1
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Sui X, Dang HT, Porey A, Trevino R, Das A, Fremin SO, Hughes WB, Thompson WT, Dhakal SK, Arman HD, Larionov OV. Acridine photocatalysis enables tricomponent direct decarboxylative amine construction. Chem Sci 2024; 15:9582-9590. [PMID: 38939159 PMCID: PMC11206229 DOI: 10.1039/d4sc02356k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/20/2024] [Indexed: 06/29/2024] Open
Abstract
Amines are centrally important motifs in medicinal chemistry and biochemistry, and indispensable intermediates and linchpins in organic synthesis. Despite their cross-disciplinary prominence, synthetic access to amine continues to rely on two-electron approaches based on reductions and additions of organometallic reagents, limiting their accessible chemical space and necessitating stepwise preassembly of synthetic precursors. We report herein a homogeneous photocatalytic tricomponent decarboxylative radical-mediated amine construction that enables modular access to α-branched secondary amines directly from the broad and structurally diverse chemical space of carboxylic acids in a tricomponent reaction with aldehydes and aromatic amines. Our studies reveal the key role of acridine photocatalysis acting in concert with copper and Brønsted acid catalytic processes in facilitating the previously inaccessible homogeneous photocatalytic reaction and provide a streamlined segue to a wide range of amines and nonproteinogenic α-amino acids.
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Affiliation(s)
- Xianwei Sui
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Hang T Dang
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Arka Porey
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Ramon Trevino
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Arko Das
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Seth O Fremin
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - William B Hughes
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - William T Thompson
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Shree Krishna Dhakal
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Hadi D Arman
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
| | - Oleg V Larionov
- Department of Chemistry, The University of Texas at San Antonio One UTSA Circle San Antonio TX 78249 USA
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2
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Jirasek M, Sharma A, Bame JR, Mehr SHM, Bell N, Marshall SM, Mathis C, MacLeod A, Cooper GJT, Swart M, Mollfulleda R, Cronin L. Investigating and Quantifying Molecular Complexity Using Assembly Theory and Spectroscopy. ACS CENTRAL SCIENCE 2024; 10:1054-1064. [PMID: 38799656 PMCID: PMC11117308 DOI: 10.1021/acscentsci.4c00120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/16/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024]
Abstract
Current approaches to evaluate molecular complexity use algorithmic complexity, rooted in computer science, and thus are not experimentally measurable. Directly evaluating molecular complexity could be used to study directed vs undirected processes in the creation of molecules, with potential applications in drug discovery, the origin of life, and artificial life. Assembly theory has been developed to quantify the complexity of a molecule by finding the shortest path to construct the molecule from building blocks, revealing its molecular assembly index (MA). In this study, we present an approach to rapidly infer the MA of molecules from spectroscopic measurements. We demonstrate that the MA can be experimentally measured by using three independent techniques: nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS), and infrared spectroscopy (IR). By identifying and analyzing the number of absorbances in IR spectra, carbon resonances in NMR, or molecular fragments in tandem MS, the MA of an unknown molecule can be reliably estimated. This represents the first experimentally quantifiable approach to determining molecular assembly. This paves the way to use experimental techniques to explore the evolution of complex molecules as well as a unique marker of where an evolutionary process has been operating.
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Affiliation(s)
- Michael Jirasek
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Abhishek Sharma
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Jessica R. Bame
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - S. Hessam M. Mehr
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Nicola Bell
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Stuart M. Marshall
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Cole Mathis
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Alasdair MacLeod
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Geoffrey J. T. Cooper
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Marcel Swart
- University
of Girona, Campus Montilivi (Ciencies), c/M.A. Capmany 69, 17003 Girona, Spain
- ICREA, Pg. Lluis Companys
23, 08010 Barcelona, Spain
| | - Rosa Mollfulleda
- University
of Girona, Campus Montilivi (Ciencies), c/M.A. Capmany 69, 17003 Girona, Spain
| | - Leroy Cronin
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
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3
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Croy A. From Local Atomic Environments to Molecular Information Entropy. ACS OMEGA 2024; 9:20616-20622. [PMID: 38737089 PMCID: PMC11080039 DOI: 10.1021/acsomega.4c02770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 05/14/2024]
Abstract
The similarity of local atomic environments is an important concept in many machine learning techniques, which find applications in computational chemistry and material science. Here, we present and discuss a connection between the information entropy and the similarity matrix of a molecule. The resulting entropy can be used as a measure of the complexity of a molecule. Exemplarily, we introduce and evaluate two specific choices for defining the similarity: one is based on a SMILES representation of local substructures, and the other is based on the SOAP kernel. By tuning the sensitivity of the latter, we can achieve good agreement between the respective entropies. Finally, we consider the entropy of two molecules in a mixture. The gain of entropy due to the mixing can be used as a similarity measure of the molecules. We compare this measure to the average and best-match kernel. The results indicate a connection between the different approaches and demonstrate the usefulness and broad applicability of the similarity-based entropy approach.
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Affiliation(s)
- Alexander Croy
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07737 Jena, Germany
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4
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Porey A, Fremin SO, Nand S, Trevino R, Hughes WB, Dhakal SK, Nguyen VD, Greco SG, Arman HD, Larionov OV. Multimodal Acridine Photocatalysis Enables Direct Access to Thiols from Carboxylic Acids and Elemental Sulfur. ACS Catal 2024; 14:6973-6980. [PMID: 38737399 PMCID: PMC11081195 DOI: 10.1021/acscatal.4c01289] [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] [Indexed: 05/14/2024]
Abstract
Development of photocatalytic systems that facilitate mechanistically divergent steps in complex catalytic manifolds by distinct activation modes can enable previously inaccessible synthetic transformations. However, multimodal photocatalytic systems remain understudied, impeding their implementation in catalytic methodology. We report herein a photocatalytic access to thiols that directly merges the structural diversity of carboxylic acids with the ready availability of elemental sulfur without substrate preactivation. The photocatalytic transformation provides a direct radical-mediated segue to one of the most biologically important and synthetically versatile organosulfur functionalities, whose synthetic accessibility remains largely dominated by two-electron-mediated processes based on toxic and uneconomical reagents and precursors. The two-phase radical process is facilitated by a multimodal catalytic reactivity of acridine photocatalysis that enables both the singlet excited state PCET-mediated decarboxylative carbon-sulfur bond formation and the previously unknown radical reductive disulfur bond cleavage by a photoinduced HAT process in the silane-triplet acridine system. The study points to a significant potential of multimodal photocatalytic systems in providing unexplored directions to previously inaccessible transformations.
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Affiliation(s)
- Arka Porey
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Seth O Fremin
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Sachchida Nand
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ramon Trevino
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - William B Hughes
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Shree Krishna Dhakal
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Viet D Nguyen
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Samuel G Greco
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Hadi D Arman
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Oleg V Larionov
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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5
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Kim H, Lee K, Kim C, Lim J, Kim WY. DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening. J Chem Inf Model 2024; 64:2432-2444. [PMID: 37651152 DOI: 10.1021/acs.jcim.3c01134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Recently emerging generative AI models enable us to produce a vast number of compounds for potential applications. While they can provide novel molecular structures, the synthetic feasibility of the generated molecules is often questioned. To address this issue, a few recent studies have attempted to use deep learning models to estimate the synthetic accessibility of many molecules rapidly. However, retrosynthetic analysis tools used to train the models rely on reaction templates automatically extracted from a large reaction database that are not domain-specific and may exhibit low chemical correctness. To overcome this limitation, we introduce DFRscore (Drug-Focused Retrosynthetic score), a deep learning-based approach for a more practical assessment of synthetic accessibility in drug discovery. The DFRscore model is trained exclusively on drug-focused reactions, providing a predicted number of minimally required synthetic steps for each compound. This approach enables practitioners to filter out compounds that do not meet their desired level of synthetic accessibility at an early stage of high-throughput virtual screening for accelerated drug discovery. The proposed strategy can be easily adapted to other domains by adjusting the synthesis planning setup of the reaction templates and starting materials.
