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Nikolova V, Dobrev S, Kircheva N, Yordanova V, Dudev T, Angelova S. Host-guest complexation of cucurbit[7]uril and cucurbit[8]uril with the antimuscarinic drugs tropicamide and atropine. J Mol Graph Model 2023; 119:108380. [PMID: 36455472 DOI: 10.1016/j.jmgm.2022.108380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/30/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Cucurbiturils are useful excipients in eye drop formulations: they can increase the water solubility of the drug, enhance drug absorption into the eye, improve aqueous stability and reduce local irritation. Effective and safe drug delivery is, however, a challenge and the information on the host (CBs)/guest (tropicamide and atropine) interactions can help improving the existing treatments and develop novel therapies not limited only to eye diseases/conditions. Since this carrier system can easily modify the properties of the drug and ensure its delivery at the targeted ocular tissue, further insight into the intimate mechanism of the host-guest recognition is crucial. The present DFT/SMD study focuses on the role of numerous factors governing this process, namely the specific position of the guest molecule in the cavity of the cucurbituril, the ionization form (non/protonated) of the antimuscarinic drug, the dielectric constant of the medium, and the size of the cavitant pore. The obtained results are in line with experimental observations and shed light on the mechanism, at atomic resolution, of recognition between the CBs and the two parasympatholytic drugs.
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Affiliation(s)
- Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria
| | - Nikoleta Kircheva
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria
| | - Victoria Yordanova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164, Sofia, Bulgaria.
| | - Silvia Angelova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria.
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2
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Auras S, Trapp O. Scorpio‐Ligand: Synthesis of Biphenyl‐Dihydroazepine Phosphoramidite Ligands for Asymmetric Hydrogenation. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stefanie Auras
- Department of Chemistry Ludwig Maximilian University Munich Butenandtstr. 5–13 DE-81377 Munich Germany
| | - Oliver Trapp
- Department of Chemistry Ludwig Maximilian University Munich Butenandtstr. 5–13 DE-81377 Munich Germany
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3
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Ozcelik A, Pereira-Cameselle R, Alonso-Gómez JL. From Allenes to Spirobifluorenes: On the Way to Device-compatible Chiroptical Systems. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999201013164534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The last decade has seen a huge growth in the construction of chiral systems to
expand the scope of chiroptical applications. Dependence of chiroptical response on molecular
conformation typically leads to low chiroptical intensities of chiral systems that feature
several conformations in solution. In this respect, allenes were employed for the preparation
of open and cyclic oligomers as well as molecular cages, presenting remarkable chiroptical
responses in solution. Their molecular chirality was also transferred to metal surfaces, yet
photoisomerization of allenes limited their further exploration. In search of a more robust
chiral axis, theoretical and experimental studies confirmed that spirobifluorenes could give
rise to stable systems with tailored optical and chiroptical properties. Additionally, incorporating
a conformational lock into spirobifluorene cyclic architectures served as an efficient
strategy towards the generation of distinct helical molecular orbitals. This review article outlines our results on developing
device-compatible chiroptical systems through axially chiral allenes and spirobifluorenes. The contribution
from other research groups is presented briefly.
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Affiliation(s)
- Ani Ozcelik
- Department of Organic Chemistry, Faculty of Chemistry, University of Vigo, Vigo, Spain
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4
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Elder FCT, Feil EJ, Snape J, Gaze WH, Kasprzyk-Hordern B. The role of stereochemistry of antibiotic agents in the development of antibiotic resistance in the environment. ENVIRONMENT INTERNATIONAL 2020; 139:105681. [PMID: 32251898 DOI: 10.1016/j.envint.2020.105681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/28/2020] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance (ABR) is now recognised as a serious global health and economic threat that is most efficiently managed via a 'one health' approach incorporating environmental risk assessment. Although the environmental dimension of ABR has been largely overlooked, recent studies have underlined the importance of non-clinical settings in the emergence and spread of resistant strains. Despite this, several research gaps remain in regard to the development of a robust and fit-for-purpose environmental risk assessment for ABR drivers such as antibiotics (ABs). Here we explore the role the environment plays in the dissemination of ABR within the context of stereochemistry and its particular form, enantiomerism. Taking chloramphenicol as a proof of principle, we argue that stereoisomerism of ABs impacts on biological properties and the mechanisms of resistance and we discuss more broadly the importance of stereochemistry (enantiomerism in particular) with respect to antimicrobial potency and range of action.
