1
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Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, Zubatyuk R, Bosko IP, Furs KV, Karpenko AD, Kornoushenko YV, Shuldau M, Yushkevich A, Benabderrahmane MB, Bousquet-Melou P, Bureau R, Charton B, Cirou BC, Gil G, Allen WJ, Sirimulla S, Watowich S, Antonopoulos N, Epitropakis N, Krasoulis A, Itsikalis V, Theodorakis S, Kozlovskii I, Maliutin A, Medvedev A, Popov P, Zaretckii M, Eghbal-Zadeh H, Halmich C, Hochreiter S, Mayr A, Ruch P, Widrich M, Berenger F, Kumar A, Yamanishi Y, Zhang KYJ, Bengio E, Bengio Y, Jain MJ, Korablyov M, Liu CH, Marcou G, Glaab E, Barnsley K, Iyengar SM, Ondrechen MJ, Haupt VJ, Kaiser F, Schroeder M, Pugliese L, Albani S, Athanasiou C, Beccari A, Carloni P, D'Arrigo G, Gianquinto E, Goßen J, Hanke A, Joseph BP, Kokh DB, Kovachka S, Manelfi C, Mukherjee G, Muñiz-Chicharro A, Musiani F, Nunes-Alves A, Paiardi G, Rossetti G, Sadiq SK, Spyrakis F, Talarico C, Tsengenes A, Wade RC, Copeland C, Gaiser J, Olson DR, Roy A, Venkatraman V, Wheeler TJ, Arthanari H, Blaschitz K, Cespugli M, Durmaz V, Fackeldey K, Fischer PD, Gorgulla C, Gruber C, Gruber K, Hetmann M, Kinney JE, Padmanabha Das KM, Pandita S, Singh A, Steinkellner G, Tesseyre G, Wagner G, Wang ZF, Yust RJ, Druzhilovskiy DS, Filimonov DA, Pogodin PV, Poroikov V, Rudik AV, Stolbov LA, Veselovsky AV, De Rosa M, De Simone G, Gulotta MR, Lombino J, Mekni N, Perricone U, Casini A, Embree A, Gordon DB, Lei D, Pratt K, Voigt CA, Chen KY, Jacob Y, Krischuns T, Lafaye P, Zettor A, Rodríguez ML, White KM, Fearon D, Von Delft F, Walsh MA, Horvath D, Brooks CL, Falsafi B, Ford B, García-Sastre A, Yup Lee S, Naffakh N, Varnek A, Klambauer G, Hermans TM. A community effort in SARS-CoV-2 drug discovery. Mol Inform 2024; 43:e202300262. [PMID: 37833243 DOI: 10.1002/minf.202300262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against COVID-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.
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2
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Hetmann M, Langner C, Durmaz V, Cespugli M, Köchl K, Krassnigg A, Blaschitz K, Groiss S, Loibner M, Ruau D, Zatloukal K, Gruber K, Steinkellner G, Gruber CC. Identification and validation of fusidic acid and flufenamic acid as inhibitors of SARS-CoV-2 replication using DrugSolver CavitomiX. Sci Rep 2023; 13:11783. [PMID: 37479788 PMCID: PMC10362000 DOI: 10.1038/s41598-023-39071-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023] Open
Abstract
In this work, we present DrugSolver CavitomiX, a novel computational pipeline for drug repurposing and identifying ligands and inhibitors of target enzymes. The pipeline is based on cavity point clouds representing physico-chemical properties of the cavity induced solely by the protein. To test the pipeline's ability to identify inhibitors, we chose enzymes essential for SARS-CoV-2 replication as a test system. The active-site cavities of the viral enzymes main protease (Mpro) and papain-like protease (Plpro), as well as of the human transmembrane serine protease 2 (TMPRSS2), were selected as target cavities. Using active-site point-cloud comparisons, it was possible to identify two compounds-flufenamic acid and fusidic acid-which show strong inhibition of viral replication. The complexes from which fusidic acid and flufenamic acid were derived would not have been identified using classical sequence- and structure-based methods as they show very little structural (TM-score: 0.1 and 0.09, respectively) and very low sequence (~ 5%) identity to Mpro and TMPRSS2, respectively. Furthermore, a cavity-based off-target screening was performed using acetylcholinesterase (AChE) as an example. Using cavity comparisons, the human carboxylesterase was successfully identified, which is a described off-target for AChE inhibitors.
