1
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Fuller AA, Dounay AB, Schirch D, Rivera DG, Hansford KA, Elliott AG, Zuegg J, Cooper MA, Blaskovich MAT, Hitchens JR, Burris-Hiday S, Tenorio K, Mendez Y, Samaritoni JG, O’Donnell MJ, Scott WL. Multi-Institution Research and Education Collaboration Identifies New Antimicrobial Compounds. ACS Chem Biol 2020; 15:3187-3196. [PMID: 33242957 PMCID: PMC7928911 DOI: 10.1021/acschembio.0c00732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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New
antibiotics are urgently needed to address increasing rates
of multidrug resistant infections. Seventy-six diversely functionalized
compounds, comprising five structural scaffolds, were synthesized
and tested for their ability to inhibit microbial growth. Twenty-six
compounds showed activity in the primary phenotypic screen at the
Community for Open Antimicrobial Drug Discovery (CO-ADD). Follow-up
testing of active molecules confirmed that two unnatural dipeptides
inhibit the growth of Cryptococcus neoformans with
a minimum inhibitory concentration (MIC) ≤ 8 μg/mL. Syntheses
were carried out by undergraduate students at five schools implementing
Distributed Drug Discovery (D3) programs. This report showcases that
a collaborative research and educational process is a powerful approach
to discover new molecules inhibiting microbial growth. Educational
gains for students engaged in this project are highlighted in parallel
to the research advances. Aspects of D3 that contribute to its success,
including an emphasis on reproducibility of procedures, are discussed
to underscore the power of this approach to solve important research
problems and to inform other coupled chemical biology research and
teaching endeavors.
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Affiliation(s)
- Amelia A. Fuller
- Santa Clara University, Department of Chemistry & Biochemistry, Santa Clara, California 95053, United States
| | - Amy B. Dounay
- Department of Chemistry and Biochemistry, Colorado College, 14 E. Cache La Poudre Street, Colorado Springs, Colorado 80903, United States
| | - Douglas Schirch
- Department of Chemistry, Goshen College, 1700 South Main Street, Goshen, Indiana 46526, United States
| | - Daniel G. Rivera
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Karl A. Hansford
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Alysha G. Elliott
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Johannes Zuegg
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Matthew A Cooper
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jacob R. Hitchens
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Sarah Burris-Hiday
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Kristiana Tenorio
- Santa Clara University, Department of Chemistry & Biochemistry, Santa Clara, California 95053, United States
| | - Yanira Mendez
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - J. Geno Samaritoni
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Martin J. O’Donnell
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - William L. Scott
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
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2
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Acheampong KK, Kokona B, Braun GA, Jacobsen DR, Johnson KA, Charkoudian LK. Colorimetric Assay Reports on Acyl Carrier Protein Interactions. Sci Rep 2019; 9:15589. [PMID: 31666546 PMCID: PMC6821831 DOI: 10.1038/s41598-019-51554-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/25/2019] [Indexed: 01/15/2023] Open
Abstract
The ability to produce new molecules of potential pharmaceutical relevance via combinatorial biosynthesis hinges on improving our understanding of acyl-carrier protein (ACP)-protein interactions. However, the weak and transient nature of these interactions makes them difficult to study using traditional spectroscopic approaches. Herein we report that converting the terminal thiol of the E. coli ACP 4'-phosphopantetheine arm into a mixed disulfide with 2-nitro-5-thiobenzoate ion (TNB-) activates this site to form a selective covalent cross-link with the active site cysteine of a cognate ketoacyl synthase (KS). The concomitant release of TNB2-, which absorbs at 412 nm, provides a visual and quantitative measure of mechanistically relevant ACP-KS interactions. The colorimetric assay can propel the engineering of biosynthetic routes to novel chemical diversity by providing a high-throughput screen for functional hybrid ACP-KS partnerships as well as the discovery of novel antimicrobial agents by enabling the rapid identification of small molecule inhibitors of ACP-KS interactions.
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Affiliation(s)
- Kofi K Acheampong
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Gabriel A Braun
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | | | - Karl A Johnson
- Department of Biology, Haverford College, Haverford, PA, 19041-1391, USA.
