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Synthetic Molecular Evolution of Cell Penetrating Peptides. Methods Mol Biol 2021; 2383:73-89. [PMID: 34766283 DOI: 10.1007/978-1-0716-1752-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Rational design and optimization of cell penetrating peptides (CPPs) is difficult to accomplish because of the lack of quantitative sequence-structure-function rules describing the activity and because of the complex, poorly understood mechanisms of CPPs. Synthetic molecular evolution is a powerful method to identify gain-of-function cell penetrating peptide variants in this situation. Synthetic molecular evolution requires the design and synthesis of iterative, knowledge-based peptide libraries and the screening of such libraries in complex orthogonal cell-based screens for improved activity. In this chapter, we describe methods for synthesizing powerful combinatorial peptide libraries for synthetic molecular evolution.
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2
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Borges A, Gillespie D, Nag A. Biological applications of amide and amino acid containing synthetic macrocycles. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1650178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ariane Borges
- Department of Chemistry, Clark University, Worcester, MA, USA
| | - Dylan Gillespie
- Department of Chemistry, Clark University, Worcester, MA, USA
| | - Arundhati Nag
- Department of Chemistry, Clark University, Worcester, MA, USA
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3
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In-solution enrichment identifies peptide inhibitors of protein-protein interactions. Nat Chem Biol 2019; 15:410-418. [PMID: 30886434 DOI: 10.1038/s41589-019-0245-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/13/2019] [Indexed: 12/14/2022]
Abstract
The use of competitive inhibitors to disrupt protein-protein interactions (PPIs) holds great promise for the treatment of disease. However, the discovery of high-affinity inhibitors can be a challenge. Here we report a platform for improving the affinity of peptide-based PPI inhibitors using non-canonical amino acids. The platform utilizes size exclusion-based enrichment from pools of synthetic peptides (1.5-4 kDa) and liquid chromatography-tandem mass spectrometry-based peptide sequencing to identify high-affinity binders to protein targets, without the need for 'reporter' or 'encoding' tags. Using this approach-which is inherently selective for high-affinity binders-we realized gains in affinity of up to ~100- or ~30-fold for binders to the oncogenic ubiquitin ligase MDM2 or HIV capsid protein C-terminal domain, which inhibit MDM2-p53 interaction or HIV capsid protein C-terminal domain dimerization, respectively. Subsequent macrocyclization of select MDM2 inhibitors rendered them cell permeable and cytotoxic toward cancer cells, demonstrating the utility of the identified compounds as functional PPI inhibitors.
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Wimley WC. Application of Synthetic Molecular Evolution to the Discovery of Antimicrobial Peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:241-255. [PMID: 30980361 DOI: 10.1007/978-981-13-3588-4_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite long-standing promise and many known examples, antimicrobial peptides (AMPs) have failed, with few exceptions, to significantly impact human medicine. Impediments to the systemic activity of AMPs include proteolysis, host cell interactions, and serum protein binding, factors that are not often considered in the early stages of AMP development. Here we discuss how synthetic molecular evolution, iterative cycles of library design, and physiologically relevant screening can be used to evolve AMPs that do not have these impediments.
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Affiliation(s)
- William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA.
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5
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The identification of high-affinity G protein-coupled receptor ligands from large combinatorial libraries using multicolor quantum dot-labeled cell-based screening. Future Med Chem 2015; 6:809-23. [PMID: 24941874 DOI: 10.4155/fmc.14.38] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs), which are involved in virtually every biological process, constitute the largest family of transmembrane receptors. Many top-selling and newly approved drugs target GPCRs. In this review, we aim to recapitulate efforts and progress in combinatorial library-assisted GPCR ligand discovery, particularly focusing on one-bead-one-compound library synthesis and quantum dot-labeled cell-based assays, which both effectively enhance the rapid identification of GPCR ligands with higher affinity and specificity.
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6
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Nallagatla SR, Heuberger B, Haque A, Switzer C. Combinatorial synthesis of thrombin-binding aptamers containing iso-guanine. ACTA ACUST UNITED AC 2009; 11:364-9. [PMID: 19243167 DOI: 10.1021/cc800178m] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A library of all possible substitutions of guanine by iso-guanine (iG) in the thrombin aptamer was prepared by split and mix synthesis. A colorimetric assay was used to screen for functional oligomers in the library. Colorimetrically active oligonucleotides were selected and sequenced by the Maxam-Gilbert method. The sequenced oligonucleotides were individually resynthesized, and their affinities for thrombin were assayed by isothermal titration calorimetry. Three aptamer sequences containing iG were found to have enhanced binding activity to human alpha-thrombin compared to the parent aptamer.