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Affiliation(s)
- Hyeongwoo Kim
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyunghoon Lee
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chansu Kim
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jaechang Lim
- HITS Incorporation, 124 Teheran-ro, Gangnam-gu, Seoul 06234, Republic of Korea
| | - Woo Youn Kim
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- HITS Incorporation, 124 Teheran-ro, Gangnam-gu, Seoul 06234, Republic of Korea
- AI Institute, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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6
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Shenvi RA. Natural Product Synthesis in the 21st Century: Beyond the Mountain Top. ACS CENTRAL SCIENCE 2024; 10:519-528. [PMID: 38559299 PMCID: PMC10979479 DOI: 10.1021/acscentsci.3c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 04/04/2024]
Abstract
Research into natural products emerged from humanity's curiosity about the nature of matter and its role in the materia medica of diverse civilizations. Plants and fungi, in particular, supplied materials that altered behavior, perception, and well-being profoundly. Many active principles remain well-known today: strychnine, morphine, psilocybin, ephedrine. The potential to circumvent the constraints of natural supply and explore the properties of these materials led to the field of natural product synthesis. This research delivered new molecules with new properties, but also led to fundamental insights into the chemistry of the nonmetal elements H, C, N, O, P, S, Se, and their combinations, i.e., organic chemistry. It also led to a potent culture focused on bigger molecules and races to the finish line, perhaps at the expense of actionable next steps. About 20 years ago, the field began to contract in the United States. Research that focused solely on chemical reaction development, especially catalysis, filled the void. After all, new reactions and mechanistic insight could be immediately implemented by the chemistry community, so it became hard to justify the lengthy procurement of a complex molecule that sat in the freezer unused. This shift coincided with a divestment of natural product portfolios by pharmaceutical companies and an emphasis in academic organic chemistry on applications-driven research, perhaps at the expense of more fundamental science. However, as bioassays and the tools of chemical biology become widespread, synthesis finds a new and powerful ally that allows us to better deliver on the premise of the field. And the hard-won insights of complex synthesis can be better encoded digitally, mined by data science, and applied to new challenges, as chemists perturb and even surpass the properties of complex natural products. The 21st century promises powerful developments, both in fundamental organic chemistry and at the interface of synthesis and biology, if the community of scientists fosters its growth. This essay tries to contextualize natural product synthesis for a broad audience, looks ahead to its transformation in the coming years, and expects the future to be bright.
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Affiliation(s)
- Ryan A. Shenvi
- Department
of Chemistry, Scripps Research, La Jolla, California 92037, United States
- Graduate
School of Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
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7
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Zhuang K, Haug GC, Wang Y, Yin S, Sun H, Huang S, Trevino R, Shen K, Sun Y, Huang C, Qin B, Liu Y, Cheng M, Larionov OV, Jin S. Cobalt-Catalyzed Carbon-Heteroatom Transfer Enables Regioselective Tricomponent 1,4-Carboamination. J Am Chem Soc 2024; 146:8508-8519. [PMID: 38382542 DOI: 10.1021/jacs.3c14828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Tricomponent cobalt(salen)-catalyzed carbofunctionalization of unsaturated substrates by radical-polar crossover has the potential to streamline access to broad classes of heteroatom-functionalized synthetic targets, yet the reaction platform has remained elusive, despite the well-developed analogous hydrofunctionalizations mediated by high-valent alkylcobalt intermediates. We report herein the development of a cobalt(salen) catalytic system that enables carbofunctionalization. The reaction entails a tricomponent decarboxylative 1,4-carboamination of dienes and provides a direct route to aromatic allylic amines by obviating preformed allylation reagents and protection of oxidation-sensitive aromatic amines. The catalytic system merges acridine photocatalysis with cobalt(salen)-catalyzed regioselective 1,4-carbofunctionalization that facilitates the crossover of the radical and polar phases of the tricomponent coupling process, revealing critical roles of the reactants, as well as ligand effects and the nature of the formal high-valent alkylcobalt species on the chemo- and regioselectivity.
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Affiliation(s)
- Kaitong Zhuang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Graham C Haug
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Yangyang Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Shuyu Yin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Huiying Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Siwen Huang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Ramon Trevino
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Kunzhi Shen
- Shenyang Photosensitive Chemical Research Institute Company Limited, 8-12 No. 6 Road, Shenyang 110141, P. R. China
| | - Yao Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Chao Huang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Bin Qin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Yongxiang Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
| | - Oleg V Larionov
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Shengfei Jin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, P. R. China
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8
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Lee AS, Elliott S, Harb H, Ward L, Foster I, Curtiss L, Assary RS. Emin: A First-Principles Thermochemical Descriptor for Predicting Molecular Synthesizability. J Chem Inf Model 2024; 64:1277-1289. [PMID: 38359461 DOI: 10.1021/acs.jcim.3c01583] [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: 02/17/2024]
Abstract
Predicting the synthesizability of a new molecule remains an unsolved challenge that chemists have long tackled with heuristic approaches. Here, we report a new method for predicting synthesizability using a simple yet accurate thermochemical descriptor. We introduce Emin, the energy difference between a molecule and its lowest energy constitutional isomer, as a synthesizability predictor that is accurate, physically meaningful, and first-principles based. We apply Emin to 134,000 molecules in the QM9 data set and find that Emin is accurate when used alone and reduces incorrect predictions of "synthesizable" by up to 52% when used to augment commonly used prediction methods. Our work illustrates how first-principles thermochemistry and heuristic approximations for molecular stability are complementary, opening a new direction for synthesizability prediction methods.
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Affiliation(s)
- Andrew S Lee
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Sarah Elliott
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Hassan Harb
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Logan Ward
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Ian Foster
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Larry Curtiss
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Rajeev S Assary
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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9
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Collins JE, Lee JW, Rocamora F, Saggu GS, Wendt KL, Pasaje CFA, Smick S, Santos NM, Paes R, Jiang T, Mittal N, Luth MR, Chin T, Chang H, McLellan JL, Morales-Hernandez B, Hanson KK, Niles JC, Desai SA, Winzeler EA, Cichewicz RH, Chakrabarti D. Antiplasmodial peptaibols act through membrane directed mechanisms. Cell Chem Biol 2024; 31:312-325.e9. [PMID: 37995692 PMCID: PMC10923054 DOI: 10.1016/j.chembiol.2023.10.025] [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: 10/28/2022] [Revised: 08/29/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Our previous study identified 52 antiplasmodial peptaibols isolated from fungi. To understand their antiplasmodial mechanism of action, we conducted phenotypic assays, assessed the in vitro evolution of resistance, and performed a transcriptome analysis of the most potent peptaibol, HZ NPDG-I. HZ NPDG-I and 2 additional peptaibols were compared for their killing action and stage dependency, each showing a loss of digestive vacuole (DV) content via ultrastructural analysis. HZ NPDG-I demonstrated a stepwise increase in DV pH, impaired DV membrane permeability, and the ability to form ion channels upon reconstitution in planar membranes. This compound showed no signs of cross resistance to targets of current clinical candidates, and 3 independent lines evolved to resist HZ NPDG-I acquired nonsynonymous changes in the P. falciparum multidrug resistance transporter, pfmdr1. Conditional knockdown of PfMDR1 showed varying effects to other peptaibol analogs, suggesting differing sensitivity.
