Fragment-Based Stabilizers of Protein–Protein Interactions through Imine-Based Tethering

Small-molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom-up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine-forming fragments. The imine bond offers a covalent anchor for site-directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65-subunit-derived peptide of NF-κB with the adapter protein 14-3-3. Those fragments that subsequently establish contacts with the p65-derived peptide, rather than with 14-3-3, efficiently stabilize the 14-3-3/p65 complex and offer novel starting points for molecular glues.     

Design of Drug-Like Protein–Protein Interaction Stabilizers Guided By Chelation-Controlled Bioactive Conformation Stabilization

Protein–protein interactions (PPIs) of 14-3-3 proteins are a model system for studying PPI stabilization. The complex natural product Fusicoccin A stabilizes many 14-3-3 PPIs but is not amenable for use in SAR studies, motivating the search for more drug-like chemical matter. However, drug-like 14-3-3 PPI stabilizers enabling such studies have remained elusive. An X-ray crystal structure of a PPI in complex with an extremely low potency stabilizer uncovered an unexpected non-protein interacting, ligand-chelated Mg²⁺ leading to the discovery of metal-ion-dependent 14-3-3 PPI stabilization potency. This originates from a novel chelation-controlled bioactive conformation stabilization effect. Metal chelation has been associated with pan-assay interference compounds (PAINS) and frequent hitter behavior, but chelation can evidently also lead to true potency gains and find use as a medicinal chemistry strategy to guide compound optimization. To demonstrate this, we exploited the effect to design the first potent, selective, and drug-like 14-3-3 PPI stabilizers.     

Rationally Designed Semisynthetic Natural Product Analogues for Stabilization of 14‐3‐3 Protein–Protein Interactions

The natural product family of fusicoccanes are stabilizers of 14‐3‐3 mediated protein–protein interactions (PPIs), some of which possess antitumor activity. In this study, the first use of molecular dynamics (MD) to rationally design PPI stabilizers with increased potency is presented. Synthesis of a focused library, with subsequent characterization by fluorescence polarization, mutational studies, and X‐ray crystallography confirmed the power of the MD‐based design approach, revealing the potential for an additional hydrogen bond with the 14‐3‐3 protein to lead to significantly increased potency. Additionally, these compounds exert their action in a cellular environment with increased potency. The newly found polar interaction could provide an anchoring point for new small‐molecule PPI stabilizers. These results facilitate the development of fusicoccanes towards drugs or tool compounds, as well as allowing the study of the fundamental principles behind PPI stabilization.     

Linking Chemical Fragments, “Gluing” Protein Complexes,Connecting across Cultures

This invited Team Profile was created by Michelle Arkin and Adam Renslo from the University of California, San Francisco in the USA and Luc Brunsveld and Christian Ottmann from the Eindhoven University of Technology in the Netherlands. They recently published an article on designing molecular glues for the 14-3-3/estrogen receptor (ER) protein-protein interaction (PPI). Molecular glues increase the binding between two proteins by binding at the PPI interface. While they hold exciting promise to induce new biology and treat disease, systematic approaches to discover glues are just becoming available. Fragment-based drug discovery has been used to discover inhibitors of PPI; here, the team demonstrated a fragment discovery and linking strategy to create a new molecular glue for 14-3-3/ER, an anticancer target. “From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions though Fragment Linking”, E. J. Visser, P. Jaishankar, E. Sijbesma, M. A. M. Pennings, E. M. F. Vandenboorn, X. Guillory, R. J. Neitz, J. Morrow, S. Dutta, A. R. Renslo, L. Brunsveld, M. R. Arkin, C. Ottmann, Angew. Chem. Int. Ed. 2023 , 62, e202308004 .     

Constrained Peptides with Target‐Adapted Cross‐Links as Inhibitors of a Pathogenic Protein–Protein Interaction

Bioactive conformations of peptides can be stabilized by macrocyclization, resulting in increased target affinity and activity. Such macrocyclic peptides proved useful as modulators of biological functions, in particular as inhibitors of protein–protein interactions (PPI). However, most peptide‐derived PPI inhibitors involve stabilized α‐helices, leaving a large number of secondary structures unaddressed. Herein, we present a rational approach towards stabilization of an irregular peptide structure, using hydrophobic cross‐links that replace residues crucially involved in target binding. The molecular basis of this interaction was elucidated by X‐ray crystallography and isothermal titration calorimetry. The resulting cross‐linked peptides inhibit the interaction between human adaptor protein 14‐3‐3 and virulence factor exoenzyme S. Taking into consideration that irregular peptide structures participate widely in PPIs, this approach provides access to novel peptide‐derived inhibitors.     

