1
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Zhang W, Ma Z, Han X, Li G. Design, synthesis and biological activity of α-nitrile substituted guaiazulene-based chalcone derivatives. Fitoterapia 2024; 178:106151. [PMID: 39098736 DOI: 10.1016/j.fitote.2024.106151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/06/2024]
Abstract
In present study, seventeen α-nitrile substituted guaiazulene-based chalcone derivatives including twelve new were designed, synthesized, and assayed for antiviral, cytotoxicity and signal pathway activities. All derivatives showed potential antiviral activity towards influenza virus or herpes simplex virus (HSV), 7 g with the substitution of nitro group showed strong effects towards H1N1 virus at 30 μM with inhibitory rate of 66.0%, 7o with thiophene exhibited potent anti HSV-1 activities with inhibitory rate of 65.8%. Moreover, several compounds exhibited inhibitory effects on tumor cells and hypoxia-inducible factor-1 (HIF1) signaling pathways. These results showed that α-nitrile substituted guaiazulene-based chalcones offered a promising framework for the further development of new highly efficient drugs.
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Affiliation(s)
- Wenjie Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zongchen Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiao Han
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Guoqiang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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2
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Adak S, Ye N, Calderone LA, Duan M, Lubeck W, Schäfer RJB, Lukowski AL, Houk KN, Pandelia ME, Drennan CL, Moore BS. A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile. Nat Chem 2024:10.1038/s41557-024-01603-z. [PMID: 39285206 DOI: 10.1038/s41557-024-01603-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 07/12/2024] [Indexed: 09/25/2024]
Abstract
Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes.
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Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Naike Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Meng Duan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Wilson Lubeck
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Rebecca J B Schäfer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - April L Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | | | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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3
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Lee S, Kang G, Han S. Development of an Easy-To-Handle Redox Active Group for Alcohols: Catalytic Transformation of Tertiary Alcohols to Nitriles. Org Lett 2024; 26:5640-5645. [PMID: 38924766 DOI: 10.1021/acs.orglett.4c01580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The generation of radical intermediates via SET-mediated deoxygenation of activated alcohol derivatives is desirable, as alcohols can be utilized in various radical-mediated reactions. Herein, we introduce α-N-phthalimido-oxy isobutyrate (NPIB) as a novel activating group for alcohols. Essentially, it is a more chemically robust alternative to Overman's N-phthalimidoyl oxalate group. The utility of the NPIB group is showcased in the conversion of tertiary alcohols to nitriles under Ir/Cu dual catalysts and in the presence of TMSCN upon blue LED irradiation. With our newly developed NPIB handle, the reactivities of N-hydroxyphthalimide esters derived from carboxylic acids would be achievable with naturally and commercially more abundant alcohol substrates.
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Affiliation(s)
- Seunghee Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gyumin Kang
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sunkyu Han
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST), Daejeon 34141, Republic of Korea
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4
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Khetmalis YM, Shobha S, Nandikolla A, Chandu A, Murugesan S, Kumar MMK, Chandra Sekhar KVG. Design, synthesis, and anti-mycobacterial evaluation of 1,8-naphthyridine-3-carbonitrile analogues. RSC Adv 2024; 14:22676-22689. [PMID: 39027042 PMCID: PMC11255784 DOI: 10.1039/d4ra04262j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
Twenty-eight compounds, viz., 1,8-naphthyridine-3-carbonitrile (ANC and ANA) derivatives, were designed and synthesized through a molecular hybridization approach. The structures of these compounds were analyzed and confirmed using 1H NMR, 13C NMR, LCMS, and elemental analyses. The synthesized compounds were evaluated by in vitro testing for their effectiveness against tuberculosis using the MABA assay, targeting the Mycobacterium tuberculosis H37Rv strain. Their minimum inhibitory concentration (MIC) was determined, showing that the tested compounds' MIC values ranged from 6.25 to ≤50 μg mL-1. Among the derivatives studied, ANA-12 demonstrated prominent anti-tuberculosis activity with a MIC of 6.25 μg mL-1. Compounds ANC-2, ANA-1, ANA 6-8, and ANA-10 displayed moderate to good anti-tuberculosis activity with MIC values of 12.5 μg mL-1. Compounds with MIC ≤ 12.5 μg mL-1 were screened against human embryonic kidney cells to assess their potential cytotoxicity. Interestingly, these compounds showed less toxicity towards normal cells, with a selectivity index value ≥ 11. To further evaluate the binding pattern in the active site of enoyl-ACP reductase (InhA) from Mtb (PDB-4TZK), a molecular docking analysis of compound ANA-12 was performed using the glide module of Schrodinger software. The stability, confirmation, and intermolecular interactions of the cocrystal ligand and the highly active compound ANA-12 on the chosen target protein were investigated through molecular dynamics simulations lasting 100 ns. In silico predictions were utilized to assess the ADMET properties of the final compounds. A suitable single crystal was developed and analyzed for compound ANA-5 to gain a deeper understanding of the compounds' structures.
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Affiliation(s)
- Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India +91 40 66303527
| | - Singarapalle Shobha
- College of Pharmaceutical Sciences, Andhra University Visakhapatnam Andhra Pradesh - 530 003 India
| | - Adinarayana Nandikolla
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India +91 40 66303527
| | - Ala Chandu
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani 333031 India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani 333031 India
| | | | - Kondapalli Venkata Gowri Chandra Sekhar
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India +91 40 66303527
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5
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Chiodi D, Ishihara Y. The role of the methoxy group in approved drugs. Eur J Med Chem 2024; 273:116364. [PMID: 38781921 DOI: 10.1016/j.ejmech.2024.116364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 05/25/2024]
Abstract
The methoxy substituent is prevalent in natural products and, consequently, is present in many natural product-derived drugs. It has also been installed in modern drug molecules with no remnant of natural product features because medicinal chemists have been taking advantage of the benefits that this small functional group can bestow on ligand-target binding, physicochemical properties, and ADME parameters. Herein, over 230 methoxy-containing small-molecule drugs, as well as several fluoromethoxy-containing drugs, are presented from the vantage point of the methoxy group. Biochemical mechanisms of action, medicinal chemistry SAR studies, and numerous X-ray cocrystal structures are analyzed to identify the precise role of the methoxy group for many of the drugs and drug classes. Although the methoxy substituent can be considered as the hybridization of a hydroxy and a methyl group, the combination of these functionalities often results in unique effects that can amount to more than the sum of the individual parts.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, Takeda Pharmaceuticals, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA, 92121, USA.
