1
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Wang X, Gao R, Li X. Catalytic Asymmetric Construction of Chiral Polysubstituted 3-Azabicyclo[3.1.1]heptanes by Copper-Catalyzed Stereoselective Formal [4π+2σ] Cycloaddition. J Am Chem Soc 2024. [PMID: 39011580 DOI: 10.1021/jacs.4c06436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The direct construction of bioisosteric compounds enriched in Csp3 content represents an attractive and dependable approach to imbuing biologically active molecules with enhanced three-dimensional characteristics, finding wide utility across the synthetic and medicinal chemistry community. Despite recent advancements in the synthesis of (aza)-bicyclo[3.1.1]heptanes (BCHeps and aza-BCHeps), which serve as meta-substituted (aza)-arene bioisosteres, the enantioselective assembly of chiral 3-aza-BCHeps remains a coveted goal yet to be achieved. Here, we disclose an unprecedented copper-catalyzed asymmetric formal [4π+2σ] cycloaddition of bicyclo[1.1.0]butanes (BCBs) and azomethine ylides, furnishing a diverse array of enantioenriched 3-aza-BCHeps with exceptional levels of diastereo- and enantioselectivites (51 examples, all >20:1 dr, mostly 97-99% ee). Both mono- and disubstituted BCBs are well compatible with this protocol, offering an enticing route for the efficient synthesis of challenging tetrasubstituted bicyclic products bearing two quaternary centers. The synthetic significance of this methodology is further demonstrated by the successful preparation of several piperidine drug analogues.
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Affiliation(s)
- Xunhua Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Rongkai Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xiaoxun Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Suzhou Institute of Shandong University, NO.388 Ruoshui Road, SIP, Suzhou, Jiangsu 215123, China
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2
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Le Roch M, Renault J, Argouarch G, Lenci E, Trabocchi A, Roisnel T, Gouault N, Lalli C. Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery. J Org Chem 2024; 89:4932-4946. [PMID: 38451837 DOI: 10.1021/acs.joc.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).
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Affiliation(s)
- Myriam Le Roch
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
| | | | | | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Thierry Roisnel
- Univ Rennes, Centre de Diffractométrie X (CDIFX), ISCR-UMR 6226, Rennes F-35000, France
| | | | - Claudia Lalli
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
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3
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Leblanc J, Boutin M, Vega C, Mathé-Allainmat M, Grosse S, Guillemont J, Lebreton J, Tessier A. A new synthetic route towards multifunctionalized cyclic amidrazones for feeding chemical space. Org Biomol Chem 2024; 22:2404-2408. [PMID: 38411004 DOI: 10.1039/d3ob02092d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
In the context of growing impetus to develop new molecular scaffolds as well as a variety of 3D fragments to escape from flatland, we have reintroduced the accessibility of the underexplored azaheterocyclic amidrazones as promising bioisosteres. Herein, we present an original and versatile approach to synthesize cyclic amidrazones functionalized at different positions of the scaffold in view of diversifying the substitution pattern towards multifunctionalization, extension or fusion of the ring system and 3D-shaping of fragments. This unprecedented synthetic route represents a sweet achievement to cover further lead-like chemical space.
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Affiliation(s)
- Johann Leblanc
- Nantes Université, CNRS, CEISAM, UMR 6230, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
| | - Margaux Boutin
- Nantes Université, CNRS, CEISAM, UMR 6230, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
| | - Clara Vega
- Nantes Université, CNRS, CEISAM, UMR 6230, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
| | - Monique Mathé-Allainmat
- Nantes Université, CNRS, CEISAM, UMR 6230, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
| | - Sandrine Grosse
- Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Jérôme Guillemont
- NovAliX on-site Janssen-Cilag, Centre de recherche Pharma, Campus de Maigremont BP615, F-27106 Val de Reuil Cedex, France
| | - Jacques Lebreton
- Nantes Université, CNRS, CEISAM, UMR 6230, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
| | - Arnaud Tessier
- Nantes Université, CNRS, CEISAM, UMR 6230, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
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4
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Choi A, Das A, Meijer AJHM, Proietti Silvestri I, Coldham I. Synthesis of enantioenriched spirocyclic 2-arylpiperidines via kinetic resolution. Org Biomol Chem 2024; 22:1602-1607. [PMID: 38314915 DOI: 10.1039/d4ob00011k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Kinetic resolution of N-Boc-spirocyclic 2-arylpiperidines with spiro substitution at C-4 was achieved with high enantiomeric ratios using the chiral base n-BuLi/sparteine. Cyclopropanation or metallaphotoredox catalysis were used to access the piperidines, which could be further functionalised without loss of enantiopurity, highlighting their use as potential 3D fragments for drug discovery.