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3
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Jimenez CJ, Tan J, Dowell KM, Gadbois GE, Read CA, Burgess N, Cervantes JE, Chan S, Jandaur A, Karanik T, Lee JJ, Ley MC, McGeehan M, McMonigal A, Palazzo KL, Parker SA, Payman A, Soria M, Verheyden L, Vo VT, Yin J, Calkins AL, Fuller AA, Stokes GY. Peptoids advance multidisciplinary research and undergraduate education in parallel: Sequence effects on conformation and lipid interactions. Biopolymers 2019; 110:e23256. [PMID: 30633339 PMCID: PMC6590334 DOI: 10.1002/bip.23256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 01/05/2023]
Abstract
Peptoids are versatile peptidomimetic molecules with wide-ranging applications from drug discovery to materials science. An understanding of peptoid sequence features that contribute to both their three-dimensional structures and their interactions with lipids will expand functions of peptoids in varied fields. Furthermore, these topics capture the enthusiasm of undergraduate students who prepare and study diverse peptoids in laboratory coursework and/or in faculty led research. Here, we present the synthesis and study of 21 peptoids with varied functionality, including 19 tripeptoids and 2 longer oligomers. We observed differences in fluorescence spectral features for 10 of the tripeptoids that correlated with peptoid flexibility and relative positioning of chromophores. Interactions of representative peptoids with sonicated glycerophospholipid vesicles were also evaluated using fluorescence spectroscopy. We observed evidence of conformational changes effected by lipids for select peptoids. We also summarize our experiences engaging students in peptoid-based projects to advance both research and undergraduate educational objectives in parallel.
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Affiliation(s)
- Christian J. Jimenez
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Jiacheng Tan
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Kalli M. Dowell
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Gillian E. Gadbois
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Cameron A. Read
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Nicole Burgess
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Jesus E. Cervantes
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Shannon Chan
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Anmol Jandaur
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Tara Karanik
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Jaenic J. Lee
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Mikaela C. Ley
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Molly McGeehan
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Ann McMonigal
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Kira L. Palazzo
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Samantha A. Parker
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Andre Payman
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Maritza Soria
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Lauren Verheyden
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Vivian T. Vo
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Jennifer Yin
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Anna L. Calkins
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Amelia A. Fuller
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
| | - Grace Y. Stokes
- Department of Chemistry & BiochemistrySanta Clara UniversitySanta ClaraCaliforniaU.S.A.
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4
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Rivas MA, Courouble VC, Baker MC, Cookmeyer DL, Fiore KE, Frost AJ, Godbe KN, Jordan MR, Krasnow EN, Mollo A, Ridings ST, Sawada K, Shroff KD, Studnitzer B, Thiele GAR, Sisto AC, Nawal S, Huff AR, Fairman R, Johnson KA, Beld J, Kokona B, Charkoudian LK. The Effect of Divalent Cations on the Thermostability of Type II Polyketide Synthase Acyl Carrier Proteins. AIChE J 2018; 64:4308-4318. [PMID: 31527922 DOI: 10.1002/aic.16402] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The successful engineering of biosynthetic pathways hinges on understanding the factors that influence acyl carrier protein (ACP) stability and function. The stability and structure of ACPs can be influenced by the presence of divalent cations, but how this relates to primary sequence remains poorly understood. As part of a course-based undergraduate research experience, we investigated the thermostability of type II polyketide synthase (PKS) ACPs. We observed an approximate 40 °C range in the thermostability amongst the 14 ACPs studied, as well as an increase in stability (5 - 26 °C) of the ACPs in the presence of divalent cations. Distribution of charges in the helix II-loop-helix III region was found to impact the enthalpy of denaturation. Taken together, our results reveal clues as to how the sequence of type II PKS ACPs relates to their structural stability, information that can be used to study how ACP sequence relates to function.
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Affiliation(s)
| | - Valentine C. Courouble
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Miranda C. Baker
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Kristen E. Fiore
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Alexander J. Frost
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Michael R. Jordan
- Dept. of Physics Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Emily N. Krasnow
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Aurelio Mollo
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Stephen T. Ridings
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Keisuke Sawada
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Kavita D. Shroff
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Bradley Studnitzer
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Grace A. R. Thiele
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Saadia Nawal
- Dept. of Chemistry Haverford College Haverford PA 19041
| | - Adam R. Huff
- Dept. of Chemistry Haverford College Haverford PA 19041
| | | | | | - Joris Beld
- Dept. of Microbiology and Immunology Drexel University College of Medicine Philadelphia PA 19102
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5
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Epstein SC, Charkoudian LK, Medema MH. A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. Stand Genomic Sci 2018; 13:16. [PMID: 30008988 PMCID: PMC6042397 DOI: 10.1186/s40793-018-0318-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.
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Affiliation(s)
- Samuel C. Epstein
- Department of Chemistry, Haverford College, Haverford, PA 19041-1391 USA
| | | | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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