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Affiliation(s)
- Felicity C T Elder
- Department of Chemistry, University of Bath, BA27AY Bath, United Kingdom
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA27AY Bath, United Kingdom
| | - JasoN Snape
- AstraZeneca Global Safety, Health and Environment, Mereside, Macclesfield SK10, 4TG, United Kingdom
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, Cornwall TR1 3HD, United Kingdom
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5
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About the Misleading Use of Stereodescriptors in Labeling the Stereoisomers of Milnacipran and Levomilnacipran. J Clin Psychopharmacol 2020; 39:673-674. [PMID: 31688383 DOI: 10.1097/jcp.0000000000001116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Ballard A, Narduolo S, Ahmed HO, Keymer NI, Asaad N, Cosgrove DA, Buurma NJ, Leach AG. Racemisation in Chemistry and Biology. Chemistry 2020; 26:3661-3687. [PMID: 31709642 DOI: 10.1002/chem.201903917] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Indexed: 11/09/2022]
Abstract
The two enantiomers of a compound often have profoundly different biological properties and thus their liability to racemisation in aqueous solutions is an important piece of information. The authors reviewed the available data concerning the process of racemisation in vivo, in the presence of biological molecules (e.g., racemase enzymes, serum albumin, cofactors and derivatives) and under purely chemical but aqueous conditions (acid, base and other aqueous systems). Mechanistic studies are described critically in light of reported kinetic data. The types of experimental measurement that can be used to effectively determine rate constants of racemisation in various conditions are discussed and the data they provide is summarised. The proposed origins of enzymatic racemisation are presented and suggest ways to promote the process that are different from processes taking place in bulk water. Experimental and computational studies that provide understanding and quantitative predictions of racemisation risk are also presented.
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Affiliation(s)
- Andrew Ballard
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Stefania Narduolo
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Hiwa O Ahmed
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK.,Pharmaceutical Chemistry Department, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Nathaniel I Keymer
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Nabil Asaad
- AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | | | - Niklaas J Buurma
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
| | - Andrew G Leach
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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7
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Saied KF, Abdelwahab SS, Hashem HE, Kandeel KA. Advancements in synthesis of pharmacologically active imidazolidin‐4‐ones and stereochemistry of their Reactions with some Reagents. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Khaled F. Saied
- Basic Science Department, Faculty of Oral and Dental MedicineNahda University Beni‐Suef Egypt
| | - Salwa S. Abdelwahab
- Faculty of Pharmaceutical Sciences and Pharmaceutical industriesFuture University Cairo Egypt
| | - Heba E. Hashem
- Department of Chemistry, Faculty of WomenAin Shams University Cairo Egypt
| | - Kamal A. Kandeel
- Department of Chemistry, Faculty of SinceAin Shams University Cairo Egypt
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8
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Ballard A, Narduolo S, Ahmad HO, Cosgrove DA, Leach AG, Buurma NJ. The problem of racemization in drug discovery and tools to predict it. Expert Opin Drug Discov 2019; 14:527-539. [PMID: 30882254 DOI: 10.1080/17460441.2019.1588881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Racemization has long been an ignored risk in drug development, probably because of a lack of convenient access to good tools for its detection and an absence of methods to predict racemization risk. As a result, the potential effects of racemization have been systematically underestimated. Areas covered: Herein, the potential effects of racemization are discussed through a review of drugs for which activity and side effects for both enantiomers are known. Subsequently, drugs known to racemize are discussed and the authors review methods to predict racemization risk. Application of a method quantitatively predicting racemization risk to databases of compounds from the medicinal chemistry literature shows that success in clinical trials is negatively correlated with racemization risk. Expert opinion: It is envisioned that a quantitative method of predicting racemization risk will remove a blind spot from the drug development pipeline. Removal of the blind spot will make drug development more efficient and result in less late-stage attrition of the drug pipeline.
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Affiliation(s)
- Andrew Ballard
- a Physical Organic Chemistry Centre , School of Chemistry, Cardiff University , Cardiff , UK
| | - Stefania Narduolo
- a Physical Organic Chemistry Centre , School of Chemistry, Cardiff University , Cardiff , UK
| | - Hiwa O Ahmad
- a Physical Organic Chemistry Centre , School of Chemistry, Cardiff University , Cardiff , UK.,b Pharmaceutical Chemistry Department , College of Pharmacy, Hawler Medical University , Erbil , Kurdistan Region , Iraq
| | | | - Andrew G Leach
- d School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - Niklaas J Buurma
- a Physical Organic Chemistry Centre , School of Chemistry, Cardiff University , Cardiff , UK
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9
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A new fundamental type of conformational isomerism. Nat Chem 2018; 10:615-624. [PMID: 29784991 DOI: 10.1038/s41557-018-0043-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/08/2018] [Indexed: 11/08/2022]
Abstract
Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term 'akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.
