1
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Tsien J, Hu C, Merchant RR, Qin T. Three-dimensional saturated C(sp 3)-rich bioisosteres for benzene. Nat Rev Chem 2024:10.1038/s41570-024-00623-0. [PMID: 38982260 DOI: 10.1038/s41570-024-00623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Benzenes, the most ubiquitous structural moiety in marketed small-molecule drugs, are frequently associated with poor 'drug-like' properties, including metabolic instability, and poor aqueous solubility. In an effort to overcome these limitations, recent developments in medicinal chemistry have demonstrated the improved physicochemical profiles of C(sp3)-rich bioisosteric scaffolds relative to arenes. In the past two decades, we have witnessed an exponential increase in synthetic methods for accessing saturated bioisosteres of monosubstituted and para-substituted benzenes. However, until recent discoveries, analogous three-dimensional ortho-substituted and meta-substituted biososteres have remained underexplored, owing to their ring strain and increased s-character hybridization. This Review summarizes the emerging synthetic methodologies to access such saturated motifs and their impact on the application of bioisosteres for ortho-substituted, meta-substituted and multi-substituted benzene rings. It concludes with a perspective on the development of next-generation bioisosteres, including those within novel chemical space.
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Affiliation(s)
- Jet Tsien
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Hu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rohan R Merchant
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - Tian Qin
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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2
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Liu Y, Wu Z, Shan JR, Yan H, Hao EJ, Shi L. Titanium catalyzed [2σ + 2π] cycloaddition of bicyclo[1.1.0]-butanes with 1,3-dienes for efficient synthesis of stilbene bioisosteres. Nat Commun 2024; 15:4374. [PMID: 38782978 PMCID: PMC11116475 DOI: 10.1038/s41467-024-48494-9] [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: 08/26/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Natural stilbenes have shown significant potential in the prevention and treatment of diseases due to their diverse pharmacological activities. Here we present a mild and effective Ti-catalyzed intermolecular radical-relay [2σ + 2π] cycloaddition of bicyclo[1.1.0]-butanes and 1,3-dienes. This transformation enables the synthesis of bicyclo[2.1.1]hexane (BCH) scaffolds containing aryl vinyl groups with excellent regio- and trans-selectivity and broad functional group tolerance, thus offering rapid access to structurally diverse stilbene bioisosteres.
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Affiliation(s)
- Yonghong Liu
- Cancer Hospital of Dalian University of Technology, 116024, Dalian, China
- School of Chemistry, Dalian University of Technology, 116024, Dalian, China
| | - Zhixian Wu
- Cancer Hospital of Dalian University of Technology, 116024, Dalian, China
- School of Chemistry, Dalian University of Technology, 116024, Dalian, China
| | - Jing-Ran Shan
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Huaipu Yan
- School of Chemistry, Dalian University of Technology, 116024, Dalian, China
| | - Er-Jun Hao
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, China.
| | - Lei Shi
- Cancer Hospital of Dalian University of Technology, 116024, Dalian, China.
- School of Chemistry, Dalian University of Technology, 116024, Dalian, China.
- Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, China.
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3
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Prysiazhniuk K, Datsenko OP, Polishchuk O, Shulha S, Shablykin O, Nikandrova Y, Horbatok K, Bodenchuk I, Borysko P, Shepilov D, Pishel I, Kubyshkin V, Mykhailiuk PK. Spiro[3.3]heptane as a Saturated Benzene Bioisostere. Angew Chem Int Ed Engl 2024; 63:e202316557. [PMID: 38251921 DOI: 10.1002/anie.202316557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 01/23/2024]
Abstract
The spiro[3.3]heptane core, with the non-coplanar exit vectors, was shown to be a saturated benzene bioisostere. This scaffold was incorporated into the anticancer drug sonidegib (instead of the meta-benzene), the anticancer drug vorinostat (instead of the phenyl ring), and the anesthetic drug benzocaine (instead of the para-benzene). The patent-free saturated analogs obtained showed a high potency in the corresponding biological assays.
