Side-chain Fragmentation Research Articles

Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase.

The sensitivity to protein inhibitors is altered by modifications or protein mutations, as represented by drug resistance. The mode of stable drug binding to the protein pocket has been experimentally clarified. However, the nature of the binding of inhibitors with reduced sensitivity remains unclear at the atomic level. In this study, we analyzed the thermodynamics and kinetics of inhibitor binding to the surface of wild-type and mutant dihydrofolate reductase (DHFR) using molecular dynamics simulations combined with Markov state modeling. A strong inhibitor of methotrexate (MTX) showed a preference for the active site of wild-type DHFR with minimal binding to unrelated (secondary) sites. Deletion of a side-chain fragment in MTX largely destabilized the active site-bound state, with clear evidence of binding to secondary sites. Similarly, the F31V mutation in DHFR diminished the specificity of MTX binding to the active site. These results reveal the presence of multiple-bound states whose stabilities are comparable to or higher than those of the unbound state, suggesting that a reduction in the binding affinity for the active site significantly elevates the fractions of these states. This study presents a theoretical model that more accurately interprets the altered drug sensitivity than the traditional two-state model.

Vinyl-addition polynorbornenes with glycerol and diethylene glycol moieties: Synthesis and structure-property study

A set of new norbornene-type monomers containing linear and branched substituents with three C–O–C fragments was synthesized in good yields from commercially available glycerol and diethylene glycol monomethyl ether. Vinyl-addition polymerization of the synthesized monomers was systematically studied, and highly active Pd-catalysts that made it possible to reach quantitative conversions of the monomers were suggested for their polymerization. As a result, robust thin membranes were successfully prepared directly from the polymerization mixtures in the air. Gas separation performance for a wide range of gases was evaluated for the synthesized polymers, and new valuable structure-property relationships were found. More specifically, these membranes display the facilitated transport of CO2 and solubility-controlled hydrocarbon separation selectivity. The increase in the amount of C–O–C fragments in side chains enhances these effects, but only in the case of the linear structure of the substituents. If the structure of side chains becomes branched, the gas permeability is reduced, the facilitated transport of CO2 is minimized, and the polymer becomes more susceptible to plasticization by butane. The facilitated transport of CO2 is due to the specific dipole-quadrupole interaction between CO2 molecules and polymer matrix. For the studied polymers, the contribution of this specific interaction to the solubility of CO2 achieves 64 %. The significant influence of alkyl tails in side chains on gas transport properties was also observed. To achieve better gas separation performance, it is desirable to incorporate short and rigid alkyl tails. Thus, among substituents containing ether moieties, linear oligoethylene glycols with methyl tails seem to be the most promising side-chain substituents for the macromolecular design of CO2-selective polymeric membrane materials. The results obtained were considered along with NMR, TGA, DSC, DMA, and WAXD data.

Discovery and structure-activity relationship studies of novel Bcl-2/Mcl-1 dual inhibitors with indole scaffold

The Bcl-2 anti-apoptotic proteins were widely overexpressed in diverse tumor cells, especially for Bcl-2 and Mcl-1, which regarding as important targets of apoptosis induction and resistance of chemotherapy. We identified novel Bcl-2/Mcl-1 dual inhibitors with indole scaffold by the optimization of hit 1. Structure modification against several moieties including hydrophobic fragment, side chain and benzoic acid fragment was conducted and the structure-activity relationship was analyzed. The representative compound 12f exhibited sub-micromolar binding affinities to Bcl-2/Mcl-1 without binding affinity to Bcl-XL. Mechanism of action studies suggested that compound 12f dose-dependently triggered apoptosis in HL-60 cells. Compound 12f represents a novel Bcl-2/Mcl-1 dual inhibitor which deserving further study.

Differentiating aspartic acid isomers and epimers with charge transfer dissociation mass spectrometry (CTD-MS).

