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Vinodkumar R, Nakate AK, Sharma H, Vanka K, Rama Krishna G, Kontham R. Brønsted Acid-Promoted Cyclodimerization of α,β-Unsaturated γ-Ketoesters: Construction of Fused Pyrano-ketal-lactones and γ-Ylidene-butenolides. ACS OMEGA 2024; 9:19859-19878. [PMID: 38737031 PMCID: PMC11079881 DOI: 10.1021/acsomega.3c08873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/12/2023] [Accepted: 01/09/2024] [Indexed: 05/14/2024]
Abstract
Unprecedented MsOH-promoted diastereoselective cascade dimerization and intramolecular lactonization of readily accessible α,β-unsaturated γ-ketoesters are presented. The results obtained in this work, control experiments, and density functional theory (DFT) calculations suggested that the initial enolization and E to Z isomerization/equilibration of olefin (C=C) of substrate α,β-unsaturated γ-ketoesters give a Z-isomer preferentially over an E-isomer. Subsequently, the Z-isomer undergoes intermolecular annulation with α,β-unsaturated γ-ketoesters via domino Michael addition/ketalization/lactonization steps to furnish fused tetracyclic pyrano-ketal-lactone. However, the Z-isomer prefers intramolecular trans-esterification in a competing pathway and gives bicyclic γ-ylidene-butenolide. The key features of this work include simple Brønsted acid catalysis, the formation of three bonds, two rings, and three contiguous stereogenic centers in a single step, DFT calculations, and the assignment of relative stereochemistry through X-ray diffraction (XRD) and two-dimensional (2D) nuclear magnetic resonance (NMR) analyses.
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Affiliation(s)
- Ramavath Vinodkumar
- Organic
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashwini K. Nakate
- Organic
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Himanshu Sharma
- Physical
and Materials Chemistry Division, CSIR-National
Chemical Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kumar Vanka
- Physical
and Materials Chemistry Division, CSIR-National
Chemical Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gamidi Rama Krishna
- Organic
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Center
for Materials Characterization, CSIR-National
Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ravindar Kontham
- Organic
Chemistry Division, CSIR-National Chemical
Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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Cong F, Sun GQ, Ye SH, Hu R, Rao W, Koh MJ. A Bimolecular Homolytic Substitution-Enabled Platform for Multicomponent Cross-Coupling of Unactivated Alkenes. J Am Chem Soc 2024; 146:10274-10280. [PMID: 38568080 DOI: 10.1021/jacs.4c02284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The construction of C(sp3)-C(sp3) bonds remains one of the most difficult challenges in cross-coupling chemistry. Here, we report a photoredox/nickel dual catalytic approach that enables the simultaneous formation of two C(sp3)-C(sp3) linkages via trimolecular cross-coupling of alkenes with alkyl halides and hypervalent iodine-based reagents. The reaction harnesses a bimolecular homolytic substitution (SH2) mechanism and chemoselective halogen-atom transfer (XAT) to orchestrate the regioselective addition of electrophilic and nucleophilic alkyl radicals across unactivated alkenes without the need for a directing auxiliary. Utility is highlighted through late-stage (fluoro)alkylation and (trideutero)methylation of C═C bonds bearing different substitution patterns, offering straightforward access to drug-like molecules comprising sp3-hybridized carbon scaffolds.
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Affiliation(s)
- Fei Cong
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Republic of Singapore, 117544
| | - Guo-Quan Sun
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Republic of Singapore, 117544
| | - Si-Han Ye
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Republic of Singapore, 117544
| | - Rui Hu
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Republic of Singapore, 117544
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Weidong Rao
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Ming Joo Koh
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Republic of Singapore, 117544
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3
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Liashuk OS, Ryzhov IA, Hryshchuk OV, Volovenko YM, Grygorenko OO. [3+2] Cycloaddition of Alkynyl Boronates and in situ Generated Azomethine Ylide. Chemistry 2024; 30:e202303504. [PMID: 38059680 DOI: 10.1002/chem.202303504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/08/2023]
Abstract
Scalable [3+2] cycloaddition of alkynyl boronates and in situ generated unstabilized azomethine ylide is reported for the first time. The selective formation of either 1 : 1 or 1 : 2 cycloaddition products was achieved by carefully optimizing the reaction conditions, mainly by controlling the reactant stoichiometry, catalyst loading, and internal temperature. The developed protocol tolerated many valuable functional groups, including TMS, protected alcohol (as ether or THP derivatives), or aldehyde (as acetal). Further common C-C and C-heteroatom bond-forming reactions, as well as scaled-up procedures demonstrate the utility of the prepared compounds as building blocks for organic synthesis and drug discovery.
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Affiliation(s)
- Oleksandr S Liashuk
- Enamine Ltd., Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Ihor A Ryzhov
- Enamine Ltd., Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Oleksandr V Hryshchuk
- Enamine Ltd., Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Yulian M Volovenko
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
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4
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Nippa DF, Atz K, Hohler R, Müller AT, Marx A, Bartelmus C, Wuitschik G, Marzuoli I, Jost V, Wolfard J, Binder M, Stepan AF, Konrad DB, Grether U, Martin RE, Schneider G. Enabling late-stage drug diversification by high-throughput experimentation with geometric deep learning. Nat Chem 2024; 16:239-248. [PMID: 37996732 PMCID: PMC10849962 DOI: 10.1038/s41557-023-01360-5] [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: 10/21/2022] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Late-stage functionalization is an economical approach to optimize the properties of drug candidates. However, the chemical complexity of drug molecules often makes late-stage diversification challenging. To address this problem, a late-stage functionalization platform based on geometric deep learning and high-throughput reaction screening was developed. Considering borylation as a critical step in late-stage functionalization, the computational model predicted reaction yields for diverse reaction conditions with a mean absolute error margin of 4-5%, while the reactivity of novel reactions with known and unknown substrates was classified with a balanced accuracy of 92% and 67%, respectively. The regioselectivity of the major products was accurately captured with a classifier F-score of 67%. When applied to 23 diverse commercial drug molecules, the platform successfully identified numerous opportunities for structural diversification. The influence of steric and electronic information on model performance was quantified, and a comprehensive simple user-friendly reaction format was introduced that proved to be a key enabler for seamlessly integrating deep learning and high-throughput experimentation for late-stage functionalization.
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Affiliation(s)
- David F Nippa
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kenneth Atz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Remo Hohler
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Alex T Müller
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Andreas Marx
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Christian Bartelmus
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Georg Wuitschik
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Irene Marzuoli
- Process Chemistry and Catalysis (PCC), F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Vera Jost
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Jens Wolfard
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Martin Binder
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Antonia F Stepan
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - David B Konrad
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Uwe Grether
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- ETH Singapore SEC Ltd, Singapore, Singapore.
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5
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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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6
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Xie A, Zhang Z, Guan J, Zhou S. Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction. Brief Bioinform 2023; 24:bbad296. [PMID: 37598424 DOI: 10.1093/bib/bbad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023] Open
Abstract
Molecular property prediction (MPP) is a crucial and fundamental task for AI-aided drug discovery (AIDD). Recent studies have shown great promise of applying self-supervised learning (SSL) to producing molecular representations to cope with the widely-concerned data scarcity problem in AIDD. As some specific substructures of molecules play important roles in determining molecular properties, molecular representations learned by deep learning models are expected to attach more importance to such substructures implicitly or explicitly to achieve better predictive performance. However, few SSL pre-trained models for MPP in the literature have ever focused on such substructures. To challenge this situation, this paper presents a Chemistry-Aware Fragmentation for Effective MPP (CAFE-MPP in short) under the self-supervised contrastive learning framework. First, a novel fragment-based molecular graph (FMG) is designed to represent the topological relationship between chemistry-aware substructures that constitute a molecule. Then, with well-designed hard negative pairs, a is pre-trained on fragment-level by contrastive learning to extract representations for the nodes in FMGs. Finally, a Graphormer model is leveraged to produce molecular representations for MPP based on the embeddings of fragments. Experiments on 11 benchmark datasets show that the proposed CAFE-MPP method achieves state-of-the-art performance on 7 of the 11 datasets and the second-best performance on 3 datasets, compared with six remarkable self-supervised methods. Further investigations also demonstrate that CAFE-MPP can learn to embed molecules into representations implicitly containing the information of fragments highly correlated to molecular properties, and can alleviate the over-smoothing problem of graph neural networks.
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Affiliation(s)
- Ailin Xie
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200438 Shanghai, China
| | - Ziqiao Zhang
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200438 Shanghai, China
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, 201804 Shanghai, China
| | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200438 Shanghai, China
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7
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Abstract
DNA-encoded libraries (DELs) are widely used in the discovery of drug candidates, and understanding their design principles is critical for accessing better libraries. Most DELs are combinatorial in nature and are synthesized by assembling sets of building blocks in specific topologies. In this study, different aspects of library topology were explored and their effect on DEL properties and chemical diversity was analyzed. We introduce a descriptor for DEL topological assignment (DELTA) and use it to examine the landscape of possible DEL topologies and their coverage in the literature. A generative topographic mapping analysis revealed that the impact of library topology on chemical space coverage is secondary to building block selection. Furthermore, it became apparent that the descriptor used to analyze chemical space dictates how structures cluster, with the effects of topology being apparent when using three-dimensional descriptors but not with common two-dimensional descriptors. This outcome points to potential challenges of attempts to predict DEL productivity based on chemical space analyses alone. While topology is rather inconsequential for defining the chemical space of encoded compounds, it greatly affects possible interactions with target proteins as illustrated in docking studies using NAD/NADP binding proteins as model receptors.
