1
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Seiler C, Stainthorp AK, Ketchen S, Jones CM, Marks K, Quirke P, Ladbury JE. The Grb2 splice variant, Grb3-3, is a negative regulator of RAS activation. Commun Biol 2022; 5:1029. [PMID: 36171279 PMCID: PMC9519967 DOI: 10.1038/s42003-022-03985-7] [Citation(s) in RCA: 2] [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: 08/20/2021] [Accepted: 09/13/2022] [Indexed: 11/24/2022] Open
Abstract
Activation of RAS is crucial in driving cellular outcomes including proliferation, differentiation, migration and apoptosis via the MAPK pathway. This is initiated on recruitment of Grb2, as part of a Grb2-Sos complex, to an up-regulated receptor tyrosine kinase (RTK), enabling subsequent interaction of Sos with the plasma membrane-localised RAS. Aberrant regulation at this convergence point for RTKs in MAPK signalling is a key driver of multiple cancers. Splicing of the GRB2 gene produces a deletion variant, Grb3-3, that is incapable of binding to RTKs. We show that, despite maintaining the ability to bind to Sos, the Grb3-3-Sos complex remains in the cytoplasm, unable to engage with RAS. Competition between Grb2 and Grb3-3 for binding to C-terminal proline-rich sequences on Sos modulates MAPK signalling. Additionally, we demonstrate that splicing is regulated by heterogenous nuclear riboproteins C1/C2, and that normal and malignant colon tissue show differential Grb3-3 expression.
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Affiliation(s)
- Caroline Seiler
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Amy K Stainthorp
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Sophie Ketchen
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Christopher M Jones
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Radiotherapy Research Group, Faculty of Medicine & Health, University of Leeds, Leeds, UK
- Leeds Cancer Centre, The Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kate Marks
- University of Leeds School of Medicine, Leeds Institute of Medical Research, Pathology and Data Analytics, University of Leeds, Leeds, UK
| | - Philip Quirke
- University of Leeds School of Medicine, Leeds Institute of Medical Research, Pathology and Data Analytics, University of Leeds, Leeds, UK
| | - John E Ladbury
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
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2
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Wen J, Liao H, Stachowski K, Hempfling JP, Qian Z, Yuan C, Foster MP, Pei D. Rational design of cell-permeable cyclic peptides containing a d-Pro-l-Pro motif. Bioorg Med Chem 2020; 28:115711. [PMID: 33069067 DOI: 10.1016/j.bmc.2020.115711] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/01/2022]
Abstract
Cyclic peptides are capable of binding to challenging targets (e.g., proteins involved in protein-protein interactions) with high affinity and specificity, but generally cannot gain access to intracellular targets because of poor membrane permeability. In this work, we discovered a conformationally constrained cyclic cell-penetrating peptide (CPP) containing a d-Pro-l-Pro motif, cyclo(AFΦrpPRRFQ) (where Φ is l-naphthylalanine, r is d-arginine, and p is d-proline). The structural constraints provided by cyclization and the d-Pro-l-Pro motif permitted the rational design of cell-permeable cyclic peptides of large ring sizes (up to 16 amino acids). This strategy was applied to design a potent, cell-permeable, and biologically active cyclic peptidyl inhibitor, cyclo(YpVNFΦrpPRR) (where Yp is l-phosphotyrosine), against the Grb2 SH2 domain. Multidimensional NMR spectroscopic and circular dichroism analyses revealed that the cyclic CPP as well as the Grb2 SH2 inhibitor assume a predominantly random coil structure but have significant β-hairpin character surrounding the d-Pro-l-Pro motif. These results demonstrate cyclo(AFΦrpPRRFQ) as an effective CPP for endocyclic (insertion of cargo into the CPP ring) or exocyclic delivery of biological cargos (attachment of cargo to the Gln side chain).
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Affiliation(s)
- Jin Wen
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Hui Liao
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Kye Stachowski
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Jordan P Hempfling
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Ziqing Qian
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, 460 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA.
| | - Dehua Pei
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA.