The ability to understand the function of a protein often relies on knowledge about its detailed structure. Sometimes, seemingly insignificant changes in the primary structure of a protein, like an amino acid substitution, can completely disrupt a protein's function. Long-lived proteins (LLPs), which can be found in critical areas of the human body, like the brain and eye, are especially susceptible to primary sequence alterations in the form of isomerization and epimerization. Because long-lived proteins do not have the corrective regeneration capabilities of most other proteins, points of isomerism and epimerization that accumulate within the proteins can severely hamper their functions and can lead to serious diseases like Alzheimer's disease, cancer and cataracts. Whereas tandem mass spectrometry (MS/MS) in the form of collision-induced dissociation (CID) generally excels at peptide characterization, MS/MS often struggles to pinpoint modifications within LLPs, especially when the differences are only isomeric or epimeric in nature. One of the most prevalent and difficult-to-identify modifications is that of aspartic acid between its four isomeric forms: L-Asp, L-isoAsp, D-Asp, and D-isoAsp. In this study, peptides containing isomers of Asp were analyzed by charge transfer dissociation (CTD) mass spectrometry to identify spectral features that could discriminate between the different isomers. For the four isomers of Asp in three model peptides, CTD produced diagnostic ions of the form cn+57 on the N-terminal side of iso-Asp residues, but not on the N-terminal side of Asp residues. Using CTD, the L- and D forms of Asp and isoAsp could also be differentiated based on the relative abundance of y- and z ions on the C-terminal side of Asp residues. Differentiation was accomplished through a chiral discrimination factor, R, which compares an ion ratio in a spectrum of one epimer or isomer to the same ion ratio in the spectrum of a different epimer or isomer. The R values obtained using CTD are as robust and statistically significant as other fragmentation techniques, like radical directed dissociation (RDD). In summary, the extent of backbone and side-chain fragments produced by CTD enabled the differentiation of isomers and epimers of Asp in a variety of peptides.

Photo-induced fragmentation of tyrosine side chains in IgG4-Fc: Effect of protein sequence, conformation and glycan structure

This account summarizes recent work on photo-induced side chain cleavage reactions of Tyr in IgG4-Fc. These processes are initiated via photo-ionization of Trp to a Trp radical cation, followed by one-electron oxidation of Tyr to a Tyr radical cation, where fragmentation of the Cα-Cβ bond leads to an intermediary glycyl radical. The latter converts into Gly via hydrogen atom transfer, or into various backbone cleavage products subsequent to the addition of oxygen. Site-directed mutation of Trp381 to Phe381 significantly reduces the yields of Tyr side chain cleavage products, underlining a critical role of Trp for these reactions. Likewise, conformational changes of IgG4-Fc induced by increasing contents of 1-propanol in the solution diminishes the yields of Tyr side chain cleavage products. Variations of the glycan structure at Asn297 had an effect on Tyr side chain cleavage, where larger glycan structures led to lower yields. This result is in interesting contrast to Trp side chain cleavage in IgG1-Fc, where larger glycan structures led to higher yields. The opposite trends for Trp and Tyr side chain cleavage as a function of glycan structure are consistent with a connection between the precursors for both reactions, radical cations of Trp and Tyr, related by electron transfer. The potential significance of these reactions for protein integrity in formulations of pharmaceutical proteins will be discussed.

Improved Protein and PTM Characterization with a Practical Electron-Based Fragmentation on Q-TOF Instruments.

Electron-based dissociation (ExD) produces uncluttered mass spectra of intact proteins while preserving labile post-translational modifications. However, technical challenges have limited this option to only a few high-end mass spectrometers. We have developed an efficient ExD cell that can be retrofitted in less than an hour into current LC/Q-TOF instruments. Supporting software has been developed to acquire, process, and annotate peptide and protein ExD fragmentation spectra. In addition to producing complementary fragmentation, ExD spectra enable many isobaric leucine/isoleucine and isoaspartate/aspartate pairs to be distinguished by side-chain fragmentation. The ExD cell preserves phosphorylation and glycosylation modifications. It also fragments longer peptides more efficiently to reveal signaling cross-talk between multiple post-translational modifications on the same protein chain and cleaves disulfide bonds in cystine knotted proteins and intact antibodies. The ability of the ExD cell to combine collisional activation with electron fragmentation enables more complete sequence coverage by disrupting intramolecular electrostatic interactions that can hold fragments of large peptides and proteins together. These enhanced capabilities made possible by the ExD cell expand the size of peptides and proteins that can be analyzed as well as the analytical certainty of characterizing their post-translational modifications.