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6
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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7
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Liu M, Li S. Nitrile biosynthesis in nature: how and why? Nat Prod Rep 2024; 41:649-671. [PMID: 38193577 DOI: 10.1039/d3np00028a] [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: 01/10/2024]
Abstract
Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.
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Affiliation(s)
- Mingyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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8
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Liang ZL, Zhang ZH, Jiao YE, Xu H, Hu HS, Zhao B. Highly Stable 72-Nuclearity Nanocages for Efficient Synthesis of Aryl Nitriles via Ni/Cu Synergistic Catalysis. J Am Chem Soc 2024; 146:10776-10784. [PMID: 38578219 DOI: 10.1021/jacs.4c00885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Seeking noble-metal-free catalysts for efficient synthesis of aryl nitriles under mild conditions poses a significant challenge due to the use of hypertoxic cyanides or high-pressure/temperature NH3/O2 in conventional synthesis processes. Herein, we developed a novel framework 1 assembled by [Ni72] nanocages with excellent solvents/pH stability. To investigate the structure-activity relationship of catalytic performance, several isostructural MOFs with different molar ratios of Ni/Cu by doping Cu2+ into framework 1 (Ni0.59Cu0.41 (2), Ni0.81Cu0.19 (3), Ni0.88Cu0.12 (4), and Ni0.92Cu0.08 (5)) were prepared. Catalytic studies revealed that catalyst 3 exhibited remarkable performance in the synthesis of aryl nitriles, utilizing a formamide alternative to hypertoxic NaCN/KCN. Notably, catalyst 3 achieved an excellent TOF value of 9.8 h-1. Furthermore, catalyst 3 demonstrated its applicability in a gram-scale experiment and maintained its catalytic performance even after six recycling cycles, owing to its high stability resulting from significant electrostatic and orbital interactions between the Ni center and ligands as well as a large SOMO-LUMO energy gap supported by DFT calculations. Control experiments and DFT calculations further revealed that the excellent catalytic performance of catalyst 3 originated from the synergistic effect of Ni/Cu. Importantly, this work not only provides a highly feasible method to construct highly stable MOFs containing multinuclear nanocages with exceptional catalytic performance but also represents the first example of a heterogeneous catalyst for the synthesis of aryl nitriles using formamide as the cyanide source.
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Affiliation(s)
- Ze-Long Liang
- Department of Chemistry, Key Laboratory of Advanced Energy Material Chemistry (Ministry of Education), and Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Zi-He Zhang
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Yue-E Jiao
- Department of Chemistry, Key Laboratory of Advanced Energy Material Chemistry (Ministry of Education), and Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Hang Xu
- Department of Chemistry, Key Laboratory of Advanced Energy Material Chemistry (Ministry of Education), and Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Han-Shi Hu
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Bin Zhao
- Department of Chemistry, Key Laboratory of Advanced Energy Material Chemistry (Ministry of Education), and Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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9
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Guin AK, Chakraborty S, Khanra S, Chakraborty S, Paul ND. Oxygen-Dependent Ligand-Controlled Iron-Catalyzed Chemoselective Synthesis of Olefins and Vinyl Nitriles. Org Lett 2024; 26:2540-2545. [PMID: 38546405 DOI: 10.1021/acs.orglett.4c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
An oxygen-dependent ligand-controlled chemoselective synthesis of vinyl nitriles and E-olefins by coupling a variety of alcohols and benzyl cyanides, catalyzed by a well-characterized, air-stable, easy-to-prepare Fe(II) catalyst (1a) bearing a redox-active arylazo pincer (L1a) is reported. The azo-moiety of the ligand backbone acts as an electron and hydrogen reservoir, enabling catalyst 1a to efficiently produce a broad spectrum of vinyl nitriles and E-olefins in moderate to good yields selectively under an oxygen and argon atmosphere, respectively.
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Affiliation(s)
- Amit Kumar Guin
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Botanic Garden, Howrah 711103, India
| | - Subhajit Chakraborty
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Botanic Garden, Howrah 711103, India
| | - Subhankar Khanra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Botanic Garden, Howrah 711103, India
| | - Santana Chakraborty
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Botanic Garden, Howrah 711103, India
| | - Nanda D Paul
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Botanic Garden, Howrah 711103, India
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10
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Kirsh J, Weaver JB, Boxer SG, Kozuch J. Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields. J Am Chem Soc 2024; 146:6983-6991. [PMID: 38415598 PMCID: PMC10941190 DOI: 10.1021/jacs.3c14775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.
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Affiliation(s)
- Jacob
M. Kirsh
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jared Bryce Weaver
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Steven G. Boxer
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jacek Kozuch
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
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11
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Lee H, Nam H, Lee SY. Enantio- and Diastereoselective Variations on α-Iminonitriles: Harnessing Chiral Cyclopropenimine-Thiourea Organocatalysts. J Am Chem Soc 2024; 146:3065-3074. [PMID: 38281151 DOI: 10.1021/jacs.3c09911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Chiral 1-pyrrolines containing a nitrile motif serve as crucial structural scaffolds in biologically active molecules and exhibit diversity as building blocks owing to their valuable functional groups; however, the asymmetric synthesis of such compounds remains largely unexplored. Herein, we present an enantio- and diastereoselective method for the synthesis of α-chiral nitrile-containing 1-pyrroline derivatives bearing vicinal stereocenters through the design and introduction of chiral cyclopropenimine-based bifunctional catalysts featuring a thiourea moiety. This synthesis entails a highly stereoselective conjugate addition of α-iminonitriles to a wide array of enones, followed by cyclocondensation, thereby affording a series of cyanopyrroline derivatives, some of which contain all-carbon quaternary centers. Moreover, we demonstrate the synthetic utility of this strategy by performing a gram-scale reaction with 1% catalyst loading, along with a variety of chemoselective transformations of the product, including the synthesis of a vildagliptin analogue. Finally, we showcase the selective synthesis of all four stereoisomers of the cyanopyrroline products through trans-to-cis isomerization, highlighting the versatility of our approach.
