Characterization of the Two Fundamental Conformations of Benzoylureas and Elucidation of the Factors That Facilitate Their Conformational Interchange

The benzoylphenylurea derivative BPU17 acts as an inhibitor of prohibitin and exhibits antifibrotic activity

Inflammation-induced choroidal neovascularization followed by the epithelial-mesenchymal transition (EMT) of retinal pigment epithelial cells (RPEs) is a cause of neovascular age-related macular degeneration (nAMD). RPE-derived myofibroblasts overproduce extracellular matrix, leading to subretinal fibrosis. We already have demonstrated that benzylphenylurea (BPU) derivatives inhibit the function of cancer-associated fibroblasts. Here, we investigated the anti-myofibroblast effects of BPU derivatives and examined such BPU activity on subretinal fibrosis. A BPU derivative, BPU17, exhibits the most potent anti-myofibroblast activity among dozens of BPU derivatives and inhibits subretinal fibrosis in a mouse model of retinal degeneration. Investigations with primary cultured RPEs reveal that BPU17 suppresses cell motility and collagen synthesis in RPE-derived myofibroblasts. These effects depend on repressing the serum response factor (SRF)/CArG-box-dependent transcription. BPU17 inhibits the expression of SRF cofactor, cysteine and glycine-rich protein 2 (CRP2), which activates the SRF function. Proteomics analysis reveals that BPU17 binds to prohibitin 1 (PHB1) and inhibits the PHB1-PHB2 interaction, resulting in mild defects in mitochondrial function. This impairment causes a decrease in the expression of CRP2 and suppresses collagen synthesis. Our findings suggest that BPU17 is a promising agent against nAMD and the close relationship between PHB function and EMT.

Novel ability of diflubenzuron as an inhibitor of mitochondrial function

Compounds classified as benzoylphenylurea (BPU), such as diflubenzuron (DFB), are used as insecticides. Although BPU disrupts molting by inhibiting chitin biosynthesis and exhibits insecticidal activity, their exact mode of action remains unknown. Since epidermal cells proliferate and morphologically change from squamous to columnar cells during the early stages of insect molting, we speculate that a transition similar to that from epithelium to mesenchyme occurs and that BPU may inhibit this transition. Here, we addressed this possibility. We found that DFB decreases actin expression in insect cells (the tissue cultures of insect integument). Detailed analysis in Schneider S2 cells reveals that DFB inhibits the expression of actin isoforms (Act5C and Act42A) and the Drosophila ortholog of myocardin-related transcription factor (Mrtf), leading to cell growth suppression. Proteomics identified the Drosophila ortholog of prohibitin (Phb1D and Phb2E) as one of the DFB-binding proteins. DFB inhibits the interaction between Phb1D and Phb2E and induces mitochondrial dysfunction. The knock-down of Phb2E suppresses the expression of Act5C, Act42A, and Mrtf, leading to cell growth inhibition. Thus, the disruption of Phb function is a possible novel target of DFB.

Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-XL and BCL-2

The BCL-2 family of proteins (including the prosurvival proteins BCL-2, BCL-X_L, and MCL-1) is an important target for the development of novel anticancer therapeutics. Despite the challenges of targeting protein-protein interaction (PPI) interfaces with small molecules, a number of inhibitors (called BH3 mimetics) have entered the clinic and the BCL-2 inhibitor, ABT-199/venetoclax, is already proving transformative. For BCL-X_L, new validated chemical series are desirable. Here, we outline the crystallography-guided development of a structurally distinct series of BCL-X_L/BCL-2 inhibitors based on a benzoylurea scaffold, originally proposed as α-helix mimetics. We describe structure-guided exploration of a cryptic "p5" pocket identified in BCL-X_L. This work yields novel inhibitors with submicromolar binding, with marked selectivity toward BCL-X_L. Extension into the hydrophobic p2 pocket yielded the most potent inhibitor in the series, binding strongly to BCL-X_L and BCL-2 (nanomolar-range half-maximal inhibitory concentration (IC₅₀)) and displaying mechanism-based killing in cells engineered to depend on BCL-X_L for survival.

Personal Accounts of Australian Drug Discovery at the Public–Private Interface

The public–private interface is a vibrant and invigorating stage for drug discovery and can allow for relatively higher risk but more rewarding research. Although adequate resourcing is a perennial challenge, persistence, optimism, and flexibility will pay dividends and can allow for a thoroughly rewarding career. In this account of chronological research experiences, selected examples are used to support this contention.