Electron-Transfer-Induced Side-Chain Cleavage in Tryptophan Facilitated through Potassium-Induced Transition-State Stabilization in the Gas Phase.

Fragmentation of transient negative ions of tryptophan molecules formed through electron transfer in collisions with potassium atoms is presented for the first time in the laboratory collision energy range of 20 up to 100 eV. In the unimolecular decomposition process, the dominating side-chain fragmentation channel is assigned to the dehydrogenated indoline anion, in contrast to dissociative electron attachment of free low-energy electrons to tryptophan. The role of the collision complex formed by the potassium cation and tryptophan negative ion in the electron transfer process is significant for the mechanisms that operate at lower collision energies. At those collision times, on the order of a few tens of fs, the collision complex may not only influence the lifetime of the anion but also stabilize specific transition states and thus alter the fragmentation patterns considerably. DFT calculations, at the BHandHLYP/6-311++G(3df,2pd) level of theory, are used to explore potential reaction pathways and the evolvement of the charge distribution along those.

Liquid Chromatography/Mass Spectrometry Analysis of Effluent Water from PFSA Membrane Fuel Cells Operated at OCV

Perfluoroalkylsulfonic acid (PFSA) ionomer membranes degrade under accelerated testing conditions such as open circuit voltage (OCV). Fluoride release rate is commonly used for evaluating the membrane degradation rate; however, many proposed degradation mechanisms should result in the release of small molecule polymer fragments. Liquid chromatography/mass spectrometry (LC/MS) methods are well suited to analyze for these fragments and provide insight into the degradation reactions. Accelerated OCV durability tests were conducted on membrane electrode assemblies made with 3M Ionomer ™ or Nafion™ XL membranes. Effluent water was analyzed for fluoride, sulfate, and trifluoroacetic acid by ion chromatography (IC) and other polymer fragments by LC/MS. The detection of partially hydrogenated side chain fragments and long chain dicarboxylic acids suggest hydrogen atoms play a significant role in these reactions. The results of this study show the possibility that more than one reaction may occur at the tertiary fluoride on the polymer backbone. The presence of a tertiary fluoride on the backbone and side chain of the Nafion™ XL membranes allows for these reactions in more than one location on this polymer. Performance loss for the Nafion™ XL samples during these tests is consistent with adsorption of ionomer fragments on the catalyst surface.

Amphiphilic Comb Polymers as New Additives in Bicontinuous Microemulsions

It has been shown that the thermodynamics of bicontinuous microemulsions can be tailored via the addition of various different amphiphilic polymers. In this manuscript, we now focus on comb-type polymers consisting of hydrophobic backbones and hydrophilic side chains. The distinct philicity of the backbone and side chains leads to a well-defined segregation into the oil and water domains respectively, as confirmed by contrast variation small-angle neutron scattering experiments. This polymer–microemulsion structure leads to well-described conformational entropies of the polymer fragments (backbone and side chains) that exert pressure on the membrane, which influences the thermodynamics of the overall microemulsion. In the context of the different polymer architectures that have been studied by our group with regards to their phase diagrams and small-angle neutron scattering, the microemulsion thermodynamics of comb polymers can be described in terms of a superposition of the backbone and side chain fragments. The denser or longer the side chain, the stronger the grafting and the more visible the brush effect of the side chains becomes. Possible applications of the comb polymers as switchable additives are discussed. Finally, a balanced philicity of polymers also motivates transmembrane migration in biological systems of the polymers themselves or of polymer–DNA complexes.

Tandem Electrospray Mass Spectrometry of Cyclic N-Substituted Oligo-β-(1→6)-D-glucosamines.

