The Role of Counter-Ions in Peptides-An Overview

Trifluoroacetic Acid as a Molecular Probe for the Dense Phase in Liquid-Liquid Phase-Separating Peptide Systems

Although trifluoroacetic acid (TFA) is not typically considered a Hofmeister reagent, it has been demonstrated to modulate biocoacervation. We show that TFA can be employed to probe specific interactions in coacervating bioinspired peptide phenylalanine (Phe) 19F-labeled at a single site, altering its liquid-liquid phase separation (LLPS) behavior. Solid-state nuclear magnetic resonance (NMR) spectroscopy revealed two dynamically distinct binding modes of TFA with Phe, resulting in a structured, dipolar-ordered complex and a more dynamic complex, highlighting the proximity between TFA and Phe. Quantum chemistry modeling of 19F chemical shift differences indicates that the structured complex is formed by the intercalation of one TFA molecule between two stacked Phe aromatic rings, possibly contributing to the stabilization of the condensed dense phase. Thus, we propose that TFA can be used as a convenient molecular probe in 19F NMR-based studies of the structure and dynamics of the dense phase in LLPS peptide systems.

Macrocyclic receptors for anion recognition

Macrocyclic receptors have emerged as versatile and efficient molecular tools for the recognition and sensing of anions, playing a pivotal role in molecular recognition and supramolecular chemistry. The following review provides an overview of the recent advances in the design, synthesis, and applications of macrocyclic receptors specifically tailored for anion recognition. The unique structural features of macrocycles, such as their well-defined structures and pre-organised binding sites, contribute to their exceptional anion-binding capabilities that have led to their application across a broad range of the chemical and biological sciences.

Histidine as a versatile excipient in the protein-based biopharmaceutical formulations

Adequate stabilization is essential for marketed protein-based biopharmaceutical formulations to withstand the various stresses that can be exerted during the pre- and post-manufacturing processes. Therefore, a suitable choice of excipient is a significant step in the manufacturing of such delicate products. Histidine, an essential amino acid, has been extensively used in protein-based biopharmaceutical formulations. The physicochemical properties of histidine are unique among amino acids and could afford multifaceted benefits to protein-based biopharmaceutical formulations. With a pKa of approximately 6.0 at the side chain, histidine has been primarily used as a buffering agent, especially for pH 5.5-6.5. Additionally, histidine exhibited several affirmative properties similar to those of carbohydrates (e.g., sucrose and trehalose) and could therefore be considered to be an alternative approach to established protein-based formulation strategies. The current review describes the general physicochemical properties of histidine, lists all commercial histidine-containing protein-based biopharmaceutical products, and discusses a brief outline of the existing research focused on the versatile applications of histidine, which can act as a buffering agent, stabilizer, cryo-/lyo-protectant, antioxidant, viscosity reducer, and solubilizing agent. The interaction between histidine and proteins in protein-based biopharmaceutical formulations, such as the Donnan effect during diafiltration of monoclonal antibody solutions and the degradation of polysorbates in histidine buffer, has also been discussed. As the first review of histidine in protein biopharmaceuticals, it helps to deepen our understanding of the opportunities and challenges associated with histidine as an excipient for protein-based biopharmaceutical formulations.

Deciphering the Concept of Solubility by Strategically Using the Counterion Effect in Charged Molecules

Solubility is an essential concept in chemistry that describes the ability of a substance to dissolve in a particular solvent. Despite its importance in many fields of science, understanding the basic principles of solubility is challenging for many undergraduate students. Notably, students often encounter difficulties in comprehending the role of counterions when dealing with charged molecules. Here, we bring the opportunity to assimilate the key concepts of solubility regarding the role of counterions by developing a straightforward, cheap, and visually appealing experiment that focuses on the strategic use of counterions to control solubility. A student questionnaire delivered encouraging results with most of students giving positive feedback in both interest and training their hands-on skills. Hence, our experiment offers a proficient understanding of the solubility concept, thus preparing undergraduate students for advanced courses in the various subject areas of chemistry.