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Affiliation(s)
- William K Weigel
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, Utah 84112, United States
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8
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Beng TK, Garcia J, Eichwald J, Borg C. Introducing a sulfone-embedded anhydride to the anhydride-imine reaction for the modular synthesis of N-heterocyclic sulfones bearing vicinal stereocenters. RSC Adv 2023; 13:14355-14360. [PMID: 37180005 PMCID: PMC10171042 DOI: 10.1039/d3ra01812a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
N-heterocyclic sulfones constitute the core of several pharmaceuticals, including the antityrpanosomal drug Nifurtimox. Their biological relevance and architectural complexity makes them valued targets and inspires the development of more selective and atom-economical strategies for their construction and post-modification. In this embodiment, we describe a flexible approach to sp3-rich N-heterocyclic sulfones, which hinges on the efficient annulation of a novel sulfone-embedded anhydride with 1,3-azadienes and aryl aldimines. Further elaboration of the lactam esters has facilitated the construction of a library of vicinally functionalized sulfone-embedded N-heterocycles.
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Affiliation(s)
- Timothy K Beng
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
| | - Jorge Garcia
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
| | - Jane Eichwald
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
| | - Claire Borg
- Department of Chemistry, Central Washington University Ellensburg WA 98926 USA
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9
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Dou L, Zhang Z, Liu D, Qian Y, Zhang Q. BCM-DTI: A fragment-oriented method for drug-target interaction prediction using deep learning. Comput Biol Chem 2023; 104:107844. [PMID: 36924586 DOI: 10.1016/j.compbiolchem.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/30/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
The identification of drug-target interaction (DTI) is significant in drug discovery and development, which is usually of high cost in time and money due to large amount of molecule and protein space. The application of deep learning in predicting DTI pairs can overcome these limitations through feature engineering. However, most works do the features extraction using the whole drug and target, which do not take the theoretical basis of pharmacological reaction that the interaction is closely related to some substructure of molecule and protein into consideration, thus poor in performance. On the other hand, some substructure-oriented studies only consider a single type of fragment, e.g., functional group. To address these issues, we propose an end-to-end predicting framework for drug-target interaction named BCM-DTI that takes diverse fragment types into account, including branch chain, common substructure and motif/fragments, and applies a feature learning module based on CNN to learn the synergistic effect between these fragments. We implement BCM-DTI on four public datasets, and the results show that BCM-DTI outperforms state-of-the-art approaches and requires lower training cost.
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Affiliation(s)
- Liang Dou
- Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Computer Science and Technology, East China Normal University, North Zhongshan Road, Shanghai, 200062, China.
| | - Zhen Zhang
- Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Computer Science and Technology, East China Normal University, North Zhongshan Road, Shanghai, 200062, China.
| | - Dan Liu
- Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Computer Science and Technology, East China Normal University, North Zhongshan Road, Shanghai, 200062, China.
| | - Ying Qian
- Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Computer Science and Technology, East China Normal University, North Zhongshan Road, Shanghai, 200062, China.
| | - Qian Zhang
- Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Computer Science and Technology, East China Normal University, North Zhongshan Road, Shanghai, 200062, China.
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10
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Yu T, Yang J, Wang Z, Ding Z, Xu M, Wen J, Xu L, Li P. Selective [2σ + 2σ] Cycloaddition Enabled by Boronyl Radical Catalysis: Synthesis of Highly Substituted Bicyclo[3.1.1]heptanes. J Am Chem Soc 2023; 145:4304-4310. [PMID: 36763965 DOI: 10.1021/jacs.2c13740] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In contrast to the traditional and widely-used cycloaddition reactions involving at least a π bond component, a [2σ + 2σ] radical cycloaddition between bicyclo[1.1.0]butanes (BCBs) and cyclopropyl ketones has been developed to provide a modular, concise, and atom-economical synthetic route to substituted bicyclo[3.1.1]heptane (BCH) derivatives that are 3D bioisosteres of benzenes and core skeleton of a number of terpene natural products. The reaction was catalyzed by a combination of simple tetraalkoxydiboron(4) compound B2pin2 and 3-pentyl isonicotinate. The broad substrate scope has been demonstrated by synthesizing a series of new highly functionalized BCHs with up to six substituents on the core with up to 99% isolated yield. Computational mechanistic investigations supported a pyridine-assisted boronyl radical catalytic cycle.
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Affiliation(s)
- Tao Yu
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
| | - Jinbo Yang
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, China
| | - Zhijun Wang
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, China
| | - Zhengwei Ding
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Ming Xu
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
| | - Jingru Wen
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
| | - Liang Xu
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, China
| | - Pengfei Li
- Frontier Institute of Science and Technology and State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710054, China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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11
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Di Filippo M, Baumann M. Carbene-controlled regioselectivity in photochemical cascades. Org Biomol Chem 2023; 21:2930-2934. [PMID: 36745509 DOI: 10.1039/d3ob00122a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A highly regioselective route to complex carbocyclic scaffolds through a continuous photochemical process is reported. Crucially, we uncovered that ortho substitutents on the right-hand aryl ring are placed away from a transient carbene species which induces the exclusive regioselectivity observed. By varying the non-symmetrically substituted aryl moiety, we demonstrate how the product outcome favors cyclobutenes for electron-poor and neutral substituents and cycloheptatrienes for more electron-rich systems. Additionally, a photochemically induced rearrangement was uncovered for highly electron-rich substrates that ultimately generates complex hydroperoxides. Overall, this facile one-step process is fast and high yielding and demonstrates the power of photochemistry towards the exploration of new chemical space.
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Affiliation(s)
- Mara Di Filippo
- University College Dublin, School of Chemistry, Science Centre South, Belfield, Dublin 4, Ireland.
| | - Marcus Baumann
- University College Dublin, School of Chemistry, Science Centre South, Belfield, Dublin 4, Ireland.
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12
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Abdiaj I, Cañellas S, Dieguez A, Linares ML, Pijper B, Fontana A, Rodriguez R, Trabanco A, Palao E, Alcázar J. End-to-End Automated Synthesis of C(sp 3)-Enriched Drug-like Molecules via Negishi Coupling and Novel, Automated Liquid-Liquid Extraction. J Med Chem 2023; 66:716-732. [PMID: 36520521 PMCID: PMC9841985 DOI: 10.1021/acs.jmedchem.2c01646] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Indexed: 12/23/2022]
Abstract
Herein, we report an end-to-end process including synthesis, work-up, purification, and post-purification with minimal human intervention using Negishi coupling as a key transformation to increase Fsp3 in bioactive molecules. The main advantages of this protocol are twofold. First, the automated sequential generation of organozinc reagents from readily available alkyl halides offers a large diversity of alkyl groups to functionalize (hetero)aryl halide scaffolds via Pd-catalyzed Negishi coupling in continuous flow. Second, a fully automated liquid-liquid extraction has been developed and successfully applied for unattended operations. The workflow was completed with mass-triggered preparative high-performance liquid chromatography HPLC, providing an efficient production line of compounds with enriched sp3 character and better drug-like properties. The modular nature allows a smooth adaptation to a wide variety of synthetic methods and protocols and makes it applicable to any medchem laboratory.
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Affiliation(s)
- Irini Abdiaj
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Santiago Cañellas
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Alejandro Dieguez
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Maria Lourdes Linares
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Brenda Pijper
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Alberto Fontana
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Raquel Rodriguez
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Andres Trabanco
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Eduardo Palao
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
| | - Jesus Alcázar
- Discovery Chemistry, Janssen Research
and Development, Janssen-Cilag, S.A., C/ Jarama 75, E-45007Toledo, Spain
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13
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Xu M, Wang Z, Sun Z, Ouyang Y, Ding Z, Yu T, Xu L, Li P. Diboron(4)-Catalyzed Remote [3+2] Cycloaddition of Cyclopropanes via Dearomative/Rearomative Radical Transmission through Pyridine. Angew Chem Int Ed Engl 2022; 61:e202214507. [PMID: 36344444 DOI: 10.1002/anie.202214507] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Indexed: 11/09/2022]
Abstract
Ring structures such as pyridine, cyclopentane or their combinations are important motifs in bioactive molecules. In contrast to previous cycloaddition reactions that necessitated a directly bonded initiating functional group, this work demonstrated a novel through-(hetero)arene radical transmission concept for selective activation of a remote bond. An efficient, metal-free and atom-economical [3+2] cycloaddition between 4-pyridinyl cyclopropanes and alkenes or alkynes has been developed for modular synthesis of pyridine-substituted cyclopentanes, cyclopentenes and bicyclo[2.1.1]hexanes that are difficult to access using known methods. This complexity-building reaction was catalyzed by a very simple and inexpensive diboron(4) compound and took place via dearomative/rearomative processes. The substrate scope was broad and more than 100 new compounds were prepared in generally high yields. Mechanistic experiments and density function theory (DFT) investigation supported a radical relay catalytic cycle involving alkylidene dihydropyridine radical intermediates and boronyl radical transfer.
