Five amphiphilic alpha-helical peptides of 18 residues containing a hydrophobic Trp residue as a fluorescence probe were designed. The peptides were made up of hydrophobic Leu and hydrophilic Lys residues of a ratio of 13:5, 11:7, 9:9, 7:11, and 5:13 (abbreviated as Hels 13-5, 11-7, 9-9, 7-11, and 5-13, respectively). These peptides generate ideal amphiphilic alpha-helical structures, which have systematically varied hydrophobic-hydrophilic balance (relative amphiphilic potential) as a result of different hydrophobicities and almost the same hydrophobic moments. Their hydrophobic-hydrophilic balance was estimated both theoretically from the calculated hydrophobicity values (or the magnitude of hydrophobic faces) and experimentally from the retention times in reverse phase high-performance liquid chromatography (RP-HPLC). Circular dichroism, liposome-lytic, and Trp-fluorescent studies in buffer and in the presence of acidic and neutral liposomes clearly showed that the increasing hydrophobic face area not only increases the affinity for lipid but also increases the trend of self-association. The structure-activity relationship estimated by means of leakage ability and hemolytic activity demonstrated that the model- and bio-membrane perturbation ability is completely parallel to the magnitude of the hydrophobic face area. The lipid-binding study in guanidine hydrochloride solution showed that the peptides with a hydrophobic face larger than the hydrophilic face (Hels 13-5 and 11-7) immerse their hydrophobic regions in lipid bilayers and that the inverse ones (Hels 7-11 and 5-13) interact only between the anionic lipid head groups and cationic peptide residues on liposome surfaces. The peptide Hel 9-9, which has exactly the same hydrophobic and hydrophilic regions, was found to be at a critical boundary among these peptides in terms of (1) behavior of peptide self-aggregation in buffer solution and membrane perturbation ability, (2) transfer from bulk solution to neutral lipid bilayers, and (3) necessity of charge interaction in lipid-peptide binding.

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Medulloblastoma (MB) is a pediatric malignant brain tumor composed of four different subgroups (WNT, SHH, Group 3, Group 4), each of which are a unique biological entity with distinct clinico-pathological, molecular, and prognostic characteristics. Although risk stratification of patients with MB based on molecular features may offer personalized therapies, conventional subgroup identification methods take too long and are unable to deliver subgroup information intraoperatively. This limitation prevents subgroup-specific adjustment of the extent or the aggressiveness of the tumor resection by the neurosurgeon. In this study, we investigated the potential of rapid tumor characterization with Picosecond infrared laser desorption mass spectrometry (PIRL-MS) for MB subgroup classification based on small molecule signatures. One hundred and thirteen ex vivo MB tumors from a local tissue bank were subjected to 10-to 15-second PIRL-MS data collection and principal component analysis with linear discriminant analysis (PCA-LDA). The MB subgroup model was established from 72 independent tumors; the remaining 41 de-identified unknown tumors were subjected to multiple, 10-second PIRL-MS samplings and real-time PCA-LDA analysis using the above model. The resultant 124 PIRL-MS spectra from each sampling event, after the application of a 95% PCA-LDA prediction probability threshold, yielded a 98.9% correct classification rate. Post-ablation histopathologic analysis suggested that intratumoral heterogeneity or sample damage prior to PIRL-MS sampling at the site of laser ablation was able to explain failed classifications. Therefore, upon translation, 10-seconds of PIRL-MS sampling is sufficient to allow personalized, subgroup-specific treatment of MB during surgery.Significance: This study demonstrates that laser-extracted lipids allow immediate grading of medulloblastoma tumors into prognostically important subgroups in 10 seconds, providing medulloblastoma pathology in an actionable manner during surgery.

In situ mass spectrometry sampling in the absence of tissue thermal damage.

WD repeat-containing protein 5 (WDR5) is an important component of the multiprotein complex essential for activating mixed-lineage leukemia 1 (MLL1). Rearrangement of the MLL1 gene is associated with onset and progression of acute myeloid and lymphoblastic leukemias, and targeting the WDR5-MLL1 interaction may result in new cancer therapeutics. Our previous work showed that binding of small molecule ligands to WDR5 can modulate its interaction with MLL1, suppressing MLL1 methyltransferase activity. Initial structure-activity relationship studies identified N-(2-(4-methylpiperazin-1-yl)-5-substituted-phenyl) benzamides as potent and selective antagonists of this protein-protein interaction. Guided by crystal structure data and supported by in silico library design, we optimized the scaffold by varying the C-1 benzamide and C-5 substituents. This allowed us to develop the first highly potent (Kdisp < 100 nM) small molecule antagonists of the WDR5-MLL1 interaction and demonstrate that N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide 16d (OICR-9429) is a potent and selective chemical probe suitable to help dissect the biological role of WDR5.

