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Belabbes A, Retamosa MG, Foubelo F, Sirvent A, Nájera C, Yus M, Sansano JM. Pseudo-multicomponent 1,3-dipolar cycloaddition involving metal-free generation of unactivated azomethine ylides. Org Biomol Chem 2023; 21:1927-1936. [PMID: 36752549 DOI: 10.1039/d3ob00023k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The pseudo-multicomponent reaction between propargyl amine, an aldehyde and an electron-deficient alkene is described. The C-H activation takes place thermally and allows the obtaining of cycloadducts in very good yields with high diastereoselectivities. The relative configuration is determined by X-ray diffraction analysis of the chiral molecule, obtained as a single diastereoisomer, using a chiral maleimide. A brief study of the stability of the possible ylides involved in the process is also mentioned, confirming the high diastereoselectivity observed. The high functional group density of these cycloadducts permits the synthesis of complex heterocycles. After allylation or propargylation of the pyrrolidine nitrogen atom, RCM-DA cycloaddition or cyclotrimerization with an alkyne is studied, respectively. In this last example, the resulting tetracyclic structures are of potential interest as drugs for the treatment of cystic fibrosis.
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Affiliation(s)
- Asmaa Belabbes
- Departamento de Química Orgánica e Instituto de Síntesis Orgánica (ISO), University of Alicante, E-03080 Alicante, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of Alicante, E-03080 Alicante, Spain
| | - María Gracia Retamosa
- Departamento de Química Orgánica e Instituto de Síntesis Orgánica (ISO), University of Alicante, E-03080 Alicante, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of Alicante, E-03080 Alicante, Spain
| | - Francisco Foubelo
- Departamento de Química Orgánica e Instituto de Síntesis Orgánica (ISO), University of Alicante, E-03080 Alicante, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of Alicante, E-03080 Alicante, Spain
| | - Ana Sirvent
- Departamento de Química Orgánica e Instituto de Síntesis Orgánica (ISO), University of Alicante, E-03080 Alicante, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of Alicante, E-03080 Alicante, Spain
| | - Carmen Nájera
- Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of Alicante, E-03080 Alicante, Spain
| | - Miguel Yus
- Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of Alicante, E-03080 Alicante, Spain
| | - José M Sansano
- Departamento de Química Orgánica e Instituto de Síntesis Orgánica (ISO), University of Alicante, E-03080 Alicante, Spain. .,Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of Alicante, E-03080 Alicante, Spain
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2
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Tsuji K, Ishii T, Kobayakawa T, Higashi-Kuwata N, Azuma C, Nakayama M, Onishi T, Nakano H, Wada N, Hori M, Shinohara K, Miura Y, Kawada T, Hayashi H, Hattori SI, Bulut H, Das D, Takamune N, Kishimoto N, Saruwatari J, Okamura T, Nakano K, Misumi S, Mitsuya H, Tamamura H. Potent and biostable inhibitors of the main protease of SARS-CoV-2. iScience 2022; 25:105365. [PMID: 36338434 PMCID: PMC9623849 DOI: 10.1016/j.isci.2022.105365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
Potent and biostable inhibitors of the main protease (Mpro) of SARS-CoV-2 were designed and synthesized based on an active hit compound 5h (2). Our strategy was based not only on the introduction of fluorine atoms into the inhibitor molecule for an increase of binding affinity for the pocket of Mpro and cell membrane permeability but also on the replacement of the digestible amide bond by a surrogate structure to increase the biostability of the compounds. Compound 3 is highly potent and blocks SARS-CoV-2 infection in vitro without a viral breakthrough. The derivatives, which contain a thioamide surrogate in the P2-P1 amide bond of these compounds (2 and 3), showed remarkably preferable pharmacokinetics in mice compared with the corresponding parent compounds. These data show that compounds 3 and its biostable derivative 4 are potential drugs for treating COVID-19 and that replacement of the digestible amide bond by its thioamide surrogate structure is an effective method.