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Affiliation(s)
- Ming Xu
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Zhijun Wang
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhaohui Sun
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yizhao Ouyang
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Zhengwei Ding
- Department of Medicinal Chemistry, School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Tao Yu
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Liang Xu
- School of Chemistry and Chemical Engineering/Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Pengfei Li
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China.,State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
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14
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Fudger A, Cakir OM, Khan Y, Sinclair A, Le Gresley A. Chemical synthesis of a library of natural product-like derivatives based on pinnaic acid and initial evaluation of their anti-cancer activity. Org Biomol Chem 2022; 20:9408-9421. [PMID: 36398757 DOI: 10.1039/d2ob01626e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Halichlorine and pinnaic acid have been shown previously to be potent inhibitors of the inflammatory enzymes cPLA2 and VCAM-1 and have also demonstrated some anti-cancer activity. They possess an almost identical azaspirocyclic core consisting of a unique 3-dimensional geometry with four stereocentres, making them compounds of interest for further study to reveal any bioactivity not yet discovered. The azaspirocyclic core was synthesised from an established protocol, from which a small library of novel analogues were synthesised and tested for activity against two cancer cell lines, HeLa and CaCo-2, along with the non-cancerous cell line HaCaT. Eleven compounds were found to be selective for CaCo-2 cells.
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Affiliation(s)
- Alex Fudger
- School of Life Sciences, Pharmacy and Chemistry, HSSCE Faculty, Kingston University, Kingston upon Thames, KT1 2EE, UK.
| | - Okan M Cakir
- School of Life Sciences, Pharmacy and Chemistry, HSSCE Faculty, Kingston University, Kingston upon Thames, KT1 2EE, UK.
| | - Yousaf Khan
- School of Life Sciences, Pharmacy and Chemistry, HSSCE Faculty, Kingston University, Kingston upon Thames, KT1 2EE, UK.
| | - Alex Sinclair
- School of Life Sciences, Pharmacy and Chemistry, HSSCE Faculty, Kingston University, Kingston upon Thames, KT1 2EE, UK.
| | - Adam Le Gresley
- School of Life Sciences, Pharmacy and Chemistry, HSSCE Faculty, Kingston University, Kingston upon Thames, KT1 2EE, UK.
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15
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Cong F, Mega RS, Chen J, Day CS, Martin R. Trifluoromethylation of Carbonyl and Unactivated Olefin Derivatives by C(sp 3 )-C Bond Cleavage. Angew Chem Int Ed Engl 2022; 62:e202214633. [PMID: 36416716 DOI: 10.1002/anie.202214633] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022]
Abstract
Herein, we report a Cu-mediated trifluoromethylation of carbonyl-type compounds and unactivated olefins enabled by visible-light irradiation via σ C(sp3 )-C bond-functionalization. The reaction is distinguished by its modularity, mild conditions and wide scope-even in the context of late-stage functionalization-thus offering a complementary approach en route to valuable C(sp3 )-CF3 architectures from easily accessible precursors.
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Affiliation(s)
- Fei Cong
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain.,Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, c/Marcel ⋅ lí Domingo, 1, 43007, Tarragona, Spain
| | - Riccardo S Mega
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain
| | - Jinhong Chen
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain.,Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, c/Marcel ⋅ lí Domingo, 1, 43007, Tarragona, Spain
| | - Craig S Day
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain.,Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, c/Marcel ⋅ lí Domingo, 1, 43007, Tarragona, Spain
| | - Ruben Martin
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007, Tarragona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluïs Companys 23, 08010, Barcelona, Spain
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16
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Barthel T, Wollenhaupt J, Lima GMA, Wahl MC, Weiss MS. Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites. J Med Chem 2022; 65:14630-14641. [PMID: 36260741 DOI: 10.1021/acs.jmedchem.2c01165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The identification of starting points for compound development is one of the key steps in early-stage drug discovery. Information-rich techniques such as crystallographic fragment screening can potentially increase the efficiency of this step by providing the structural information of the binding mode of the ligands in addition to the mere binding information. Here, we present the crystallographic screening of our 1000-plus-compound F2X-Universal Library against the complex of the yeast spliceosomal Prp8 RNaseH-like domain and the snRNP assembly factor Aar2. The observed 269 hits are distributed over 10 distinct binding sites on the surface of the protein-protein complex. Our work shows that hit clusters from large-scale crystallographic fragment screening campaigns identify known interaction sites with other proteins and suggest putative additional interaction sites. Furthermore, the inherent binding pose validation within the hit clusters may accelerate downstream compound optimization.
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Affiliation(s)
- Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | | | - Markus C Wahl
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany.,Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany
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17
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Melnykov KP, Voloshyna OV, Vashchenko BV, Demchuk OP, Hryshchuk OV, Grygorenko OO. 4,4‐Difluorospiro[2.2]pentan‐1‐yl – A Fluorinated Substituent to Expand the Synthetic and Medicinal Chemists’ Toolbox. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200863] [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)
- Kostiantyn P. Melnykov
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
| | - Olena V. Voloshyna
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
| | - Bohdan V. Vashchenko
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
| | | | | | - Oleksandr O Grygorenko
- Taras Shevchenko National University of Kyiv: Kiivs'kij nacional'nij universitet imeni Tarasa Sevcenka Chemical Faculty UKRAINE
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18
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Shennan BDA, Berheci D, Crompton JL, Davidson TA, Field JL, Williams BA, Dixon DJ. Branching out: redox strategies towards the synthesis of acyclic α-tertiary ethers. Chem Soc Rev 2022; 51:5878-5929. [PMID: 35770619 DOI: 10.1039/d1cs00669j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Acyclic α-tertiary ethers represent a highly prevalent functionality, common to high-value bioactive molecules, such as pharmaceuticals and natural products, and feature as crucial synthetic handles in their construction. As such their synthesis has become an ever-more important goal in synthetic chemistry as the drawbacks of traditional strong base- and acid-mediated etherifications have become more limiting. In recent years, the generation of highly reactive intermediates via redox approaches has facilitated the synthesis of highly sterically-encumbered ethers and accordingly these strategies have been widely applied in α-tertiary ether synthesis. This review summarises and appraises the state-of-the-art in the application of redox strategies enabling acyclic α-tertiary ether synthesis.
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Affiliation(s)
- Benjamin D A Shennan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Diana Berheci
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Jessica L Crompton
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Timothy A Davidson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Joshua L Field
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Benedict A Williams
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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19
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Isert C, Atz K, Jiménez-Luna J, Schneider G. QMugs, quantum mechanical properties of drug-like molecules. Sci Data 2022; 9:273. [PMID: 35672335 PMCID: PMC9174255 DOI: 10.1038/s41597-022-01390-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 05/17/2022] [Indexed: 12/16/2022] Open
Abstract
Machine learning approaches in drug discovery, as well as in other areas of the chemical sciences, benefit from curated datasets of physical molecular properties. However, there currently is a lack of data collections featuring large bioactive molecules alongside first-principle quantum chemical information. The open-access QMugs (Quantum-Mechanical Properties of Drug-like Molecules) dataset fills this void. The QMugs collection comprises quantum mechanical properties of more than 665 k biologically and pharmacologically relevant molecules extracted from the ChEMBL database, totaling ~2 M conformers. QMugs contains optimized molecular geometries and thermodynamic data obtained via the semi-empirical method GFN2-xTB. Atomic and molecular properties are provided on both the GFN2-xTB and on the density-functional levels of theory (DFT, ωB97X-D/def2-SVP). QMugs features molecules of significantly larger size than previously-reported collections and comprises their respective quantum mechanical wave functions, including DFT density and orbital matrices. This dataset is intended to facilitate the development of models that learn from molecular data on different levels of theory while also providing insight into the corresponding relationships between molecular structure and biological activity. Measurement(s) | Quantum Mechanics | Technology Type(s) | density functional theory |
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20
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Jonnalagadda SK, Huwaimel BI, Jonnalagadda S, Garrison JC, Trippier PC. Access to Highly Strained Tricyclic Ketals Derived from Coumarins. J Org Chem 2022; 87:4476-4482. [PMID: 35258961 PMCID: PMC8996706 DOI: 10.1021/acs.joc.2c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthesis of highly strained fused substituted dihydrobenzopyran cyclopropyl lactones derived from coumarin carboxylates are reported. The substrate scope tolerates a variety of 6- and 8-substituents on the coumarin ring. Substitution at the 5- or 7-position is resistant to tricyclic lactone formation except with 7-methyl substitution. Benzamide-containing coumarins afford the tricyclic ketal. A plausible mechanism is proposed for the formation of the fused lactone: intramolecular rearrangement of trans cyclopropyl methyl ketones with phenolic acetate via the formation of a hemiacetal.