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Affiliation(s)
- M Hetmann
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - C Langner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - V Durmaz
- Innophore, San Francisco, CA, USA
| | | | - K Köchl
- Innophore, San Francisco, CA, USA
| | | | | | - S Groiss
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - M Loibner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - D Ruau
- NVIDIA, Santa Clara, CA, USA
| | - K Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - K Gruber
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - G Steinkellner
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - C C Gruber
- Innophore, San Francisco, CA, USA.
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
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3
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Köchl K, Schopper T, Durmaz V, Parigger L, Singh A, Krassnigg A, Cespugli M, Wu W, Yang X, Zhang Y, Wang WWS, Selluski C, Zhao T, Zhang X, Bai C, Lin L, Hu Y, Xie Z, Zhang Z, Yan J, Zatloukal K, Gruber K, Steinkellner G, Gruber CC. Optimizing variant-specific therapeutic SARS-CoV-2 decoys using deep-learning-guided molecular dynamics simulations. Sci Rep 2023; 13:774. [PMID: 36641503 PMCID: PMC9840421 DOI: 10.1038/s41598-023-27636-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
Treatment of COVID-19 with a soluble version of ACE2 that binds to SARS-CoV-2 virions before they enter host cells is a promising approach, however it needs to be optimized and adapted to emerging viral variants. The computational workflow presented here consists of molecular dynamics simulations for spike RBD-hACE2 binding affinity assessments of multiple spike RBD/hACE2 variants and a novel convolutional neural network architecture working on pairs of voxelized force-fields for efficient search-space reduction. We identified hACE2-Fc K31W and multi-mutation variants as high-affinity candidates, which we validated in vitro with virus neutralization assays. We evaluated binding affinities of these ACE2 variants with the RBDs of Omicron BA.3, Omicron BA.4/BA.5, and Omicron BA.2.75 in silico. In addition, candidates produced in Nicotiana benthamiana, an expression organism for potential large-scale production, showed a 4.6-fold reduction in half-maximal inhibitory concentration (IC50) compared with the same variant produced in CHO cells and an almost six-fold IC50 reduction compared with wild-type hACE2-Fc.
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Affiliation(s)
- Katharina Köchl
- Innophore GmbH, 8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria
| | | | | | | | - Amit Singh
- Innophore GmbH, 8010, Graz, Austria
- Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria
| | | | | | - Wei Wu
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Xiaoli Yang
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Yanchong Zhang
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Welson Wen-Shang Wang
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Crystal Selluski
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Tiehan Zhao
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Xin Zhang
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Caihong Bai
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Leon Lin
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Yuxiang Hu
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Zhiwei Xie
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Zaihui Zhang
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Jun Yan
- SignalChem Lifesciences Corp., 110-13120 Vanier Place, Richmond, BC, V6V 2J2, Canada
| | - Kurt Zatloukal
- Diagnostic- and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, 8010, Graz, Austria
| | - Karl Gruber
- Innophore GmbH, 8010, Graz, Austria
- Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010, Graz, Austria
| | - Georg Steinkellner
- Innophore GmbH, 8010, Graz, Austria.
- Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, 8010, Graz, Austria.
| | - Christian C Gruber
- Innophore GmbH, 8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria.
- Institute of Molecular Bioscience, University of Graz, 8010, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, 8010, Graz, Austria.