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3
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Komnatnyy VV, Nielsen TE, Qvortrup K. Bead-based screening in chemical biology and drug discovery. Chem Commun (Camb) 2018; 54:6759-6771. [PMID: 29888365 DOI: 10.1039/c8cc02486c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.
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Affiliation(s)
- Vitaly V Komnatnyy
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
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4
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Bedewy W, Liao H, Abou-Taleb NA, Hammad SF, Nasr T, Pei D. Generation of a cell-permeable cycloheptapeptidyl inhibitor against the peptidyl-prolyl isomerase Pin1. Org Biomol Chem 2018; 15:4540-4543. [PMID: 28517007 DOI: 10.1039/c7ob00430c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cyclic peptides are capable of binding and modulating challenging drug targets including protein-protein interactions. However, their lack of membrane permeability prevents their application against intracellular targets. In this study, we show that it is possible to design a cell-permeable and biologically active cycloheptapeptide inhibitor against the intracellular enzyme peptidyl-prolyl isomerase Pin1 by integrating cell-penetrating and target-binding sequences.
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Affiliation(s)
- Walaa Bedewy
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.
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5
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Strategies for transitioning macrocyclic peptides to cell-permeable drug leads. Curr Opin Biotechnol 2017; 48:242-250. [DOI: 10.1016/j.copbio.2017.07.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/17/2017] [Accepted: 07/20/2017] [Indexed: 11/23/2022]
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6
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Qian Z, Dougherty PG, Pei D. Targeting intracellular protein-protein interactions with cell-permeable cyclic peptides. Curr Opin Chem Biol 2017; 38:80-86. [PMID: 28388463 DOI: 10.1016/j.cbpa.2017.03.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for conventional drug modalities, because small molecules generally do not bind to their large, flat binding sites with high affinity, whereas monoclonal antibodies cannot cross the cell membrane to reach the targets. Cyclic peptides in the 700-2000 molecular-weight range have the sufficient size and a balanced conformational flexibility/rigidity for binding to flat PPI interfaces with antibody-like affinity and specificity. Several powerful cyclic peptide library technologies were developed over the past decade to rapidly discover potent, specific cyclic peptide ligands against proteins of interest including those involved in PPIs. Methods are also being developed to enhance the membrane permeability of cyclic peptides through both passive diffusion and active transport mechanisms. Integration of the permeability-enhancing elements into cyclic peptide design has led to an increasing number of cell-permeable and biologically active cyclic peptides against intracellular PPIs. In this account, we review the recent developments in the design and synthesis of cell-permeable cyclic peptides.
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Affiliation(s)
- Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Patrick G Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, United States.
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7
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Macrocycles as protein-protein interaction inhibitors. Biochem J 2017; 474:1109-1125. [PMID: 28298556 DOI: 10.1042/bcj20160619] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
Macrocyclic compounds such as cyclic peptides have emerged as a new and exciting class of drug candidates for inhibition of intracellular protein-protein interactions, which are challenging targets for conventional drug modalities (i.e. small molecules and proteins). Over the past decade, several complementary technologies have been developed to synthesize macrocycle libraries and screen them for binding to therapeutically relevant targets. Two different approaches have also been explored to increase the membrane permeability of cyclic peptides. In this review, we discuss these methods and their applications in the discovery of macrocyclic compounds against protein-protein interactions.