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Affiliation(s)
| | | | | | | | - Oleh Shablykin
- Enamine Ltd., Winston Churchill Str. 78, 02094, Kyiv, Ukraine
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, 02094, Kyiv, Ukraine
| | | | | | | | - Petro Borysko
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
| | | | - Iryna Pishel
- Bienta, Winston Churchill Str. 78, 02094, Kyiv, Ukraine
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4
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Semeno VV, Vasylchenko VO, Fesun IM, Ruzhylo LY, Kipriianov MO, Melnykov KP, Skreminskyi A, Iminov R, Mykhailiuk P, Vashchenko BV, Grygorenko OO. Bicyclo[m.n.k]alkane Building Blocks as Promising Benzene and Cycloalkane Isosteres: Multigram Synthesis, Physicochemical and Structural Characterization. Chemistry 2024; 30:e202303859. [PMID: 38149408 DOI: 10.1002/chem.202303859] [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: 11/20/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 12/28/2023]
Abstract
Electrophilic double bond functionalization - intramolecular enolate alkylation sequence was used to obtain a series of bridged and fused bicyclo[m.n.k]alkane derivatives (i. e., bicyclo[4.1.1]octanes, bicyclo[2.2.1]heptanes, bicyclo[3.2.1]octanes, bicyclo[3.1.0]hexanes, and bicyclo[4.2.0]heptanes). The scope and limitations of the method were established, and applicability to the multigram synthesis of target bicyclic compounds was illustrated. Using the developed protocols, over 50 mono- and bifunctional building blocks relevant to medicinal chemistry were prepared. The synthesized compounds are promising isosteres of benzene and cycloalkane rings, which is confirmed by their physicochemical and structural characterization (pKa , LogP, and exit vector parameters (EVP)). "Rules of thumb" for the upcoming isosteric replacement studies were proposed.
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Affiliation(s)
- Volodymyr V Semeno
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | | | - Ihor M Fesun
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
| | - Liudmyla Yu Ruzhylo
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- National Technical University of Ukraine " Igor Sikorsky Kyiv Polytechnic Institute", Beresteiskyi Ave. 37, Kyїv, 03056, Ukraine
| | - Mykhailo O Kipriianov
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- National Technical University of Ukraine " Igor Sikorsky Kyiv Polytechnic Institute", Beresteiskyi Ave. 37, Kyїv, 03056, Ukraine
| | - Kostiantyn P Melnykov
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | | | - Rustam Iminov
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
| | | | - Bohdan V Vashchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
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5
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Levterov VV, Panasiuk Y, Sahun K, Stashkevych O, Badlo V, Shablykin O, Sadkova I, Bortnichuk L, Klymenko-Ulianov O, Holota Y, Lachmann L, Borysko P, Horbatok K, Bodenchuk I, Bas Y, Dudenko D, Mykhailiuk PK. 2-Oxabicyclo[2.2.2]octane as a new bioisostere of the phenyl ring. Nat Commun 2023; 14:5608. [PMID: 37783681 PMCID: PMC10545790 DOI: 10.1038/s41467-023-41298-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/30/2023] [Indexed: 10/04/2023] Open
Abstract
The phenyl ring is a basic structural element in chemistry. Here, we show the design, synthesis, and validation of its new saturated bioisostere with improved physicochemical properties - 2-oxabicyclo[2.2.2]octane. The design of the structure is based on the analysis of the advantages and disadvantages of the previously used bioisosteres: bicyclo[1.1.1]pentane, bicyclo[2.2.2]octane, and cubane. The key synthesis step is the iodocyclization of cyclohexane-containing alkenyl alcohols with molecular iodine in acetonitrile. 2-Oxabicyclo[2.2.2]octane core is incorporated into the structure of Imatinib and Vorinostat (SAHA) drugs instead of the phenyl ring. In Imatinib, such replacement leads to improvement of physicochemical properties: increased water solubility, enhanced metabolic stability, and reduced lipophilicity. In Vorinostat, such replacement results in a new bioactive analog of the drug. This study enhances the repertoire of available saturated bioisosteres of (hetero)aromatic rings for the use in drug discovery projects.
