Stabilizer‐Guided Inhibition of Protein–Protein Interactions

The discovery of novel protein–protein interaction (PPI) modulators represents one of the great molecular challenges of the modern era. PPIs can be modulated by either inhibitor or stabilizer compounds, which target different though proximal regions of the protein interface. In principle, protein–stabilizer complexes can guide the design of PPI inhibitors (and vice versa). In the present work, we combine X‐ray crystallographic data from both stabilizer and inhibitor co‐crystal complexes of the adapter protein 14‐3‐3 to characterize, down to the atomic scale, inhibitors of the 14‐3‐3/Tau PPI, a potential drug target to treat Alzheimer’s disease. The most potent compound notably inhibited the binding of phosphorylated full‐length Tau to 14‐3‐3 according to NMR spectroscopy studies. Our work sets a precedent for the rational design of PPI inhibitors guided by PPI stabilizer–protein complexes while potentially enabling access to new synthetically tractable stabilizers of 14‐3‐3 and other PPIs.     

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.     

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.     

Synthesis,and Helix or Hairpin‐Turn Secondary Structures of ‘Mixed’ α/β‐Peptides Consisting of Residues with Proteinogenic Side Chains and of 2‐Amino‐2‐methylpropanoic Acid (Aib)

Twelve peptides, 1 – 12 , have been synthesized, which consist of alternating sequences of α‐ and β‐amino acid residues carrying either proteinogenic side chains or geminal dimethyl groups (Aib). Two peptides, 13 and 14 , containing 2‐methyl‐3‐aminobutanoic acid residues or a ‘random mix’ of α‐, β²‐, and β³‐amino acid moieties were also prepared. The new compounds were fully characterized by CD (Figs. 1 and 2), and ¹H‐ and ¹³C‐NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). In two cases, 3 and 14 , we discovered novel types of turn structures with nine‐ and ten‐membered H‐bonded rings forming the actual turns. In two other cases, 8 and 11 , we found 14/15‐helices, which had been previously disclosed in mixed α/β‐peptides containing unusual β‐amino acids with non‐proteinogenic side chains. The helices are formed by peptides containing the amino acid moiety Aib in every other position, and their backbones are primarily not held together by H‐bonds, but by the intrinsic conformations of the containing amino acid building blocks. The structures offer new possibilities of mimicking peptide–protein and protein–protein interactions (PPI).     

An Efficient and Facile Synthesis of Functionalized Indole‐3‐yl Pyrazole Derivatives Starting from 3‐Cyanoacetylindole

The versatile hitherto reported 3‐(1H‐indol‐3‐yl)‐1H‐pyrazol‐5‐amine ( 4 ) was synthesized by the reaction of 3‐cyanoacetylindole ( 3 ) with hydrazine hydrate in refluxing ethanol and used as a key intermediate for the synthesis of novel pyrazolo[1,5‐a ]pyrimidines via its reactions with appropriate 1,3‐biselectrophilic reagents or through three‐component condensations with triethyl orthoformate and compounds possessing an activated methylene group. Besides, the applicability and synthetic potency of ( 4 ) to attain polyfunctionally substituted imidazo[1,2‐b ]pyrazole, pyrazolo[1,5‐a ][1,3]diazepine and pyrazolo[1,5‐c ][1,3,5]thiadiazine derivatives of an expected pharmaceutical interest have been investigated. The mechanistic aspects for the formation of the newly synthesized compounds are discussed.     