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Affiliation(s)
- Anthony Choi
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
| | - Anjan Das
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
| | | | | | - Iain Coldham
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
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5
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Sedenkova KN, Leschukov DN, Grishin YK, Zefirov NA, Gracheva YA, Skvortsov DA, Hrytseniuk YS, Vasilyeva LA, Spirkova EA, Shevtsov PN, Shevtsova EF, Lukmanova AR, Spiridonov VV, Markova AA, Nguyen MT, Shtil AA, Zefirova ON, Yaroslavov AA, Milaeva ER, Averina EB. Verubulin (Azixa) Analogues with Increased Saturation: Synthesis, SAR and Encapsulation in Biocompatible Nanocontainers Based on Ca 2+ or Mg 2+ Cross-Linked Alginate. Pharmaceuticals (Basel) 2023; 16:1499. [PMID: 37895970 PMCID: PMC10610134 DOI: 10.3390/ph16101499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Tubulin-targeting agents attract undiminished attention as promising compounds for the design of anti-cancer drugs. Verubulin is a potent tubulin polymerization inhibitor, binding to colchicine-binding sites. In the present work, a series of verubulin analogues containing a cyclohexane or cycloheptane ring 1,2-annulated with pyrimidine moiety and various substituents in positions 2 and 4 of pyrimidine were obtained and their cytotoxicity towards cancer and non-cancerous cell lines was estimated. The investigated compounds revealed activity against various cancer cell lines with IC50 down to 1-4 nM. According to fluorescent microscopy data, compounds that showed cytotoxicity in the MTT test disrupt the normal cytoskeleton of the cell in a pattern similar to that for combretastatin A-4. The hit compound (N-(4-methoxyphenyl)-N,2-dimethyl-5,6,7,8-tetrahydroquinazolin-4-amine) was encapsulated in biocompatible nanocontainers based on Ca2+ or Mg2+ cross-linked alginate and it was demonstrated that its cytotoxic activity was preserved after encapsulation.
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Affiliation(s)
- Kseniya N Sedenkova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Denis N Leschukov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Yuri K Grishin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Nikolay A Zefirov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Yulia A Gracheva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry A Skvortsov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | - Lilja A Vasilyeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Spirkova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences (IPAC RAS), 142432 Chernogolovka, Russia
| | - Pavel N Shevtsov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences (IPAC RAS), 142432 Chernogolovka, Russia
| | - Elena F Shevtsova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences (IPAC RAS), 142432 Chernogolovka, Russia
| | - Alina R Lukmanova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vasily V Spiridonov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alina A Markova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Minh T Nguyen
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Alexander A Shtil
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Institute of Cyber Intelligence Systems, National Research Nuclear University MEPhI, 115409 Moscow, Russia
| | - Olga N Zefirova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | - Elena R Milaeva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena B Averina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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6
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Zhang Z, Zhang SL, Wu C, Li HH, Zha L, Shi J, Liu X, Qin HL, Tang W. Sulfur-fluoride exchange (SuFEx)-enabled lead discovery of AChE inhibitors by fragment linking strategies. Eur J Med Chem 2023; 257:115502. [PMID: 37224761 DOI: 10.1016/j.ejmech.2023.115502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/06/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
SuFEx click chemistry has been a method for the rapid synthesis of functional molecules with desirable properties. Here, we demonstrated a workflow that allows for in situ synthesis of sulfonamide inhibitors based on SuFEx reaction for high-throughput testing of their cholinesterase activity. According to fragment-based drug discovery (FBDD), sulfonyl fluorides [R-SO2F] with moderate activity were identified as fragment hits, rapidly diversified into 102 analogs in SuFEx reactions, and the sulfonamides were directly screened to yield drug-like inhibitors with 70-fold higher potency (IC50 = 94 nM). Moreover, the improved molecule J8-A34 can ameliorate cognitive function in Aβ1-42-induced mouse model. Since this SuFEx linkage reaction succeeds on picomole scale for direct screening, this methodology can accelerate the development of robust biological probes and drug candidates.
