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Rosenberger L, Jenniches J, von Essen C, Khutia A, Kühn C, Marx A, Georgi K, Hirsch AKH, Hartmann RW, Badolo L. Metabolic profiling of S-praziquantel: Structure elucidation using the crystalline sponge method in combination with mass spectrometry and nuclear magnetic resonance. Drug Metab Dispos 2022; 50:320-326. [PMID: 35115299 DOI: 10.1124/dmd.121.000663] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/15/2022] [Indexed: 11/22/2022] Open
Abstract
Praziquantel (PZQ) is the drug of choice for treatment of the neglected tropical disease schistosomiasis. Although the drug has been extensively used over several decades and its metabolism well studied (several oxidative metabolites are known from literature), the knowledge of the complete structure of some of its metabolites remains elusive. Conventional techniques like nuclear magnetic resonance (NMR) or liquid chromatography mass spectrometry (LC-MS) were used in the past to investigate phase I and phase II metabolites of PZQ. These techniques are either limited to provide the complete molecular structure (LC-MS) or require large amount of sample material (NMR), which are not always available when in vitro systems are used for investigation of the metabolites. In this study, we describe new structures of S-PZQ metabolites generated in vitro from human liver microsomes (HLM) using the crystalline sponge method (CS-XRD). After chromatographic separation and purification of the oxidative metabolites, ultra-performance liquid chromatography (UPLC)-quadrupole time-of-flight mass spectrometry (qTOF) analysis was conducted to narrow down the position of oxidation to a certain part of the molecule. To determine the exact position of hydroxylation, singe-crystal X-ray diffraction (SC-XRD) analysis of the crystalline sponges (CS) and absorbed analyte was used to identify the structure of S-PZQ and its metabolites. CS-XRD allowed for complete structure elucidation of the known metabolites S-trans-4'-hydroxy PZQ (M1), S-cis-4'-hydroxy PZQ (M2) and S-/R-11b-hydroxy PZQ (M6) as well as the unknown metabolites S-9-hydroxy PZQ (M3) and S-7-hydroxy S-PZQ (M4). For comparison of structural elucidation techniques, one metabolite (M3) was additionally analyzed using NMR. Significance Statement The information content of the metabolic pathway of praziquantel is still limited. The crystalline sponge method allowed the complete structural elucidation of three known and two unknown metabolites of S-praziquantel, using only trace amounts of analyte material, as demonstrated in this study.
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Affiliation(s)
| | | | | | | | | | | | | | - Anna K H Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland, Germany
| | - Rolf W Hartmann
- Helmholtz-Institute for Pharmaceutical Research Saarland, Germany
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Rosenberger L, von Essen C, Khutia A, Kühn C, Georgi K, Hirsch AKH, Hartmann RW, Badolo L. Crystalline sponge affinity screening: A fast tool for soaking condition optimization without the need of X-ray diffraction analysis. Eur J Pharm Sci 2021; 164:105884. [PMID: 34161782 DOI: 10.1016/j.ejps.2021.105884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 11/28/2022]
Abstract
Structural elucidation of small molecules only available in low quantity (nanogram) is one of the big advantages of the crystalline sponge method. The optimization of various soaking parameters is crucial for effective analyte absorption and repetitive positioning in the pores of the crystal. Time-consuming X-ray diffraction measurements are necessary for data collection and confirmation of successful guest inclusion. In this work, we report a screening method to select optimal soaking conditions without the need of single-crystal X-ray diffraction analysis for individual compounds and mixtures. 14 substances were chosen as test compounds. Parallel guest soaking of individual compounds and mixtures was conducted using various soaking conditions. After evaporation of solvent, excessive material was removed, and guest molecules released through dissolution of the framework. Liquid chromatography-tandem mass spectrometry allowed the estimation of analyte trapped in the pores and the selection of optimal soaking condition dependent on the highest amount of analyte to crystal size (affinity factor). The tool allowed subsequent crystallographic analysis of ten compounds with minimal experiment time. Additionally, a study to examine the lower limit of detection of the crystalline sponge method was conducted. Determination of two target analytes was possible using only 5 ng of sample. Our study shows the potential of an affinity screening to prioritize soaking parameters by estimation of the guest concentration in a single crystal for one or multiple target compounds within a short period of time.
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Affiliation(s)
- Lara Rosenberger
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany; Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Carolina von Essen
- Innovation Center, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Anupam Khutia
- Innovation Center, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Clemens Kühn
- Innovation Center, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany.
