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Latendresse M, Malerich JP, Herson J, Krummenacker M, Szeto J, Vu VA, Collins N, Madrid PB. SynRoute: A Retrosynthetic Planning Software. J Chem Inf Model 2023; 63:5484-5495. [PMID: 37635298 PMCID: PMC10498441 DOI: 10.1021/acs.jcim.3c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Indexed: 08/29/2023]
Abstract
Computer-assisted synthetic planning has seen major advancements that stem from the availability of large reaction databases and artificial intelligence methodologies. SynRoute is a new retrosynthetic planning software tool that uses a relatively small number of general reaction templates, currently 263, along with a literature-based reaction database to find short, practical synthetic routes for target compounds. For each reaction template, a machine learning classifier is trained using data from the Pistachio reaction database to predict whether new computer-generated reactions based on the template are likely to work experimentally in the laboratory. This reaction generation methodology is used together with a vectorized Dijkstra-like search of top-scoring routes organized by synthetic strategies for easy browsing by a synthetic chemist. SynRoute was able to find routes for an average of 83% of compounds based on selection of random subsets of drug-like compounds from the ChEMBL database. Laboratory evaluation of 12 routes produced by SynRoute, to synthesize compounds not from the previous random subsets, demonstrated the ability to produce feasible overall synthetic strategies for all compounds evaluated.
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Affiliation(s)
| | | | - James Herson
- SRI International, 333 Ravenswood Ave, Menlo Park, California 94025, United States
| | - Markus Krummenacker
- SRI International, 333 Ravenswood Ave, Menlo Park, California 94025, United States
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McNaughton AD, Joshi RP, Knutson CR, Fnu A, Luebke KJ, Malerich JP, Madrid PB, Kumar N. Machine Learning Models for Predicting Molecular UV-Vis Spectra with Quantum Mechanical Properties. J Chem Inf Model 2023; 63:1462-1471. [PMID: 36847578 DOI: 10.1021/acs.jcim.2c01662] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Accurate understanding of ultraviolet-visible (UV-vis) spectra is critical for the high-throughput synthesis of compounds for drug discovery. Experimentally determining UV-vis spectra can become expensive when dealing with a large quantity of novel compounds. This provides us an opportunity to drive computational advances in molecular property predictions using quantum mechanics and machine learning methods. In this work, we use both quantum mechanically (QM) predicted and experimentally measured UV-vis spectra as input to devise four different machine learning architectures, UVvis-SchNet, UVvis-DTNN, UVvis-Transformer, and UVvis-MPNN, and assess the performance of each method. We find that the UVvis-MPNN model outperforms the other models when using optimized 3D coordinates and QM predicted spectra as input features. This model has the highest performance for predicting UV-vis spectra with a training RMSE of 0.06 and validation RMSE of 0.08. Most importantly, our model can be used for the challenging task of predicting differences in the UV-vis spectral signatures of regioisomers.
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Affiliation(s)
- Andrew D McNaughton
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rajendra P Joshi
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carter R Knutson
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Anubhav Fnu
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kevin J Luebke
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Urbina F, Batra K, Luebke KJ, White JD, Matsiev D, Olson LL, Malerich JP, Hupcey MAZ, Madrid PB, Ekins S. UV-adVISor: Attention-Based Recurrent Neural Networks to Predict UV-Vis Spectra. Anal Chem 2021; 93:16076-16085. [PMID: 34812602 DOI: 10.1021/acs.analchem.1c03741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet-visible (UV-Vis) absorption spectra are routinely collected as part of high-performance liquid chromatography (HPLC) analysis systems and can be used to identify chemical reaction products by comparison to the reference spectra. Here, we present UV-adVISor as a new computational tool for predicting the UV-Vis spectra from a molecule's structure alone. UV-Vis prediction was approached as a sequence-to-sequence problem. We utilized Long-Short Term Memory and attention-based neural networks with Extended Connectivity Fingerprint Diameter 6 or molecule SMILES to generate predictive models for the UV spectra. We have produced two spectrum datasets (dataset I, N = 949, and dataset II, N = 2222) using different compound collections and spectrum acquisition methods to train, validate, and test our models. We evaluated the prediction accuracy of the complete spectra by the correspondence of wavelengths of absorbance maxima and with a series of statistical measures (the best test set median model parameters are in parentheses for model II), including RMSE (0.064), R2 (0.71), and dynamic time warping (DTW, 0.194) of the entire spectrum curve. Scrambling molecule structures with the experimental spectra during training resulted in a degraded R2, confirming the utility of the approaches for prediction. UV-adVISor is able to provide fast and accurate predictions for libraries of compounds.
