling has proved able to fill this gap providing a breeding ground to rationally address compounds targeting hAQP4. In this review, we give an overview of the important advances obtained in this field through the application of Molecular Dynamics (MD) and other complementary modeling techniques. The case studies presented herein are discussed with the aim of providing important clues for computational chemists and biophysicists interested in this field and looking for new challenges.
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Affiliation(s)
- Giuseppe Felice Mangiatordi
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
| | - Domenico Alberga
- Institut de Recherche de Chimie Paris CNRS Chimie ParisTech, PSL Research University, 11 rue P. et M. Curie, F-75005 Paris, France.
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
| | - Gianluca Lattanzi
- INFN-Sez. di Bari and Dipartimento di Medicina Clinica e Sperimentale, University of Foggia, Viale Pinto, 71122 Foggia, Italy.
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
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Kurkcuoglu Z, Doruker P. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins. PLoS One 2016; 11:e0158063. [PMID: 27348230 PMCID: PMC4922591 DOI: 10.1371/journal.pone.0158063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/09/2016] [Indexed: 01/03/2023] Open
Abstract
Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7-15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4-3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its "parents" up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5-2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, 34342, Turkey
- * E-mail: (ZK); (PD)
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, 34342, Turkey
- * E-mail: (ZK); (PD)
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Amendola G, Di Maio D, La Pietra V, Cosconati S. Best Matching Protein Conformations and Docking Programs for a Virtual Screening Campaign Against SMO Receptor. Mol Inform 2016; 35:340-9. [DOI: 10.1002/minf.201501021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/14/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Giorgio Amendola
- DiSTABiF; Seconda Università degli Studi di Napoli; Via Vivaldi 43 81100 Caserta Italy
| | - Danilo Di Maio
- Istituto Nazionale di Fisica Nucleare (INFN); sezione di Pisa; Largo Bruno Pontecorvo 3 56127 Pisa Italy
- Scuola Normale Superiore; Piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Valeria La Pietra
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Via D. Montesano 49 80131 Naples Italy
| | - Sandro Cosconati
- DiSTABiF; Seconda Università degli Studi di Napoli; Via Vivaldi 43 81100 Caserta Italy
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21
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Bolia A, Ozkan SB. Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility. J Chem Inf Model 2016; 56:734-46. [PMID: 26971620 DOI: 10.1021/acs.jcim.5b00587] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present an induced fit docking approach called Adaptive BP-Dock that integrates perturbation response scanning (PRS) with the flexible docking protocol of RosettaLigand in an adaptive manner. We first perturb the binding pocket residues of a receptor and obtain a new conformation based on the residue response fluctuation profile using PRS. Next, we dock a ligand to this new conformation by RosettaLigand, where we repeat these steps for several iterations. We test this approach on several protein test sets including difficult unbound docking cases such as HIV-1 reverse transcriptase and HIV-1 protease. Adaptive BP-Dock results show better correlation with experimental binding affinities compared to other docking protocols. Overall, the results imply that Adaptive BP-Dock can easily capture binding induced conformational changes by simultaneous sampling of protein and ligand conformations. This can provide faster and efficient docking of novel targets for rational drug design.
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Affiliation(s)
- Ashini Bolia
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - S Banu Ozkan
- Department of Physics, Center for Biological Physics, Arizona State University , Tempe, Arizona 85287, United States
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22
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Abdizadeh H, Atilgan C. Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single microstate. Phys Chem Chem Phys 2016; 18:7916-26. [DOI: 10.1039/c5cp05107j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PRS identifies regions contacting rapidly evolving residues that mechanically manipulate dissociation from the pathogen in the human transferrin–bacterial receptor complex.
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Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences
- Sabanci University
- Tuzla
- Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences
- Sabanci University
- Tuzla
- Turkey
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23
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Li Z, Bolia A, Maxwell JD, Bobkov AA, Ghirlanda G, Ozkan SB, Margulis CJ. A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs. Biochemistry 2015; 54:6951-60. [PMID: 26507789 DOI: 10.1021/acs.biochem.5b00635] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mutations in the hinge region of cyanovirin-N (CVN) dictate its preferential oligomerization state. Constructs with the Pro51Gly mutation preferentially exist as monomers, whereas wild-type cyanovirin can form domain-swapped dimers under certain conditions. Because the hinge region is an integral part of the high-affinity binding site of CVN, we investigated whether this mutation affects the shape, flexibility, and binding affinity of domain B for dimannose. Our studies indicate that the capability of monomeric wild-type CVN to resist mechanical perturbations is enhanced when compared to that of constructs in which the hinge region is more flexible. Our computational results also show that enhanced flexibility leads to blocking of the binding site by allowing different rotational isomeric states of Asn53. Moreover, at higher temperatures, this observed flexibility leads to an interaction between Asn53 and Asn42, further hindering access to the binding site. On the basis of these results, we predicted that binding affinity for dimannose would be more favorable for cyanovirin constructs containing a wild-type hinge region, whereas affinity would be impaired in the case of mutants containing Pro51Gly. Experimental characterization by isothermal titration calorimetry of a set of cyanovirin mutants confirms this hypothesis. Those possessing the Pro51Gly mutation are consistently inferior binders.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Ashini Bolia
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Jason D Maxwell
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Andrey A Bobkov
- Sanford Burnham Medical Research Institute , 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Giovanna Ghirlanda
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University , Tempe, Arizona 85287, United States
| | - Claudio J Margulis
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
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24