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Affiliation(s)
- Jennifer E Collins
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA
| | - Jin Woo Lee
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, Norman OK 73019, USA
| | - Frances Rocamora
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Gagandeep S Saggu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20852, USA
| | - Karen L Wendt
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, Norman OK 73019, USA
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sebastian Smick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Natalia Mojica Santos
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA
| | - Raphaella Paes
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA
| | - Tiantian Jiang
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Nimisha Mittal
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeline R Luth
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Taylor Chin
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Howard Chang
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - James L McLellan
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Beatriz Morales-Hernandez
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Kirsten K Hanson
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX 78249, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sanjay A Desai
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20852, USA
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Institute for Natural Products Applications & Research Technologies, University of Oklahoma, Norman OK 73019, USA.
| | - Debopam Chakrabarti
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA.
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10
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Gillard RM, Zhang J, Steel R, Wang J, Strull JL, Cai B, Chakraborty N, Boger DL. Aryl Annulation: A Powerful Simplifying Retrosynthetic Disconnection. SYNTHESIS-STUTTGART 2024; 56:118-133. [PMID: 38144170 PMCID: PMC10745204 DOI: 10.1055/a-1959-2088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Retrosynthetic deconstruction of a core aromatic ring is an especially simplifying retrosynthetic step, reducing the complexity of the precursor synthetic target. Moreover, when implemented to provide a penultimate intermediate, it enables late-stage divergent aryl introductions, permitting deep-seated core aryl modifications ordinarily accessible only by independent synthesis. Herein, we highlight the use of a ketone carbonyl group as the functionality to direct such late-stage divergent aryl introductions onto a penultimate intermediate with a projected application in the total synthesis of vinblastine and its presently inaccessible analogs containing indole replacements. Although the studies highlight this presently unconventional strategy with an especially challenging target in mind, the increase in molecular complexity (intricacy) established by the synthetic implementation of the powerful retrosynthetic disconnection, the use of a ketone as the precursor enabling functionality, and with adoption of either conventional or new wave (hetero)aromatic annulations combine to define a general and powerful strategy suited for wide-spread implementation with near limitless scope in target diversification.
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Affiliation(s)
- Rachel M. Gillard
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jianjun Zhang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Richard Steel
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jocelyn Wang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jessica L. Strull
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bin Cai
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nilanjana Chakraborty
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dale L. Boger
- Department of Chemistry and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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11
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Tong G, Griffin S, Sader A, Crowell AB, Beavers K, Watson J, Buchan Z, Chen S, Shenvi RA. C5 methylation confers accessibility, stability and selectivity to picrotoxinin. Nat Commun 2023; 14:8308. [PMID: 38097583 PMCID: PMC10721898 DOI: 10.1038/s41467-023-44030-3] [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: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Minor changes to complex structures can exert major influences on synthesis strategy and functional properties. Here we explore two parallel series of picrotoxinin (PXN, 1) analogs and identify leads with selectivity between mammalian and insect ion channels. These are the first SAR studies of PXN despite its >100-year history and are made possible by advances in total synthesis. We observe a remarkable stabilizing effect of a C5 methyl, which completely blocks C15 alcoholysis via destabilization of an intermediate twist-boat conformer; suppression of this secondary hydrolysis pathway increases half-life in plasma. C5 methylation also decreases potency against vertebrate ion channels (γ-Aminobutyric acid type A (GABAA) receptors) but maintains or increases antagonism of homologous invertebrate GABA-gated chloride channels (resistance to dieldrin (RDL) receptors). Optimal 5MePXN analogs appear to change the PXN binding pose within GABAARs by disruption of a hydrogen bond network. These discoveries were made possible by the lower synthetic burden of 5MePXN (2) and were illuminated by the parallel analog series, which allowed characterization of the role of the synthetically simplifying C5 methyl in channel selectivity. These are the first SAR studies to identify changes to PXN that increase the GABAA-RDL selectivity index.
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Affiliation(s)
- Guanghu Tong
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Samantha Griffin
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana, 46268, USA
| | - Avery Sader
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana, 46268, USA
| | - Anna B Crowell
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, Ohio, 44074, USA
| | - Ken Beavers
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana, 46268, USA
| | - Jerry Watson
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana, 46268, USA
| | - Zachary Buchan
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana, 46268, USA
| | - Shuming Chen
- Department of Chemistry and Biochemistry, Oberlin College, 119 Woodland Street, Oberlin, Ohio, 44074, USA.
| | - Ryan A Shenvi
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA.
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12
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Maujean T, Kannaboina P, Green AI, Burslem GM. Lead-oriented synthesis of epigenetic relevant scaffolds. Chem Commun (Camb) 2023; 59:14555-14558. [PMID: 37991354 PMCID: PMC10842704 DOI: 10.1039/d3cc04317g] [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] [Indexed: 11/23/2023]
Abstract
A simple and rational method to rank lead-likeness of molecules using continuous evaluation functions was hereby developed. This strategy proved to be competitive against known methods and finally helped in driving synthetic efforts towards candidates of interest for epigenetic applications against HDAC6, BRD4 and EZH2.
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Affiliation(s)
- Timothé Maujean
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
| | - Prakash Kannaboina
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
| | - Adam I Green
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
| | - George M Burslem
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
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13
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Xie J, Pahl A, Krzyzanowski A, Krupp A, Liu J, Koska S, Schölermann B, Zhang R, Bonowski J, Sievers S, Strohmann C, Ziegler S, Grigalunas M, Waldmann H. Synthetic Matching of Complex Monoterpene Indole Alkaloid Chemical Space. Angew Chem Int Ed Engl 2023; 62:e202310222. [PMID: 37818743 DOI: 10.1002/anie.202310222] [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: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are endowed with high structural and spatial complexity and characterized by diverse biological activities. Given this complexity-activity combination in MIAs, rapid and efficient access to chemical matter related to and with complexity similar to these alkaloids would be highly desirable, since such compound classes might display novel bioactivity. We describe the design and synthesis of a pseudo-natural product (pseudo-NP) collection obtained by the unprecedented combination of MIA fragments through complexity-generating transformations, resulting in arrangements not currently accessible by biosynthetic pathways. Cheminformatic analyses revealed that both the pseudo-NPs and the MIAs reside in a unique and common area of chemical space with high spatial complexity-density that is only sparsely populated by other natural products and drugs. Investigation of bioactivity guided by morphological profiling identified pseudo-NPs that inhibit DNA synthesis and modulate tubulin. These results demonstrate that the pseudo-NP collection occupies similar biologically relevant chemical space that Nature has endowed MIAs with.
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Affiliation(s)
- Jianing Xie
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Adrian Krzyzanowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Anna Krupp
- Faculty of Chemistry, Inorganic Chemistry, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Jie Liu
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Sandra Koska
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Ruirui Zhang
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Jana Bonowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Compound Management and Screening Center (COMAS), Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry, Inorganic Chemistry, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Slava Ziegler
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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14
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Abadi N, Ruzzenenti F. Complex Networks and Interacting Particle Systems. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1490. [PMID: 37998182 PMCID: PMC10670629 DOI: 10.3390/e25111490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Complex networks is a growing discipline aimed at understanding large interacting systems. One of its goals is to establish a relation between the interactions of a system and the networks structure that emerges. Taking a Lennard-Jones particle system as an example, we show that when interactions are governed by a potential, the notion of structure given by the physical arrangement of the interacting particles can be interpreted as a binary approximation to the interaction potential. This approximation simplifies the calculation of the partition function of the system and allows to study the stability of the interaction structure. We compare simulated results with those from the approximated partition function and show how the network and system perspective complement each other. With this, we draw a direct connection between the interactions of a molecular system and the network structure it forms and assess the degree to which it describes the system. We conclude by discussing the advantages and limitations of this method for weighted networks, as well as how this concept might be extended to more general systems.
