Investigation of Sequence Clipping and Structural Heterogeneity of an HIV Broadly Neutralizing Antibody by a Comprehensive LC-MS Analysis

CAP256 is one of the highly potent, broadly neutralizing monoclonal antibodies (bNAb) designed for HIV-1 therapy. During the process development of one of the constructs, an unexpected product-related impurity was observed via microfluidics gel electrophoresis. A panel of complementary LC-MS analyses was applied for the comprehensive characterization of CAP256 which included the analysis of the intact and reduced protein, the middle-up approach, and a set of complementary peptide mapping techniques and verification of the disulfide bonds. The designed workflow allowed to identify a clip within a protruding acidic loop in the CDR-H3 region of the heavy chain, which can lead to the decrease of bNAb potency. This characterization explained the origin of the additional species reflected by the reducing gel profile. An intra-loop disulfide bond linking the two fragments was identified, which explained why the non-reducing capillary electrophoresis (CE) profile was not affected. The extensive characterization of CAP256 post-translational modifications was performed to investigate a possible cause of CE profile complexity and to illustrate other structural details related to this molecule’s biological function. Two sites of the engineered Tyr sulfation were verified in the antigen-binding loop, and pyroglutamate formation was used as a tool for monitoring the extent of antibody clipping. Overall, the comprehensive LC-MS study was crucial to (1) identify the impurity as sequence clipping, (2) pinpoint the clipping location and justify its susceptibility relative to the molecular structure, (3) lead to an upstream process optimization to mitigate product quality risk, and (4) ultimately re-engineer the sequence to be clip-resistant.

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High-throughput capillary electrophoresis analysis of biopharmaceuticals utilizing sequential injections

The complexity of biotherapeutic products implies an ever-increasing list of product quality attributes that need to be monitored and characterized. In addition, the growing interest in implementing process analytical technology in biopharmaceutical production has further increased the testing burden, together with the need for rapid testing that can facilitate real-time or near-real-time decision-making. Capillary electrophoresis (CE) has made a place in biopharmaceutical analysis but is regarded as a low-throughput method, with the instrument dead time constituting more than 80% of the total time of analysis. In this study, the dead time of CE was utilized to analyse 3 mAb samples in a single-CE run. This approach resulted in an up to 77% reduction in the total analysis time and increased the productivity by up to 300%, compared to traditional single CE-ultraviolet runs, without compromising resolution or relative peak areas. Additionally, good method reproducibility was observed. The compatibility of the method has been demonstrated with protein A eluate and cation exchange chromatography fractions. We, thus, propose that sequential injections can be applied for fast and robust CE analysis of biopharmaceuticals.     

Analysis and numerical simulation for a class of time fractional diffusion equation via tension spline

In this work, we prove the weak and strong convergence of a sequence generated by a modified S-iteration process for finding a common fixed point of two G-nonexpansive mappings in a uniformly convex Banach space with a directed graph. We also give some numerical examples for supporting our main theorem and compare convergence rate between the studied iteration and the Ishikawa iteration.     

Enhanced permeation, leaf retention, and plant protease inhibitor activity with bicontinuous microemulsions

Bicontinuous microemulsions (BCMEs) have excellent solubulizing properties along with low interfacial tension and aqueous content that can be controlled. In this work, water soluble plant protease inhibitor (PI), well characterized for its activity against insect pests, was incorporated into a BCME system and explored for permeation on hydrophobic leaf surfaces and protease inhibition activity. The bicontinuous nature of the microemulsion containing water:2-propanol:1-butanol (55:35:10 w/w) was characterized using conductivity and self-diffusion coefficient measurements. The PI was soluble in the water-rich bicontinuous domains, stable in the microemulsions, and protease inhibition activity was retained for a prolonged duration. The microemulsions ensured greater wettability and a wider spread of the PI on hydrophobic leaf surfaces as revealed by contact angle measurements. Significantly, trypsin inhibition activity assays of the PI recovered from the leaves after delivery from the microemulsion indicated a significant increase in the PI retention on the leaf. This BCME enabled greater leaf permeation and retention of the PI can be attributed to a temporary disruption of the waxy leaf surface followed by self-repair without causing any long term damage to the plant.     