High throughput methods to measure the propensity of compounds to form intramolecular hydrogen bonding

Implementation of IMHB considerations in drug discovery needs robust and validated descriptors to experimentally verify the propensity of compounds to exhibit IMHBs. The first part of the paper presents an overview of the most common techniques to measure the propensity of compounds to form IMHBs. Then we review and discuss recently proposed high throughput (HT) physicochemical descriptors (i.e. Δlog Poct-tol, EPSA and log k'80 PLRP-S) which provide the same information. Analysis of the available data enabled us to extract guidelines for the application of these descriptors in drug discovery programs.

Bifunctional Thioureas with α-Trifluoromethyl or Methyl Groups: Comparison of Catalytic Performance in Michael Additions

Thioureas are an important scaffold in organocatalysis because of their ability to form hydrogen bonds that activate substrates and fix them in a defined position, which allows a given reaction to occur. Structures that enhance the acidity of the thiourea are usually used to increase the hydrogen-bonding properties, such as 3,5-bis(trifluoromethyl)phenyl and boronate ureas. Herein, we report the synthesis of bifunctional thioureas with a chiral moiety that include either a trifluoromethyl or methyl group. Their catalytic performance in representative Michael addition reactions was used in an effort to compare the electronic effects of the fluorination at the methyl group. The observed differences concerning yields and ee values cannot be attributed solely to the different steric environments; theoretical results indicate distinct interactions within the corresponding transition states. The calculated transition states show that the fluorinated catalysts have stronger N-H···O and C-H···F hydrogen bonds, while the nonfluorinated systems have C-H···π contacts. These results have shown that a variety of hydrogen-bonding interactions are important in determining the yield and selectivity of thiourea organocatalysis. These details can be further exploited in catalyst design.

Novel acylureidoindolin-2-one derivatives as dual Aurora B/FLT3 inhibitors for the treatment of acute myeloid leukemia

A series of 6-acylureido derivatives containing a 3-(pyrrol-2-ylmethylidene)indolin-2-one scaffold were synthesized as potential dual Aurora B/FLT3 inhibitors by replacing the 6-arylureido moiety in 6-arylureidoindolin-2-one-based multi-kinase inhibitors. (Z)-N-(2-(pyrrolidin-1-yl)ethyl)-5-((6-(3-(2-fluoro-4-methoxybenzoyl)ureido)-2-oxoindolin-3-ylidene)methyl)-2,4-dimethyl-1H-pyrrole-3-carboxamide (54) was identified as a dual Aurora B/FLT3 inhibitor (IC50 = 0.4 nM and 0.5 nM, respectively). Compound 54 also exhibited potent cytotoxicity with single-digit nanomolar IC50 values against the FLT3 mutant-associated human acute myeloid leukemia (AML) cell lines MV4-11 (FLT3-ITD) and MOLM-13 (FLT3-ITD). Compound 54 also specifically induced extrinsic apoptosis by inhibiting the phosphorylation of the Aurora B and FLT3 pathways in MOLM-13 cells. Compound 54 had a moderate pharmacokinetic profile. The mesylate salt of 54 efficiently inhibited tumor growth and reduced the mortality of BALB/c nude mice (subcutaneous xenograft model) that had been implanted with AML MOLM-13 cells. Compound 54 is more potent than sunitinib not only against FLT3-WT AML cells but also active against sunitinib-resistant FLT3-ITD AML cells. This study demonstrates the significance of dual Aurora B/FLT3 inhibitors for the development of potential agents to treat AML.

De-novo designed library of benzoylureas as inhibitors of BCL-XL: synthesis, structural and biochemical characterization

The prosurvival BCL-2 proteins are attractive yet challenging targets for medicinal chemists. Their involvement in the initiation and progression of many, if not all, tumors makes them prime targets for developing new anticancer therapies. We present our approach based on de novo structure-based drug design. Using known structural information from complexes engaging opposing members of the BCL-2 family of proteins, we designed peptidomimetic compounds using a benzoylurea scaffold to reproduce key interactions between these proteins. A library stemming from the initial de novo designed scaffold led to the discovery of ligands with low micromolar potency (KD = 4 μM) and selectivity for BCL-XL. These compounds bind in the canonical BH3 binding groove in a binding mode distinct from previously known BCL-2 inhibitors. The results of our study provide insight into the design of a new class of antagonists targeting a challenging class of protein-protein interactions.

α-Helix mimetics: outwards and upwards

α-Helices are common secondary structural elements forming key parts of the large, generally featureless interfacial regions of many therapeutically-relevant protein-protein interactions (PPIs). The rational design of helix mimetics is an appealing small-molecule strategy for the mediation of aberrant PPIs, however the first generation of scaffolds presented a relatively small number of residues on a single recognition surface. Increasingly, helices involved in PPIs are found to have more complex binding modes, utilizing two or three recognition surfaces, or binding with extended points of contact. To address these unmet needs the design and synthesis of new generations of multi-sided, extended, and supersecondary structures are underway.