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Affiliation(s)
- Sravan K Jonnalagadda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States
| | - Bader I Huwaimel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States.,Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 81442, Kingdom of Saudi Arabia
| | - Shirisha Jonnalagadda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States
| | - Jered C Garrison
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States.,Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States.,Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States.,UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska 68106, United States
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21
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Mannchen MD, Ghiviriga I, Abboud KA, Grenning AJ. 1,2,4-Trifunctionalized Cyclohexane Synthesis via a Diastereoselective Reductive Cope Rearrangement and Functional Group Interconversion Strategy. Org Lett 2021; 23:8804-8809. [PMID: 34719933 DOI: 10.1021/acs.orglett.1c03310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Polyfunctionalized cyclohexanes are privileged scaffolds in drug discovery. Reported herein is a method for synthesizing 1,2,4-trifunctionalized cyclohexanes via diastereoselective reductive Cope rearrangement. The scaffolds obtained can be derivatized by orthogonal functional group interconversion to cyclohexanes bearing a 1-amide, 2-branched arylallyl, and variable 4-functional group.
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Affiliation(s)
- Michael D Mannchen
- Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
| | - Ion Ghiviriga
- Center for NMR Spectroscopy, Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
| | - Khalil A Abboud
- Center for X-ray Crystallography, Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
| | - Alexander J Grenning
- Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
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22
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23
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Nguyen T, Gamage TF, Decker AM, Finlay DB, Langston TL, Barrus D, Glass M, Harris DL, Zhang Y. Rational design of cannabinoid type-1 receptor allosteric modulators: Org27569 and PSNCBAM-1 hybrids. Bioorg Med Chem 2021; 41:116215. [PMID: 34015703 DOI: 10.1016/j.bmc.2021.116215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/22/2021] [Accepted: 05/07/2021] [Indexed: 11/25/2022]
Abstract
Allosteric modulation offers an alternate approach to target the cannabinoid type-1 receptor (CB1) for therapeutic benefits. Examination of the two widely studied prototypic CB1 negative allosteric modulators (NAMs) Org27569 and PSNCBAM-1 revealed structural resemblance and similar structure-activity relationships (SARs). In silico docking and dynamics simulation studies using the crystal structure of CB1 co-bound with CP55,940 and Org27569 suggested that Org27569 and PSNCBAM-1 occupied the same binding pocket and several common interactions were present in both series with the CB1 receptor. A new scaffold was therefore designed by merging the key structural features from the two series and the hybrids retained these binding features in the in silico docking studies. In addition, one such hybrid displayed similar functions to Org27569 in dynamic simulations by preserving a key R2143.50-D3386.30 salt bridge and maintaining an antagonist-like Helix3-Helix6 interhelical distance. Based on these results, a series of hybrids were synthesized and assessed in calcium mobilization, [35S]GTPγS binding and cAMP assays. Several compounds displayed comparable potencies to Org27569 and PSNCBAM-1 in these assays. This work offers new insight of the SAR requirement at the allosteric site of the CB1 receptor and provides a new scaffold that can be optimized for the development of future CB1 allosteric modulators.
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Affiliation(s)
- Thuy Nguyen
- Research Triangle Institute, Research Triangle Park, NC 27709, USA
| | - Thomas F Gamage
- Research Triangle Institute, Research Triangle Park, NC 27709, USA
| | - Ann M Decker
- Research Triangle Institute, Research Triangle Park, NC 27709, USA
| | - David B Finlay
- Department of Pharmacology and Toxicology, University of Otago, Dunedin 9054, New Zealand
| | | | - Daniel Barrus
- Research Triangle Institute, Research Triangle Park, NC 27709, USA
| | - Michelle Glass
- Department of Pharmacology and Toxicology, University of Otago, Dunedin 9054, New Zealand
| | - Danni L Harris
- Research Triangle Institute, Research Triangle Park, NC 27709, USA.
| | - Yanan Zhang
- Research Triangle Institute, Research Triangle Park, NC 27709, USA.
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24
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Diallo BN, Glenister M, Musyoka TM, Lobb K, Tastan Bishop Ö. SANCDB: an update on South African natural compounds and their readily available analogs. J Cheminform 2021; 13:37. [PMID: 33952332 PMCID: PMC8097257 DOI: 10.1186/s13321-021-00514-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND South African Natural Compounds Database (SANCDB; https://sancdb.rubi.ru.ac.za/ ) is the sole and a fully referenced database of natural chemical compounds of South African biodiversity. It is freely available, and since its inception in 2015, the database has become an important resource to several studies. Its content has been: used as training data for machine learning models; incorporated to larger databases; and utilized in drug discovery studies for hit identifications. DESCRIPTION Here, we report the updated version of SANCDB. The new version includes 412 additional compounds that have been reported since 2015, giving a total of 1012 compounds in the database. Further, although natural products (NPs) are an important source of unique scaffolds, they have a major drawback due to their complex structure resulting in low synthetic feasibility in the laboratory. With this in mind, SANCDB is, now, updated to provide direct links to commercially available analogs from two major chemical databases namely Mcule and MolPort. To our knowledge, this feature is not available in other NP databases. Additionally, for easier access to information by users, the database and website interface were updated. The compounds are now downloadable in many different chemical formats. CONCLUSIONS The drug discovery process relies heavily on NPs due to their unique chemical organization. This has inspired the establishment of numerous NP chemical databases. With the emergence of newer chemoinformatic technologies, existing chemical databases require constant updates to facilitate information accessibility and integration by users. Besides increasing the NPs compound content, the updated SANCDB allows users to access the individual compounds (if available) or their analogs from commercial databases seamlessly.
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Affiliation(s)
- Bakary N'tji Diallo
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, 6140, South Africa
| | - Michael Glenister
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, 6140, South Africa
| | - Thommas M Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, 6140, South Africa
| | - Kevin Lobb
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, 6140, South Africa.,Department of Chemistry, Rhodes University, Makhanda/Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, 6140, South Africa.
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25
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Synthesis of sp3-rich chemical libraries based upon 1,2-diazetidines. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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26
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Hamilton DJ, Dekker T, Klein HF, Janssen GV, Wijtmans M, O'Brien P, de Esch IJP. Escape from planarity in fragment-based drug discovery: A physicochemical and 3D property analysis of synthetic 3D fragment libraries. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 38:77-90. [PMID: 34895643 DOI: 10.1016/j.ddtec.2021.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/30/2021] [Accepted: 05/19/2021] [Indexed: 06/14/2023]
Abstract
Fragment-based drug discovery (FBDD) has grown into a well-established approach in the pursuit of new therapeutics. Key to the success of FBDD is the low molecular complexity of the initial hits and this has resulted in fragment libraries that mainly contain compounds with a two-dimensional (2D) shape. In an effort to increase the chemical diversity and explore the impact of increased molecular complexity on the hit rate of fragment library screening, several academic and industrial groups have designed and synthesised novel fragments with a three-dimensional (3D) shape. This review provides an overview of 25 synthetic 3D fragment libraries from the recent literature. We calculate and compare physicochemical properties and descriptors that are typically used to measure molecular three-dimensionality such as fraction sp3 (Fsp3), plane of best fit (PBF) scores and principal moment of inertia (PMI) plots. Although the libraries vary widely in structure and properties, some key common features can be identified which may have utility in designing the next generation of 3D fragment libraries.
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Affiliation(s)
- David J Hamilton
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Tom Dekker
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Hanna F Klein
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Guido V Janssen
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.
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27
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Cong F, Lv XY, Day CS, Martin R. Dual Catalytic Strategy for Forging sp2–sp3 and sp3–sp3 Architectures via β-Scission of Aliphatic Alcohol Derivatives. J Am Chem Soc 2020; 142:20594-20599. [DOI: 10.1021/jacs.0c11172] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Fei Cong
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avenida Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Xin-Yang Lv
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avenida Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Craig S. Day
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avenida Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, c/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Ruben Martin
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avenida Països Catalans 16, 43007 Tarragona, Spain
- ICREA, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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28
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O’Hagan S, Kell DB. Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products. Mar Drugs 2020; 18:E582. [PMID: 33238416 PMCID: PMC7700180 DOI: 10.3390/md18110582] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
It is known that at least some fluorophores can act as 'surrogate' substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the 'natural' substrates of 'orphan' transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly 'drug-like', and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores along with standard fingerprinting methods and the Tanimoto similarity metric. Results: The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug, as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the "quantitative estimate of drug likeness" technique. It is concluded that this set of fluorophores does overlap with a significant part of both the drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities.
