Optimal Collision Energies and Bioinformatics Tools for Efficient Bottom-up Sequence Validation of Monoclonal Antibodies

Rigorous validation of amino acid sequence is fundamental in the characterization of original and biosimilar protein biopharmaceuticals. Widely accepted workflows are based on bottom-up mass spectrometry, and they often require multiple techniques and significant manual work. Here, we demonstrate that optimization of a set of tandem mass spectroscopy (MS/MS) collision energies and automated combination of all available information in the measurements can increase the sequence validated by one technique close to the inherent limits. We created a software (called "Serac") that consumes results of the Mascot database search engine and identifies the amino acids validated by bottom-up MS/MS experiments using the most rigorous, industrially acceptable definition of sequence coverage (we term this "confirmed sequence coverage"). The software can combine spectra at the level of amino acids or fragment ions to exploit complementarity, provides full transparency to justify validation, and reduces manual effort. With its help, we investigated collision energy dependence of confirmed sequence coverage of individual peptides and full proteins on trypsin-digested monoclonal antibody samples (rituximab and trastuzumab). We found the energy dependence to be modest, but we demonstrated the benefit of using spectra taken at multiple energies. We describe a workflow based on 2-3 LC-MS/MS runs, carefully selected collision energies, and a fragment ion level combination, which yields ∼85% confirmed sequence coverage, 25%-30% above that from a basic proteomics protocol. Further increase can mainly be expected from alternative digestion enzymes or fragmentation techniques, which can be seamlessly integrated to the processing, thereby allowing effortless validation of full sequences.

Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate-based inhibitors

A series of carbamate-based inhibitors of glutamate carboxypeptidase II (GCPII) were designed and synthesized using ZJ-43, N-[[[(1S)-1-carboxy-3-methylbutyl]amino]carbonyl]-l-glutamic acid, as a molecular template in order to better understand the impact of replacing one of the two nitrogen atoms in the urea-based GCPII inhibitor with an oxygen atom. Compound 7 containing a C-terminal 2-oxypentanedioic acid was more potent than compound 5 containing a C-terminal glutamic acid (2-aminopentanedioic acid) despite GCPII's preference for peptides containing an N-terminal glutamate as substrates. Subsequent crystallographic analysis revealed that ZJ-43 and its two carbamate analogs 5 and 7 with the same (S,S)-stereochemical configuration adopt a nearly identical binding mode while (R,S)-carbamate analog 8 containing a d-leucine forms a less extensive hydrogen bonding network. QM and QM/MM calculations have identified no specific interactions in the GCPII active site that would distinguish ZJ-43 from compounds 5 and 7 and attributed the higher potency of ZJ-43 and compound 7 to the free energy changes associated with the transfer of the ligand from bulk solvent to the protein active site as a result of the lower ligand strain energy and solvation/desolvation energy. Our findings underscore a broader range of factors that need to be taken into account in predicting ligand-protein binding affinity. These insights should be of particular importance in future efforts to design and develop GCPII inhibitors for optimal inhibitory potency.

Selection of Collision Energies in Proteomics Mass Spectrometry Experiments for Best Peptide Identification: Study of Mascot Score Energy Dependence Reveals Double Optimum

Collision energy is a key parameter determining the information content of beam-type collision induced dissociation tandem mass spectrometry (MS/MS) spectra, and its optimal choice largely affects successful peptide and protein identification in MS-based proteomics. For an MS/MS spectrum, quality of peptide match based on sequence database search, often characterized in terms of a single score, is a complex function of spectrum characteristics, and its collision energy dependence has remained largely unexplored. We carried out electrospray ionization-quadrupole-time of flight (ESI-Q-TOF)-MS/MS measurements on 2807 peptides from tryptic digests of HeLa and E. coli at 21 different collision energies. Agglomerative clustering of the resulting Mascot score versus energy curves revealed that only few of them display a single, well-defined maximum; rather, they feature either a broad plateau or two clear peaks. Nonlinear least-squares fitting of one or two Gaussian functions allowed the characteristic energies to be determined. We found that the double peaks and the plateaus in Mascot score can be associated with the different energy dependence of b- and y-type fragment ion intensities. We determined that the energies for optimum Mascot scores follow separate linear trends for the unimodal and bimodal cases with rather large residual variance even after differences in proton mobility are taken into account. This leaves room for experiment optimization and points to the possible influence of further factors beyond m/ z.

Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase

Oxygenation of aromatic rings using O₂ is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenzyme A epoxidase, BoxB. The calculations revealed four possible pathways for attacking the aromatic ring: (a) electrophilic (2e^-) attack by a bis(μ-oxo)-diiron(IV) species (Q pathway); (b) electrophilic (2e^-) attack via the σ* orbital of a μ-η²:η²-peroxo-diiron(III) intermediate (Pσ* pathway); (c) radical (1e^-) attack via the π*-orbital of a superoxo-diiron(II,III) species (Pπ* pathway); (d) radical (1e^-) attack of a partially quenched bis(μ-oxo)-diiron(IV) intermediate (Q' pathway). The results allowed earlier work of de Visser on olefin epoxidation by diiron complexes and QM-cluster studies of Liao and Siegbahn on BoxB to be put into a broader perspective. Parallels with epoxidation using organic peracids were also examined. Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.

