Mimicking LysC Proteolysis by 'Arginine Modification-cum-Trypsin Digestion': Comparison of Bottom-up & Middle-down Proteomic Approaches by ESI Q-TOF MS.

BACKGROUND: Middle-down (MD) proteomics is an emerging approach for reliable identification of post-translational modifications and isoforms, as this approach focuses on proteolytic peptides containing > 25-30 amino acid residues (a.a.r.), which are longer than typical tryptic peptides. Such longer peptides can be obtained by AspN, GluC, and LysC proteases. Additionally, some special proteases were developed specifically to effect MD approach, e.g., OmpT, Sap9, etc. However, these proteases are expensive. Herein we report a cost-effective strategy 'arginine modification- cum trypsin digestion', which can produce longer tryptic peptides resembling LysC peptides derived from proteins. OBJECTIVE: The aim of this study is to obtain proteolytic peptides that resemble LysC peptides by using 'trypsin', which is a less expensive protease. METHODS: This strategy is based on the simple principle that trypsin cannot act at the C-termini of those arginines in proteins, whose sidechain guanidine groups are modified by 1,2-cyclohexanedione or phenylglyoxal. RESULTS: As a proof of concept, we demonstrate this strategy on four models: ß-casein (bovine), ß- lactoglobulin (bovine), ovalbumin (chick) and transferrin (human), by electrospray ionization-mass spectrometry (ESI-MS) involving hybrid quadrupole time-of-flight. From the ESI-MS of these models, we obtained several arginine modified tryptic peptides, whose lengths are in the range of 30-60 a.a.r. The collision induced dissociation MS/MS characteristics of some of the arginine modified longer tryptic peptides are compared with the unmodified standard tryptic peptides. CONCLUSION: The strategy demonstrated in this proof-of-concept study is not only useful to obtain longer tryptic peptides that mimic LysC proteolytic peptides, but also facilitates in enhancing the probability of missed cleavages by the trypsin. Hence, this method aids in evading the possibility of obtaining very short peptides that are <5-10 a.a.r. Therefore, this is indeed a cost-effective alternative/ substitute for LysC proteolysis and, in turn, for those MD proteomic studies that utilize LysC. Additionally, this methodology can be fruitful for mass spectrometry-based de novo protein and peptide sequencing.

Gas-phase basicity and proton affinity measurements of Alzheimer's disease drugs by the extended kinetic method and a theoretical investigation.

This study has been carried out to obtain the thermochemical parameters of drugs used for Alzheimer's disease. The measurement of gas-phase basicity (GB) and proton affinity (PA) values of four important and commercially available drugs for Alzheimer's disease namely, rivastigmine, galantamine, memantine, and tacrine, is attempted for the first time. This study also includes the measurement of GB and PA values for the proposed drug curcumin, a natural product. We calculated the GB and PA values for all these drugs by applying electrospray ionization tandem mass spectrometry (ESI-MS/MS) with the extended kinetic method. Since, all these drugs possessing amino groups (basic nature), the PA values for all these drugs are high i.e., the PA values range from 923.6 to 979.7 kJ/mol and the GB values range from 886.2 to 943.3 kJ/mol. The GB and PA values obtained from the mass spectrometric experiments are well supported with the theoretical calculations. A high-level theoretical B3LYP/6-311 + G(d,p) method is used for the PA and GB calculation and the deviations are in the acceptable range.

Characterization of degradation products of silodosin under stress conditions by liquid chromatography/Fourier transform mass spectrometry.

