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Bayarsaikhan B, Zsidó BZ, Börzsei R, Hetényi C. Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols. Int J Mol Sci 2024; 25:5945. [PMID: 38892133 PMCID: PMC11172440 DOI: 10.3390/ijms25115945] [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: 04/24/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Histones are keys to many epigenetic events and their complexes have therapeutic and diagnostic importance. The determination of the structures of histone complexes is fundamental in the design of new drugs. Computational molecular docking is widely used for the prediction of target-ligand complexes. Large, linear peptides like the tail regions of histones are challenging ligands for docking due to their large conformational flexibility, extensive hydration, and weak interactions with the shallow binding pockets of their reader proteins. Thus, fast docking methods often fail to produce complex structures of such peptide ligands at a level appropriate for drug design. To address this challenge, and improve the structural quality of the docked complexes, post-docking refinement has been applied using various molecular dynamics (MD) approaches. However, a final consensus has not been reached on the desired MD refinement protocol. In this present study, MD refinement strategies were systematically explored on a set of problematic complexes of histone peptide ligands with relatively large errors in their docked geometries. Six protocols were compared that differ in their MD simulation parameters. In all cases, pre-MD hydration of the complex interface regions was applied to avoid the unwanted presence of empty cavities. The best-performing protocol achieved a median of 32% improvement over the docked structures in terms of the change in root mean squared deviations from the experimental references. The influence of structural factors and explicit hydration on the performance of post-docking MD refinements are also discussed to help with their implementation in future methods and applications.
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Affiliation(s)
- Bayartsetseg Bayarsaikhan
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Rita Börzsei
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
- National Laboratory for Drug Research and Development, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
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2
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Szél V, Zsidó BZ, Jeszenői N, Hetényi C. Target-ligand binding affinity from single point enthalpy calculation and elemental composition. Phys Chem Chem Phys 2023; 25:31714-31725. [PMID: 37964670 DOI: 10.1039/d3cp04483a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Reliable target-ligand binding thermodynamics data are essential for successful drug design and molecular engineering projects. Besides experimental methods, a number of theoretical approaches have been introduced for the generation of binding thermodynamics data. However, available approaches often neglect electronic effects or explicit water molecules influencing target-ligand interactions. To handle electronic effects within a reasonable time frame, we introduce a fast calculator QMH-L using a single target-ligand complex structure pre-optimized at the molecular mechanics level. QMH-L is composed of the semi-empirical quantum mechanics calculation of binding enthalpy with predicted explicit water molecules at the complex interface, and a simple descriptor based on the elemental composition of the ligand. QMH-L estimates the target-ligand binding free energy with a root mean square error (RMSE) of 0.94 kcal mol-1. The calculations also provide binding enthalpy values and they were compared with experimental binding thermodynamics data collected from the most reliable isothermal titration calorimetry studies of systems including various protein targets and challenging, large peptide ligands with a molecular weight of up to 2-3 thousand. The single point enthalpy calculations of QMH-L require modest computational resources and are based on short runs with open source and/or free software like Gromacs, Mopac, MobyWat, and Fragmenter. QMH-L can be applied for fast, automated scoring of drug candidates during a virtual screen, enthalpic engineering of new ligands or thermodynamic explanation of complex interactions.
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Affiliation(s)
- Viktor Szél
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Norbert Jeszenői
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
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3
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Zsidó BZ, Bayarsaikhan B, Börzsei R, Hetényi C. Construction of Histone-Protein Complex Structures by Peptide Growing. Int J Mol Sci 2023; 24:13831. [PMID: 37762134 PMCID: PMC10530865 DOI: 10.3390/ijms241813831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structures of histone complexes are master keys to epigenetics. Linear histone peptide tails often bind to shallow pockets of reader proteins via weak interactions, rendering their structure determination challenging. In the present study, a new protocol, PepGrow, is introduced. PepGrow uses docked histone fragments as seeds and grows the full peptide tails in the reader-binding pocket, producing atomic-resolution structures of histone-reader complexes. PepGrow is able to handle the flexibility of histone peptides, and it is demonstrated to be more efficient than linking pre-docked peptide fragments. The new protocol combines the advantages of popular program packages and allows fast generation of solution structures. AutoDock, a force-field-based program, is used to supply the docked peptide fragments used as structural seeds, and the building algorithm of Modeller is adopted and tested as a peptide growing engine. The performance of PepGrow is compared to ten other docking methods, and it is concluded that in situ growing of a ligand from a seed is a viable strategy for the production of complex structures of histone peptides at atomic resolution.