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Affiliation(s)
| | | | - Kateryna Sahun
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
| | | | - Valentyn Badlo
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
| | - Oleh Shablykin
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
- V. P. Kukhar IBOPC of the NASciences of Ukraine, Academician Kukhar Str. 1, 02094, Kyiv, Ukraine
| | - Iryna Sadkova
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
| | - Lina Bortnichuk
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
| | | | - Yuliia Holota
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
| | | | - Petro Borysko
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
| | | | - Iryna Bodenchuk
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
| | - Yuliia Bas
- Taras Shevchenko National University of Kyiv, Chemistry Department, Volodymyrska 64, 01601, Kyiv, Ukraine
| | - Dmytro Dudenko
- Enamine Ltd., Winston Churchill street 78, 02094, Kyiv, Ukraine
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6
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Kim K, You E, Hong S. Nucleophilic C4-selective (hetero) arylation of pyridines for facile synthesis of heterobiaryls. Front Chem 2023; 11:1254632. [PMID: 37720719 PMCID: PMC10502421 DOI: 10.3389/fchem.2023.1254632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
The synthesis of heterobiaryl compounds holds significant value in organic chemistry due to their extensive range of applications. Herein, we report a highly efficient strategy for conducting C4-selective (hetero) arylation of pyridines using N-aminopyridinium salts. The reaction proceeds readily at room temperature in the presence of a base, thus eliminating the requirement for catalysts or oxidants. This method allows for the installation of various electron-rich (hetero) aryl groups on pyridines, resulting in the streamlined synthesis of highly valuable C4-(hetero) aryl pyridine derivatives, which are otherwise challenging to acquire via conventional methods. This simple and straightforward method will facilitate access to a range of heterobiaryl compounds thereby promoting their application in various scientific disciplines.
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Affiliation(s)
- Kewon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Euna You
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Sungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, Republic of Korea
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7
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Radhoff N, Daniliuc CG, Studer A. Lewis Acid Catalyzed Formal (3+2)-Cycloaddition of Bicyclo[1.1.0]butanes with Ketenes. Angew Chem Int Ed Engl 2023; 62:e202304771. [PMID: 37166141 DOI: 10.1002/anie.202304771] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/12/2023]
Abstract
Design, synthesis and application of benzene bioisosteres have attracted a lot of attention in the past 20 years. Recently, bicyclo[2.1.1]hexanes have emerged as highly attractive bioisosteres for ortho- and meta-substituted benzenes. Herein we report a mild, scalable and transition-metal-free protocol for the construction of highly substituted bicyclo[2.1.1]hexan-2-ones through Lewis acid catalyzed (3+2)-cycloaddition of bicyclo[1.1.0]-butane ketones with disubstituted ketenes. The reaction shows high functional group tolerance as documented by the successful preparation of various 3-alkyl-3-aryl as well as 3,3-bisalkyl bicyclo[2.1.1]hexan-2-ones (26 examples, up to 89 % yield). Postfunctionalization of the exocyclic ketone moiety is also demonstrated.
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Affiliation(s)
- Niklas Radhoff
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstraße 40, 48149, Münster, Germany
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstraße 40, 48149, Münster, Germany
| | - Armido Studer
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstraße 40, 48149, Münster, Germany
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8
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Advances in nonclassical phenyl bioisosteres for drug structural optimization. Future Med Chem 2022; 14:1681-1692. [PMID: 36317661 DOI: 10.4155/fmc-2022-0188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The phenyl group is the most prevalent ring system and plays an essential role as a pharmacophore or scaffold in marketed drugs. However, the indiscriminate employment of phenyl is also a major cause of poor physicochemical properties of active molecules. Nonclassical phenyl bioisosteres (NPBs) have emerged as effective replacements for phenyl in structural optimization due to their unique steric structures and physicochemical properties. Herein, the effects of widely reported NPBs on physicochemical properties and biological activities, including bicyclo[1.1.1]pentane (BCP), bicyclo[2.1.1]hexanes (BCH), bicyclo[2.2.2]octane (BCO), cubane (CUB) and closo-carboborane, are reviewed. Issues that require consideration while using NPBs and practical solutions to problems frequently encountered in structural optimization using NPBs are also discussed.