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Affiliation(s)
- Subba Rao Nallagatla
- Department of Chemistry, University of California, Riverside, California 92521, USA
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Marani MM, Oliveira E, Côte S, Camperi SA, Albericio F, Cascone O. Identification of protein-binding peptides by direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of peptide beads selected from the screening of one bead–one peptide combinatorial libraries. Anal Biochem 2007; 370:215-22. [PMID: 17888393 DOI: 10.1016/j.ab.2007.07.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2007] [Revised: 07/27/2007] [Accepted: 07/30/2007] [Indexed: 10/23/2022]
Abstract
A fast and inexpensive strategy for the identification of peptide ligands by direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of peptide beads screened from one bead-one peptide combinatorial libraries is herein described. Streptavidin was used as the model protein. A combinatorial library of 6561 peptides was synthesized on ChemMatrix resin by the divide-couple-recombine method. 4-Hydroxymethylbenzoic acid was used as the linker and five residues of Gly were incorporated at the C termini to increase the final peptide molecular weight. Positive control peptides with the HPQ motif and negative control peptides without the HPQ motif evidenced that the linker and the five residues of Gly have neither impaired the specific binding nor facilitated unspecific binding. After screening the library, positive beads were isolated and washed with 8M guanidine hydrochloride. The beads were sliced into two or four pieces, deposited onto the stainless steel MALDI sample plate, and treated with ammonia vapor to release the peptides. In addition, 26 beads picked at random from the library were subjected to the same treatment. All samples were analyzed by MALDI-TOF-MS and the peptides were unambiguously identified with very good reproducibility between the bead pieces, thus evidencing the good homogeneity of the bead. All sequences obtained from the screening contained HPQ.
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Affiliation(s)
- Mariela M Marani
- Institute for Research in Biomedicine, Barcelona Science Park, Josep Samitier 1, 08028 Barcelona, Spain
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8
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Kumaresan PR, Lam KS. Screening chemical microarrays: methods and applications. MOLECULAR BIOSYSTEMS 2006; 2:259-70. [PMID: 16880944 DOI: 10.1039/b602004f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Pappanaicken R Kumaresan
- Division of Hematology & Oncology, Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 4501 X Street, Sacramento, CA 95817, USA
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9
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Kritzer JA, Stephens OM, Guarracino DA, Reznik SK, Schepartz A. beta-Peptides as inhibitors of protein-protein interactions. Bioorg Med Chem 2005; 13:11-6. [PMID: 15582447 PMCID: PMC2853017 DOI: 10.1016/j.bmc.2004.09.009] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Accepted: 09/08/2004] [Indexed: 01/10/2023]
Abstract
We became interested several years ago in exploring whether 14-helical beta-peptide foldamers could bind protein surfaces and inhibit protein-protein interactions, and if so, whether their affinities and specificities would compare favorably with those of natural or miniature proteins. This exploration was complicated initially by the absence of a suitable beta-peptide scaffold, one that possessed a well-defined 14-helical structure in water and tolerated the diverse sequence variation required to generate high-affinity protein surface ligands. In this perspective, we describe our approach to the design of adaptable beta-peptide scaffolds with high levels of 14-helix structure in water, track the subsequent development of 14-helical beta-peptide protein-protein interaction inhibitors, and examine the potential of this strategy for targeting other therapeutically important proteins.
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Affiliation(s)
| | - Olen M. Stephens
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | | | - Samuel K. Reznik
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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Martin SE, Peterson BR. A colorimetric enzyme-linked on-bead assay for identification of synthetic substrates of protein tyrosine kinases. J Pept Sci 2002; 8:227-33. [PMID: 12043997 DOI: 10.1002/psc.376] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Protein tyrosine kinases play key roles in the progression of numerous human diseases including several types of cancers. We report here a simple colorimetric assay for tyrosine kinase activity employing synthetic peptide substrates prepared on Tentagel synthesis beads. Phosphorylation of compounds on beads was detected with an antiphosphotyrosine antibody complexed with a secondary antibody-alkaline phosphatase conjugate. This assay may prove useful for the identification and characterization of synthetic substrates of this important class of enzymes.
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Affiliation(s)
- Scott E Martin
- Department of Chemistry, The Pennsylvania State University, University Park 16802, USA
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Floyd CD, Leblanc C, Whittaker M. Combinatorial chemistry as a tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2000; 36:91-168. [PMID: 10818672 DOI: 10.1016/s0079-6468(08)70046-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.