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Affiliation(s)
- Hooseung Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyeongwoo Nam
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Sarah Yunmi Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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12
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Mao R, Taylor DM, Wackelin DJ, Wu SJ, Sicinski KM, Arnold FH. Biocatalytic, Stereoconvergent Alkylation of ( Z/E)-Trisubstituted Silyl Enol Ethers. NATURE SYNTHESIS 2024; 3:256-264. [PMID: 39130128 PMCID: PMC11309014 DOI: 10.1038/s44160-023-00431-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/04/2023] [Indexed: 08/13/2024]
Abstract
Alkene functionalization has garnered significant attention due to the versatile reactivity of C=C bonds. A major challenge is the selective conversion of isomeric alkenes into chiral products. Researchers have devised various biocatalytic strategies to transform isomeric alkenes into stereopure compounds; while selective, the enzymes often specifically convert one alkene isomer, thereby diminishing overall yield. To increase the overall yield, scientists have introduced additional driving forces to interconvert alkene isomers. This improves the yield of biocatalytic alkene functionalization at the cost of increased energy consumption and chemical waste. Developing a stereoconvergent enzyme for alkene functionalization offers an ideal solution, although such catalysts are rarely reported. Here we present engineered hemoproteins derived from a bacterial cytochrome P450 that efficiently catalyze the stereoconvergent α-carbonyl alkylation of isomeric silyl enol ethers, producing stereopure products. Through screening and directed evolution, we generated P450BM3 variant SCA-G2, which catalyzes stereoconvergent carbene transfer in E. coli, with high efficiency and stereoselectivity toward various Z/E mixtures of silyl enol ethers. In contrast to established stereospecific transformations that leave one isomer unreacted, SCA-G2 converts both isomers to a stereopure product. This biocatalytic approach simplifies the synthesis of chiral α-branched ketones by eliminating the need for stoichiometric chiral auxiliaries, strongly basic alkali-metal enolates, and harsh conditions, delivering products with high efficiency and excellent chemo- and stereoselectivities.
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Affiliation(s)
| | | | | | - Sophia J. Wu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Kathleen M. Sicinski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
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13
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He Y, Jin H, Ju F. Toxicological effects and underlying mechanisms of chlorination-derived metformin byproducts in Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167281. [PMID: 37758144 DOI: 10.1016/j.scitotenv.2023.167281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
Abstract
Chlorination-derived byproducts of the emerging contaminant metformin, such as (3E)-3-(chloroimino)-N,N-dimethyl-3H-1,2,4-triazol-5-amine (3,3-CDTA) and N-cyano-N,N-dimethylcarbaminmidic chloride (NCDC), occur in global waters and are toxic to organisms, from bacteria to mice. However, the mechanisms underlying their toxicity remain unknown. Here, we explored the toxicological effects and potential molecular mechanisms of 3,3-CDTA and NCDC at milligram concentrations, using Escherichia coli as a model organism. Compared with metformin (>300 mg/L), 3,3-CDTA and NCDC exerted stronger toxicity to E. coli, with a 4-h half maximal inhibitory concentration of 2.97 mg/L and 75.7 mg/L, respectively. Both byproducts disrupted E. coli cellular structures and components, decreased membrane potential and adenosine triphosphate (ATP) biosynthesis, and led to excessive reactive oxidative species (ROS), as well as the ROS-scavenging enzymes superoxide dismutase and catalase. Proteomic analysis and molecular docking supported these biomarker responses in the byproduct-treated E. coli, and indicated potential damage to DNA/RNA processes, while also provided novel insights into the toxicological and detoxified-byproduct effects at the proteome level. The toxicity-related events of NCDC and 3,3-CDTA included membrane disruption, oxidative stress, and abnormal protein expression. This study is the first to examine the toxicological effects of chlorination-derived metformin byproducts in E. coli and the associated pathways involved; thereby broadening our understanding regarding the toxicity and transformation risks of metformin throughout its entire life process.
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Affiliation(s)
- Yuanzhen He
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Hui Jin
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Research Centre for Industries of the Future, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China.
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14
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Feral A, Martin AR, Desfoux A, Amblard M, Vezenkov LL. Covalent-reversible peptide-based protease inhibitors. Design, synthesis, and clinical success stories. Amino Acids 2023; 55:1775-1800. [PMID: 37330416 DOI: 10.1007/s00726-023-03286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated human peptidases are implicated in a large variety of diseases such as cancer, hypertension, and neurodegeneration. Viral proteases for their part are crucial for the pathogens' maturation and assembly. Several decades of research were devoted to exploring these precious therapeutic targets, often addressing them with synthetic substrate-based inhibitors to elucidate their biological roles and develop medications. The rational design of peptide-based inhibitors offered a rapid pathway to obtain a variety of research tools and drug candidates. Non-covalent modifiers were historically the first choice for protease inhibition due to their reversible enzyme binding mode and thus presumably safer profile. However, in recent years, covalent-irreversible inhibitors are having a resurgence with dramatic increase of their related publications, preclinical and clinical trials, and FDA-approved drugs. Depending on the context, covalent modifiers could provide more effective and selective drug candidates, hence requiring lower doses, thereby limiting off-target effects. Additionally, such molecules seem more suitable to tackle the crucial issue of cancer and viral drug resistances. At the frontier of reversible and irreversible based inhibitors, a new drug class, the covalent-reversible peptide-based inhibitors, has emerged with the FDA approval of Bortezomib in 2003, shortly followed by 4 other listings to date. The highlight in the field is the breathtakingly fast development of the first oral COVID-19 medication, Nirmatrelvir. Covalent-reversible inhibitors can hipothetically provide the safety of the reversible modifiers combined with the high potency and specificity of their irreversible counterparts. Herein, we will present the main groups of covalent-reversible peptide-based inhibitors, focusing on their design, synthesis, and successful drug development programs.