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9
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Kotha S, Gaikwad V. Synthesis of Unusual Amino Acid Derivatives Containing Bicyclo[2.2.2]octane Unit by the Diels‐Alder Approach Involving Pentacene. ChemistrySelect 2022. [DOI: 10.1002/slct.202201114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sambasivarao Kotha
- Department of Chemistry Indian Institute of Technology, Bombay Powai Mumbai 400076 India
| | - Vidyasagar Gaikwad
- Department of Chemistry Indian Institute of Technology, Bombay Powai Mumbai 400076 India
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10
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Abdallah M, Hamed MM, Frakolaki E, Katsamakas S, Vassilaki N, Bartenschlager R, Zoidis G, Hirsch AKH, Abdel-Halim M, Abadi AH. Redesigning of the cap conformation and symmetry of the diphenylethyne core to yield highly potent pan-genotypic NS5A inhibitors with high potency and high resistance barrier. Eur J Med Chem 2021; 229:114034. [PMID: 34959173 DOI: 10.1016/j.ejmech.2021.114034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022]
Abstract
Herein, we report the discovery of several NS5A inhibitors with potency against HCV genotype 1b in the picomolar range. Compounds (15, 33) were of extremely high potency against HCV genotype 1b (EC50 ≈ 1 pM), improved activity against genotype 3a (GT 3a) and good metabolic stability. We studied the impact of changing the cap conformation relative to the diphenylethyne core and/or compound symmetry on both potency and metabolic stability. The analogs obtained exhibited improved potency against HCV genotypes 1a, 1b, 3a and 4a compared to the clinically approved candidate daclatasvir with EC50 values in the low picomolar range and SI50s > 7 orders of magnitude. Compound 15, a symmetrically m-, m'-substituted diphenyl ethyne analog, was 150-fold more potent than daclatasvir against GT 3a, while compound 33, an asymmetrically m-, p-substituted diphenyl ethyne analog, was 35-fold more potent than daclatasvir against GT 3a. In addition, compound 15 exhibited a higher resistance barrier than daclatasvir against genotype 1b.
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Affiliation(s)
- Mennatallah Abdallah
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt
| | - Mostafa M Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus E8.1, 66123, Saarbrücken, Germany
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521, Athens, Greece
| | - Sotirios Katsamakas
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, 11521, Athens, Greece
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, Germany
| | - Grigoris Zoidis
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece.
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, Saarbrücken, 66123, Germany
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, 11835, Egypt.
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11
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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12
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Ratni H, Baumann K, Bellotti P, Cook XA, Green LG, Luebbers T, Reutlinger M, Stepan AF, Vifian W. Phenyl bioisosteres in medicinal chemistry: discovery of novel γ-secretase modulators as a potential treatment for Alzheimer's disease. RSC Med Chem 2021; 12:758-766. [PMID: 34124674 PMCID: PMC8152580 DOI: 10.1039/d1md00043h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
Phenyl rings are one of the most prevalent structural moieties in active pharmaceutical ingredients, even if they often contribute to poor physico-chemical properties. Herein, we propose the use of a bridged piperidine (BP) moiety as a phenyl bioisostere, which could also be seen as a superior phenyl alternative as it led to strongly improved drug like properties, in terms of solubility and lipophilicity. Additionally, this BP moiety compares favorably to the recently reported saturated phenyl bioisosteres. We applied this concept to our γ-secretase modulator (GSM) project for the potential treatment of Alzheimer's disease delivering clinical candidates.