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Affiliation(s)
| | | | | | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti Út 12, 7624 Pécs, Hungary; (B.Z.Z.); (B.B.); (R.B.)
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4
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Zsidó BZ, Bayarsaikhan B, Börzsei R, Szél V, Mohos V, Hetényi C. The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering. Int J Mol Sci 2023; 24:11784. [PMID: 37511543 PMCID: PMC10381018 DOI: 10.3390/ijms241411784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
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Affiliation(s)
- Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Bayartsetseg Bayarsaikhan
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Violetta Mohos
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
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5
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Chen W, He H, Wang J, Wang J, Chang CEA. Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics. Phys Chem Chem Phys 2023; 25:2098-2109. [PMID: 36562309 PMCID: PMC9970846 DOI: 10.1039/d2cp04584b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Developing a ligand with high affinity for a specific protein target is essential for drug design, and water molecules are well known to play a key role in protein-drug recognition. However, predicting the role of particularly ordered water molecules in drug binding remains challenging. Furthermore, hydration free energy contributed from the water network, including the second shell of water molecules, is far from being well studied. In this research we focused on these aspects to accurately and efficiently evaluate water effects in protein-ligand binding affinity. We developed a new strategy using a free-energy calculation method, VM2. We successfully predicted the stable ordered water molecules in a number of protein systems: PDE 10a, HSP90, tryptophan synthase (TRPS), CDK2 and Factor Xa. In some of these, the second shell of water molecules appeared to be critical in protein-ligand binding. We also applied the strategy to largely improve binding free energy calculation using the MM/PBSA method. When applying MM/PBSA alone for two systems, CDK2 and Factor Xa, the computed binding free energy resulted in poor to moderate R2 values with experimental data. However, including water free energy correction greatly improved the free energy calculation. Furthermore, our work helped to explain how xk263 is a 1000 times faster binder to HIVp than ritonavir, a potentially useful tool for investigating binding kinetics. Our studies reveal the importance of fully considering water effects in therapeutic developments in pharmaceutical and biotechnology industries and for fundamental research in protein-ligand recognition.
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Affiliation(s)
- Wei Chen
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Huan He
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Jing Wang
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Jiahui Wang
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Chia-en A. Chang
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA,Corresponding Authors Wei Chen: School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, China. , Chia-en A. Chang: Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA.
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6
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Bálint M, Zsidó BZ, van der Spoel D, Hetényi C. Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design. Int J Mol Sci 2022; 23:ijms23137313. [PMID: 35806314 PMCID: PMC9267029 DOI: 10.3390/ijms23137313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
The human genome codes only a few thousand druggable proteins, mainly receptors and enzymes. While this pool of available drug targets is limited, there is an untapped potential for discovering new drug-binding mechanisms and modes. For example, enzymes with long binding cavities offer numerous prerequisite binding sites that may be visited by an inhibitor during migration from a bulk solution to the destination site. Drug design can use these prerequisite sites as new structural targets. However, identifying these ephemeral sites is challenging. Here, we introduce a new method called NetBinder for the systematic identification and classification of prerequisite binding sites at atomic resolution. NetBinder is based on atomistic simulations of the full inhibitor binding process and provides a networking framework on which to select the most important binding modes and uncover the entire binding mechanism, including previously undiscovered events. NetBinder was validated by a study of the binding mechanism of blebbistatin (a potent inhibitor) to myosin 2 (a promising target for cancer chemotherapy). Myosin 2 is a good test enzyme because, like other potential targets, it has a long internal binding cavity that provides blebbistatin with numerous potential prerequisite binding sites. The mechanism proposed by NetBinder of myosin 2 structural changes during blebbistatin binding shows excellent agreement with experimentally determined binding sites and structural changes. While NetBinder was tested on myosin 2, it may easily be adopted to other proteins with long internal cavities, such as G-protein-coupled receptors or ion channels, the most popular current drug targets. NetBinder provides a new paradigm for drug design by a network-based elucidation of binding mechanisms at an atomic resolution.
