Continuous evolution of compact protein degradation tags regulated by selective molecular glues.

Conditional protein degradation tags (degrons) are usually >100 amino acids long or are triggered by small molecules with substantial off-target effects, thwarting their use as specific modulators of endogenous protein levels. We developed a phage-assisted continuous evolution platform for molecular glue complexes (MG-PACE) and evolved a 36-amino acid zinc finger (ZF) degron (SD40) that binds the ubiquitin ligase substrate receptor cereblon in complex with PT-179, an orthogonal thalidomide derivative. Endogenous proteins tagged in-frame with SD40 using prime editing are degraded by otherwise inert PT-179. Cryo-electron microscopy structures of SD40 in complex with ligand-bound cereblon revealed mechanistic insights into the molecular basis of SD40's activity and specificity. Our efforts establish a system for continuous evolution of molecular glue complexes and provide ZF tags that overcome shortcomings associated with existing degrons.

Proteolysis-targeting chimeras with reduced off-targets.

Proteolysis-targeting chimeras (PROTACs) are molecules that induce proximity between target proteins and E3 ligases triggering target protein degradation. Pomalidomide, a widely used E3 ligase recruiter in PROTACs, can independently degrade other proteins, including zinc-finger (ZF) proteins, with vital roles in health and disease. This off-target degradation hampers the therapeutic applicability of pomalidomide-based PROTACs, requiring development of PROTAC design rules that minimize off-target degradation. Here we developed a high-throughput platform that interrogates off-target degradation and found that reported pomalidomide-based PROTACs induce degradation of several ZF proteins. We generated a library of pomalidomide analogues to understand how functionalizing different positions of the phthalimide ring, hydrogen bonding, and steric and hydrophobic effects impact ZF protein degradation. Modifications of appropriate size on the C5 position reduced off-target ZF degradation, which we validated through target engagement and proteomics studies. By applying these design principles, we developed anaplastic lymphoma kinase oncoprotein-targeting PROTACs with enhanced potency and minimal off-target degradation.

Small-molecule binding and sensing with a designed protein family.

Despite transformative advances in protein design with deep learning, the design of small-molecule-binding proteins and sensors for arbitrary ligands remains a grand challenge. Here we combine deep learning and physics-based methods to generate a family of proteins with diverse and designable pocket geometries, which we employ to computationally design binders for six chemically and structurally distinct small-molecule targets. Biophysical characterization of the designed binders revealed nanomolar to low micromolar binding affinities and atomic-level design accuracy. The bound ligands are exposed at one edge of the binding pocket, enabling the de novo design of chemically induced dimerization (CID) systems; we take advantage of this to create a biosensor with nanomolar sensitivity for cortisol. Our approach provides a general method to design proteins that bind and sense small molecules for a wide range of analytical, environmental, and biomedical applications.

Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing.

The targeted deletion, replacement, integration or inversion of genomic sequences could be used to study or treat human genetic diseases, but existing methods typically require double-strand DNA breaks (DSBs) that lead to undesired consequences, including uncontrolled indel mixtures and chromosomal abnormalities. Here we describe twin prime editing (twinPE), a DSB-independent method that uses a prime editor protein and two prime editing guide RNAs (pegRNAs) for the programmable replacement or excision of DNA sequences at endogenous human genomic sites. The two pegRNAs template the synthesis of complementary DNA flaps on opposing strands of genomic DNA, which replace the endogenous DNA sequence between the prime-editor-induced nick sites. When combined with a site-specific serine recombinase, twinPE enabled targeted integration of gene-sized DNA plasmids (>5,000 bp) and targeted sequence inversions of 40 kb in human cells. TwinPE expands the capabilities of precision gene editing and might synergize with other tools for the correction or complementation of large or complex human pathogenic alleles.

Enantioselective Cyclobutenylation of Olefins Using N-Sulfonyl-1,2,3-Triazoles as Vicinal Dicarbene Equivalents.

Cyclobutenes are highly useful synthetic intermediates as well as important motifs in bioactive small molecules. Herein, we report a regio-, chemo-, and enantioselective synthesis of cyclobutenes from olefins using N-sulfonyl-1,2,3-triazoles as vicinal dicarbene equivalents or alkyne [2 + 2] cycloaddition surrogates. Terminal and cis-olefins can be transformed into enantioenriched cyclopropanes via rhodium catalysis. Then, in one pot, treatment of these intermediates with tosyl hydrazide and base effects diazo formation followed by rhodium-catalyzed ring expansion to yield enantioenriched cyclobutenes. These cyclobutenes can be transformed into highly substituted, enantioenriched cyclobutanes, including structures relevant to natural product scaffolds.

The cascade unzipping of ladderane reveals dynamic effects in mechanochemistry.