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8
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Qvortrup K, Nielsen TE. In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katrine Qvortrup
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
| | - Thomas E. Nielsen
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
- Singapore Centre on Environmental Life Sciences Engineering; Nanyang Technological University; 637551 Singapore Singapore
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9
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Qvortrup K, Nielsen TE. In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors. Angew Chem Int Ed Engl 2016; 55:4472-5. [DOI: 10.1002/anie.201511308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 02/02/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Katrine Qvortrup
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
| | - Thomas E. Nielsen
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
- Singapore Centre on Environmental Life Sciences Engineering; Nanyang Technological University; 637551 Singapore Singapore
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10
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Giguère S, Laviolette F, Marchand M, Tremblay D, Moineau S, Liang X, Biron É, Corbeil J. Machine learning assisted design of highly active peptides for drug discovery. PLoS Comput Biol 2015; 11:e1004074. [PMID: 25849257 PMCID: PMC4388847 DOI: 10.1371/journal.pcbi.1004074] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 12/05/2014] [Indexed: 01/15/2023] Open
Abstract
The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning approaches can greatly assist in the process and even partly replace expensive laboratory experiments by learning a predictor with existing data or with a smaller amount of data generation. Unfortunately, once the model is learned, selecting peptides having the greatest predicted bioactivity often requires a prohibitive amount of computational time. For this combinatorial problem, heuristics and stochastic optimization methods are not guaranteed to find adequate solutions. We focused on recent advances in kernel methods and machine learning to learn a predictive model with proven success. For this type of model, we propose an efficient algorithm based on graph theory, that is guaranteed to find the peptides for which the model predicts maximal bioactivity. We also present a second algorithm capable of sorting the peptides of maximal bioactivity. Extensive analyses demonstrate how these algorithms can be part of an iterative combinatorial chemistry procedure to speed up the discovery and the validation of peptide leads. Moreover, the proposed approach does not require the use of known ligands for the target protein since it can leverage recent multi-target machine learning predictors where ligands for similar targets can serve as initial training data. Finally, we validated the proposed approach in vitro with the discovery of new cationic antimicrobial peptides. Source code freely available at http://graal.ift.ulaval.ca/peptide-design/. Part of the complexity of drug discovery is the sheer chemical diversity to explore combined to all requirements a compound must meet to become a commercial drug. Hence, it makes sense to automate this chemical exploration endeavor in a wise, informed, and efficient fashion. Here, we focused on peptides as they have properties that make them excellent drug starting points. Machine learning techniques may replace expensive in-vitro laboratory experiments by learning an accurate model of it. However, computational models also suffer from the combinatorial explosion due to the enormous chemical diversity. Indeed, applying the model to every peptides would take an astronomical amount of computer time. Therefore, given a model, is it possible to determine, using reasonable computational time, the peptide that has the best properties and chance for success? This exact question is what motivated our work. We focused on recent advances in kernel methods and machine learning to learn a model that already had excellent results. We demonstrate that this class of model has mathematical properties that makes it possible to rapidly identify and sort the best peptides. Finally, in-vitro and in-silico results are provided to support and validate this theoretical discovery.
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Affiliation(s)
- Sébastien Giguère
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
- * E-mail:
| | - François Laviolette
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
| | - Mario Marchand
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
| | - Denise Tremblay
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Canada
| | - Sylvain Moineau
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Canada
| | - Xinxia Liang
- Faculty of Pharmacy, Université Laval, Québec, Canada
| | - Éric Biron
- Faculty of Pharmacy, Université Laval, Québec, Canada
| | - Jacques Corbeil
- Department of Molecular Medicine, Université Laval, Québec, Canada
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11
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Foster AD, Ingram JD, Leitch EK, Lennard KR, Osher EL, Tavassoli A. Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery. ACTA ACUST UNITED AC 2015; 20:563-76. [DOI: 10.1177/1087057114566803] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/11/2014] [Indexed: 12/23/2022]
Abstract
The identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for screening libraries of macromolecules created using chemical biology approaches. Not only can the production of the library be directly interfaced with a cell-based assay, but these libraries also require significantly fewer resources to generate and maintain. In this context, cyclic peptides are increasingly viewed as ideal scaffolds and have proven capability against challenging targets such as protein-protein interactions. Here we discuss a range of methods used for the creation of cyclic peptide libraries and detail examples of their successful implementation.
