Protein Engineering Laboratory

Laboratory

Fluorescent D-Amino Acids for Super-resolution Microscopy of the Bacterial Cell Wall

Juliette Griffie, Suliana Manley, Jiangtao Qiao, Luc Reymond, Ophélie Rutschmann, Faustine Ambroisine Charline Ryckebusch, Willi Leopold Stepp, Chen Zhang

Fluorescent D-amino acids (FDAAs) have previ-ously been developed to enable in situ highlighting of locations of bacterial cell wall growth. Most bacterial cells lie at the edge of the diffraction limit of visible light; thus, resolving the precise details of peptidoglycan (PG) biosynthesis requires super-resolution micros-copy after probe incorporation. Single molecule localization microscopy (SMLM) has stringent requirements on the fluorophore photophysical properties and therefore has remained challenging in this context. Here, we report the synthesis and characterization of new FDAAs compatible with one-step labeling and SMLM imaging. We demonstrate the incorporation of our probes and their utility for visualizing PG at the nanoscale in Gram-negative, Gram-positive, and mycobacteria species. This improved FDAA toolkit will endow researchers with a nanoscale perspective on the spatial distribution of PG biosynthesis for a broad range of bacterial species.

AMER CHEMICAL SOC2022

Solid-phase peptide synthesis on disulfide-linker resin followed by reductive release affords pure thiol-functionalized peptides

Zsolt Bognár, Christian Heinis, Manuel Leonardo Merz, Ganesh Kumar Mothukuri, Alexander Lund Nielsen, Peter Matei Frisius Pânzar

Thiol groups are suitable handles for site-selectively modifying, immobilizing or cyclizing individual peptides or entire peptide libraries. A limiting step in producing the thiol-functionalized peptides is the chromatographic purification, which is particularly laborious and costly if many peptides or even large libraries are to be produced. Herein, we present a strategy in which thiol-functionalized peptides are obtained in >90% purity and free of reducing agent, without a single chromatographic purification step. In brief, peptides are synthesized on a solid support linked via a disulfide bridge, the side-chain protecting groups are eliminated and washed away while the peptides remain on resin, and rather pure peptides are released from the solid support by reductive cleavage of the disulfide linker. Application of a volatile reducing agent, 1,4-butanedithiol (BDT), enabled removal of the agent by evaporation. We demonstrate that the approach is suited for the parallel synthesis of many peptides and that peptides containing a second thiol group can directly be cyclized by bis-electrophilic alkylating reagents for producing libraries of cyclic peptides.

ROYAL SOC CHEMISTRY2022

Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale

Alessandro Angelini, Zsolt Bognár, Julien Bortoli Chapalay, Cristina Diaz Perlas, Sevan Mleh Habeshian, Christian Heinis, Manuel Leonardo Merz, Ganesh Kumar Mothukuri, Gontran Sangouard, Mischa Schüttel, Gerardo Turcatti, Jonathan Patrice Vesin

Macrocycles have excellent potential as therapeutics due to their ability to bind challenging targets. However, generating macrocycles against new targets is hindered by a lack of large macrocycle libraries for high-throughput screening. To overcome this, we herein established a combinatorial approach by tethering a myriad of chemical fragments to peripheral groups of structurally diverse macrocyclic scaffolds in a combinatorial fashion, all at a picomole scale in nanoliter volumes using acoustic droplet ejection technology. In a proof-of-concept, we generate a target-tailored library of 19,968 macrocycles by conjugating 104 carboxylic-acid fragments to 192 macrocyclic scaffolds. The high reaction efficiency and small number of side products of the acylation reactions allowed direct assay without purification and thus a large throughput. In screens, we identify nanomolar inhibitors against thrombin (Ki = 44 ± 1 nM) and the MDM2:p53 protein-protein interaction (Kd MDM2 = 43 ± 18 nM). The increased efficiency of macrocycle synthesis and screening and general applicability of this approach unlocks possibilities for generating leads against any protein target.

2022

Cyclative Release Strategy to Obtain Pure Cyclic Peptides Directly from the Solid Phase

Sevan Mleh Habeshian, Christian Heinis, Manuel Leonardo Merz, Ganesh Ashokrao Sable

The synthesis of large numbers of cyclic peptides-required, for example, in screens for drug development-is currently limited by the need of chromatographic purification of individual peptides. Herein, we have developed a strategy in which cyclic peptides are released from the solid phase in the pure form and do not need purification. Peptides with an N-terminal thiol group are synthesized on the solid phase via a C-terminal disulfide linker, their sidechain-protecting groups are removed while the peptides remain on the solid phase, and the peptides are finally released via a cyclative mechanism by the addition of a base that deprotonates the N-terminal thiol group and triggers an intramolecular disulfide-exchange reaction. The method yields disulfide-cyclized peptides, a format on which many important peptide drugs such as o based. We demonstrate that the method is applicable for facile synthesis in 96-well plates and allows for synthesis and screening of hundreds of cyclic peptides.