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Affiliation(s)
- Steve O’Hagan
- Department of Chemistry, The University of Manchester, Manchester M13 9PT, UK;
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Molecular, Integrative and Systems Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
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Matos MS, Anastácio JD, Allwood JW, Carregosa D, Marques D, Sungurtas J, McDougall GJ, Menezes R, Matias AA, Stewart D, dos Santos CN. Assessing the Intestinal Permeability and Anti-Inflammatory Potential of Sesquiterpene Lactones from Chicory. Nutrients 2020; 12:E3547. [PMID: 33228214 PMCID: PMC7699524 DOI: 10.3390/nu12113547] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/16/2022] Open
Abstract
Cichorium intybus L. has recently gained major attention due to large quantities of health-promoting compounds in its roots, such as inulin and sesquiterpene lactones (SLs). Chicory is the main dietary source of SLs, which have underexplored bioactive potential. In this study, we assessed the capacity of SLs to permeate the intestinal barrier to become physiologically available, using in silico predictions and in vitro studies with the well-established cell model of the human intestinal mucosa (differentiated Caco-2 cells). The potential of SLs to modulate inflammatory responses through modulation of the nuclear factor of activated T-cells (NFAT) pathway was also evaluated, using a yeast reporter system. Lactucopicrin was revealed as the most permeable chicory SL in the intestinal barrier model, but it had low anti-inflammatory potential. The SL with the highest anti-inflammatory potential was 11β,13-dihydrolactucin, which inhibited up to 54% of Calcineurin-responsive zinc finger (Crz1) activation, concomitantly with the impairment of the nuclear accumulation of Crz1, the yeast orthologue of human NFAT.
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Affiliation(s)
- Melanie S. Matos
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal; (M.S.M.); (J.D.A.); (D.C.); (R.M.); (A.A.M.)
| | - José D. Anastácio
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal; (M.S.M.); (J.D.A.); (D.C.); (R.M.); (A.A.M.)
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal;
| | - J. William Allwood
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences, The James Hutton Institute, Dundee DD2 5DA, UK; (J.W.A.); (J.S.); (G.J.M.); (D.S.)
| | - Diogo Carregosa
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal; (M.S.M.); (J.D.A.); (D.C.); (R.M.); (A.A.M.)
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal;
| | - Daniela Marques
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal;
| | - Julie Sungurtas
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences, The James Hutton Institute, Dundee DD2 5DA, UK; (J.W.A.); (J.S.); (G.J.M.); (D.S.)
| | - Gordon J. McDougall
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences, The James Hutton Institute, Dundee DD2 5DA, UK; (J.W.A.); (J.S.); (G.J.M.); (D.S.)
| | - Regina Menezes
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal; (M.S.M.); (J.D.A.); (D.C.); (R.M.); (A.A.M.)
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal;
| | - Ana A. Matias
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal; (M.S.M.); (J.D.A.); (D.C.); (R.M.); (A.A.M.)
| | - Derek Stewart
- Plant Biochemistry and Food Quality Group, Environmental and Biochemical Sciences, The James Hutton Institute, Dundee DD2 5DA, UK; (J.W.A.); (J.S.); (G.J.M.); (D.S.)
| | - Cláudia Nunes dos Santos
- Instituto de Biologia Experimental e Tecnológica (iBET), Av. República, Qta. Marquês, 2780-157 Oeiras, Portugal; (M.S.M.); (J.D.A.); (D.C.); (R.M.); (A.A.M.)
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal;
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30
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Medina-Franco JL, Saldívar-González FI. Cheminformatics to Characterize Pharmacologically Active Natural Products. Biomolecules 2020; 10:E1566. [PMID: 33213003 PMCID: PMC7698493 DOI: 10.3390/biom10111566] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 12/19/2022] Open
Abstract
Natural products have a significant role in drug discovery. Natural products have distinctive chemical structures that have contributed to identifying and developing drugs for different therapeutic areas. Moreover, natural products are significant sources of inspiration or starting points to develop new therapeutic agents. Natural products such as peptides and macrocycles, and other compounds with unique features represent attractive sources to address complex diseases. Computational approaches that use chemoinformatics and molecular modeling methods contribute to speed up natural product-based drug discovery. Several research groups have recently used computational methodologies to organize data, interpret results, generate and test hypotheses, filter large chemical databases before the experimental screening, and design experiments. This review discusses a broad range of chemoinformatics applications to support natural product-based drug discovery. We emphasize profiling natural product data sets in terms of diversity; complexity; acid/base; absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties; and fragment analysis. Novel techniques for the visual representation of the chemical space are also discussed.
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Affiliation(s)
- José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico;
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31
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Saldívar-González FI, Huerta-García CS, Medina-Franco JL. Chemoinformatics-based enumeration of chemical libraries: a tutorial. J Cheminform 2020; 12:64. [PMID: 33372622 PMCID: PMC7590480 DOI: 10.1186/s13321-020-00466-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022] Open
Abstract
Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper aims to examine the fundamental concepts of library design and describe how to enumerate virtual libraries using open source tools. To exemplify the enumeration of chemical libraries, we emphasize the use of pre-validated or reported reactions and accessible chemical reagents. This tutorial shows a step-by-step procedure for anyone interested in designing and building chemical libraries with or without chemoinformatics experience. The aim is to explore various methodologies proposed by synthetic organic chemists and explore affordable chemical space using open-access chemoinformatics tools. As part of the tutorial, we discuss three examples of design: a Diversity-Oriented-Synthesis library based on lactams, a bis-heterocyclic combinatorial library, and a set of target-oriented molecules: isoindolinone based compounds as potential acetylcholinesterase inhibitors. This manuscript also seeks to contribute to the critical task of teaching and learning chemoinformatics.
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Affiliation(s)
- Fernanda I. Saldívar-González
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510 Mexico, Mexico
| | - C. Sebastian Huerta-García
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510 Mexico, Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510 Mexico, Mexico
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32
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Lengacher R, Csucker J, Hernández-Valdés D, Spingler B, Braband H, Alberto R. Expanding the Cyclopentadienyl Framework: 99mTc/Re Complexes with Orthogonal Functions for Bioconjugation. Bioconjug Chem 2020; 32:1393-1398. [PMID: 32997491 DOI: 10.1021/acs.bioconjchem.0c00468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of bifunctional cyclopentadienes of the type 1,3-EtOCO-HCp-linker-NH2 were synthesized. In this series, the linker length (distance between the amine functionalities and the cyclopentadiene) has been systematically varied (CH2)n (n = 1-3). The corresponding Re complexes [(η5-C5H3RR')Re(CO)3] (R = -COOEt, R' = -linker-NH2) were synthesized and structurally characterized. They exhibit extraordinary stability toward water and air. All bifunctional cyclopentadienes have been labeled with the [99mTc(CO)3]+ moiety. Whereas the reactions with ethylene and propylene linked cyclopentadiene under mild reaction conditions led to the products in high radiochemical purity (>96%) without applying further purification protocols, harsher reaction conditions were required for the synthesis of the methylene-linked cyclopentadiene compound. Masking the amine in the methylene-linked cyclopentadiene by an amide bond bypasses this problem. The very hydrophilic characters of these complexes were assessed by KOW analysis. The reported cyclopentadienes and their complexes offer a robust and versatile platform for (radio)metal incorporation into biologically active lead structures.
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Affiliation(s)
- Raphael Lengacher
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Joshua Csucker
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Daniel Hernández-Valdés
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Bernhard Spingler
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Henrik Braband
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Roger Alberto
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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33
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Ferrara SJ, Scanlan TS. A CNS-Targeting Prodrug Strategy for Nuclear Receptor Modulators. J Med Chem 2020; 63:9742-9751. [DOI: 10.1021/acs.jmedchem.0c00868] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Skylar J. Ferrara
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Thomas S. Scanlan
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
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34
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Palchykov VA, Gaponova RG, Omelchenko IV, Kasyan LI. Synthesis of new azapolycyclic scaffolds via the domino aminolysis of dicyclopentadiene diepoxide in water. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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35
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Li X, Shi Z, Wu J, Wu J, He C, Hao X, Duan C. Lighting up metallohelices: from DNA binders to chemotherapy and photodynamic therapy. Chem Commun (Camb) 2020; 56:7537-7548. [PMID: 32573609 DOI: 10.1039/d0cc02194f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The design of novel agents that specifically target DNA and interrupt its normal biological processes is an attractive goal in drug design. Among the promising metallodrugs, metal-directed self-assembled metallohelices with defined three-dimensional stereochemical structures display unique structure-inherent and unprecedented noncovalent targeting abilities towards DNA, resulting in excellent anticancer or antibiotic activities. A newly burgeoning hotspot is focusing on lighting them up by embedding luminescent metal ions as the vertices. The photoactive metallohelices that combine strong interactions toward DNA targets and efficient 1O2 quantum yield may provide new motivation in diagnostic and photodynamic therapy (PDT) areas. This perspective focuses on research progress on metallohelices as DNA binders and chemotherapeutic agents, and highlights recent advances in fabricating luminescent examples for PDT. The relative assembly strategies are also discussed and compared. Finally, perspectives on the future development of the lit-up metallohelices are presented.
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Affiliation(s)
- Xuezhao Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China.