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Affiliation(s)
| | | | | | | | | | - Ali Tavassoli
- Chemistry, University of Southampton, Southampton, UK
- Cancer Sciences, University of Southampton, Southampton, UK
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12
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The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.54] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Menegatti S, Ward KL, Naik AD, Kish WS, Blackburn RK, Carbonell RG. Reversible cyclic peptide libraries for the discovery of affinity ligands. Anal Chem 2013; 85:9229-37. [PMID: 24000940 DOI: 10.1021/ac401954k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A novel strategy is presented for the identification of cyclic peptide ligands from combinatorial libraries of reversible cyclic depsipeptides. A method for the solid-phase synthesis of individual cyclic depsipeptides and combinatorial libraries of these compounds is proposed, which employs lactic acid (Lact) and the dipeptide ester (Nα-Ac)-Ser(Ala)- as linkers for dilactonization. Upon alkaline treatment of the beads selected by screening a model library, the cyclic depsipeptides are linearized and released from the solid support to the liquid phase, to be sequenced via single-step tandem mass spectrometry (MS/MS). The protocol presented for library synthesis provides for wide structural diversity. Two model sequences, VVWVVK and AAWAAR, were chosen to present different structural examples for depsipeptide libraries and demonstrate the process of sequence determination by mass spectrometry. Further, a case study using the IgG binding cyclic depsipeptide cyclo[(Nα-Ac)-S(A)-RWHYFK-Lact-E] is presented to demonstrate the process of library screening and sequence determination on the selected beads. Finally, a method is shown for synthesis of the irreversible cyclic peptide corresponding to the proposed depsipeptide structure, to make the ligand stable to the aqueous acid and alkaline conditions encountered in affinity chromatographic applications. The cyclic peptide ligand was synthesized on a poly(methacrylate) resin and used for chromatographic binding of the target IgG.
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Affiliation(s)
- Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, ‡Department of Molecular and Structural Biochemistry, and §Biomanufacturing Training and Education Center, North Carolina State University , Raleigh, North Carolina 27695, United States
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14
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Chu CY, Chang CP, Chou YT, Handoko, Hu YL, Lo LC, Lin JJ. Development and evaluation of novel phosphotyrosine mimetic inhibitors targeting the Src homology 2 domain of signaling lymphocytic activation molecule (SLAM) associated protein. J Med Chem 2013; 56:2841-9. [PMID: 23470190 DOI: 10.1021/jm301610q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Specific interactions between Src homology 2 (SH2) domain-containing proteins and the phosphotyrosine-containing counterparts play significant role in cellular protein tyrosine kinase (PTK) signaling pathways. The SH2 domain inhibitors could potentially serve as drug candidates in treating human diseases. Here we have incorporated a novel phosphotyrosine mimetic, which is an unusual amino acid carrying a cyclosaligenyl (cycloSal) phosphodiester moiety, into dipeptides to investigate the inhibitory effect on SH2 domain-containing proteins. A plate-based assay was also established to screen for inhibitors that disrupt the interaction between a phosphopeptide of SLAM (signaling lymphocytic activation molecule) and its interacting protein SAP (SLAM-associated protein). We identified a number of inhibitors with IC50 values in the range of 17-35 μM, implying that the cycloSal phosphodiester-carrying amino acid could mimic the phosphotyrosyl residue. Our results also raise the possibility of integrating the newly developed phosphotyrosine mimetic moiety into inhibitors designed for other SH2 domain-containing proteins.
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Affiliation(s)
- Chi-Yuan Chu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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15
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Chung BKW, Hickey JL, Scully CCG, Zaretsky S, Yudin AK. Bicycle synthesis through peptide macrocyclization using aziridine aldehydes followed by late stage disulfide bond installation. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00054k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a method that can be applied to generate medium-sized peptidomimetic macrocycles equipped with disulfide bonds.
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Affiliation(s)
| | | | | | - Serge Zaretsky
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
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16
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Menegatti S, Hussain M, Naik AD, Carbonell RG, Rao BM. mRNA display selection and solid-phase synthesis of Fc-binding cyclic peptide affinity ligands. Biotechnol Bioeng 2012; 110:857-70. [DOI: 10.1002/bit.24760] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 12/25/2022]
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17
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Liu X, Dix M, Speers AE, Bachovchin DA, Zuhl AM, Cravatt BF, Kodadek TJ. Rapid development of a potent photo-triggered inhibitor of the serine hydrolase RBBP9. Chembiochem 2012; 13:2082-93. [PMID: 22907802 DOI: 10.1002/cbic.201200445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Indexed: 11/09/2022]
Abstract
The serine hydrolases constitute a large class of enzymes that play important roles in physiology. There is great interest in the development of potent and selective pharmacological inhibitors of these proteins. Traditional active-site inhibitors often have limited selectivity within this superfamily and are tedious and expensive to discover. Using the serine hydrolase RBBP9 as a model target, we designed a rapid and relatively inexpensive route to highly selective peptoid-based inhibitors that can be activated by visible light. This technology provides rapid access to photo-activated tool compounds capable of selectively blocking the function of particular serine hydrolases.
