Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests.

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SILAC-Pulse Proteolysis: A Mass Spectrometry-Based Method for Discovery and Cross-Validation in Proteome-Wide Studies of Ligand Binding

Reported here is the use of stable isotope labeling with amino acids in cell culture (SILAC) and pulse proteolysis (PP) for detection and quantitation of protein–ligand binding interactions on the proteomic scale. The incorporation of SILAC into PP enables the PP technique to be used for the unbiased detection and quantitation of protein–ligand binding interactions in complex biological mixtures (e.g., cell lysates) without the need for prefractionation. The SILAC-PP technique is demonstrated in two proof-of-principle experiments using proteins in a yeast cell lysate and two test ligands including a well-characterized drug, cyclosporine A (CsA), and a non-hydrolyzable adenosine triphosphate (ATP) analogue, adenylyl imidodiphosphate (AMP-PNP). The well-known tight-binding interaction between CsA and cyclophilin A was successfully detected and quantified in replicate analyses, and a total of 33 proteins from a yeast cell lysate were found to have AMP-PNP-induced stability changes. In control experiments, the method’s false positive rate of protein target discovery was found to be in the range of 2.1% to 3.6%. SILAC-PP and the previously reported stability of protein from rates of oxidation (SPROX) technique both report on the same thermodynamic properties of proteins and protein–ligand complexes. However, they employ different probes and mass spectrometry-based readouts. This creates the opportunity to cross-validate SPROX results with SILAC-PP results, and vice-versa. As part of this work, the SILAC-PP results obtained here were cross-validated with previously reported SPROX results on the same model systems to help differentiate true positives from false positives in the two experiments. Graphical Abstract

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A fast method for large‐scale De Novo peptide and miniprotein structure prediction

Although peptides have many biological and biomedical implications, an accurate method predicting their equilibrium structural ensembles from amino acid sequences and suitable for large‐scale experiments is still missing. We introduce a new approach—PEP‐FOLD—to the de novo prediction of peptides and miniproteins. It first predicts, in the terms of a Hidden Markov Model‐derived structural alphabet, a limited number of local conformations at each position of the structure. It then performs their assembly using a greedy procedure driven by a coarse‐grained energy score. On a benchmark of 52 peptides with 9–23 amino acids, PEP‐FOLD generates lowest‐energy conformations within 2.8 and 2.3 Å Cα root‐mean‐square deviation from the full nuclear magnetic resonance structures (NMR) and the NMR rigid cores, respectively, outperforming previous approaches. For 13 miniproteins with 27–49 amino acids, PEP‐FOLD reaches an accuracy of 3.6 and 4.6 Å Cα root‐mean‐square deviation for the most‐native and lowest‐energy conformations, using the nonflexible regions identified by NMR. PEP‐FOLD simulations are fast—a few minutes only—opening therefore, the door to in silico large‐scale rational design of new bioactive peptides and miniproteins. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Advances and Drawbacks of the Adaptation to Serum-Free Culture of CHO-K1 Cells for Monoclonal Antibody Production

Currently, mammalian cell technology has become the focus of biopharmaceutical production, with strict regulatory scrutiny of the techniques employed. Major concerns about the presence of animal-derived components in the culture media led to the development of serum-free (SF) culture processes. However, cell adaptation to SF conditions is still a major challenge and limiting step of process development. Thus, this study aims to assess the impact of SF adaptation on monoclonal antibody (mAb) production, identify the most critical steps of cell adaptation to the SF EX-CELL medium, and create basic process guidelines. The success of SF adaptation was dependent on critical steps that included accentuated cell sensitivity to common culture procedures (centrifugation, trypsinization), initial cell concentration, time given at each step of serum reduction, and, most importantly, medium supplements used to support adaptation. Indeed, only one of the five supplement combinations assessed (rhinsulin, ammonium metavanadate, nickel chloride, and stannous chloride) succeeded for the Chinese hamster ovary-K1 cell line used. This work also revealed that the chemically defined EX-CELL medium benefits mAb production in comparison with the general purpose Dulbecco’s Modified Eagle’s Medium, but the complete removal of serum attenuates these positive effects.     

Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents

We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (1) robust targeting of peptide N-termini and lysyl side chains, (2) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (3) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (4) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da, are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition, we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally, we provide exemplar data that extend the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers.

A Rapid Tandem Mass Spectrometric Assay for Determination of Ursolic Acid – Application to Analysis of Ursolic Acid in Four Species of Staphylea L. and Leaves of Staphylea Pinnata L. Gathered During Ontogenesis

Plant extracts of Staphylea L. exhibit a number of biological activities which are presumably attributed to ursolic acid. A rapid and specific tandem mass spectrometric (MS-MS) assay for the quantification of ursolic acid in the leaves of four species of Staphylea L. (Bladdernut) and in the leaves of S. pinnata L. during ontogenesis, was developed and validated. The samples were analyzed by flow injection analysis without chromatographic separation using a transport liquid of methanol/water/formic acid (80:20:0.1 v/v/v) at a flow-rate of 0.2 mL min⁻¹. The run cycle time was ~2-3 min injection-to-injection. Quantification was achieved using multiple reaction monitoring at MRM transition m/z 439 > 203. Calibration curves were linear over the concentration range of 2–20 μg mL⁻¹ with a lower limit of quantification of 2 μg mL⁻¹ (1.8 ± 0.297, RSD: 0.165). Validation data showed that the RSD% values were in the range of 1.8 to 6.8%, whereas the % DEVs ranged from −18 to −2% indicating reasonable and acceptable precision and accuracy, respectively. A recovery percent of 106.8 ± 10.3 of ursolic acid from spiked extracts samples, indicated the specificity and reliability of tandem mass procedure for determination of ursolic acid in the plant extracts. The derived data of sample analysis showed different contents of ursolic acid among various Staphylea species. The highest content of ursolic acid was found in the leaves extract of S. pinnata L. Additionally, the highest amount of ursolic acid accumulated in the leaves of S. pinnata L. was in the August /September period of the year. Smaller amounts of ursolic acid were found in samples collected before and after that time. The results obtained serve as a justification of determining the most appropriate time for collecting plant material as a source of ursolic acid.     

Reply to the comment on ‘Pople versus Dunning basis-sets for group IA metal hydrides and some other second row hydrides: The case against a De Facto standard’ by R.A. Klein and M.A. Zottola [Chem. Phys. Lett. 419 (2006) 254–258]

In their Comment on our recent Letter [R.A. Klein, M.A. Zottola, Chem. Phys. Lett. 419 (2006) 254–258], Feller and Peterson point out that density functional theory combined with the Pople triple split-valence basis-set 6-311++G(2d,p), does indeed perform well in comparison to second-order perturbation and coupled cluster theory in combination with correlation-consistent basis-sets for the prediction of bond lengths and harmonic frequencies but does not provide acceptable accuracy for dissociation energies. MPW1PW91/6-311++G(2d,p) is, therefore, highly suitable and computationally efficient for generating starting structures for subsequent single-point (SP) calculations at higher and more computationally expensive levels of theory.