Serendipitous discovery of light-induced (In Situ) formation of an Azo-bridged dimeric sulfonated naphthol as a potent PTP1B inhibitor

Background

Protein tyrosine phosphatases (PTPs) like dual specificity phosphatase 5 (DUSP5) and protein tyrosine phosphatase 1B (PTP1B) are drug targets for diseases that include cancer, diabetes, and vascular disorders such as hemangiomas. The PTPs are also known to be notoriously difficult targets for designing inihibitors that become viable drug leads. Therefore, the pipeline for approved drugs in this class is minimal. Furthermore, drug screening for targets like PTPs often produce false positive and false negative results.

Results

Studies presented herein provide important insights into: (a) how to detect such artifacts, (b) the importance of compound re-synthesis and verification, and (c) how in situ chemical reactivity of compounds, when diagnosed and characterized, can actually lead to serendipitous discovery of valuable new lead molecules. Initial docking of compounds from the National Cancer Institute (NCI), followed by experimental testing in enzyme inhibition assays, identified an inhibitor of DUSP5. Subsequent control experiments revealed that this compound demonstrated time-dependent inhibition, and also a time-dependent change in color of the inhibitor that correlated with potency of inhibition. In addition, the compound activity varied depending on vendor source. We hypothesized, and then confirmed by synthesis of the compound, that the actual inhibitor of DUSP5 was a dimeric form of the original inhibitor compound, formed upon exposure to light and oxygen. This compound has an IC₅₀ of 36 μM for DUSP5, and is a competitive inhibitor. Testing against PTP1B, for selectivity, demonstrated the dimeric compound was actually a more potent inhibitor of PTP1B, with an IC₅₀ of 2.1 μM. The compound, an azo-bridged dimer of sulfonated naphthol rings, resembles previously reported PTP inhibitors, but with 18-fold selectivity for PTP1B versus DUSP5.

Conclusion

We report the identification of a potent PTP1B inhibitor that was initially identified in a screen for DUSP5, implying common mechanism of inhibitory action for these scaffolds.

Electronic supplementary material

The online version of this article (doi:10.1186/s12858-017-0083-3) contains supplementary material, which is available to authorized users.

Critical Role of the Secondary Binding Pocket in Modulating the Enzymatic Activity of DUSP5 toward Phosphorylated ERKs

DUSP5 is an inducible nuclear dual-specificity phosphatase that specifically interacts with and deactivates extracellular signal-regulated kinases ERK1 and ERK2, which are responsible for cell proliferation, differentiation, and survival. The phosphatase domain (PD) of DUSP5 has unique structural features absent from other nuclear DUSPs, such as the presence of a secondary anion-binding site in the proximity of the reaction center and a glutamic acid E264 positioned next to the catalytic cysteine C263, as well as a remote intramolecular disulfide linkage. The overall 400 ns molecular dynamics simulations indicate that the secondary binding site of DUSP5 PD acts as an allosteric regulator of the phosphatase activity of DUSP5. Our studies have identified E264 as a critical constituent of the dual binding pocket, which regulates the catalytic activity of DUSP5 by forming a salt bridge with arginine R269. Molecular dynamics studies showed that initial occupation of the secondary binding pocket leads to the breakage of the salt bridge, which then allows the occupation of the active site. Indeed, biochemical analysis using the pERK assay on mutant E264Q demonstrated that mutation of glutamic acid E264 leads to an increase in the DUSP5 catalytic activity. The role of the secondary binding site in assembling the DUSP5-pERK pre-reactive complex was further demonstrated by molecular dynamics simulations that showed that the remote C197-C219 disulfide linkage controls the structure of the secondary binding pocket based on its redox state (i.e., disulfide/dithiol) and, in turn, the enzymatic activity of DUSP5.

