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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 27628

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Special Issue Editors

Prof. Dr. Josef Jampilek

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1. Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia
2. Department of Chemical Biology, Faculty of Science, Palacky University, Olomouc, Slechtitelu 27, 78371 Olomouc, Czech Republic
Interests: medicinal chemistry; drug design; structure–activity relationships; pharmaceutical analysis; polymorphism; drug bioavailability; ADME; nanoparticles; nanoformulations; controlled/targeted delivery
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Dr. Jiri Kos

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Guest Editor

Faculty of Medicine, Masaryk University, Brno, Czech Republic
Interests: medicinal chemistry; analytical chemistry; intermolecular interactions; NMR

Special Issue Information

Dear Colleagues,

Knowledge of the interactions between molecules is undoubtedly the driving force behind all contemporary biomedical and biological sciences. Chemical biology/biological chemistry has become an important multidisciplinary bridge between chemistry and biology dealing with the study of small molecules, peptidomimetics or peptides, and their interactions in biological systems.

This Special Issue is intended for all researchers involved in the structure and analysis of biomolecules, the design and development of biologically active compounds and materials, and their interactions. Both works of a theoretical nature and manuscripts dealing with the mentioned topics at the level of in vitro/ex vivo and in vivo are welcome. Papers dealing with the structure of receptors and the enzymatic cascade are also invited.

Prof. Dr. Josef Jampilek
Dr. Jiri Kos
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

design bioactive molecules
bioactive materials
targeting
theoretical analysis of biomolecular structure
analytical and biophysical methods
structure and dynamics of biomolecules
intermolecular interactions
molecular biology/biochemistry
chemical biology/biological chemistry

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Published Papers (9 papers)

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Editorial

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4 pages, 1944 KiB

Open AccessEditorial

Editorial of Special Issue “Current Trends in Chemistry Towards Biology”

by Jiri Kos and Josef Jampilek

Int. J. Mol. Sci. 2024, 25(13), 7307; https://doi.org/10.3390/ijms25137307 - 3 Jul 2024

Viewed by 735

Abstract

One of the definitions of chemical biology is that it is a scientific discipline spanning the fields of chemistry, biology, and physics; it primarily involves the application of chemical techniques, tools, analyses, and often compounds (also known as chemical probes), which are produced [...] Read more.

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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Research

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15 pages, 2245 KiB

Open AccessArticle

Recovering What Matters: High Protein Recovery after Endotoxin Removal from LPS-Contaminated Formulations Using Novel Anti-Lipid A Antibody Microparticle Conjugates

by Cristiane Casonato Melo, Alexandra C. Fux, Martin Himly, Neus G. Bastús, Laura Schlahsa, Christiane Siewert, Victor Puntes, Albert Duschl, Isabel Gessner and Jonathan A. Fauerbach

Int. J. Mol. Sci. 2023, 24(18), 13971; https://doi.org/10.3390/ijms241813971 - 12 Sep 2023

Cited by 2 | Viewed by 2452

Abstract

Endotoxins or lipopolysaccharides (LPS), found in the outer membrane of Gram-negative bacterial cell walls, can stimulate the human innate immune system, leading to life-threatening symptoms. Therefore, regulatory limits for endotoxin content apply to injectable pharmaceuticals, and excess LPS must be removed before commercialization. The majority of available endotoxin removal systems are based on the non-specific adsorption of LPS to charged and/or hydrophobic surfaces. Albeit effective to remove endotoxins, the lack of specificity can result in the unwanted loss of essential proteins from the pharmaceutical formulation. In this work, we developed microparticles conjugated to anti-Lipid A antibodies for selective endotoxin removal. Anti-Lipid A particles were characterized using flow cytometry and microscopy techniques. These particles exhibited a depletion capacity > 6 ×10³ endotoxin units/mg particles from water, as determined with two independent methods (Limulus Amebocyte Lysate test and nanoparticle tracking analysis). Additionally, we compared these particles with a non-specific endotoxin removal system in a series of formulations of increasing complexity: bovine serum albumin in water < insulin in buffer < birch pollen extracts. We demonstrated that the specific anti-Lipid A particles show a higher protein recovery without compromising their endotoxin removal capacity. Consequently, we believe that the specificity layer integrated by the anti-Lipid A antibody could be advantageous to enhance product yield. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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25 pages, 2375 KiB

Open AccessArticle

Easy and Versatile Technique for the Preparation of Stable and Active Lipase-Based CLEA-like Copolymers by Using Two Homofunctional Cross-Linking Agents: Application to the Preparation of Enantiopure Ibuprofen

by Oussama Khiari, Nassima Bouzemi, José María Sánchez-Montero and Andrés R. Alcántara

Int. J. Mol. Sci. 2023, 24(17), 13664; https://doi.org/10.3390/ijms241713664 - 4 Sep 2023

