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Peřina M, Börzsei R, Henrietta Ágoston, Hlogyik T, Poór M, Rigó R, Özvegy-Laczka C, Batta G, Hetényi C, Vojáčková V, Jorda R, Mernyák E. Synthesis and estrogenic activity of BODIPY-labeled estradiol conjugates. Eur J Pharm Sci 2024; 199:106813. [PMID: 38797442 DOI: 10.1016/j.ejps.2024.106813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Novel BODIPY-estradiol conjugates have been synthesized by selecting position C-3-O for labeling. The conjugation strategy was based on Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) or etherification. Estradiol derivatives used as azide partners bearing an ω-azidoalkyl function through C4-C8-long linkers have been prepared. CuAAC reactions of estradiol azides with BODIPY alkyne furnished fluorescent 3-O-labeled conjugates bearing the triazole ring as a coupling moiety. Williamson etherifications of 3-O-(ω-bromoalkyl)-17β-estradiol derivatives with BODIPY-OH resulted in labeled conjugates connected with an ether moiety. Interactions of the conjugates with estrogen receptor (ER) were investigated using molecular docking calculations in comparison with estradiol. The conjugates occupied both the classical and alternative binding sites on human ERα, with slightly lower binding affinity to references estradiol and diethystilbestrol. All compounds have displayed reasonable estrogenic activity. They increased the proliferation of ER-positive breast cancer cell line MCF7 contrary to ER-negative SKBR-3 cell line. The most potent compound 13a induced the transcriptional activity of ER in dose-dependent manner in dual luciferase recombinant reporter model and increased progesterone receptor's expression, proving the retained estrogenic activity. The fluorescence of candidate compound 13a co-localised with the ERα. The newly synthesized labeled compounds might serve as good starting point for further development of fluorescent probes for modern biological applications. In addition to studying steroid uptake and transport in cells, e.g. in the processes of biodegradation of estrogen-hormones micropollutants, they could also be utilized in examination of estrogen-binding proteins.
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Affiliation(s)
- Miroslav Peřina
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27 78371 Olomouc, Czech Republic
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12 H-7624 Pécs, Hungary
| | - Henrietta Ágoston
- Department of Inorganic, Organic and Analytical Chemistry, University of Szeged, Dóm tér 7‒8 H-6720 Szeged, Hungary
| | - Tamás Hlogyik
- Department of Inorganic, Organic and Analytical Chemistry, University of Szeged, Dóm tér 7‒8 H-6720 Szeged, Hungary
| | - Miklós Poór
- Department of Laboratory Medicine, Medical School, University of Pécs, Ifjúság útja 13, Pécs H-7624, Hungary; Molecular Medicine Research Group, János Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, Pécs H-7624, Hungary
| | - Réka Rigó
- Drug resistance research group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - Csilla Özvegy-Laczka
- Drug resistance research group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - Gyula Batta
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1 H-4032 Debrecen, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12 H-7624 Pécs, Hungary
| | - Veronika Vojáčková
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27 78371 Olomouc, Czech Republic
| | - Radek Jorda
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27 78371 Olomouc, Czech Republic.
| | - Erzsébet Mernyák
- Department of Inorganic, Organic and Analytical Chemistry, University of Szeged, Dóm tér 7‒8 H-6720 Szeged, Hungary; Department of Pharmacognosy, University of Szeged, Eötvös u. 6 H-6720 Szeged, Hungary.