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Affiliation(s)
- Anthony Feral
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
| | | | | | - Muriel Amblard
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
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15
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Taniguchi T, Agbo DO. Vibrational circular dichroism spectroscopy in the C-D, XY, and XYZ stretching region. Phys Chem Chem Phys 2023; 25:28567-28575. [PMID: 37861094 DOI: 10.1039/d3cp04287a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is a powerful technique for structural analysis of chiral molecules, but information available from VCD spectra of large molecular systems can be limited by severe overlap of vibrational bands. While common chiral molecules do not absorb in the 1900-2400 cm-1 region, observation of VCD signals in this spectrally-isolated region is possible for molecules containing C-D, XY, and XYZ chromophores. Thus, a strategic introduction of these chromophores to a target molecule may produce VCD signals informative for molecular structures. VCD spectroscopy in the 1900-2400 cm-1 region is a rather unexplored research field and its basic properties remain to be investigated. This perspective article discusses insight obtained so far on the usefulness and physicochemical aspects of VCD spectroscopy in this region with briefly summarizing previous experimental VCD studies including classic examples as well as our recent results. We show that anharmonic effects such as overtones and combination bands often complicate VCD patterns. On the other hand, some molecules exhibit characteristic VCD signals that can be well interpreted by harmonic DFT spectral calculations for structural analysis. This article also discusses several examples of the use of this region for studying solute-solvent interactions and for VCD signal augmentation.
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Affiliation(s)
- Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan.
| | - Davidson Obinna Agbo
- Graduate School of Life Science, Hokkaido University, North 21 West 11, Sapporo 001-0021, Japan
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16
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Burton NR, Polasky DA, Shikwana F, Ofori S, Yan T, Geiszler DJ, Veiga Leprevost FD, Nesvizhskii AI, Backus KM. Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics. J Am Chem Soc 2023; 145:21303-21318. [PMID: 37738129 DOI: 10.1021/jacs.3c05797] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Mass spectrometry-based chemoproteomics has emerged as an enabling technology for functional biology and drug discovery. To address limitations of established chemoproteomics workflows, including cumbersome reagent synthesis and low throughput sample preparation, here, we established the silane-based cleavable isotopically labeled proteomics (sCIP) method. The sCIP method is enabled by a high yielding and scalable route to dialkoxydiphenylsilane fluorenylmethyloxycarbonyl (DADPS-Fmoc)-protected amino acid building blocks, which enable the facile synthesis of customizable, isotopically labeled, and chemically cleavable biotin capture reagents. sCIP is compatible with both MS1- and MS2-based quantitation, and the sCIP-MS2 method is distinguished by its click-assembled isobaric tags in which the reporter group is encoded in the sCIP capture reagent and balancer in the pan cysteine-reactive probe. The sCIP-MS2 workflow streamlines sample preparation with early stage isobaric labeling and sample pooling, allowing for high coverage and increased sample throughput via customized low cost six-plex sample multiplexing. When paired with a custom FragPipe data analysis workflow and applied to cysteine-reactive fragment screens, sCIP proteomics revealed established and unprecedented cysteine-ligand pairs, including the discovery that mitochondrial uncoupling agent FCCP acts as a covalent-reversible cysteine-reactive electrophile.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Flowreen Shikwana
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
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17
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Reisenbauer J, Finkelstein P, Ebert MO, Morandi B. Mechanistic Investigation of the Nickel-Catalyzed Transfer Hydrocyanation of Alkynes. ACS Catal 2023; 13:11548-11555. [PMID: 37671177 PMCID: PMC10476158 DOI: 10.1021/acscatal.3c02977] [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: 06/30/2023] [Revised: 07/28/2023] [Indexed: 09/07/2023]
Abstract
The implementation of HCN-free transfer hydrocyanation reactions on laboratory scales has recently been achieved by using HCN donor reagents under nickel- and Lewis acid co-catalysis. More recently, malononitrile-based HCN donor reagents were shown to undergo the C(sp3)-CN bond activation by the nickel catalyst in the absence of Lewis acids. However, there is a lack of detailed mechanistic understanding of the challenging C(sp3)-CN bond cleavage step. In this work, in-depth kinetic and computational studies using alkynes as substrates were used to elucidate the overall reaction mechanism of this transfer hydrocyanation, with a particular focus on the activation of the C(sp3)-CN bond to generate the active H-Ni-CN transfer hydrocyanation catalyst. Comparisons of experimentally and computationally derived 13C kinetic isotope effect data support a direct oxidative addition mechanism of the nickel catalyst into the C(sp3)-CN bond facilitated by the coordination of the second nitrile group to the nickel catalyst.
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Affiliation(s)
| | | | | | - Bill Morandi
- ETH Zürich, Vladimir-Prelog-Weg 3, HCI, 8093 Zürich, Switzerland
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18
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Adak S, Ye N, Calderone LA, Schäfer RJB, Lukowski AL, Pandelia ME, Drennan CL, Moore BS. Oxidative rearrangement of tryptophan to indole nitrile by a single diiron enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551874. [PMID: 37577561 PMCID: PMC10418191 DOI: 10.1101/2023.08.03.551874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Nitriles are uncommon in nature and are typically constructed from oximes via the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third strategy of nitrile biosynthesis featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the 'eagle-killing' neurotoxin, aetokthonotoxin, AetD converts the alanyl side chain of 5,7-dibromo-L-tryptophan to a nitrile. Employing a combination of structural, biochemical, and biophysical techniques, we characterized AetD as a non-heme diiron enzyme that belongs to the emerging Heme Oxygenase-like Diiron Oxidase and Oxygenase (HDO) superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation that we propose proceeds via an aziridine intermediate. Our work presents a new paradigm for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other HDO enzymes.
