Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs).

Helix mimicry provides probes to perturb protein-protein interactions (PPIs). Helical conformations can be stabilized by joining side chains of non-terminal residues (stapling) or via capping fragments. Nature exclusively uses capping, but synthetic helical mimics are heavily biased towards stapling. This study comprises: (i) creation of a searchable database of unique helical N-caps (ASX motifs, a protein structural motif with two intramolecular hydrogen-bonds between aspartic acid/asparagine and following residues); (ii) testing trends observed in this database using linear peptides comprising only canonical L-amino acids; and, (iii) novel synthetic N-caps for helical interface mimicry. Here we show many natural ASX motifs comprise hydrophobic triangles, validate their effect in linear peptides, and further develop a biomimetic of them, Bicyclic ASX Motif Mimics (BAMMs). BAMMs are powerful helix inducing motifs. They are synthetically accessible, and potentially useful to a broad section of the community studying disruption of PPIs using secondary structure mimics.

Dual-Capped Helical Interface Mimics.

Disruption of protein-protein interactions is medicinally important. Interface helices may be mimicked in helical probes featuring enhanced rigidities, binding to protein targets, stabilities in serum, and cell uptake. This form of mimicry is dominated by stapling between side chains of helical residues: there has been less progress on helical N-caps, and there were no generalizable C-caps. Conversely, in natural proteins, helicities are stabilized and terminated by C- and N-caps but not staples. Bicyclic caps previously introduced by us enable interface helical mimicry featuring rigid synthetic caps at both termini in this work. An unambiguously helical dual-capped system proved to be conformationally stable, binding cyclins A and E, and showed impressive cellular uptake. In addition, the dual-capped mimic was completely resistant to proteolysis in serum over an extended period when compared with "gold standard" hydrocarbon-stapled controls. Dual-capped peptidomimetics are a new, generalizable paradigm for helical interface probe design.

A fluorescent electrophile for CLIPS: self indicating TrkB binders.

Combination of cysteine-containing peptides with electrophiles provides efficient access to cyclo-organopeptides. However, there are no routes to intrinsically fluorescent cyclo-organopeptides containing robust, brilliant fluorophores emitting at wavelengths longer than cellular autofluorescence. We show such fluorescent cyclo-organopeptides can be made via SNAr reactions of cysteine-containing peptides with a BODIPY system. Seven compounds of this type were prepared to test as probes; six contained peptide sequences corresponding to loop regions in brain-derived neurotrophic factor and neurotrophic factor 4 (BDNF and NT-4) which bind tropomyocin receptor kinase B (TrkB). Cellular assays in serum-free media indicated two of the six key compounds induced survival of HEK293 cells stably transfected with TrkB whereas a control did not. The two compounds inducing cell survival bound TrkB on those cells (Kd ∼40 and 47 nM), illustrating how intrinsically fluorescent cyclo-organopeptides can be assayed for quantifiable binding to surface receptors in cell membrane environments.

Cyanine Dye Conjugation Enhances Crizotinib Localization to Intracranial Tumors, Attenuating NF-κB-Inducing Kinase Activity and Glioma Progression.

Glioblastoma (GBM) is a highly aggressive form of brain cancer with a poor prognosis and limited treatment options. The ALK and c-MET inhibitor Crizotinib has demonstrated preclinical therapeutic potential for newly diagnosed GBM, although its efficacy is limited by poor penetration of the blood brain barrier. Here, we identify Crizotinib as a novel inhibitor of nuclear factor-κB (NF-κB)-inducing kinase, which is a key regulator of GBM growth and proliferation. We further show that the conjugation of Crizotinib to a heptamethine cyanine dye, or a near-infrared dye (IR-Crizotinib), attenuated glioma cell proliferation and survival in vitro to a greater extent than unconjugated Crizotinib. Moreover, we observed increased IR-Crizotinib localization to orthotopic mouse xenograft GBM tumors, which resulted in impaired tumor growth in vivo. Overall, IR-Crizotinib exhibited improved intracranial chemotherapeutic delivery and tumor localization with concurrent inhibition of NIK and noncanonical NF-κB signaling, thereby reducing glioma growth in vitro, as well as in vivo, and increasing survival in a preclinical rodent model.