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Affiliation(s)
- Ziwen Zhang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Shi-Long Zhang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Chengyao Wu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Huan-Huan Li
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Liang Zha
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Jingbo Shi
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China
| | - Xinhua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China.
| | - Hua-Li Qin
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, China.
| | - Wenjian Tang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, 230032, China.
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7
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Dekker T, Janssen MAC, Sutherland C, Aben RWM, Scheeren HW, Blanco-Ania D, Rutjes FPJT, Wijtmans M, de Esch IJP. An Automated, Open-Source Workflow for the Generation of (3D) Fragment Libraries. ACS Med Chem Lett 2023; 14:583-590. [PMID: 37197454 PMCID: PMC10184156 DOI: 10.1021/acsmedchemlett.2c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/27/2023] [Indexed: 05/19/2023] Open
Abstract
The recent success of fragment-based drug discovery (FBDD) is inextricably linked to adequate library design. To guide the design of our fragment libraries, we have constructed an automated workflow in the open-source KNIME software. The workflow considers chemical diversity and novelty of the fragments, and can also take into account the three-dimensional (3D) character. This design tool can be used to create large and diverse libraries but also to select a small number of representative compounds as a focused set of unique screening compounds to enrich existing fragment libraries. To illustrate the procedures, the design and synthesis of a 10-membered focused library is reported based on the cyclopropane scaffold, which is underrepresented in our existing fragment screening library. Analysis of the focused compound set indicates significant shape diversity and a favorable overall physicochemical profile. By virtue of its modular setup, the workflow can be readily adjusted to design libraries that focus on properties other than 3D shape.
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Affiliation(s)
- Tom Dekker
- Amsterdam
Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Mathilde A. C.
H. Janssen
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Christina Sutherland
- Amsterdam
Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rene W. M. Aben
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans W. Scheeren
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Daniel Blanco-Ania
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Floris P. J. T. Rutjes
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maikel Wijtmans
- Amsterdam
Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Amsterdam
Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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8
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Chopra A, Bauman JD, Ruiz FX, Arnold E. Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. J Med Chem 2023; 66:6013-6024. [PMID: 37115705 PMCID: PMC10184123 DOI: 10.1021/acs.jmedchem.2c01681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
X-ray crystallographic fragment screening (XCFS) uses fragment-sized molecules (∼60 to 300 Da) to access binding sites on proteins that may be inaccessible to larger drug-like molecules (>300 Da). Previous studies have shown that fragments containing halogen atoms bind more often to proteins than non-halogenated fragments. Here, we designed the Halo Library containing 46 halogenated fragments (including the "universal fragment" 4-bromopyrazole), a majority of which have been reported to bind to or inhibit one or more targets. The library was screened against the crystals of HIV-1 reverse transcriptase with the drug rilpivirine, yielding an overall hit rate of 26%. Two new binding sites were discovered, and several hot spots were identified. This small library may thus provide a convenient tool for rapidly assessing the feasibility of a target for XCFS, mapping hot spots and cryptic sites, as well as finding fragment binders that can be useful for developing drug leads.
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Affiliation(s)
- Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Joseph D Bauman
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Francesc X Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, United States
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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9
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Tarifa L, Pilar Del Río M, Asensio L, López JA, Ciriano MA, Geer AM, Tejel C. Iridium-Catalyzed Regio- and Diastereoselective Synthesis of C-Substituted Piperazines. ACS Catal 2023; 13:3148-3152. [PMID: 36910865 PMCID: PMC9990149 DOI: 10.1021/acscatal.2c05895] [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: 11/30/2022] [Revised: 02/08/2023] [Indexed: 02/18/2023]
Abstract
Piperazine rings are essential motifs frequently found in commercial drugs. However, synthetic methodologies are mainly limited to N-substituted piperazines, preventing structural diversity. Disclosed herein is a straightforward catalytic method for the synthesis of complex C-substituted piperazines based on an uncommon head-to-head coupling of easily prepared imines. This 100% atom-economic process allows the selective formation of a sole diastereoisomer, a broad substrate scope, and a good functional group tolerance employing a bench-stable iridium catalyst under mild reaction conditions. Key to the success is the addition of N-oxides to the reaction mixture, as they notably enhance the catalytic activity and selectivity.