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Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Naike Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Logan A. Calderone
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Rebecca J. B. Schäfer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - April L. Lukowski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 01239, United States
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
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19
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Bera S, Datta HK, Dastidar P. Nitrile-Containing Terpyridyl Zn(II)-Coordination Polymer-Based Metallogelators Displaying Helical Structures: Synthesis, Structures, and "Druglike" Action against B16-F10 Melanoma Cells. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25098-25109. [PMID: 35723469 DOI: 10.1021/acsami.2c05338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
An attempt has been made to develop a self-drug-delivery system against melanoma from a series of metallogelators derived from coordination polymers. Thus, a series of coordination polymers (CP1-CP6) derived from a nitrile-containing terpyridyl ligand (L) and transition metal salts (Cu(I)/Zn(II)) have been synthesized and thoroughly characterized by a number of physicochemical techniques including single crystal X-ray diffraction. Reactions of the ingredients of the coordination polymers guided by their single crystal structures produced four metallogels (CPG2-CPG5) which were characterized by dynamic rheology and TEM. The metallogelator CPG3 turned out to be the best suited for further studies as revealed from MTT assay against melanoma (B16-F10) and macrophage (RAW 264.7) cells. Various experiments (scratch, cell cycle, nuclear condensation, annexin V-FITC/PI, mitochondrial membrane potential, Ho-efflux assays) not only supported the "druglike" action against melanoma B16-F10 cells but also suggested that the mechanism of cancer cell death was via mitochondrial membrane potential depolarization-driven apoptosis. Because melanoma B16-F10 is a model cell line for human skin cancer, the metallogel CPG3 may, therefore, be further developed for such treatment.
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Affiliation(s)
- Sourabh Bera
- School of Chemical Sciences, Indian Association for the Cultivation of Science (IACS), 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Hemanta Kumar Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science (IACS), 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Parthasarathi Dastidar
- School of Chemical Sciences, Indian Association for the Cultivation of Science (IACS), 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
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20
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Alfano AI, Pelliccia S, Rossino G, Chianese O, Summa V, Collina S, Brindisi M. Continuous-Flow Technology for Chemical Rearrangements: A Powerful Tool to Generate Pharmaceutically Relevant Compounds. ACS Med Chem Lett 2023; 14:326-337. [PMID: 36923914 PMCID: PMC10009796 DOI: 10.1021/acsmedchemlett.3c00010] [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: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
The efficacy, safety, and scale-up of several chemical rearrangements remain unsolved problems due to the associated handling of hazardous, toxic, and pollutant chemicals and high-risk intermediates. For many years batch processes have been considered the only possibility to drive these reactions, but continuous-flow technology has emerged, for both academic laboratories and pharmaceutical companies, as a powerful tool for easy, controlled, and safer chemistry protocols, helping to minimize the formation of side products and increase reaction yields. This Technology Note summarizes recently reported chemical rearrangements using continuous-flow approaches, with a focus on Curtius, Hofmann, and Schmidt reactions. Flow protocols, general advantages and safety aspects, and reaction scope for the generation of both privileged scaffolds and active pharmaceutical ingredients will be showcased.
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Affiliation(s)
- Antonella Ilenia Alfano
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Sveva Pelliccia
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Orazio Chianese
- Genetic S.p.A., Via Canfora, 64, 84084 Fisciano (Salerno), Italy
| | - Vincenzo Summa
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Margherita Brindisi
- Department of Pharmacy (DoE 2023-2027), University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
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21
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Ishii H, Yamasaki T, Okamura T, Zhang Y, Kurihara Y, Ogawa M, Nengaki N, Zhang MR. Evaluation and improvement of CuI-mediated 11 C-cyanation. J Labelled Comp Radiopharm 2023; 66:95-107. [PMID: 36791689 DOI: 10.1002/jlcr.4016] [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: 09/15/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023]
Abstract
CuI-mediated 11 C-cyanation was evaluated by synthesizing [11 C]perampanel ([11 C]5) as a model compound and compared with previous reports. To a DMF solution with 5'-(2-bromophenyl)-1'-phenyl-[2,3'-bipyridin]-6'(1'H)-one (4) and CuI, [11 C]NH4 CN in a stream of ammonia/nitrogen (5:95, v/v) gas was bubbled. Subsequently, the reaction mixture was heated at 180°C for 5 min. After HPLC purification, [11 C]5 was obtained in 7.2 ± 1.0% (n = 4) non-decay corrected radiochemical yield with >99% radiochemical purity and a molar activity of 98 ± 28 GBq/μmol. In vivo evaluations of [11 C]5 were performed using small animals. PET scans to check the kinetics of [11 C]5 in the whole body of mice suggested that [11 C]5 spreads rapidly into the brain, heart, and lungs and then accumulates in the small intestine. To evaluate the performance of CuI-mediated 11 C-cyanation reaction, bromobenzene (6a) was selected as the model compound; however, it failed. Therefore, optimization of the reaction conditions has been performed, and consequently, the addition of K2 CO3 and prolonging the reaction time improved the radiochemical yield about double. With this improved method, CuI-mediated 11 C-cyanation of various (hetero)aromatic bromides was performed to exhibit the tolerance of most functional groups and to provide 11 C-cyanated products in good to moderate radiochemical yields.