Conformational preference of glycinamide in solution: an answer derived from combined experimental and computational studies

Conformational problems are often subtle but very important in controlling many intricate features in chemistry and biochemistry. We have performed the conformational analysis of glycinamide using NMR experiments and computational studies. (1)H NMR experiments suggest the prevalence of intramolecular hydrogen bonded conformation of glycinamide (2B) in acetonitrile, whereas, non-intramolecular hydrogen bonded conformation 2A is favoured in dimethylsulfoxide. The NOESY experiments carried out for glycinamide in DMSO-d6, showed stronger NOE interaction of the NHa-atom of amide group with CH2 than that of NHb-atom confirming the presence of conformer 2A. DFT calculations performed with explicit DMSO molecules also suggested a clear preference for the conformer 2A. The molecular dynamics simulations performed with the explicit DMSO molecules also showed that the intermolecular hydrogen bonding exists between the solvent and solute molecules to stabilize the conformer 2A. The present study sheds light on the debate of conformational preference of neutral glycinamide in the present literature.

Strategies for the development of conotoxins as new therapeutic leads

Peptide toxins typically bind to their target ion channels or receptors with high potency and selectivity, making them attractive leads for therapeutic development. In some cases the native peptide as it is found in the venom from which it originates can be used directly, but in many instances it is desirable to truncate and/or stabilize the peptide to improve its therapeutic properties. A complementary strategy is to display the key residues that make up the pharmacophore of the peptide toxin on a non-peptidic scaffold, thereby creating a peptidomimetic. This review exemplifies these approaches with peptide toxins from marine organisms, with a particular focus on conotoxins.

Chitin synthesis inhibitors: old molecules and new developments

Abstract  Chitin is the most abundant natural aminopolysaccharide and serves as a structural component of extracellular matrices. It is found in fungal septa, spores, and cell walls, and in arthropod cuticles and peritrophic matrices, squid pens, mollusk shells, nematode egg shells, and some protozoan cyst walls. As prokaryotes, plants and vertebrates including humans do not produce chitin, its synthesis is considered as an attractive target site for fungicides, insecticides, and acaricides. Although no chitin synthesis inhibitor has been developed into a therapeutic drug to treat fungal infections in humans, a larger number of compounds have been successfully launched worldwide to combat arthropod pests in agriculture and forestry. This review summarizes the latest advances on the mode of action of chitin synthesis inhibitors with a special focus on those molecules that act on a postcatalytic step of chitin synthesis.

Identification of compounds with anti-proliferative activity against Trypanosoma brucei brucei strain 427 by a whole cell viability based HTS campaign

Human African Trypanosomiasis (HAT) is caused by two trypanosome sub-species, Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense. Drugs available for the treatment of HAT have significant issues related to difficult administration regimes and limited efficacy across species and disease stages. Hence, there is considerable need to find new alternative and less toxic drugs. An approach to identify starting points for new drug candidates is high throughput screening (HTS) of large compound library collections. We describe the application of an Alamar Blue based, 384-well HTS assay to screen a library of 87,296 compounds against the related trypanosome subspecies, Trypanosoma brucei brucei bloodstream form lister 427. Primary hits identified against T.b. brucei were retested and the IC₅₀ value compounds were estimated for T.b. brucei and a mammalian cell line HEK293, to determine a selectivity index for each compound. The screening campaign identified 205 compounds with greater than 10 times selectivity against T.b. brucei. Cluster analysis of these compounds, taking into account chemical and structural properties required for drug-like compounds, afforded a panel of eight compounds for further biological analysis. These compounds had IC₅₀ values ranging from 0.22 µM to 4 µM with associated selectivity indices ranging from 19 to greater than 345. Further testing against T.b. rhodesiense led to the selection of 6 compounds from 5 new chemical classes with activity against the causative species of HAT, which can be considered potential candidates for HAT early drug discovery. Structure activity relationship (SAR) mining revealed components of those hit compound structures that may be important for biological activity. Four of these compounds have undergone further testing to 1) determine whether they are cidal or static in vitro at the minimum inhibitory concentration (MIC), and 2) estimate the time to kill.