PROTAC-mediated CDK degradation differentially impacts cancer cell cycles due to heterogeneity in kinase dependencies.

BACKGROUND: Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibition yields differential cellular responses in multiple tumor models due to redundancy in cell cycle. We investigate whether the differential requirements of CDKs in multiple cell lines function as determinant of response to pharmacological agents that target these kinases. METHODS: We utilized proteolysis-targeted chimeras (PROTACs) that are conjugated with palbociclib (Palbo-PROTAC) to degrade both CDK4 and CDK6. FN-POM was synthesized by chemically conjugating pomalidomide moiety with a multi-kinase inhibitor, FN-1501. Patient derived PDAC organoids and PDX model were utilized to investigate the effect of FN-POM in combination with palbociclib. RESULTS: Palbo-PROTAC mediates differential impact on cell cycle in different tumor models, indicating that the dependencies to CDK4 and 6 kinases are heterogenous. Cyclin E overexpression uncouples cell cycle from CDK4/6 and drives resistance to palbo-PROTAC. Elevated expression of P16INK4A antagonizes PROTAC-mediated degradation of CDK4 and 6. FN-POM degrades cyclin E and CDK2 and inhibits cell cycle progression in P16INK4A-high tumor models. Combination of palbociclib and FN-POM cooperatively inhibit tumor cell proliferation via RB activation. CONCLUSION: Resistance to CDK4/6 inhibition could be overcome by pharmacologically limiting Cyclin E/CDK2 complex and proves to be a potential therapeutic approach.

Cytotoxicities of Tumor-Seeking Dyes: Impact on Future Clinical Trials.

Heptamethine (Cy7) dyes with meso-Cl substituents injected intravenously (iv) into mice accumulate in tumors and persist there over several days. We believe this occurs via meso-Cl displacement by the only free cysteine residues of albumin; therefore, conjugating tumor-seeking dyes with fragments can increase selective therapeutic delivery to tumors and drug residence. This strategy has elevated significance recently because the first tumor-seeking dye-drug conjugate has moved into clinical trials. Options for further clinical research include modifying the dye, and use of preformed albumin adducts instead of dyes alone. Herein we show correlations of cytotoxicities, lipophilicities, organelle localization, apoptosis, cell-cycle arrest, wound healing/migration assays, and reactivities/affinities with human serum albumin are difficult to observe. However, our studies arrived at an important conclusion: preformed dye-drug-HSA adducts are less cytotoxic, and therefore preferable for subsequent clinical work, relative to direct injection of meso-Cl-containing forms.

A, B, C's of Trk Receptors and Their Ligands in Ocular Repair.

Neurotrophins are a family of closely related secreted proteins that promote differentiation, development, and survival of neurons, which include nerve growth factor (NGF), brain-derived neurotrophic factor, neurotrophin-3, and neurotrophin-4. All neurotrophins signal through tropomyosin receptor kinases (TrkA, TrkB, and TrkC) which are more selective to NGF, brain-derived neurotrophic factor, and neurotrophin-3, respectively. NGF is the most studied neurotrophin in the ocular surface and a human recombinant NGF has reached clinics, having been approved to treat neurotrophic keratitis. Brain-derived neurotrophic factor, neurotrophin-3, and neurotrophin-4 are less studied neurotrophins in the ocular surface, even though brain-derived neurotrophic factor is well characterized in glaucoma, retina, and neuroscience. Recently, neurotrophin analogs with panTrk activity and TrkC selectivity have shown promise as novel drugs for treating dry eye disease. In this review, we discuss the biology of the neurotrophin family, its role in corneal homeostasis, and its use in treating ocular surface diseases. There is an unmet need to investigate parenteral neurotrophins and its analogs that activate TrkB and TrkC selectively.