Cited by 1 | Viewed by 2287

Abstract

An easy and versatile method was designed and applied successfully to obtain access to lipase-based cross-linked-enzyme aggregate-like copolymers (CLEA-LCs) using one-pot, consecutive cross-linking steps using two types of homobifunctional cross-linkers (glutaraldehyde and putrescine), mediated with amine activation through pH alteration (pH jump) as a key step in the process. Six lipases were utilised in order to assess the effectiveness of the technique, in terms of immobilization yields, hydrolytic activities, thermal stability and application in kinetic resolution. A good retention of catalytic properties was found for all cases, together with an important thermal and storage stability improvement. Particularly, the CLEA-LCs derived from Candida rugosa lipase showed an outstanding behaviour in terms of thermostability and capability for catalysing the enantioselective hydrolysis of racemic ibuprofen ethyl ester, furnishing the eutomer (S)-ibuprofen with very high conversion and enantioselectivity. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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21 pages, 2320 KiB

Open AccessArticle

Electrochemical Kinetics and Detection of Paracetamol by Stevensite-Modified Carbon Paste Electrode in Biological Fluids and Pharmaceutical Formulations

by Moaad Gharous, Loubna Bounab, Fernando J. Pereira, Mohamed Choukairi, Roberto López and A. Javier Aller

Int. J. Mol. Sci. 2023, 24(14), 11269; https://doi.org/10.3390/ijms241411269 - 10 Jul 2023

Cited by 12 | Viewed by 2117

Abstract

Paracetamol (PCT), or acetaminophen, is an important drug used worldwide for various clinical purposes. However, the excessive or indiscriminate use of PCT can provoke liver and kidney dysfunction; hence, it is essential to determine the amount of this target in biological samples. In this work, we develop a quick, simple, and sensitive voltammetric method using chemically modified electrodes to determine PCT in complex matrices, including human serum and commercial solid formulations. We modify the carbon paste electrode with stevensite monoclinic clay mineral (Stv-CPE), using cyclic voltammetry, differential pulse voltammetry, and electrochemical impedance spectroscopy to characterise and detect PCT. The kinetics study provides a better electrochemical characterisation of the electrode behaviour, finding the detection and quantitation limits of 0.2 μM and 0.5 μM under favourable conditions. Further, the best linear working concentration range is 0.6–100 μM for PCT, applying the proposed method to the quantitative determination of PCT content in reference tablet formulations and biological samples for validation. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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15 pages, 3549 KiB

Open AccessArticle

Structural and Biological Features of G-Quadruplex Aptamers as Promising Inhibitors of the STAT3 Signaling Pathway

by Veronica Esposito, Daniela Benigno, Ivana Bello, Elisabetta Panza, Mariarosaria Bucci, Antonella Virgilio and Aldo Galeone

Int. J. Mol. Sci. 2023, 24(11), 9524; https://doi.org/10.3390/ijms24119524 - 30 May 2023

Cited by 3 | Viewed by 2220

Abstract

In this paper, we investigate the structural and biological features of G-quadruplex (G4) aptamers as promising antiproliferative compounds affecting the STAT3 signalling pathway. Targeting the STAT3 protein through high-affinity ligands to reduce its levels or activity in cancer has noteworthy therapeutic potential. T40214 (STAT) [(G₃C)₄] is a G4 aptamer that can influence STAT3 biological outcomes in an efficient manner in several cancer cells. To explore the effects of an extra cytidine in second position and/or of single site-specific replacements of loop residues in generating aptamers that can affect the STAT3 biochemical pathway, a series of STAT and STATB [GCG₂(CG₃)₃C] analogues containing a thymidine residue instead of cytidines was prepared. NMR, CD, UV, and PAGE data suggested that all derivatives adopt dimeric G4 structures like that of unmodified T40214 endowed with higher thermal stability, keeping the resistance in biological environments substantially unchanged, as shown by the nuclease stability assay. The antiproliferative activity of these ODNs was tested on both human prostate (DU145) and breast (MDA-MB-231) cancer cells. All derivatives showed similar antiproliferative activities on both cell lines, revealing a marked inhibition of proliferation, particularly at 72 h at 30 µM. Transcriptomic analysis aimed to evaluate STAT’s and STATB’s influence on the expression of many genes in MDA-MB-231 cells, suggested their potential involvement in STAT3 pathway modulation, and thus their interference in different biological processes. These data provide new tools to affect an interesting biochemical pathway and to develop novel anticancer and anti-inflammatory drugs. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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20 pages, 13933 KiB

Open AccessArticle

The Design, Synthesis and Application of Nitrogen Heteropolycyclic Compounds with UV Resistance Properties

by Biao Yang, Xinbo Yang, Yuchuan Li and Siping Pang

Int. J. Mol. Sci. 2023, 24(9), 7882; https://doi.org/10.3390/ijms24097882 - 26 Apr 2023