RATIONALE: Silodosin (SDN) is a novel α1 -adrenoceptor antagonist in the treatment of benign prostatic hyperplasia (BPH). The presence of degradation products in a drug affects not only the quality, but also the safety and efficacy of drug formulation. Thus, it is essential to develop an efficient analytical method which could be useful to selectively separate, identify and characterise of all possible degradation products of SDN which is mandatory in drug development processes. METHODS: SDN was subjected to forced degradation under hydrolytic (acid, base and neutral), oxidative, photolytic and thermal stress conditions. Separation of the drug and degradation products was achieved by a liquid chromatography (LC) method using an Acquity UPLC® BEH C18 (2.1 × 100 mm, 1.7 µm; Waters) column with mobile phase consisting of 0.1% formic acid (FA) in water (A) and 0.1% FA in acetonitrile (ACN) and methanol (MeOH) (1:1) (B) as organic modifier at a flow rate of 0.15 mL min-1 in gradient elution mode. Identification and characterization of the degradation products was performed by mass spectrometry methods using an LTQ-Orbitrap mass spectrometer. RESULTS: A total of five degradation products (DP1 to DP5) were formed under various stress conditions and their structures were proposed with the help of tandem mass spectrometry (MS/MS) experiments and high-resolution mass spectral data. A common degradation product (DP1) was observed under acidic and basic degradation conditions. DP2 was observed under acidic, DP4 and DP5 were observed under basic hydrolytic conditions, whereas DP3 was observed under oxidative conditions. CONCLUSIONS: SDN was found to be labile under hydrolytic and oxidative conditions. The structures of all the degradation products were proposed. The most rational mechanisms for the formation of the degradation products under different stress conditions have been established. The proposed method can be effectively used to carry out the determination and detection of SDN and its degradation products. Copyright © 2017 John Wiley & Sons, Ltd.

Mitochondria-targeted esculetin alleviates mitochondrial dysfunction by AMPK-mediated nitric oxide and SIRT3 regulation in endothelial cells: potential implications in atherosclerosis.

Mitochondria-targeted compounds are emerging as a new class of drugs that can potentially alter the pathophysiology of those diseases where mitochondrial dysfunction plays a critical role. We have synthesized a novel mitochondria-targeted esculetin (Mito-Esc) with an aim to investigate its effect during oxidative stress-induced endothelial cell death and angiotensin (Ang)-II-induced atherosclerosis in ApoE(-/-) mice. Mito-Esc but not natural esculetin treatment significantly inhibited H2O2- and Ang-II-induced cell death in human aortic endothelial cells by enhancing NO production via AMPK-mediated eNOS phosphorylation. While L-NAME (NOS inhibitor) significantly abrogated Mito-Esc-mediated protective effects, Compound c (inhibitor of AMPK) significantly decreased Mito-Esc-mediated increase in NO production. Notably, Mito-Esc promoted mitochondrial biogenesis by enhancing SIRT3 expression through AMPK activation; and restored H2O2-induced inhibition of mitochondrial respiration. siSIRT3 treatment not only completely reversed Mito-Esc-mediated mitochondrial biogenetic marker expressions but also caused endothelial cell death. Furthermore, Mito-Esc administration to ApoE(-/-) mice greatly alleviated Ang-II-induced atheromatous plaque formation, monocyte infiltration and serum pro-inflammatory cytokines levels. We conclude that Mito-Esc is preferentially taken up by the mitochondria and preserves endothelial cell survival during oxidative stress by modulating NO generation via AMPK. Also, Mito-Esc-induced SIRT3 plays a pivotal role in mediating mitochondrial biogenesis and perhaps contributes to its anti-atherogenic effects.

Evaluating the cation binding strength and selectivity of calix[4]pyrroles: a computational and ESI-MS/MS study.

The cation binding strength of calix[4]pyrroles in the gas phase has been evaluated by computational studies and further substantiated by ESI mass spectrometry experiments. The DFT optimized geometries of [CP + X](+) complexes are found to be stable in a 1,3-alternate conformation through cation-π interactions and interestingly CPs are found to be better cation receptor than calix[4]arenes. The binding energy values of [CP + X](+) complexes computed at B2PLYP/TZVP//M05-2X/TZVP follows the binding order, Li(+) > Na(+) > K(+) > Rb(+) > Cs(+). The diameter of Li(+) matches very well with the cavity size of CP and thus is optimally disposed to interact simultaneously with all four pyrrole rings through multiple cation-π interactions. However, other cations, due to the increase in their size, drift away from the cavity center towards the rim of the cavity exhibiting weak cation-π interactions. Energy decomposition analysis (EDA) reveals that the electrostatic and polarization effects act as the major driving force in these interactions. The important outcome of the current study is that the stability of precursor and product ions is found to be crucial in the experimental evaluation of binding affinity of Li(+) and Na(+) complexes of CP. The ESI-MS/MS experiments on the cation complexes of different substituted CPs revealed that the binding strength of CPs towards cations is also dependant on the substituents at the meso-position.