Synthetic helical peptide capping strategies.

Relatively small mimics of interface secondary structures can be used to disrupt protein-protein interactions (PPIs). This strategy is valuable because many PPIs are pivotal in cell biology and contemporary medicinal chemistry. Small peptides tend to have random coil conformations in solution, so the entropy costs are high for them to order into states binding protein receptors. Consequently, peptides constrained in conformations resembling interface secondary structures are favored for enhanced affinities to PPI components. Helices are commonly found at PPI interfaces. The two general strategies that have emerged for imposing helical constraints in probes, capping and stapling, are often confused because both involve formation of macrocyclic rings. This review considers parameters that distinguish capping from stapling. Capping motifs terminate helices and project the adjacent peptide units in non-helical orientations, but stapling enforces helical motifs in ways that enable adjacent peptide fragments to extend helices. There is no evidence that stapling is more effective than capping for helix mimicry, but stapling is used more frequently. This imbalance may be because no strategies have emerged for synthetic C-capping with compact unit; if convenient and effective C-capping strategies were available then capping strategies should be more widely used.

Fluorescent PARP Inhibitors Applied To Intracranial Glioblastoma: Accumulation and Persistence In Vivo.

Rucaparib-containing fluorescent probes (1-3) inhibit PARP1 in cell models. One of these (1) was tested in a murine model and shown to permeate into implanted intracranial glioblastoma tumors and persist there for at least 24 h.

QuatCy-I2 and MHI-I2 in Photodynamic Therapy.

MHI-I2 (1) and QuatCy-I2 (2) were compared in terms of properties important for early-stage photodynamic therapy preclinical candidates. Thus, experiments were performed to monitor dark cytotoxicities, light/dark cytotoxicity ratios, selectivity of localization in tumors over other organs, and clearance from the plasma.

Antibody-dependent cellular phagocytosis of tropomyosin receptor kinase C (TrkC) expressing cancer cells for targeted immunotherapy.

Conventional cancer therapies such as chemotherapy are non-selective and induce immune system anergy, which lead to serious side effects and tumor relapse. It is a challenge to prime the body's immune system in the cancer-bearing subject to produce cancer antigen-targeting antibodies, as most tumor-associated antigens are expressed abundantly in cancer cells and some of normal cells. This study illustrates how hapten-based pre-immunization (for anti-hapten antibodies production) combined with cancer receptor labeling with hapten antigen constructs can elicit antibody-dependent cellular phagocytosis (ADCP). Thus, the hapten antigen 2,4-dinitrophenol (DNP) was covalently combined with a cancer receptor-binding dipeptide (IYIY) to form a dipeptide-hapten construct (IYIY-DNP, MW = 1322.33) that targets the tropomyosin receptor kinase C (TrkC)-expressed on the surface of metastatic cancer cells. IYIY-DNP facilitated selective association of RAW264.7 macrophages to the TrkC expressing 4T1 cancer cells in vitro, forming cell aggregates in the presence of anti-DNP antibodies, suggesting initiation of anti-DNP antibody-dependent cancer cell recognition of macrophages by the IYIY-DNP. In in vivo, IYIY-DNP at 10 mg/kg suppressed growth of 4T1 tumors in DNP-immunized BALB/c mice by 45% (p < 0.05), when comparing the area under the tumor growth curve to that of the saline-treated DNP-immunized mice. Meanwhile, IYIY-DNP at 10 mg/kg had no effect on TrkC-negative 67NR tumor-bearing mice immunized with DNP. Tumor growth suppression activity of IYIY-DNP in DNP-immunized mice was associated with an increase in the anti-DNP IgG (7.3 × 106 ± 1.6 U/mL) and IgM (0.9 × 106 ± 0.07 U/mL) antibodies after five cycles of DNP treatment, demonstrated potential for hapten-based pre-immunization then treatment with IYIY-DNP to elicit ADCP for improved immunotherapy of TrkC expressing cancers.

Fluorescent kinase inhibitors as probes in cancer.