New Heterocyclic Compounds Derived from 4,6‐Diamino‐3‐cyano‐2‐methylthiopyridine and their Biological Activity

Treatment of 4,6‐diamino‐3‐cyano‐2‐methylthiopyridine ( 1 ) with aqueous KOH or hydrazine hydrate afforded the corresponding nicotinamide 2 and pyrazolo[3,4‐b]pyridine 3 , respectively. Reaction of compound 1 with bromine, sulfuryl chloride, formaldehyde, or aromatic diazonium salts gave 5‐bromopyridine 4 , 5‐chloropyridine 5 , dipyridylmethane 6 , and azo dyes 7 , 8 , 9 , 10 , respectively. Compound 1 reacted with diketones to yield the corresponding butenylamino derivative 11 and amides 12 , 13 , 14 , 15 , respectively. Treatment of butanamide 13 with diazonium salts or a mixture of urea and aromatic aldehyde in the presence of drops of HCl as a catalyst yielded the corresponding arylhydrazones 16 , 17 , 18 , 19 , pyrimidines 20 , 21 , 22 , 23 , 24 , and 1,8‐naphthyridine 25 , respectively. The potency of the results as anti‐inflammatory and antifungal agents have been evaluated. The compounds have been characterized based on their spectral and elemental analysis.     

Copper‐Free Huisgen Cycloaddition for the 14‐3‐3‐Templated Synthesis of Fusicoccin‐Peptide Conjugates

Mid‐sized molecules have emerged as an attractive chemical space and potentially provide a robust basis for the development of synthetic agents to control intracellular protein interactions. However, the limited cell permeability and chemical tractability of such agents remain to be addressed. We envisioned that target‐templated synthesis of such mid‐sized molecules might provide a solution. Here, we exploited a copper‐free Huisgen cycloaddition for template synthesis using a peptide fragment containing a 4,8‐diazacyclononyne (DACN) moiety and an azide‐containing fusicoccin derivative in the presence or absence of recombinant 14‐3‐3ζ protein in vitro. Time‐course changes in the yield of products demonstrated that the reaction was accelerated in the presence of 14‐3‐3 and one of the regioisomers was generated predominantly, supporting the template effect.     

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.     

Design and Synthesis of 3‐Aryl‐5‐Alicylic‐[1,2,4]‐oxadiazoles as Novel Platelet Aggregation Inhibitors

A series of 4‐[2‐(alicyclic‐[1,2,4]oxadiazol‐3‐yl)phenoxy]‐butyric acids were synthesized from N‐hydroxy‐2‐isopropoxy benzamidine in 4 steps with good yields. These [1,2,4]oxadiazoles are novel platelet aggregation inhibitors preventing human platelet aggregation induced by thromboxane derivative U44,619 and adenosine diphosphate. A structure‐activity‐relationship study revealed that the potency for these 5‐oxadiazoles increases with the increase in the ring size of the alicylic rings. Derivative 8f may be useful as a template for the design of more potent anti‐platelet agents.     

Synthesis and Solid‐state Reaction of 1‐[3′‐(Benzotriazol‐2″‐yl)‐4′ ‐hydroxybenzoyl]‐3‐methyl‐5‐pyrazolones

A new kind of UV stabilizers, 1‐(3′‐(benzotriazol‐2″‐yl)‐4′‐hydroxy‐benzoyl)‐3‐methyl‐5‐pyrazolones (1a‐d), was synthesized with the aim to bind them chemically to certain polymers. The reaction of 1d with substituted benzaldehydes 4 in the molten state at 150°C and in the solid state at room temperature produced the condensation products l‐(3′‐(5″‐chlorobenzotriazol‐2″‐yl)‐4′‐hydroxyl‐5′‐chlorobenzoyl)‐3‐methyl‐4‐arylmethylene‐5‐pyrazolones (2) and 4,4′‐arylmethylene‐bis [1‐(3′‐(5″‐chloro‐benzotriazol‐2″‐yl)‐4′‐hydroxy‐5′‐chloro‐benzoyl)‐3‐methyl‐5‐pyrazolone] s (3), respectively, as the major product. On the other hand, the reaction of 1d with 4 at 50°C in chloroform solution proceeded non‐selectively to give a mixture of 2 and 3.     