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4
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Durmaz V, Köchl K, Krassnigg A, Parigger L, Hetmann M, Singh A, Nutz D, Korsunsky A, Kahler U, König C, Chang L, Krebs M, Bassetto R, Pavkov-Keller T, Resch V, Gruber K, Steinkellner G, Gruber CC. Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference. Sci Rep 2022; 12:14534. [PMID: 36008461 PMCID: PMC9406262 DOI: 10.1038/s41598-022-18507-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/08/2022] [Indexed: 01/16/2023] Open
Abstract
To date, more than 263 million people have been infected with SARS-CoV-2 during the COVID-19 pandemic. In many countries, the global spread occurred in multiple pandemic waves characterized by the emergence of new SARS-CoV-2 variants. Here we report a sequence and structural-bioinformatics analysis to estimate the effects of amino acid substitutions on the affinity of the SARS-CoV-2 spike receptor binding domain (RBD) to the human receptor hACE2. This is done through qualitative electrostatics and hydrophobicity analysis as well as molecular dynamics simulations used to develop a high-precision empirical scoring function (ESF) closely related to the linear interaction energy method and calibrated on a large set of experimental binding energies. For the latest variant of concern (VOC), B.1.1.529 Omicron, our Halo difference point cloud studies reveal the largest impact on the RBD binding interface compared to all other VOC. Moreover, according to our ESF model, Omicron achieves a much higher ACE2 binding affinity than the wild type and, in particular, the highest among all VOCs except Alpha and thus requires special attention and monitoring.
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Affiliation(s)
| | | | | | | | - Michael Hetmann
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, 8010, Graz, Austria
| | - Amit Singh
- Innophore GmbH, 8010, Graz, Austria.,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | | | | | | | - Lee Chang
- AWS Diagnostic Development Initiative-Global Social Impact, Seattle, WA, 98109, USA
| | - Marius Krebs
- Amazon Web Services EMEA SARL, 80807, Muenchen, Germany
| | | | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
| | | | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,Field of Excellence BioHealth-University of Graz, 8010, Graz, Austria
| | - Georg Steinkellner
- Innophore GmbH, 8010, Graz, Austria. .,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
| | - Christian C Gruber
- Innophore GmbH, 8010, Graz, Austria. .,Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.
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5
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Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten J, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening. iScience 2021; 24:102021. [PMID: 33426509 PMCID: PMC7783459 DOI: 10.1016/j.isci.2020.102021] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics, and targeting multiple points in the viral life cycle could help tackle the current, as well as future, coronaviruses. Here, we leverage our recently developed, ultra-large-scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kendra E. Leigh
- Max Planck Institute of Biophysics, Frankfurt am Main, Hessen 60438, Germany
| | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Saarland 66123, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | | | | | - Anthony Calderaio
- VirtualFlow Organization, https://virtual-flow.org/, Boston, MA 02115, USA
| | | | - Alexander Rose
- Mol∗ Consortium, https://molstar.org, San Diego, CA 92109, USA
| | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin 14195, Germany
- Institute of Mathematics, Technical University Berlin, Berlin 10587, Germany
| | - J.J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz 8010, Austria
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Ryan Yust
- Google, Mountain View, CA 94043, USA
| | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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6
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Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten JJ, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening. ChemRxiv 2020:12682316. [PMID: 33200116 PMCID: PMC7668741 DOI: 10.26434/chemrxiv.12682316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/24/2020] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | | | | | | | | | | | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Justin J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
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7
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Spahn V, Del Vecchio G, Labuz D, Rodriguez-Gaztelumendi A, Massaly N, Temp J, Durmaz V, Sabri P, Reidelbach M, Machelska H, Weber M, Stein C. A nontoxic pain killer designed by modeling of pathological receptor conformations. Science 2017; 355:966-969. [PMID: 28254944 DOI: 10.1126/science.aai8636] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/30/2017] [Indexed: 12/12/2022]
Abstract
Indiscriminate activation of opioid receptors provides pain relief but also severe central and intestinal side effects. We hypothesized that exploiting pathological (rather than physiological) conformation dynamics of opioid receptor-ligand interactions might yield ligands without adverse actions. By computer simulations at low pH, a hallmark of injured tissue, we designed an agonist that, because of its low acid dissociation constant, selectively activates peripheral μ-opioid receptors at the source of pain generation. Unlike the conventional opioid fentanyl, this agonist showed pH-sensitive binding, heterotrimeric guanine nucleotide-binding protein (G protein) subunit dissociation by fluorescence resonance energy transfer, and adenosine 3',5'-monophosphate inhibition in vitro. It produced injury-restricted analgesia in rats with different types of inflammatory pain without exhibiting respiratory depression, sedation, constipation, or addiction potential.