Fluorescent dyes attached to kinase inhibitors (KIs) can be used to probe kinases in vitro, in cells, and in vivo. Ideal characteristics of the dyes vary with their intended applications. Fluorophores used in vitro may inform on kinase active site environments, hence the dyes used should be small and have minimal impact on modes of binding. These probes may have short wavelength emissions since blue fluorophores are perfectly adequate in this context. Thus, for instance, KI fragments that mimic nucleobases may be modified to be fluorescent with minimal perturbation to the kinase inhibitor structure. However, progressively larger dyes, that emit at longer wavelengths, are required for cellular and in vivo work. In cells, it is necessary to have emissions above autofluorescence of biomolecules, and near infrared dyes are needed to enable excitation and observation through tissue in vivo. This review is organized to describe probes intended for applications in vitro, in cells, then in vivo. The readers will observe that the probes featured tend to become larger and responsive to the near infared end of the spectrum as the review progresses. Readers may also be surprised to realize that relatively few dyes have been used for fluorophore-kinase inhibitor conjugates, and the area is open for innovations in the types of fluorophores used.

Hows and Whys of Tumor-Seeking Dyes.

Active targeting uses molecular fragments that bind receptors overexpressed on cell surfaces to deliver cargoes, and this selective delivery to diseased over healthy tissue is valuable in diagnostic imaging and therapy. For instance, targeted near-infrared (near-IR) dyes can mark tissue to be excised in surgery, and radiologists can use active targeting to concentrate agents for positron emission tomography (PET) in tumor tissue to monitor tumor metastases. Selective delivery to diseased tissue is also valuable in some treatments wherein therapeutic indexes (toxic/effective doses) are key determinants of efficacy. However, active targeting will only work for cells expressing the pivotal cell surface receptor that is targeted. That is a problem because tumors, even ones derived from the same organ, are not homogeneous, patient-to-patient variability is common, and heterogeneity can occur even in the same patient, so monotherapy with one actively targeted agent is unlikely to be uniformly effective. A particular category of fluorescent heptamethine cyanine-7 (Cy-7) dyes, here called tumor seeking dyes, offer a way to circumvent this problem because they selectively accumulate in any solid tumor. Furthermore, they persist in tumor tissue for several days, sometimes longer than 72 h. Consequently, tumor seeking dyes are near-IR fluorescent targeting agents that, unlike mAbs (monoclonal antibodies), accumulate in any solid lesion, thus overcoming tumor heterogeneity, and persist there for long periods, circumventing the rapid clearance problems that bedevil low molecular mass drugs. Small molecule imaging agents and drugs attached to tumor-seeking dyes have high therapeutic indices and long residence times in cancer cells and tumor tissue. All this sounds too good to be true. We believe most of this is true, but the controversy is associated with how and why these characteristics arise. Prior to our studies, the prevailing hypothesis, often repeated, was that tumor seeking dyes are uptaken by organic anion transporting polypeptides (OATPs) overexpressed on cancer cells. This Account summarizes evidence indicating tumor seeking Cy-7 dyes have exceptional accumulation and persistence properties because they covalently bind to albumin in vivo. That adduct formation provides a convenient way to form albumin-bound pharmaceuticals labeled with near-IR fluorophores which can be tracked in vivo. This understanding may facilitate more rapid developments of generally applicable actively targeted reagents.

Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules.

Small molecule probe development is pivotal in biomolecular science. Research described here was undertaken to develop a non-peptidic chemotype, piptides, that is amenable to convenient, iterative solid-phase syntheses, and useful in biomolecular probe discovery. Piptides can be made from readily accessible pip acid building blocks and have good proteolytic and pH stabilities. An illustrative application of piptides against a protein-protein interaction (PPI) target was explored. The Exploring Key Orientations (EKO) strategy was used to evaluate piptide candidates for this. A library of only 14 piptides contained five members that disrupted epidermal growth factor (EGF) and its receptor, EGFR, at low micromolar concentrations. These piptides also caused apoptotic cell death, and antagonized EGF-induced phosphorylation of intracellular tyrosine residues in EGFR.