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Affiliation(s)
- Hideki Ishii
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Tomoteru Yamasaki
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Toshimitsu Okamura
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yiding Zhang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yusuke Kurihara
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- SHI Accelerator Service Ltd., Tokyo, Japan
| | - Masanao Ogawa
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- SHI Accelerator Service Ltd., Tokyo, Japan
| | - Nobuki Nengaki
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- SHI Accelerator Service Ltd., Tokyo, Japan
| | - Ming-Rong Zhang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
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22
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Bonatto V, Lameiro RF, Rocho FR, Lameira J, Leitão A, Montanari CA. Nitriles: an attractive approach to the development of covalent inhibitors. RSC Med Chem 2023; 14:201-217. [PMID: 36846367 PMCID: PMC9945868 DOI: 10.1039/d2md00204c] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Nitriles have broad applications in medicinal chemistry, with more than 60 small molecule drugs on the market containing the cyano functional group. In addition to the well-known noncovalent interactions that nitriles can perform with macromolecular targets, they are also known to improve drug candidates' pharmacokinetic profiles. Moreover, the cyano group can be used as an electrophilic warhead to covalently bind an inhibitor to a target of interest, forming a covalent adduct, a strategy that can present benefits over noncovalent inhibitors. This approach has gained much notoriety in recent years, mainly with diabetes and COVID-19-approved drugs. Nevertheless, the application of nitriles in covalent ligands is not restricted to it being the reactive center, as it can also be employed to convert irreversible inhibitors into reversible ones, a promising strategy for kinase inhibition and protein degradation. In this review, we introduce and discuss the roles of the cyano group in covalent inhibitors, how to tune its reactivity and the possibility of achieving selectivity only by replacing the warhead. Finally, we provide an overview of nitrile-based covalent compounds in approved drugs and inhibitors recently described in the literature.
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Affiliation(s)
- Vinícius Bonatto
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Rafael F Lameiro
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Fernanda R Rocho
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Jerônimo Lameira
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
- Institute of Biological Science, Federal University of Pará Rua Augusto Correa S/N Belém PA Brazil
| | - Andrei Leitão
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group, São Carlos Institute of Chemistry, University of São Paulo Avenue Trabalhador Sancarlense, 400 13566-590 São Carlos/SP Brazil
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23
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Wu X, Chen W, Holmberg-Douglas N, Bida GT, Tu X, Ma X, Wu Z, Nicewicz DA, Li Z. 11C, 12C and 13C-Cyanation of Electron-Rich Arenes via Organic Photoredox Catalysis. Chem 2023; 9:343-362. [PMID: 36777049 PMCID: PMC9913897 DOI: 10.1016/j.chempr.2022.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As a non-invasive imaging technology, positron emission tomography (PET) plays a crucial role in personalized medicine, including early diagnosis, patient screening, and treatment monitoring. The advancement of PET research depends on the discovery of new PET agents, which requires the development of simple and efficient radiolabeling methods in many cases. As bioisosteres for halogen and carbonyl moieties, nitriles are important functional groups in pharmaceutical and agrochemical compounds. Here, we disclose a mild organophotoredox-catalyzed method for efficient cyanation of a broad spectrum of electron-rich arenes, including abundant and readily available veratroles and pyrogallol trimethyl ethers. Notably, the transformations not only are compatible with various affordable 12C and 13C-cyanide sources, but also could be applied to carbon-11 synthons to incorporate [11C]nitriles into arenes. The aryl [11C]nitriles can be further derivatized to [11C]carboxylic acids, [11C]amides, and [11C]alkyl amines. The newly developed reaction can serve as a powerful tool for generating new PET agents.
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Affiliation(s)
- Xuedan Wu
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Wei Chen
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Natalie Holmberg-Douglas
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-3290, United States
| | - Gerald Thomas Bida
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Xianshuang Tu
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Xinrui Ma
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - Zhanhong Wu
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
| | - David A. Nicewicz
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-3290, United States
| | - Zibo Li
- Biomedical Research Imaging Center, Department of Radiology, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, USA
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24
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Zhang M, Zhou Q, Luo H, Tang ZL, Xu X, Wang XC. C3-Cyanation of Pyridines: Constraints on Electrophiles and Determinants of Regioselectivity. Angew Chem Int Ed Engl 2023; 62:e202216894. [PMID: 36517651 DOI: 10.1002/anie.202216894] [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: 11/17/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Methods for C-H cyanation of pyridines are rare. Here, we report a method for C3-selective cyanation of pyridines by a tandem process with the reaction of an in situ generated dihydropyridine with a cyano electrophile as the key step. The method is suitable for late-stage functionalization of pyridine drugs. The low reduction potential of the electrophile and effective transfer of the nitrile group were found to be essential for the success of this method. We studied the reaction mechanism in detail by means of control experiments and theoretical calculations and found that a combination of electronic and steric factors determined the regioselectivity of reactions involving C2-substituted pyridines.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Haihe Laboratory of Sustainable Chemical Transformations, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Qingyang Zhou
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Heng Luo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Haihe Laboratory of Sustainable Chemical Transformations, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zi-Lu Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Haihe Laboratory of Sustainable Chemical Transformations, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Xiufang Xu
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Xiao-Chen Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Haihe Laboratory of Sustainable Chemical Transformations, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, 94 Weijin Road, Tianjin, 300071, China
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25
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Saad MH, El-Moselhy TF, S El-Din N, Mehany ABM, Belal A, Abourehab MAS, Tawfik HO, El-Hamamsy MH. Discovery of new symmetrical and asymmetrical nitrile-containing 1,4-dihydropyridine derivatives as dual kinases and P-glycoprotein inhibitors: synthesis, in vitro assays, and in silico studies. J Enzyme Inhib Med Chem 2022; 37:2489-2511. [PMID: 36093880 PMCID: PMC9481151 DOI: 10.1080/14756366.2022.2120478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Two new series of symmetric (1a-h) and asymmetric (2a-l) 1,4-DHP derivatives were designed, synthesised, and evaluated as anticancer agents. In vitro anticancer screening of target compounds via National cancer institute “NCI” revealed that analogues 1g, 2e, and 2l demonstrated antiproliferative action with mean growth inhibition percentage “GI%” = 41, 28, and 64, respectively. The reversal doxorubicin (DOX) effects of compounds 1g, 2e, and 2l were examined and illustrated better cytotoxic activity with IC50 =1.12, 3.64, and 3.57 µM, respectively. The most active anticancer analogues, 1g, 2e, and 2l, were inspected for their putative mechanism of action by estimating their epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER-2), and Bruton’s tyrosine kinase (BTK) inhibitory activities. Furthermore, the antimicrobial activity of target compounds was assessed against six different pathogens, followed by determining the minimum inhibitory concentration “MIC” values for the most active analogues. Molecular docking study was achieved to understand mode of interactions between selected inhibitors and different biological targets.