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Affiliation(s)
- V Spahn
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany
| | - G Del Vecchio
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany
| | - D Labuz
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany
| | - A Rodriguez-Gaztelumendi
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany
| | - N Massaly
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany
| | - J Temp
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany
| | - V Durmaz
- Computational Molecular Design, Zuse-Institut Berlin, Takustrasse 7, Berlin, 14195, Germany
| | - P Sabri
- Computational Molecular Design, Zuse-Institut Berlin, Takustrasse 7, Berlin, 14195, Germany
| | - M Reidelbach
- Computational Molecular Design, Zuse-Institut Berlin, Takustrasse 7, Berlin, 14195, Germany
| | - H Machelska
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany
| | - M Weber
- Computational Molecular Design, Zuse-Institut Berlin, Takustrasse 7, Berlin, 14195, Germany
| | - C Stein
- Department of Anesthesiology and Critical Care Medicine, Charité-Universitätsmedizin Berlin Campus Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 30, Berlin 12203, Germany.
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8
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Heye K, Becker D, Lütke Eversloh C, Durmaz V, Ternes TA, Oetken M, Oehlmann J. Effects of carbamazepine and two of its metabolites on the non-biting midge Chironomus riparius in a sediment full life cycle toxicity test. Water Res 2016; 98:19-27. [PMID: 27064208 DOI: 10.1016/j.watres.2016.03.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 06/05/2023]
Abstract
The antiepileptic drug carbamazepine (CBZ) and its main metabolites carbamazepine-10,11-epoxide (EP-CBZ) and 10,11-dihydro-10,11-dihydroxy-carbamazepine (DiOH-CBZ) were chosen as test substances to assess chronic toxicity on the non-biting midge Chironomus riparius. All the three substances were tested in a 40-day sediment full life cycle test (according to OECD 233) in which mortality, emergence, fertility, and clutch size were evaluated. In addition, these parameters were considered to calculate the population growth rate which represents an integrated measure to assess population relevant effects. With an LC50 of 0.20 mg/kg (time-weighted mean), the metabolite EP-CBZ was significantly more toxic than the parent substance CBZ (LC50: 1.1 mg/kg). Especially mortality, emergence, and fertility showed to be sensitive parameters under the exposure to CBZ and EP-CBZ. By using classical molecular dynamics (MD) simulations, the binding of CBZ to the ecdysone receptor was investigated as one possible mode of action (MoA) but appeared to be unlikely. The second metabolite DiOH-CBZ did not cause any effects within the tested concentration rage (0.17-1.2 mg/kg). Even though CBZ was less toxic compared to EP-CBZ, CBZ is found in the environment at much higher concentrations and therefore causes a higher potential risk for sediment dwelling organisms compared to its metabolites. Nevertheless, the current study illustrates the importance of including commonly found metabolites into the risk assessment of parent substances.
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Affiliation(s)
- Katharina Heye
- Goethe University Frankfurt am Main, Department Aquatic Toxicology, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany.
| | - Dennis Becker
- Goethe University Frankfurt am Main, Department Aquatic Toxicology, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | | | - Vedat Durmaz
- Zuse Institute Berlin (ZIB), Takustraße 7, 14195 Berlin, Germany
| | - Thomas A Ternes
- German Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Matthias Oetken
- Goethe University Frankfurt am Main, Department Aquatic Toxicology, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Goethe University Frankfurt am Main, Department Aquatic Toxicology, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
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9
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Koschek K, Durmaz V, Krylova O, Wieczorek M, Gupta S, Richter M, Bujotzek A, Fischer C, Haag R, Freund C, Weber M, Rademann J. Peptide-polymer ligands for a tandem WW-domain, an adaptive multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands. Beilstein J Org Chem 2015; 11:837-47. [PMID: 26124884 PMCID: PMC4464424 DOI: 10.3762/bjoc.11.93] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 12/22/2022] Open
Abstract
Three polymers, poly(N-(2-hydroxypropyl)methacrylamide) (pHPMA), hyperbranched polyglycerol (hPG), and dextran were investigated as carriers for multivalent ligands targeting the adaptive tandem WW-domain of formin-binding protein (FBP21). Polymer carriers were conjugated with 3–9 copies of the proline-rich decapeptide GPPPRGPPPR-NH2 (P1). Binding of the obtained peptide–polymer conjugates to the tandem WW-domain was investigated employing isothermal titration calorimetry (ITC) to determine the binding affinity, the enthalpic and entropic contributions to free binding energy, and the stoichiometry of binding for all peptide–polymer conjugates. Binding affinities of all multivalent ligands were in the µM range, strongly amplified compared to the monovalent ligand P1 with a KD > 1 mM. In addition, concise differences were observed, pHPMA and hPG carriers showed moderate affinity and bound 2.3–2.8 peptides per protein binding site resulting in the formation of aggregates. Dextran-based conjugates displayed affinities down to 1.2 µM, forming complexes with low stoichiometry, and no precipitation. Experimental results were compared with parameters obtained from molecular dynamics simulations in order to understand the observed differences between the three carrier materials. In summary, the more rigid and condensed peptide–polymer conjugates based on the dextran scaffold seem to be superior to induce multivalent binding and to increase affinity, while the more flexible and dendritic polymers, pHPMA and hPG are suitable to induce crosslinking upon binding.