A Supramolecular Stabilizer of the 14‐3‐3ζ/ERα Protein‐Protein Interaction with a Synergistic Mode of Action

We report on a stabilizer of the interaction between 14‐3‐3ζ and the Estrogen Receptor alpha (ERα). ERα is a driver in the majority of breast cancers and 14‐3‐3 proteins are negative regulators of this nuclear receptor, making the stabilization of this protein‐protein interaction (PPI) an interesting strategy. The stabilizer ( 1 ) consists of three symmetric peptidic arms containing an arginine mimetic, previously described as the GCP motif. 1 stabilizes the 14‐3‐3ζ/ERα interaction synergistically with the natural product Fusicoccin‐A and was thus hypothesized to bind to a different site. This is supported by computational analysis of 1 binding to the binary complex of 14‐3‐3 and an ERα‐derived phosphopeptide. Furthermore, 1 shows selectivity towards 14‐3‐3ζ/ERα interaction over other 14‐3‐3 client‐derived phosphomotifs. These data provide a solid support of a new binding mode for a supramolecular 14‐3‐3ζ/ERα PPI stabilizer.     

Biosensor-based small molecule fragment screening with biolayer interferometry

Biosensor-based fragment screening is a valuable tool in the drug discovery process. This method is advantageous over many biochemical methods because primary hits can be distinguished from non-specific or non-ideal interactions by examining binding profiles and responses, resulting in reduced false-positive rates. Biolayer interferometry (BLI), a technique that measures changes in an interference pattern generated from visible light reflected from an optical layer and a biolayer containing proteins of interest, is a relatively new method for monitoring small molecule interactions. The BLI format is based on a disposable sensor that is immersed in 96-well or 384-well plates. BLI has been validated for small molecule detection and fragment screening with model systems and well-characterized targets where affinity constants and binding profiles are generally similar to those obtained with surface plasmon resonsance (SPR). Screens with challenging targets involved in protein–protein interactions including BCL-2, JNK1, and eIF4E were performed with a fragment library of 6,500 compounds, and hit rates were compared for these targets. For eIF4E, a protein containing a PPI site and a nucleotide binding site, results from a BLI fragment screen were compared to results obtained in biochemical HTS screens. Overlapping hits were observed for the PPI site, and hits unique to the BLI screen were identified. Hit assessments with SPR and BLI are described.     

A Supramolecular Stabilizer of the 14-3-3ζ/ERα Protein-Protein Interaction with a Synergistic Mode of Action

We report on a stabilizer of the interaction between 14-3-3ζ and the Estrogen Receptor alpha (ERα). ERα is a driver in the majority of breast cancers and 14-3-3 proteins are negative regulators of this nuclear receptor, making the stabilization of this protein-protein interaction (PPI) an interesting strategy. The stabilizer ( 1 ) consists of three symmetric peptidic arms containing an arginine mimetic, previously described as the GCP motif. 1 stabilizes the 14-3-3ζ/ERα interaction synergistically with the natural product Fusicoccin-A and was thus hypothesized to bind to a different site. This is supported by computational analysis of 1 binding to the binary complex of 14-3-3 and an ERα-derived phosphopeptide. Furthermore, 1 shows selectivity towards 14-3-3ζ/ERα interaction over other 14-3-3 client-derived phosphomotifs. These data provide a solid support of a new binding mode for a supramolecular 14-3-3ζ/ERα PPI stabilizer.     

An optimised small-molecule stabiliser of the 14-3-3-PMA2 protein-protein interaction

Modulation of protein-protein interactions (PPIs) is a highly demanding, but also a very promising approach in chemical biology and targeted drug discovery. In contrast to inhibiting PPIs with small, chemically tractable molecules, stabilisation of these interactions can only be achieved with complex natural products, like rapamycin, FK506, taxol, forskolin, brefeldin and fusicoccin. Fusicoccin stabilises the activatory complex of the plant H(+)-ATPase PMA2 and 14-3-3 proteins. Recently, we have shown that the stabilising effect of fusicoccin could be mimicked by a trisubstituted pyrrolinone (pyrrolidone1, 1). Here, we report the synthesis, functional activity and crystal structure of derivatives of 1 that stabilise the 14-3-3-PMA2 complex. With a limited compound collection three modifications that are important for activity enhancement could be determined: 1) conversion of the pyrrolinone scaffold into a pyrazole, 2) introduction of a tetrazole moiety to the phenyl ring that contacts PMA2, and 3) addition of a bromine to the phenyl ring that exclusively contacts the 14-3-3 protein. The crystal structure of a pyrazole derivative of 1 in complex with 14-3-3 and PMA2 revealed that the more rigid core of this molecule positions the stabiliser deeper into the rim of the interface, enlarging especially the contact surface to PMA2. Combination of the aforementioned features gave rise to a molecule (37) that displays a threefold increase in stabilising the 14-3-3-PMA2 complex over 1. Compound 37 and the other active derivatives show no effect on two other important 14-3-3 protein-protein interactions, that is, with CRaf and p53. This is the first study that describes the successful optimisation of a PPI stabiliser identified by screening.     