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Affiliation(s)
- Noam Abadi
- Integrated Research on Energy, Environment and Society (IREES), Energy and Sustainability Research Institute Groningen (ESRIG), University of Groningen, Nijenborgh 6, 9747 AG Groningen, The Netherlands;
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15
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Krzyzanowski A, Pahl A, Grigalunas M, Waldmann H. Spacial Score─A Comprehensive Topological Indicator for Small-Molecule Complexity. J Med Chem 2023; 66:12739-12750. [PMID: 37651653 PMCID: PMC10544027 DOI: 10.1021/acs.jmedchem.3c00689] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Indexed: 09/02/2023]
Abstract
The fraction of sp3-hybridized carbons (Fsp3) and the fraction of stereogenic carbons (FCstereo) are two widely employed scores of molecular complexity with strong links to biologically relevant features. However, they do not comprehensively express molecular topology, and they often do not match the chemical intuition of complexity. We propose the spacial score (SPS) as an empirical scoring system that builds upon the principle underlying Fsp3 and FCstereo and expresses the spacial complexity of a compound in a uniform manner on a highly granular scale. The size-normalized SPS (nSPS) can differentiate distributions of natural products and synthetic compounds and is applicable in the analysis of biological activity data. Analysis of the ChEMBL database revealed general trends of increasing selectivity and potency with increasing nSPS. SPS can also be used advantageously in planning and analysis of synthesis programs for direct comparison of chemical transformations and intermediates in reaction sequences.
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Affiliation(s)
- Adrian Krzyzanowski
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
- Faculty
of Chemistry, Chemical Biology Technical
University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
| | - Axel Pahl
- Compound
Management and Screening Center, Max Planck
Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Michael Grigalunas
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
- Faculty
of Chemistry, Chemical Biology Technical
University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
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16
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Docherty JH, Lister TM, Mcarthur G, Findlay MT, Domingo-Legarda P, Kenyon J, Choudhary S, Larrosa I. Transition-Metal-Catalyzed C-H Bond Activation for the Formation of C-C Bonds in Complex Molecules. Chem Rev 2023. [PMID: 37163671 DOI: 10.1021/acs.chemrev.2c00888] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Site-predictable and chemoselective C-H bond functionalization reactions offer synthetically powerful strategies for the step-economic diversification of both feedstock and fine chemicals. Many transition-metal-catalyzed methods have emerged for the selective activation and functionalization of C-H bonds. However, challenges of regio- and chemoselectivity have emerged with application to highly complex molecules bearing significant functional group density and diversity. As molecular complexity increases within molecular structures the risks of catalyst intolerance and limited applicability grow with the number of functional groups and potentially Lewis basic heteroatoms. Given the abundance of C-H bonds within highly complex and already diversified molecules such as pharmaceuticals, natural products, and materials, design and selection of reaction conditions and tolerant catalysts has proved critical for successful direct functionalization. As such, innovations within transition-metal-catalyzed C-H bond functionalization for the direct formation of carbon-carbon bonds have been discovered and developed to overcome these challenges and limitations. This review highlights progress made for the direct metal-catalyzed C-C bond forming reactions including alkylation, methylation, arylation, and olefination of C-H bonds within complex targets.
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Affiliation(s)
- Jamie H Docherty
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Thomas M Lister
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Gillian Mcarthur
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Michael T Findlay
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Pablo Domingo-Legarda
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Jacob Kenyon
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Shweta Choudhary
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Igor Larrosa
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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17
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Dang HT, Nguyen VD, Haug GC, Arman HD, Larionov OV. Decarboxylative Triazolation Enables Direct Construction of Triazoles from Carboxylic Acids. JACS AU 2023; 3:813-822. [PMID: 37006773 PMCID: PMC10052276 DOI: 10.1021/jacsau.2c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 06/19/2023]
Abstract
Triazoles have major roles in chemistry, medicine, and materials science, as centrally important heterocyclic motifs and bioisosteric replacements for amides, carboxylic acids, and other carbonyl groups, as well as some of the most widely used linkers in click chemistry. Yet, the chemical space and molecular diversity of triazoles remains limited by the accessibility of synthetically challenging organoazides, thereby requiring preinstallation of the azide precursors and restricting triazole applications. We report herein a photocatalytic, tricomponent decarboxylative triazolation reaction that for the first time enables direct conversion of carboxylic acids to triazoles in a single-step, triple catalytic coupling with alkynes and a simple azide reagent. Data-guided inquiry of the accessible chemical space of decarboxylative triazolation indicates that the transformation can improve access to the structural diversity and molecular complexity of triazoles. Experimental studies demonstrate a broad scope of the synthetic method that includes a variety of carboxylic acid, polymer, and peptide substrates. When performed in the absence of alkynes, the reaction can also be used to access organoazides, thereby obviating preactivation and specialized azide reagents and providing a two-pronged approach to C-N bond-forming decarboxylative functional group interconversions.
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18
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Grant PS, Meyrelles R, Gajsek O, Niederacher G, Maryasin B, Maulide N. Biomimetic Cationic Cyclopropanation Enables an Efficient Chemoenzymatic Synthesis of 6,8-Cycloeudesmanes. J Am Chem Soc 2023; 145:5855-5863. [PMID: 36854118 PMCID: PMC10021018 DOI: 10.1021/jacs.2c13116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Cationic cyclopropanation involves the γ-elimination at carbocations to form a new σ-C-C bond through proton loss. While exceedingly rare in bulk solution, it is recognized as one of the main biosynthetic cyclopropanation pathways. Despite the rich history of bioinspired synthetic chemistry, cationic cyclopropanation has not been appropriated for the synthetic toolbox, likely due to the preference of carbocations to undergo competing E1 β-elimination pathways. Here, we present an in-depth synthetic and computational study of cationic cyclopropanation, focusing on the 6,8-cycloeudesmanes as a platform for this investigation. We were able to apply biomimetic cationic cyclopropanation to the synthesis of several 6,8-cycloeudesmanes and non-natural analogues─in doing so, we showcase the power of this transformation in the preparation of complex cyclopropanes.
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Affiliation(s)
- Phillip S Grant
- Institute of Organic Chemistry, University of Vienna, Vienna 1090, Austria
| | - Ricardo Meyrelles
- Institute of Organic Chemistry, University of Vienna, Vienna 1090, Austria.,Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria.,Vienna Doctoral School in Chemistry, University of Vienna, Vienna 1090, Austria
| | - Oliver Gajsek
- Institute of Biological Chemistry, University of Vienna, Vienna 1090, Austria.,Vienna Doctoral School in Chemistry, University of Vienna, Vienna 1090, Austria
| | - Gerhard Niederacher
- Institute of Biological Chemistry, University of Vienna, Vienna 1090, Austria
| | - Boris Maryasin
- Institute of Organic Chemistry, University of Vienna, Vienna 1090, Austria.,Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Nuno Maulide
- Institute of Organic Chemistry, University of Vienna, Vienna 1090, Austria
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19
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Reddy DS, Novitskiy IM, Kutateladze AG. Complexity-Building Photoinduced Cascade Involving C sp2-C sp3 Coupling of Aromatic Amides via [2 + 2] Reactivity of ESIPT-Generated o-Azaxylylenes. Org Lett 2023; 25:1131-1135. [PMID: 36763986 DOI: 10.1021/acs.orglett.3c00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
A new mode for complexity-building photochemical cascades which offers experimentally simple transition metal-free intramolecular Csp2-Csp3 cross coupling of aromatic amides is attained via an unprecedented [2 + 2] reactivity of ESIPT-generated azaxylylenes. Coupled with short and straightforward postphotochemical modifications of the primary photoproducts, these cascades allow for a significant step-normalized growth of molecular complexity while accessing diverse and complex polyheterocyclic molecular architectures.