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Affiliation(s)
- Luis Tarifa
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - M Pilar Del Río
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Laura Asensio
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - José A López
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Miguel A Ciriano
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Ana M Geer
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Cristina Tejel
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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10
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Dekker T, Harteveld JW, Wágner G, de Vries MCM, Custers H, van de Stolpe AC, de Esch IJP, Wijtmans M. Green Drug Discovery: Novel Fragment Space from the Biomass-Derived Molecule Dihydrolevoglucosenone (Cyrene TM). Molecules 2023; 28:molecules28041777. [PMID: 36838763 PMCID: PMC9967789 DOI: 10.3390/molecules28041777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Biomass-derived molecules can provide a basis for sustainable drug discovery. However, their full exploration is hampered by the dominance of millions of old-fashioned screening compounds in classical high-throughput screening (HTS) libraries frequently utilized. We propose a fragment-based drug discovery (FBDD) approach as an efficient method to navigate biomass-derived drug space. Here, we perform a proof-of-concept study with dihydrolevoglucosenone (CyreneTM), a pyrolysis product of cellulose. Diverse synthetic routes afforded a 100-membered fragment library with a diversity in functional groups appended. The library overall performs well in terms of novelty, physicochemical properties, aqueous solubility, stability, and three-dimensionality. Our study suggests that Cyrene-based fragments are a valuable green addition to the drug discovery toolbox. Our findings can help in paving the way for new hit drug candidates that are based on renewable resources.
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11
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Yu T, Yang J, Wang Z, Ding Z, Xu M, Wen J, Xu L, Li P. Selective [2σ + 2σ] Cycloaddition Enabled by Boronyl Radical Catalysis: Synthesis of Highly Substituted Bicyclo[3.1.1]heptanes. J Am Chem Soc 2023; 145:4304-4310. [PMID: 36763965 DOI: 10.1021/jacs.2c13740] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In contrast to the traditional and widely-used cycloaddition reactions involving at least a π bond component, a [2σ + 2σ] radical cycloaddition between bicyclo[1.1.0]butanes (BCBs) and cyclopropyl ketones has been developed to provide a modular, concise, and atom-economical synthetic route to substituted bicyclo[3.1.1]heptane (BCH) derivatives that are 3D bioisosteres of benzenes and core skeleton of a number of terpene natural products. The reaction was catalyzed by a combination of simple tetraalkoxydiboron(4) compound B2pin2 and 3-pentyl isonicotinate. The broad substrate scope has been demonstrated by synthesizing a series of new highly functionalized BCHs with up to six substituents on the core with up to 99% isolated yield. Computational mechanistic investigations supported a pyridine-assisted boronyl radical catalytic cycle.
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Affiliation(s)
- Tao Yu
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
| | - Jinbo Yang
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, China
| | - Zhijun Wang
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, China
| | - Zhengwei Ding
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Ming Xu
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
| | - Jingru Wen
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
| | - Liang Xu
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, China
| | - Pengfei Li
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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12
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Barchi JJ, Strain CN. The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation. Front Mol Biosci 2023; 10:1117850. [PMID: 36845552 PMCID: PMC9950641 DOI: 10.3389/fmolb.2023.1117850] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
A variety of glycan structures cover the surface of all cells and are involved in myriad biological processes, including but not limited to, cell adhesion and communication, protein quality control, signal transduction and metabolism, while also being intimately involved in innate and adaptive immune functions. Immune surveillance and responses to foreign carbohydrate antigens, such as capsular polysaccharides on bacteria and surface protein glycosylation of viruses, are the basis of microbial clearance, and most antimicrobial vaccines target these structures. In addition, aberrant glycans on tumors called Tumor-Associated Carbohydrate Antigens (TACAs) elicit immune responses to cancer, and TACAs have been used in the design of many antitumor vaccine constructs. A majority of mammalian TACAs are derived from what are referred to as mucin-type O-linked glycans on cell-surface proteins and are linked to the protein backbone through the hydroxyl group of either serine or threonine residues. A small group of structural studies that have compared mono- and oligosaccharides attached to each of these residues have shown that there are distinct differences in conformational preferences assumed by glycans attached to either "unmethylated" serine or ß-methylated threonine. This suggests that the linkage point of antigenic glycans will affect their presentation to the immune system as well as to various carbohydrate binding molecules (e.g., lectins). This short review, followed by our hypothesis, will examine this possibility and extend the concept to the presentation of glycans on surfaces and in assay systems where recognition of glycans by proteins and other binding partners can be defined by different attachment points that allow for a range of conformational presentations.