Automated site-directed drug design: The generation of a basic set of fragments to be used for automated structure assembly

Summary If a method is to be developed to assemble putative ligands structures in site-directed drug design, from molecular graphs generated in the site, then basic building blocks are needed. Structure assembly is a combinatoric process that needs to be optimised if it is to be tractable. What has to be determined is whether small molecular fragments can have transferable properties from one molecule to another. In this paper we determine all possible combinations of 3-, 4- and 5-atom aliphatic fragments from a small set of atoms H, C, N, O, F or Cl. The frequency of occurrence of these candidate fragments is searched for in the Cambridge Structural Database. A similar analysis is performed on charged fragments. A more restricted search is carried out for P and S and aromatic structures. A basic set of fragments can be derived that have a significant frequency in known crystal structures. The transferability of fragment properties is discussed in subsequent papers.     

Semisynthesis II - formation of a covalently linked 1–12/106–129 -fragment of hen egg-white lysozyme

Methoxycarbonylsulphenyl chloride has been shown to cleave reduced Hen egg-white lysozyme into two fragments, rather than the 1–12, 13–105 and 106–129 fragments which would have been anticipated. The covalently linked 1–12/106–129 and 13-105 fragments are produced by initial cleavage at methionines 12 and 105 resulting in the generation of two homoserine lactone residues in place of the methionines. The homoserine lactone at position 12 then couples to the alpha amino group of asparagine-106 to give a covalently linked 1–12/106–129 fragment which has been characterised by a variety of techniques.     

Double anomeric effects and a hydrogen‐bonded supramolecular motif in N,N′‐bis(3‐nitrophenyl)methanediamine

In the title compound, C₁₃H₁₂N₄O₄, the molecule lies on a crystallographic twofold axis. Molecules are linked into complex sheets parallel to (100) via one N—H...O and two C—H...O hydrogen bonds. Within the molecule, the 3‐nitroanilino fragment is essentially planar, and the C—N—C—N—C fragment assumes a nearly perpendicular/perpendicular conformation, with C—N—C—N torsion angles of 81.18 (18)°, which is controlled by a pair of adjacent anomeric interactions. The findings constitute the first demonstration of two anomeric effects existing in one N—C—N unit.     

Inhibitor mediated protein degradation

The discovery of drugs that cause the degradation of their target proteins has been largely serendipitous. Here we report that the tert-butyl carbamate-protected arginine (Boc(3)Arg) moiety provides a general strategy for the design of degradation-inducing inhibitors. The covalent inactivators ethacrynic acid and thiobenzofurazan cause the specific degradation of glutathione-S-transferase when linked to Boc(3)Arg. Similarly, the degradation of dihydrofolate reductase is induced when cells are treated with the noncovalent inhibitor trimethoprim linked to Boc(3)Arg. Degradation is rapid and robust, with 30%-80% of these abundant target proteins consumed within 1.3-5 hr. The proteasome is required for Boc(3)Arg-mediated degradation, but ATP is not necessary and the ubiquitin pathways do not appear to be involved. These results suggest that the Boc(3)Arg moiety may provide a general strategy to construct inhibitors that induce targeted protein degradation.     

The nature of interactions in the ionic crystal of 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium

The hybrid variation -- perturbation many-body interaction energy decomposition scheme has been applied to analyze the physical nature of interactions in the ionic 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium crystal, which can be regarded as a model for a large group of aromatic quaternary nitrogen salts. In the crystal structure the sodium ions and water molecules of adjacent unit cells form a positively charged "inorganic layer" with the sodium ions clustered together along the ab faces with the organic (negative) part in between. This puzzling crystal packing is due to a strong favorable interaction between the water molecule and the sodium ions and a substantial charge transfer from the carbanions that balances out the destabilizing sodium-sodium ion repulsion. Although the majority of cohesion energy of the crystal structure comes from the electrostatic interactions of ions, the resulting net stabilization also depends heavily on the nonadditive delocalization components, due to a counterbalance between the two-body delocalization and exchange effects. The estimated nonadditivity of interactions varies between 12% and 22%.     

Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I(3) and the single-component molecular conductor [Au(tmdt)(2)]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.     

Polyoxoanions functionalized by diorganotin groups: the tetrameric, chiral tungstoarsenate(III), [{Sn(CH3)2(H2O)}2{Sn(CH3)2}As3(alpha-AsW9O33)4]21-

The tetrameric, hybrid organic-inorganic tungstoarsenate(III) [{Sn(CH3)2(H2O)}2{Sn(CH3)2}As3(alpha-AsW9O33)4]21- is composed of four (B-alpha-AsW9O33) fragments that are linked by three dimethyltin groups and three As(III) atoms resulting in an unprecedented, chiral polyoxoanion assembly with C1 symmetry.     