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Affiliation(s)
- Kohei Tsuji
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takahiro Ishii
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Chika Azuma
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Miyuki Nakayama
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takato Onishi
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroki Nakano
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Naoya Wada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Miki Hori
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kouki Shinohara
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yutaro Miura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuma Kawada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hironori Hayashi
- Department of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Shin-ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nobutoki Takamune
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Junji Saruwatari
- Division of Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Kenta Nakano
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences, Kumamoto University Hospital, Chuo-ku, Kumamoto 860-8556, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
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Kuhn B, Haap W, Obst-Sander U, Kramer C, Stahl M. What We Learned in 25 Years of Interactive Molecular Design Sessions. ChemMedChem 2021; 16:2760-2763. [PMID: 34374230 DOI: 10.1002/cmdc.202100351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/12/2022]
Abstract
We retrace Prof. François Diederich's consultancy work for Roche and its impact over the years he worked with us. François Diederich uniquely shaped our approach to molecular design, and interactions with him and his research group at ETH Zurich have created deep insights into molecular recognition. Herein we share how his style and approach continue to inspire us.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Wolfgang Haap
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Ulrike Obst-Sander
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Christian Kramer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Martin Stahl
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
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4
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Richardson P. Applications of fluorine to the construction of bioisosteric elements for the purposes of novel drug discovery. Expert Opin Drug Discov 2021; 16:1261-1286. [PMID: 34074189 DOI: 10.1080/17460441.2021.1933427] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction There continues to be an exponential rise in the number of small molecule drugs that contain either a fluorine atom or a fluorinated fragment. While the unique properties of fluorine enable the precise modulation of a molecule's physicochemical properties, strategic bioisosteric replacement of fragments with fluorinated moieties represents an area of significant growth.Areas covered This review discusses the strategic employment of fluorine substitution in the design and development of bioisosteres in medicinal chemistry. In addition, the classic exploitation of trifluoroethylamine group as an amide bioisostere is discussed. In each of the case studies presented, emphasis is placed on the context-dependent influence of the fluorinated fragment on the overall properties/binding of the compound of interest.Expert opinion Whereas utilization of bioisosteric replacements to modify molecular structures is commonplace within drug discovery, the overarching lesson to be learned is that the chances of success with this strategy significantly increase as the knowledge of the structure/environment of the biological target grows. Coupled to this, breakthroughs and learnings achieved using bioisosteres within a specific program are context-based, and though may be helpful in guiding future intuition, will not necessarily be directly translated to future programs. Another important point is to bear in mind what implications a structural change based on a bioisosteric replacement will have on the candidate molecule. Finally, the development of new methods and reagents for the controlled regioselective introduction of fluorine and fluorinated moieties into biologically relevant compounds particularly in drug discovery remains a contemporary challenge in organic chemistry.
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5
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Chabour I, Nájera C, Sansano JM. Diastereoselective multicomponent phosphoramidate-aldehyde-dienophile (PAD) process for the synthesis of polysubstituted cyclohex-2-enyl-amine derivatives. Tetrahedron 2020. [DOI: 10.1016/j.tet.2019.130801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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6
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Cai Z, Huang X, He W. Crystal structure of 3-fluoro-3-methyl-1-((2-nitrophenyl)sulfonyl)-5,5-diphenylpiperidine, C24H23FN2O4S. Z KRIST-NEW CRYST ST 2019. [DOI: 10.1515/ncrs-2019-0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractC24H23FN2O4S, orthorhombic, Pbca (no. 19), a = 14.3646(18) Å, b = 15.5927(19) Å, c = 19.645(3) Å, V = 4400.1(10) Å3, Z = 8, Rgt(F) = 0.0349, wRref(F2) = 0.0982, T = 296(2) K.
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Affiliation(s)
- Zedong Cai
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, Xi an 710032, P.R. China
| | - Xie Huang
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, Xi an 710032, P.R. China
| | - Wei He
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, Xi an 710032, P.R. China
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7
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Zhang H, Wan X, Shen Q. Asymmetric Difluoromethylthiolation of Carbon Nucleophiles with Optically Pure Difluoromethylthiolating Reagents Derived from Camphorsultam. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900298] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- He Zhang
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic ChemistryUniversity of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu Shanghai 200032 China
| | - Xiaolong Wan
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic ChemistryUniversity of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu Shanghai 200032 China
| | - Qilong Shen
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic ChemistryUniversity of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu Shanghai 200032 China
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8
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Wade AD, Rizzi A, Wang Y, Huggins DJ. Computational Fluorine Scanning Using Free-Energy Perturbation. J Chem Inf Model 2019; 59:2776-2784. [PMID: 31046267 DOI: 10.1021/acs.jcim.9b00228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We present perturbative fluorine scanning, a computational fluorine scanning approach using free-energy perturbation. This method can be applied to molecular dynamics simulations of a single compound and make predictions for the best binders out of numerous fluorinated analogues. We tested the method on nine test systems: renin, DPP4, menin, P38, factor Xa, CDK2, AKT, JAK2, and androgen receptor. The predictions were in excellent agreement with more rigorous alchemical free-energy calculations and in good agreement with experimental data for most of the test systems. However, the agreement with experiment was very poor in some of the test systems, and this highlights the need for improved force fields in addition to accurate treatment of tautomeric and protonation states. The method is of particular interest due to the wide use of fluorine in medicinal chemistry to improve binding affinity and ADME properties. The promising results on this test case suggest that perturbative fluorine scanning will be a useful addition to the available arsenal of free-energy methods.