Mitochondrial-targeted curcuminoids: a strategy to enhance bioavailability and anticancer efficacy of curcumin.

Although the anti-cancer effects of curcumin has been shown in various cancer cell types, in vitro, pre-clinical and clinical studies showed only a limited efficacy, even at high doses. This is presumably due to low bioavailability in both plasma and tissues, particularly due to poor intracellular accumulation. A variety of methods have been developed to achieve the selective targeting of drugs to cells and mitochondrion. We used a novel approach by conjugation of curcumin to lipophilic triphenylphosphonium (TPP) cation to facilitate delivery of curcumin to mitochondria. TPP is selectively taken up by mitochondria driven by the membrane potential by several hundred folds. In this study, three mitocurcuminoids (mitocurcuminoids-1, 2, and 3) were successfully synthesized by tagging TPP to curcumin at different positions. ESI-MS analysis showed significantly higher uptake of the mitocurcuminoids in mitochondria as compared to curcumin in MCF-7 breast cancer cells. All three mitocurcuminoids exhibited significant cytotoxicity to MCF-7, MDA-MB-231, SKNSH, DU-145, and HeLa cancer cells with minimal effect on normal mammary epithelial cells (MCF-10A). The IC50 was much lower for mitocurcuminoids when compared to curcumin. The mitocurcuminoids induced significant ROS generation, a drop in ΔØm, cell-cycle arrest and apoptosis. They inhibited Akt and STAT3 phosphorylation and increased ERK phosphorylation. Mitocurcuminoids also showed upregulation of pro-apoptotic BNIP3 expression. In conclusion, the results of this study indicated that mitocurcuminoids show substantial promise for further development as a potential agent for the treatment of various cancers.

Concomitant nitrene and carbene insertion accompanying ring expansion: spectroscopic, X-ray, and computational studies.

Reinvestigation of the thermolysis of azido-meta-hemipinate (I) yielded, in addition to known II, unusual products III and IV. These products are formed via a rare intramolecular nitrene insertion into an adjacent methoxy C-H bond followed by an intermolecular reaction during a ring-expansion and a ring-extrusion reaction followed by a carbene insertion. The structures of the new compounds were confirmed using a battery of techniques, including HRMS (ESI-QTOF) and 2D NMR as well as X-ray crystallography for compound IV. Density functional theory methods were used to support the proposed mechanism of formation of the products.

Iodine-catalyzed tandem synthesis of terminal acetals and glycol mono esters from olefins.

A new metal-free protocol is described for the synthesis of terminal acetals by tandem oxidative rearrangement of olefins using oxone as an oxidant in the presence of iodine. Moreover, a one-pot procedure for the preparation of glycol mono esters from olefins is also presented for the first time using the same reagent system.

Differential interactions of isomeric amino sugars with insulin studied under electrospray ionisation mass spectrometry.

Protein-ligand interactions were studied for bovine insulin-amino sugar systems under electrospray ionisation mass spectrometry conditions. The isomeric amino sugars showed differences in the relative abundance of 1:1 protein-ligand complex formation. The electrospray ionisation and tandem mass spectrometry results of the complex clearly demonstrated that the differences in the interaction of isomeric sugars with insulin are mainly due to the differences in their gas-phase basicity. The same phenomenon is replicated in the formation of complexes between insulin and other ligands, such as amino acids, as well as in the binding of the amino sugars with amyloid ß 1-40 peptide.

Differentiation of diasteromeric α-sulfanyl-ß-amino acid derivatives by electrospray ionization tandem mass spectrometry.