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Affiliation(s)
- D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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20
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Singh M, Gaskins B, Johnson DR, Elles CG, Boskovic Z. Synthesis of Cycloheptatriene-Containing Azetidine Lactones. J Org Chem 2022; 87:15001-15010. [PMID: 35605105 PMCID: PMC10091648 DOI: 10.1021/acs.joc.2c00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We prepared a collection of complex cycloheptatriene-containing azetidine lactones by applying two key photochemical reactions: "aza-Yang" cyclization and Buchner carbene insertion into aromatic rings. While photolysis of phenacyl amines leads to a rapid charge transfer and elimination, we found that a simple protonation of the amine enables the formation of azetidinols as single diastereomers. We provide evidence, through ultrafast spectroscopy, for the electron transfer from free amines in the excited state. Further, we characterize the aza-Yang reaction by establishing the dependence of the initial reaction rates on the rates of photon absorption. An unanticipated change in reactivity in morpholine analogues is explained through interactions with the tosylate anion. The Buchner reaction proceeds with a slight preference for one diastereomer over the other, and successful reaction requires electron-donating carbene-stabilizing substituents. Overall, 16 compounds were prepared over seven steps. Guided by an increase in structural complexity, efforts such as this one extend the reach of chemists into unexplored chemical space and provide useful quantities of new compounds for studies focused on their properties.
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Affiliation(s)
- Manvendra Singh
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Bryce Gaskins
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Daniel R Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Christopher G Elles
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Zarko Boskovic
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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21
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Woo S, Landwehr EM, Shenvi RA. Synthesis of psychotropic alkaloids from Galbulimima. Tetrahedron 2022; 126:133064. [PMID: 37807979 PMCID: PMC10552879 DOI: 10.1016/j.tet.2022.133064] [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] [Indexed: 10/31/2022]
Abstract
Efficient syntheses of valuable natural products open gateways from kind learning environments to wicked worlds, where long-term, interdisciplinary research questions can be asked and answered. In this Perspective, we discuss the Galbulimima (GB) alkaloids, metabolites of a rainforest canopy tree that exhibit potent but poorly understood effects in humans, including accounts of hallucination. Recent syntheses from our group have opened up GB alkaloid chemical space for investigation by way of new cross-coupling reactions and gram-scale target production. Although natural product synthesis can be challenging, its objective is obvious. Realization of long-term, enabling goals will be a circuitous journey at the interface of chemistry, pharmacology and neuroscience-a potent mix to foster discovery in the coming century.
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Affiliation(s)
- Stone Woo
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Eleanor M. Landwehr
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
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22
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Scott KA, Groch JR, Bao J, Marshall CM, Allen RA, Nick SJ, Lauta NR, Williams RE, Qureshi MH, Delost MD, Njardarson JT. Minimalistic graphical presentation approach for total syntheses. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Nguyen VD, Haug GC, Greco SG, Trevino R, Karki GB, Arman HD, Larionov OV. Decarboxylative Sulfinylation Enables a Direct, Metal-Free Access to Sulfoxides from Carboxylic Acids. Angew Chem Int Ed Engl 2022; 61:e202210525. [PMID: 36006859 PMCID: PMC9588746 DOI: 10.1002/anie.202210525] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 12/14/2022]
Abstract
The intermediate oxidation state of sulfoxides is central to the plethora of their applications in chemistry and medicine, yet it presents challenges for an efficient synthetic access, limiting the structural diversity of currently available sulfoxides. Here, we report a data-guided development of direct decarboxylative sulfinylation that enables the previously inaccessible functional group interconversion of carboxylic acids to sulfoxides in a reaction with sulfinates. Given the broad availability of carboxylic acids and the growing synthetic potential of sulfinates, the direct decarboxylative sulfinylation is poised to improve the structural diversity of synthetically accessible sulfoxides. The reaction is facilitated by a kinetically favored sulfoxide formation from the intermediate sulfinyl sulfones, despite the strong thermodynamic preference for the sulfone formation, unveiling the previously unknown and chemoselective radicalophilic sulfinyl sulfone reactivity.
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Affiliation(s)
- Viet D Nguyen
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Graham C Haug
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Samuel G Greco
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Ramon Trevino
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Guna B Karki
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Hadi D Arman
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Oleg V Larionov
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
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24
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Arai N. Formation of
anti‐Bredt
‐type Azabicyclo[4.2.0]octene Frameworks through Photochemical Intramolecular [2+2] Cycloaddition between Indole and a Distal Double Bond of Allene. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4574] [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)
- Noriyoshi Arai
- Division of Applied Chemistry, Faculty of Engineering Hokkaido University, Sapporo Hokkaido Japan
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25
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Digitalizing Structure–Symmetry Relations at the Formation of Endofullerenes in Terms of Information Entropy Formalism. Symmetry (Basel) 2022. [DOI: 10.3390/sym14091800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Information entropy indices are widely used for numerical descriptions of chemical structures, though their applications to the processes are scarce. We have applied our original information entropy approach to filling fullerenes with a guest atom. The approach takes into account both the topology and geometry of the fullerene structures. We have studied all possible types of such fillings and found that information entropy (ΔhR) and symmetry changes correlate. ΔhR is negative, positive or zero if symmetry is increased, reduced or does not change, respectively. The ΔhR value and structural reorganization entropy, a contribution to ΔhR, are efficient parameters for the digital classification of the fullerenes involved into the filling process. Based on the calculated values, we have shown that, as the symmetry of the fullerene cage becomes higher, the structural changes due to the filling it with a guest atom become larger. The corresponding analytical expressions and numerical data are discussed.
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26
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Nguyen VD, Haug GC, Greco SG, Trevino R, Karki GB, Arman HD, Larionov O. Decarboxylative Sulfinylation Enables a Direct, Metal‐Free Access to Sulfoxides from Carboxylic Acids. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Viet D. Nguyen
- The University of Texas at San Antonio Department of Chemistry 78249 San Antonio UNITED STATES
| | - Graham C. Haug
- The University of Texas at San Antonio Deoartment of Chemistry 1 utsa circle 78249 SAN ANTONIO UNITED STATES
| | - Samuel G. Greco
- The University of Texas at San Antonio Department of Chemistry UNITED STATES
| | - Ramon Trevino
- The University of Texas at San Antonio Department of Chemistry UNITED STATES
| | - Guna B. Karki
- The University of Texas at San Antonio Department of Chemistry UNITED STATES
| | - Hadi D. Arman
- The University of Texas at San Antonio Department of Chemistry UNITED STATES
| | - Oleg Larionov
- University of Texas at San Antonio Department of Chemistry One UTSA Circle 78249 San Antonio UNITED STATES
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27
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Chen D, Hao G, Song B. Finding the Missing Property Concepts in Pesticide-Likeness. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10090-10099. [PMID: 35971945 DOI: 10.1021/acs.jafc.2c02757] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Poor bioavailability of pesticides is one of the major bottlenecks in the development of pesticides. Applications of the concept of pesticide-likeness have been widely accepted as one of the ways to break the bottleneck. At present, the evaluation of pesticide-likeness is mainly based on absorption, distribution, metabolism, excretion, and toxicity (ADME-T) property concepts of pesticides. However, a few significant property concepts of pesticides are ignored in the research of pesticide-likeness. Herein, we summarize the current study of ADME-T and other property concepts and analyze physicochemical properties for pesticides in the last 30 years, such as Fsp3, log P, and chiral centers. On the basis of these analyses, we propose that molecular complexity and residual property concepts of pesticides should be considered in the pesticide-likeness study. We hope that this work can help pesticide researchers and students, who are less knowledgeable in the field, to assess pesticide-likeness.
