1
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Cheng S, Dong C, Ma Y, Xu X, Zhao Y. Skeletal Transformations of Terpenoid Forskolin Employing an Oxidative Rearrangement Strategy. J Org Chem 2024; 89:5741-5745. [PMID: 38568052 DOI: 10.1021/acs.joc.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The skeletal transformations of diterpenoid forskolin were achieved by employing an oxidative rearrangement strategy. A library of 36 forskolin analogues with structural diversity was effectively generated. Computational analysis shows that 12 CTD compounds with unique scaffolds and ring systems were produced during the course of this work.
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Affiliation(s)
- Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Chenhu Dong
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Yujie Ma
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Xiaoyu Xu
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China
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2
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Zhang X, Ma X, Zhang W. Decarboxylative 1,3-dipolar cycloaddition of amino acids for the synthesis of heterocyclic compounds. Beilstein J Org Chem 2023; 19:1677-1693. [PMID: 38025085 PMCID: PMC10644012 DOI: 10.3762/bjoc.19.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
The [3 + 2] cycloadditions of stabilized azomethine ylides (AMYs) derived from amino esters are well-established. However, the reactions of semi-stabilized AMYs generated from decarboxylative condensation of α-amino acids with arylaldehydes are much less explored. The [3 + 2] adducts of α-amino acids could be used for a second [3 + 2] cycloaddition as well as for other post-condensation modifications. This article highlights our recent work on the development of α-amino acid-based [3 + 2] cycloaddition reactions of N-H-type AMYs in multicomponent, one-pot, and stepwise reactions for the synthesis of diverse heterocycles related to some bioactive compounds and natural products.
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Affiliation(s)
- Xiaofeng Zhang
- Center for Green Chemistry and Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
- Department of Medicinal Chemistry, Cerevel Therapeutics, 222 Jacobs St Suite 200, Cambridge, MA 02141, USA
| | - Xiaoming Ma
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Wei Zhang
- Center for Green Chemistry and Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
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3
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Maji B, Gangopadhyay SA, Lee M, Shi M, Wu P, Heler R, Mok B, Lim D, Siriwardena SU, Paul B, Dančík V, Vetere A, Mesleh MF, Marraffini LA, Liu DR, Clemons PA, Wagner BK, Choudhary A. A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9. Cell 2019; 177:1067-1079.e19. [PMID: 31051099 PMCID: PMC7182439 DOI: 10.1016/j.cell.2019.04.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 09/17/2018] [Accepted: 04/03/2019] [Indexed: 12/26/2022]
Abstract
The precise control of CRISPR-Cas9 activity is required for a number of genome engineering technologies. Here, we report a generalizable platform that provided the first synthetic small-molecule inhibitors of Streptococcus pyogenes Cas9 (SpCas9) that weigh <500 Da and are cell permeable, reversible, and stable under physiological conditions. We developed a suite of high-throughput assays for SpCas9 functions, including a primary screening assay for SpCas9 binding to the protospacer adjacent motif, and used these assays to screen a structurally diverse collection of natural-product-like small molecules to ultimately identify compounds that disrupt the SpCas9-DNA interaction. Using these synthetic anti-CRISPR small molecules, we demonstrated dose and temporal control of SpCas9 and catalytically impaired SpCas9 technologies, including transcription activation, and identified a pharmacophore for SpCas9 inhibition using structure-activity relationships. These studies establish a platform for rapidly identifying synthetic, miniature, cell-permeable, and reversible inhibitors against both SpCas9 and next-generation CRISPR-associated nucleases.
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Affiliation(s)
- Basudeb Maji
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Soumyashree A Gangopadhyay
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Miseon Lee
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mengchao Shi
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Peng Wu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Beverly Mok
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sachini U Siriwardena
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bishwajit Paul
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vlado Dančík
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amedeo Vetere
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 11231, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
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4
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Si Y, Xu D, Bum-Erdene K, Ghozayel MK, Yang B, Clemons PA, Meroueh SO. Chemical Space Overlap with Critical Protein-Protein Interface Residues in Commercial and Specialized Small-Molecule Libraries. ChemMedChem 2019; 14:119-131. [PMID: 30548204 PMCID: PMC7175409 DOI: 10.1002/cmdc.201800537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/29/2018] [Indexed: 12/14/2022]
Abstract
There is growing interest in the use of structure-based virtual screening to identify small molecules that inhibit challenging protein-protein interactions (PPIs). In this study, we investigated how effectively chemical library members docked at the PPI interface mimic the position of critical side-chain residues known as "hot spots". Three compound collections were considered, a commercially available screening collection (ChemDiv), a collection of diversity-oriented synthesis (DOS) compounds that contains natural-product-like small molecules, and a library constructed using established reactions (the "screenable chemical universe based on intuitive data organization", SCUBIDOO). Three different tight PPIs for which hot-spot residues have been identified were selected for analysis: uPAR⋅uPA, TEAD4⋅Yap1, and CaV α⋅CaV β. Analysis of library physicochemical properties was followed by docking to the PPI receptors. A pharmacophore method was used to measure overlap between small-molecule substituents and hot-spot side chains. Fragment-like conformationally restricted small molecules showed better hot-spot overlap for interfaces with well-defined pockets such as uPAR⋅uPA, whereas better overlap was observed for more complex DOS compounds in interfaces lacking a well-defined binding site such as TEAD4⋅Yap1. Virtual screening of conformationally restricted compounds targeting uPAR⋅uPA and TEAD4⋅Yap1 followed by experimental validation reinforce these findings, as the best hits were fragment-like and had few rotatable bonds for the former, while no hits were identified for the latter. Overall, such studies provide a framework for understanding PPIs in the context of additional chemical matter and new PPI definitions.