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Affiliation(s)
- Fabio Urbina
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kushal Batra
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States.,Computer Science, NC State University, Raleigh, North Carolina 27606, United States
| | - Kevin J Luebke
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jason D White
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Daniel Matsiev
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Lori L Olson
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Maggie A Z Hupcey
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Peter B Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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Collins N, Stout D, Lim JP, Malerich JP, White JD, Madrid PB, Latendresse M, Krieger D, Szeto J, Vu VA, Rucker K, Deleo M, Gorfu Y, Krummenacker M, Hokama LA, Karp P, Mallya S. Fully Automated Chemical Synthesis: Toward the Universal Synthesizer. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00143] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nathan Collins
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - David Stout
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jin-Ping Lim
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jeremiah P. Malerich
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Jason D. White
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Mario Latendresse
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - David Krieger
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Judy Szeto
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Vi-Anh Vu
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Kristina Rucker
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Michael Deleo
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Yonael Gorfu
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Markus Krummenacker
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Leslie A. Hokama
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Peter Karp
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sahana Mallya
- SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
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Rhee SW, Bradford WW, Malerich JP, Tanga MJ. Carbon-14 labeling of K777•HCl, a therapeutic agent for Chagas disease. J Labelled Comp Radiopharm 2013; 56:461-3. [DOI: 10.1002/jlcr.3107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Sung-Whi Rhee
- SRI International; Biosciences Division; 333-Ravenswood Ave; Menlo Park; CA; 94025; USA
| | - Wallace W. Bradford
- SRI International; Biosciences Division; 333-Ravenswood Ave; Menlo Park; CA; 94025; USA
| | - Jeremiah P. Malerich
- SRI International; Biosciences Division; 333-Ravenswood Ave; Menlo Park; CA; 94025; USA
| | - Mary J. Tanga
- SRI International; Biosciences Division; 333-Ravenswood Ave; Menlo Park; CA; 94025; USA
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Malerich JP, Li J, Joder D, Vieria ÉLM, Keesen TSL, Vaidyanathan R, Gollob KJ, Tanga MJ. Antileishmanial Activity of Natural Product-Like Naphthoquinones. Drug Dev Res 2013. [DOI: 10.1002/ddr.21067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jeremiah P. Malerich
- SRI International; Center for Infectious Disease and Biodefense Research; 333 Ravenswood Avenue; Menlo Park; California; 94025; USA
| | - Jinfang Li
- SRI International; Center for Infectious Disease and Biodefense Research; 140 Research Drive; Harrisonburg; Virginia; 22802; USA
| | - Dallas Joder
- SRI International; Center for Infectious Disease and Biodefense Research; 140 Research Drive; Harrisonburg; Virginia; 22802; USA
| | | | - Tatjana S. L. Keesen
- Biochemistry and Immunology Department; Universidade Federal de Minas Gerais; Belo Horizonte; MG; Brazil
| | - Rajeev Vaidyanathan
- SRI International; Center for Infectious Disease and Biodefense Research; 140 Research Drive; Harrisonburg; Virginia; 22802; USA
| | | | - Mary J. Tanga
- SRI International; Center for Infectious Disease and Biodefense Research; 333 Ravenswood Avenue; Menlo Park; California; 94025; USA
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Affiliation(s)
- Mario Latendresse
- SRI International,
333 Ravenswood Ave., Menlo Park,
California 94025, United States
| | - Jeremiah P. Malerich
- SRI International,
333 Ravenswood Ave., Menlo Park,
California 94025, United States
| | - Mike Travers
- SRI International,
333 Ravenswood Ave., Menlo Park,
California 94025, United States
| | - Peter D. Karp
- SRI International,
333 Ravenswood Ave., Menlo Park,
California 94025, United States
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Rhee SW, Iyer RP, Coughlin JE, Padmanabhan S, Malerich JP, Tanga MJ. Synthesis of a 35S-labeled dinucleoside phosphorothioate prodrug, an orally bioavailable anti-HBV agent. J Labelled Comp Radiopharm 2012. [DOI: 10.1002/jlcr.2925] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sung-Whi Rhee
- SRI International; 333 Ravenswood Avenue; Menlo Park; CA; 94025; USA
| | | | - John E. Coughlin
- Spring Bank Pharmaceuticals, INC.; S-7, 113 Cedar Street; Milford; MA; 01757; USA
| | | | | | - Mary J. Tanga
- SRI International; 333 Ravenswood Avenue; Menlo Park; CA; 94025; USA
