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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 6471

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Special Issue Editors

Prof. Dr. Josef Jampilek

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Guest Editor

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
Special Issues, Collections and Topics in MDPI journals

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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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

Published Papers (6 papers)

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Research

Open AccessArticle

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

Cristiane Casonato Melo

and

Jonathan A. Fauerbach

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

Viewed by 439

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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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

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 - 04 Sep 2023

Viewed by 945

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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Open AccessArticle

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

and

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

Viewed by 694

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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Open AccessArticle

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

and

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

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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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Open AccessArticle

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

and

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

Viewed by 816

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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Open AccessCommunication

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

and

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

Viewed by 2183

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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