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Affiliation(s)
- H Ratni
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - K Baumann
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - P Bellotti
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - X A Cook
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - L G Green
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - T Luebbers
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - M Reutlinger
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - A F Stepan
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
| | - W Vifian
- pRED, Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. Grenzacherstrasse 124 4070 Basel Switzerland (+41) 61 688 2748
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13
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Abe T, Hirao S. Rapid access to indole-fused bicyclo[2.2.2]octanones by merging the umpolung strategy and molecular iodine as a green catalyst. Org Biomol Chem 2021; 18:4193-4197. [PMID: 32458925 DOI: 10.1039/d0ob01038c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One-pot synthesis of indole-fused bicyclo[2.2.2]octanones from DiMeOIN and 2-cyclohexen-1-one is accomplished under an iodine catalyst. The simple and metal-free conditions provide a practical tool to construct Csp3-rich complex molecules via coupling cyclization.
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Affiliation(s)
- Takumi Abe
- Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-tobetsu, Hokkaido 0610293, Japan.
| | - Seiya Hirao
- Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-tobetsu, Hokkaido 0610293, Japan.
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14
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Sodano TM, Combee LA, Stephenson CRJ. Recent Advances and Outlook for the Isosteric Replacement of Anilines. ACS Med Chem Lett 2020; 11:1785-1788. [PMID: 33062152 DOI: 10.1021/acsmedchemlett.9b00687] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Many promising drug candidates and pharmaceutical compounds fail due to idiosyncratic adverse drug reactions (IADRs), often arising from the formation of reactive metabolites. Among the "structural alerts" responsible, anilines are well-known to undergo deleterious metabolic processing, yet isosteric replacement strategies remain limited. Herein we discuss current art and potential new avenues of saturated isosteres to mitigate aniline-related toxicities.
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Affiliation(s)
- Taylor M. Sodano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Logan A. Combee
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Corey R. J. Stephenson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Abstract
The replacement of para-substituted benzenes with saturated bi- and polycyclic bioisosteres - bicyclo[1.1.1]pentane, bicyclo[2.2.2]octane and cubane, - often increases the potency, selectivity and metabolic stability of bioactive compounds. The currently remaining challenge for chemists, however, is to rationally design, synthesize and validate the saturated bioisosteres for ortho- and meta-substituted benzenes.
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16
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Ramdas V, Talwar R, Banerjee M, Joshi AA, Das AK, Walke DS, Borhade P, Dhayagude U, Loriya R, Gote G, Bommakanti A, Sivaram A, Agarwal G, Goswami A, Nigade P, Mehta M, Patil V, Modi D, Kumar H, Mallurwar S, Dash A, Modi F, Kuldharan S, Srivastava P, Singh M, Narasimham L, Gundu J, Sharma S, Kamboj RK, Palle VP. Discovery and Characterization of Potent Pan-Genotypic HCV NS5A Inhibitors Containing Novel Tricyclic Central Core Leading to Clinical Candidate. J Med Chem 2019; 62:10563-10582. [PMID: 31710479 DOI: 10.1021/acs.jmedchem.9b01562] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The identification of a novel class of potent pan-genotypic NS5A inhibitors with good pharmacokinetic profile suitable for potential use in treating HCV infections is disclosed here. The present series of compounds are with less complex tricyclic central core, identified through a systematic SAR study carried out on biphenyl moiety. The SAR outcome has confirmed the requirement of near planar and linear conformation of the molecule to achieve the best pan-genotypic activity. In addition, SAR with substituted imidazoles on improvement of antiviral activity is disclosed. The newly identified compounds 12, 16, 19-21 have shown desirable pharmacokinetic profiles with a favorable uptake of compounds in liver and maintained a significant concentration for up to 8 h in the liver. In addition, compounds 20 and 21 have shown superior pan-genotypic anti-HCV activity compared to ledipasvir and daclatasvir. Additional characterization and preliminary safety assessment resulted in the identification of compound 20 as a potential clinical candidate.