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Affiliation(s)
| | - Tarek F El-Moselhy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Nabaweya S El-Din
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Ahmed B M Mehany
- Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Amany Belal
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Minia University, Minia, Egypt
| | - Haytham O Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Mervat H El-Hamamsy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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26
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Duran-Camacho G, Hethcox JC. Nickel-Catalyzed Cyanation of (Hetero)aryl Bromides Using DABAL-Me 3 as a Soluble Reductant. Org Lett 2022; 24:8397-8400. [DOI: 10.1021/acs.orglett.2c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Geraldo Duran-Camacho
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - J. Caleb Hethcox
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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27
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Zhang W, Vadlakonda S, Wu M, Chintareddy V, Vogeti LN, Juarez L, Muppa S, Parker C, Kellogg-Yelder D, Williams J, Polach K, Chen X, Raman K, Babu Y, Kotian P. Discovery and Optimization of Orally Bioavailable and Potent Plasma Kallikrein Inhibitors Bearing a Quaternary Carbon. Bioorg Med Chem 2022; 73:117035. [DOI: 10.1016/j.bmc.2022.117035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
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28
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Ring replacement recommender: Ring modifications for improving biological activity. Eur J Med Chem 2022; 238:114483. [DOI: 10.1016/j.ejmech.2022.114483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022]
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29
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Margaret McCutcheon M, Freindorf M, Kraka E. Bonding in Nitrile Photo-dissociating Ruthenium Drug Candidates --A Local Vibrational Mode Study. J Chem Phys 2022; 157:014301. [DOI: 10.1063/5.0094567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we investigated bonding features 15 ruthenium complexes of the type [Ru(tpy)(L)-(CH3CN)]n+, containing the tridentate tpy ligand (tpy = 2,2':6',2'--terpyridine) and various bidentate ancillary ligands, 12 compounds originally synthesized by Loftus et al. (J. Phys. Chem. C 123, 10291-10299 (2019)) complemented with three additional complexes. The main focus of our work was to relate these local features to the experimental data of Loftus et al. which assess the efficiency of nitrile release in an indirect way via observed quantum yields for ruthenium water association after nitrile release. As a tool to quantitatively assess Ru-NC and Ru-L bonding we utilized the local vibrational mode analysis complemented by the topological analysis of the electron density and the natural bond orbital analysis. Interestingly, the stronger Ru-NC bonds have the greater observed quantum yields, leading to the conclusion that the observed quantum yields are a result of a complex interplay of several processes excluding a direct relationship between QY and Ru-NC or Ru-L bond strengths. We identified the ST splitting as one of the key players and not the Ru-NC bond strength, as one may have thought. In summary, this work has presented a modern computational tool set for the investigation of bonding features applied to nitrile photo-dissociating ruthenium drug candidates forming a valuable basis for future design and fine tuning of nitrile releasing ruthenium compounds, as well as for the understanding of how local properties affect overall experimental outcomes.
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Affiliation(s)
| | | | - Elfi Kraka
- Chemistry, Southern Methodist University, United States of America
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30
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Zhou Y, Gao CF, Ma H, Nie J, Ma JA, Zhang FG. Quadruple Functionalized Pyrazole Pharmacophores via One-pot Regioselective [3 + 2] Cycloaddition of Fluorinated Nitrile Imines and Dicyanoalkenes. Chem Asian J 2022; 17:e202200436. [PMID: 35603760 DOI: 10.1002/asia.202200436] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/22/2022] [Indexed: 11/08/2022]
Abstract
Here we present a quadruple functionalization approach for the modular construction of fully substituted N 1 -aryl 3-di/trifluoro-methyl-4/5-cyanopyrazole pharmacophores from readily available hydrazonyl chlorides and dicyanoalkenes. The realization of this [3 + 2] cycloaddition reaction hinges upon the employment of N -aryl di/trifluoromethyl nitrile imines as the 1,3-dipoles to bypass external synthetic steps and dicyanoalkenes as the dipolarophiles to tune the regioselectivity. This one-pot strategy offers access to a divergent library of cyano analogues of prevalent 3-di/trifluoromethyl pyrazole pharmacophores, among which several compounds have shown potent inhibitory activity towards cyclooxygenase 2 (COX-2) compared with marketed drug Celecoxib.
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Affiliation(s)
- Yin Zhou
- Tianjin University, Department of Chemistry, CHINA
| | | | - Hai Ma
- China Academy of Chinese Medical Sciences Institute of Chinese Materia Medica, Chemistry, CHINA
| | - Jing Nie
- Tianjin University, Department of Chemistry, CHINA
| | - Jun-An Ma
- Tianjin University, Department of Chemistry, School of Science,, No. 92, Weijin Road, 300072, Tianjin, CHINA
| | - Fa-Guang Zhang
- Tianjin University, Department of Chemistry, 92 WEIJIN Road, 300072, Tianjin, CHINA
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31
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Scotti C, Barlow JW. Natural Products Containing the Nitrile Functional Group and Their Biological Activities. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221099973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The importance of nitriles as a key class of chemicals with applications across the sciences is widely appreciated. The natural world is an underappreciated source of chemically diverse nitriles. With this in mind, this review describes novel nitrile-containing molecules isolated from natural sources from 1998 to 2021, as well as a discussion of the biological activity of these compounds. This study gathers 192 molecules from varied origins across the plant, animal, and microbial worlds. Their biological activity is extremely diverse, with many potential medicinal applications.
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Affiliation(s)
- Camille Scotti
- Ecole Nationale Supérieure de Chimie de Mulhouse, Université de Haute Alsace, Mulhouse, France
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - James W. Barlow
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
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32
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Weaver JB, Kozuch J, Kirsh JM, Boxer SG. Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments. J Am Chem Soc 2022; 144:7562-7567. [PMID: 35467853 PMCID: PMC10082610 DOI: 10.1021/jacs.2c00675] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C≡N bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.