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Affiliation(s)
- Dongyu Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Gefei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
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28
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Zhang S, Luo ZH, Wang WT, Qian L, Liao JY. Simultaneous Construction of C-N Axial and Central Chirality via Silver-Catalyzed Desymmetrizative [3 + 2] Cycloaddition of Prochiral N-Aryl Maleimides with Activated Isocyanides. Org Lett 2022; 24:4645-4649. [PMID: 35724978 DOI: 10.1021/acs.orglett.2c01761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we report an unprecedented strategy for the simultaneous construction of a remote C-N stereogenic axis and three contiguous stereogenic carbon centers via silver-catalyzed desymmetrizative [3 + 2] cycloaddition of prochiral N-aryl maleimides with activated isocyanides. This method features operational simplicity, wide substrate scope, high efficiency, and good to excellent stereoselectivity. Notably, it represents the first example of catalytic enantioselective synthesis of C-N atropisomers with the use of activated isocyanides.
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Affiliation(s)
- Sen Zhang
- College of Pharmaceutical Sciences, and Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Zhang-Hong Luo
- College of Pharmaceutical Sciences, and Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Wen-Tao Wang
- College of Pharmaceutical Sciences, and Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Linghui Qian
- College of Pharmaceutical Sciences, and Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058
| | - Jia-Yu Liao
- College of Pharmaceutical Sciences, and Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China, 310058.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, China, 310018
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29
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Theoretical Prediction of Gastrointestinal Absorption of Phytochemicals. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2022. [DOI: 10.3390/ijpb13020016] [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 discovery of bioactive compounds for non-invasive therapy has been the goal of research groups focused on pharmacotherapy. Phytonutrients have always been attractive for researchers because they are a significant source of bioactive phytochemicals. Still, it is challenging to determine which components show high biomedical activity and bioavailability after administration. However, based on the chemical structure of these phytochemicals, their physicochemical properties can be calculated to predict the probability of gastrointestinal (GI) absorption after oral administration. Indeed, different researchers have proposed several rules (e.g., Lipinski’s, Veber’s, Ghose’s, and Muegge’s rules) to attain these predictions, but only for synthetic compounds. Most phytochemicals do not fully comply with these rules even though they show high bioactivity and high GI absorption experimentally. Here, we propose a detailed methodology using scientifically validated web-based platforms to determine the physicochemical properties of five phytochemicals found in ginger, echinacea, and tobacco. Furthermore, we analyzed the calculated data and established a protocol based on the integration of these classical rules, plus other extended parameters, that we called the Phytochemical Rule, to obtain a more reliable prediction of the GI absorption of natural compounds. This methodology can help evaluate bioactive phytochemicals as potential drug candidates and predict their oral bioavailability in patients.
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30
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Lenci E, Trabocchi A. Diversity‐Oriented Synthesis and Chemoinformatics: A Fruitful Synergy towards Better Chemical Libraries. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elena Lenci
- Universita degli Studi di Firenze Department of Chemistry Via della Lastruccia 1350019Italia 50019 Sesto Fiorentino ITALY
| | - Andrea Trabocchi
- University of Florence: Universita degli Studi di Firenze Department of Chemistry "Ugo Schiff" ITALY
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31
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Todorovic M, Rivollier P, Wong AAWL, Wang Z, Pryyma A, Nguyen TT, Newell KC, Froelich J, Perrin DM. Rationally Designed Amanitins Achieve Enhanced Cytotoxicity. J Med Chem 2022; 65:10357-10376. [PMID: 35696491 DOI: 10.1021/acs.jmedchem.1c02226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
For 70 years, α-amanitin, the most cytotoxic peptide in its class, has been without a synthetic rival; through synthesis, we address the structure-activity relationships to inform the design of new amatoxins and disclose analogues that are more cytotoxic than the natural product when evaluated on CHO, HEK293, and HeLa cells, whereas on liver-derived HepG2 cells, the same toxins show diminished cytotoxicity.
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Affiliation(s)
- Mihajlo Todorovic
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Paul Rivollier
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Antonio A W L Wong
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Zhou Wang
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Alla Pryyma
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Tuan Trung Nguyen
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Kayla C Newell
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - Juliette Froelich
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
| | - David M Perrin
- Chemistry Department, 2036 Main Mall, The University of British Columbia, 2036 Main Mall, Vancouver, BC V6T-1Z1, Canada
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32
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Woo S, Shenvi RA. Synthesis and target annotation of the alkaloid GB18. Nature 2022; 606:917-921. [PMID: 35551513 PMCID: PMC10036212 DOI: 10.1038/s41586-022-04840-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/06/2022] [Indexed: 11/08/2022]
Abstract
Ingestion of alkaloid metabolites from the bark of Galbulimima (GB) sp. leads to psychotropic and excitatory effects in humans1-4. Limited, variable supply of GB alkaloids5, however, has impeded their biological exploration and clinical development6. Here we report a solution to the supply of GB18, a structural outlier and putative psychotropic principle of Galbulimima bark. Efficient access to its challenging tetrahedral attached-ring motif required the development of a ligand-controlled endo-selective cross-electrophile coupling and a diastereoselective hydrogenation of a rotationally dynamic pyridine. Reliable, gram-scale access to GB18 enabled its assignment as a potent antagonist of κ- and μ-opioid receptors-the first new targets in 35 years-and lays the foundation to navigate and understand the biological activity of Galbulimima metabolites.
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Affiliation(s)
- Stone Woo
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Ryan A Shenvi
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
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33
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Gu Y, Zheng S, Xu Z, Yin Q, Li L, Li J. An efficient curriculum learning-based strategy for molecular graph learning. Brief Bioinform 2022; 23:6562682. [DOI: 10.1093/bib/bbac099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/18/2022] [Accepted: 02/27/2022] [Indexed: 12/14/2022] Open
Abstract
Abstract
Computational methods have been widely applied to resolve various core issues in drug discovery, such as molecular property prediction. In recent years, a data-driven computational method-deep learning had achieved a number of impressive successes in various domains. In drug discovery, graph neural networks (GNNs) take molecular graph data as input and learn graph-level representations in non-Euclidean space. An enormous amount of well-performed GNNs have been proposed for molecular graph learning. Meanwhile, efficient use of molecular data during training process, however, has not been paid enough attention. Curriculum learning (CL) is proposed as a training strategy by rearranging training queue based on calculated samples' difficulties, yet the effectiveness of CL method has not been determined in molecular graph learning. In this study, inspired by chemical domain knowledge and task prior information, we proposed a novel CL-based training strategy to improve the training efficiency of molecular graph learning, called CurrMG. Consisting of a difficulty measurer and a training scheduler, CurrMG is designed as a plug-and-play module, which is model-independent and easy-to-use on molecular data. Extensive experiments demonstrated that molecular graph learning models could benefit from CurrMG and gain noticeable improvement on five GNN models and eight molecular property prediction tasks (overall improvement is 4.08%). We further observed CurrMG’s encouraging potential in resource-constrained molecular property prediction. These results indicate that CurrMG can be used as a reliable and efficient training strategy for molecular graph learning.