Active targeted ligand-aza-BODIPY conjugate for near-infrared photodynamic therapy in melanoma.

Active targeting compound, a non-iodinated derivative of IK-IK-I2-azaBODIPY (1a) was previously reported to preferentially bind melanoma over healthy cells. In this study, we evaluate the photodynamic therapy (PDT) efficiency on melanoma cells of 1a, together with its reversed sequence compound KI-KI-I2-azaBODIPY (1b) and a non-targeted control I2-azaBODIPY-NH2 (2). All three test compounds possess absorption wavelengths in the near-infrared (NIR) region (λmax between 678 and 687 nm) which alleviate melanin interference and allow deeper tissue penetration. In vitro studies revealed 1a and 1b are promising photosensitizers with enhanced singlet oxygen generation, have increased uptake by B16-F10 melanoma cells via clathrin-mediated endocytosis and good photocytotoxic efficacies. Ex vivo biodistribution assays showed both 1a and 1b accumulated in the tumour. In B16-F10 tumour bearing-C57BL/6 mice, 10 mg/kg of 1b and light irradiation was found to reduce tumour volume by up to 23% at day-3. Doubling the dosage of 1b (20 mg/kg) enhanced the antitumour effect, showing 96% maximum tumour volume reduction at day-7 and tumour growth suppression for up to 12 days.

Unconventional Secondary Structure Mimics: Ladder-Rungs.

Secondary structures tend to be recognizable because they have repeating structural motifs, but mimicry of these does not have to follow such well-defined patterns. Bioinformatics studies to match side-chain orientations of a novel hydantoin triazole chemotype (1) to protein-protein interfaces revealed it tends to align well across parallel and antiparallel sheets, like rungs on a ladder. One set of these overlays was observed for the protein-protein interaction uPA⋅uPAR. Consequently, chemotype 1 was made with appropriate side-chains to mimic uPA at this interface. Biophysical assays indicate these compounds did in fact bind uPAR, and elicit cellular responses that affected invasion, migration, and wound healing.

Role of Albumin in Accumulation and Persistence of Tumor-Seeking Cyanine Dyes.

Some heptamethine cyanine dyes accumulate in solid tumors in vivo and persist there for several days. The reasons why they accumulate and persist in tumors were incompletely defined, but explanations based on uptake into cancer cells via organic anion transporting polypeptides (OATPs) have been widely discussed. All cyanine-based "tumor-seeking dyes" have a chloride centrally placed on the heptamethine bridge (a "meso-chloride"). We were intrigued and perplexed by the correlation between this particular functional group and tumor uptake, so the following study was designed. It features four dyes (1-Cl, 1-Ph, 5-Cl, and 5-Ph) with complementary properties. Dye 1-Cl is otherwise known as MHI-148, and 1-Ph is a close analog wherein the meso-chloride has been replaced by a phenyl group. Data presented here shows that both 1-Cl and 1-Ph form noncovalent adducts with albumin, but only 1-Cl can form a covalent one. Both dyes 5-Cl and 5-Ph have a methylene (CH2) unit replaced by a dimethylammonium functionality (N+Me2). Data presented here shows that both these dyes 5 do not form tight noncovalent adducts with albumin, and only 5-Cl can form a covalent one (though much more slowly than 1-Cl). In tissue culture experiments, uptake of dyes 1 is more impacted by the albumin in the media than by the pan-OATP uptake inhibitor (BSP) that has been used to connect uptake of tumor-seeking dyes in vivo with the OATPs. Uptake of 1-Cl in media containing fluorescein-labeled albumin gave a high degree of colocalization of intracellular fluorescence. No evidence was found for the involvement of OATPs in uptake of the dyes into cells in media containing albumin. In an in vivo tumor model, only the two dyes that can form albumin adducts (1-Cl and 5-Cl) gave intratumor fluorescence that persisted long enough to be clearly discerned over the background (∼4 h); this fluorescence was still observed at 48 h. Tumors could be imaged with a higher contrast if 5-Cl is used instead of 1-Cl, because 5-Cl is cleared more rapidly from healthy tissues. Overall, the evidence is consistent with in vitro and in vivo results and indicates that the two dyes in the test series that accumulate in tumors and persist there (1-Cl and 5-Cl, true tumor-seeking dyes) do so as covalent albumin adducts trapped in tumor tissue via uptake by some cancer cells and via the enhanced permeability and retention (EPR) effect.