A set of diastereomeric α-sulfanyl-ß-amino acid derivatives, which are important building blocks for pharmaceuticals with potent biological activity, are studied by electrospray ionization tandem mass spectrometry. The collision induced dissociation (CID) spectra of [M+H](+), [M+NH(4)](+), [M+Na](+) and [M+Li](+) of the diastereomers were studied, among them the CID of [M+Na](+) and [M+Li](+) showed consistent differences in the relative abundance of characteristic ions that enabled distinction of the anti isomers from syn isomers. The decomposition pathways for the diagnostic ions were arrived at based on high-resolution mass spectrometry data, multiple mass spectrometry data, deuterium labeling experiments and the mass shift in accordance with the substituents located at different places. Loss of (R(1)-C(6)H(4)-CH=NH) and (Cat-NH-SO(2)R(2)) from [M+Cat](+), where Cat=Na and Li, and the product ions as a results of McLafferty rearrangement involving either >S=O or >C=O group were found to be diagnostic. The McLafferty rearrangement product ions involving >S=O group were more abundant in syn isomers while those involving >C=O group were more abundant in anti isomer. The selectivity observed in the decomposition of [M+Li](+) ions was found to be similar to that of [M+Na](+) ions, but in few cases the differences are marginal in the decomposition [M+Li](+) ions.

Chiral discrimination of drugs by DNA tetranucleotides under electrospray ionisation conditions.

The DNA tetranucleotides, extended versions of GCA at the 3'-end or 5'-end, were used as chiral selectors for the chiral discrimination of atenolol, DOPA, tamsulosin, valacyclovir and zolmitriptan. Chiral discrimination was achieved by investigating the collision-induced dissociation spectra of the [X+Y-2H](2-) ion generated by electrospraying a solution mixture of tetranucleotide (X) and R- or S-analyte drug (Y). The relative abundances of the precursor ion and the product ion, resulting from the loss of drug, were considered for measuring the degree of chiral discrimination. Among all the tetranucleotides studied, AGCA showed the highest chiral discrimination. The present study emphasised the position of an adenine base in the tetranucleotide in chiral discrimination. The suitability of the method for the measurement of optical purity was also demonstrated in the case of zolmitriptan.

Estimation of gas-phase acidities of deoxyribonucleosides: an experimental and theoretical study.

We determined the gas-phase acidities (DeltaH(acid)) of four deoxyribonucleosides, i.e., 2'-deoxyadenosine (dA), 2'-deoxyguanosine (dG), 2'-deoxycytidine (dC), and 2'-deoxythymidine (dT) by applying the extended kinetic method. The negatively charged proton-bound hetero-dimeric anions, [A - H - B](-) of the deoxyribonucleosides (A) and reference compounds (B) were generated under electrospray ionization conditions. Collision-induced dissociation spectra of [A - H - B](-) were recorded at four different collision energies using a triple quadrupole mass spectrometer. The abundance ratios of the individual monomeric product ions were used to determine the DeltaH(acid) of the deoxyribonucleosides. The obtained DeltaH(acid) value follows the order dA > dC > dT > dG. The DeltaG(acid) (298 K) values were determined by using DeltaG(acid) = DeltaH(acid) - TDeltaS(acid) where the DeltaH(acid) and DeltaS(acid) values were determined directly from the kinetic method plots. The DeltaH(acid) values were also predicted for the deoxyribonucleosides at the B3LYP/6-311+G**//B3LYP/6-311G** level of theory. The acidity trend obtained from the computational investigation shows good agreement with that obtained experimentally by the extended kinetic method. Theoretical calculations provided the most preferred deprotonation site as C5'-OH from sugar moiety in case of dA, and as -NH(2) (dC and dG) or -NH- (dT) from nitrogenous base moiety in the case of other deoxyribonucleosides.

Exploration of mononucleotides as fixed ligands towards chiral discrimination of hexose monosaccharides by the kinetic method.