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Affiliation(s)
- Katharina Koschek
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany ; Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany ; Fraunhofer Institute for Manufacturing Technology and Advanced Materials (IFAM), Wiener Str. 12, 28359 Bremen, Germany
| | - Vedat Durmaz
- Konrad-Zuse-Zentrum für Informationstechnik Berlin, Numerical Analysis and Modelling, Takustr. 7, 14195 Berlin, Germany
| | - Oxana Krylova
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Marek Wieczorek
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany ; Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Shilpi Gupta
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
| | - Martin Richter
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany ; Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Alexander Bujotzek
- Konrad-Zuse-Zentrum für Informationstechnik Berlin, Numerical Analysis and Modelling, Takustr. 7, 14195 Berlin, Germany
| | - Christina Fischer
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
| | - Rainer Haag
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany
| | - Christian Freund
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany ; Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Marcus Weber
- Konrad-Zuse-Zentrum für Informationstechnik Berlin, Numerical Analysis and Modelling, Takustr. 7, 14195 Berlin, Germany
| | - Jörg Rademann
- Institute of Pharmacy & Institute of Chemistry and Biochemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195 Berlin, Germany ; Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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10
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Durmaz V. Markov model-based polymer assembly from force field-parameterized building blocks. J Comput Aided Mol Des 2014; 29:225-32. [PMID: 25428569 DOI: 10.1007/s10822-014-9817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very work-intensive and time-consuming. Using the example of polyglycerol, I present a polymer decomposition strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantum-chemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers.
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Affiliation(s)
- Vedat Durmaz
- Zuse-Institut Berlin, Takustraße 7, Berlin, 14195, Germany,
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11
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Abstract
Small molecules can have a significant effect on human metabolic processes. Computational drug design aims at constructing specialized small molecules that selectively and efficiently address specific proteins. The basic ideas of computational molecular design are presented and it will be shown how a virtual protein can be computer designed. This virtual protein can be used to predict the binding affinity of given small molecules without having to synthesize them in a laboratory. Modern computational drug design goes far beyond the lock and key principle. Possible future developments are discussed and a current successful example of computational drug design in the field of painkiller medication is demonstrated.