Human African Sleeping Sickness (HAT) is a disease caused by sub-species of Trypanosoma. The disease affects developing countries within Africa, mainly occurring in rural regions that lack resources to purchase drugs for treatment. Drugs that are currently available have significant side effects, and treatment regimes are lengthy and not always transferrable to the field. In consideration of these factors, new drugs are urgently needed for the treatment of HAT. To discover compounds suitable for drug discovery, cultured trypanosomes can be tested against libraries of compounds to identify candidates for further biological analysis. We have utilised a 384-well format, Alamar Blue viability assay to screen a large non-proprietary compound collection against Trypanosoma brucei brucei bloodstream form lister 427. The assay was shown to be reproducible, with reference compounds exhibiting activity in agreement with previously published results. Primary screening hits were retested against T.b. brucei and HEK293 mammalian cells in order to assess selectivity against the parasite. Selective hits were characterised by chemical analysis, taking into consideration drug-like properties amenable to further progression. Priority compounds were tested against a panel of protozoan parasites, including Trypanosoma brucei rhodesiense, Trypanosoma cruzi, Leishmania donovani and Plasmodium falciparum. Five new compound classes were discovered that are amenable to progression in the drug discovery process for HAT.

Studies of the solvatochromic emission properties of N-aroylurea derivatives II: influence of hydrogen-bonding interactions

The solvatochromic emission properties of five naphthoylurea derivatives with different substitution patterns at the naphthoylurea functionality were investigated, with a particular focus on the influence of inter- and intramolecular H-bonding interactions. The bathochromic shifts of the emission maxima correlate well with the acceptor number or Catalán's acidity of the solvent (Δλ = 47-86 nm), indicating an excited species with a pronounced negative charge that is stabilized by H-bond donating (HBD) solvents. In media with restricted free volume the formation of the charged species is not favored, because the required conformational change to establish an intramolecular charge transfer (ICT) between the fluorophore and the acylurea substituent is hindered, and the emission mainly originates from the locally excited state. This relationship between the alignment of the naphthoyl carbonyl functionality relative to the naphthyl ring and the spectroscopic shift was confirmed by the comparison of the ground state conformation and the emission spectra of the naphthoylurea derivatives in the solid state. Time-resolved experiments revealed different excited entities, whose lifetimes are significantly influenced by the HBD properties and the temperature of the environment. With few exceptions the naphthoylurea derivatives exhibit only two emissive species in the nanosecond range. All experimental data point to conformational relaxation and solvent reorganization leading to the cis and trans isomers of one preferential conformer with respect to the acylurea unit. The structure of the preferred conformation is mainly determined by the possible inter- or intramolecular H-bonds and is therefore also strongly influenced by the HBD and H-bond accepting (HBA) properties of the polar solvents. As the NH groups of the acylurea functionality contribute mainly to the entire inter- and intramolecular H-bond arrangement the variation of the substitution pattern of the urea unit, specifically the presence and position of the NH groups, leads to derivatives with significantly different steady-state and time-resolved emission properties.

Solid-phase synthesis of disubstituted N-acylureas from resin-bound ureas and acyl chlorides

Acylureas (ureides) are valued for their important biological activities. Whereas cyclic acylureas have frequently been the object of solid-phase chemistry, only few reports have focused on the solid-supported preparation of acyclic representatives. We have prepared different types of acylureas on Rink amide resin in three or four steps. The products are either N-acylated (9, 18), N-acylated-N'-alkylated (10, 19), or N-acylated-N-alkylated (22). Characteristic NMR parameters of isomeric acylureas 10, 19, and 22 are discussed.

Disrupting protein-protein interactions with non-peptidic, small molecule alpha-helix mimetics

Many biological processes are regulated by protein-protein interactions (PPIs) and as such their misregulation can cause a multitude of diseases. Often the interactions between large proteins are mediated by small protein secondary structural domains, which project a minimum number of specifically arranged residues into the complementary surface of an interacting protein. Nature has the advantage of time, and over time has optimized those secondary structures, such as alpha-helices, beta-sheets and beta-strands, found at the interfaces of PPIs. Inspired by Nature's extensive optimization, chemists have used these secondary structures as templates in the design of small molecules that may act as structural and functional mimics of large rhenylogically organized protein secondary structures. Herein recent applications of the indane, terphenyl, terphenyl-inspired templates, polycyclic ether and benzodiazepinedione scaffolds, as non-peptidic, small molecule alpha-helix mimetics, to disrupt PPIs are detailed.

Mu-conotoxins as leads in the development of new analgesics

Voltage-gated sodium channels (VGSCs) contain a specific binding site for a family of cone shell toxins known as mu-conotoxins. As some VGSCs are involved in pain perception and mu-conotoxins are able to block these channels, mu-conotoxins show considerable potential as analgesics. Recent studies have advanced our understanding of the three-dimensional structures and structure-function relationships of the mu-conotoxins, including their interaction with VGSCs. Truncated peptide analogues of the native toxins have been created in which secondary structure elements are stabilized by non-native linkers such as lactam bridges. Ultimately, it would be desirable to capture the favourable analgesic properties of the native toxins, in particular their potency and channel sub-type selectivity, in non-peptide mimetics. Such mimetics would constitute lead compounds in the development of new therapeutics for the treatment of pain.