Microbial lipopeptides: their pharmaceutical and biotechnological potential, applications, and way forward

As lead molecules, cyclic lipopeptides with antibacterial, antifungal, and antiviral properties have garnered a lot of attention in recent years. Because of their potential, cyclic lipopeptides have earned recognition as a significant class of antimicrobial compounds with applications in pharmacology and biotechnology. These lipopeptides, often with biosurfactant properties, are amphiphilic, consisting of a hydrophilic moiety, like a carboxyl group, peptide backbone, or carbohydrates, and a hydrophobic moiety, mostly a fatty acid. Besides, several lipopeptides also have cationic groups that play an important role in biological activities. Antimicrobial lipopeptides can be considered as possible substitutes for antibiotics that are conventional to address the current drug-resistant issues as pharmaceutical industries modify the parent antibiotic molecules to render them more effective against antibiotic-resistant bacteria and fungi, leading to the development of more resistant microbial strains. Bacillus species produce lipopeptides, which are secondary metabolites that are amphiphilic and are typically synthesized by non-ribosomal peptide synthetases (NRPSs). They have been identified as potential biocontrol agents as they exhibit a broad spectrum of antimicrobial activity. A further benefit of lipopeptides is that they can be produced and purified biotechnologically or biochemically in a sustainable manner using readily available, affordable, renewable sources without harming the environment. In this review, we discuss the biochemical and functional characterization of antifungal lipopeptides, as well as their various modes of action, method of production and purification (in brief), and potential applications as novel antibiotic agents.

Polymyxins with Potent Antibacterial Activity against Colistin-Resistant Pathogens: Fine-Tuning Hydrophobicity with Unnatural Amino Acids

In view of the increased prevalence of antimicrobial resistance among human pathogens, antibiotics against multidrug-resistant (MDR) bacteria are in urgent demand. In particular, the rapidly emerging resistance to last-resort antibiotic colistin, used for severe Gram-negative MDR infections, is critical. Here, a series of polymyxins containing unnatural amino acids were explored, and some analogues exhibited excellent antibacterial activity against Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. Hydrophobicity of the compounds within this series (as measured by retention in reversed-phase analytical HPLC) exhibited a discernible correlation with their antimicrobial activity. This trend was particularly pronounced for colistin-resistant pathogens. The most active compounds demonstrated competitive activity against a panel of Gram-negative pathogens, while exhibiting low in vitro cytotoxicity. Importantly, most of these hits also retained (or even had increased) potency against colistin-susceptible strains. These findings infer that fine-tuning hydrophobicity may enable the design of polymyxin analogues with favorable activity profiles.

The Study of Antistaphylococcal Potential of Omiganan and Retro-Omiganan Under Flow Conditions

Staphylococcus aureus is considered one of the leading pathogens responsible for infections in humans and animals. The heterogeneous nature of diseases caused by these bacteria is due to the occurrence of multiple strains, differentiated by several mechanisms of antibiotic resistance and virulence factors. One of these is the ability to form biofilm. Biofilm-associated bacteria exhibit a different phenotype that protects them from external factors such as the activity of immune system or antimicrobial substances. Moreover, it has been shown that the majority of persistent and recurrent infections are associated with the presence of the biofilm. Omiganan, an analog of indolicidin - antimicrobial peptide (AMP) derived from bovine neutrophil granules, was found to exhibit high antistaphylococcal and antibiofilm potential. Furthermore, its analog with a reversed sequence (retro-omiganan) was found to display enhanced activity against a variety of pathogens. Based on experience of our group, we found out that counterion exchange can improve the antistaphylococcal activity of AMPs. The aim of this study was to investigate the activity of both compounds against S. aureus biofilm under flow conditions. The advantage of this approach was that it offered the opportunity to form and characterize the biofilm under more controlled conditions. To do this, unique flow cells made of polydimethylsiloxane (PDMS) were developed. The activity against pre-formed biofilm as well as AMPs-treated bacteria was measured. Also, the incorporation of omiganan and retro-omiganan into the channels was conducted to learn whether or not it would inhibit the development of biofilm. The results of the microbiological tests ultimately confirmed the high potential of the omiganan and its retro-analog as well as the importance of counterion exchange in terms of antimicrobial examination. We found out that retro-omiganan trifluoroacetate had the highest biofilm inhibitory properties, however, acetates of both compounds exhibited the highest activity against planktonic and biofilm cultures. Moreover, the developed methodology of investigation under flow conditions allows the implementation of the studies under flow conditions to other compounds.