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Affiliation(s)
- Alexander D Wade
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Andrea Rizzi
- Tri-Institutional Training Program in Computational Biology and Medicine , New York , New York 10065 , United States.,Computational and Systems Biology Program , Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center , New York , New York 10065 , United States
| | - Yuanqing Wang
- Physiology, Biophysics, and System Biology Program , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - David J Huggins
- TCM Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom.,Tri-Institutional Therapeutics Discovery Institute , Belfer Research Building , 413 East 69th Street, 16th Floor , Box 300, New York , New York 10021 , United States.,Department of Physiology and Biophysics , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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9
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Selva V, Chabour I, Nájera C, Sansano JM. Diastereoselective multicomponent Amine-Aldehyde-Dienophile (AAD) process for the synthesis of polysubstituted cyclohex-2-enylamines. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.01.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Nájera C, Sansano JM. Synthesis of pyrrolizidines and indolizidines by multicomponent 1,3-dipolar cycloaddition of azomethine ylides. PURE APPL CHEM 2018. [DOI: 10.1515/pac-2018-0710] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
Different multicomponent 1,3-dipolar cycloadditions (1,3-DC) of cyclic α-amino acid derivatives with aldehydes and dipolarophiles have been described as efficient and simple methodologies for the synthesis of the pyrrolidine unit of pyrrolizidines and indolizidines. When free cyclic α-amino acids are used, a thermal promoted decarboxylative process generates in situ the corresponding non-stabilized azomethine ylides, which afforded the corresponding pyrrolizidines and indolizidines with a hydrogen in the bicyclic units. This methodology has been employed to the synthesis of complex systems including spiro derivatives when ketones are used as carbonyl component. In addition, working with cyclic α-amino acid derived esters, the three-component 1,3-DC takes place under milder reaction conditions giving the corresponding pyrrolizidines and indolizidines with an alkoxycarbonyl group in the bridge adjacent carbon to the nitrogen. This methodology can be carried out by a double consecutive or stepwise 1,3-DC to provide pyrrolizidines via the precursor prolinates. The conformation of the azomethine ylide controls the endo/exo diastereoselectivity of the 1,3-DC.
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Affiliation(s)
- Carmen Nájera
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Universidad de Alicante , Apdo. 99 , Alicante 03080 , Spain
| | - José Miguel Sansano
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Universidad de Alicante , Apdo. 99 , Alicante 03080 , Spain
- Instituto de Síntesis Orgánica, Universidad de Alicante , Apdo. 99 , Alicante 03080 , Spain
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11
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Sugimoto K. [Development of Novel Preparations for Nitrogen Heterocycles Based on Cascade Reactions]. YAKUGAKU ZASSHI 2018; 138:1151-1161. [PMID: 30175759 DOI: 10.1248/yakushi.18-00122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nitrogen heterocycles are important skeletons in biologically active compounds such as medicines and natural alkaloids. However, in terms of the efficiency of the synthetic process, the many synthetic steps required to achieve the target compounds with complex architectures pose a significant problem. To overcome this challenge, novel approaches were developed to afford biologically active heterocycles, 1,2-diazepines, pyrroloisoquinolines, and pyrrolizidines utilizing cascade reactions that enable multiple bond formation in a one-pot process. This review discusses three one-pot reactions: 1) 1,2-diazepine synthesis from cyclobutenones and lithiodiazoesters via cascade 4π-8π electrocyclization; 2) synthesis of pyrroloisoquinolines from alkynylimino esters triggered by gold-catalyzed azomethine ylide formation; and 3) pyrrolizidine synthesis via three-component coupling reactions of iminoesters, acetylenes, and maleimides through the gold-catalyzed azomethine ylide generation/[3+2]-cycloaddition/enamine cyclization reaction.
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Affiliation(s)
- Kenji Sugimoto
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama
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12
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Selva V, Selva E, Merino P, Nájera C, Sansano JM. Sequential Metal-Free Thermal 1,3-Dipolar Cycloaddition of Unactivated Azomethine Ylides. Org Lett 2018; 20:3522-3526. [DOI: 10.1021/acs.orglett.8b01292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Verónica Selva
- Departamento de Química Orgánica. Facultad de Ciencias, Universidad de Alicante, 03080 Alicante, Spain
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Instituto de Síntesis Orgánica (ISO), 03080 Alicante, Spain
| | - Elisabet Selva
- Departamento de Química Orgánica. Facultad de Ciencias, Universidad de Alicante, 03080 Alicante, Spain
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Instituto de Síntesis Orgánica (ISO), 03080 Alicante, Spain
- Medalchemy, S. L. Avenida Ancha de Castelar, 46-EA, San Vicente del Raspeig, 03690 Alicante, Spain
| | - Pedro Merino
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI). Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Carmen Nájera
- Departamento de Química Orgánica. Facultad de Ciencias, Universidad de Alicante, 03080 Alicante, Spain
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
| | - José M. Sansano
- Departamento de Química Orgánica. Facultad de Ciencias, Universidad de Alicante, 03080 Alicante, Spain
- Centro de Innovación en Química Avanzada (ORFEO-CINQA)
- Instituto de Síntesis Orgánica (ISO), 03080 Alicante, Spain
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13
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Fluorine walk: The impact of fluorine in quinolone amides on their activity against African sleeping sickness. Eur J Med Chem 2018; 152:377-391. [DOI: 10.1016/j.ejmech.2018.04.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/12/2018] [Accepted: 04/26/2018] [Indexed: 11/17/2022]
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14
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Johnson TW, Gallego RA, Edwards MP. Lipophilic Efficiency as an Important Metric in Drug Design. J Med Chem 2018; 61:6401-6420. [DOI: 10.1021/acs.jmedchem.8b00077] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ted W. Johnson
- Oncology Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Rebecca A. Gallego
- Oncology Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
| | - Martin P. Edwards
- Oncology Medicinal Chemistry, Pfizer Inc., 10770 Science Center Drive, La Jolla, California 92121, United States
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15
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Entropy drives selective fluorine recognition in the fluoroacetyl-CoA thioesterase from Streptomyces cattleya. Proc Natl Acad Sci U S A 2018; 115:E2193-E2201. [PMID: 29453276 DOI: 10.1073/pnas.1717077115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorinated small molecules play an important role in the design of bioactive compounds for a broad range of applications. As such, there is strong interest in developing a deeper understanding of how fluorine affects the interaction of these ligands with their targets. Given the small number of fluorinated metabolites identified to date, insights into fluorine recognition have been provided almost entirely by synthetic systems. The fluoroacetyl-CoA thioesterase (FlK) from Streptomyces cattleya thus provides a unique opportunity to study an enzyme-ligand pair that has been evolutionarily optimized for a surprisingly high 106 selectivity for a single fluorine substituent. In these studies, we synthesize a series of analogs of fluoroacetyl-CoA and acetyl-CoA to generate nonhydrolyzable ester, amide, and ketone congeners of the thioester substrate to isolate the role of fluorine molecular recognition in FlK selectivity. Using a combination of thermodynamic, kinetic, and protein NMR experiments, we show that fluorine recognition is entropically driven by the interaction of the fluorine substituent with a key residue, Phe-36, on the lid structure that covers the active site, resulting in an ∼5- to 20-fold difference in binding (KD). Although the magnitude of discrimination is similar to that found in designed synthetic ligand-protein complexes where dipolar interactions control fluorine recognition, these studies show that hydrophobic and solvation effects serve as the major determinant of naturally evolved fluorine selectivity.