The most recent version of the kinetic method, i.e. fixed ligand method, is applied towards chiral discrimination of three pairs of enantiomeric hexose monosaccharides under mass spectral conditions. Naturally occurring mononucleotides are used as fixed ligands (FL) and the amino acids are selected as the chiral references (ref) to discriminate the analyte (A), the enantiomers of glucose, mannose and galactose. Chiral discrimination is achieved by investigating the collision-induced dissociation spectra of trimeric complex ion, [Ni(II)(FL)(ref)(A)-H](+) generated by electrospraying the solution mixture of D- or L- analyte (A), FL, amino acid (ref) and NiCl(2). The relative abundance of product ions resulting from the competitive loss of reference amino acid and analyte are considered for measuring the degree of chiral discrimination by applying the kinetic method. L-Asp, L-Thr, L-Glu, L-Trp and L-Ser are found as suitable reference compounds. Among the tested mononucleotides (5'AMP, 5'GMP, 5'CMP, 5'UMP and 5'TMP), 5'GMP is found to be the best for the studied analytes. Chiral discrimination is found to depend on the nature of the monosaccharide, the functional groups present in the side chain of reference amino acids and the configuration of reference amino acids.

Chiral discrimination of alpha-amino acids by the DNA triplet GCA using amino acids as a co-selector.

The DNA triplet GCA is successfully used as a chiral selector for the chiral discrimination of amino acids using amino acids themselves as a co-selector. Chiral discrimination was achieved by investigating the collision-induced dissociation spectra of the [X(A) + X(R) + 2Y - 2H](2-) ion generated by electrospraying a mixture of analyte amino acid (X(A)), reference amino acid (X(R)) and GCA (Y). The relative abundances of fragment ions resulting from the competitive loss of reference and X(A)'s are considered for measuring the degree of chiral discrimination. GCA successfully shows D-selectivity for all the amino acids, except Tyr and Lys. The success of the method lies in the selection of a suitable 10(R) that has closer GCA binding affinity to that of analyte. The degree of discrimination by GCA is improved in the presence of the reference, and the chirality of the reference does not change the selectivity of GCA. The suitability of the method for the measurement of optical purity is also demonstrated.

Chiral discrimination of D- and L-amino acids using iodinated tyrosines as chiral references: effect of iodine substituent.

L-Tyrosine and iodinated L-tyrosines, i.e., 3-iodo-L-tyrosine and 3,5-diiodo-L-tyrosine, are successfully used as chiral references for the chiral discrimination of aliphatic, acidic, and aromatic amino acids. Chiral discrimination is achieved by investigating the collision-induced dissociation spectra of the trimeric complex [Cu(II)(ref)(2)(A) - H](+) ion generated by electro spraying the mixture of D- or L-analyte amino acid (A), chiral reference ligand (ref) and M(II)Cl(2) (M = Ni and Cu). The relative abundances of fragment ions resulted by the competitive loss of reference and analyte amino acids are considered for measuring the degree of chiral discrimination by applying the kinetic method. The chiral discrimination ability increases as the number of iodine atom increases on the aromatic ring of the reference and the discrimination is better with Cu when compared with Ni. A large chiral discrimination is obtained for aliphatic and aromatic amino acids using iodinated L-tyrosine as the reference. Computational studies on the different stabilities of the diastereomeric complexes also support the observed differences measured by the kinetic method. The suitability of the method in the measurement of enantiomeric excess over the range of 2% to 100% ee with relative error 0.28% to 1.6% is also demonstrated.

Chiral discrimination of alpha-amino acids by the DNA triplet GCA.

The DNA triplet GCA is successfully used for the first time as a chiral selector for the chiral discrimination and optical purity measurement of some alpha-amino acids by investigating the collision-induced dissociation spectra of the sodiated ternary complex ion formed by electrospray ionization.

Unraveling adaptive evolution: how a single point mutation affects the protein coregulation network.

Understanding the mechanisms of evolution requires identification of the molecular basis of the multiple (pleiotropic) effects of specific adaptive mutations. We have characterized the pleiotropic effects on protein levels of an adaptive single-base pair substitution in the coding sequence of a signaling pathway gene in the bacterium Pseudomonas fluorescens SBW25. We find 52 proteomic changes, corresponding to 46 identified proteins. None of these proteins is required for the adaptive phenotype. Instead, many are found within specific metabolic pathways associated with fitness-reducing (that is, antagonistic) effects of the mutation. The affected proteins fall within a single coregulatory network. The mutation 'rewires' this network by drawing particular proteins into tighter coregulating relationships. Although these changes are specific to the mutation studied, the quantitatively altered proteins are also affected in a coordinated way in other examples of evolution to the same niche.