The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation

Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.

Designing Formulation Strategies for Enhanced Stability of Therapeutic Peptides in Aqueous Solutions: A Review

Over the past few decades, there has been a tremendous increase in the utilization of therapeutic peptides. Therapeutic peptides are usually administered via the parenteral route, requiring an aqueous formulation. Unfortunately, peptides are often unstable in aqueous solutions, affecting stability and bioactivity. Although a stable and dry formulation for reconstitution might be designed, from a pharmaco-economic and practical convenience point of view, a peptide formulation in an aqueous liquid form is preferred. Designing formulation strategies that optimize peptide stability may improve bioavailability and increase therapeutic efficacy. This literature review provides an overview of various degradation pathways and formulation strategies to stabilize therapeutic peptides in aqueous solutions. First, we introduce the major peptide stability issues in liquid formulations and the degradation mechanisms. Then, we present a variety of known strategies to inhibit or slow down peptide degradation. Overall, the most practical approaches to peptide stabilization are pH optimization and selecting the appropriate type of buffer. Other practical strategies to reduce peptide degradation rates in solution are the application of co-solvency, air exclusion, viscosity enhancement, PEGylation, and using polyol excipients.

Photoinduced Processes in Lysine-Tryptophan-Lysine Tripeptide with L and D Tryptophan

Optical isomers of short peptide Lysine-Tryptophan-Lysine (Lys-{L/D-Trp}-Lys) and Lys-Trp-Lys with an acetate counter-ion were used to study photoinduced intramolecular and intermolecular processes of interest in photobiology. A comparison of L- and D-amino acid reactivity is also the focus of scientists' attention in various specialties because today, the presence of amyloid proteins with D-amino acids in the human brain is considered one of the leading causes of Alzheimer's disease. Since aggregated amyloids, mainly Aβ42, are highly disordered peptides that cannot be studied with traditional NMR and X-ray techniques, it is trending to explore the reasons for differences between L- and D-amino acids using short peptides, as in our article. Using NMR, chemically induced dynamic nuclear polarization (CIDNP) and fluorescence techniques allowed us to detect the influence of tryptophan (Trp) optical configuration on the peptides fluorescence quantum yields, bimolecular quenching rates of Trp excited state, and the photocleavage products formation. Thus, compared with the D-analog, the L-isomer shows a greater Trp excited state quenching efficiency with the electron transfer (ET) mechanism. There are experimental confirmations of the hypothesis about photoinduced ET between Trp and the CONH peptide bond, as well as between Trp and another amide group.

Understanding the Role of Self-Assembly and Interaction with Biological Membranes of Short Cationic Lipopeptides in the Effective Design of New Antibiotics

This study investigates short cationic antimicrobial lipopeptides composed of 2-4 amino acid residues and C12-C18 fatty acids attached to the N-terminal part of the peptides. The findings were discussed in the context of the relationship among biological activity, self-assembly, stability, and membrane interactions. All the lipopeptides showed the ability to self-assemble in PBS solution. In most cases, the critical aggregation concentration (CAC) much surpassed the minimal inhibitory concentration (MIC) values, suggesting that monomers are the main active form of lipopeptides. The introduction of β-alanine into the peptide sequence resulted in a compound with a high propensity to fibrillate, which increased the peptide stability and activity against S. epidermidis and C. albicans and reduced the cytotoxicity against human keratinocytes. The results of our study indicated that the target of action of lipopeptides is the bacterial membrane. Interestingly, the type of peptide counterion may affect the degree of penetration of the lipid bilayer. In addition, the binding of the lipopeptide to the membrane of Gram-negative bacteria may lead to the release of calcium ions necessary for stabilization of the lipopolysaccharide layer.