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16
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Ivanova MV, Bayle A, Besset T, Pannecoucke X, Poisson T. Copper-Mediated Introduction of the CF2
PO(OEt)2
Motif: Scope and Limitations. Chemistry 2017; 23:17318-17338. [DOI: 10.1002/chem.201703542] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Maria V. Ivanova
- Normandie Univ; INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014); 76000 Rouen France
| | - Alexandre Bayle
- Normandie Univ; INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014); 76000 Rouen France
| | - Tatiana Besset
- Normandie Univ; INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014); 76000 Rouen France
| | - Xavier Pannecoucke
- Normandie Univ; INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014); 76000 Rouen France
| | - Thomas Poisson
- Normandie Univ; INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014); 76000 Rouen France
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17
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Organic Dye-Catalyzed Atom Transfer Radical Addition–Elimination (ATRE) Reaction for the Synthesis of Perfluoroalkylated Alkenes. Org Lett 2017; 19:4295-4298. [DOI: 10.1021/acs.orglett.7b01952] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Zafrani Y, Yeffet D, Sod-Moriah G, Berliner A, Amir D, Marciano D, Gershonov E, Saphier S. Difluoromethyl Bioisostere: Examining the “Lipophilic Hydrogen Bond Donor” Concept. J Med Chem 2017; 60:797-804. [DOI: 10.1021/acs.jmedchem.6b01691] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yossi Zafrani
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Dina Yeffet
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Gali Sod-Moriah
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Anat Berliner
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Dafna Amir
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Daniele Marciano
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Eytan Gershonov
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Sigal Saphier
- The Department of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
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19
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Medvedeva SM, Shikhaliev KS. (3+2) Cycloaddition reactions in the synthesis of C(4)–N(5)-condensed tetrahydropyrrolo[3,4-c]pyrrole-1,3-diones (microreview). Chem Heterocycl Compd (N Y) 2016. [DOI: 10.1007/s10593-016-1949-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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New halogenated tris-(phenylalkyl)amines as h5-HT2B receptor ligands. Bioorg Med Chem Lett 2016; 26:3216-3219. [PMID: 27261181 DOI: 10.1016/j.bmcl.2016.05.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 11/20/2022]
Abstract
A series of compounds in which various halogen substituents were incorporated into a phenyl ring of a tris-(phenylalkyl)amine scaffold, was synthesized and evaluated for affinity to h5-HT2 receptors. In general, all compounds were found to have good affinity for the 5-HT2B receptor and were selective over 5-HT2A and 5-HT2C receptors. Compound 9i was the most selective compound in this study and is the highest affinity 5-HT2B receptor ligand bearing a tris-(phenylalkyl)amine scaffold to date.
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21
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Stehouwer JS, Goodman MM. Fluorine-18 Radiolabeled PET Tracers for Imaging Monoamine Transporters: Dopamine, Serotonin, and Norepinephrine. PET Clin 2016; 4:101-28. [PMID: 20216936 DOI: 10.1016/j.cpet.2009.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review focuses on the development of fluorine-18 radiolabeled PET tracers for imaging the dopamine transporter (DAT), serotonin transporter (SERT), and norepinephrine transporter (NET). All successful DAT PET tracers reported to date are members of the 3β-phenyl tropane class and are synthesized from cocaine. Currently available carbon-11 SERT PET tracers come from both the diphenylsulfide and 3β-phenyl nortropane class, but so far only the nortropanes have found success with fluorine-18 derivatives. NET imaging has so far employed carbon-11 and fluorine-18 derivatives of reboxetine but due to defluorination of the fluorine-18 derivatives further research is still necessary.