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Affiliation(s)
- Yubing Si
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, 46202, USA
| | - Khuchtumur Bum-Erdene
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mona K Ghozayel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Baocheng Yang
- Henan Provincial Key Laboratory of Nanocomposites and Applications, Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan, 450006, China
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Samy O Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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5
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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6
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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7
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Fu C, Lora N, Kirchhoefer PL, Lee DR, Altenhofer E, Barnes CL, Hungerford NL, Krenske EH, Harmata M. (4+3) Cycloaddition Reactions of N‐Alkyl Oxidopyridinium Ions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chencheng Fu
- Department of Chemistry University of Missouri-Columbia Columbia MO 65211 USA
| | - Nestor Lora
- Department of Chemistry University of Missouri-Columbia Columbia MO 65211 USA
| | | | - Dong Reyoul Lee
- Department of Chemistry University of Missouri-Columbia Columbia MO 65211 USA
| | - Erich Altenhofer
- Department of Chemistry University of Missouri-Columbia Columbia MO 65211 USA
| | - Charles L. Barnes
- Department of Chemistry University of Missouri-Columbia Columbia MO 65211 USA
| | - Natasha L. Hungerford
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD 4072 Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD 4072 Australia
| | - Michael Harmata
- Department of Chemistry University of Missouri-Columbia Columbia MO 65211 USA
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8
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Fu C, Lora N, Kirchhoefer PL, Lee DR, Altenhofer E, Barnes CL, Hungerford NL, Krenske EH, Harmata M. (4+3) Cycloaddition Reactions of N-Alkyl Oxidopyridinium Ions. Angew Chem Int Ed Engl 2017; 56:14682-14687. [PMID: 28929559 DOI: 10.1002/anie.201708320] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Indexed: 11/07/2022]
Abstract
N-Methylation of methyl 5-hydroxynicotinate followed by reaction with a diene in the presence of triethylamine afforded (4+3) cycloadducts in good to excellent yields. High regioselectivity was observed with 1-substituted and 1,2-disubstituted butadienes. Density functional theory calculations indicate that the cycloaddition involves concerted addition of the diene onto the oxidopyridinium ion. The process provides rapid access to bicyclic nitrogenous structures resembling natural alkaloids.
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Affiliation(s)
- Chencheng Fu
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Nestor Lora
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | | | - Dong Reyoul Lee
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Erich Altenhofer
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Charles L Barnes
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Natasha L Hungerford
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Michael Harmata
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
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Duvall JR, VerPlank L, Ludeke B, McLeod SM, Lee MD, Vishwanathan K, Mulrooney CA, Le Quement S, Yu Q, Palmer MA, Fleming P, Fearns R, Foley MA, Scherer CA. Novel diversity-oriented synthesis-derived respiratory syncytial virus inhibitors identified via a high throughput replicon-based screen. Antiviral Res 2016; 131:19-25. [PMID: 27059228 DOI: 10.1016/j.antiviral.2016.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 03/27/2016] [Accepted: 03/29/2016] [Indexed: 01/23/2023]
Abstract
Respiratory syncytial virus (RSV) infections affect millions of children and adults every year. Despite the significant disease burden, there are currently no safe and effective vaccines or therapeutics. We employed a replicon-based high throughput screen combined with live-virus triaging assays to identify three novel diversity-oriented synthesis-derived scaffolds with activity against RSV. One of these small molecules is shown to target the RSV polymerase (L protein) to inhibit viral replication and transcription; the mechanisms of action of the other small molecules are currently unknown. The compounds described herein may provide attractive inhibitors for lead optimization campaigns.
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Affiliation(s)
- Jeremy R Duvall
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Lynn VerPlank
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Barbara Ludeke
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States
| | - Sarah M McLeod
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Maurice D Lee
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Karthick Vishwanathan
- AstraZeneca R&D Boston, Early Clinical Development, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Carol A Mulrooney
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Sebastian Le Quement
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Qin Yu
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Michelle A Palmer
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Paul Fleming
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Rachel Fearns
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States
| | - Michael A Foley
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Christina A Scherer
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States.
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