| | - Katrin Georgi
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Anna K H Hirsch
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf W Hartmann
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Lassina Badolo
- Discovery and Development Technologies (DDTech), Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
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Rosenberger L, von Essen C, Khutia A, Kühn C, Urbahns K, Georgi K, Hartmann RW, Badolo L. Crystalline Sponges as a Sensitive and Fast Method for Metabolite Identification: Application to Gemfibrozil and its Phase I and II Metabolites. Drug Metab Dispos 2020; 48:587-593. [DOI: 10.1124/dmd.120.091140] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/20/2020] [Indexed: 11/22/2022] Open
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Sakurai F, Khutia A, Kikuchi T, Fujita M. X‐ray Structure Analysis of N‐Containing Nucleophilic Compounds by the Crystalline Sponge Method. Chemistry 2017; 23:15035-15040. [DOI: 10.1002/chem.201704176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Fumie Sakurai
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
| | - Anupam Khutia
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubara-cho Tokyo Akishima-shi 196–8628 Japan
| | - Makoto Fujita
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
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Abstract
Crystalline sponges are porous metal complexes that can absorb and orient common organic molecules in their pores and make them observable by conventional X-ray structure analysis (crystalline sponge method). In this study, all of the steps in the crystalline sponge method, including sponge crystal preparation, pore-solvent exchange, guest soaking, data collection and crystallographic analysis, are carefully examined and thoroughly optimized to provide reliable and meaningful chemical information as chemical crystallography. Major improvements in the method have been made in the guest-soaking and data-collection steps. In the soaking step, obtaining a high site occupancy of the guest is particularly important, and dominant parameters for guest soaking (e.g. temperature, time, concentration, solvents) therefore have to be optimized for every sample compound. When standard conditions do not work, a high-throughput method is useful for efficiently optimizing the soaking conditions. The X-ray experiments are also carefully re-examined. Significant improvement of the guest data quality is achieved by complete data collection at high angle regions. The appropriate disorder treatment of the most flexible ZnI2 portions of the host framework and refinement of the solvents filling the remaining void are also particularly important for obtaining better data quality. A benchmark test for the crystalline sponge method toward an achiral molecule is proposed with a guaiazulene guest, in which the guest structure (with ∼ 100% site occupancy) is refined without applying any restraints or constraints. The obtained data quality with R int = 0.0279 and R 1 = 0.0379 is comparable with that of current conventional crystallographic analysis for small molecules. Another benchmark test for this method toward a chiral molecule is also proposed with a santonin guest. The crystallographic data obtained [R int = 0.0421, R 1 = 0.0312, Flack (Parsons) = -0.0071 (11)] represents the potential ability of this method for reliable absolute structure determination.
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Affiliation(s)
- Manabu Hoshino
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Anupam Khutia
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hongzhu Xing
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuhide Inokuma
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Herbst A, Khutia A, Janiak C. Brønsted Instead of Lewis Acidity in Functionalized MIL-101Cr MOFs for Efficient Heterogeneous (nano-MOF) Catalysis in the Condensation Reaction of Aldehydes with Alcohols. Inorg Chem 2014; 53:7319-33. [DOI: 10.1021/ic5006456] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Annika Herbst
- Institut
für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Anupam Khutia
- Institut
für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Christoph Janiak
- Institut
für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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Khutia A, Shen WZ, Das N, Sanz Miguel PJ, Lippert B. Rationalizing the formation and versatility of multinuclear metal complexes of bis(1-methyluracil-5-yl)methane as hybrids between classical calix[n]arenes and metallacalixaromatics. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.01.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Khutia A, Janiak C. Programming MIL-101Cr for selective and enhanced CO2adsorption at low pressure by postsynthetic amine functionalization. Dalton Trans 2014; 43:1338-47. [DOI: 10.1039/c3dt52365a] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jeremias F, Khutia A, Henninger SK, Janiak C. MIL-100(Al, Fe) as water adsorbents for heat transformation purposes—a promising application. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm15615f] [Citation(s) in RCA: 295] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Khutia A, Sanz Miguel PJ, Lippert B. “Directed” Assembly of Metallacalix[n]arenes with Pyrimidine Nucleobase Ligands of Low Symmetry: Metallacalix[n]arene Derivatives of cis-[a2M(cytosine-N3)2]2+ (M=PtII, PdII; n=4 and 6). Chemistry 2011; 17:4195-204. [DOI: 10.1002/chem.201002722] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Indexed: 11/06/2022]
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Khutia A, Sanz Miguel PJ, Lippert B. “Directed” Assembly of Metallacalix[n]arenes with Pyrimidine Nucleobase Ligands of Low Symmetry: Interchanging Metals in Mixed-Metal Metallacalix[4]arenes and Incorporating Additional Metals at the Exocyclic Groups. Chemistry 2011; 17:4205-16. [DOI: 10.1002/chem.201002723] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Indexed: 11/05/2022]
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Khutia A, Miguel PJS, Lippert B. Influence of PtII and PdII coordination on the equilibrium of 2,2′-dipyridylketone (dpk) with its hydrated gem-diol form (dpk·H2O). Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2010.02.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Khutia A, Sanz Miguel PJ, Lippert B. Isomerism with Metallacalix[4]arenes of the Nonsymmetrical Pyrimidine Nucleobase Cytosine: How Connectivity and Rotamer State Determine the Topology of Multinuclear Derivatives. Inorg Chem 2010; 49:7635-7. [DOI: 10.1021/ic100794s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anupam Khutia
- Fakultät Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
| | | | - Bernhard Lippert
- Fakultät Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
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Das N, Sanz Miguel PJ, Khutia A, Lazar M, Lippert B. Hybrids between classical and metallacalix[4]arenes based on uracil and cis-PtIIL2 entities (L = P(Ph)3 or L2 = 2,2′-bipyridine). Dalton Trans 2009:9120-2. [DOI: 10.1039/b916178n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Joseph R, Ramanujam B, Acharya A, Khutia A, Rao CP. Experimental and Computational Studies of Selective Recognition of Hg2+ by Amide Linked Lower Rim 1,3-Dibenzimidazole Derivative of Calix[4]arene: Species Characterization in Solution and that in the Isolated Complex, Including the Delineation of the Nanostructures. J Org Chem 2008; 73:5745-58. [DOI: 10.1021/jo800073g] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [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)
- Roymon Joseph
- Department of Chemistry Indian Institute of Technology Bombay,Powai,Mumbai 400076,India
| | - Balaji Ramanujam
- Department of Chemistry Indian Institute of Technology Bombay,Powai,Mumbai 400076,India
| | - Amitabha Acharya
- Department of Chemistry Indian Institute of Technology Bombay,Powai,Mumbai 400076,India
| | - Anupam Khutia
- Department of Chemistry Indian Institute of Technology Bombay,Powai,Mumbai 400076,India
| | - Chebrolu P. Rao
- Department of Chemistry Indian Institute of Technology Bombay,Powai,Mumbai 400076,India
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