Cited by 2 | Viewed by 1932

Abstract

Exposure to ultraviolet (UV) light is known to cause skin aging, skin damage, cancer, and eye diseases, as well as polymer material aging. Therefore, significant attention has been devoted to the research and development of UV absorbers. Considering the robust hydrogen bonding and conjugated structure present in nitrogen-containing polycyclic compounds, these compounds have been selected as potential candidates for exploring ultraviolet absorption properties. After structural optimization and the simulation of ultraviolet absorption spectra, four tris-[1,2,4]-triazolo-[1,3,5]-triazine (TTTs) derivatives, namely TTTB, TTTD, TTTJ, and TTTL, were selected as the preferred compounds and synthesized. The structure of the compound was determined using various analytical techniques, including FTIR, ¹HNMR, ¹³CNMR, HRMS, and XRD. Subsequently, composite films of polyvinyl chloride (PVC) and TTTs were produced using a simple solvent casting technique. The PVC films were subjected to UV age testing by exposing them to an ultraviolet aging chamber. The age-resistant performance of the fabricated films was evaluated using an ultraviolet spectrophotometer and Fourier infrared spectrum instrument. The findings suggest that TTTs exhibit a noteworthy capacity for absorbing ultraviolet radiation. The TTTL compound exhibits a superior UV absorption performance compared to commercially available UV absorbers such as UV-0 and UV-327 in the market. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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10 pages, 2304 KiB

Open AccessCommunication

A Practical Method for Amino Acid Analysis by LC-MS Using Precolumn Derivatization with Urea

by Runjin Zhao, Biling Huang, Gang Lu, Songsen Fu, Jianxi Ying and Yufen Zhao

Int. J. Mol. Sci. 2023, 24(8), 7332; https://doi.org/10.3390/ijms24087332 - 15 Apr 2023

Cited by 4 | Viewed by 5313

Abstract

Amino acid (AA) analysis is important in biochemistry, food science, and clinical medicine. However, due to intrinsic limitations, AAs usually require derivatization to improve their separation and determination. Here, we present a liquid chromatography-mass spectrometry (LC-MS) method for the derivatization of AAs using the simple agent urea. The reactions proceed quantitatively under a wide range of conditions without any pretreatment steps. Urea-derivatized products (carbamoyl amino acids) of 20 AAs exhibit better separation on reversed-phase columns and increased response in a UV detector compared to underivatized ones. We applied this approach to AA analysis in complex samples using a cell culture media as a model, and it showed potential for the determination of oligopeptides. This fast, simple, and inexpensive method should be useful for AA analysis in complex samples. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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Review

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29 pages, 2526 KiB

Open AccessReview

Recent Analytical Methodologies in Lipid Analysis

by Ivana Gerhardtova, Timotej Jankech, Petra Majerova, Juraj Piestansky, Dominika Olesova, Andrej Kovac and Josef Jampilek

Int. J. Mol. Sci. 2024, 25(4), 2249; https://doi.org/10.3390/ijms25042249 - 13 Feb 2024

Cited by 7 | Viewed by 8334

Abstract

Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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Other

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15 pages, 756 KiB

Open AccessCase Report

A Tissue Distribution Study of Propafenone in an Intentional Fatal Poisoning Case

by Žofia Nižnanská, Alexandra Hengerics Szabó, Marián Masár, Roman Szucs, Ján Šikuta and Ľuboš Nižnanský

Int. J. Mol. Sci. 2024, 25(10), 5202; https://doi.org/10.3390/ijms25105202 - 10 May 2024

Cited by 3 | Viewed by 948

Abstract

Propafenone (PPF) belongs to the class 1C antiarrhythmics and can cause electrocardiogram-associated adverse/toxic effects. Cases of PPF intoxication are rarely investigated. We developed a novel and selective GC-MS/MS method for the determination of PPF and its tissue distribution in an intentional fatal poisoning case, which is applicable to PPF quantification in the range of therapeutic to lethal concentrations in complex post-mortem samples. A simple and effective sample pretreatment was applied to all analyzed samples. PPF was determined without the need for dilution, even in highly complex samples containing a wide range of analyte concentrations. Quantification was performed using the standard addition method, developed and validated according to the ICH M10 guidelines. The obtained results indicated that the PPF concentration in the serum from blood taken while alive, before therapy, was the highest ever reported in the literature. Despite the intensive therapy after the patients’ admission, the PPF concentrations in the lungs, spleen, femoral blood and cardiac blood were fatal or abnormally high. On the other hand, the concentrations in the liver and skeletal muscle were lower or approximately the same as observed in cases with therapeutic doses. To the best of our knowledge, the distribution of PPF has not been investigated in fatal intoxication cases and can be helpful in clinical or forensic toxicology. Full article

(This article belongs to the Special Issue Current Trends in Chemistry towards Biology)

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