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Affiliation(s)
- Vidya Ramdas
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Rashmi Talwar
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Moloy Banerjee
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Advait Arun Joshi
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Amit Kumar Das
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Deepak Sahebrao Walke
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Prashant Borhade
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Usha Dhayagude
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Rajesh Loriya
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Ganesh Gote
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Apparao Bommakanti
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Aruna Sivaram
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Gautam Agarwal
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Arnab Goswami
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Prashant Nigade
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Maneesh Mehta
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Vinod Patil
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Dipak Modi
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Hemant Kumar
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Sadanand Mallurwar
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Amruta Dash
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Falguni Modi
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Sandip Kuldharan
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Pratima Srivastava
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Minakshi Singh
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Lakshmi Narasimham
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Jayasagar Gundu
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Sharad Sharma
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Rajender Kumar Kamboj
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
| | - Venkata P Palle
- Novel Drug Discovery & Development , Lupin Ltd. , Lupin Research Park, Survey No. 46 A/47 A, Village Nande, Taluka Mulshi , Pune 412115 , India
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17
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Lu Z, Duan JJW, Xiao H, Neels J, Wu DR, Weigelt CA, Sack JS, Khan J, Ruzanov M, An Y, Yarde M, Karmakar A, Vishwakrishnan S, Baratam V, Shankarappa H, Vanteru S, Babu V, Basha M, Kumar Gupta A, Kumaravel S, Mathur A, Zhao Q, Salter-Cid LM, Carter PH, Murali Dhar T. Identification of potent, selective and orally bioavailable phenyl ((R)-3-phenylpyrrolidin-3-yl)sulfone analogues as RORγt inverse agonists. Bioorg Med Chem Lett 2019; 29:2265-2269. [DOI: 10.1016/j.bmcl.2019.06.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 11/25/2022]
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18
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You Y, Kim HS, Park JW, Keum G, Jang SK, Kim BM. Sulfur(vi) fluoride exchange as a key reaction for synthesizing biaryl sulfate core derivatives as potent hepatitis C virus NS5A inhibitors and their structure-activity relationship studies. RSC Adv 2018; 8:31803-31821. [PMID: 35548241 PMCID: PMC9085918 DOI: 10.1039/c8ra05471a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/28/2018] [Indexed: 12/25/2022] Open
Abstract
Extremely potent, new hepatitis C virus (HCV) nonstructural 5A (NS5A) featuring substituted biaryl sulfate core structures was designed and synthesized. Based on the previously reported novel HCV NS5A inhibitors featuring biaryl sulfate core structures which exhibit two-digit picomolar half-maximal effective concentration (EC50) values against HCV genotype 1b and 2a, the new inhibitors equipped with the sulfate core structures containing diversely substituted aryl groups were explored. In this study, highly efficient, chemoselective coupling reactions between an arylsulfonyl fluoride and an aryl silyl ether, known as the sulfur(vi) fluoride exchange (SuFEx) reaction, were utilized. Among the inhibitors prepared based on the SuFEx chemistry, compounds 14, 15 and 29 exhibited two-digit picomolar EC50 values against GT-1b and single digit or sub nanomolar activities against the HCV GT-2a strain. Nonsymmetrical inhibitors containing an imidazole and amide moieties on each side of the sulfate core structures were also synthesized. In addition, a biotinylated probe targeting NS5A protein was prepared for labeling using the same synthetic methodology.
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Affiliation(s)
- Youngsu You
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 South Korea
| | - Hee Sun Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology Pohang 37673 South Korea
| | - Jung Woo Park
- Supercomputing Modeling & Simulation Center, Division of Data Analysis, Korea Institute of Science and Technology Information (KISTI) 245 Daehak-ro, Yuseong-gu Daejeon 34141 South Korea
| | - Gyochang Keum
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST) Hwarangno 14-gil 5, Seongbuk-gu Seoul 02455 South Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology Pohang 37673 South Korea
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 South Korea
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19
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Auberson YP, Brocklehurst C, Furegati M, Fessard TC, Koch G, Decker A, La Vecchia L, Briard E. Improving Nonspecific Binding and Solubility: Bicycloalkyl Groups and Cubanes as para-Phenyl Bioisosteres. ChemMedChem 2017; 12:590-598. [PMID: 28319646 DOI: 10.1002/cmdc.201700082] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/17/2017] [Indexed: 11/09/2022]
Abstract
Bicycloalkyl groups have been previously described as phenyl group bioisosteres. This article describes the synthesis of new building blocks allowing their introduction into complex molecules, and explores their use as a means to modify the physicochemical properties of drug candidates and improve the quality of imaging agents. In particular, the replacement of an aromatic ring with a bicyclo[1.1.1]pentane-1,3-diyl (BCP) group improves aqueous solubility by at least 50-fold, and markedly decreases nonspecific binding (NSB) as measured by CHI(IAM), the chromatographic hydrophobicity index on immobilized artificial membranes. Structural variations with the bicyclo[2.2.2]octane-1,4-diyl group led to more lipophilic molecules and did not show the same benefits regarding NSB or solubility, whereas substitutions with cubane-1,4-diyl showed improvements for both parameters. These results confirm the potential advantages of both BCP and cubane motifs as bioisosteric replacements for optimizing para-phenyl-substituted molecules.