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Affiliation(s)
- C D Floyd
- British Biotech Pharmaceuticals Limited, Oxford, U.K
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Vetter SW, Keng YF, Lawrence DS, Zhang ZY. Assessment of protein-tyrosine phosphatase 1B substrate specificity using "inverse alanine scanning". J Biol Chem 2000; 275:2265-8. [PMID: 10644673 DOI: 10.1074/jbc.275.4.2265] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An "inverse alanine scanning" peptide library approach has been developed to assess the substrate specificity of protein-tyrosine phosphatases (PTPases). In this method each Ala moiety in the parent peptide, Ac-AAAApYAAAA-NH(2), is separately and sequentially replaced by the 19 non-Ala amino acids to generate a library of 153 well defined peptides. The relatively small number of peptides allows the acquisition of explicit kinetic data for all library members, thereby furnishing information about the contribution of individual amino acids with respect to substrate properties. The approach was applied to protein-tyrosine phosphatase 1B (PTP1B) as a first example, and the highly potent peptide substrate Ac-ELEFpYMDYE-NH(2) (k(cat)/K(m) 2.2 +/- 0.05 x 10(7) M(-1) s(-1)) has been identified. More importantly, several heretofore unknown features of the substrate specificity of PTP1B were revealed. This includes the ability of PTP1B to accommodate acidic, aromatic, and hydrophobic residues at the -1 position, a strong nonpreference for Lys and Arg residues in any position, and the first evidence that residues well beyond the +1 position contribute to substrate efficacy.
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Affiliation(s)
- S W Vetter
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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13
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Kundu B, Khare SK, Rastogi SK. Combinatorial chemistry: Polymer supported synthesis of peptide and non-peptide libraries. PROGRESS IN DRUG RESEARCH 1999; 53:89-156. [PMID: 10616297 DOI: 10.1007/978-3-0348-8735-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
In recent years, combinatorial chemistry has emerged as a powerful tool for accelerating drug discovery. While industry is rapidly embracing the technology, researchers continue to develop novel library methods including resins, linkers, tagging and deconvolution techniques. Newer strategies involving computer-customized combinatorial libraries offer enormous potential for the design of more "focused" and "smart" chemical libraries with maximal diversity. In addition, miniaturized systems for synthesizing chemical libraries are also being developed, which has made it possible to carry out reactions at submicroliter volumes.
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Affiliation(s)
- B Kundu
- Division of Medicinal Chemistry, Central Drug Research Institute, Lucknow, India
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Dolle RE. Comprehensive survey of chemical libraries yielding enzyme inhibitors, receptor agonists and antagonists, and other biologically active agents: 1992 through 1997. ACTA ACUST UNITED AC 1999. [DOI: 10.1007/978-94-017-0735-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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15
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Dolle RE. Comprehensive survey of chemical libraries yielding enzyme inhibitors, receptor agonists and antagonists, and other biologically active agents: 1992 through 1997. Mol Divers 1998; 3:199-233. [PMID: 9850519 DOI: 10.1023/a:1009699413828] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This review is a historical accounting of chemical libraries from which biologically active agents have been obtained. The comprehensive tabulation includes citations as early as 1992, when the first descriptions of biologically active libraries were disclosed, and continues through 1997. Four tables are provided listing libraries screened against (1) proteolytic enzymes, (2) non-proteolytic enzymes, (3) G-protein coupled receptors (GPCRs), and (4) other targets not classified in the first three tables (e.g. non-GPCRs, integrins, antiinfectives). A name, generic structure, and size is provided for each library citation, accompanied by the molecular screen and the structure and potency of the most active library member. In total, 86 libraries are presented with 60% of the contributions reported from pharmaceutical and biotechnology companies. Approximately 70% of the libraries have used alpha-amino acid synthons in their construction and 85% of the libraries include one or more amide bonds.
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Affiliation(s)
- R E Dolle
- Department of Chemistry, Pharmacopeia, Inc., Princeton, NJ 08540, USA.
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Lam KS, Lebl M, Krchnák V. The "One-Bead-One-Compound" Combinatorial Library Method. Chem Rev 1997; 97:411-448. [PMID: 11848877 DOI: 10.1021/cr9600114] [Citation(s) in RCA: 507] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kit S. Lam
- Arizona Cancer Center, Department of Medicine, Department of Microbiology and Immunology, 1501 N. Campbell Avenue, Tucson, Arizona 85724, and Houghten Pharmaceuticals Inc., 3550 General Atomics Court, San Diego, California 92121
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Abstract
This review serves to highlight the recent examples of combinatoric methodology as applied to the discovery and optimization of enzyme inhibitors. Early research efforts focused on the identification of polypeptides from libraries as inhibitors of proteases. As solution- and solid-phase chemistries gain in sophistication, libraries containing less peptidic structural motifs have been created. A recurring design stratagem relies on the synthesis of libraries incorporating pharmacophores with known affinity for the target enzyme. Screening of these structure-based libraries has led to the discovery of small-molecule inhibitors of both proteolytic and non-proteolytic enzymes alike. Two tables are provided listing the enzyme targeted libraries through 1996. A name, generic structure and size is given for each library citation, accompanied by the enzyme screen and the structure and potency of the most active library member.
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Affiliation(s)
- R E Dolle
- Department of Chemistry, Pharmacopeia Inc., Princeton, NJ 08540, USA
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