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Affiliation(s)
- Xiaodan Liu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
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18
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Bédard F, Girard A, Biron É. A Convenient Approach to Prepare Topologically Segregated Bilayer Beads for One-Bead Two-Compound Combinatorial Peptide Libraries. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-012-9316-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Abstract
Developing short peptides into useful probes and therapeutic leads remains a difficult challenge. Structural rigidification is a proven method for improving the properties of short peptides. In this work, we report a strategy for stabilizing peptide macrocycles by introducing side-chain-to-side-chain staples to produce peptide bicycles with higher affinity, selectivity, and resistance to degradation. We have applied this strategy to G1, an 11-residue peptide macrocycle that binds the Src homology 2 (SH2) domain of growth-factor-bound protein 2 (Grb2). Several homodetic peptide bicycles were synthesized entirely on-resin with high yields. Two rounds of iterative design produced peptide bicycle BC1, which is 60 times more potent than G1 and 200 times more selective. Moreover, BC1 is completely intact after 24 hours in buffered human serum, conditions under which G1 is completely degraded. Our peptide-bicycle approach holds promise for the development of selective inhibitors of SH2 domains and other phosophotyrosine (pTyr)-binding proteins, as well as inhibitors of many other protein-protein interactions.
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Affiliation(s)
- Justin S. Quartararo
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA 02155 USA, Fax: (617) 627-3443
| | - Pianpian Wu
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA 02155 USA, Fax: (617) 627-3443
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA 02155 USA, Fax: (617) 627-3443
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20
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Simpson LS, Kodadek T. A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry. Tetrahedron Lett 2012; 53:2341-2344. [PMID: 22736872 DOI: 10.1016/j.tetlet.2012.02.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many macrocyclic depsipeptides or related compounds have interesting medicinal properties and often display more favorable pharmacokinetic properties than linear analogues. Therefore, there is considerable interest in the development of large combinatorial libraries of macrocyclic peptidomimetic compounds. However, such molecules cannot be easily sequenced by tandem mass spectrometry, making it difficult to identify hits isolated from library screens using one bead one compound libraries. Here we report a strategy to solve this problem by placing a methionine in both the linker connecting the cyclic molecule to the bead as well as within the cycle itself. Treatment with CNBr both linearizes the molecule at a specific position and releases the molecule from the bead, making its characterization by tandem MALDI mass spectrometry straightforward.
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Affiliation(s)
- Levi S Simpson
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9185
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21
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Feliu L, Oliveras G, Cirac AD, Besalú E, Rosés C, Colomer R, Bardají E, Planas M, Puig T. Antimicrobial cyclic decapeptides with anticancer activity. Peptides 2010; 31:2017-26. [PMID: 20708052 DOI: 10.1016/j.peptides.2010.07.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/30/2010] [Accepted: 07/30/2010] [Indexed: 11/27/2022]
Abstract
Antimicrobial peptides have been considered as potential candidates for cancer therapy. We report here the cytotoxicity of a library of 66 antibacterial cyclodecapeptides on human carcinoma cell lines, and their effects on apoptosis [as assessed by cleavage of poly(ADP-ribose) polymerase (PARP)] and cell signaling proteins (p53 and ERK1/2) in cultured human cervical carcinoma cells. A design of experiments approach permitted to analyze the results of a subset of 16 peptides and define rules for high anticancer activity against MDA-MB-231 breast carcinoma cells. Eight peptides were identified with IC(50) values ranging from 18.5 to 57.5 μM against the five cell lines tested, being HeLa cells the most sensitive. Among these sequences, BPC88, BPC96, BPC98, and BPC194 displayed specificity and high cytotoxicity against HeLa cells (IC(50) of 22.5-38.5 μM), showed low hemolytic activity and low cytotoxicity to non-malignant fibroblasts, and were stable to proteases in human serum. Induction of apoptosis by these peptides was observed and the apoptotic effect of BPC88 and BPC96 caused a marked decrease on the activated form of ERK1/2 kinase and an induction of p53. We further showed that BPC96 at low doses synergized the cytotoxic effect of cisplatin. These findings suggest that cyclic decapeptides may represent novel anticancer agents providing a new strategy in cancer therapy.