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Affiliation(s)
- Yves P Auberson
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 141 Klybeckstrasse, 4057, Basel, Switzerland
| | - Cara Brocklehurst
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 141 Klybeckstrasse, 4057, Basel, Switzerland
| | - Markus Furegati
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 141 Klybeckstrasse, 4057, Basel, Switzerland
| | - Thomas C Fessard
- SpiroChem AG, Swiss Federal Institute of Technology (ETH) Zürich, LOC-HCI-H337, Wolfgang-Pauli Str. 10, 8093, Zürich, Switzerland
| | - Guido Koch
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 141 Klybeckstrasse, 4057, Basel, Switzerland
| | - Andrea Decker
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 141 Klybeckstrasse, 4057, Basel, Switzerland
| | - Luigi La Vecchia
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 141 Klybeckstrasse, 4057, Basel, Switzerland
| | - Emmanuelle Briard
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 141 Klybeckstrasse, 4057, Basel, Switzerland
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20
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Tereshchenko AD, Myronchuk JS, Leitchenko LD, Knysh IV, Tokmakova GO, Litsis OO, Tolmachev A, Liubchak K, Mykhailiuk P. Synthesis of 3-oxadiazolyl/triazolyl morpholines: Novel scaffolds for drug discovery. Tetrahedron 2017. [DOI: 10.1016/j.tet.2016.12.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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You Y, Kim HS, Bae IH, Lee SG, Jee MH, Keum G, Jang SK, Kim BM. New potent biaryl sulfate-based hepatitis C virus inhibitors. Eur J Med Chem 2016; 125:87-100. [PMID: 27657807 DOI: 10.1016/j.ejmech.2016.09.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
Abstract
The discovery of a new series of potent hepatitis C virus (HCV) NS5A inhibitors containing biaryl sulfone or sulfate cores is reported. Structure-activity relationship (SAR) studies on inhibitors containing various substitution patterns of the sulfate or sulfone core structure established that m-,m'- substituted biaryl sulfate core-based inhibitors containing an amide moiety (compound 20) or an imidazole moiety (compound 24) showed extremely high potency. Compound 20 demonstrated double-digit pM potencies against both genotype 1b (GT-1b) and 2a (GT-2a). Compound 24 also exhibited double-digit pM potencies against GT-1b and sub nM potencies against GT-2a. Furthermore, compounds 20 and 24 exhibited no cardiotoxicity in an hERG ligand binding assay and showed acceptable plasma stability and no mutagenic potential in the Ames test. In addition, these compounds showed distinctive additive effects in combination treatment with the NS5B targeting drug sofosbuvir (Sovaldi®). The results of this study showed that the compounds 20 and 24 could be effective HCV inhibitors.
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Affiliation(s)
- Youngsu You
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Hee Sun Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Il Hak Bae
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Seung Gi Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Min Hyeok Jee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Gyochang Keum
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, South Korea
| | - Sung Key Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, South Korea.
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, South Korea.
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22
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Discovery of ravidasvir (PPI-668) as a potent pan-genotypic HCV NS5A inhibitor. Bioorg Med Chem Lett 2016; 26:4508-4512. [DOI: 10.1016/j.bmcl.2016.07.066] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/17/2022]
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