Protein-protein interactions that regulate gene expression in the nucleus are increasingly recognized as potential therapeutic targets but present unique challenges. Effective targeting requires molecules capable of interacting with large protein surfaces while remaining small enough to pass through the nuclear pore, for which peptidomimetics are promising candidates. De novo design strategies often focus on projecting hot-spot residues using well-defined, rigid scaffolds; however, other critical properties-such as solubility, charge, or local flexibility-are often overlooked. Our approach employs α/β-peptidomimetics to enable fine-tuning of these properties by generating manageable-sized soluble libraries. Using the KIX domain of the coactivator proteins p300/CBP as a model system, we demonstrate that our strategy allows modular optimization of hot-spot, solvent-exposed, and structure-inducing residues, thereby tuning affinity and binding-site selectivity. Coactivator proteins often use multivalency to enhance affinity and selectivity, which we exploit by creating dimers from our initial hits. We show that both static libraries and template-directed dynamic covalent chemistry facilitate the screening of multivalent ligands that closely mimic the native interaction partners. Our design strategy, built on α/β-peptide building blocks, represents a promising approach to develop de novo ligands against proteins characterized by high plasticity and multivalent interactions.

Theoretical models of prebiotic evolution propose that catalytic modulation can influence autocatalytic replication cycles. We hypothesized that a protein catalyst could create a favorable environment for proximity-controlled, dissipative replication of primitive peptides. This setup, in principle, allows competitive selection by making the catalyst a limited resource. Here, we show that a structurally flexible and promiscuous protein, calmodulin, catalyzes UVA light-driven replication in a helical foldamer-based replicator system. The protein accelerates both non-autocatalytic synthesis and autocatalytic replication, with autocatalysis being the dominant pathway. The system demonstrates light-intensity-dependent competitive selection, where replicators compete for scarce binding sites on the catalyst. This mechanism enables efficient selection even within a large replicator pool. Our results provide evidence that the specific catalyst-replicator interactions envisioned in Eigen's hypercycle model can be approximated under dissipative conditions in catalyzed primitive replicator systems.

Non-cephem drugs with 1,3-thiazine-derived rings are very rare, although a number of bioactive 1,3-thiazine derivatives are known. Similarly, 1,4-thiazepine-derived drugs are rare, but many 1,4-thiazepine derivatives show interesting biological activities. Therefore, our aim was the synthesis of such N,S-heterocycles using a versatile and short (1–3 steps) literature method. First, a three-component reaction of a cycloalkene, a thioamide, and an aldehyde provided 5,6-dihydro-4H-1,3-thiazines. Afterwards, Staudinger ketene–imine cycloaddition with chloroketene resulted in β-lactam-fused 1,3-thiazinanes. Finally, treatment with sodium methoxide induced ring expansion, yielding 4,5,6,7-tetrahydro-1,4-thiazepines. This synthetic pathway generates 3–5 new chiral centers with the help of pericyclic reactions, and almost every cycloaddition proceeded in a diastereoselective manner. Two-dimensional NOESY as well as single-crystal X-ray diffraction enabled unequivocal determination of the stereochemistry of all synthesized compounds.

In this study, a set of spiro[5,8-methanoquinazoline-2,3′-indoline]-2′,4-dione derivatives 3a–p were synthesized starting from unsubstituted and N-methyl-substituted diendo- and diexo-2-aminonorbornene carboxamides, as well as various substituted isatins. The typical method involves a condensation reaction of alicyclic aminocarboxamide and isatin in the presence of a catalyst, using a solvent and an acceptable temperature. We developed a cost-effective and ecologically benign high-speed ball milling (HSBM), microwave irradiation (MW), and continuous flow (CF) technique to synthesize spiroquinazolinone molecule 3a. The structures of the synthesized compounds 3a–p were determined using 1D and 2D NMR spectroscopies. Furthermore, docking studies and absorption, distribution, metabolism, and toxicity (ADMET) predictions were used in this work. In agreement with the corresponding features found in the case of both the SARS-CoV-2 main protease (RCSB Protein Data Bank: 6LU7) and human mast cell tryptase (RCSB Protein Data Bank: 2ZA5) based on the estimated total energy and binding affinity, H bonds, and hydrophobicity in silico, compound 3d among our 3a–g, 3i–k, and 3m derivatives was found to be our top-rated compound.

Arsenic is highly toxic and a significant threat to human health, but certain bacteria have developed defense mechanisms initiated by As-III binding to As-III-sensing proteins of the ArsR family. The transcriptional regulator AfArsR responds to As-III and Sb-III by coordinating the metalloids with three cysteines, located in a short sequence of the same monomer chain. Here, we characterize the binding of As-III and Hg-II to a model peptide encompassing this fragment of the protein via solution equilibrium and spectroscopic/spectrometric techniques (pH potentiometry, UV, CD, NMR, PAC, EXAFS, and ESI-MS) combined with DFT calculations and MD simulations. Coordination of As-III changes the peptide structure from a random-coil to a well-defined structure of the complex. A trigonal pyramidal AsS3 binding site is formed with almost exactly the same structure as observed in the crystal structure of the native protein, implying that the peptide possesses all of the features required to mimic the As-III recognition and response selectivity of AfArsR. Contrary to this, binding of Hg-II to the peptide does not lead to a well-defined structure of the peptide, and the atoms near the metal binding site are displaced and reoriented in the Hg-II model. Our model study suggests that structural organization of the metal site by the inducer ion is a key element in the mechanism of the metalloid-selective recognition of this protein.