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2
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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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3
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Yepes-Molina L, Teruel JA, Johanson U, Carvajal M. Brassica oleracea L. var. italica Aquaporin Reconstituted Proteoliposomes as Nanosystems for Resveratrol Encapsulation. Int J Mol Sci 2024; 25:1987. [PMID: 38396666 PMCID: PMC10888208 DOI: 10.3390/ijms25041987] [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: 01/15/2024] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Aquaporins (AQPs), membrane proteins responsible for facilitating water transport, found in plant membrane vesicles (MV), have been related to the functionality and stability of MV. We focused on AQPs obtained from broccoli, as they show potential for biotechnological applications. To gain further insight into the role of AQPs in MV, we describe the heterologous overexpression of two broccoli AQPs (BoPIP1;2 and BoPIP2;2) in Pichia pastoris, resulting in their purification with high yield (0.14 and 0.99 mg per gram cells for BoPIP1;2 and BoPIP2;2). We reconstituted AQPs in liposomes to study their functionality, and the size of proteoliposomes did not change concerning liposomes. BoPIP2;2 facilitated water transport, which was preserved for seven days at 4 °C and at room temperature but not at 37 °C. BoPIP2;2 was incorporated into liposomes to encapsulate a resveratrol extract, resulting in increased entrapment efficiency (EE) compared to conventional liposomes. Molecular docking was utilized to identify binding sites in PIP2s for resveratrol, highlighting the role of aquaporins in the improved EE. Moreover, interactions between plant AQP and human integrin were shown, which may increase internalization by the human target cells. Our results suggest AQP-based alternative encapsulation systems can be used in specifically targeted biotechnological applications.
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Affiliation(s)
- Lucia Yepes-Molina
- Aquaporins Group, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS), CSIC, Campus de Espinardo, E-30100 Murcia, Spain;
| | - José A. Teruel
- Department of Biochemistry and Molecular Biology, Facultad de Veterinaria, Universidad de Murcia, E-30100 Murcia, Spain;
| | - Urban Johanson
- Division of Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Micaela Carvajal
- Aquaporins Group, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS), CSIC, Campus de Espinardo, E-30100 Murcia, Spain;
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4
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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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Wang P, Wu R, Jia Y, Tang P, Wei B, Zhang Q, Wang VYF, Yan R. Inhibition and structure-activity relationship of dietary flavones against three Loop 1-type human gut microbial β-glucuronidases. Int J Biol Macromol 2022; 220:1532-1544. [PMID: 36096258 DOI: 10.1016/j.ijbiomac.2022.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/28/2022] [Accepted: 09/04/2022] [Indexed: 02/07/2023]
Abstract
Gut microbial β-glucuronidases (GUSs) inhibition is a new approach for managing some diseases and medication therapy. However, the structural and functional complexity of GUSs have posed tremendous challenges to discover specific or broad-spectrum GUSs inhibitors using Escherichia coli GUS (EcoGUS) alone. This study first assessed the effects of twenty-one dietary flavones employing three Loop 1-type GUSs of different taxonomic origins, which were considered to be the main GUSs involved in deglucuronidation of small molecules, on p-nitrophenyl-β-D-glucuronide hydrolysis and a structure-activity relationship is preliminarily proposed based on both in vitro assays and a docking study with representative compounds. EcoGUS and Staphylococcus pasteuri GUS showed largely similar inhibition propensities with potencies positively correlating with the total hydroxyl groups and those at ring B of flavones, while docking results revealed strong interactions developed via ring A and/or C. Streptococcus agalactiae GUS (SagaGUS) exhibited distinct inhibition propensities, displaying late-onset inhibition and steep dose-response profiles with most tested compounds. The α-helix in loop 1 region of SagaGUS which causes spatial hindrance but offers a hydrophobic surface for contacting with the carbonyl group on ring C of flavones is believed to be essential for the allosteric inhibition of SagaGUS. Taken together, the study with a series of flavones revealed varied preferences for GUSs belonging to the same Loop 1-type, highlighting the necessity of adopting multi-GUSs instead of EcoGUS alone for screening broad-spectrum GUSs inhibitors or tailoring the inhibition based on specific GUS structure.
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Affiliation(s)
- Panpan Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao.
| | - Rongrong Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao.
| | - Yifei Jia
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao
| | - Puipui Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao
| | - Bin Wei
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao.
| | - Qingwen Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao.
| | | | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao.