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Affiliation(s)
- Jared Bryce Weaver
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Jacek Kozuch
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Jacob M Kirsh
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
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33
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Brogi S, Ibba R, Rossi S, Butini S, Calderone V, Gemma S, Campiani G. Covalent Reversible Inhibitors of Cysteine Proteases Containing the Nitrile Warhead: Recent Advancement in the Field of Viral and Parasitic Diseases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082561. [PMID: 35458759 PMCID: PMC9029279 DOI: 10.3390/molecules27082561] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 12/29/2022]
Abstract
In the field of drug discovery, the nitrile group is well represented among drugs and biologically active compounds. It can form both non-covalent and covalent interactions with diverse biological targets, and it is amenable as an electrophilic warhead for covalent inhibition. The main advantage of the nitrile group as a warhead is mainly due to its milder electrophilic character relative to other more reactive groups (e.g., -CHO), reducing the possibility of unwanted reactions that would hinder the development of safe drugs, coupled to the ease of installation through different synthetic approaches. The covalent inhibition is a well-assessed design approach for serine, threonine, and cysteine protease inhibitors. The mechanism of hydrolysis of these enzymes involves the formation of a covalent acyl intermediate, and this mechanism can be exploited by introducing electrophilic warheads in order to mimic this covalent intermediate. Due to the relevant role played by the cysteine protease in the survival and replication of infective agents, spanning from viruses to protozoan parasites, we will review the most relevant and recent examples of protease inhibitors presenting a nitrile group that have been introduced to form or to facilitate the formation of a covalent bond with the catalytic cysteine active site residue.
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Affiliation(s)
- Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (S.B.); (V.C.)
| | - Roberta Ibba
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Sara Rossi
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (S.B.); (V.C.)
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
- Correspondence:
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (R.I.); (S.R.); (S.B.); (G.C.)
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34
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Sochacka-Ćwikła A, Mączyński M, Regiec A. FDA-Approved Small Molecule Compounds as Drugs for Solid Cancers from Early 2011 to the End of 2021. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072259. [PMID: 35408658 PMCID: PMC9000317 DOI: 10.3390/molecules27072259] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 01/09/2023]
Abstract
Solid cancers are the most common types of cancers diagnosed globally and comprise a large number of deaths each year. The main challenge currently in drug development for tumors raised from solid organs is to find more selective compounds, which exploit specific molecular targets. In this work, the small molecule drugs registered by the Food and Drug Administration (FDA) for solid cancers treatment between 2011 and 2022 were identified and analyzed by investigating a type of therapy they are used for, as well as their structures and mechanisms of action. On average, 4 new small molecule agents were introduced each year, with a few exceptions, for a total of 62 new drug approvals. A total of 50 of all FDA-approved drugs have also been authorized for use in the European Union by the European Medicines Agency (EMA). Our analysis indicates that many more anticancer molecules show a selective mode of action, i.e., 49 targeted agents, 5 hormone therapies and 3 radiopharmaceuticals, compared to less specific cytostatic action, i.e., 5 chemotherapeutic agents. It should be emphasized that new medications are indicated for use mainly for monotherapy and less for a combination or adjuvant therapies. The comprehensive data presented in this review can serve for further design and development of more specific targeted agents in clinical usage for solid tumors.
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35
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Hethcox JC, Sifri RJ. Air-Tolerant Nickel-Catalyzed Cyanation of (Hetero)aryl Halides Enabled by Polymethylhydrosiloxane, a Green Reductant. J Org Chem 2022; 87:4951-4954. [PMID: 35316048 DOI: 10.1021/acs.joc.1c02939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An air-tolerant nickel-catalyzed cyanation of aryl bromides is reported. The reaction uses a NiCl2/Xantphos catalyst in combination with substoichiometric quantities of zinc cyanide and polymethylhydrosiloxane. This silane is a green, homogeneous alternative to the traditional, insoluble solid reductant zinc and renders the reaction tolerant to air. The reaction can be performed under an air atmosphere, obviating the need for degassing, a glovebox, or Schlenk techniques. The reaction scope is broad, proceeding in good yields with a variety of (hetero)arenes.
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Affiliation(s)
- J Caleb Hethcox
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Renee J Sifri
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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36
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Nie H, Sun L, Zhang M, Song C. TfOH-promoted cyclocondensation reaction of 2-arylacetonitriles. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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León Sandoval A, Politano F, Witko ML, Leadbeater NE. Preparation of nitriles from aldehydes using ammonium persulfate by means of a nitroxide-catalysed oxidative functionalisation reaction. Org Biomol Chem 2022; 20:667-671. [PMID: 34989384 DOI: 10.1039/d1ob02187g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A methodology for the preparation of nitriles from aldehydes by means of an oxidative functionalisation reaction is reported. It employs ammonium persulfate as both the primary oxidant and the nitrogen source, and a catalytic amount of a nitroxide. It is applicable to a range of structurally diverse (hetero)aromatic aldehydes furnishing the nitrile products in 30-97% isolated yield. Given the ready accessibility of aldehydes and that ammonium persulfate is cheap and less toxic than many other reagents for generating nitriles, this methodology offers a simple and easy to use approach to this valuable class of compounds.
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Affiliation(s)
- Arturo León Sandoval
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA.
| | - Fabrizio Politano
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA.
| | - Mason L Witko
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA.
| | - Nicholas E Leadbeater
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA.
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38
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Unsal Tan O, Zengin M. Insights into the chemistry and therapeutic potential of acrylonitrile derivatives. Arch Pharm (Weinheim) 2021; 355:e2100383. [PMID: 34763365 DOI: 10.1002/ardp.202100383] [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: 10/04/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022]
Abstract
Acrylonitrile is a fascinating scaffold widely found in many natural products, drugs, and drug candidates with various biological activities. Several drug molecules such as entacapone, rilpivirine, teriflunomide, and so forth, bearing an acrylonitrile moiety have been marketed. In this review, diverse synthetic strategies for constructing desired acrylonitriles are discussed, and the different biological activities and medicinal significance of various acrylonitrile derivatives are critically evaluated. The information gathered is expected to provide rational guidance for the development of clinically useful agents from acrylonitriles.
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Affiliation(s)
- Oya Unsal Tan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Merve Zengin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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