Room-temperature tetragonal non-collinear Heusler antiferromagnet Pt2MnGa

Antiferromagnetic spintronics is a rapidly growing field, which actively introduces new principles of magnetic storage. Despite that, most applications have been suggested for collinear antiferromagnets. In this study, we consider an alternative mechanism based on long-range helical order, which allows for direct manipulation of the helicity vector. As the helicity of long-range homogeneous spirals is typically fixed by the Dzyaloshinskii-Moriya interactions, bi-stable spirals (left- and right-handed) are rare. Here, we report a non-collinear room-temperature antiferromagnet in the tetragonal Heusler group. Neutron diffraction reveals a long-period helix propagating along its tetragonal axis. Ab-initio analysis suggests its pure exchange origin and explains its helical character resulting from a large basal plane magnetocrystalline anisotropy. The actual energy barrier between the left- and right-handed spirals is relatively small and might be easily overcome by magnetic pulse, suggesting Pt2MnGa as a potential candidate for non-volatile magnetic memory.

Identification of inhibitors that target dual-specificity phosphatase 5 provide new insights into the binding requirements for the two phosphate pockets

BACKGROUND

Dual-specificity phosphatase-5 (DUSP5) plays a central role in vascular development and disease. We present a p-nitrophenol phosphate (pNPP) based enzymatic assay to screen for inhibitors of the phosphatase domain of DUSP5.

METHODS

pNPP is a mimic of the phosphorylated tyrosine on the ERK2 substrate (pERK2) and binds the DUSP5 phosphatase domain with a Km of 7.6 ± 0.4 mM. Docking followed by inhibitor verification using the pNPP assay identified a series of polysulfonated aromatic inhibitors that occupy the DUSP5 active site in the region that is likely occupied by the dual-phosphorylated ERK2 substrate tripeptide (pThr-Glu-pTyr). Secondary assays were performed with full length DUSP5 with ERK2 as substrate.

RESULTS

The most potent inhibitor has a naphthalene trisulfonate (NTS) core. A search for similar compounds in a drug database identified suramin, a dimerized form of NTS. While suramin appears to be a potent and competitive inhibitor (25 ± 5 μM), binding to the DUSP5 phosphatase domain more tightly than the monomeric ligands of which it is comprised, it also aggregates. Further ligand-based screening, based on a pharmacophore derived from the 7 Å separation of sulfonates on inhibitors and on sulfates present in the DUSP5 crystal structure, identified a disulfonated and phenolic naphthalene inhibitor (CSD (3) _2320) with IC₅₀ of 33 μM that is similar to NTS and does not aggregate.

CONCLUSIONS

The new DUSP5 inhibitors we identify in this study typically have sulfonates 7 Å apart, likely positioning them where the two phosphates of the substrate peptide (pThr-Glu-pTyr) bind, with one inhibitor also positioning a phenolic hydroxyl where the water nucleophile may reside. Polysulfonated aromatic compounds do not commonly appear in drugs and have a tendency to aggregate. One FDA-approved polysulfonated drug, suramin, inhibits DUSP5 and also aggregates. Docking and modeling studies presented herein identify polysulfonated aromatic inhibitors that do not aggregate, and provide insights to guide future design of mimics of the dual-phosphate loops of the ERK substrates for DUSPs.

A snapshot of ubiquitin chain elongation: lysine 48-tetra-ubiquitin slows down ubiquitination

We have explored the mechanisms of polyubiquitin chain assembly with reconstituted ubiquitination of IκBα and β-catenin by the Skp1-cullin 1-βTrCP F-box protein (SCF(βTrCP)) E3 ubiquitin (Ub) ligase complex. Competition experiments revealed that SCF(βTrCP) formed a complex with IκBα and that the Nedd8 modified E3-substrate platform engaged in dynamic interactions with the Cdc34 E2 Ub conjugating enzyme for chain elongation. Using "elongation intermediates" containing β-catenin linked with Ub chains of defined length, it was observed that a Lys-48-Ub chain of a length greater than four, but not its Lys-63 linkage counterparts, slowed the rate of additional Ub conjugation. Thus, the Ub chain length and linkage impact kinetic rates of chain elongation. Given that Lys-48-tetra-Ub is packed into compact conformations due to extensive intrachain interactions between Ub subunits, this topology may limit the accessibility of SCF(βTrCP)/Cdc34 to the distal Ub Lys-48 and result in slowed elongation.