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Affiliation(s)
- Lidia Feliu
- LIPPSO, Department of Chemistry, University of Girona, Campus Montilivi, E-17071 Girona, Spain
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22
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Cho S, Choi J, Kim A, Lee Y, Kwon YU. Efficient solid-phase synthesis of a series of cyclic and linear peptoid-dexamethasone conjugates for the cell permeability studies. ACTA ACUST UNITED AC 2010; 12:321-6. [PMID: 20210299 DOI: 10.1021/cc9001857] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic peptides and their cyclic analogs have received a great deal of attention because of their numerous interesting biological activities and their challenging chemical synthesis. It has also been hypothesized that they might improve the cell permeability compared to linear molecules by providing internal hydrogen bonding and generally decreasing the conformational flexibility. In this study, a series of cyclic and linear peptoid-dexamethasone conjugates were rationally designed and efficiently synthesized on solid-phase for systematic cell permeability studies using reporter gene-based assays. These model compounds should be used to reveal how the cell permeability of cyclic molecules is affected by several physicochemical properties, especially, the reduced conformational flexibility and the ring size. In addition, the synthetic strategy that was adopted in this study can also provide a robust platform for postchemical modifications of various molecular scaffolds in solid-phase or solution-phase syntheses.
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Affiliation(s)
- Suekyung Cho
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, South Korea
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23
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Chen X, Tan PH, Zhang Y, Pei D. On-bead screening of combinatorial libraries: reduction of nonspecific binding by decreasing surface ligand density. ACTA ACUST UNITED AC 2010; 11:604-11. [PMID: 19397369 DOI: 10.1021/cc9000168] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
On-bead screening of one-bead-one-compound (OBOC) libraries provides a powerful method for the rapid identification of active compounds against molecular or cellular targets. However, on-bead screening is susceptible to interference from nonspecific binding, which results in biased screening data and false positives. In this work, we have found that a major source of nonspecific binding is derived from the high ligand loading on the library beads, which permits a macromolecular target (e.g., a protein) to simultaneously interact with multiple ligands on the bead surface. To circumvent this problem, we have synthesized a phosphotyrosyl (pY)-containing peptide library on spatially segregated TentaGel microbeads, which feature a 10-fold reduced peptide loading on the bead surface but a normal peptide loading in the bead interior. The library was screened against a panel of 10 Src homology 2 (SH2) domains including those of Csk and Fyn kinases and adaptor protein SLAP, and the specific recognition motif(s) was successfully identified for each of the domains. In contrast, when the SH2 domains were screened against a control library that contained unaltered (high) ligand loading at the bead surface, six of them exhibited varying degrees of sequence biases, ranging from minor perturbation in the relative abundance of different sequences to the exclusive selection of false positive sequences that have no measurable affinity to the target protein. These results indicate that reduction of the ligand loading on the bead surface represents a simple, effective strategy to largely eliminate the interference from nonspecific binding, while preserving sufficient amounts of materials in the bead interior for compound identification. This finding should further expand the utility of OBOC libraries in biomedical research.
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Affiliation(s)
- Xianwen Chen
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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24
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Liu T, Liu Y, Kao HY, Pei D. Membrane permeable cyclic peptidyl inhibitors against human Peptidylprolyl Isomerase Pin1. J Med Chem 2010; 53:2494-501. [PMID: 20180533 DOI: 10.1021/jm901778v] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Peptidylprolyl isomerase Pin1 regulates the function and/or stability of phosphoproteins by altering the conformation of specific pSer/pThr-Pro peptide bonds. In this work, a cyclic peptide library was synthesized and screened against the catalytic domain of human Pin1. The selected inhibitors contained a consensus motif of D-pThr-Pip-Nal (where Pip is L-piperidine-2-carboxylic acid and Nal is L-2-naphthylalanine). Representative compounds were tested for binding to Pin1 by isothermal titration calorimetry and inhibition of Pin1 activity, and the most potent inhibitors had K(D) (and K(I)) values in the low nanomolar range. Treatment of breast cancer cells with the inhibitors, which were rendered membrane permeable by attachment of an octaarginine sequence, inhibited cell proliferation and increased the protein levels of two previously established Pin1 substrates, PML and SMRT. Finally, a second generation of cell permeable Pin1 inhibitors was designed by replacing the noncritical residues within the cyclic peptide ring with arginine residues and shown to have antiproliferative activity against the cancer cells.