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Affiliation(s)
| | - Caitlin N. Strain
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute at Frederick, Frederick, MD, United States
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13
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Xu M, Wang Z, Sun Z, Ouyang Y, Ding Z, Yu T, Xu L, Li P. Diboron(4)-Catalyzed Remote [3+2] Cycloaddition of Cyclopropanes via Dearomative/Rearomative Radical Transmission through Pyridine. Angew Chem Int Ed Engl 2022; 61:e202214507. [PMID: 36344444 DOI: 10.1002/anie.202214507] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Indexed: 11/09/2022]
Abstract
Ring structures such as pyridine, cyclopentane or their combinations are important motifs in bioactive molecules. In contrast to previous cycloaddition reactions that necessitated a directly bonded initiating functional group, this work demonstrated a novel through-(hetero)arene radical transmission concept for selective activation of a remote bond. An efficient, metal-free and atom-economical [3+2] cycloaddition between 4-pyridinyl cyclopropanes and alkenes or alkynes has been developed for modular synthesis of pyridine-substituted cyclopentanes, cyclopentenes and bicyclo[2.1.1]hexanes that are difficult to access using known methods. This complexity-building reaction was catalyzed by a very simple and inexpensive diboron(4) compound and took place via dearomative/rearomative processes. The substrate scope was broad and more than 100 new compounds were prepared in generally high yields. Mechanistic experiments and density function theory (DFT) investigation supported a radical relay catalytic cycle involving alkylidene dihydropyridine radical intermediates and boronyl radical transfer.
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Affiliation(s)
- Ming Xu
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Zhijun Wang
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhaohui Sun
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yizhao Ouyang
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Zhengwei Ding
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Tao Yu
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Liang Xu
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Pengfei Li
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China.,State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
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14
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Jones SP, Firth JD, Wheldon MC, Atobe M, Hubbard RE, Blakemore DC, De Fusco C, Lucas SCC, Roughley SD, Vidler LR, Whatton MA, Woolford AJA, Wrigley GL, O'Brien P. Exploration of piperidine 3D fragment chemical space: synthesis and 3D shape analysis of fragments derived from 20 regio- and diastereoisomers of methyl substituted pipecolinates. RSC Med Chem 2022; 13:1614-1620. [PMID: 36545433 PMCID: PMC9749955 DOI: 10.1039/d2md00239f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Fragment-based drug discovery is now widely adopted for lead generation in the pharmaceutical industry. However, fragment screening collections are often predominantly populated with flat, 2D molecules. Herein, we report the synthesis of piperidine-based 3D fragment building blocks - 20 regio- and diastereoisomers of methyl substituted pipecolinates using simple and general synthetic methods. cis-Piperidines, accessed through a pyridine hydrogenation were transformed into their trans-diastereoisomers using conformational control and unified reaction conditions. Additionally, diastereoselective lithiation/trapping was utilised to access trans-piperidines. Analysis of a virtual library of fragments derived from the 20 cis- and trans-disubstituted piperidines showed that it consisted of 3D molecules with suitable molecular properties to be used in fragment-based drug discovery programs.
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Affiliation(s)
- S. Paul Jones
- Department of Chemistry, University of YorkHeslingtonYorkYO10 5DDUK
| | - James D. Firth
- Department of Chemistry, University of YorkHeslingtonYorkYO10 5DDUK
| | - Mary C. Wheldon
- Department of Chemistry, University of YorkHeslingtonYorkYO10 5DDUK
| | - Masakazu Atobe
- Department of Chemistry, University of YorkHeslingtonYorkYO10 5DDUK,Asahi Kasei Pharma Corporation632-1 Mifuku, IzunokuniShizuoka 410-2321Japan
| | - Roderick E. Hubbard
- Department of Chemistry, University of YorkHeslingtonYorkYO10 5DDUK,Vernalis (R&D) Ltd.Granta Park, AbingtonCambridgeCB21 6GBUK
| | | | - Claudia De Fusco
- Bayer AG, Research and Development, Pharmaceuticals, Synthetic Modalities13353BerlinGermany
| | - Simon C. C. Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZenecaCambridgeCB4 0WGUK
| | | | - Lewis R. Vidler
- Amphista TherapeuticsThe Cori Building, Granta Park, Great AbingtonCambridge CB21 6GQUK
| | - Maria Ann Whatton
- Evotec (UK) LtdDorothy Crowfoot Hodgkin Campus, 114 Innovation Drive, Milton Park, AbingdonOxonOX14 4RZUK
| | | | | | - Peter O'Brien
- Department of Chemistry, University of YorkHeslingtonYorkYO10 5DDUK
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