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22
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Giroud M, Harder M, Kuhn B, Haap W, Trapp N, Schweizer WB, Schirmeister T, Diederich F. Fluorine Scan of Inhibitors of the Cysteine Protease Human Cathepsin L: Dipolar and Quadrupolar Effects in the π-Stacking of Fluorinated Phenyl Rings on Peptide Amide Bonds. ChemMedChem 2016; 11:1042-7. [DOI: 10.1002/cmdc.201600132] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/23/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - Michael Harder
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - Bernd Kuhn
- Small Molecule Research; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124, Building 92 4070 Basel Switzerland
| | - Wolfgang Haap
- Small Molecule Research; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124, Building 92 4070 Basel Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - W. Bernd Schweizer
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
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23
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Arntson KE, Pomerantz WCK. Protein-Observed Fluorine NMR: A Bioorthogonal Approach for Small Molecule Discovery. J Med Chem 2015; 59:5158-71. [PMID: 26599421 DOI: 10.1021/acs.jmedchem.5b01447] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The (19)F isotope is 100% naturally abundant and is the second most sensitive and stable NMR-active nucleus. Unlike the ubiquitous hydrogen atom, fluorine is nearly absent in biological systems, making it a unique bioorthogonal atom for probing molecular interactions in biology. Over 73 fluorinated proteins have been studied by (19)F NMR since the seminal studies of Hull and Sykes in 1974. With advances in cryoprobe production and fluorinated amino acid incorporation strategies, protein-based (19)F NMR offers opportunities to the medicinal chemist for characterizing and ultimately discovering new small molecule protein ligands. This review will highlight new advances using (19)F NMR for characterizing small molecule interactions with both small and large proteins as well as detailing NMR resonance assignment challenges and amino acid incorporation approaches.
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Affiliation(s)
- Keith E Arntson
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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24
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Mancebo-Aracil J, Nájera C, Castelló LM, Sansano JM, Larrañaga O, de Cózar A, Cossío FP. Regio and diastereoselective multicomponent 1,3-dipolar cycloadditions between prolinate hydrochlorides, aldehydes and dipolarophiles for the direct synthesis of pyrrolizidines. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.10.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Sugimoto K, Yamamoto N, Tominaga D, Matsuya Y. Three-Component Domino Process for the Pyrrolizine Skeleton via [3 + 2]-Cycloaddition–Enamine Cyclization Triggered by a Gold Catalyst. Org Lett 2015; 17:1320-3. [DOI: 10.1021/acs.orglett.5b00320] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kenji Sugimoto
- Graduate
School of Medicine
and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Nozomi Yamamoto
- Graduate
School of Medicine
and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Daisuke Tominaga
- Graduate
School of Medicine
and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yuji Matsuya
- Graduate
School of Medicine
and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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26
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Hyohdoh I, Furuichi N, Aoki T, Itezono Y, Shirai H, Ozawa S, Watanabe F, Matsushita M, Sakaitani M, Ho PS, Takanashi K, Harada N, Tomii Y, Yoshinari K, Ori K, Tabo M, Aoki Y, Shimma N, Iikura H. Fluorine Scanning by Nonselective Fluorination: Enhancing Raf/MEK Inhibition while Keeping Physicochemical Properties. ACS Med Chem Lett 2013; 4:1059-63. [PMID: 24900605 DOI: 10.1021/ml4002419] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/22/2013] [Indexed: 11/30/2022] Open
Abstract
A facile methodology effective in obtaining a set of compounds monofluorinated at various positions (fluorine scan) by chemical synthesis is reported. Direct and nonselective fluorination reactions of our lead compound 1a and key intermediate 2a worked efficiently to afford a total of six monofluorinated derivatives. All of the derivatives kept their physicochemical properties compared with the lead 1a and one of them had enhanced Raf/MEK inhibitory activity. Keeping physicochemical properties could be considered a benefit of monofluorinated derivatives compared with chlorinated derivatives, iodinated derivatives, methylated derivatives, etc. This key finding led to the identification of compound 14d, which had potent tumor growth inhibition in a xenograft model, excellent PK profiles in three animal species, and no critical toxicity.
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Affiliation(s)
- Ikumi Hyohdoh
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Noriyuki Furuichi
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Toshihiro Aoki
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Yoshiko Itezono
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Haruyoshi Shirai
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Sawako Ozawa
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Fumio Watanabe
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masayuki Matsushita
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Masahiro Sakaitani
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Pil-Su Ho
- C&C Research Laboratories, DRC Natural Sciences Campus, Sungkyunkwan University, 300 Cheoncheon-dong, Jangan-gu, Suwon, Gyeonggi-do 440-746, Republic of Korea
| | - Kenji Takanashi
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Naoki Harada
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Yasushi Tomii
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kiyoshi Yoshinari
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Kazutomo Ori
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Mitsuyasu Tabo
- Research Division, Chugai Pharmaceutical Co., Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Yuko Aoki
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Nobuo Shimma
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
| | - Hitoshi Iikura
- Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
- Research Division, Chugai Pharmaceutical Co., Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
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27
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Liang T, Neumann CN, Ritter T. Introduction of fluorine and fluorine-containing functional groups. Angew Chem Int Ed Engl 2013; 52:8214-64. [PMID: 23873766 DOI: 10.1002/anie.201206566] [Citation(s) in RCA: 1965] [Impact Index Per Article: 178.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Indexed: 01/20/2023]
Abstract
Over the past decade, the most significant, conceptual advances in the field of fluorination were enabled most prominently by organo- and transition-metal catalysis. The most challenging transformation remains the formation of the parent C-F bond, primarily as a consequence of the high hydration energy of fluoride, strong metal-fluorine bonds, and highly polarized bonds to fluorine. Most fluorination reactions still lack generality, predictability, and cost-efficiency. Despite all current limitations, modern fluorination methods have made fluorinated molecules more readily available than ever before and have begun to have an impact on research areas that do not require large amounts of material, such as drug discovery and positron emission tomography. This Review gives a brief summary of conventional fluorination reactions, including those reactions that introduce fluorinated functional groups, and focuses on modern developments in the field.