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Affiliation(s)
- Mónika Bálint
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden;
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
- Correspondence:
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7
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Zsidó B, Börzsei R, Szél V, Hetényi C. Determination of Ligand Binding Modes in Hydrated Viral Ion Channels to Foster Drug Design and Repositioning. J Chem Inf Model 2021; 61:4011-4022. [PMID: 34313421 PMCID: PMC8389532 DOI: 10.1021/acs.jcim.1c00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Indexed: 12/29/2022]
Abstract
Target-based design and repositioning are mainstream strategies of drug discovery. Numerous drug design and repositioning projects have been launched to fight the ongoing COVID-19 pandemic. The resulting drug candidates have often failed due to the misprediction of their target-bound structures. The determination of water positions of such structures is particularly challenging due to the large number of possible drugs and the diversity of their hydration patterns. To answer this challenge and help correct predictions, we introduce a new protocol HydroDock, which can build hydrated drug-target complexes from scratch. HydroDock requires only the dry target and drug structures and produces their complexes with appropriately positioned water molecules. As a test application of the protocol, we built the structures of amantadine derivatives in complex with the influenza M2 transmembrane ion channel. The repositioning of amantadine derivatives from this influenza target to the SARS-CoV-2 envelope protein was also investigated. Excellent agreement was observed between experiments and the structures determined by HydroDock. The atomic resolution complex structures showed that water plays a similar role in the binding of amphipathic amantadine derivatives to transmembrane ion channels of both influenza A and SARS-CoV-2. While the hydrophobic regions of the channels capture the bulky hydrocarbon group of the ligand, the surrounding waters direct its orientation parallel with the axes of the channels via bridging interactions with the ionic ligand head. As HydroDock supplied otherwise undetermined structural details, it can be recommended to improve the reliability of future design and repositioning of antiviral drug candidates and many other ligands with an influence of water structure on their mechanism of action.
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Affiliation(s)
- Balázs
Zoltán Zsidó
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
- Department
of Pharmacology, Faculty of Pharmacy, University
of Pécs, Szigeti
út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
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8
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Spoel D, Zhang J, Zhang H. Quantitative predictions from molecular simulations using explicit or implicit interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1560] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- David Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology Uppsala University Uppsala Sweden
| | - Jin Zhang
- Department of Chemistry Southern University of Science and Technology Shenzhen China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering University of Science and Technology Beijing Beijing China
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Kim KH. Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies. J Comput Aided Mol Des 2021; 35:371-396. [PMID: 33712973 DOI: 10.1007/s10822-021-00377-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
It is frequently mentioned that QSARs have not generally lived up to expectations, especially in cases where high predictability is expected yet failed to deliver satisfactory results. Even though outliers can provide an increased opportunity in drug discovery research, outliers in SAR and QSAR can contort predictions and affect the accuracy if proper attention is not given. The percentages of outliers in QSARs have not changed appreciably over the last decade. In our previous studies, we suggested two possible sources of outliers in SAR and QSAR. In this paper, we suggest an additional possible source of outliers in QSAR. We presented several literature examples that show one or more water molecules that play a critical role in protein-ligand binding interactions as observed in their crystal structures. These examples illustrate that failing to account for the effects of water molecules in protein-ligand interactions could mislead interpretation and possibly yield outliers in SAR and QSAR. Examples include cases where QSAR, considering the role of water molecules in protein-ligand crystal structures, provided deeper insight into the understanding and interpretation of the developed QSAR.