High-resolution electrospray mass spectra (MS and MS/MS CID) of positive ions of a series of protonated, ammoniated, and metallated molecules of cyclic N-substituted oligo-β-(1→6)-D-glucosamines differing in cycle size and N-acyl substituents were registered and interpreted. It was shown that the main type of fragmentation is a cleavage of glycosidic bonds of a cycle, and in some cases fragmentation of amide side chains is possible. If labile fragments in substituents (e.g., carbohydrate chains) are present, a decay of the cycle and an elimination of labile fragments are of comparable possibility. It was found that in some cases rearrangements with loss of an internal carbohydrate residue (IRL), or an internal part of a side chain, are feasible.

White-rot fungus Phanerochaete chrysosporium metabolizes chloropyridinyl-type neonicotinoid insecticides by an N-dealkylation reaction catalyzed by two cytochrome P450s

We previously identified a cytochrome P450 (CYP) derived from the white-rot fungus Phanerochaete chrysosporium as involved in degradation of acetamiprid, a neonicotinoid (NEO) insecticide. In the present study, we investigated biodegradation of other NEOs by P. chrysosporium, and attempted to identify the CYP enzyme responsible for NEO degradation. P. chrysosporium was able to degrade some NEOs (acetamiprid, clothianidin, imidacloprid, and thiacloprid) in nutrient-rich medium. Two CYPs in P. chrysosporium (PcCYPs), CYP5037B3 and CYP5147A3, were identified as major isozymes involved in metabolism of three neonicotinoids that have in common a chloropyridinyl moiety (acetamiprid, imidacloprid, and thiacloprid) by screening yeast that heterologously express PcCYPs. Both PcCYPs catalyzed cleavage of the chloropyridinyl moiety and side chain of the three NEOs by N-dealkylation, resulting in 6-chloro-3-pyridinemethanol and respective side chain fragments. In a culture of P. chrysosporium, 97 % and 74 % of imidacloprid and thiacloprid were modified to form degradation products, and one of these, 6-chloro-3-pyridinemethanol, was further degraded. These two PcCYPs catalyzed almost the same reaction but their substrate specificity and expression pattern are slightly different. Altogether, we found that P. chrysosporium degrades NEOs via the activity of at least two different CYP isozymes.

HETEROCYCLIC ANALOGS OF 5,12-NAPHTHACENEQUINONE 16*. SYNTHESIS AND PROPERTIES OF NEW DNA LIGANDS BASED ON 4,11-DIAMINOANTHRA[2,3- b ]THIOPHENE-5,10-DIONE

A divergent route for the synthesis of new derivatives of 4,11-diaminoanthra[2,3-b]thiophene-5,10-dione was developed based on the introduction of cyclic amines to the terminal positions of 4,11-aminoalkyl groups. Modification of the side chains of anthra[2,3-b]thiophene-5,10-dione increases the affinity of ligands to DNA duplex and decreases the affinity to G-quadruplexes. An analysis of the structure–activity relationship showed that 2-(piperidin-1-yl)ethylamine is the most promising side chain fragment for the development of new double-stranded DNA ligands. The ability of new ligands to bind to DNA duplex correlates with inhibition of tumor cell growth, which indicates the prospects for a further search for new antitumor compounds or chemical probes for duplex-forming nucleic acid sequences among 4,11-diaminoanthra[2,3-b]thiophene-5,10-diones.

Fast fragmentation during surface-induced dissociation: An examination of peptide size and structure

We present the results of direct dynamics simulations of surface-induced dissociation for protonated versions of AnK, KAn (n = 1, 3, and 5), AcA7K, and AcKA7 for collisions with a fluorinated self-assembled monolayer surface. We focus on elucidating fast fragmentation events, which takes place in coincidence with the collision event. Such events generate a large number of products, and hence, are not easily understood through chemical intuition. Our simulations show distinct differences between the AnK/AcA7K and KAn/AcKA7 series of peptides, with the former being more reactive, and the latter more selective. Backbone rearrangements and sidechain fragmentation are also seen.