Availability: The source code is available in https://github.com/gu-yaowen/CurrMG.
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Affiliation(s)
- Yaowen Gu
- Institute of Medical Information (IMI), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100020, China
| | - Si Zheng
- Institute of Medical Information (IMI), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100020, China
- Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Zidu Xu
- Institute of Medical Information (IMI), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100020, China
| | - Qijin Yin
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Liang Li
- Key Laboratory of Antibiotic Bioengineering of National Health and Family Planning Commission (NHFPC), Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100020, China
| | - Jiao Li
- Institute of Medical Information (IMI), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100020, China
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34
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Kumar Jha A, Deeksha, Inani H, Easwar S. An isatin Aldol Adduct as a precursor to α,α’-Difunctionalized Methyl Vinyl Ketones. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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35
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Landwehr EM, Baker MA, Oguma T, Burdge HE, Kawajiri T, Shenvi RA. Concise syntheses of GB22, GB13, and himgaline by cross-coupling and complete reduction. Science 2022; 375:1270-1274. [PMID: 35298242 PMCID: PMC10036211 DOI: 10.1126/science.abn8343] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Neuroactive metabolites from the bark of Galbulimima belgraveana occur in variable distributions among trees and are not easily accessible through chemical synthesis because of elaborate bond networks and dense stereochemistry. Previous syntheses of complex congeners such as himgaline have relied on iterative, stepwise installation of multiple methine stereocenters. We decreased the synthetic burden of himgaline chemical space to nearly one-third of the prior best (7 to 9 versus 19 to 31 steps) by cross-coupling high fraction aromatic building blocks (high Fsp2) followed by complete, stereoselective reduction to high fraction sp3 products (high Fsp3). This short entry into Galbulimima alkaloid space should facilitate extensive chemical exploration and biological interrogation.
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Affiliation(s)
| | - Meghan A. Baker
- Department of Chemistry, Scripps Research, La Jolla, United States
| | - Takuya Oguma
- Department of Chemistry, Scripps Research, La Jolla, United States
| | - Hannah E. Burdge
- Department of Chemistry, Scripps Research, La Jolla, United States
| | | | - Ryan A. Shenvi
- Department of Chemistry, Scripps Research, La Jolla, United States
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36
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37
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Abstract
![]()
Natural products
are the result of Nature’s exploration
of biologically relevant chemical space through evolution and an invaluable
source of bioactive small molecules for chemical biology and medicinal
chemistry. Novel concepts for the discovery of new bioactive compound
classes based on natural product structure may enable exploration
of wider biologically relevant chemical space. The pseudo-natural
product concept merges the relevance of natural product structure
with efficient exploration of chemical space by means of fragment-based
compound development to inspire the discovery of new bioactive chemical
matter through de novo combination of natural product
fragments in unprecedented arrangements. The novel scaffolds retain
the biological relevance of natural products but are not obtainable
through known biosynthetic pathways which can lead to new chemotypes
that may have unexpected or unprecedented bioactivities. Herein, we
cover the workflow of pseudo-natural product design and development,
highlight recent examples, and discuss a cheminformatic analysis in
which a significant portion of biologically active synthetic compounds
were found to be pseudo-natural products. We compare the concept to
natural evolution and discuss pseudo-natural products as the human-made
equivalent, i.e. the chemical evolution of natural product structure.
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Affiliation(s)
- Michael Grigalunas
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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38
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Reddy DS, Novitskiy IM, Kutateladze AG. Maximizing Step‐Normalized Increases in Molecular Complexity: Formal [4+2+2+2] Photoinduced Cyclization Cascade to Access Polyheterocycles Possessing Privileged Substructures. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- D. Sai Reddy
- Department of Chemistry and Biochemistry University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Ivan M. Novitskiy
- Department of Chemistry and Biochemistry University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Andrei G. Kutateladze
- Department of Chemistry and Biochemistry University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
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Abstract
Abstract
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging intramolecular H-bonds. AutoDock-GPU and Vina can model macrocyclic ligands flexibly, without requiring the enumeration of macrocyclic conformers before docking. Here, we characterize the performance of the method for handling macrocyclic compounds, which is implemented and the default behaviour for ligand preparation with our ligand preparation pipeline, Meeko. A pseudoatom is used to encode bond geometry and produce an anisotropic closure force for macrocyclic rings. This method is evaluated on a diverse set of small molecule and peptide macrocycles, ranging from 7- to 33-membered rings, showing little accuracy loss compared to rigid redocking of the X-ray macrocycle conformers. This suggests that for conformationally flexible macrocycles with unknown binding modes, this method can be effectively used to predict the macrocycle conformation.
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40
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Reddy DS, Novitskiy IM, Kutateladze AG. Maximizing Step-Normalized Increases in Molecular Complexity: Formal [4+2+2+2] Photoinduced Cyclization Cascade to Access Polyheterocycles Possessing Privileged Substructures. Angew Chem Int Ed Engl 2021; 61:e202112573. [PMID: 34850525 DOI: 10.1002/anie.202112573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 11/10/2022]
Abstract
A new complexity building photoinduced cascade which amounts to an unprecedented formal [4+2+2+2] cycloaddition topology is developed to access complex nitrogen polyheterocycles. This photocascade is initiated by the excited state intramolecular proton transfer (ESIPT) in aromatic amino ketones with tethered dual unsaturated pendants, i.e. pyrrole and alkenic moieties, resulting in the formation of four σ-bonds and setting six new stereogenic centers in a single experimentally simple photochemical step with up to 220 mcbit complexity increases.
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Affiliation(s)
- D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Denver, CO 80208, USA
| | - Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Denver, CO 80208, USA
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Denver, CO 80208, USA
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41
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Molecular size and molecular structure: Discriminating their changes upon chemical reactions in terms of information entropy. J Mol Graph Model 2021; 110:108052. [PMID: 34715466 DOI: 10.1016/j.jmgm.2021.108052] [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: 09/15/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022]
Abstract
Structural descriptors take the central place in the digitalization of chemical reactions. Information entropy is one of such descriptors that has been a seminal for numerous derivative indices. Previously, we have studied the rules of calculating information entropies of molecular ensembles based on the corresponding values of constituting molecules and found that the complexity of the ensemble has the contributions from the molecular structure and the size of the molecules. Considering chemical reaction as the conversion of one molecular ensemble to another allows calculating the change in information entropy as well as its components associated with molecular-structure and molecular-size changes. We demonstrate that both total information entropy change and its contributions are characteristic for the selected classes of chemical reactions and exemplify this approach with the cycloaddition and exchange reactions widespread in organic chemistry.
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42
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Wang X, Hu N, Kong W, Song B, Li S. Facile and divergent optimization of chromazonarol enabled the identification of simplified drimane meroterpenoids as novel pharmaceutical leads. Eur J Med Chem 2021; 227:113912. [PMID: 34653771 DOI: 10.1016/j.ejmech.2021.113912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/22/2022]
Abstract
The diversity of drimane hydroquinones was significantly expanded by the facile construction of (+)-chromazonarol relevant natural products, isomers, and analogues for the discovery of new pharmaceutical leads. The structure-activity relationship of (+)-chromazonarol relevant (non)-natural products was delineated via the synergistic interaction of the programmable synthesis and bioactivity-guided screening. The first divergent derivatization of (+)-chromazonarol demonstrated that the phenolic hydroxyl group is one inviolable requirement for antifungal effect. Pinpoint modification of (+)-yahazunol manifested the position of hydroxyl group was crucial for both antifungal and antitumor activities. (+)-Albaconol, (+)-neoalbaconol, and two (+)-yahazunol isomers (24 and 25) proved to be the novel pharmaceutical leads. The probable macromolecular targets were estimated to deliver new information about the biological potentials resident in (+)-yahazunol relevant products. This work also featured the first synthesis of (+)-albaconol and (+)-neoalbaconol, the first biological exploration of (+)-dictyvaric acid and improved preparation of (+)-8-epi-puupehedione and a promising pelorol analogue.