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10
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The role of water in ligand binding. Curr Opin Struct Biol 2020; 67:1-8. [PMID: 32942197 DOI: 10.1016/j.sbi.2020.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
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Zsidó BZ, Hetényi C. Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome. Int J Mol Sci 2020; 21:ijms21114134. [PMID: 32531926 PMCID: PMC7311975 DOI: 10.3390/ijms21114134] [Citation(s) in RCA: 5] [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: 05/28/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Development of valid structure–activity relationships (SARs) is a key to the elucidation of pathomechanisms of epigenetic diseases and the development of efficient, new drugs. The present review is based on selected methodologies and applications supplying molecular structure, binding affinity and biological activity data for the development of new SARs. An emphasis is placed on emerging trends and permanent challenges of new discoveries of SARs in the context of proteins as epigenetic drug targets. The review gives a brief overview and classification of the molecular background of epigenetic changes, and surveys both experimental and theoretical approaches in the field. Besides the results of sophisticated, cutting edge techniques such as cryo-electron microscopy, protein crystallography, and isothermal titration calorimetry, examples of frequently used assays and fast screening techniques are also selected. The review features how different experimental methods and theoretical approaches complement each other and result in valid SARs of the epigenome.
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12
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Kunstmann S, Engström O, Wehle M, Widmalm G, Santer M, Barbirz S. Increasing the Affinity of an O-Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein. Chemistry 2020; 26:7263-7273. [PMID: 32189378 PMCID: PMC7463171 DOI: 10.1002/chem.202000495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/09/2020] [Indexed: 12/30/2022]
Abstract
Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D 1 H,1 H-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.
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Affiliation(s)
- Sonja Kunstmann
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Current address: Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads2800 Kgs.LyngbyDenmark
| | - Olof Engström
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Marko Wehle
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Göran Widmalm
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Mark Santer
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Stefanie Barbirz
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
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13
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Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles. Microorganisms 2019; 8:microorganisms8010059. [PMID: 31905784 PMCID: PMC7023208 DOI: 10.3390/microorganisms8010059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/25/2022] Open
Abstract
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.
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14
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Horváth I, Jeszenői N, Bálint M, Paragi G, Hetényi C. A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level. Int J Mol Sci 2019; 20:ijms20184384. [PMID: 31489952 PMCID: PMC6770515 DOI: 10.3390/ijms20184384] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 12/22/2022] Open
Abstract
Optimization of the enthalpy component of binding thermodynamics of drug candidates is a successful pathway of rational molecular design. However, the large size and missing hydration structure of target-ligand complexes often hinder such optimizations with quantum mechanical (QM) methods. At the same time, QM calculations are often necessitated for proper handling of electronic effects. To overcome the above problems, and help the QM design of new drugs, a protocol is introduced for atomic level determination of hydration structure and extraction of structures of target-ligand complex interfaces. The protocol is a combination of a previously published program MobyWat, an engine for assigning explicit water positions, and Fragmenter, a new tool for optimal fragmentation of protein targets. The protocol fostered a series of fast calculations of ligand binding enthalpies at the semi-empirical QM level. Ligands of diverse chemistry ranging from small aromatic compounds up to a large peptide helix of a molecular weight of 3000 targeting a leukemia protein were selected for systematic investigations. Comparison of various combinations of implicit and explicit water models demonstrated that the presence of accurately predicted explicit water molecules in the complex interface considerably improved the agreement with experimental results. A single scaling factor was derived for conversion of QM reaction heats into binding enthalpy values. The factor links molecular structure with binding thermodynamics via QM calculations. The new protocol and scaling factor will help automated optimization of binding enthalpy in future molecular design projects.
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Affiliation(s)
- István Horváth
- Chemistry Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary.
| | - Norbert Jeszenői
- Institute of Physiology, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Mónika Bálint
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Gábor Paragi
- MTA-SZTE Biomimetic Systems Research Group, Dóm tér 8, 6720 Szeged, Hungary.
- Institute of Physics, University of Pécs, Ifjúság útja 6, 7624 Pécs, Hungary.