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36
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Prosser K, Stokes RW, Cohen SM. Evaluation of 3-Dimensionality in Approved and Experimental Drug Space. ACS Med Chem Lett 2020; 11:1292-1298. [PMID: 32551014 PMCID: PMC7294711 DOI: 10.1021/acsmedchemlett.0c00121] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/18/2020] [Indexed: 11/28/2022] Open
Abstract
The 3-dimensional (3D) structure of therapeutics and other bioactive molecules is an important factor in determining the strength and selectivity of their protein-ligand interactions. Previous efforts have considered the strain introduced and tolerated through conformational changes induced upon protein binding. Herein, we present an analysis of 3-dimentionality for energy-minimized structures from the DrugBank and ligands bound to proteins identified in the Protein Data Bank (PDB). This analysis reveals that the majority of molecules found in both the DrugBank and the PDB tend toward linearity and planarity, with few molecules having highly 3D conformations. Decidedly 3D geometries have been historically difficult to achieve, likely due to the synthetic challenge of making 3D organic molecules, and other considerations, such as adherence to the 'rule-of-five'. This has resulted in the dominance of planar and/or linear topologies of the molecules described here. Strategies to address the generally flat nature of these data sets are explored, including the use of 3D organic fragments and inorganic scaffolds as a means of accessing privileged 3D space. This work highlights the potential utility of libraries with greater 3D topological diversity so that the importance of molecular shape to biological behavior can be more fully understood in drug discovery campaigns.
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Affiliation(s)
- Kathleen
E. Prosser
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Ryjul W. Stokes
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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Dean C, Rajkumar S, Roesner S, Carson N, Clarkson GJ, Wills M, Jones M, Shipman M. Readily accessible sp 3-rich cyclic hydrazine frameworks exploiting nitrogen fluxionality. Chem Sci 2020; 11:1636-1642. [PMID: 32206282 PMCID: PMC7069508 DOI: 10.1039/c9sc04849a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Increased molecular complexity correlates with improved chances of success in the drug development process. Here, a strategy for the creation of sp3-rich, non-planar heterocyclic scaffolds suitable for drug discovery is described that obviates the need to generate multiple stereogenic centers with independent control. Asymmetric transfer hydrogenation using a tethered Ru-catalyst is used to efficiently produce a range of enantiopure cyclic hydrazine building blocks (up to 99% ee). Iterative C-N functionalization at the two nitrogen atoms of these compounds produces novel hydrazine and hydrazide based chemical libraries. Wide chemical diversification is possible through variation in the hydrazine structure, use of different functionalization chemistries and coupling partners, and controlled engagement of each nitrogen of the hydrazine in turn. Principal Moment of Inertia (PMI) analysis of this small hydrazine library reveals excellent shape diversity and three-dimensionality. NMR and crystallographic studies confirm these frameworks prefer to orient their substituents in three-dimensional space under the control of a single stereogenic center through exploitation of the fluxional behavior of the two nitrogen atoms.
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Affiliation(s)
- Conor Dean
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Sundaram Rajkumar
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Stefan Roesner
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Nessa Carson
- AMRI UK, Ltd. , Erl Wood Manor , Windlesham , Surrey GU20 6PH , UK
| | - Guy J Clarkson
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Martin Wills
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Matthew Jones
- Eli Lilly & Company Ltd. , Erl Wood Manor , Windlesham , Surrey GU20 6PH , UK
| | - Michael Shipman
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
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Mandal D, Gupta R, Jaiswal AK, Young RD. Frustrated Lewis-Pair-Meditated Selective Single Fluoride Substitution in Trifluoromethyl Groups. J Am Chem Soc 2020; 142:2572-2578. [DOI: 10.1021/jacs.9b12167] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Dipendu Mandal
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Richa Gupta
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Amit K. Jaiswal
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Rowan D. Young
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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Troelsen NS, Shanina E, Gonzalez-Romero D, Danková D, Jensen ISA, Śniady KJ, Nami F, Zhang H, Rademacher C, Cuenda A, Gotfredsen CH, Clausen MH. The 3F Library: Fluorinated Fsp 3 -Rich Fragments for Expeditious 19 F NMR Based Screening. Angew Chem Int Ed Engl 2019; 59:2204-2210. [PMID: 31724281 DOI: 10.1002/anie.201913125] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/11/2019] [Indexed: 11/08/2022]
Abstract
Fragment-based drug discovery (FBDD) is a popular method in academia and the pharmaceutical industry for the discovery of early lead candidates. Despite its wide-spread use, the approach still suffers from laborious screening workflows and a limited diversity in the fragments applied. Presented here is the design, synthesis, and biological evaluation of the first fragment library specifically tailored to tackle both these challenges. The 3F library of 115 fluorinated, Fsp3 -rich fragments is shape diverse and natural-product-like with desirable physicochemical properties. The library is perfectly suited for rapid and efficient screening by NMR spectroscopy in a two-stage workflow of 19 F NMR and subsequent 1 H NMR methods. Hits against four diverse protein targets are widely distributed among the fragment scaffolds in the 3F library and a 67 % validation rate was achieved using secondary assays. This collection is the first synthetic fragment library tailor-made for 19 F NMR screening and the results demonstrate that the approach should find broad application in the FBDD community.
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Affiliation(s)
- Nikolaj S Troelsen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Elena Shanina
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424, Potsdam, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Diego Gonzalez-Romero
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus UAM, 28049, Madrid, Spain
| | - Daniela Danková
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Ida S A Jensen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Katarzyna J Śniady
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Faranak Nami
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Hengxi Zhang
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424, Potsdam, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Christoph Rademacher
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424, Potsdam, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Ana Cuenda
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Campus UAM, 28049, Madrid, Spain
| | - Charlotte H Gotfredsen
- NMR Center⋅DTU, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
| | - Mads H Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kongens, Lyngby, Denmark
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40
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Troelsen NS, Shanina E, Gonzalez‐Romero D, Danková D, Jensen ISA, Śniady KJ, Nami F, Zhang H, Rademacher C, Cuenda A, Gotfredsen CH, Clausen MH. The 3F Library: Fluorinated Fsp
3
‐Rich Fragments for Expeditious
19
F NMR Based Screening. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201913125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nikolaj S. Troelsen
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Elena Shanina
- Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14424 Potsdam Germany
- Department of Biology, Chemistry and PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Diego Gonzalez‐Romero
- Department of Immunology and OncologyCentro Nacional de Biotecnología/CSIC Campus UAM 28049 Madrid Spain
| | - Daniela Danková
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Ida S. A. Jensen
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Katarzyna J. Śniady
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Faranak Nami
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Hengxi Zhang
- Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14424 Potsdam Germany
- Department of Biology, Chemistry and PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Christoph Rademacher
- Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14424 Potsdam Germany
- Department of Biology, Chemistry and PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Ana Cuenda
- Department of Immunology and OncologyCentro Nacional de Biotecnología/CSIC Campus UAM 28049 Madrid Spain
| | - Charlotte H. Gotfredsen
- NMR Center⋅DTUDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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41
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Morrison CN, Prosser KE, Stokes RW, Cordes A, Metzler-Nolte N, Cohen SM. Expanding medicinal chemistry into 3D space: metallofragments as 3D scaffolds for fragment-based drug discovery. Chem Sci 2019; 11:1216-1225. [PMID: 34123246 PMCID: PMC8148059 DOI: 10.1039/c9sc05586j] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/12/2019] [Indexed: 01/02/2023] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful strategy for the identification of new bioactive molecules. FBDD relies on fragment libraries, generally of modest size, but of high chemical diversity. Although good chemical diversity in FBDD libraries has been achieved in many respects, achieving shape diversity - particularly fragments with three-dimensional (3D) structures - has remained challenging. A recent analysis revealed that >75% of all conventional, organic fragments are predominantly 1D or 2D in shape. However, 3D fragments are desired because molecular shape is one of the most important factors in molecular recognition by a biomolecule. To address this challenge, the use of inert metal complexes, so-called 'metallofragments' (mFs), to construct a 3D fragment library is introduced. A modest library of 71 compounds has been prepared with rich shape diversity as gauged by normalized principle moment of inertia (PMI) analysis. PMI analysis shows that these metallofragments occupy an area of fragment space that is unique and highly underrepresented when compared to conventional organic fragment libraries that are comprised of orders of magnitude more molecules. The potential value of this metallofragment library is demonstrated by screening against several different types of proteins, including an antiviral, an antibacterial, and an anticancer target. The suitability of the metallofragments for future hit-to-lead development was validated through the determination of IC50 and thermal shift values for select fragments against several proteins. These findings demonstrate the utility of metallofragment libraries as a means of accessing underutilized 3D fragment space for FBDD against a variety of protein targets.
