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Eyilcim O, Gunay F, Gunkara OT, Ng YY, Ulucan O, Erden I. Design and synthesis of novel 1,2,3,4-tetrazines as new anti-leukemia cancer agents. Chem Biol Drug Des 2023; 102:1186-1201. [PMID: 37730958 DOI: 10.1111/cbdd.14328] [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: 04/04/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 09/22/2023]
Abstract
A series of novel 1,2,3,4-tetrazines were designed and synthesized. 1 H-NMR spectroscopy, 13 C NMR spectroscopy, and HRMS were used to determine the structures of this novel compounds. Computational approaches suggested that DHFR is a putative target for the newly synthesized 11 compounds. Extensive molecular dynamics simulations followed by molecular docking simulations were employed to evaluate DHFR as a potential target protein. The anticancer activities of the compounds were evaluated against five different types of leukemia cell lines (Jurkat, Nalm-6, Reh, K562, and Molt-4) and one non-leukemic cell line (Hek293T) by MTT test in vitro and imatinib was used as a control drug. Among these compounds, 3a exhibited the best activity against all the leukemic cell lines, except Reh cell line. For Nalm-6, K562, Jurkat, and Molt-4 cell lines, IC50 values were found to be 15.98, 19.12, 23.15, and 25.80 μM, respectively. Our work focuses on the synthesis of original and novel 1,2,3,4-tetrazine derivatives while contributing to the ongoing effort to discover more potent new antileukemia agents.
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Affiliation(s)
- Oznur Eyilcim
- Department of Chemistry, Faculty of Science and Arts, Yildiz Technical University, Istanbul, Turkey
| | - Fulya Gunay
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Istanbul Bilgi University, Istanbul, Turkey
| | - Omer Tahir Gunkara
- Department of Chemistry, Faculty of Science and Arts, Yildiz Technical University, Istanbul, Turkey
| | - Yuk Yin Ng
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Istanbul Bilgi University, Istanbul, Turkey
| | - Ozlem Ulucan
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Istanbul Bilgi University, Istanbul, Turkey
| | - Ihsan Erden
- San Francisco State University, Department of Chemistry & Biochemistry, San Francisco, California, USA
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Hollander M, Rasp D, Aziz M, Helms V. ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures. J Chem Inf Model 2021; 61:1555-1559. [PMID: 33844545 DOI: 10.1021/acs.jcim.1c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface pockets, cavities, and tunnels in the 3D structures of proteins play integral functional roles such as enabling enzymatic catalysis, ligand binding, or transport of ions or small molecules across biomembranes. ProPores2 facilitates understanding and analysis of these processes by identifying pores and lining residues, determining their axes, and opening closed connections via side-chain rotation. The fast stand-alone tool introduces a novel mode for pore identification, improved axis determination, and additional features such as parallel batch processing and a graphical user interface. The new web service features an integrated and customizable protein viewer with an option to analyze and view more than one structure at once. This feature facilitates side-by-side comparisons of pores in different conformations of the same protein or of identified pores before and after opening gates within the same protein. ProPores2 is freely and publicly available at https://service.bioinformatik.uni-saarland.de/propores.
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Affiliation(s)
- Markus Hollander
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66041 Saarbrücken, Germany
| | - David Rasp
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66041 Saarbrücken, Germany
| | - Moomal Aziz
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66041 Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66041 Saarbrücken, Germany
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3
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Wang KW, Hall CK. Characterising the throat diameter of through-pores in network structures using a percolation criterion. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1654140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Kye Won Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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Ariz-Extreme I, Hub JS. Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B 2017; 121:1506-1519. [PMID: 28128570 DOI: 10.1021/acs.jpcb.6b11279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
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5
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Johnson QR, Lindsay RJ, Nellas RB, Shen T. Pressure-induced conformational switch of an interfacial protein. Proteins 2016; 84:820-7. [DOI: 10.1002/prot.25031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 02/04/2016] [Accepted: 03/01/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Quentin R. Johnson
- UT-ORNL Graduate School of Genome Science and Technology; University of Tennessee; Knoxville Tennessee 37996
- Oak Ridge National Laboratory; Center for Molecular Biophysics; Oak Ridge Tennessee 37830
| | - Richard J. Lindsay
- Oak Ridge National Laboratory; Center for Molecular Biophysics; Oak Ridge Tennessee 37830
- Department of Biochemistry and Cellular & Molecular Biology; University of Tennessee; Knoxville Tennessee 37996
| | - Ricky B. Nellas
- Institute of Chemistry, University of the Philippines Diliman; Quezon City Philippines
| | - Tongye Shen
- Oak Ridge National Laboratory; Center for Molecular Biophysics; Oak Ridge Tennessee 37830
- Department of Biochemistry and Cellular & Molecular Biology; University of Tennessee; Knoxville Tennessee 37996
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Nguyen D, Helms V, Lee PH. PRIMSIPLR: Prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins. Proteins 2014; 82:1503-11. [DOI: 10.1002/prot.24520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/08/2014] [Accepted: 01/16/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Duy Nguyen
- Center for Bioinformatics; Saarland University; D-66041 Saarbrücken Germany
| | - Volkhard Helms
- Center for Bioinformatics; Saarland University; D-66041 Saarbrücken Germany
| | - Po-Hsien Lee
- Center for Bioinformatics; Saarland University; D-66041 Saarbrücken Germany
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Benkaidali L, Andre F, Maouche B, Siregar P, Benyettou M, Maurel F, Petitjean M. Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models. Bioinformatics 2013; 30:792-800. [DOI: 10.1093/bioinformatics/btt644] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu CM, Otyepka M, Koča J. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform 2013; 5:39. [PMID: 23953065 PMCID: PMC3765717 DOI: 10.1186/1758-2946-5-39] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/13/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. RESULTS We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. CONCLUSION Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz.
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Affiliation(s)
- David Sehnal
- National Centre for Biomolecular Research, Faculty of Science and CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.
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Johnson QR, Nellas RB, Shen T. Solvent-Dependent Gating Motions of an Extremophilic Lipase from Pseudomonas aeruginosa. Biochemistry 2012; 51:6238-45. [DOI: 10.1021/bi300557y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Quentin R. Johnson
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville,
Tennessee 37996, United States
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37830, United States
| | - Ricky B. Nellas
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37830, United States
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Tongye Shen
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37830, United States
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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Berka K, Hanák O, Sehnal D, Banás P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vareková R, Koca J, Otyepka M. MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res 2012; 40:W222-7. [PMID: 22553366 PMCID: PMC3394309 DOI: 10.1093/nar/gks363] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.
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Affiliation(s)
- Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
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