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
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15
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Zhong H, Wang Z, Wang X, Liu H, Li D, Liu H, Yao X, Hou T. Importance of a crystalline water network in docking-based virtual screening: a case study of BRD4. Phys Chem Chem Phys 2019; 21:25276-25289. [DOI: 10.1039/c9cp04290c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a member of the bromodomain and extra terminal domain (BET) protein family, bromodomain-containing protein 4 (BRD4) is an epigenetic reader and can recognize acetylated lysine residues in histones.
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Affiliation(s)
- Haiyang Zhong
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- College of Pharmaceutical Sciences
| | - Zhe Wang
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Xuwen Wang
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Hui Liu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Huanxiang Liu
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000
- China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- State Key Laboratory of Quality Research in Chinese Medicine
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
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16
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Brysbaert G, Blossey R, Lensink MF. The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues. Front Mol Biosci 2018; 5:88. [PMID: 30364190 PMCID: PMC6193073 DOI: 10.3389/fmolb.2018.00088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/18/2018] [Indexed: 12/13/2022] Open
Abstract
The relevance of water molecules for the recognition and the interaction of biomolecules is widely appreciated. In this paper we address the role that water molecules associated to protein complexes play for the functional relevance of residues by considering their residue interaction networks (RINs). These are commonly defined on the basis of the amino acid composition of the proteins themselves, disregarding the solvation state of the protein. We determine properties of the RINs of two protein complexes, colicin E2/Im2 and barnase/barstar, with and without associated water molecules, using a previously developed methodology and its associated application RINspector. We find that the inclusion of water molecules in RINs leads to an increase in the number of central residues which adds a novel mechanism to the relevance of water molecules for protein function.
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Affiliation(s)
- Guillaume Brysbaert
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
| | - Ralf Blossey
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
| | - Marc F Lensink
- CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France
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17
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Kunstmann S, Gohlke U, Broeker NK, Roske Y, Heinemann U, Santer M, Barbirz S. Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site. J Am Chem Soc 2018; 140:10447-10455. [DOI: 10.1021/jacs.8b03719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonja Kunstmann
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ulrich Gohlke
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Nina K. Broeker
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Stefanie Barbirz
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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18
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Fischer NM, Polêto MD, Steuer J, van der Spoel D. Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations. Nucleic Acids Res 2018; 46:4872-4882. [PMID: 29718375 PMCID: PMC6007214 DOI: 10.1093/nar/gky221] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/16/2018] [Accepted: 04/23/2018] [Indexed: 01/11/2023] Open
Abstract
The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na+ or Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (ΔG‡ for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.
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Affiliation(s)
- Nina M Fischer
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Marcelo D Polêto
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Bento Gonçalves 9500, BR-91500-970 Porto Alegre, Brazil
| | - Jakob Steuer
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
- Department of Chemistry, University of Konstanz, Universitätstraße 10, D-78457 Konstanz, Germany
| | - David van der Spoel
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
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19
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Jeszenői N, Schilli G, Bálint M, Horváth I, Hetényi C. Analysis of the influence of simulation parameters on biomolecule-linked water networks. J Mol Graph Model 2018; 82:117-128. [DOI: 10.1016/j.jmgm.2018.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/27/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
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20
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Bálint M, Jeszenői N, Horváth I, van der Spoel D, Hetényi C. Systematic exploration of multiple drug binding sites. J Cheminform 2017; 9:65. [PMID: 29282592 PMCID: PMC5745209 DOI: 10.1186/s13321-017-0255-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/16/2017] [Indexed: 02/06/2023] Open
Abstract
Background Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple binding sites is often challenging. Blind docking has been widely used for fast mapping of the entire target surface for multiple binding sites. Reliability of blind docking is limited by approximations of hydration models, simplified handling of molecular flexibility, and imperfect search algorithms. Results To overcome such limitations, the present study introduces Wrap ‘n’ Shake (WnS), an atomic resolution method that systematically “wraps” the entire target into a monolayer of ligand molecules. Functional binding sites are extracted by a rapid molecular dynamics shaker. WnS is tested on biologically important systems such as mitogen-activated protein, tyrosine-protein kinases, key players of cellular signaling, and farnesyl pyrophosphate synthase, a target of antitumor agents.![]() Electronic supplementary material The online version of this article (10.1186/s13321-017-0255-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mónika Bálint
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.,Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Norbert Jeszenői
- MTA NAP-B Molecular Neuroendocrinology Group, Institute of Physiology, Szentágothai Research Center, Center for Neuroscience, University of Pécs, Szigeti út 12, Pecs, 7624, Hungary
| | - István Horváth
- Chemistry Doctoral School, University of Szeged, Dugonics tér 13, Szeged, 6720, Hungary
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, University of Uppsala, Box 596, 75124, Uppsala, Sweden
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.
