Coiled coils are a versatile class of α‐helical protein motifs characterized by recurring sequence patterns that direct their assembly into defined oligomeric bundles and underpin a wide range of biological functions. The well‐established sequence‐structure relationships governing coiled‐coil formation enable predictive control over stability, specificity, and oligomerization state, making them attractive and chemically tractable building blocks for biosensor design in applications ranging from single‐molecule detection to synthetic biochemical circuits and functional nanomaterials. After revisiting the theoretical foundations of coiled‐coil architecture, this review outlines strategies to engineer programmable binding interfaces that can be rationally tuned to generate orthogonal, high–affinity interaction pairs, enabling flexible and modular biosensor platforms. Particular emphasis is placed on recent advances in computational and data‐driven design approaches, including machine‐learning and AI‐based strategies, alongside established rational and empirical methods for coiled‐coil construction. These complementary design principles underpin the development of coiled‐coil‐based biosensors and are discussed together with selected application examples to illustrate how engineered coiled‐coil interactions support sensitive and specific molecular recognition as well as switchable control in synthetic biology and chemical biology. Overall, this review highlights coiled coils as programmable, stable, and highly designable scaffolds at the interface of molecular engineering, computation, and chemical biology.
Limitations in the druggability of challenging protein targets, coupled with recognition of the diverse roles of noncoding RNAs in cellular regulation and disease have spurred interest in RNA as a druggable macromolecule. The rapidly emerging field of RNA‐targeted small‐molecule therapeutics is now exploring induced proximity mechanisms in the form of RNA‐targeting chimeras that recruit effector proteins to catalyze RNA decay. Inspired by “molecular glue” natural products such as rapamycin and cyclosporin A, which induce protein–protein interactions to sterically modulate protein function, we propose the new application of immunophilin recruitment to alter RNA function. Here in, we report the design and characterization of heterobifunctional molecules that induce highly cooperative RNA‐FKBP12 ternary complexes and describe efforts to assess their impact on RNA metabolism. We also evaluate applications and report off‐target liabilities associated with the chosen RNA ligand for our heterobifunctional series. Finally, we discuss the challenges faced and highlight opportunities for future success in the RNA space.
Sensitive detection of protease activity in complex biological environments remains challenging due to signal instability, background interference, and the lack of internal calibration. Here, we report a self‐referenced, white‐light–emitting surface defect‐engineered nanocluster assembly for selective and ratiometric detection of proteinase K activity and inhibition. Manganese‐doped, zinc‐mediated gold nanocluster (Zn Au NC) assemblies functionalized with bovine serum albumin (BSA) generate tricolor emission from BSA, the nanocluster core, and Mn 2+ , producing near‐white‐light fluorescence that serves as an intrinsic internal reference. Proteinase K induces coordinated spectral changes, including enhanced and blueshifted BSA emission with simultaneous quenching of Zn Au NC and Mn 2+ emissions, resulting in systematic chromaticity shifts and a robust ratiometric response. Mechanistic studies attribute these changes to proteolytic cleavage of BSA and disruption of the nanocluster assembly, corroborated by circular dichroism measurements. The platform exhibits high selectivity for proteinase K , enables inhibitor detection, and performs reliably in fetal bovine serum. This self‐calibrated nanocluster platform provides a versatile strategy for enzyme‐responsive sensing with potential applications in biochemical diagnostics and inhibitor screening.
Cyclic peptides are powerful scaffolds for chemical biology and drug discovery. Genetically encoded display (phage, ribosome, mRNA, and yeast) enables high‐throughput screening of peptide libraries. Yet expanding their accessible chemical space depends not only on library size but also on the cyclization chemistry, which selects the conformations the library samples and makes linkage choice a primary design variable. Cyclization most often relies on cysteine through disulfides, thiol‐reactive linkers, or metal‐thiolate bonds. Enzymatic head‐to‐tail ligation and noncanonical amino acids (ncAAs) provide cysteine‐free macrocyclization through amide bonds, but each imposes practical limits such as motif constraints or reliance on genetic code expansion. In this perspective, we examine photoinduced aromatic crosslinking as a complementary, cysteine‐independent strategy. Recent fluorotryptophan photochemistry shows that irradiation drives diaryl bond formation between fluorinated tryptophan and proximal phenylalanine or tyrosine, generating intrinsically fluorescent macrocycles and enabling an optical readout of cyclization yield. Fluorotryptophan is a conservative modification that can be introduced at native Trp codons, which may avoid the genetic code expansion. Antimicrobial peptides offer a demanding test case: their function depends on backbone rigidity, amphipathic face presentation, and membrane interaction, all of which an aromatic crosslink could influence.
The high‐risk human papillomavirus (HPV) early protein 6 (E6) viral oncoprotein is a key player in HPV‐mediated cancers and is the major driver of cervical, anal, and a substantial portion of head and neck cancers. HPV E6 recruits the cellular ubiquitin E3‐ligase E6‐associated protein (E6AP), also termed UBE3A, and this E6/E6AP complex in turn recruits the tumor suppressor p53, resulting in the ubiquitin‐mediated degradation of p53. The cysteine‐rich E6 protein presents an attractive target for chemical intervention through covalent, cysteine‐reactive chemistries. While previous studies have uncovered peptidic covalent inhibitors of E6, we sought to determine whether we could identify nonpeptidic functional binders. We screened a library of cysteine‐reactive covalent ligands and identified a pyrazoline hit, EN218, bearing a chloroacetamide cysteine‐reactive warhead. Evaluation of pyrazoline analogs led to the development of an improved molecule, ( S )‐WX48A, that stereoselectively reacted with C58 on E6 to inhibit E6‐mediated p53 ubiquitination. While this molecule is still in an early stage and requires further medicinal chemistry optimization to exert on‐target cellular activity, our study demonstrates that E6 can be directly and stereoselectively targeted with a covalent nonpeptidic small‐molecule and provides a foundation for developing more drug‐like E6 inhibitors for HPV therapy.