Mechanical and electronic approaches to improve the sensitivity of microcantilever sensors

Advances in the field of micro electro mechanical systems and their uses now offer unique opportunities in the design of ultrasensitive analytical tools. The analytical community continues to search for cost-effective, reliable, and even portable analytical techniques that can give reliable and fast response results for a variety of chemicals and biomolecules. Microcantilevers （MCLs） have emerged as a unique platform for label-free chem-sensor or bioassay. Several electronic designs, including piezoresistive, piezoelectric, and capacitive approaches, have been applied to measure the bending or frequency change of the MCLs upon exposure to chemicals. This review summarizes mechanical, fabrication, and electronics approaches to increase the sensitivity of MCL sensors.     

Ring-chain isomerism in conjugated guanylhydrazones: Experimental and theoretical study

Treatment of 1,3-diaryl-propene-2-one with aminoguanidine under acidic conditions for a short reaction period (1?h) delivers - in accordance with a literature report - the corresponding guanylhydrazones. However, when the reaction time was increased to 12?h, formation of the ring annulated product 4,5-dihydro-1H-pyrazole-1-carboximidamide was observed. This is the first case of ring-chain isomerism in conjugated guanylhydrazones. The acyclic conjugated guanylhydrazone and the corresponding annulated product (4,5-dihydro-1H-pyrazole-1-carboximidamide) could be clearly distinguished by means of UV and NMR spectroscopy. The formation of the ring isomer was further confirmed by single crystal XRD analysis. The time-dependent ¹H NMR study indicated the gradual transformation of the open-chain compound into the cyclic one. The mechanistic insights into the formation of these two products were explored using quantum chemical methods which revealed that the ring isomer is thermodynamically more stable than the open-chain isomer by 6–11?kcal/mol and the barrier for cyclization was found to be 31.37?kcal/mol.     

Vibrational dynamics and heat capacity in poly(L‐lactic acid)

Poly(L ‐lactic acid) (PLLA) (? CH(CH₃) ? COO? )_n is a biodegradable polymer, which exhibits many applications in the biomedical field and where thermoplastics are employed. A comprehensive study of the normal modes and their dispersion in PLLA using Wilson′s GF matrix method as modified by Higgs is being reported. Assignments of calculated normal modes have been made and characteristic features of dispersion curves are discussed. Heat capacity has been calculated via density‐of‐states using Debye relation in the temperature range 10–250 K, which is in fairly good agreement with the experimental data. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 175–182, 2010     

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes

A nonredundant dataset of ∼300 high (up to 2.5 Å) resolution X-ray structures of RNA : protein complexes were analyzed for hydrogen bonds between amino-acid residues and canonical ribonucleotides (rNs). The identified 17100 contacts were classified based on the identity (rA, rC, rG or rU) and interacting fragment (base, sugar, or ribose) of the rN, the nature (polar or nonpolar) and interacting moiety (main chain or side chain) of the amino-acid residue, as well as the rN and amino-acid atoms participating in the hydrogen bonding. 80 possible hydrogen-bonding combinations (4 (rNs)×20 (amino acids)) involve a wide variety of RNA and protein types and are present in multiple occurrences in almost all PDB files. Comparison with the analogously-selected DNA:protein complexes reveals that the absence of 2′-OH group in DNA mainly accounts for the differences in DNA:protein and RNA : protein hydrogen bonding. Search for intrinsically-stable base:amino acid pairs containing single or multiple hydrogen bonds reveals 37 unique pairs, which may act as well-defined RNA : protein interaction motifs. Overall, our work collectively analyzes the largest set of nucleic acid-protein hydrogen bonds to date, and therefore highlights several trends that may help frame structural rules governing the physiochemical characteristics of RNA : protein recognition.