Expanding medicinal chemistry into 3D space: metallofragments as 3D scaffolds for fragment-based drug discovery

Fragment-based drug discovery (FBDD) is a powerful strategy for the identification of new bioactive molecules. FBDD relies on fragment libraries, generally of modest size, but of high chemical diversity. Although good chemical diversity in FBDD libraries has been achieved in many respects, achieving shape diversity – particularly fragments with three-dimensional (3D) structures – has remained challenging. A recent analysis revealed that >75% of all conventional, organic fragments are predominantly 1D or 2D in shape. However, 3D fragments are desired because molecular shape is one of the most important factors in molecular recognition by a biomolecule. To address this challenge, the use of inert metal complexes, so-called ‘metallofragments’ (mFs), to construct a 3D fragment library is introduced. A modest library of 71 compounds has been prepared with rich shape diversity as gauged by normalized principle moment of inertia (PMI) analysis. PMI analysis shows that these metallofragments occupy an area of fragment space that is unique and highly underrepresented when compared to conventional organic fragment libraries that are comprised of orders of magnitude more molecules. The potential value of this metallofragment library is demonstrated by screening against several different types of proteins, including an antiviral, an antibacterial, and an anticancer target. The suitability of the metallofragments for future hit-to-lead development was validated through the determination of IC₅₀ and thermal shift values for select fragments against several proteins. These findings demonstrate the utility of metallofragment libraries as a means of accessing underutilized 3D fragment space for FBDD against a variety of protein targets.

Fragment-based drug discovery (FBDD) using 3-dimensional metallofragments is a new strategy for the identification of bioactive molecules.     

Novel strategy for three-dimensional fragment-based lead discovery

Fragment-based drug design (FBDD) is considered a promising approach in lead discovery. However, for a practical application of this approach, problems remain to be solved. Hence, a novel practical strategy for three-dimensional lead discovery is presented in this work. Diverse fragments with spatial positions and orientations retained in separately adjacent regions were generated by deconstructing well-aligned known inhibitors in the same target active site. These three-dimensional fragments retained their original binding modes in the process of new molecule construction by fragment linking and merging. Root-mean-square deviation (rmsd) values were used to evaluate the conformational changes of the component fragments in the final compounds and to identify the potential leads as the main criteria. Furthermore, the successful validation of our strategy is presented on the basis of two relevant tumor targets (CDK2 and c-Met), demonstrating the potential of our strategy to facilitate lead discovery against some drug targets.     

Oligo(p‐phenylene‐ethynylene)‐Derived Super‐π‐Gelators with Tunable Emission and Self‐Assembled Polymorphic Structures

Linear π‐conjugated oligomers are known to form organogels through noncovalent interactions. Herein, we report the effect of π‐repeat units on the gelation and morphological properties of three different oligo(p‐phenylene‐ethynylene)s: OPE3 , OPE5 , and OPE7 . All of these molecules form fluorescent gels in nonpolar solvents at low critical gel concentrations, thereby resulting in a blue gel for OPE3 , a green gel for OPE5 , and a greenish yellow gel for OPE7 . The molecule–molecule and molecule–substrate interactions in these OPEs are strongly influenced by the conjugation length of the molecules. Silicon wafer suppresses substrate–molecule interactions whereas a mica surface facilitates such interactions. At lower concentrations, OPE3 formed vesicular assemblies and OPE5 gave entangled fibers, whereas OPE7 resulted in spiral assemblies on a mica surface. At higher concentrations, OPE3 and OPE5 resulted in super‐bundles of fibers and flowerlike short‐fiber agglomerates when different conditions were applied. The number of polymorphic structures increases on increasing the conjugation length, as seen in the case of OPE7 with n=5, which resulted in a variety of exotic structures, the formation of which could be controlled by varying the substrate, concentration, and humidity.     

Structural analysis of rapamycin and related compounds using [M + Li]+ ions generated by liquid secondary ion mass spectrometry

Cationization of the macrocyclic immunosuppressant rapamycin with lithium ion upon liquid secondary ion mass spectrometric ionization yields a number of fragment ions, which are observable in the full-scan spectrum. These are clearly assigned using B/E linked scanning (fragment ion scanning), B²/E linked scanning (precursor ion scanning) and peak matching for accurate mass measurement. Many of the fragments are produced by processes that open the macrocyclic ring, and it is possible to observe several different pieces of the molecule as fragment ions. The diversity of fragments produced facilitates the elucidation of new rapamycin-like structures through mass spectrometry. Three structurally modified rapamycin analogues have been examined by this technique, and the modifications to the molecule may be located based on the nominal masses of their fragments.