Synthesis,Characterization, and Anti‐inflammatory Activity of Novel Isoxazolyl‐4‐(2‐oxo‐2,3‐dihydro‐1H‐3‐indolyl)pyrrole‐3‐carboxylates

A series of novel isoxazolyl‐4‐(2‐oxo‐2,3‐dihydro‐1H‐3‐indolyl)pyrrole‐3‐carboxylates ( 17a – i) were synthesized by a three‐component reaction of 4‐amino‐3‐methyl‐5‐styrylisoxazole 14 , β‐keto ester 15 , and 3‐phenacylideneoxindole 16 , in the presence of CAN catalyst in ethanol. The structures of the synthesized compounds have been established on the basis of spectral and analytical data. The title compounds 17a – i were evaluated for their anti‐inflammatory activity. Compounds 17b and 17c exhibited potent anti‐inflammatory activity as that of standard drug.     

Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.     

Reactions of 1‐(3‐aryl‐3‐oxopropenyl)azulenes and 1‐cinnamoylazulenes with malononitrile: Synthesis of 1‐(2‐aryl‐4‐pyridyl)azulenes and 1‐(4‐aryl‐2‐pyridyl)azulenes

The reactions of 1‐formyl‐3‐methoxycarbonylazulene ( 1 ) with acetophenones 3a‐e gave 1‐(3‐aryl‐3‐oxopropenyl)‐3‐methoxycarbonylazulenes 4a‐e which reacted with malononitrile in the presence of sodium methoxide to afford 1‐(2‐aryl‐4‐pyridyl)‐3‐methoxycarbonylazulenes 9a‐d , except for 4′‐nitro‐substituted compounds. Heating of the compounds 9a‐d in 100% phosphoric acid yielded 1‐(2‐aryl‐4‐pyridyl)azulenes 10a‐d . In a similar manner, 1‐(4‐aryl‐2‐pyridyl)azulenes 12a‐1 and 1‐[4‐(2‐furyl)‐ and 4‐(2‐thienyl)‐2‐pyridyl)]azulenes 14a,b were obtained.     

Synthesis of 2‐[4‐(Imidazolin‐2‐Ylideneamino)Benzyl]‐Indan‐1‐Ones as Novel Potent Prostacyclin Antagonists

Prostacyclin is involved in many pathological conditions, such as sensitization of inflammation induced pain and isovolumetic distention. Therefore, antagonism of prostacyclin action may be useful in the alleviation of these conditions. In this study, novel potent prostacyclin antagonists, 2‐[4‐(imidazolin‐2‐ylideneamino)benzyl]‐indan‐1‐ones were synthesized from their respective substituted indanones in three steps. The construction of the amino‐imidazole moiety of these derivatives is achieved by using in situ generation of chloro‐imidazole and reaction with their respective anilines. Thus, these N‐substituted 2‐imidazolines can be prepared safely and efficiently. Moreover, these compounds show potent prostacyclin antagonistic activity by inhibition of prostacyclin agonist induced ERK_1/2 phosphorylation in human erythroleukemia cells. Moreover, we observed an increase in activity with the increase in electro‐donating property of the substitution on the indanone aromatic ring. Prostacyclin antagonists with increased potency may be designed based on these findings. These compounds may also be invaluable tools for the study of the physiological functions of prostacyclin.     

Comparative α‐Helicity of Cyclic Pentapeptides in Water

Helix‐constrained polypeptides have attracted great interest for modulating protein–protein interactions (PPI). It is not known which are the most effective helix‐inducing strategies for designing PPI agonists/antagonists. Cyclization linkers (X₁–X₅) were compared here, using circular dichroism and 2D NMR spectroscopy, for α‐helix induction in simple model pentapeptides, Ac‐cyclo(1,5)‐[X₁‐Ala‐Ala‐Ala‐X₅]‐NH₂, in water. In this very stringent test of helix induction, a Lys1→Asp5 lactam linker conferred greatest α‐helicity, hydrocarbon and triazole linkers induced a mix of α‐ and 3₁₀‐helicity, while thio‐ and dithioether linkers produced less helicity. The lactam‐linked cyclic pentapeptide was also the most effective α‐helix nucleator attached to a 13‐residue model peptide.     