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Affiliation(s)
- Theresa Liang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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28
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29
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Matsuzaki K, Furukawa T, Tokunaga E, Matsumoto T, Shiro M, Shibata N. Highly Enantioselective Monofluoromethylation of C2-Arylindoles Using FBSM under Chiral Phase-Transfer Catalysis. Org Lett 2013; 15:3282-5. [DOI: 10.1021/ol4013102] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kohei Matsuzaki
- Department of Frontier Materials, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan, and Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
| | - Tatsuya Furukawa
- Department of Frontier Materials, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan, and Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
| | - Etsuko Tokunaga
- Department of Frontier Materials, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan, and Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
| | - Takashi Matsumoto
- Department of Frontier Materials, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan, and Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
| | - Motoo Shiro
- Department of Frontier Materials, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan, and Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
| | - Norio Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan, and Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo 196-8666, Japan
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30
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Chopin N, Médebielle M, Pilet G. Bidentate and Tetradentate β‐Aminovinyl Trifluoromethylated Ketones and Their Copper(II) Complexes: Synthesis, Characterization and Redox Chemistry. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201101385] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nicolas Chopin
- Université de Lyon and Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), UMR CNRS‐UCBL‐INSA Lyon 5246, Equipe “Synthèse de Molécules d'Intérêt Thérapeutique (SMITH)”, Bât. Curien, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne cedex, France
| | - Maurice Médebielle
- Université de Lyon and Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), UMR CNRS‐UCBL‐INSA Lyon 5246, Equipe “Synthèse de Molécules d'Intérêt Thérapeutique (SMITH)”, Bât. Curien, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne cedex, France
| | - Guillaume Pilet
- Université de Lyon and Université Claude Bernard Lyon 1, Laboratoire des multiMatériaux et Interfaces, UMR CNRS‐UCBL, 5615, Bât. Chevreul, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne cedex, France
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31
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Salonen LM, Holland MC, Kaib PSJ, Haap W, Benz J, Mary JL, Kuster O, Schweizer WB, Banner DW, Diederich F. Molecular recognition at the active site of factor Xa: cation-π interactions, stacking on planar peptide surfaces, and replacement of structural water. Chemistry 2011; 18:213-22. [PMID: 22162109 DOI: 10.1002/chem.201102571] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Indexed: 11/10/2022]
Abstract
Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i)=2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.
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Affiliation(s)
- Laura M Salonen
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland
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32
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Sotriffer C, Matter H. The Challenge of Affinity Prediction: Scoring Functions for Structure-Based Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Xu M, Lill MA. Significant enhancement of docking sensitivity using implicit ligand sampling. J Chem Inf Model 2011; 51:693-706. [PMID: 21375306 DOI: 10.1021/ci100457t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficient and accurate quantification of protein-ligand interactions using computational methods is still a challenging task. Two factors strongly contribute to the failure of docking methods to predict free energies of binding accurately: the insufficient incorporation of protein flexibility coupled to ligand binding and the neglected dynamics of the protein-ligand complex in current scoring schemes. We have developed a new methodology, named the 'ligand-model' concept, to sample protein conformations that are relevant for binding structurally diverse sets of ligands. In the ligand-model concept, molecular-dynamics (MD) simulations are performed with a virtual ligand, represented by a collection of functional groups that binds to the protein and dynamically changes its shape and properties during the simulation. The ligand model essentially represents a large ensemble of different chemical species binding to the same target protein. Representative protein structures were obtained from the MD simulation, and docking was performed into this ensemble of protein conformation. Similar binding poses were clustered, and the averaged score was utilized to rerank the poses. We demonstrate that the ligand-model approach yields significant improvements in predicting native-like binding poses and quantifying binding affinities compared to static docking and ensemble docking simulations into protein structures generated from an apo MD simulation.
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Affiliation(s)
- Mengang Xu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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34
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Wang J, Lin D, Zhou S, Ding X, Soloshonok VA, Liu H. Asymmetric synthesis of sterically and electronically demanding linear ω-trifluoromethyl containing amino acids via alkylation of chiral equivalents of nucleophilic glycine and alanine. J Org Chem 2010; 76:684-7. [PMID: 21182272 DOI: 10.1021/jo102031b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An operationally convenient, scalable asymmetric synthesis of linear, ω-trifluoromethyl-containing amino acids, which were not previously produced in their enantiomerically pure form, has been developed via alkylation of chiral equivalents of nucleophilic glycine and alanine. The simplicity of the experimental procedures and high stereochemical outcome (yields up to 90% and diastereoselectivity up to 99%) of the presented method render these fluorinated amino acids readily available for systematic medicinal chemistry studies and de novo peptide design.