(3 + 1)D superspace description of the incommensurate modulation in the premartensite phase of Ni2MnGa: a high resolution synchrotron x-ray powder diffraction study

Le Bail and Rietveld analysis of high resolution synchrotron x-ray powder diffraction (SXRPD) data shows unambiguous signatures of the failure of the commensurate 3M modulation model. Using (3 + 1) dimensional superspace group formalism, we have not only confirmed the incommensurate modulation in the premartensite phase with a modulation wavevector of q = 0.337 61(5)c* but also determined the superspace group (Immm(00γ)s00), atomic positions and amplitude of modulations for the incommensurate premartensite phase of Ni2MnGa for the first time. Our results may have important implications in the understanding of the martensitic transition and hence the magnetic field induced strains.

Bulk electronic structure of quasicrystals

We use hard x-ray photoemission to resolve a controversial issue regarding the mechanism for the formation of quasicrystalline solids, i.e., the existence of a pseudogap at the Fermi level. Our data from icosahedral fivefold Al-Pd-Mn and Al-Cu-Fe quasicrystals demonstrate the presence of a pseudogap, which is not observed in surface sensitive low energy photoemission because the spectrum is affected by a metallic phase near the surface. In contrast to Al-Pd-Mn, we find that in Al-Cu-Fe the pseudogap is fully formed; i.e., the density of states reaches zero at E(F) indicating that it is close to the metal-insulator phase boundary.

High energy resolution bandpass photon detector for inverse photoemission spectroscopy

We report a bandpass ultraviolet photon detector for inverse photoemission spectroscopy with energy resolution of 82 ± 2 meV. The detector (Sr(0.7)Ca(0.3)F(2)/acetone) consists of Sr(0.7)Ca(0.3)F(2) entrance window with energy transmission cutoff of 9.85 eV and acetone as detection gas with 9.7 eV photoionization threshold. The response function of the detector, measured using synchrotron radiation, has a nearly Gaussian shape. The n = 1 image potential state of Cu(100) and the Fermi edge of silver have been measured to demonstrate the improvement in resolution compared to the CaF(2)/acetone detector. To show the advantage of improved resolution of the Sr(0.7)Ca(0.3)F(2)/acetone detector, the metal to semiconductor transition in Sn has been studied. The pseudogap in the semiconducting phase of Sn could be identified, which is not possible with the CaF(2)/acetone detector because of its worse resolution.

An ultrahigh vacuum compatible sample holder for studying complex metal surfaces

We present a design of a compact and versatile sample holder meant for studying complex (ternary) metallic crystals that require sputtering and annealing to high temperatures under ultrahigh vacuum (10(-10) mbar range) for obtaining the clean, ordered and stoichiometric surface. A resistive heater is fixed to the sample holder and not to the sample plate, and thus can be thoroughly degassed initially to high temperatures without heating the sample. The heater, which is mounted vertically on the sample holder frame, slides into the sample plate of rectangular cross-section during sample transfer. For efficient cooling that is required for adlayer deposition, Cu braids can be pressed on the sample plate from both sides through a screw mechanism. The sample holder has 5 degrees of freedom including a tilt rotation. The sample holder has been used to study different metal surfaces such as ferromagnetic shape memory alloys, alkali metal and Mn adlayers on Al-Pd-Mn quasicrystal, aluminum metal, and Al-Mn alloys. Here, our recent results on temperature dependent low energy electron diffraction study of Ni(2)MnGa(100) are presented.

Pathfinding by cranial nerve VII (facial) motorneurons in the chick hindbrain

Cranial nerve VII (facial) motorneurons begin extending axons through rhombomeres 4 and 5 (R4 and R5) in the chick hindbrain on the second day of incubation. Without crossing the midline, facial motorneuron axons extend laterally from a ventromedial cell body location. All facial motorneuron axons leave the hindbrain through a discrete exit site in R4. To examine the importance of the exit site in R4 on motorneuron pathfinding, we ablated R4 before motorneuron axonogenesis. We find that mechanisms intrinsic to R5 direct the initial lateral orientation of R5 motorneuron axons. Upon reaching a particular lateral position, all R5 motorneuron axons must turn. In normal embryos the axons all turn rostrally to reach the nerve exit in R4. In embryos with R4 ablated, sometimes the axons turn rostrally and sometimes they turn caudally. A model combining permissive fields and chemotropic cues is presented to account for our observations.