Current methods for proteomimetic engineering rely on structure-based design. Here we describe a design strategy that allows the construction of proteomimetics against challenging targets without a priori characterization of the target surface. Our approach employs (i) a 100-membered photoreactive foldamer library, the members of which act as local surface mimetics, and (ii) the subsequent affinity maturation of the primary hits using systems chemistry. Two surface-oriented proteinogenic side chains drove the interactions between the short helical foldamer fragments and the proteins. Diazirine-based photo-crosslinking was applied to sensitively detect and localize binding even to shallow and dynamic patches on representatively difficult targets. Photo-foldamers identified functionally relevant protein interfaces, allosteric and previously unexplored targetable regions on the surface of STAT3 and an oncogenic K-Ras variant. Target-templated dynamic linking of foldamer hits resulted in two orders of magnitude affinity improvement in a single step. The dimeric K-Ras ligand mimicked protein-like catalytic functions. The photo-foldamer approach thus enables the highly efficient mapping of protein-protein interaction sites and provides a viable starting point for proteomimetic ligand development without a priori structural hypotheses.

Single-stranded DNA-binding protein (SSB) is a bacterial interaction hub and an appealing target for antimicrobial therapy. Understanding the structural adaptation of the disordered SSB C-terminus (SSB-Ct) to DNA metabolizing enzymes (e.g., ExoI and RecO) is essential for designing high-affinity SSB mimetic inhibitors. Molecular dynamics simulations revealed the transient interactions of SSB-Ct with two hot spots on ExoI and RecO. The residual flexibility of the peptide–protein complexes allows adaptive molecular recognition. Scanning with non-canonical amino acids revealed that modifications at both termini of SSB-Ct could increase the affinity, supporting the two-hot-spot binding model. Combining unnatural amino acid substitutions on both segments of the peptide resulted in enthalpy-enhanced affinity, accompanied by enthalpy–entropy compensation, as determined by isothermal calorimetry. NMR data and molecular modeling confirmed the reduced flexibility of the improved affinity complexes. Our results highlight that the SSB-Ct mimetics bind to the DNA metabolizing targets through the hot spots, interacting with both of segments of the ligands.

The concept of chemically evolvable replicators is central to abiogenesis. Chemical evolvability requires three essential components: energy-harvesting mechanisms for nonequilibrium dissipation, kinetically asymmetric replication and decomposition pathways, and structure-dependent selective templating in the autocatalytic cycles. We observed a UVA light-fueled chemical system displaying sequence-dependent replication and replicator decomposition. The system was constructed with primitive peptidic foldamer components. The photocatalytic formation-recombination cycle of thiyl radicals was coupled with the molecular recognition steps in the replication cycles. Thiyl radical-mediated chain reaction was responsible for the replicator death mechanism. The competing and kinetically asymmetric replication and decomposition processes led to light intensity-dependent selection far from equilibrium. Here, we show that this system can dynamically adapt to energy influx and seeding. The results highlight that mimicking chemical evolution is feasible with primitive building blocks and simple chemical reactions.

Evolvability of the chemical replicator systems requires non-equilibrium energy dissipation, effective death pathways and transfer of structural information in the autocatalytic cycles. We engineered a chemical network with peptidic foldamer components, where UV light fuelled dissipative sequence-dependent exponential replication and replicator decomposition. The light-harvesting formation-recombination cycle of the thiyl radicals was coupled with the molecular recognition steps in the replication cycles. Thiyl radical-mediated chain reaction was responsible for the replicator death. The competing and kinetically asymmetric replication and decomposition processes led to light intensity-dependent selection and competitive exclusion. Dynamic adaptation to the energy input and the selection factor maximised the dissipation rate in the regime of exponential growth. The results contribute to the development of chemically evolvable replicator systems.

Ubiquitination of proliferating cell nuclear antigen (PCNA) triggers pathways of DNA damage tolerance, including mutagenic translesion DNA synthesis, and comprises a cascade of reactions involving the E1 ubiquitin-activating enzyme Uba1, the E2 ubiquitin-conjugating enzyme Rad6, and the E3 ubiquitin ligase Rad18. We report here the discovery of a series of xanthenes that inhibit PCNA ubiquitination, Rad6∼ubiquitin thioester formation, and the Rad6–Rad18 interaction. Structure-activity relationship experiments across multiple assays reveal chemical and structural features important for different activities along the pathway to PCNA ubiquitination. The compounds that inhibit these processes are all a subset of the xanthen-3-ones we tested. These small molecules thus represent first-in-class probes of Rad6 function and the association of Rad6 and Rad18, the latter being a new inhibitory activity discovered for a small molecule, in the PCNA ubiquitination cascade and potential therapeutic agents to contain cancer progression.