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Affiliation(s)
- Jiang Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu chong zhi Road, Shanghai 201203, People's Republic of China
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35
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Prateeptongkum S, Driller K, Jackstell R, Spannenberg A, Beller M. Efficient Synthesis of Biologically Interesting 3,4-Diaryl-Substituted Succinimides and Maleimides: Application of Iron-Catalyzed Carbonylations. Chemistry 2010; 16:9606-15. [DOI: 10.1002/chem.201000369] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Mikami K, Murase T, Zhai L, Itoh Y, Ito S. Highly enantioselective synthesis of α-(perfluoroalkyl)amines via hydrogenation of enamide precursors in the presence of chiraphos-rhodium catalyst. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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37
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Vulpetti A, Hommel U, Landrum G, Lewis R, Dalvit C. Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine. J Am Chem Soc 2009; 131:12949-59. [DOI: 10.1021/ja905207t] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anna Vulpetti
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Ulrich Hommel
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Gregory Landrum
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Richard Lewis
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Claudio Dalvit
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
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38
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Matter H, Nazaré M, Güssregen S, Will D, Schreuder H, Bauer A, Urmann M, Ritter K, Wagner M, Wehner V. Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein-Ligand Binding Affinity. Angew Chem Int Ed Engl 2009; 48:2911-6. [DOI: 10.1002/anie.200806219] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Matter H, Nazaré M, Güssregen S, Will D, Schreuder H, Bauer A, Urmann M, Ritter K, Wagner M, Wehner V. Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein-Ligand Binding Affinity. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806219] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Salonen LM, Bucher C, Banner DW, Haap W, Mary JL, Benz J, Kuster O, Seiler P, Schweizer WB, Diederich F. Cation-pi interactions at the active site of factor Xa: dramatic enhancement upon stepwise N-alkylation of ammonium ions. Angew Chem Int Ed Engl 2009; 48:811-4. [PMID: 19101972 DOI: 10.1002/anie.200804695] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura M Salonen
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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Salonen L, Bucher C, Banner D, Haap W, Mary JL, Benz J, Kuster O, Seiler P, Schweizer W, Diederich F. Kation-π-Wechselwirkungen im aktiven Zentrum von Faktor Xa: drastische Verstärkung durch stufenweise N-Alkylierung von Ammoniumionen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804695] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Benito D, Matheu MI, Morère A, Díaz Y, Castillón S. Towards the preparation of 2″-deoxy-2″-fluoro-adenophostin A. Study of the glycosylation reaction. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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A fluorine scan of non-peptidic inhibitors of neprilysin: Fluorophobic and fluorophilic regions in an enzyme active site. J Fluor Chem 2008. [DOI: 10.1016/j.jfluchem.2008.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Berkowitz DB, Karukurichi KR, de la Salud-Bea R, Nelson DL, McCune CD. Use of Fluorinated Functionality in Enzyme Inhibitor Development: Mechanistic and Analytical Advantages. J Fluor Chem 2008; 129:731-742. [PMID: 19727327 PMCID: PMC2598403 DOI: 10.1016/j.jfluchem.2008.05.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
On the one hand, owing to its electronegativity, relatively small size, and notable leaving group ability from anionic intermediates, fluorine offers unique opportunities for mechanism-based enzyme inhibitor design. On the other, the "bio-orthogonal" and NMR-active 19-fluorine nucleus allows the bioorganic chemist to follow the mechanistic fate of fluorinated substrate analogues or inhibitors as they are enzymatically processed. This article takes an overview of the field, highlighting key developments along these lines. It begins by highlighting new screening methodologies for drug discovery that involve appropriate tagging of either substrate or the target protein itself with (19)F-markers, that then report back on turnover and binding, respectively, via an the NMR screen. Taking this one step further, substrate-tagging with fluorine can be done is such a manner as to provide stereochemical information on enzyme mechanism. For example, substitution of one of the terminal hydrogens in phosphoenolpyruvate, provides insight into the, otherwise latent, facial selectivity of C-C bond formation in KDO synthase. Perhaps, most importantly, from the point of view of this discussion, appropriately tailored fluorinated functionality can be used to form to stabilized "transition state analogue" complexes with a target enzymes. Thus, 5-fluorinated pyrimidines, alpha-fluorinated ketones, and 2-fluoro-2-deoxysugars each lead to covalent adduction of catalytic active site residues in thymidylate synthase, serine protease and glycosidase enzymes, respectively. In all such cases, (19)F NMR allows the bioorganic chemist to spectrally follow "transition state analogue" formation. Finally, the use of specific fluorinated functionality to engineer "suicide substrates" is highlighted in a discussion of the development of the alpha-(2'Z-fluoro)vinyl trigger for amino acid decarboxylase inactivation. Here (19)F NMR allows the bioorganic chemist to glean useful partition ratio data directly out of the NMR tube.