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Affiliation(s)
- Christine N Morrison
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Kathleen E Prosser
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Anna Cordes
- Lehrstuhl für Anorganische Chemie 1, Bioanorganische Chemie, Ruhr-Universität Bochum Universitätsstraße 150 44801 Bochum Germany
| | - Nils Metzler-Nolte
- Lehrstuhl für Anorganische Chemie 1, Bioanorganische Chemie, Ruhr-Universität Bochum Universitätsstraße 150 44801 Bochum Germany
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
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42
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Rice S, Cox DJ, Marsden SP, Nelson A. Unified synthesis of diverse building blocks for application in the discovery of bioactive small molecules. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.130513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Li X, Payne DT, Ampolu B, Bland N, Brown JT, Dutton MJ, Fitton CA, Gulliver A, Hale L, Hamza D, Jones G, Lane R, Leach AG, Male L, Merisor EG, Morton MJ, Quy AS, Roberts R, Scarll R, Schulz-Utermoehl T, Stankovic T, Stevenson B, Fossey JS, Agathanggelou A. Derivatisation of parthenolide to address chemoresistant chronic lymphocytic leukaemia. MEDCHEMCOMM 2019; 10:1379-1390. [PMID: 32952998 PMCID: PMC7478165 DOI: 10.1039/c9md00297a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022]
Abstract
Parthenolide is a natural product that exhibits anti-leukaemic activity, however, its clinical use is limited by its poor bioavailability. It may be extracted from feverfew and protocols for growing, extracting and derivatising it are reported. A novel parthenolide derivative with good bioavailability and pharmacological properties was identified through a screening cascade based on in vitro anti-leukaemic activity and calculated "drug-likeness" properties, in vitro and in vivo pharmacokinetics studies and hERG liability testing. In vitro studies showed the most promising derivative to have comparable anti-leukaemic activity to DMAPT, a previously described parthenolide derivative. The newly identified compound was shown to have pro-oxidant activity and in silico molecular docking studies indicate a prodrug mode of action. A synthesis scheme is presented for the production of amine 7 used in the generation of 5f.
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Affiliation(s)
- Xingjian Li
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Daniel T Payne
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Badarinath Ampolu
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Nicholas Bland
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Jane T Brown
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Mark J Dutton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Catherine A Fitton
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Abigail Gulliver
- Winterbourne Botanic Garden, University of Birmingham, 58 Edgbaston Park Road, Edgbaston, Birmingham, West Midlands B15 2RT, UK
| | - Lee Hale
- Winterbourne Botanic Garden, University of Birmingham, 58 Edgbaston Park Road, Edgbaston, Birmingham, West Midlands B15 2RT, UK
| | - Daniel Hamza
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Geraint Jones
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Rebecca Lane
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Louise Male
- X-Ray Crystallography Facility, School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Elena G Merisor
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Michael J Morton
- ApconiX Ltd, Alderly Park, Nether Alderly, Cheshire, SK10 4TG, UK
| | - Alex S Quy
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Ruth Roberts
- ApconiX Ltd, Alderly Park, Nether Alderly, Cheshire, SK10 4TG, UK
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Rosanna Scarll
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | | | - Tatjana Stankovic
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Brett Stevenson
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - John S Fossey
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Angelo Agathanggelou
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
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44
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Shershnev I, Dar'in D, Chuprun S, Kantin G, Bakulina O, Krasavin M. The use of ∝-diazo-γ-butyrolactone in the Büchner-Curtius-Schlotterbeck reaction of cyclic ketones: A facile entry into spirocyclic scaffolds. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Pasturaud K, Rkein B, Sanselme M, Sebban M, Lakhdar S, Durandetti M, Legros J, Chataigner I. The facile dearomatization of nitroaromatic compounds using lithium enolates of unsaturated ketones in conjugate additions and (4+2) formal cycloadditions. Chem Commun (Camb) 2019; 55:7494-7497. [PMID: 31185071 DOI: 10.1039/c9cc02924a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The dearomatization of conventional nitroarenes by lithiated enolates derived from methyl vinyl ketones easily takes place, following a formal (4+2) cycloaddition process. While nitroindoles react readily with in situ generated conjugated enolates, the deaggregation of these latter species using HMPA extends the reaction scope to the more aromatic nitronaphthalenes and pyridines.
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Affiliation(s)
- Karine Pasturaud
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Batoul Rkein
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | | | - Muriel Sebban
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Sami Lakhdar
- Normandie Univ., LCMT, ENSICAEN, UNICAEN, CNRS, 6, Boulevard Maréchal Juin, Caen 14000, France
| | - Muriel Durandetti
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Julien Legros
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
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46
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Ling T, Lang WH, Craig J, Potts MB, Budhraja A, Opferman J, Bollinger J, Maier J, Marsico TD, Rivas F. Studies of Jatrogossone A as a Reactive Oxygen Species Inducer in Cancer Cellular Models. JOURNAL OF NATURAL PRODUCTS 2019; 82:1301-1311. [PMID: 31084028 DOI: 10.1021/acs.jnatprod.8b01087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Natural products continue to provide a platform to study biological systems. A bioguided study of cancer cell models led us to a new member of the jatrophane natural products from Jatropha gossypiifolia, which was independently identified and characterized as jatrogossone A (1). Purification and structure elucidation was performed by column chromatography and high-performance liquid chromatography-mass spectrometry and NMR techniques, and the structure was confirmed via X-ray crystallography. The unique molecular scaffold of jatrogossone A prompted an evaluation of its mode of action. Cytotoxicity assays demonstrated that jatrogossone A displays selective antiproliferative activity against cancer cell models in the low micromolar range with a therapeutic window. Jatrogossone A (1) affects mitochondrial membrane potential (ΔΨm) in a time- and dose-dependent manner. This natural product induces radical oxygen species (ROS) selectively in cancer cellular models, with minimal ROS induction in noncancerous cells. Compound 1 induces ROS in the mitochondria, as determined by colocalization studies, and it induces mitophagy. It promotes also in vitro cell death by causing cell arrest at the G2/M stage, caspase (3/7) activation, and PARP-1 cleavage. The combined findings provide a potential mechanism by which 1 relies on upregulation of mitochondrial ROS to potentiate cytotoxic effects through intracellular signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Travis D Marsico
- Department of Biological Sciences , Arkansas State University , Jonesboro , Arkansas 72467 , United States
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47
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Sun AW, Hess SN, Stoltz BM. Enantioselective synthesis of gem-disubstituted N-Boc diazaheterocycles via decarboxylative asymmetric allylic alkylation. Chem Sci 2019; 10:788-792. [PMID: 30774872 PMCID: PMC6345351 DOI: 10.1039/c8sc03967d] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/29/2018] [Indexed: 11/28/2022] Open
Abstract
An enantioselective synthesis of diverse N4-Boc-protected α,α-disubstituted piperazin-2-ones using the palladium-catalyzed decarboxylative allylic alkylation reaction has been achieved. Using a chiral Pd-catalyst derived from an electron deficient PHOX ligand, chiral piperazinones are synthesized in high yields and enantioselectivity. The chiral piperazinone products can be deprotected and reduced to valuable gem-disubstituted piperazines. This reaction is further extended to enable the enantioselective synthesis of α,α-disubstituted tetrahydropyrimidin-2-ones, which are hydrolyzed into corresponding chiral β2,2-amino acids.
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Affiliation(s)
- Alexander W Sun
- Warren and Katherine Schlinger Laboratory for Chemistry and Chemical Engineering , Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , USA .
| | - Stephan N Hess
- Warren and Katherine Schlinger Laboratory for Chemistry and Chemical Engineering , Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , USA .
| | - Brian M Stoltz
- Warren and Katherine Schlinger Laboratory for Chemistry and Chemical Engineering , Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , USA .
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48
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Kearney SE, Zahoránszky-Kőhalmi G, Brimacombe KR, Henderson MJ, Lynch C, Zhao T, Wan K, Itkin Z, Dillon C, Shen M, Cheff D, Lee T, Bougie D, Cheng K, Coussens N, Dorjsuren D, Eastman R, Huang R, Iannotti M, Karavadhi S, Klumpp-Thomas C, Roth J, Sakamuru S, Sun W, Titus S, Yasgar A, Zhang YQ, Zhao J, Andrade R, Brown MK, Burns N, Cha JK, Mevers E, Clardy J, Clement J, Crooks P, Cuny G, Ganor J, Moreno J, Morrill L, Picazo E, Susick R, Garg N, Goess B, Grossman R, Hughes C, Johnston J, Joullie M, Kinghorn AD, Kingston D, Krische M, Kwon O, Maimone T, Majumdar S, Maloney K, Mohamed E, Murphy B, Nagorny P, Olson D, Overman L, Brown L, Snyder J, Porco J, Rivas F, Ross S, Sarpong R, Sharma I, Shaw J, Xu Z, Shen B, Shi W, Stephenson C, Verano A, Tan D, Tang Y, Taylor R, Thomson R, Vosburg D, Wu J, Wuest W, Zakarian A, Zhang Y, Ren T, Zuo Z, Inglese J, Michael S, Simeonov A, Zheng W, Shinn P, Jadhav A, Boxer M, Hall MD, Xia M, Guha R, Rohde JM. Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space. ACS CENTRAL SCIENCE 2018; 4:1727-1741. [PMID: 30648156 PMCID: PMC6311695 DOI: 10.1021/acscentsci.8b00747] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 05/20/2023]
Abstract
Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The assay data generated were analyzed using a variety of quality control metrics, and the resultant assay profiles were explored using statistical methods, such as clustering and compound promiscuity analyses. Individual compounds were then sorted by structural class and activity profiles. Differential behavior based on these classifications, as well as noteworthy activities, are outlined herein. One such highlight is the activity of (-)-2(S)-cathafoline, which was found to stabilize calcium levels in the endoplasmic reticulum. The workflow described here illustrates a pilot effort to broadly survey the biological potential of natural products by utilizing the power of automation and high-throughput screening.