The fragment-centric design promises a means to develop complex xenobiotic protein surface mimetics, but it is challenging to find locally biomimetic structures. To address this issue, foldameric local surface mimetic (LSM) libraries were constructed. Protein affinity patterns, ligand promiscuity and protein druggability were evaluated using pull-down data for targets with various interaction tendencies and levels of homology. LSM probes based on H14 helices exhibited sufficient binding affinities for the detection of both orthosteric and non-orthosteric spots, and overall binding tendencies correlated with the magnitude of the target interactome. Binding was driven by two proteinogenic side chains and LSM probes could distinguish structurally similar proteins with different functions, indicating limited promiscuity. Binding patterns displayed similar side chain enrichment values to those for native protein-protein interfaces implying locally biomimetic behavior. These analyses suggest that in a fragment-centric approach foldameric LSMs can serve as useful probes and building blocks for undruggable protein interfaces.

We developed and implemented a reconstituted system to screen for modulators of the ubiquitination of proliferating cell nuclear antigen, a process that activates pathways of DNA damage tolerance and drug resistance. We identified the primary putatively health-beneficial green tea polyphenol epigallocatechin gallate (EGCG) and certain related small molecules as potent inhibitors of ubiquitination. EGCG directly and reversibly targets the ubiquitin-activating enzyme Uba1, blocking formation of the Uba1~ubiquitin thioester conjugate and thus ubiquitination and in the cell. Structure–activity relationship profiles across multiple biochemical and cellular assays for a battery of EGCG analogues revealed distinct chemical and mechanism-of-action clusters of molecules, with catechin gallates, alkyl gallates, and myricetin potently inhibiting ubiquitination. This study defines a number of related though distinct first-in-class inhibitors of ubiquitination, each series with its own unique activity pattern and mechanistic signature.

Melampyrum barbatum Waldst. & Kit. ex Willd. (Scrophulariaceae) has been used in traditional medicine for the treatment of rheumatic complaints and different skin diseases. In the course of our study the anti-inflammatory activity of the aerial parts of M barbatum was evaluated. A MeOH extract was prepared and consecutively partitioned with CHCl3, EtOAc and n-BuOH. The fractions were assayed in in vivo carrageenan-induced rat paw oedema model. The intraperitoneally administered n-BuOH phase exerted marked inhibitory effect (33.6 %, p < 0.01). Multistep chromatographic separation afforded mussaenoside and aucubine from n-BuOH fraction. Moreover, 8-epiloganin, loganic acid and mussaenoside were obtained from EtOAc fraction and apigenin, luteolin, benzoic acid and galactitol from CHCl3 fraction. These data validate the ethnomedicinal use of M barbatum for the treatment of inflammatory diseases and reveal that iridoids and flavonoids could be responsible for the anti-inflammatory effect of this species.

Melampyrum barbatum Waldst. & Kit. ex Willd. (Scrophulariaceae) has been used in traditional medicine for the treatment of rheumatic complaints and different skin diseases. In the course of our study the anti-inflammatory activity of the aerial parts of M. barbatum was evaluated. A MeOH extract was prepared and consecutively partitioned with CHCl 3 , EtOAc and n -BuOH. The fractions were assayed in in vivo carrageenan-induced rat paw oedema model. The intraperitoneally administered n -BuOH phase exerted marked inhibitory effect (33.6 %, p < 0.01). Multistep chromatographic separation afforded mussaenoside and aucubine from n -BuOH fraction. Moreover, 8-epiloganin, loganic acid and mussaenoside were obtained from EtOAc fraction and apigenin, luteolin, benzoic acid and galactitol from CHCl 3 fraction. These data validate the ethnomedicinal use of M. barbatum for the treatment of inflammatory diseases and reveal that iridoids and flavonoids could be responsible for the anti-inflammatory effect of this species.

Engineering water-soluble stand-alone β-sandwich mimetics is a current challenge because of the difficulties associated with tailoring long-range interactions. In this work, single cis-(1R,2S)-2-aminocyclohexanecarboxylic acid mutations were introduced into the edge strands of the eight-stranded β-sandwich mimetic structures from the betabellin family. Temperature-dependent NMR and CD measurements, together with thermodynamic analyses, demonstrated that the modified peripheral strands exhibited an irregular and partially disordered structure but were able to exert sufficient shielding on the hydrophobic core to retain the predominantly β-sandwich structure. Although the frustrated interactions decreased the free energy of unfolding, the temperature of the maximum stabilities increased to or remained at physiologically relevant temperatures. We found that the irregular peripheral strands were able to prevent edge-to-edge association and fibril formation in the aggregation-prone model. These findings establish a β-sandwich stabilization and aggregation inhibition approach, which does not interfere with the pillars of the peptide bond or change the net charge of the peptide.

A ZnCl2-catalyzed diastereoselective Joullié-Ugi three-component reaction from 2 H-azirines, isocyanides, and carboxylic acids was established. The protocol allows the preparation of highly and diversely functionalized N-acylaziridine-2-carboxamide derivatives in up to 82% isolated yields. Moreover, the applicability of N-acylaziridines is demonstrated through a variety of transformations.