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Affiliation(s)
- David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304
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Zürcher M, Diederich F. Structure-Based Drug Design: Exploring the Proper Filling of Apolar Pockets at Enzyme Active Sites. J Org Chem 2008; 73:4345-61. [DOI: 10.1021/jo800527n] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Zürcher
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| | - François Diederich
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
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Riss PJ, Rösch F. A convenient chemo-enzymatic synthesis and 18F-labelling of both enantiomers of trans-1-toluenesulfonyloxymethyl-2-fluoromethyl-cyclopropane. Org Biomol Chem 2008; 6:4567-74. [DOI: 10.1039/b812777h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Fluorine substituents have become a widespread and important drug component, their introduction facilitated by the development of safe and selective fluorinating agents. Organofluorine affects nearly all physical and adsorption, distribution, metabolism, and excretion properties of a lead compound. Its inductive effects are relatively well understood, enhancing bioavailability, for example, by reducing the basicity of neighboring amines. In contrast, exploration of the specific influence of carbon-fluorine single bonds on docking interactions, whether through direct contact with the protein or through stereoelectronic effects on molecular conformation of the drug, has only recently begun. Here, we review experimental progress in this vein and add complementary analysis based on comprehensive searches in the Cambridge Structural Database and the Protein Data Bank.
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Affiliation(s)
- Klaus Müller
- Pharmaceuticals Division, Discovery Chemistry, F. Hoffmann-La Roche, CH-4070 Basel, Switzerland.
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48
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Morgenthaler M, Schweizer E, Hoffmann-Röder A, Benini F, Martin RE, Jaeschke G, Wagner B, Fischer H, Bendels S, Zimmerli D, Schneider J, Diederich F, Kansy M, Müller K. Predicting and Tuning Physicochemical Properties in Lead Optimization: Amine Basicities. ChemMedChem 2007; 2:1100-15. [PMID: 17530727 DOI: 10.1002/cmdc.200700059] [Citation(s) in RCA: 371] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This review describes simple and useful concepts for predicting and tuning the pK(a) values of basic amine centers, a crucial step in the optimization of physical and ADME properties of many lead structures in drug-discovery research. The article starts with a case study of tricyclic thrombin inhibitors featuring a tertiary amine center with pK(a) values that can be tuned over a wide range, from the usual value of around 10 to below 2 by (remote) neighboring functionalities commonly encountered in medicinal chemistry. Next, the changes in pK(a) of acyclic and cyclic amines upon substitution by fluorine, oxygen, nitrogen, and sulfur functionalities, as well as carbonyl and carboxyl derivatives are systematically analyzed, leading to the derivation of simple rules for pK(a) prediction. Electronic and stereoelectronic effects in cyclic amines are discussed, and the emerging computational methods for pK(a) predictions are briefly surveyed. The rules for tuning amine basicities should not only be of interest in drug-discovery research, but also to the development of new crop-protection agents, new amine ligands for organometallic complexes, and in particular, to the growing field of amine-based organocatalysis.
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Affiliation(s)
- Martin Morgenthaler
- Laboratorium für Organische Chemie, ETH Zürich, HCI, Hönggerberg, 8093 Zürich, Switzerland
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Xiao N, Jiang ZX, Yu YB. Enantioselective synthesis of (2R, 3S)- and (2S, 3R)-4,4,4-trifluoro-N-Fmoc-O-tert-butyl-threonine and their racemization-free incorporation into oligopeptides via solid-phase synthesis. Biopolymers 2007; 88:781-96. [PMID: 17702025 PMCID: PMC2892391 DOI: 10.1002/bip.20825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An efficient method for the enantioselective synthesis of (2R, 3S)- and (2S, 3R)-4,4,4-trifluoro-N-Fmoc-O-tert-butyl-threonine on multigram scales was developed. Absolute configurations of the two stereoisomers were ascertained by X-ray crystallography. Racemization-free coupling conditions for the incorporation of tfT into oligopeptides were then explored. For solution-phase synthesis, tfT racemization was not an issue under conventional coupling conditions. For solid-phase synthesis, the following conditions were identified to achieve racemization-free synthesis: if tfT (3.0 equiv) was not the first amino acid to be linked to the resin (1.0 equiv), the condition is 2.7 equiv DIC/3.0 equiv HOBt as the coupling reagent at 0 degrees C for 20 h; if tfT (3.0 equiv) was the first amino acid to be linked to the resin (1.0 equiv), then 1.0 equiv of CuCl(2) needs to be added to the coupling reagent.
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Affiliation(s)
- Nu Xiao
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, U. S. A
| | - Zhong-Xing Jiang
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, U. S. A
| | - Y. Bruce Yu
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, U. S. A
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 20101, U. S. A
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Hoffmann-Röder A, Schweizer E, Egger J, Seiler P, Obst-Sander U, Wagner B, Kansy M, Banner DW, Diederich F. Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups into the P Pocket. ChemMedChem 2006; 1:1205-15. [PMID: 17001711 DOI: 10.1002/cmdc.200600124] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics followed by oxidation/deoxyfluorination, as well as oxidation/reduction/deoxyfluorination sequences. In contrast, the incorporation of perfluoroalkyl groups required a stereoselective nucleophilic addition reaction at the "upper" carbonyl group of the tricycles, thereby yielding scaffolds with an additional OH, F, or OMe group, respectively. All newly prepared inhibitors showed potent biological activity, with inhibitory constants (K(i) values) in the range of 0.008-0.163 microM. The X-ray crystal structure of a protein-ligand complex revealed the exact positioning of a difluoromethyl substituent in the tight P pocket. Fluorophilic characteristics are attributed to this hydrophobic pocket, although the potency of the inhibitors was found to be modulated by steric rather than electronic factors.
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Affiliation(s)
- Anja Hoffmann-Röder
- Institut für Organische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
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