The impact of counterions in biological activity: case study of antibacterial alkylguanidino ureas

Abstract

Trifluoroacetic acid (TFA), due to its strong acidity and low boiling point, is extensively used in protecting groups-based synthetic strategies. Indeed, synthetic compounds bearing basic functions, such as amines or guanidines (commonly found in peptido or peptidomimetic derivatives), developed in the frame of drug discovery programmes, are often isolated as trifluoroacetate (TF-Acetate) salts and their biological activity is assessed as such in in vitro, ex vivo, or in vivo experiments. However, the presence of residual amounts of TFA was reported to potentially affect the accuracy and reproducibility of a broad range of cellular assays (e. g. antimicrobial susceptibility testing, and cytotoxicity assays) limiting the further development of these derivatives. Furthermore, the impact of the counterion on biological activity, including TF-Acetate, is still controversial. Herein, we present a focused case study aiming to evaluate the activity of an antibacterial AlkylGuanidino Urea (AGU) compound obtained as TF-Acetate (1a) and hydrochloride (1b) salt forms to highlight the role of counterions in affecting the biological activity. We also prepared and tested the corresponding free base (1c). The exchange of the counterions applied to polyguanidino compounds represents an unexplored and challenging field, which required significant efforts for the successful optimization of reliable methods of preparation, also reported in this work. In the end, the biological evaluation revealed a quite similar biological profile for the salt derivatives 1a and 1b and a lower potency was found for the free base 1c.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s11030-022-10505-6.

A story of peptides, lipophilicity and chromatography - back and forth in time

Peptides, as part of the beyond the rule of 5 (bRo5) chemical space, represent a unique class of pharmaceutical compounds. Because of their exceptional position in the chemical space between traditional small molecules (molecular weight (MW) < 500 Da) and large therapeutic proteins (MW > 5000 Da), peptides became promising candidates for targeting challenging binding sites, including even targets traditionally considered as undruggable - e.g. intracellular protein-protein interactions. However, basic knowledge about physicochemical properties that are important for a drug to be membrane permeable is missing but would enhance the drug discovery process of bRo5 molecules. Consequently, there is a demand for quick and simple lipophilicity determination methods for peptides. In comparison to the traditional lipophilicity determination methods via shake flask and in silico prediction, chromatography-based methods could have multiple benefits such as the requirement of low analyte amount, insensitivity to impurities and high throughput. Herein we elucidate the role of peptide lipophilicity and different lipophilicity values. Further, we summarize peptide analysis via common chromatographic techniques, in specific reversed phase liquid chromatography, hydrophilic interaction liquid chromatography and supercritical fluid chromatography and their role in drug discovery and development process.

Synthetic pharmaceutical peptides characterization by chromatography principles and method development

As per United States Food and Drug Administration, any polymer/chain composed of 40 or fewer amino acids is called as a peptide, where more than 40 amino acids are considered as proteins. In many occasions there is a change in the source of manufacturing of the peptide active pharmaceutical ingredient, where one has to prove the sameness of that product with the existing formulation by considering several aspects like presence of impurities/degradation products, extent of aggregations etc. For the same, several chromatographic characterization techniques such as; Reverse phase high performance liquid chromatography-ultraviolet/high resolution mass spectrometry, supercritical fluid chromatography, size exclusion chromatography, Ion exchange chromatography etc are widely used in pharmaceutical industry. It is well known that the method development of peptide molecules is often challenging as many variables are to be kept in mind which can affect the separation, recovery and stability of molecule. The present review focuses on the basics of peptide degradation and method development by using various chromatographic techniques for characterization. It also covers a deep insight of method development parameters and variables to be considered which might directly or indirectly affect the chromatographic separation and recovery, and also provides a guide on selection of chromatographic parameters. This article is protected by copyright. All rights reserved.