Isolation and characterization of cotiaractivase, a novel low molecular weight prothrombin activator from the venom of Bothrops cotiara.

In this study, we isolated a novel prothrombin activator from the venom of Bothrops cotiara, a Brazilian lance-headed pit viper (Cotiara, Jararaca preta, Biocotiara), which we have designated "cotiaractivase" (prefix: cotiar- from B. cotiara; suffix: -activase, from prothrombin activating activity). Cotiaractivase was purified using a phenyl-Superose hydrophobic interaction column followed by a Mono-Q anion exchange column. It is a single-chain polypeptide with a molecular weight of 22,931 Da as measured by mass spectroscopy. Cotiaractivase generated active alpha-thrombin from purified human prothrombin in a Ca2+-dependent manner as assessed by S2238 chromogenic substrate assay and SDS-PAGE. Cotiaractivase cleaved prothrombin at positions Arg271-Thr272 and Arg320-Ile321, which are also cleaved by factor Xa. However, the rate of thrombin generation by cotiaractivase was approximately 60-fold less than factor Xa alone and 17 x 10(6)-fold less than the prothrombinase complex. The enzymatic activity of cotiaractivase was inhibited by the chelating agent EDTA, whereas the serine protease inhibitor PMSF had no effect on its activity, suggesting that it is a metalloproteinase. Interestingly, S2238 inhibited cotiaractivase activity non-competitively, suggesting that this toxin contains an exosite that allows it to bind prothrombin independently of its active site. Tandem mass spectrometry and N-terminal sequencing of purified cotiaractivase identified peptides that were identical to regions of the cysteine-rich and disintegrin-like domains of known snake venom metalloproteinases. Cotiaractivase is a unique low molecular weight snake venom prothrombin activator that likely belongs to the metalloproteinase family of proteins.

Nef-mediated lipid raft exclusion of UbcH7 inhibits Cbl activity in T cells to positively regulate signaling.

Lentiviral Nef increases T cell signaling activity, but the molecular nature of the stimulus involved is incompletely described. We explored CD4 T cell lipid raft composition in the presence and absence of Nef. Here, the E2 ubiquitin-conjugating enzyme UbcH7, which acts in conjunction with c-Cbl, is absent from lipid rafts. This Nef-mediated exclusion is associated with failure of ubiquitination of activated Vav. In the presence of Nef, lipid raft Cdc42 is activated and forms a ternary complex between the c-Cbl-interacting protein p85Cool-1/betaPix and c-Cbl, displacing UbcH7 from rafts. Suppression of p85Cool-1/betaPix expression restores UbcH7 raft localization and Vav ubiquitination and diminishes Cdc42 activity. Moreover, p85Cool-1/betaPix knockdown attenuates HIV replication. Thresholds for activation of signaling involve the intricate balance of positive and negative regulators. Here we provide evidence for Nef disruption of a negative regulator of T cell signaling in promoting HIV replication.

Extensive analysis of the human platelet proteome by two-dimensional gel electrophoresis and mass spectrometry.

Platelets play a key role in the control of bleeding and wound healing, contributing to the formation of vascular plugs. Under pathologic circumstances, they are involved in thrombotic disorders, including heart disease. Since platelets do not have a nucleus, proteomics offers a powerful alternative approach to provide data on protein expression in these cells, helping to address their biology. In this publication we extend the previously reported analysis of the pI 4-5 region of the human platelet proteome to the pI 5-11 region. By using narrow pI range two-dimensional electrophoresis (2-DE) for protein separation followed by high-throughput tandem mass spectrometry (MS/MS) for protein identification, we were able to identify 760 protein features, corresponding to 311 different genes, resulting in the annotation of 54% of the pI 5-11 range 2-DE proteome map. We evaluated the physicochemical properties and functions of the identified platelet proteome. Importantly, the main group of proteins identified is involved in intracellular signalling and regulation of the cytoskeleton. In addition, 11 hypothetical proteins are reported. In conclusion, this study provides a unique inventory of the platelet proteome, contributing to our understanding of platelet function and building the basis for the identification of new drug targets.