Force can induce remarkable non-destructive transformations along a polymer, but we have a limited understanding of the energy transduction and product distribution in tandem mechanochemical reactions. Ladderanes consist of multiple fused cyclobutane rings and have recently been used as monomeric motifs to develop polymers that drastically change their properties in response to force. Here we show that [4]-ladderane always exhibits 'all-or-none' cascade mechanoactivations and the same stereochemical distribution of the generated dienes under various conditions and within different polymer backbones. Transition state theory fails to capture the reaction kinetics and explain the observed stereochemical distributions. Ab initio steered molecular dynamics reveals unique non-equilibrium dynamic effects: energy transduction from the first cycloreversion substantially accelerates the second cycloreversion, and bifurcation on the force-modified potential energy surface leads to the product distributions. Our findings illustrate the rich chemistry in closely coupled multi-mechanophores and an exciting potential for effective energy transduction in tandem mechanochemical reactions.

Synthesis and Mechanochemical Activation of Ladderene-Norbornene Block Copolymers.

We have recently reported a polymechanophore system, polyladderene (PLDE), which dramatically transforms into polyacetylene (PA) upon mechanical stimulation. Herein, we optimized conditions to synthesize unprecedented block copolymers (BCPs) containing a force-responsive block by sequential ring-opening metathesis polymerization of different norbornenes and bromoladderene. Successful extension from PLDE to other blocks required careful timing and low temperatures to preserve the reactivity of the PLDE-appended catalyst. The PLDE-containing BCPs were sonochemically activated into visually soluble PA with a maximum absorption λ ≥ 600 nm and unique absorption patterns corresponding to noncontinuous activation of ladderene units. Access to polymechanophore BCPs paves the way for new stress-responsive materials with solution and solid state self-assembly behaviors and incorporation of polymechanophores into other materials.

Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability.

Ladderane lipids are unique to anaerobic ammonium-oxidizing (anammox) bacteria and are enriched in the membrane of the anammoxosome, an organelle thought to compartmentalize the anammox process, which involves the toxic intermediate hydrazine (N2H4). Due to the slow growth rate of anammox bacteria and difficulty of isolating pure ladderane lipids, experimental evidence of the biological function of ladderanes is lacking. We have synthesized two natural and one unnatural ladderane phosphatidylcholine lipids and compared their thermotropic properties in self-assembled bilayers to distinguish between [3]- and [5]-ladderane function. We developed a hydrazine transmembrane diffusion assay using a water-soluble derivative of a hydrazine sensor and determined that ladderane membranes are as permeable to hydrazine as straight-chain lipid bilayers. However, pH equilibration across ladderane membranes occurs 5-10 times more slowly than across straight-chain lipid membranes. Langmuir monolayer analysis and the rates of fluorescence recovery after photobleaching suggest that dense ladderane packing may preclude formation of proton/hydroxide-conducting water wires. These data support the hypothesis that ladderanes prevent the breakdown of the proton motive force rather than blocking hydrazine transmembrane diffusion in anammox bacteria.

Mechanochemical unzipping of insulating polyladderene to semiconducting polyacetylene.

Biological systems sense and respond to mechanical stimuli in a complex manner. In an effort to develop synthetic materials that transduce mechanical force into multifold changes in their intrinsic properties, we report on a mechanochemically responsive nonconjugated polymer that converts to a conjugated polymer via an extensive rearrangement of the macromolecular structure in response to force. Our design is based on the facile mechanochemical unzipping of polyladderene, a polymer inspired by a lipid natural product structure and prepared via direct metathesis polymerization. The resultant polyacetylene block copolymers exhibit long conjugation length and uniform trans-configuration and self-assemble into semiconducting nanowires. Calculations support a tandem unzipping mechanism of the ladderene units.

Chemical Synthesis and Self-Assembly of a Ladderane Phospholipid.

Ladderane lipids produced by anammox bacteria constitute some of the most structurally fascinating yet poorly studied molecules among biological membrane lipids. Slow growth of the producing organism and the inherent difficulty of purifying complex lipid mixtures have prohibited isolation of useful amounts of natural ladderane lipids. We have devised a highly selective total synthesis of ladderane lipid tails and a full phosphatidylcholine to enable biophysical studies on chemically homogeneous samples of these molecules. Additionally, we report the first proof of absolute configuration of a natural ladderane.

Stereocontrolled synthesis of syn-ß-Hydroxy-α-amino acids by direct aldolization of pseudoephenamine glycinamide.

ß-Hydroxy-α-amino acids figure prominently as chiral building blocks in chemical synthesis and serve as precursors to numerous important medicines. Reported herein is a method for the synthesis of ß-hydroxy-α-amino acid derivatives by aldolization of pseudoephenamine glycinamide, which can be prepared from pseudoephenamine in a one-flask protocol. Enolization of (R,R)- or (S,S)-pseudoephenamine glycinamide with lithium hexamethyldisilazide in the presence of LiCl followed by addition of an aldehyde or ketone substrate affords aldol addition products that are stereochemically homologous with L- or D-threonine, respectively. These products, which are typically solids, can be obtained in stereoisomerically pure form in yields of 55-98 %, and are readily transformed into ß-hydroxy-α-amino acids by mild hydrolysis or into 2-amino-1,3-diols by reduction with sodium borohydride. This new chemistry greatly facilitates the construction of novel antibiotics of several different classes.