Transformation of Zwitterionic Pyridine Derivatives to a Spiro-Fused Ring System: Azoniabenzo[de]fluorine. Synthesis and Mechanistic Rationalization

Reaction of aryl- and benzylsulfanopyridinium amidates bearing a methyl group in position 6 with 2 equiv of diphenylketene afforded a spiro-fused ring system: azoniabenzo[de]fluorine. By use of an excess amount of ketene, a distinct reaction was observed via which a 1H-pyrrolo[3,2-b]pyridin-2(3H)-one derivative was furnished. The structure of the tetracyclic spiro-fused ring system was unambiguously confirmed by X-ray diffraction, and its formation was rationalized by DFT calculations.

Reactivity of the binuclear non-heme iron active site of Δ⁹ desaturase studied by large-scale multireference ab initio calculations

The results of density matrix renormalization group complete active space self-consistent field (DMRG-CASSCF) and second-order perturbation theory (DMRG-CASPT2) calculations are presented on various structural alternatives for the O-O and first C-H activating step of the catalytic cycle of the binuclear nonheme iron enzyme Δ(9) desaturase. This enzyme is capable of inserting a double bond into an alkyl chain by double hydrogen (H) atom abstraction using molecular O2. The reaction step studied here is presumably associated with the highest activation barrier along the full pathway; therefore, its quantitative assessment is of key importance to the understanding of the catalysis. The DMRG approach allows unprecedentedly large active spaces for the explicit correlation of electrons in the large part of the chemically important valence space, which is apparently conditio sine qua non for obtaining well-converged reaction energetics. The derived reaction mechanism involves protonation of the previously characterized 1,2-μ peroxy Fe(III)Fe(III) (P) intermediate to a 1,1-μ hydroperoxy species, which abstracts an H atom from the C10 site of the substrate. An Fe(IV)-oxo unit is generated concomitantly, supposedly capable of the second H atom abstraction from C9. In addition, several popular DFT functionals were compared to the computed DMRG-CASPT2 data. Notably, many of these show a preference for heterolytic C-H cleavage, erroneously predicting substrate hydroxylation. This study shows that, despite its limitations, DMRG-CASPT2 is a significant methodological advancement toward the accurate computational treatment of complex bioinorganic systems, such as those with the highly open-shell diiron active sites.

Curvature correction for microiterative optimizations with QM/MM electronic embedding

One of the most common methods to treat the electrostatic effect of the environment in QM/MM calculations is to include the MM atoms as point charges in the QM Hamiltonian. In this case, a microiterative geometry optimization ignoring the QM contributions to the forces in the relaxation of the environment cannot yield exact stationary points. One solution that has been suggested in the literature is based on using a constant additive correction to the MM gradient during the microiterations, determined in the preceding macroiteration. Here, we analyze the convergence properties of the gradient correction method and point out that a smooth relaxation is not ensured if the curvature of the approximate, MM-based description of the potential energy surface of the environment is too small in comparison with the exact one. We suggest a computationally cheap second-order correction that uses an estimated Hessian from the Davidon-Fletcher-Powell method to tackle the problems caused by the too small curvature. Test calculations on four metalloenzymatic systems (∼100 QM atoms, ∼2000 relaxed MM atoms, ∼20,000 atoms in total) show that our approach efficiently restores the convergence where gradient correction alone would lead to oscillations.

Rearrangement of aryl- and benzylthiopyridinium imides with participation of a methyl substituent

6-Methyl substituted 2-aryl- and 2-benzylthiopyridinium N-imides reacted with an excess of isocyanates to give N,N-disubstituted exocyclic1H-imidazo[4,5-b]pyridin-2(3H)-ones. The products easily underwent spontaneous [1,5] hydrogen shift to provide the heteroaromatic imidazopyridinone isomers. The transformation implied the initial formation of [1,2,4]triazolo[2,3-a]pyridinium salt, followed by deprotonation and carbamoylation of the methylene moiety, and, finally, a rearrangement following a [1,3] sigmatropic pattern. Mechanistic considerations suggest and some experimental findings reveal the nonconcerted two-step mechanism of the ring transformation step.

Computing reliable energetics for conjugate addition reactions

The performance of various density functionals along with second-order perturbation treatments has been tested for a set of conjugate addition reactions relevant to stereoselective organocatalysis. It is shown that B3LYP predictions seriously underestimate the reaction energies, whereas two newly designed functionals (M05-2X and M06-2X) and the SCS-MP2 method provide very accurate data. These new methods represent promising alternative approaches in future mechanistic studies.

Comments on “Observation of the surface stress induced in microcantilevers by electrochemical redox processes” by F. Tian, J.H. Pei, D.L. Hedden, G.M. Brown, T. Thundat

Critical remarks have been formulated in connection with the surface stress measurements reported by Tian et al. It has been shown that due to the shortcomings of the experimental procedure some conclusions of the authors are hardly acceptable.