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Affiliation(s)
- Sung-Whi Rhee
- Biosciences Division; SRI International; 333 Ravenswood Ave.; Menlo Park; CA; 94025-3135; USA
| | - Jeremiah P. Malerich
- Biosciences Division; SRI International; 333 Ravenswood Ave.; Menlo Park; CA; 94025-3135; USA
| | - Jung-Joon Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB); 125 Gwahangno; Yuseong-gu; Daejon; Korea
| | - Mary J. Tanga
- Biosciences Division; SRI International; 333 Ravenswood Ave.; Menlo Park; CA; 94025-3135; USA
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Chopra S, Matsuyama K, Tran T, Malerich JP, Wan B, Franzblau SG, Lun S, Guo H, Maiga MC, Bishai WR, Madrid PB. Evaluation of gyrase B as a drug target in Mycobacterium tuberculosis. J Antimicrob Chemother 2012; 67:415-21. [PMID: 22052686 PMCID: PMC3254195 DOI: 10.1093/jac/dkr449] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES New classes of drugs are needed to treat tuberculosis (TB) in order to combat the emergence of resistance to existing agents and shorten the duration of therapy. Targeting DNA gyrase is a clinically validated therapeutic approach using fluoroquinolone antibiotics to target the gyrase subunit A (GyrA) of the heterotetramer. Increasing resistance to fluoroquinolones has driven interest in targeting the gyrase subunit B (GyrB), which has not been targeted for TB. The biological activities of two potent small-molecule inhibitors of GyrB have been characterized to validate its targeting as a therapeutic strategy for treating TB. MATERIALS AND METHODS Novobiocin and aminobenzimidazole 1 (AB-1) were tested for their activity against Mycobacterium tuberculosis (Mtb) H37Rv and other mycobacteria. AB-1 and novobiocin were also evaluated for their interaction with rifampicin and isoniazid as well as their potential for cytotoxicity. Finally, AB-1 was tested for in vivo efficacy in a murine model of TB. RESULTS Novobiocin and AB-1 have both been shown to be active against Mtb with MIC values of 4 and 1 mg/L, respectively. Only AB-1 exhibited time-dependent bactericidal activity against drug-susceptible and drug-resistant mycobacteria, including a fluoroquinolone-resistant strain. AB-1 had potent activity in the low oxygen recovery assay model for non-replicating persistent Mtb. Additionally, AB-1 has no interaction with isoniazid and rifampicin, and has no cross-resistance with fluoroquinolones. In a murine model of TB, AB-1 significantly reduced lung cfu counts in a dose-dependent manner. CONCLUSIONS Aminobenzimidazole inhibitors of GyrB exhibit many of the characteristics required for their consideration as a potential front-line antimycobacterial therapeutic.
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Affiliation(s)
- Sidharth Chopra
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Karen Matsuyama
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Tran Tran
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Jeremiah P. Malerich
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
| | - Baojie Wan
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, USA
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL, USA
| | - Shichun Lun
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
| | - Haidan Guo
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
| | - Mariama C. Maiga
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, USA
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Suite Z310 Doris Duke Building, 719 Umbilo Road, Durban, 4001, Republic of South Africa
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA
| | - Peter B. Madrid
- Center for Infectious Disease and Biodefense Research, Bioscience Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
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Glaser BT, Malerich JP, Duellman SJ, Fong J, Hutson C, Fine RM, Keblansky B, Tang MJ, Madrid PB. A high-throughput fluorescence polarization assay for inhibitors of gyrase B. ACTA ACUST UNITED AC 2011; 16:230-8. [PMID: 21245469 DOI: 10.1177/1087057110392038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
DNA gyrase, a type II topoisomerase that introduces negative supercoils into DNA, is a validated antibacterial drug target. The holoenzyme is composed of 2 subunits, gyrase A (GyrA) and gyrase B (GyrB), which form a functional A(2)B(2) heterotetramer required for bacterial viability. A novel fluorescence polarization (FP) assay has been developed and optimized to detect inhibitors that bind to the adenosine triphosphate (ATP) binding domain of GyrB. Guided by the crystal structure of the natural product novobiocin bound to GyrB, a novel novobiocin-Texas Red probe (Novo-TRX) was designed and synthesized for use in a high-throughput FP assay. The binding kinetics of the interaction of Novo-TRX with GyrB from Francisella tularensis has been characterized, as well as the effect of common buffer additives on the interaction. The assay was developed into a 21-µL, 384-well assay format and has been validated for use in high-throughput screening against a collection of Food and Drug Administration-approved compounds. The assay performed with an average Z' factor of 0.80 and was able to identify GyrB inhibitors from a screening library.