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Affiliation(s)
- K Andrae
- Computational Molecular Design, Zuse Institute Berlin (ZIB), Takusstr. 7, 14195, Berlin, Deutschland
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12
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Durmaz V, Schmidt S, Sabri P, Piechotta C, Weber M. Hands-off Linear Interaction Energy Approach to Binding Mode and Affinity Estimation of Estrogens. J Chem Inf Model 2013; 53:2681-8. [DOI: 10.1021/ci400392p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vedat Durmaz
- Department
of Numerical Analysis and Modelling, ZIB Zuse Institute Berlin, 14195 Berlin, Germany
| | - Sebastian Schmidt
- Department
of Analytical Chemistry, BAM Federal Institute for Materials Research and Testing, 12205 Berlin, Germany
| | - Peggy Sabri
- Department
of Numerical Analysis and Modelling, ZIB Zuse Institute Berlin, 14195 Berlin, Germany
| | - Christian Piechotta
- Department
of Analytical Chemistry, BAM Federal Institute for Materials Research and Testing, 12205 Berlin, Germany
| | - Marcus Weber
- Department
of Numerical Analysis and Modelling, ZIB Zuse Institute Berlin, 14195 Berlin, Germany
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13
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Andrae K, Durmaz V, Fackeldey K, Scharkoi O, Weber M. [Medicine from the computer]. Schmerz 2013; 27:409-13. [PMID: 23903763 DOI: 10.1007/s00482-013-1342-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Small molecules can have a significant effect on human metabolic processes. Computational drug design aims at constructing specialized small molecules that selectively and efficiently address specific proteins. The basic ideas of computational molecular design are presented and it will be shown how a virtual protein can be computer designed. This virtual protein can be used to predict the binding affinity of given small molecules without having to synthesize them in a laboratory. Modern computational drug design goes far beyond the lock and key principle. Possible future developments are discussed and a current successful example of computational drug design in the field of painkiller medication is demonstrated.
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Affiliation(s)
- K Andrae
- Computational Molecular Design, Zuse Institute Berlin, Takustr. 7, 14195, Berlin, Deutschland
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14
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Köppen R, Riedel J, Proske M, Drzymala S, Rasenko T, Durmaz V, Weber M, Koch M. Photochemical trans-/cis-isomerization and quantitation of zearalenone in edible oils. J Agric Food Chem 2012; 60:11733-11740. [PMID: 23157684 DOI: 10.1021/jf3037775] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The emphasis of the present work was to investigate the photochemical conversion of trans- to cis-zearalenone in edible oils under real-life conditions. For quantitation purposes a cis-zearalenone standard was synthesized and characterized for its identity and purity (≥95%) by (1)H NMR, X-ray crystallography, HPLC fluorescence and mass spectrometric detection. In a sample survey of 12 edible oils (9 corn oils, 3 hempseed oils) from local supermarkets all corn oils contained trans-zearalenone (median 194 μg/kg), but no cis-zearalenone was detected. For alteration studies trans-zearalenone contaminated corn oils were exposed to sunlight over 4 and 30 weeks, revealing an obvious shift toward cis-zearalenone up to a cis/trans ratio of 9:1 by storage in colorless glass bottles. Irradiation experiments of trans-zearalenone in different organic solvents confirmed the preferred formation of cis-zearalenone possibly caused by entropic effects rather than by enthalpic entities as investigated by quantum chemical and classical force field simulations.
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Affiliation(s)
- Robert Köppen
- Federal Institute for Materials Research and Testing, Richard-Willstätter-Strasse 11, D-12489 Berlin, Germany
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15
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Nagas E, Uyanik O, Durmaz V, Cehreli ZC. Effect of plunger diameter on the push-out bond values of different root filling materials. Int Endod J 2011; 44:950-5. [DOI: 10.1111/j.1365-2591.2011.01913.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Weber M, Becker R, Durmaz V, Köppen R. Classical hybrid Monte-Carlo simulation of the interconversion of hexabromocyclododecane stereoisomers. Molecular Simulation 2008. [DOI: 10.1080/08927020802208968] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Kartal N, Durmaz V. Evaluation of the apical leakage of isobutyl cyanoacrylate when used as a root canal sealant. J Marmara Univ Dent Fac 1990; 1:31-3. [PMID: 2129913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The sealing properties of isobutyl cyanoacrylate were evaluated in extracted single-rooted human teeth. In the experimental group, instrumented root canals were obturated with isobutyl cyanoacrylate and gutta-percha by using the lateral condensation technique. In the control group instrumented root canals were obturated with gutta-percha only. The penetration of radioactive 131I was evaluated by an autoradiographic technique. No leakage was observed in the experimental group. This study shows that isobutyl cyanoacrylate is a good apical sealant.
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Affiliation(s)
- N Kartal
- Faculty of Dentistry, Marmara University, Istanbul, Turkey
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18
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Durmaz V. [Oligodynamic effects of metals]. MIKROBIYOL BUL 1975; 9:321-5. [PMID: 1230638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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