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6
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Ongtanasup T, Prommee N, Jampa O, Limcharoen T, Wanmasae S, Nissapatorn V, Paul AK, Pereira MDL, Wilairatana P, Nasongkla N, Eawsakul K. The Cholesterol-Modulating Effect of the New Herbal Medicinal Recipe from Yellow Vine ( Coscinium fenestratum (Goetgh.)), Ginger ( Zingiber officinale Roscoe.), and Safflower ( Carthamus tinctorius L.) on Suppressing PCSK9 Expression to Upregulate LDLR Expression in HepG2 Cells. PLANTS (BASEL, SWITZERLAND) 2022; 11:1835. [PMID: 35890469 PMCID: PMC9318486 DOI: 10.3390/plants11141835] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
PCSK9 is a promising target for developing novel cholesterol-lowering drugs. We developed a recipe that combined molecular docking, GC-MS/MS, and real-time PCR to identify potential PCSK9 inhibitors for herb ratio determination. Three herbs, Carthamus tinctorius, Coscinium fenestratum, and Zingiber officinale, were used in this study. This work aimed to evaluate cholesterol-lowering through a PCSK9 inhibitory mechanism of these three herbs for defining a suitable ratio. Chemical constituents were identified using GC-MS/MS. The PCSK9 inhibitory potential of the compounds was determined using molecular docking, real-time PCR, and Oil red O staining. It has been shown that most of the active compounds of C. fenestratum and Z. officinale inhibit PCSK9 when extracted with water, and C. fenestratum has been shown to yield tetraacetyl-d-xylonic nitrile (27.92%) and inositol, 1-deoxy-(24.89%). These compounds could inhibit PCSK9 through the binding of 6 and 5 hydrogen bonds, respectively, while the active compound in Z. officinale is 2-Formyl-9-[.beta.-d-ribofuranosyl] hypoxanthine (4.37%) inhibits PCSK9 by forming 8 hydrogen bonds. These results suggest that a recipe comprising three parts C. fenestratum, two parts Z. officinale, and one part C. tinctorius is a suitable herbal ratio for reducing lipid levels in the bloodstream through a PCSK9 inhibitory mechanism.
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Affiliation(s)
- Tassanee Ongtanasup
- School of Medicine, Walailak University, Nakhon Si Thammarat 80160, Thailand; (T.O.); (T.L.)
- Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat 80160, Thailand; or
| | - Nuntika Prommee
- Division of Applied Thai Traditional Medicine, Faculty of Public Health, Naresuan University, Phitsanulok 65000, Thailand;
| | - Onkamon Jampa
- Tak Community College, Nong Bua Tai 63000, Thailand;
| | - Thanchanok Limcharoen
- School of Medicine, Walailak University, Nakhon Si Thammarat 80160, Thailand; (T.O.); (T.L.)
| | - Smith Wanmasae
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand;
| | - Veeranoot Nissapatorn
- Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat 80160, Thailand; or
- School of Allied Health Sciences, World Union for Herbal Drug Discovery (WUHeDD), Nakhon Si Thammarat 80160, Thailand
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Maria de Lourdes Pereira
- CICECO—Aveiro Institute of Materials, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Norased Nasongkla
- Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Komgrit Eawsakul
- School of Medicine, Walailak University, Nakhon Si Thammarat 80160, Thailand; (T.O.); (T.L.)
- Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat 80160, Thailand; or
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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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8
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Börzsei R, Zsidó BZ, Bálint M, Helyes Z, Pintér E, Hetényi C. Exploration of Somatostatin Binding Mechanism to Somatostatin Receptor Subtype 4. Int J Mol Sci 2022; 23:ijms23136878. [PMID: 35805885 PMCID: PMC9266823 DOI: 10.3390/ijms23136878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
Somatostatin (also named as growth hormone-inhibiting hormone or somatotropin release-inhibiting factor) is a regulatory peptide important for the proper functioning of the endocrine system, local inflammatory reactions, mood and motor coordination, and behavioral responses to stress. Somatostatin exerts its effects via binding to G-protein-coupled somatostatin receptors of which the fourth subtype (SSTR4) is a particularly important receptor mediating analgesic, anti-inflammatory, and anti-depressant effects without endocrine actions. Thus, SSTR4 agonists are promising drug candidates. Although the knowledge of the atomic resolution-binding modes of SST would be essential for drug development, experimental elucidation of the structures of SSTR4 and its complexes is still awaiting. In the present study, structures of the somatostatin–SSTR4 complex were produced using an unbiased, blind docking approach. Beyond the static structures, the binding mechanism of SST was also elucidated in the explicit water molecular dynamics (MD) calculations, and key binding modes (external, intermediate, and internal) were distinguished. The most important residues on both receptor and SST sides were identified. An energetic comparison of SST binding to SSTR4 and 2 offered a residue-level explanation of receptor subtype selectivity. The calculated structures show good agreement with available experimental results and indicate that somatostatin binding is realized via prerequisite binding modes and an induced fit mechanism. The identified binding modes and the corresponding key residues provide useful information for future drug design targeting SSTR4.
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Affiliation(s)
- Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
| | - Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
| | - Mónika Bálint
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
- Algonist Gmbh, 1030 Vienna, Austria
- PharmInVivo Ltd., 7624 Pécs, Hungary
| | - Erika Pintér
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
- Algonist Gmbh, 1030 Vienna, Austria
- PharmInVivo Ltd., 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, 7624 Pécs, Hungary; (R.B.); (B.Z.Z.); (M.B.); (Z.H.); (E.P.)
- János Szentágothai Research Centre & Centre for Neuroscience, University of Pécs, 7624 Pécs, Hungary
- Correspondence:
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Aguayo-Ortiz R, Dominguez L. Unveiling the Possible Oryzalin-Binding Site in the α-Tubulin of Toxoplasma gondii. ACS OMEGA 2022; 7:18434-18442. [PMID: 35694483 PMCID: PMC9178734 DOI: 10.1021/acsomega.2c00729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/11/2022] [Indexed: 06/09/2023]
Abstract
Dinitroaniline derivatives have been widely used as herbicidal agents to control weeds and grass. Previous studies demonstrated that these compounds also exhibit good antiparasitic activity against some protozoan parasites. Oryzalin (ORY), a representative dinitroaniline derivative, exerts its antiprotozoal activity against Toxoplasma gondii by inhibiting the microtubule polymerization process. Moreover, the identification of ORY-resistant T. gondii lines obtained by chemical mutagenesis confirmed that this compound binds selectively to α-tubulin. Based on experimental information reported so far and a multiple sequence analysis carried out in this work, we propose that the pironetin (PIR) site is the potential ORY-binding site. Therefore, we employed state-of-the-art computational approaches to characterize the interaction profile of ORY at the proposed site in the α-tubulin of T. gondii. An exhaustive search for other possible binding sites was performed using the Wrap "N" Shake method, which showed that ORY exhibits highest stability and affinity for the PIR site. Moreover, our molecular dynamics simulations revealed that the dipropylamine substituent of ORY interacts with a hydrophobic pocket, while the sulfonamide group formed hydrogen bonds with water molecules at the site entrance. Overall, our results suggest that ORY binds to the PIR site on the α-tubulin of the protozoan parasite T. gondii. This information will be very useful for designing less toxic and more potent antiprotozoal agents.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Laura Dominguez
- Departamento
de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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10
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Aguayo-Ortiz R, Guzmán-Ocampo DC, Dominguez L. Insights into the binding of morin to human γD-crystallin. Biophys Chem 2021; 282:106750. [PMID: 34999344 DOI: 10.1016/j.bpc.2021.106750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022]
Abstract