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21
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Jukič M, Konc J, Gobec S, Janežič D. Identification of Conserved Water Sites in Protein Structures for Drug Design. J Chem Inf Model 2017; 57:3094-3103. [DOI: 10.1021/acs.jcim.7b00443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI−1000, Ljubljana, Slovenia
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
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22
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Ansari MY, Dikhit MR, Sahoo GC, Ali V, Das P. Recent advancement and treatment of leishmaniasis based on pharmacoinformatics approach: Current and future outlook. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Poór M, Kunsági-Máté S, Bálint M, Hetényi C, Gerner Z, Lemli B. Interaction of mycotoxin zearalenone with human serum albumin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 170:16-24. [PMID: 28365492 DOI: 10.1016/j.jphotobiol.2017.03.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 01/05/2023]
Abstract
Zearalenone (ZEN) is a mycotoxin produced mainly by Fusarium species. Fungal contamination of cereals and plants can result in the formation of ZEN, leading to its presence in different foods, animal feeds, and drinks. Because ZEN is an endocrine disruptor, it causes reproductive disorders in farm animals and hyperoestrogenic syndromes in humans. Despite toxicokinetic properties of ZEN were studied in more species, we have no information regarding the interaction of ZEN with serum albumin. Since albumin commonly plays an important role in the toxicokinetics of different toxins, interaction of ZEN with albumin has of high biological importance. Therefore the interaction of ZEN with human serum albumin (HSA) was investigated using spectroscopic methods, ultrafiltration, and molecular modeling studies. Fluorescence spectroscopic studies demonstrate that ZEN forms complex with HSA. Binding constant (K) of ZEN-HSA complex was quantified with fluorescence quenching technique. The determined binding constant (logK=5.1) reflects the strong interaction of ZEN with albumin suggesting the potential biological importance of ZEN-HSA complex formation. Based on the results of the investigations with site markers as well as docking studies, ZEN occupies a non-conventional binding site on HSA. Considering the above listed observations, we should keep in mind this interaction if we would like to precisely understand the toxicokinetic behavior of ZEN.
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Affiliation(s)
- Miklós Poór
- Department of Pharmacology, University of Pécs, Faculty of Pharmacy, Szigeti út 12, Pécs H-7624, Hungary; Department of Pharmacology and Pharmacotherapy, University of Pécs, Medical School, Szigeti út 12, Pécs H-7624, Hungary.
| | - Sándor Kunsági-Máté
- Department of General and Physical Chemistry, University of Pécs, Ifjúság útja 6, Pécs H-7624, Hungary; János Szentágothai Research Center, Ifjúság útja 20, Pécs H-7624, Hungary
| | - Mónika Bálint
- Department of Pharmacology and Pharmacotherapy, University of Pécs, Medical School, Szigeti út 12, Pécs H-7624, Hungary; Department of Biochemistry, Eötvös Loránd University, Pázmány sétány 1/C, Budapest H-1117, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, University of Pécs, Medical School, Szigeti út 12, Pécs H-7624, Hungary; MTA-ELTE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Pázmány sétány 1/C, Budapest H-1117, Hungary
| | - Zsófia Gerner
- Department of General and Physical Chemistry, University of Pécs, Ifjúság útja 6, Pécs H-7624, Hungary
| | - Beáta Lemli
- Department of General and Physical Chemistry, University of Pécs, Ifjúság útja 6, Pécs H-7624, Hungary; János Szentágothai Research Center, Ifjúság útja 20, Pécs H-7624, Hungary
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