Antiplasmodial diterpenoid alkaloid from Aconitum heterophyllum Wall. ex Royle: Isolation, characterization, and UHPLC-DAD based quantification

ETHNOPHARMACOLOGICAL RELEVANCE

Aconitum heterophyllum Wall. ex Royle is a traditionally important medicinal plant having numerous therapeutic actions as documented in Ayurveda. This plant is traditionally known for combating worm infestation, fever, respiratory tract disease, vomiting, diarrhoea, diabetes, skin disorders, anaemia, and joint disorders. Further, it has been used alone and in combination with other plants to prepare various anti-malarial formulations. However, there is no report on the assessment of its anti-plasmodial activity, and the metabolite(s) responsible for this activity.

AIM OF THE STUDY

The main aim of this study was to conduct phytochemical investigation of A. heterophyllum roots for the preparation of extract, fractions, and isolation of pure molecules to identify active fractions/molecules responsible for the anti-plasmodial activity, and development of UHPLC-DAD based analytical method which can be used for the quantification of marker compounds in the extracts and fractions.

MATERIALS AND METHODS

Hydroalcoholic extract (1:1 v/v) and fractions (n-hexane, chloroform, ethyl acetate, n-butanol, and water) were prepared from the dried powdered roots of A. heterophyllum. Fractions were further subjected to silica gel column chromatography to isolate pure specialized secondary metabolites from this plant. All extracts, fractions, and pure molecules were evaluated against the chloroquine resistant Pf INDO and chloroquine sensitive Pf3D7 strains in culture for calculating their IC₅₀ values. UHPLC-DAD based analytical method was also developed for the first time for the quantification of marker compounds and quality assessment of this commercially important Himalayan medicinal plant.

RESULTS

Phytochemical investigation of A. heterophyllum root led to the isolation of six specialized metabolites viz. 2-O-cinnamoyl hetisine (1), atisinium (2), 4-oxabicyclo [3.2.2] nona-1(7),5,8-triene (3), atisinium cinnamate (4), aconitic acid (5), and atisinium formate (6). Compound 1 is a new hetisine type diterpenoid alkaloid, compounds 4 and 6 are new counter ionic forms observed with atisinium ion, and compound 3 is being reported for the first time from this genus. Chloroform fraction was found to be the most active with IC₅₀ (μg/mL) 1.01 (Pf INDO) and 1.32 (Pf3D7). The molecule 2-O-cinnamoyl hetisine (1), a new diterpenoid alkaloid isolated from chloroform fraction, showed promising antiplasmodial activities with IC₅₀ (μM) 1.92 (Pf INDO) and 10.8 (Pf 3D7). The activity of chloroform fraction was further validated by the developed UHPLC-DAD based method as the quantity of 2-O-cinnamoyl hetisine (1) was higher in the chloroform fraction (≅200 mg/g) than in all other fractions (<7 mg/g). Atisinium (2) and 2-O-cinnamoyl hetisine (1) were found to be the main marker compounds of this plant based on quantity and antiplasmodial activity, respectively.

CONCLUSION

This study provides the scientific rationale for the traditional use of this plant in treating malaria. Further, this study revealed that the anti-malarial potential of this plant might be due to the presence of diterpenoid alkaloids.

A New Approach to Supramolecular Structure Determination in Pharmaceutical Preparation of Self-Assembling Peptides: A Case Study of Lanreotide Autogel

The supramolecular structure in peptides’ prolonged-released gel formulations is the most critical parameter for the determination of the pharmaceutical profile of the drug. Here, we report our investigation on lanreotide Autogel as a case study. For the first time, we describe the use of the pulsed field gradient (PFG) diffusion-ordered spectroscopy (DOSY) magic-angle spinning NMR to characterize the supramolecular self-assembly and molecular mobility of different samples of lanreotide Autogel formulations prepared according to different formulation protocols. The diffusion coefficient was used to calculate the hydrodynamic radii of supramolecular assemblies and build relative molecular models. DOSY data were integrated with NMR imaging (MRI) measurements and atomic force microscopy (AFM) imaging.