Heterocyclic analogs of 5,12-naphthacenequinone 16*. Synthesis and properties of new DNA ligands based on 4,11-diaminoanthra[2,3-b]thiophene-5,10-dione

A divergent route for the synthesis of new derivatives of 4,11-diaminoanthra[2,3-b]thiophene-5,10-dione was developed based on the introduction of cyclic amines to the terminal positions of 4,11-aminoalkyl groups. Modification of the side chains of anthra[2,3-b]-thiophene-5,10-dione increases the affinity of ligands to DNA duplex and decreases the affinity to G-quadruplexes. An analysis of the structure–activity relationship showed that 2-(piperidin-1-yl)ethylamine is the most promising side chain fragment for the development of new double-stranded DNA ligands. The ability of new ligands to bind to DNA duplex correlates with inhibition of tumor cell growth, which indicates the prospects for a further search for new antitumor compounds or chemical probes for duplex-forming nucleic acid sequences among 4,11-diaminoanthra[2,3-b]thiophene-5,10-diones.

Synthesis of Gemini analogs of 19-norcalcitriol and their platinum(II) complexes

Hormonally active vitamin D3 metabolite, calcitriol, plays an important role in calcium-phosphate homeostasis, immune system actions and cell differentiation. Although anticancer activity of calcitriol is well documented and thousands of its analogs have been synthesized, none has been approved as a potential drug against cancer. Therefore, we attempted to introduce the cytotoxic effect to the calcitriol molecule by its linking to cisplatin. Herein, we present the synthesis of vitamin D compounds, designed on the basis of molecular modeling and docking experiments to the vitamin D receptor, and characterized by the presence of significantly different two side chains attached to C-20. In this study, a new synthetic approach to Gemini analogs was developed. Preparation of the target 19-norcalcitriol compounds involved separate syntheses of several building blocks (the A-ring, C/D-rings and side-chain fragments). The convergent synthetic strategy was used to combine these components by the different coupling processes, the crucial one being Wittig-Horner reaction of the Grundmann ketone analog with the known 2-methylene A-ring phosphine oxide. Due to the nature of the constructed steroidal side chains (bidentate ligands), which allowed coordination of metal ions, the first conjugate-type platinum(II) complexes of the vitamin D analogs were also successfully prepared and characterized. The target vitamin D compounds, displaying significant affinity for a vitamin D receptor, were assessed in vitro for their anti-proliferative activities towards several cell lines.

Modeling the Effects of O-Sulfonation on the CID of Serine.

We present the results of direct dynamics simulations and DFT calculations aimed at elucidating the effect of O-sulfonation on the collision-induced dissociation for serine. Toward this end, direct dynamics simulations of both serine and sulfoserine were performed at multiple collision energies and theoretical mass spectra obtained. Comparisons to experimental results are favorable for both systems. Peaks related to the sulfo group are identified and the reaction dynamics explored. In particular, three significant peaks (m/z 106, 88, and 81) seen in the theoretical mass spectrum directly related to the sulfo group are analyzed as well as major peaks shared by both systems. Our analysis shows that the m/z 106 peaks result from intramolecular rearrangements, intermolecular proton transfer among complexes composed of initial fragmentation products, and at high energy side-chain fragmentation. The m/z 88 peak was found to contain multiple constitutional isomers, including a previously unconsidered, low energy structure. It was also observed that the RM1 semiempirical method was not able to obtain all of the major peaks seen in experimens for sulfoserine. In contrast, PM6 did obtain all major experimental peaks.

Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine.

Arginine has significant effects on fragmentation patterns of the protonated peptide due to its high basicity guanidine tail. In this article, thermal dissociation of the singly protonated glycine-arginine dipeptide (GR-H+) was investigated by performing direct dynamics simulations at different vibrational temperatures of 2000–3500 K. Fourteen principal fragmentation mechanisms containing side-chain and backbone fragmentation were found and discussed in detail. The mechanism involving partial or complete loss of a guanidino group dominates side-chain fragmentation, while backbone fragmentation mainly involves the three cleavage sites of a1-x1+, a2+-x0, and b1-y1+. Fragmentation patterns for primary dissociation have been compared with experimental results, and the peak that was not identified by the experiment has been assigned by our simulation. Kinetic parameters for GR-H+ unimolecular dissociation may be determined by direct dynamics simulations, which are helpful in exploring the complex biomolecules.