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Affiliation(s)
- Xia Wang
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China; Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Weigang 1, Xuanwu District, Nanjing, 210095, China
| | - Nvdan Hu
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Wenlong Kong
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Baoan Song
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Shengkun Li
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China; Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Weigang 1, Xuanwu District, Nanjing, 210095, China.
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43
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Information Entropy in Chemistry: An Overview. ENTROPY 2021; 23:e23101240. [PMID: 34681964 PMCID: PMC8534366 DOI: 10.3390/e23101240] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
Basic applications of the information entropy concept to chemical objects are reviewed. These applications deal with quantifying chemical and electronic structures of molecules, signal processing, structural studies on crystals, and molecular ensembles. Recent advances in the mentioned areas make information entropy a central concept in interdisciplinary studies on digitalizing chemical reactions, chemico-information synthesis, crystal engineering, as well as digitally rethinking basic notions of structural chemistry in terms of informatics.
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44
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Huang S, Wen H, Tian Y, Wang P, Qin W, Yan H. Organocatalytic Enantioselective Construction of Chiral Azepine Skeleton Bearing Multiple‐Stereogenic Elements. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shengli Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Haojun Wen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Yuhong Tian
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Pengfei Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Wenling Qin
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Hailong Yan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
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45
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products-Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021; 60:15705-15723. [PMID: 33644925 PMCID: PMC8360037 DOI: 10.1002/anie.202016575] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/27/2021] [Indexed: 01/05/2023]
Abstract
Pseudo-natural products (PNPs) combine natural product (NP) fragments in novel arrangements not accessible by current biosynthesis pathways. As such they can be regarded as non-biogenic fusions of NP-derived fragments. They inherit key biological characteristics of the guiding natural product, such as chemical and physiological properties, yet define small molecule chemotypes with unprecedented or unexpected bioactivity. We iterate the design principles underpinning PNP scaffolds and highlight their syntheses and biological investigations. We provide a cheminformatic analysis of PNP collections assessing their molecular properties and shape diversity. We propose and discuss how the iterative analysis of NP structure, design, synthesis, and biological evaluation of PNPs can be regarded as a human-driven branch of the evolution of natural products, that is, a chemical evolution of natural product structure.
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Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: School of Physical and Chemical SciencesUniversity of CanterburyPrivate Bag 4800Christchurch8140New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: Department of ChemistryTechnical University of Denmark, kemitorvet 2072800 Kgs.LyngbyDenmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
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46
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Huang S, Wen H, Tian Y, Wang P, Qin W, Yan H. Organocatalytic Enantioselective Construction of Chiral Azepine Skeleton Bearing Multiple-Stereogenic Elements. Angew Chem Int Ed Engl 2021; 60:21486-21493. [PMID: 34235834 DOI: 10.1002/anie.202108040] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Indexed: 12/19/2022]
Abstract
Enantioselective construction of molecules bearing multiple stereogenic elements is increasingly related to the synthesis of enantiopure natural products, pharmaceuticals, and functional materials. However, atom-economical and enantioselective approaches to install multiple stereogenic elements in a small molecular template by limited chemical transformation remain challenging. We describe an organocatalytic enantioselective method for the preparation of polychiral molecules bearing four types of stereogenic elements in fused azepines via vinylidene ortho-quinone methide (VQM)-mediated intramolecular electrophilic aromatic substitution. This method was proved robust with a wide range of substrate scope (46-92 % yield), with excellent diastereoselectivity (>20:1 dr) and enantioselectivity achieved (up to 97 % ee). Optical properties and Ru3+ -induced fluorescence responses of these compounds suggest their potential applications in optoelectronic materials and heavy metal ion detection.
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Affiliation(s)
- Shengli Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Haojun Wen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yuhong Tian
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Pengfei Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Wenling Qin
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Hailong Yan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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47
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Wakamiya Y, Oishi T. Total Synthesis of Amphidinol 3. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuma Wakamiya
- Discovery Chemistry Department, Chugai Pharmaceutical Co., Ltd
| | - Tohru Oishi
- Department of Chemistry, Faculty of Science, Kyushu University
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48
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Yang S, Schaeffer G, Mattia E, Markovitch O, Liu K, Hussain AS, Ottelé J, Sood A, Otto S. Chemical Fueling Enables Molecular Complexification of Self-Replicators*. Angew Chem Int Ed Engl 2021; 60:11344-11349. [PMID: 33689197 PMCID: PMC8251556 DOI: 10.1002/anie.202016196] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/09/2021] [Indexed: 12/21/2022]
Abstract
Unravelling how the complexity of living systems can (have) emerge(d) from simple chemical reactions is one of the grand challenges in contemporary science. Evolving systems of self-replicating molecules may hold the key to this question. Here we show that, when a system of replicators is subjected to a regime where replication competes with replicator destruction, simple and fast replicators can give way to more complex and slower ones. The structurally more complex replicator was found to be functionally more proficient in the catalysis of a model reaction. These results show that chemical fueling can maintain systems of replicators out of equilibrium, populating more complex replicators that are otherwise not readily accessible. Such complexification represents an important requirement for achieving open-ended evolution as it should allow improved and ultimately also new functions to emerge.
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Affiliation(s)
- Shuo Yang
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Gael Schaeffer
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Elio Mattia
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Omer Markovitch
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
- Origins CenterUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Kai Liu
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Andreas S. Hussain
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Jim Ottelé
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Ankush Sood
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Sijbren Otto
- Centre for Systems ChemistryStratingh InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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49
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Serafini M, Cargnin S, Massarotti A, Tron GC, Pirali T, Genazzani AA. What's in a Name? Drug Nomenclature and Medicinal Chemistry Trends using INN Publications. J Med Chem 2021; 64:4410-4429. [PMID: 33847110 PMCID: PMC8154580 DOI: 10.1021/acs.jmedchem.1c00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 12/13/2022]
Abstract
The World Health Organization assigns international nonproprietary names (INN), also known as common names, to compounds upon request from drug developers. Structures of INNs are publicly available and represent a source, albeit underused, to understand trends in drug research and development. Here, we explain how a common drug name is composed and analyze chemical entities from 2000 to 2021. In the analysis, we describe some changes that intertwine chemical structure, newer therapeutic targets (e.g., kinases), including a significant increase in the use of fluorine and of heterocycles, and some other evolutionary modifications, such as the progressive increase in molecular weight. Alongside these, small signs of change can be spotted, such as the rise in spirocyclic scaffolds and small rings and the emergence of unconventional structural moieties that might forecast the future to come.
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Affiliation(s)
| | | | | | - Gian Cesare Tron
- Department of Pharmaceutical
Sciences, Università del Piemonte
Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Tracey Pirali
- Department of Pharmaceutical
Sciences, Università del Piemonte
Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Armando A. Genazzani
- Department of Pharmaceutical
Sciences, Università del Piemonte
Orientale, Largo Donegani 2, 28100 Novara, Italy
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50
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Yang S, Schaeffer G, Mattia E, Markovitch O, Liu K, Hussain AS, Ottelé J, Sood A, Otto S. Chemical Fueling Enables Molecular Complexification of Self‐Replicators**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shuo Yang
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gael Schaeffer
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Elio Mattia
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- Origins Center University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Kai Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Andreas S. Hussain
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ankush Sood
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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