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Affiliation(s)
- Tao Liu
- The Ohio State University, Columbus, Ohio 43210, USA
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25
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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26
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Single bead labeling method for combining confocal fluorescence on-bead screening and solution validation of tagged one-bead one-compound libraries. ACTA ACUST UNITED AC 2009; 16:724-35. [PMID: 19635409 DOI: 10.1016/j.chembiol.2009.06.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 06/05/2009] [Accepted: 06/11/2009] [Indexed: 11/21/2022]
Abstract
Screening of one-bead one-compound libraries by incubating beads with fluorescently labeled target protein requires isolation and structure elucidation of a large number of primary hit beads. However, the potency of the identified ligands is only revealed after time consuming and expensive larger scale resynthesis and testing in solution. Often, many of the resynthesized compounds turn out to be weak target binders in solution due to large differences between surface and solution binding affinities. For an industry style high-throughput screening (HTS) process a high false positive rate is detrimental. We have therefore combined single bead and single molecule/single cell techniques into an integrated HTS process in which the picomole amount of substance contained on one isolated hit bead is sufficient for quality control, structure determination, and precise affinity determination to the target protein in solution.
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27
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Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem 2009; 81:4200-9. [PMID: 19413302 PMCID: PMC2765223 DOI: 10.1021/ac900114t] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural and non-natural cyclic peptides are a crucial component in drug discovery programs because of their considerable pharmaceutical properties. Cyclosporin, microcystins, and nodularins are all notable pharmacologically important cyclic peptides. Because these biologically active peptides are often biosynthesized nonribosomally, they often contain nonstandard amino acids, thus increasing the complexity of the resulting tandem mass spectrometry data. In addition, because of the cyclic nature, the fragmentation patterns of many of these peptides showed much higher complexity when compared to related counterparts. Therefore, at the present time it is still difficult to annotate cyclic peptides MS/MS spectra. In this current work, an annotation program was developed for the annotation and characterization of tandem mass spectra obtained from cyclic peptides. This program, which we call MS-CPA is available as a web tool (http://lol.ucsd.edu/ms-cpa_v1/Input.py). Using this program, we have successfully annotated the sequence of representative cyclic peptides, such as seglitide, tyrothricin, desmethoxymajusculamide C, dudawalamide A, and cyclomarins, in a rapid manner and also were able to provide the first-pass structure evidence of a newly discovered natural product based on predicted sequence. This compound is not available in sufficient quantities for structural elucidation by other means such as NMR. In addition to the development of this cyclic annotation program, it was observed that some cyclic peptides fragmented in unexpected ways resulting in the scrambling of sequences. In summary, MS-CPA not only provides a platform for rapid confirmation and annotation of tandem mass spectrometry data obtained with cyclic peptides but also enables quantitative analysis of the ion intensities. This program facilitates cyclic peptide analysis, sequencing, and also acts as a useful tool to investigate the uncommon fragmentation phenomena of cyclic peptides and aids the characterization of newly discovered cyclic peptides encountered in drug discovery programs.
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Affiliation(s)
- Wei-Ting Liu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0636, USA
| | - Julio Ng
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093-0404, USA
| | - Dario Meluzzi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0636, USA
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093-0404, USA
| | - Marcelino Gutierrez
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0204, USA
| | - Thomas L. Simmons
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0204, USA
| | - Andrew W. Schultz
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0204, USA
| | - Roger G. Linington
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0204, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093-0636, USA
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0204, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093-0636, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093-0404, USA
| | - Pieter C. Dorrestein
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0636, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0204, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093-0636, USA
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