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Biomolecules
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Current Progress in Protein Studies in the Context of Civilization...
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Current Progress in Protein Studies in the Context of Civilization Problems: From In Silico to In Vivo

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins".

Deadline for manuscript submissions: closed (30 December 2023) | Viewed by 5671

Special Issue Editor

Prof. Dr. Agnieszka A. Kaczor

E-Mail Website
Guest Editor
Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, PL-20093 Lublin, Poland
Interests: computer-aided drug design; medicinal chemistry; molecular modeling; CNS agents; GPCRs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Undoubtedly, proteins are the building blocks of life. Knowledge of their structure and properties enables not only an understanding of biological processes at the molecular level, but also the design of drugs, progress in fertilizers and food industry and other branches of modern industry. It can be thus stated that the development of protein science is key to solve many of civilization’s problems.

In particular, proteins constitute the main group of molecular targets for approved drugs. Effective drug design is facilitated when the 3D structure of a drug target is known from experimental or molecular modeling studies. Nowadays, diverse techniques of molecular modeling constitute important computational tools to study proteins in complex systems under native-like conditions at a molecular level. MD simulations have been exploited to elucidate the dynamic nature of protein systems, taking into account interactions with chemically diverse ligands, solvent effects, allosteric modulation of ions, membrane effects and, last but not least, the formation of higher-order complexes.

In the light of the above in this Special Issue of Biomolecules, we would like to illustrate the progress in protein science in the context of civilization problems. Manuscripts (both reviews and original work) that address the application of a variety of methods are welcome: from computational modeling and in vitro studies to behavioral studies.

Dr. Agnieszka A. Kaczor
Guest Editor

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. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • molecular modeling
  • civilization diseases
  • proteomics
  • structural bioinformatics
  • proteins

Published Papers (3 papers)

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Research

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18 pages, 7833 KiB  
Article
Molecular Modeling Studies to Probe the Binding Hypothesis of Novel Lead Compounds against Multidrug Resistance Protein ABCB1
by Yasmeen Cheema, Kenneth J. Linton and Ishrat Jabeen
Biomolecules 2024, 14(1), 114; https://doi.org/10.3390/biom14010114 - 16 Jan 2024
Viewed by 1020
Abstract
The expression of drug efflux pump ABCB1/P-glycoprotein (P-gp), a transmembrane protein belonging to the ATP-binding cassette superfamily, is a leading cause of multidrug resistance (MDR). We previously curated a dataset of structurally diverse and selective inhibitors of ABCB1 to develop a pharmacophore model [...] Read more.
The expression of drug efflux pump ABCB1/P-glycoprotein (P-gp), a transmembrane protein belonging to the ATP-binding cassette superfamily, is a leading cause of multidrug resistance (MDR). We previously curated a dataset of structurally diverse and selective inhibitors of ABCB1 to develop a pharmacophore model that was used to identify four novel compounds, which we showed to be potent and efficacious inhibitors of ABCB1. Here, we dock the inhibitors into a model structure of the human transporter and use molecular dynamics (MD) simulations to report the conformational dynamics of human ABCB1 induced by the binding of the inhibitors. The binding hypotheses are compared to the wider curated dataset and those previously reported in the literature. Protein–ligand interactions and MD simulations are in good agreement and, combined with LipE profiling, statistical and pharmacokinetic analyses, are indicative of potent and selective inhibition of ABCB1. Full article
(This article belongs to the Special Issue Current Progress in Protein Studies in the Context of Civilization Problems: From In Silico to In Vivo)
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23 pages, 1444 KiB  
Article
Xanthine–Dopamine Hybrid Molecules as Multitarget Drugs with Potential for the Treatment of Neurodegenerative Diseases
by Michał Załuski, Tadeusz Karcz, Anna Drabczyńska, Christin Vielmuth, Agnieszka Olejarz-Maciej, Monika Głuch-Lutwin, Barbara Mordyl, Agata Siwek, Grzegorz Satała, Christa E. Müller and Katarzyna Kieć-Kononowicz
Biomolecules 2023, 13(7), 1079; https://doi.org/10.3390/biom13071079 - 05 Jul 2023
Cited by 1 | Viewed by 1531
Abstract
Multitarget drugs based on a hybrid dopamine–xanthine core were designed as potential drug candidates for the treatment of neurodegenerative diseases. Monoamine oxidase B (MAO-B) inhibitors with significant ancillary A2A adenosine receptor (A2AAR) antagonistic properties were further developed to exhibit additional [...] Read more.
Multitarget drugs based on a hybrid dopamine–xanthine core were designed as potential drug candidates for the treatment of neurodegenerative diseases. Monoamine oxidase B (MAO-B) inhibitors with significant ancillary A2A adenosine receptor (A2AAR) antagonistic properties were further developed to exhibit additional phosphodiesterase-4 and -10 (PDE4/10) inhibition and/or dopamine D2 receptor (D2R) agonistic activity. While all of the designed compounds showed MAO-B inhibition in the nanomolar range mostly combined with submicromolar A2AAR affinity, significant enhancement of PDE-inhibitory and D2R-agonistic activity was additionally reached for some compounds through various structural modifications. The final multitarget drugs also showed promising antioxidant properties in vitro. In order to evaluate their potential neuroprotective effect, representative ligands were tested in a cellular model of toxin-induced neurotoxicity. As a result, protective effects against oxidative stress in neuroblastoma cells were observed, confirming the utility of the applied strategy. Further evaluation of the newly developed multitarget ligands in preclinical models of Alzheimer’s and Parkinson’s diseases is warranted. Full article
(This article belongs to the Special Issue Current Progress in Protein Studies in the Context of Civilization Problems: From In Silico to In Vivo)
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Review