Crystallin aggregation in the eye lens is one of the leading causes of cataract formation. The increase in the human γD-crystallin (HγDC) aggregation propensity has been associated with the oligomerization of its partially folded and fully unfolded structure. A recent study demonstrated that the binding of flavonoid morin (MOR) to HγDC inhibits the fibrillation of this protein. In this work, we carry out an exhaustive search for the possible binding site of MOR on HγDC by combining an ensemble docking approach with the Wrap 'N' Shake protocol. In agreement with previous results, we found a potential MOR-binding site in the cleft formed between the N-terminal and C-terminal domains of HγDC. MOR preference for the cleft residues was observed even with the interface-opened intermediate conformers of HγDC. In addition, metadynamics simulations were carried out to corroborate the stabilizing activity of MOR on HγDC structure and to identify the structural regions implicated during the unfolding inhibition. Overall, this study provides relevant insights into the identification of new HγDC aggregation inhibitors.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Dulce C Guzmán-Ocampo
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
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11
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Zsidó BZ, Börzsei R, Pintér E, Hetényi C. Prerequisite Binding Modes Determine the Dynamics of Action of Covalent Agonists of Ion Channel TRPA1. Pharmaceuticals (Basel) 2021; 14:988. [PMID: 34681212 PMCID: PMC8540651 DOI: 10.3390/ph14100988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/16/2022] Open
Abstract
Transient receptor potential ankyrin 1 (TRPA1) is a transmembrane protein channeling the influx of calcium ions. As a polymodal nocisensor, TRPA1 can be activated by thermal, mechanical stimuli and a wide range of chemically damaging molecules including small volatile environmental toxicants and endogenous algogenic lipids. After activation by such compounds, the ion channel opens up, its central pore widens allowing calcium influx into the cytosol inducing signal transduction pathways. Afterwards, the calcium influx desensitizes irritant evoked responses and results in an inactive state of the ion channel. Recent experimental determination of structures of apo and holo forms of TRPA1 opened the way towards the design of new agonists, which can activate the ion channel. The present study is aimed at the elucidation of binding dynamics of agonists using experimental structures of TRPA1-agonist complexes at the atomic level applying molecular docking and dynamics methods accounting for covalent and non-covalent interactions. Following a test of docking methods focused on the final, holo structures, prerequisite binding modes were detected involving the apo forms. It was shown how reversible interactions with prerequisite binding sites contribute to structural changes of TRPA1 leading to covalent bonding of agonists. The proposed dynamics of action allowed a mechanism-based forecast of new, druggable binding sites of potent agonists.
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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; (B.Z.Z.); (E.P.)
| | - Rita Börzsei
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary;
| | - Erika Pintér
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary; (B.Z.Z.); (E.P.)
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary; (B.Z.Z.); (E.P.)
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12
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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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13
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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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14
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Evans DJ, Yovanno RA, Rahman S, Cao DW, Beckett MQ, Patel MH, Bandak AF, Lau AY. Finding Druggable Sites in Proteins Using TACTICS. J Chem Inf Model 2021; 61:2897-2910. [PMID: 34096704 DOI: 10.1021/acs.jcim.1c00204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structure-based drug discovery efforts require knowledge of where drug-binding sites are located on target proteins. To address the challenge of finding druggable sites, we developed a machine-learning algorithm called TACTICS (trajectory-based analysis of conformations to identify cryptic sites), which uses an ensemble of molecular structures (such as molecular dynamics simulation data) as input. First, TACTICS uses k-means clustering to select a small number of conformations that represent the overall conformational heterogeneity of the data. Then, TACTICS uses a random forest model to identify potentially bindable residues in each selected conformation, based on protein motion and geometry. Lastly, residues in possible binding pockets are scored using fragment docking. As proof-of-principle, TACTICS was applied to the analysis of simulations of the SARS-CoV-2 main protease and methyltransferase and the Yersinia pestis aryl carrier protein. Our approach recapitulates known small-molecule binding sites and predicts the locations of sites not previously observed in experimentally determined structures. The TACTICS code is available at https://github.com/Albert-Lau-Lab/tactics_protein_analysis.