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10
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Barabás B, Kurdi R, Zucchi C, Pályi G. Isotope chirality in long-armed multifunctional organosilicon ("Cephalopod") molecules. Chirality 2018; 30:913-922. [PMID: 29733469 DOI: 10.1002/chir.22865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 01/10/2023]
Abstract
Long-armed multifunctional organosilicon molecules display self-replicating and self-perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry.
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Affiliation(s)
- Béla Barabás
- Department of Mathematics, University of Technology and Economics, Budapest, Hungary
| | - Róbert Kurdi
- Institute of Environmental Engineering, University of Pannonia, Veszprém, Hungary
| | - Claudia Zucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Gyula Pályi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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11
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Testa B. Emergent chemodiversity: The case of stereoisomerism in acyclic alkanes. Chirality 2017; 29:415-421. [PMID: 28675534 DOI: 10.1002/chir.22718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 11/07/2022]
Abstract
The objective of this pen-and-paper study is to witness the emergence of stereoisomeric properties when comparing lower to higher families of homologs. Specifically, the study compares all acyclic hexanes (five constitutional isomers, a.k.a. regioisomers), all nine heptanes, all 18 octanes, all 35 nonanes, and all 75 decanes. The first part of the work examines the nature and number of stereoisomeric properties seen to emerge in chemical structures featuring one chiral center (i.e., enantiomerism) or two such centers, in which case more complex stereoisomeric features emerge (enantiomerism, diastereoisomerism, pseudoasymmetry, and meso-isomers). The first emergence of chirality (i.e., enantiomerism) occurred in some heptanes. Diastereoisomerism and meso-isomers appear with some octanes, while a pseudoasymmetric center exists in a decane regioisomer. The second part of the work is an attempt to rationalize the numbers of regioisomers, chiral centers, and stereoisomers as these numbers grow from one family of regioisomers to the higher ones. Far from being random, such increases prove regular and ordered.
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Affiliation(s)
- Bernard Testa
- Department of Pharmacy, Lausanne University Hospital, Lausanne, Switzerland
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12
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Mannige RV. An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h). PeerJ 2017; 5:e3327. [PMID: 28533975 PMCID: PMC5436576 DOI: 10.7717/peerj.3327] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/18/2017] [Indexed: 12/19/2022] Open
Abstract
The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ = − 100° left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.
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Affiliation(s)
- Ranjan V Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Multiscale Institute, Redwood City, CA, United States
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13
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Testa B, Vistoli G, Pedretti A. Mechanisms and pharmaceutical consequences of processes of stereoisomerisation — A didactic excursion. Eur J Pharm Sci 2016; 88:101-23. [DOI: 10.1016/j.ejps.2016.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 11/29/2022]
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14
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Walz S, Weis S, Franz M, Rominger F, Trapp O. Investigation of the enantiomerization barriers of the phthalimidone derivatives EM12 and lenalidomide by dynamic electrokinetic chromatography. Electrophoresis 2015; 36:796-804. [DOI: 10.1002/elps.201400499] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Sarah Walz
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Heidelberg Germany
| | - Sylvia Weis
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Heidelberg Germany
| | - Mareike Franz
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Heidelberg Germany
| | - Frank Rominger
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Heidelberg Germany
| | - Oliver Trapp
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Heidelberg Germany
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15
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Abstract
Stereochemical factors are known to play a significant role in the metabolism of drugs and other xenobiotics. Following Prelog's lead, types of metabolic stereoselectivity can be categorized as (i) substrate stereoselectivity (the differential metabolism of two or more stereoisomeric substrates) and (ii) product stereoselectivity (the differential formation of two or more stereoisomeric metabolites from a single substrate). Combinations of the two categories exist as (iii) substrate-product stereoselectivities, meaning that product stereoselectivity itself is substrate stereoselective. Here, published examples of metabolic stereoselectivities are examined in the light of these concepts. In parallel, a graphical scheme is presented with a view to facilitate learning and help researchers to solve classification problems.
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Affiliation(s)
- Bernard Testa
- Department of Pharmacy, Lausanne University Hospital , Lausanne , Switzerland
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16
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Testa B, Vistoli G, Pedretti A. Small Molecules as Exemplars of Emergent Properties and Diversification into the ‘Adjacent Possible’. Chem Biodivers 2014; 11:1309-29. [DOI: 10.1002/cbdv.201400177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Indexed: 11/11/2022]
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