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Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis. Future Med Chem 2015; 7:2317-31. [DOI: 10.4155/fmc.15.150] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket classifications to efficiently generate RCEs. Materials & Methods: We assessed our protocols on two well-characterized protein targets showing local active site flexibility, dihydrofolate reductase and large collective movements, CDK2. The performance of the RCEs was validated by distinguishing known ligands of dihydrofolate reductase and CDK2 among a dataset of diverse chemical decoys. Results & discussion: Our results show that different simulation protocols can be efficient for generation of RCEs depending on different kind of protein flexibility.[Formula: see text]
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25
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Xiong X, Yuan H, Zhang Y, Xu J, Ran T, Liu H, Lu S, Xu A, Li H, Jiang Y, Lu T, Chen Y. Protein flexibility oriented virtual screening strategy for JAK2 inhibitors. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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26
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Kumar A, Glembo TJ, Ozkan SB. The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin. Biophys J 2015; 109:1273-81. [PMID: 26255589 PMCID: PMC4576160 DOI: 10.1016/j.bpj.2015.06.060] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/18/2015] [Accepted: 06/30/2015] [Indexed: 12/26/2022] Open
Abstract
Determining the three-dimensional structure of myoglobin, the first solved structure of a protein, fundamentally changed the way protein function was understood. Even more revolutionary was the information that came afterward: protein dynamics play a critical role in biological functions. Therefore, understanding conformational dynamics is crucial to obtaining a more complete picture of protein evolution. We recently analyzed the evolution of different protein families including green fluorescent proteins (GFPs), β-lactamase inhibitors, and nuclear receptors, and we observed that the alteration of conformational dynamics through allosteric regulation leads to functional changes. Moreover, proteome-wide conformational dynamics analysis of more than 100 human proteins showed that mutations occurring at rigid residue positions are more susceptible to disease than flexible residue positions. These studies suggest that disease-associated mutations may impair dynamic allosteric regulations, leading to loss of function. Thus, in this study, we analyzed the conformational dynamics of the wild-type light chain subunit of human ferritin protein along with the neutral and disease forms. We first performed replica exchange molecular dynamics simulations of wild-type and mutants to obtain equilibrated dynamics and then used perturbation response scanning (PRS), where we introduced a random Brownian kick to a position and computed the fluctuation response of the chain using linear response theory. Using this approach, we computed the dynamic flexibility index (DFI) for each position in the chain for the wild-type and the mutants. DFI quantifies the resilience of a position to a perturbation and provides a flexibility/rigidity measurement for a given position in the chain. The DFI analysis reveals that neutral variants and the wild-type exhibit similar flexibility profiles in which experimentally determined functionally critical sites act as hinges in controlling the overall motion. However, disease mutations alter the conformational dynamic profile, making hinges more loose (i.e., softening the hinges), thus impairing the allosterically regulated dynamics.
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Affiliation(s)
- Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - Tyler J Glembo
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona.
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Abstract
Drug discovery utilizes chemical biology and computational drug design approaches for the efficient identification and optimization of lead compounds. Chemical biology is mostly involved in the elucidation of the biological function of a target and the mechanism of action of a chemical modulator. On the other hand, computer-aided drug design makes use of the structural knowledge of either the target (structure-based) or known ligands with bioactivity (ligand-based) to facilitate the determination of promising candidate drugs. Various virtual screening techniques are now being used by both pharmaceutical companies and academic research groups to reduce the cost and time required for the discovery of a potent drug. Despite the rapid advances in these methods, continuous improvements are critical for future drug discovery tools. Advantages presented by structure-based and ligand-based drug design suggest that their complementary use, as well as their integration with experimental routines, has a powerful impact on rational drug design. In this article, we give an overview of the current computational drug design and their application in integrated rational drug development to aid in the progress of drug discovery research.
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Affiliation(s)
- Stephani Joy Y Macalino
- National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul, 120-750, Korea
| | - Vijayakumar Gosu
- National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul, 120-750, Korea
| | - Sunhye Hong
- National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul, 120-750, Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul, 120-750, Korea.
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28
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Abdizadeh H, Guven G, Atilgan AR, Atilgan C. Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability. J Enzyme Inhib Med Chem 2015; 30:867-73. [DOI: 10.3109/14756366.2014.979345] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Haleh Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Gokce Guven
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul, Turkey
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29
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Grinter SZ, Zou X. Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design. Molecules 2014; 19:10150-76. [PMID: 25019558 PMCID: PMC6270832 DOI: 10.3390/molecules190710150] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/13/2014] [Accepted: 07/02/2014] [Indexed: 11/16/2022] Open
Abstract
The docking methods used in structure-based virtual database screening offer the ability to quickly and cheaply estimate the affinity and binding mode of a ligand for the protein receptor of interest, such as a drug target. These methods can be used to enrich a database of compounds, so that more compounds that are subsequently experimentally tested are found to be pharmaceutically interesting. In addition, like all virtual screening methods used for drug design, structure-based virtual screening can focus on curated libraries of synthesizable compounds, helping to reduce the expense of subsequent experimental verification. In this review, we introduce the protein-ligand docking methods used for structure-based drug design and other biological applications. We discuss the fundamental challenges facing these methods and some of the current methodological topics of interest. We also discuss the main approaches for applying protein-ligand docking methods. We end with a discussion of the challenging aspects of evaluating or benchmarking the accuracy of docking methods for their improvement, and discuss future directions.
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Affiliation(s)
- Sam Z Grinter
- Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
| | - Xiaoqin Zou
- Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
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