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Affiliation(s)
- Daniel J Evans
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Remy A Yovanno
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - David W Cao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Morgan Q Beckett
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - Milan H Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Afif F Bandak
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Albert Y Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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15
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Dandekar BR, Mondal J. Capturing Protein-Ligand Recognition Pathways in Coarse-Grained Simulation. J Phys Chem Lett 2020; 11:5302-5311. [PMID: 32520567 DOI: 10.1021/acs.jpclett.0c01683] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein-ligand recognition is dynamic and complex. A key approach in deciphering the mechanism underlying the recognition process is to capture the kinetic process of the ligand in its act of binding to its designated protein cavity. Toward this end, ultralong all-atom molecular dynamics simulation has recently emerged as a popular method of choice because of its ability to record these events at high spatial and temporal resolution. However, success via this route comes at an exorbitant computational cost. Herein, we demonstrate that coarse-grained models of the protein, when systematically optimized to maintain its tertiary fold, can capture the complete process of spontaneous protein-ligand binding from bulk media to the cavity at crystallographic precision and within wall clock time that is orders of magnitude shorter than that of all-atom simulations. The exhaustive sampling of ligand exploration in protein and solvent, harnessed by coarse-grained simulation, leads to elucidation of new ligand recognition pathways and discovery of non-native binding poses.
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Affiliation(s)
- Bhupendra R Dandekar
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500046, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500046, India
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16
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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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17
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A Comprehensive Computational Platform to Guide Drug Development Using Graph-Based Signature Methods. Methods Mol Biol 2020. [PMID: 32006280 DOI: 10.1007/978-1-0716-0270-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
High-throughput computational techniques have become invaluable tools to help increase the overall success, process efficiency, and associated costs of drug development. By designing ligands tailored to specific protein structures in a disease of interest, an understanding of molecular interactions and ways to optimize them can be achieved prior to chemical synthesis. This understanding can help direct crucial chemical and biological experiments by maximizing available resources on higher quality leads. Moreover, predicting molecular binding affinity within specific biological contexts, as well as ligand pharmacokinetics and toxicities, can aid in filtering out redundant leads early on within the process. We describe a set of computational tools which can aid in drug discovery at different stages, from hit identification (EasyVS) to lead optimization and candidate selection (CSM-lig, mCSM-lig, Arpeggio, pkCSM). Incorporating these tools along the drug development process can help ensure that candidate leads are chemically and biologically feasible to become successful and tractable drugs.
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18
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Bálint M, Horváth I, Mészáros N, Hetényi C. Towards Unraveling the Histone Code by Fragment Blind Docking. Int J Mol Sci 2019; 20:ijms20020422. [PMID: 30669446 PMCID: PMC6358888 DOI: 10.3390/ijms20020422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/11/2019] [Accepted: 01/16/2019] [Indexed: 12/02/2022] Open
Abstract
Histones serve as protein spools for winding the DNA in the nucleosome. High variability of their post-translational modifications result in a unique code system often responsible for the pathomechanisms of epigenetics-based diseases. Decoding is performed by reader proteins via complex formation with the N-terminal peptide tails of histones. Determination of structures of histone-reader complexes would be a key to unravel the histone code and the design of new drugs. However, the large number of possible histone complex variations imposes a true challenge for experimental structure determination techniques. Calculation of such complexes is difficult due to considerable size and flexibility of peptides and the shallow binding surfaces of the readers. Moreover, location of the binding sites is often unknown, which requires a blind docking search over the entire surface of the target protein. To accelerate the work in this field, a new approach is presented for prediction of the structure of histone H3 peptide tails docked to their targets. Using a fragmenting protocol and a systematic blind docking method, a collection of well-positioned fragments of the H3 peptide is produced. After linking the fragments, reconstitution of anchoring regions of the target-bound H3 peptide conformations was possible. As a first attempt of combination of blind and fragment docking approaches, our new method is named fragment blind docking (FBD).
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Affiliation(s)
- Mónika Bálint
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - István Horváth
- Chemistry Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary.
| | - Nikolett Mészáros
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
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