Prediction of peptides retention behavior in reversed-phase liquid chromatography based on their hydrophobicity

A novel peptide pair-based rapid fluorescent diagnostic system for malaria Plasmodium falciparum detection

Advanced diagnostic materials, such as aptamers, are required due to the scarcity of efficient diagnostic antibodies and the low sensitivity of rapid diagnostic kits at detecting the malaria parasite, Plasmodium falciparum.

METHODS

Two peptides M2.9 [(KPTAEQTESPELQSAPEN) and M2.17 (KILFNVYSPLGCTCECWV)] were designed using simple epitope prediction tools and modified against the merozoite surface antigen 2 of P. falciparum (Pf.MSP2) by 3-dimensional modeling based on binding affinity. Based on five prediction tools for hydropathy, M2.17 was selected as an appropriate capture peptide. A peptide-based fluorescence-linked immunosorbent assay (FLISA) and a peptide pair-based fluorescent immunochromatographic test strip (FICT) were developed to detect P. falciparum 3D7 (drug-sensitive) and P. falciparum K1 (multi drugs-resistant) strains.

RESULTS

Bioinformatic analysis of two peptides demonstrated the potential binding affinity with the merozoite surface protein 2 of P. falciparum (Pf.MSP2) with a positive hydropathy value. The limit of detection (LOD) of FLISA was 10 parasites/μL and of a peptide pair-linked rapid FICT system was 5 and 200 parasites/μL for P. falciparum 3D7 and K1, respectively. Compared to commercial rapid detection systems (RDTs), a peptide pair-linked FICT system exhibited a 20-fold greater efficiency in detecting P. falciparum 3D7 and specifically discriminated another protozoan spp.

CONCLUSION

A peptide pair-linked rapid diagnostic strip could be an alternative to conventional RDTs for monitoring wild-type and drug-resistant malaria parasites.

Ready-to-use Models Built Using a Diverse Set of 266 Aroma Compounds for the Estimation of Gas Chromatographic Retention Indices for the 50%-Cyanopropylphenyl-50%-Dimethylpolysiloxane Stationary Phase

Retention index prediction based on the molecule structure is not often used in practice due to low accuracy, the need to use paid software to calculate molecular descriptors (MD), and the narrow applicability domain of many models. In recent years, relatively accurate and versatile deep learning (DL)-based models have emerged. These models are now used in practice as an additional criterion in gas chromatography-mass spectrometry identification. The DB-225ms stationary phase (usually described as 50%-cyanopropylphenyl-50%-dimethylpolysiloxane in available sources) is widely used, but ready-to-use retention index estimation models are not available for it. This study presents such models. The models are linear and use simple constitutional MD and retention indices predicted by DL for the DB-WAX and DB-624 stationary phases as MD (we show that it is their use that allows us to achieve satisfactory accuracy). The accuracy obtained for a completely unseen hold-out test set: root mean square error 73.2; mean absolute error 45.7; median absolute error 22.0. The models were trained using a retention data set of 266 volatile compounds. All calculations can be performed using the convenient open-source software CHERESHNYA. The final equations are implemented as a spreadsheet and a code snippet and are available online: https://doi.org/10.6084/m9.figshare.26800789.

Evaluation of the antiviral activity of new dermaseptin analogs against Zika virus

Zika virus represents the primary cause of infection during pregnancy and can lead to various neurological disorders such as microcephaly and Guillain-Barré syndrome affecting both children and adults. This infection is also associated with urological and nephrological problems. So far, evidence of mosquito-borne Zika virus infection has been reported in a total of 89 countries and territories. However, surveillance efforts primarily concentrate on outbreaks that this virus can cause, yet the measures implemented are typically limited. Currently, there are no specific treatments or vaccines designed for the prevention or treatment of Zika virus infection or its associated disease. The development of effective therapeutic agents presents an urgent need. Importantly, an alternative for advancing the discovery of new molecules could be dermaseptins, a family of antimicrobial peptides known for their potential antiviral properties. In this study, we carried out the synthesis of dermaseptins and their analogs and subsequently assessed the bioactivity tests against Zika virus (ZIKV PF13) of dermaseptins B2 and S4 and their derivatives. The cytotoxicity of these peptides was investigated on HMC3 cell line and HeLa cells by CellTiter-Glo® Luminescent Cell Viability Assay. Thereafter, we evaluated the antiviral activity caused by the action of our dermaseptins on the viral envelope using the Fluorescence Activated Cell Sorting (FACS). The cytotoxicity of our molecules was concentration-dependent at microgram concentrations Expect for dermaseptin B2 and its derivative which present no toxicity against HeLa and HMC3 cell lines. It was observed that all tested analogs from S4 family exhibited antiviral activity with low concentrations ranging from 3 to 12.5 μg/ml , unlike the native B2 and its derivative which increased the infectivity. Pre-incubating of dermaseptins with ZIKV PF13 before infection revealed that these derivatives inhibit the initial stages of virus infection. In summary, these results suggest that dermaseptins could serve as novel lead structures for the development of potent antiviral agents against Zika virus infections.