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22 pages, 1516 KiB  
Review
The Role of Oxytocin and Vasopressin in Drug-Induced Reward—Implications for Social and Non-Social Factors
by Olga Wronikowska-Denysiuk, Weronika Mrozek and Barbara Budzyńska
Biomolecules 2023, 13(3), 405; https://doi.org/10.3390/biom13030405 - 21 Feb 2023
Cited by 2 | Viewed by 2497
Abstract
Drug abuse is a worldwide problem that leads to negative physical, mental, and economic consequences. Although pharmacological strategies for drug addiction management have been widely studied, therapeutic options with high efficacy and a low side-effects profile are still limited. Recently, there has been [...] Read more.
Drug abuse is a worldwide problem that leads to negative physical, mental, and economic consequences. Although pharmacological strategies for drug addiction management have been widely studied, therapeutic options with high efficacy and a low side-effects profile are still limited. Recently, there has been a growing interest in oxytocin (OT) and vasopressin (AVP) systems as potential therapeutic targets for the treatment of drug abuse. OT and AVP are hypothalamic neuropeptides involved in numerous physiological processes. Additionally, studies show that these neurohormones are highly implicated in the modulation of a wide range of behaviors. Interestingly, ample evidence has shown that both, OT and AVP are able to decrease the consumption of different drugs of abuse, as well as to ameliorate their rewarding and reinforcing effects. Furthermore, OT and AVP have been strongly involved in prosocial effects and social reward. In particular, OT has been shown to be able to shift drug-induced reward into social-induced reward, mainly due to its interaction with the dopaminergic system. This phenomenon is also reflected in the results of clinical trials where intranasal OT shows promising efficacy in managing substance use disorder. Therefore, the aim of this review is to comprehensively characterize the involvement of OT and AVP in the rewarding and other behavioral effects of drugs of abuse in animal models, with a particular highlight on the impact of social factors on the observed effects. Understanding this relationship may contribute to higher drug development success rates, as a result of a more profound and deliberate studies design. Full article
(This article belongs to the Special Issue Current Progress in Protein Studies in the Context of Civilization Problems: From In Silico to In Vivo)
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