AMER CHEMICAL SOC2022

Systematic Tuning of Rhodamine Spirocyclization for Super-resolution Microscopy

Kai Johnsson, Lu Wang

Rhodamines are the most important class of fluorophores for applications in live-cell fluorescence microscopy. This is mainly because rhodamines exist in a dynamic equilibrium between a fluorescent zwitterion and a nonfluorescent but cell-permeable spirocyclic form. Different imaging applications require different positions of this dynamic equilibrium, and an adjustment of the equilibrium poses a challenge for the design of suitable probes. We describe here how the conversion of the ortho-carboxy moiety of a given rhodamine into substituted acyl benzenesulfonamides and alkylamides permits the systematic tuning of the equilibrium of spirocyclization with unprecedented accuracy and over a large range. This allows one to transform the same rhodamine into either a highly fluorogenic and cell-permeable probe for live-cell-stimulated emission depletion (STED) microscopy or a spontaneously blinking dye for single-molecule localization microscopy (SMLM). We used this approach to generate differently colored probes optimized for different labeling systems and imaging applications.

AMER CHEMICAL SOC2021

In Vitro-Evolved Peptides Bind Monomeric Actin and Mimic Actin-Binding Protein Thymosin-β4

Davide Bertoldo, Raphael Johannes Gübeli, Christian Heinis, Ganesh Kumar Mothukuri, Jonas Alfred Karl Wilbs

Actin is the most abundant protein in eukaryotic cells and is key to many cellular functions. The filamentous form of actin (F-actin) can be studied with help of natural products that specifically recognize it, as for example fluorophore-labeled probes of the bicyclic peptide phalloidin, but no synthetic probes exist for the monomeric form of actin (G-actin). Herein, we have panned a phage display library consisting of more than 10 billion bicyclic peptides against G-actin and isolated binders with low nanomolar affinity and greater than 1000-fold selectivity over F-actin. Sequence analysis revealed a strong similarity to a region of thymosin-β4, a protein that weakly binds G-actin, and competition binding experiments confirmed a common binding region at the cleft between actin subdomains 1 and 3. Together with F-actin-specific peptides that we also isolated, we evaluated the G-actin peptides as probes in pull-down, imaging, and competition binding experiments. While the F-actin peptides were applied successfully for capturing actin in cell lysates and for imaging, the G-actin peptides did not bind in the cellular context, most likely due to competition with thymosin-β4 or related endogenous proteins for the same binding site.

2021

Towards the Development of Orally Available Peptide Therapeutics

Christian Heinis, Xudong Kong

Peptides have a number of attractive properties that make them an interesting modality for drug development, including their ability to bind challenging targets, their high target specificity, and their non-toxic metabolic products. However, a major limitation of peptides as drugs is their typically poor oral availability, hindering their convenient and flexible application as pills. Of the more than 60 approved peptide drugs, the large majority is not orally applicable. The oral delivery of peptides is hampered by their metabolic instability and/or limited intestinal uptake. In this article, we review the barriers peptides need to overcome after their oral administration to reach disease targets, we highlight two recent successes of pharma companies in developing orally applicable peptide drugs, and we discuss efforts of our laboratory towards the generation of bioavailable cyclic peptides.

2021

SLC25A51 is a mammalian mitochondrial NAD(+) transporter

Kai Johnsson, Liang Wang

Mitochondria require nicotinamide adenine dinucleotide (NAD(+)) to carry out the fundamental processes that fuel respiration and mediate cellular energy transduction. Mitochondrial NAD(+) transporters have been identified in yeast and plants(1,2), but their existence in mammals remains controversial(3-5). Here we demonstrate that mammalian mitochondria can take up intact NAD(+), and identify SLC25A51 (also known as MCART1)-an essential(6,7) mitochondrial protein of previously unknown function-as a mammalian mitochondrial NAD(+) transporter. Loss of SLC25A51 decreases mitochondrial-but not whole-cell-NAD(+) content, impairs mitochondrial respiration, and blocks the uptake of NAD(+) into isolated mitochondria. Conversely, overexpression of SLC25A51 or SLC25A52 (a nearly identical paralogue of SLC25A51) increases mitochondrial NAD(+) levels and restores NAD(+) uptake into yeast mitochondria lacking endogenous NAD(+) transporters. Together, these findings identify SLC25A51 as a mammalian transporter capable of importing NAD(+) into mitochondria.

NATURE RESEARCH2020

Protein Engineering Laboratory

Fluorescent D-Amino Acids for Super-resolution Microscopy of the Bacterial Cell Wall

Solid-phase peptide synthesis on disulfide-linker resin followed by reductive release affords pure thiol-functionalized peptides

Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale

Cyclative Release Strategy to Obtain Pure Cyclic Peptides Directly from the Solid Phase

Systematic Tuning of Rhodamine Spirocyclization for Super-resolution Microscopy

Chemical Biology and Drug Discovery Symposium at the LS2 Annual Meeting 2021

In Vitro-Evolved Peptides Bind Monomeric Actin and Mimic Actin-Binding Protein Thymosin-β4

Towards the Development of Orally Available Peptide Therapeutics

SLC25A51 is a mammalian mitochondrial NAD(+) transporter

Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale

Solid-phase peptide synthesis on disulfide-linker resin followed by reductive release affords pure thiol-functionalized peptides

Fluorescent D-Amino Acids for Super-resolution Microscopy of the Bacterial Cell Wall

Systematic Tuning of Rhodamine Spirocyclization for Super-resolution Microscopy

Chemical Biology and Drug Discovery Symposium at the LS2 Annual Meeting 2021

SLC25A51 is a mammalian mitochondrial NAD(+) transporter

Cyclative Release Strategy to Obtain Pure Cyclic Peptides Directly from the Solid Phase

In Vitro-Evolved Peptides Bind Monomeric Actin and Mimic Actin-Binding Protein Thymosin-β4

Towards the Development of Orally Available Peptide Therapeutics