A facile and sensitive mass spectrometric method has been developed for the dereplication of natural products. The method provides information about the molecular formula and substructure of a precursor molecule and its fragments, which are invaluable aids in dereplication of natural products at their early stages of purification and characterization. Collision-induced MS/MS technique is used to fragment a precursor ion into several product ions, and individual product ions are selected and subjected to collision-induced MS/MS/MS analysis. This method enables the identification of the fragmentation pathway of a precursor molecule from its first-generation fragments (MS/MS), through to the nth generation product ions (MSn). It also allows for the identification of the corresponding neutral products released (neutral losses). Elements used in the molecular formula analysis include C, H, N, O, and S, as most natural products are constituted by these five elements. High-resolution mass separation and accurate mass measurements afforded the unique identification of molecular formula of small neutral products. Through sequential add-up of the molecular formulas of the small neutral products, the molecular formula of the precursor ion and its productions were uniquely determined. The molecular formula of the precursor molecule was then reversely used to identify or confirm the molecular formula of the neutral products and that of the productions. The molecular formula of the neutral fragments allowed for the identification of substructures, leading to a rapid and efficient characterization of precursor natural product. The method was applied to paclitaxel (C47H51NO14; 853 amu) to identify its molecular formula and its substructures, and to characterize its potential fragmentation pathways. The method was further validated by correctly identifying the molecular formula of minocycline (C23H27N3O7; 457 amu) and piperacillin (C23H27N5O7S; 517 amu).

Cellular organelles, such as the Golgi apparatus and the endoplasmic reticulum, adopt characteristic structures depending on their function. While the tubular shapes of these structures result from complex proteinlipid interactions that are not fully understood, some fundamental machinery must be required. We show here that a de novo-designed 18-mer amphipathic ␣-helical peptide, Hel 13-5, transforms spherical liposomes made from a Golgi-specific phospholipid mixture into nanotubules on the scale of and resembling the shape of the nanotubules that form the Golgi apparatus. Furthermore, we show that that the size and the shape of such nanotubules depend on lipid composition and peptide properties such as length and the ratio of hydrophobic to hydrophilic amino acids. Although the question of precisely how nature engineers organellar membranes remains unknown, our simple novel system provides a basic set of tools to begin addressing this question.Cellular organelles like the Golgi apparatus and the endoplasmic reticulum adopt characteristic structures depending on their function (1, 2). For example, extensive membrane nanotubules, typically 50 -70 nm in diameter and up to several m in length, have been observed to form the Golgi complex, the trans Golgi network, and the connections between the Golgi stacks. The morphological engineering of these membranes involve complex interactions between proteins and lipids that are not yet understood (3, 4). However, there must be some fundamental machinery required to form such structures.We recently described the properties of a de novo-designed 18-mer peptide, Hel 13-5 (5, 6). This peptide can adopt an ideal ␣-helix having a 240°hydrophobic sector region (Fig. 1A). It forms a self-association state in buffer solution by adopting this amphipathic structure (70% ␣-helical structure by CD), and it binds to model-and biomembranes with high affinity. In the present study, we show that Hel 13-5 induces nanotubular structures, not only for PC liposomes, but also for various naturally occurring phospholipids. Most importantly, we demonstrate that Hel 13-5 transforms spherical liposomes made from a Golgi-specific phospholipid mixture into nanotubules on the scale of, and resembling the shape of, the nanotubules of the Golgi apparatus. MATERIALS AND METHODSReagents-Peptide was synthesized by the Fmoc 1 strategy based on the solid phase technique starting from Fmoc-PAL-PEG resin using a PerSeptive 9050 automatic peptide synthesizer described previously (5). The stock solutions of Hel peptides were prepared as follows: the powders were damped with a small amount of 30% acidic acid and then diluted in buffer (5 mM Tes/100 mM NaCl, pH 7.4). The peptide concentrations in the buffer solution were determined from the UV absorbance of Trp at 280 nm (⑀ ϭ 5500).Turbidity Measurement-A lipid solution in chloroform was filmed in a round bottom flask by drying in a stream of N 2 gas. The lipid film was hydrated with the Tes buffer by vortexing. The turbid liposome solution obtained was then dilu...

The core or the building block is an important component in drug development. In this article, we propose and review p-aminobenzoic acid (PABA) as a building block used in the design of drugs or drug candidates. PABA is frequently found as a structure moiety in drugs. For example, in a database of 12,111 commercial drugs, 1.5% (184 drugs) were found to contain the PABA moiety. These drugs have a wide range of therapeutic uses, such as: sun-screening, antibacterial, antineoplastic, local anesthetic, anticonvulsant, anti-arrhythmic, anti-emetic, gastrokinetic, antipsychotic, neuroleptic, and migraine prophylactic. This article reviews the molecular targets and the mechanisms of these activities. Drugs containing PABA also show a wide range of structural diversity. Of the 184 PABA containing drugs identified, 95 different substitutions were found at the carboxylic group and 61 were found at the amino group of the building block. Substitution on the aromatic ring was also diverse. 13, 3, and 13 different side chains were found to modify positions 2, 3 and 5 of the aromatic ring respectively. In some drugs, the amino group is further substituted to form tertiary amine (4 different side chains). Substitutions at the carboxyl and amino groups of PABA are particularly suitable for the generation of combinatorial libraries. Just by reshuffling the identified side chains of the 184 PABA containing drugs, 4.5 million compounds can be generated. Consequently, PABA fits well as a building block for a general chemical library of "drug-like" molecules with a wide range of functional and structural diversity.