One‐pot synthesis of conjugated poly(3‐hexylthiophene)‐b‐poly(phenyl isocyanide) hybrid rod–rod block copolymers and its self‐assembling properties

In this article, the synthesis of a series of conjugated rod–rod block copolymers based on poly(3‐hexylthiophene) (P3HT) and poly(phenyl isocyanide) (PPI) building blocks in a single pot is presented. Ni‐catalyzed Grignard metathesis polymerization of 2,5‐dibromo‐3‐hexylthiophene and subsequent addition of 4‐isocyanobenzoyl‐2‐aminoisobutyric acid decyl ester in the presence of Ni(dppp)Cl₂ as a single catalyst afford P3HT‐b‐PPI with tunable molecular weights and compositions. In solid state, microphase separation occurred as differential scanning calorimetric analysis of P3HT‐b‐PPI revealed two glass transition temperatures. In solutions, the copolymers can self‐assemble into spherical aggregates with P3HT core and PPI shell in tetrahydrofuran and exhibit amorphous state in CHCl₃. However, atomic force microscopy revealed that the block copolymers self‐assemble into nanofibrils on the substrate. These unique features warrant the resultant conjugated rod–rod copolymers' potential study in organic photovoltaic and other electronic devices. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2939–2947     

Utility of Benzoxazin‐4‐one and 3‐Aminoquinazolin‐4‐one Derivatives as Precursors for Construction of Potent Insecticidal Heterocycles

In demanding to develop new insecticidal agents, both of 2‐pentylbenzoxazin‐4‐one 1 and 3‐amino‐2‐pentylquinazolin‐4‐one 6 derivatives were subjected to react with different nucleophilic agents, for example, ammonia, o‐phenylenediamine, hydrazine hydrate, and hydroxylamine hydrochloride, and sulfur nucleophile, for example, phosphorous pentasulfide, to construct different heterocyclic systems. The structural elucidations of the synthesized compounds were ascertained from the elemental analyses and the spectral data. Assessment of the biological potency for some of the synthesized compounds as insecticidal agents was evaluated against two different insects named Mythimna separata and Nilaparvata lugens.     

Synthesis and Penicillin‐binding Protein Inhibitory Assessment of Dipeptidic 4‐Phenyl‐β‐lactams from α‐Amino Acid‐derived Imines

Monocyclic β‐lactams revive the research field on antibiotics, which are threatened by the emergence of resistant bacteria. A six‐step synthetic route was developed, providing easy access to new 3‐amino‐1‐carboxymethyl‐4‐phenyl‐β‐lactams, of which the penicillin‐binding protein (PBP) inhibitory potency was demonstrated biochemically.     

Synthesis and anti‐HIV activity of n‐(3‐amino‐3,4‐dihydro‐4‐oxopyrimidin‐2‐yl)‐4‐chloro‐2‐mercapto‐5‐methylbenzenesulfonamide derivatives

A series of N‐(3‐amino‐3,4‐dihydro‐4‐oxopyrimidin‐2‐yl)‐4‐chloro‐2‐mercapto‐5‐methylbenzenesulfonamide derivatives 10‐17 have been synthesized as potential anti‐HIV agents. The in vitro anti‐HIV‐1 activity of these compounds has been tested at the national Cancer Institute (Bethesda, MD), and the structure‐activity relationships are discussed. The selected N‐[3‐amino‐3,4‐dihydro‐6‐(tert‐butyl)‐4‐oxothieno[2,3‐e]pyrimidin‐2‐yl]‐4‐chloro‐2‐metcapto‐5‐methylbenzenesulfonamide ( 14 ) showed good anti‐HIV‐1 activity with 50% effective concentration (EC₅₀) value of 15 μM and weak cytotoxic effect (IC₅₀ = 106 μM).