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Affiliation(s)
- Sara E. Kearney
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Gergely Zahoránszky-Kőhalmi
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Kyle R. Brimacombe
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J. Henderson
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Caitlin Lynch
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Tongan Zhao
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Kanny
K. Wan
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
- Department
of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Zina Itkin
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Christopher Dillon
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Min Shen
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dorian
M. Cheff
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Tobie
D. Lee
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Danielle Bougie
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ken Cheng
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Nathan
P. Coussens
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dorjbal Dorjsuren
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Richard
T. Eastman
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ruili Huang
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Michael
J. Iannotti
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Surendra Karavadhi
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Carleen Klumpp-Thomas
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jacob
S. Roth
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Srilatha Sakamuru
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Wei Sun
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Steven
A. Titus
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Adam Yasgar
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ya-Qin Zhang
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jinghua Zhao
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rodrigo
B. Andrade
- Department
of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - M. Kevin Brown
- Department
of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Noah
Z. Burns
- Department
of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
| | - Jin K. Cha
- Department
of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Emily
E. Mevers
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Jon Clardy
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Jason
A. Clement
- Natural
Products Discovery Institute, Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Peter
A. Crooks
- University
of Arkansas for Medical Sciences, 4301 West Markham Street 522, Little Rock, Arkansas 72205, United States
| | - Gregory
D. Cuny
- Department
of Pharmacological and Pharmaceutical Sciences, University of Houston, 4849 Calhoun Road, Houston, Texas 77204, United
States
| | - Jake Ganor
- Diamond
Age Corp., 344 East Louisiana
Street, McKinney, Texas 75069, United States
| | - Jesus Moreno
- Department
of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Lucas
A. Morrill
- Department
of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Elias Picazo
- Department
of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Robert
B. Susick
- Department
of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Neil
K. Garg
- Department
of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Brian
C. Goess
- Department
of Chemistry, Furman University, 3300 Poinsett Highway, Greenville, South Carolina 29613, United States
| | - Robert
B. Grossman
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Chambers
C. Hughes
- Scripps
Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jeffrey
N. Johnston
- Department
of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Madeleine
M. Joullie
- Department
of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - A. Douglas Kinghorn
- College
of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - David
G.I. Kingston
- Department
of Chemistry, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Michael
J. Krische
- Chemistry
Department, The University of Texas at Austin, 105 East 24th Street STOP A5300, Austin, Texas 78712, United States
| | - Ohyun Kwon
- Department
of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Thomas
J. Maimone
- Department
of Chemistry, University of California Berkeley, 826 Latimer Hall, Berkeley, California 94720, United States
| | - Susruta Majumdar
- Department
of Molecular Pharmacology and Neurology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Center for
Clinical Pharmacology, St Louis College
of Pharmacy and Washington University School of Medicine, 2 Pharmacy Place, St. Louis, Missouri 63110, United States
| | - Katherine
N. Maloney
- Department
of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - Enas Mohamed
- University
of Mississippi School of Pharmacy, 2500 North State Street, Jackson, Mississippi 39216, United States
| | - Brian
T. Murphy
- College
of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, Illinois 60607, United States
| | - Pavel Nagorny
- Department
of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - David
E. Olson
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- School of
Medicine, Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Center for
Neuroscience, University of California,
Davis, 1544 Newton Court, Davis, California 95618, United States
| | - Larry
E. Overman
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Lauren
E. Brown
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John
K. Snyder
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John
A. Porco
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Fatima Rivas
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Samir
A. Ross
- University
of Mississippi School of Pharmacy, 2500 North State Street, Jackson, Mississippi 39216, United States
| | - Richmond Sarpong
- Department
of Chemistry, University of California Berkeley, 841-A Latimer Hall, Berkeley, California 94720, United States
| | - Indrajeet Sharma
- Department
of Chemistry and Biochemistry, and Institute of Natural Products and
Research Technologies, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jared
T. Shaw
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Zhengren Xu
- Department
of Chemistry, Florida Campus, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Ben Shen
- Department
of Chemistry, Florida Campus, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Wei Shi
- Department
of Chemistry and Biochemistry, University
of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Corey
R.J. Stephenson
- Department
of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Alyssa
L. Verano
- Pharmacology
Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Derek
S. Tan
- Pharmacology
Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Chemical
Biology Program, Sloan Kettering Institute and Tri-Institutional Research
Program, Memorial Sloan Kettering Cancer
Center, 1275 York Avenue, New York, New York 10065, United States
| | - Yi Tang
- Department
of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Richard
E. Taylor
- Department
of Chemistry and Biochemistry and the Warren Family Research Center
for Drug Discovery and Development, University
of Notre Dame, 305 McCourtney
Hall, Notre Dame, Indiana 46556, United States
| | - Regan
J. Thomson
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - David
A. Vosburg
- Department
of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Jimmy Wu
- Department
of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - William
M. Wuest
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
- Emory Antibiotic
Resistance Center, Emory University School
of Medicine, 201 Dowman
Drive, Atlanta, Georgia 30322, United States
| | - Armen Zakarian
- Santa
Barbara
Department of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
| | - Yufeng Zhang
- School of
Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, New Territories, Hong Kong SAR
| | - Tianjing Ren
- School of
Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, New Territories, Hong Kong SAR
| | - Zhong Zuo
- School of
Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Sha Tin, New Territories, Hong Kong SAR
| | - James Inglese
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Sam Michael
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Wei Zheng
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Paul Shinn
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew
B. Boxer
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
- Phone: 301-480-9928. Fax: 301-217-5736.
E-mail:
| | - Menghang Xia
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rajarshi Guha
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jason M. Rohde
- National
Center for Advancing Translational Sciences, National Institutes of
Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
- Phone: 301-319-9272. Fax: 301-319-9449. E-mail:
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QSAR of 1,4-benzoxazin-3-one antimicrobials and their drug design perspectives. Bioorg Med Chem 2018; 26:6105-6114. [PMID: 30471830 DOI: 10.1016/j.bmc.2018.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/05/2018] [Accepted: 11/12/2018] [Indexed: 11/23/2022]
Abstract
Synthetic derivatives of 1,4-benzoxazin-3-ones have been shown to possess promising antimicrobial activity, whereas their natural counterparts were found lacking in this respect. In this work, quantitative structure-activity relationships (QSAR) of natural and synthetic 1,4-benzoxazin-3-ones as antimicrobials were established. Data published in literature were curated into an extensive dataset of 111 compounds. Descriptor selection was performed by a genetic algorithm. QSAR models revealed differences in requirements for activity against fungi, gram-positive and gram-negative bacteria. Shape, VolSurf, and H-bonding property descriptors were frequently picked in all models. The models obtained for gram-positive and gram-negative bacteria showed good predictive power (Q2Ext 0.88 and 0.85, respectively). Based on the models generated, an additional set of 1,4-benzoxazin-3-ones, for which no antimicrobial activity had been determined in literature, were evaluated in silico. Additionally, newly designed lead compounds with a 1,4-benzoxazin-3-one scaffold were generated in silico by varying the positions and combinations of substituents. Two of these were predicted to be up to 5 times more active than any of the compounds in the current dataset. The 1,4-benzoxazin-3-one scaffold was concluded to possess potential for the design of new antimicrobial compounds with potent antibacterial activity, a multitarget mode of action, and possibly reduced susceptibility to gram negatives' efflux pumps.
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50
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Wales SM, Adcock HV, Lewis W, Hamza D, Moody CJ. Nitrogen-Bridged, Natural Product Like Octahydrobenzofurans and Octahydroindoles: Scope and Mechanism of Bridge-Forming Reductive Amination via Caged Heteroadamantanes. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Steven. M. Wales
- School of Chemistry, University Park; University of Nottingham; 2RD Nottingham, NG7 United Kingdom
| | - Holly V. Adcock
- Biocity; Sygnature Discovery Ltd; Pennyfoot Street Nottingham, NG1 1GF United Kingdom
| | - William Lewis
- School of Chemistry, University Park; University of Nottingham; 2RD Nottingham, NG7 United Kingdom
| | - Daniel Hamza
- Biocity; Sygnature Discovery Ltd; Pennyfoot Street Nottingham, NG1 1GF United Kingdom
| | - Christopher J. Moody
- School of Chemistry, University Park; University of Nottingham; 2RD Nottingham, NG7 United Kingdom
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