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Preparation of Bacterial Cell-Surface Displayed Semisynthetic Cyclic Peptides. Methods Mol Biol 2021. [PMID: 34596850 DOI: 10.1007/978-1-0716-1689-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Semisynthetic cyclic peptides bearing both non-proteinogenic and genetically encoded amino acids are excellent ligands for peptide-based drug discovery. While semisynthesis expands the chemical space, genetic encoding allows access to a large library via randomization at the nucleic acid level. Selection of novel binders of such macrocyclic ligands requires linking their genotype to phenotype. In this chapter, we report a bacterial cell-surface display system to present cyclic peptides composed of synthetic and genetically encoded fragments. The synthetic fragment along with the split intein partner and an aminooxy moiety is ligated and cyclized with the recombinant backbone containing an unnatural amino acid by protein trans-splicing and intramolecular oxime ligation, respectively. A pH-shift protocol was applied to accelerate on surface cyclization. This method will enable generation of semisynthetic cyclic peptide libraries and their selection by fluorescence-activated cell sorting.
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Reyes Romero A, Ruiz-Moreno AJ, Groves MR, Velasco-Velázquez M, Dömling A. Benchmark of Generic Shapes for Macrocycles. J Chem Inf Model 2020; 60:6298-6313. [PMID: 33270455 PMCID: PMC7768607 DOI: 10.1021/acs.jcim.0c01038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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Macrocycles
target proteins that are otherwise considered undruggable
because of a lack of hydrophobic cavities and the presence of extended
featureless surfaces. Increasing efforts by computational chemists
have developed effective software to overcome the restrictions of
torsional and conformational freedom that arise as a consequence of
macrocyclization. Moloc is an efficient algorithm, with an emphasis
on high interactivity, and has been constantly updated since 1986
by drug designers and crystallographers of the Roche biostructural
community. In this work, we have benchmarked the shape-guided algorithm
using a dataset of 208 macrocycles, carefully selected on the basis
of structural complexity. We have quantified the accuracy, diversity,
speed, exhaustiveness, and sampling efficiency in an automated fashion
and we compared them with four commercial (Prime, MacroModel, molecular
operating environment, and molecular dynamics) and four open-access
(experimental-torsion distance geometry with additional “basic
knowledge” alone and with Merck molecular force field minimization
or universal force field minimization, Cambridge Crystallographic
Data Centre conformer generator, and conformator) packages. With three-quarters
of the database processed below the threshold of high ring accuracy,
Moloc was identified as having the highest sampling efficiency and
exhaustiveness without producing thousands of conformations, random
ring splitting into two half-loops, and possibility to interactively
produce globular or flat conformations with diversity similar to Prime,
MacroModel, and molecular dynamics. The algorithm and the Python scripts
for full automatization of these parameters are freely available for
academic use.
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Affiliation(s)
- Atilio Reyes Romero
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
| | - Angel Jonathan Ruiz-Moreno
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands.,Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Trasnacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Circuito Exterior S/N, Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico.,Programa de Doctorado en Ciencias Biomédicas, UNAM, Av. Universidad 3000, Circuito Exterior S/N. Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Matthew R Groves
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
| | - Marco Velasco-Velázquez
- Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Trasnacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Circuito Exterior S/N, Delegación Coyoacán, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Alexander Dömling
- Drug Design, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, XB20, 9713 AV Groningen, The Netherlands
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