Isolation and characterization of the insecticidal, two-domain toxin LaIT3 from the Liocheles australasiae scorpion venom.

A novel insecticidal peptide (LaIT3) was isolated from the Liocheles australasiae venom. The primary structure of LaIT3 was determined by a combination of Edman degradation and MS/MS de novo sequencing analysis. Discrimination between Leu and Ile in MS/MS analysis was achieved based on the difference in side chain fragmentation assisted by chemical derivatization. LaIT3 was determined to be an 84-residue peptide with three intrachain disulfide bonds. The sequence similarity search revealed that LaIT3 belongs to the scorpine-like peptides consisting of two structural domains: an N-terminal α-helical domain and a C-terminal cystine-stabilized domain. As observed for most of the scorpine-like peptides, LaIT3 showed significant antibacterial activity against Escherichia coli, which is likely to be caused by its membrane-disrupting property.

Effects of Glycan Structure on the Stability and Receptor Binding of an IgG4-Fc.

A series of well-defined N-glycosylated IgG4-Fc variants were utilized to investigate the effect of glycan structure on their physicochemical properties (conformational stability and photostability) and interactions with an Fc γ receptor IIIA (FcγRIIIA). High mannose (HM, GlcNAc2Man(8+n) [n= 0-4]), Man5 (GlcNAc2Man5), GlcNAc1, and N297Q IgG4-Fc were prepared in good quality. The physical stability of these IgG4-Fc variants was examined with differential scanning calorimetry and intrinsic fluorescence spectroscopy. Photostability was assessed after photoirradiation between 295 and 340 nm (λ max= 305 nm), and HPLC-MS/MS analysis of specific products was performed. The size of glycans at Asn297 affects the yields of light-induced Tyr side-chain fragmentation products, where the yields decreased in the following order: N297Q > GlcNAc1 > Man5 > HM. These yields correlate with the thermal stability of the glycoforms. The HM and Man5 glycoforms display increased affinity for FcγRIIIA by at least 14.7-fold compared with GlcNAc1 IgG4-Fc. The affinities measured for the HM and Man5 IgG4-Fc (0.39-0.52 μM) are similar to those measured for fucosylated IgG1. Dependent on the mechanisms of action of IgG4 therapeutics, such glycoforms may need to be carefully monitored. The nonglycosylated N297Q IgG4-Fc did not present measurable affinity to FcγRIIIA.

Peptide Sequence Influence on the Differentiation of Valine and Norvaline by Hot Electron Capture Dissociation.

Isomeric amino acid residues such as valine (Val) and norvaline (Nva) are common in recombinant proteins. The mis-incorporation of Nva for leucine (Leu) causes heterogeneity and in some cases even toxicity. Previous studies have shown that hot electron capture dissociation (HECD) is able to differentiate Val from Nva by producing diagnostic w ions on custom designed synthetic model peptides. To broaden the utilization of HECD in proteomic studies and to define the critical structural features, a thorough investigation was performed on representative peptides including specifically designed synthetic peptides as well as biological peptides bearing tryptic digest-like features and peptides with post-translational modifications. Experimental evidence confirmed that the formation of a w ion is directly dependent upon the presence of the corresponding z ion. The results suggested that a charge carrier residue at the C-terminus is promoting the formation of diagnostic w ions for Nva. Thus, peptides resulting from trypsin digestion, with arginine (Arg) or lysine (Lys) at the C-terminus, can be analyzed using the HECD method. Post-translational modification (PTM) such as phosphorylation did not prevent the generation of the requisite side chain fragmentation w ions. These results suggest the general applicability of HECD for unambiguous identification of Val and Nva especially in structure characterization of therapeutic proteins.