Access to Diverse Glutamic Acid Dendrons and a Janus Peptide Dendrimer Using an Atypical Solid Phase Synthesis

The negligible cytotoxicity of anion surface-linked dendrons makes glutamic acid-based dendrons a potential candidate for materials and biological applications. Despite the inherent drawbacks of the conventional solution phase synthesis of glutamic acid-based dendrons, there have been no advancements in these protocols. Herein, we demonstrate the first-ever convergent solid phase synthesis of dendrons, up to fourth generation, having glutamic acid branching points produced by preactivation of dicarboxylic acid groups with N-hydroxysuccinimide and simultaneous coupling with amine groups of two growing peptide chains, with excellent yields (30-70%). In addition to the general advantages, such as the easy workup, a final single purification step, and an overall short synthesis duration, the convergent solid phase synthesis allowed us to chemically synthesize glutamic acid branching-based dendrons that cannot be accessed by standard divergent solid phase synthesis. This method has also been validated for its application in synthesizing hard-to-achieve Janus peptide dendrimers in a single stretch on a solid support. Our work corroborates the efficacy of controlled -COOH activation to accomplish an atypical solid phase synthesis of diverse glutamic acid dendrons in a convergent fashion. This is the first example of a Janus peptide dendrimer being synthesized on a solid support, utilizing both convergent and divergent approaches simultaneously.

Deep learning framework for peak detection at the intact level of therapeutic proteins

While automated peak detection functionalities are available in commercially accessible software, achieving optimal true positive rates frequently necessitates visual inspection and manual adjustments. In the initial phase of this study, hetero-variants (glycoforms) of a monoclonal antibody were distinguished using liquid chromatography-mass spectrometry, revealing discernible peaks at the intact level. To comprehensively identify each peak (hetero-variant) in the intact-level analysis, a deep learning approach utilizing convolutional neural networks (CNNs) was employed in the subsequent phase of the study. In the current case study, utilizing conventional software for peak identification, five peaks were detected using a 0.5 threshold, whereas seven peaks were identified using the CNN model. The model exhibited strong performance with a probability area under the curve (AUC) of 0.9949, surpassing that of partial least squares discriminant analysis (PLS-DA) (probability AUC of 0.8041), and locally weighted regression (LWR) (probability AUC of 0.6885) on the data acquired during experimentation in real-time. The AUC of the receiver operating characteristic curve also illustrated the superior performance of the CNN over PLS-DA and LWR.

Evaluation of the Antibacterial Activity of New Dermaseptin Derivatives against Acinetobacter baumannii

Nosocomial infections represent one of the biggest health problems nowadays. Acinetobacter baumannii is known as an opportunistic pathogen in humans, affecting people with compromised immune systems, and is becoming increasingly important as a hospital-derived infection. It is known that in recent years, more and more bacteria have become multidrug-resistant (MDR) and, for this reason, the development of new drugs is a priority. However, these products must not affect the human body, and therefore, cytotoxicity studies are mandatory. In this context, antimicrobial peptides with potential antibacterial proprieties could be an alternative. In this research, we describe the synthesis and the bioactivity of dermaseptins and their derivatives against Acinetobacter baumannii. The cytotoxicity of these compounds was investigated on the HEp-2 cell line by MTT cell viability assay. Thereafter, we studied the morphological alterations caused by the action of one of the active peptides on the bacterial membrane using atomic force microscopy (AFM). The cytotoxicity of dermaseptins was concentration-dependent at microgram concentrations. It was observed that all tested analogs exhibited antibacterial activity with Minimum Inhibitory Concentrations (MICs) ranging from 3.125 to 12.5 μg/mL and Minimum Bactericidal Concentrations (MBCs) ranging from 6.25 to 25 μg/mL. Microscopic images obtained by AFM revealed morphological changes on the surface of the treated bacteria caused by K4S4(1-16), as well as significant surface alterations. Overall, these findings demonstrate that dermaseptins might constitute new lead structures for the development of potent antibacterial agents against Acinetobacter baumannii infections.

Simultaneous effect of different chromatographic conditions on the chromatographic retention of pentapeptide derivatives (HGRFG and NPNPT)

Introduction: Oligopeptides exhibit great prospects for clinical application and its separation is of great importance in new drug development. Methods: To accurately predict the retention of pentapeptides with analogous structures in chromatography, the retention times of 57 pentapeptide derivatives in seven buffers at three temperatures and four mobile phase compositions were measured via reversed-phase high-performance liquid chromatography. The parameters ( k H A , k A , and p K a ) of the acid-base equilibrium were obtained by fitting the data corresponding to a sigmoidal function. We then studied the dependence of these parameters on the temperature (T), organic modifier composition (φ, methanol volume fraction), and polarity ( P m N parameter). Finally, we proposed two six-parameter models with (1) pH and T and (2) pH and φ or P m N as the independent variables. These models were validated for their prediction capacities by linearly fitting the predicted retention factor k-value and the experimental k-value. Results: The results showed that log k H A and log k A exhibited linear relationships with 1 / T , φ or P m N for all pentapeptides, especially for the acid pentapeptides. In the model of pH and T, the correlation coefficient (R²) of the acid pentapeptides was 0.8603, suggesting a certain prediction capability of chromatographic retention. Moreover, in the model of pH and φ or P m N , the R² values of the acid and neutral pentapeptides were greater than 0.93, and the average root mean squared error was approximately 0.3, indicating that the k-values could be effectively predicted. Discussion: In summary, the two six-parameter models were appropriate to characterize the chromatographic retention of amphoteric compounds, especially the acid or neutral pentapeptides, and could predict the chromatographic retention of pentapeptide compounds.