Small molecules targeting the NEDD8·NAE protein-protein interaction.

Ubiquitination is a major controller of protein homeostasis in cells. Some ubiquitination pathways are modulated by a NEDDylation cascade, that also features E1 - 3 enzymes. The E1 enzyme in the NEDDylation cascade involves a protein-protein interaction (PPI) between NEDD8 (similar to ubiquitin) and NAE (NEDD8 Activating Enzyme). A small molecule inhibitor of the ATP binding site in NAE is in clinical trials. We hypothesized a similar effect could be induced by disrupting the NEDD8·NAE PPI, though, to the best of our knowledge, no small molecules have been reported to disrupt this to date. In the research described here, Exploring Key Orientations (EKO) was used to evaluate several chemotype designs for their potential to disrupt NEDD8·NAE; specifically, for their biases towards orientation of side-chains in similar ways to protein segments at the interface. One chemotype design was selected, and a targeted library of 24 compounds was made around this theme via solid phase synthesis. An entry level hit for disrupting NEDD8·NAE was identified from this library on the basis of its ability to bind NAE (K i of 6.4 ± 0.3 µM from fluorescence polarization), inhibit NEDDylation, suppress formation of the corresponding E1 - 3 complexes as monitored by cell-based immunoblotting, and cytotoxicity to K562 leukemia cells via early stage apoptosis. The cell-based immunoblot assay also showed the compound caused NEDD8 to accumulate in cells, presumably due to inhibition of the downstream pathways involving the E1 enzyme. The affinity and cellular activities of the hit compound are modest, but is interesting as first in class for this mode of inhibition of NEDDylation, and as another illustration of the way EKO can be used to evaluate user-defined chemotypes as potential inhibitors of PPIs.

TrkC-Targeted Kinase Inhibitors And PROTACs.

A small molecule motif (IY-IY), which binds the tropomyosin receptor kinase C (TrkC), was used to deliver the promiscuous kinase inhibitor (KI) dasatinib into breast cancer. Conjugates with noncleavable (1) and cleavable (2) linkers were compared in cellular assays and shown to have more impact on the cell viabilities of TrkC+ breast cancer cells over TrkC- epithelial cells. The IY-IY fragment was also used to recruit the E3 ligase cereblon, giving a potent proteolysis targeting chimeric (PROTAC) for TrkC degradation in metastatic breast cancer cells.

Distribution and Community Assembly of Trees Along an Andean Elevational Gradient.

Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated how patterns of tree diversity and structure change along an elevation gradient using taxonomic and phylogenetic diversity metrics. We sampled 595 individuals (36 families; 53 genera; 88 species) across 15 plots along an elevational gradient (2440-3330 m) in Ecuador. Seventy species were sequenced for the rbcL and matK gene regions to generate a phylogeny. Species richness, Shannon-Weaver diversity, Simpson's Dominance, Simpson's Evenness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD) were evaluated for each plot. Values were correlated with elevation and standardized effect sizes (SES) of MPD and MNTD were generated, including and excluding tree fern species, for comparisons across elevation. Taxonomic and phylogenetic metrics found that species diversity decreases with elevation. We also found that overall the community has a non-random phylogenetic structure, dependent on the presence of tree ferns, with stronger phylogenetic clustering at high elevations. Combined, this evidence supports the ideas that tree ferns have converged with angiosperms to occupy the same habitat and that an increased filtering of clades has led to more closely related angiosperm species at higher elevations.