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Affiliation(s)
- Martin J. Deetz
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame, IN, 46656, USA
| | - Marco Jonas
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame, IN, 46656, USA
| | - Jeremiah P. Malerich
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame, IN, 46656, USA
| | - Bradley D. Smith
- a Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame, IN, 46656, USA
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Konishi H, Lam TY, Malerich JP, Rawal VH. Enantioselective alpha-amination of 1,3-dicarbonyl compounds using squaramide derivatives as hydrogen bonding catalysts. Org Lett 2010; 12:2028-31. [PMID: 20359172 DOI: 10.1021/ol1005104] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalytic enantioselective alpha-hydrazination of 1,3-dicarbonyl compounds with azodicarboxylates was investigated in the presence of our newly developed hydrogen bonding catalyst, squaramide 3j. High yields and high enantioselectivities were achieved with low catalyst loading under mild conditions.
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Affiliation(s)
- Hideyuki Konishi
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, USA
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Affiliation(s)
- Ye Zhu
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave. Chicago, IL 60637, USA
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Abstract
Thioureas represent the dominant platform for hydrogen bond promoted asymmetric catalysts. A large number of reactions, reported in scores of publications, have been successfully promoted by chiral thioureas. The present paper reports the use of squaramides as a highly effective new scaffold for the development of chiral hydrogen bond donor catalysts. Squaramide catalysts are very simple to prepare. The (-)-cinchonine modified squaramide (5), easily prepared through a two-step process from methyl squarate, was shown to be an effective catalyst, even at catalyst loadings as low as 0.1 mol%, for the conjugate addition reactions of 1,3-dicarbonyl compounds to beta-nitrostyrenes. The addition products were obtained in high yields and excellent enantioselectivities.
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Affiliation(s)
- Jeremiah P Malerich
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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Abstract
Given the prevalence of the indole nucleus in biologically active compounds, the direct C3-functionalization of 2,3-disubstituted indoles represents an important problem. Described is a general, high-yielding method for the palladium-catalyzed beta-allylation of carba- and heterocycle fused indoles, including complex natural product substrates.
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Affiliation(s)
- Natsuko Kagawa
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
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Malerich JP, Maimone TJ, Elliott GI, Trauner D. Biomimetic Synthesis of Antimalarial Naphthoquinones. J Am Chem Soc 2007; 129:1836. [DOI: 10.1021/ja069018l] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
The total synthesis of naphthoquinone natural products isolated from the Bignoniaceae plant family is described. Pinnatal, isopinnatal, sterekunthals A and B, pyranokunthones A and B, and anthrakunthone have been prepared along the lines of a biosynthetic proposal involving pericyclic reactions as key steps. The first case of catalysis in oxa 6pi electrocyclizations is reported.
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Affiliation(s)
- Jeremiah P Malerich
- Department of Chemistry, University of California-Berkeley, Berkeley, California 94720-1460, USA
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Abstract
Concise biomimetic syntheses of the antimalarial naphthoquinones (+/-)-pinnatal and (+/-)-sterekunthal A are described.
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Affiliation(s)
- Jeremiah P Malerich
- Center for new Directions in Organic Synthesis, Department of Chemistry, University of California-Berkeley, Berkeley, California 94720-1460, USA
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Abstract
The barrier for rotation about an N-alkylcarbamate C(carbonyl)-N bond is around 16 kcal/mol. In the case of an N-phenylcarbamate, the rotational barrier is lowered to 12.5 kcal/mol, but with N-(2-pyrimidyl)carbamates the barriers are so low (<9 kcal/mol) that the syn and anti rotamers cannot be observed as separate signals by 500 MHz NMR spectroscopy at 183 K. X-ray and computational data show that the N-(2-pyrimidyl) carbamates have C(carbonyl)-N bonds that are on average 0.03 A longer than for related N-phenylcarbamates. The computational results trace the origin of the effect to increased single bond character for the C(carbonyl)-N bond due to the increased electron-withdrawing ability of the pyrimidyl ring.
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Affiliation(s)
- Martin J Deetz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46656, USA
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