Recent developments in capillary and microchip electroseparations of peptides (2019-mid 2021)

The review provides a comprehensive overview of developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, microscale isolation, and physicochemical characterization of peptides from 2019 up to approximately the middle of 2021. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis, such as sample preparation, sorption suppression, EOF control, and detection, are presented. New developments in the individual CE and CEC methods are demonstrated and several types of their applications are shown. They include qualitative and quantitative analysis, determination in complex biomatrices, monitoring of chemical and enzymatic reactions and physicochemical changes, amino acid, sequence, and chiral analyses, and peptide mapping of proteins. In addition, micropreparative separations and determination of significant physicochemical parameters of peptides by CE and CEC methods are described.

Carboxylic Acid Counterions in FDA-Approved Pharmaceutical Salts

Salification is one of the powerful and widely employed approaches to improve the biopharmaceutical properties of drugs. The FDA's eighty-year trajectory of new drug approvals depicts around one-third of the drugs clinically used as their pharmaceutical salts. Among various cationic and anionic counterions used in FDA-approved pharmaceutical salts, the carboxylic acids have significantly contributed. A total of 94 pharmaceutical salts discovered during 1943-2020 comprises carboxylic acids as counterions with a major contribution of acetate, maleate, tartrate, fumarate, and succinate. Hydrocodone tartrate is the first FDA-approved carboxylate salt approved in 1943. Overall, the analysis shows that fifteen carboxylic acid counterions are present in FDA-approved pharmaceutical salts with a major share of acetate (18 drugs). This review provides an account of FDA-approved carboxylate salts from 1939 to 2020. The decade-wise analysis indicates that 1991-2000 contributed a maximum number of carboxylate salts (24) and least (3) in 1939-1950. The technical advantage of carboxylate salts over free-base or other counterions is also discussed. Graphical Abstract.

Facilitated Buccal Insulin Delivery via Hydrophobic Ion-Pairing Approach: In vitro and ex vivo Evaluation

BACKGROUND

The clinical use of therapeutic peptides has been limited because of their inefficient delivery approaches and, therefore, inadequate delivery to target sites. Buccal administration of therapeutic peptides offers patients a potential alternative to the current invasive routes of administration.

PURPOSE

The aim of the study was to fabricate hydrophobic ion-pairing (HIP)-nanocomplexes (C1 and C2) utilizing anionic bile salts and cationic peptides, and to assess their permeability across TR146 buccal cell layers and porcine buccal tissue.

METHODS

C1 and C2-nanocomplexes were fabricated using the HIP approach. In addition, their physiochemical and morphological attributes, in vitro and ex vivo permeability properties, and qualitative and quantitative cellular uptake were evaluated and compared. The localization of C1 and C2-nanocomplexes in porcine buccal tissue was determined using confocal laser scanning microscopy.

RESULTS

The C1-nanocomplex was the superior nanocarrier and significantly enhanced the transport of insulin across TR146 cell layers and porcine buccal tissue, exhibiting a 3.00- and 51.76-fold increase in permeability coefficient, respectively, when compared with insulin solution (p < 0.01). C1-nanocomplex was more efficient than C2-nanocomplex at facilitating insulin permeability, with a 2.18- and 27.64-fold increase across TR146 cell layers and porcine buccal tissue, respectively. The C1-nanocomplex demonstrated immense uptake and localization of insulin in TR146 cells and porcine buccal tissue, as evidenced by a highly intense fluorescence in TR146 cells, and a great shift of fluorescence intensity towards the inner region of buccal tissue over time. The increase in fluorescence intensity was observed in the order of C1 > C2 > insulin solution.

CONCLUSION

In this study, we highlighted the efficacy of potential nanocarriers in addressing the daunting issues associated with the invasive administration of insulin and indicated a promising strategy for the buccal administration and delivery of this life-saving peptide hormone.