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Molecules
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The Application of Molecular Modeling in Chemistry Science
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The Application of Molecular Modeling in Chemistry Science

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (31 May 2026) | Viewed by 1028

Editors

Prof. Dr. Wim Buijs

E-Mail Website
Guest Editor
Independent Researcher, Lochlehn 237, 6105 Leutasch, Austria
Interests: molecular modeling; CO2 capture; cannabinoids; catalysis; oxidation; industrial chemistry; renewables; teaching
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Alicja Nowaczyk

E-Mail Website
Guest Editor
Department of Organic Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 2 dr. A. Jurasza St., 85-094 Bydgoszcz, Poland
Interests: organic and medicinal chemistry; computational chemistry and molecular modeling of GAT, MAT, VGIC; predictive modelling of detailed mechanisms of action and pharmacological effec-tiveness of biologically active compounds and chemical reaction pathways; neuropharmacology; cardiovascular; safety pharmacology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Thanks to the rise of computational power and decreasing cost of computers, computational chemistry has evolved into a tool capable of changing the way chemical research and teaching are carried out. A wide variety of methods and tools have become available. These can not only improve our understanding of basic chemical concepts but are also applicable to real experimental problems in academic and industrial research. The properties of molecules and molecular ensembles can be determined with sufficient accuracy to be useful in limiting the amount of experimental work involved in catalysis, drug discovery, and the development of new materials. These include thermodynamic properties, spectroscopical properties, and reaction kinetics, to mention just a few. Visualization plays an important role in many areas, particularly in teaching. Computational chemistry has the potential to become a universal (visual) language, uniting the different descriptions of similar chemical phenomena in disciplines like physical chemistry, organic chemistry, inorganic chemistry and biochemistry, catalysis and biocatalysis, and pharmacokinetics.

We welcome authors to submit original articles and short communications, as well as a limited number of review articles, on new approaches and methods of computational chemistry for research and teaching. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on the website.

Prof. Dr. Wim Buijs
Prof. Dr. Alicja Nowaczyk
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly 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

  • visualization
  • molecular mechanics
  • quantum mechanics
  • molecular dynamics
  • biomolecular modeling
  • drug development
  • catalysis
  • material modeling
  • thermodynamics
  • method development

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Published Papers (2 papers)

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Research

21 pages, 3398 KB  
Article
Mechanistic Elucidation of BBOX-Catalyzed Hydroxylation and THP-Induced Oxidative Rearrangement via QM/MM Calculations
by Zheng Ruan, Hong Li, Yongjun Liu, Xianghui Zhang and Xinyi Li
Molecules 2026, 31(11), 1941; https://doi.org/10.3390/molecules31111941 - 3 Jun 2026
Viewed by 248
Abstract
Carnitine plays an essential role in fatty acid metabolism, and its biosynthesis is tightly regulated by γ-butyrobetaine hydroxylase (BBOX), an Fe(II)/α-ketoglutarate-dependent dioxygenase. BBOX is the target of mildronate (THP), a clinically used drug for treating ischemic heart diseases. However, the detailed mechanisms of [...] Read more.
Carnitine plays an essential role in fatty acid metabolism, and its biosynthesis is tightly regulated by γ-butyrobetaine hydroxylase (BBOX), an Fe(II)/α-ketoglutarate-dependent dioxygenase. BBOX is the target of mildronate (THP), a clinically used drug for treating ischemic heart diseases. However, the detailed mechanisms of BBOX-catalyzed hydroxylation and the atypical oxidative rearrangement underlying THP inhibition remain elusive. In this study, we employed combined quantum mechanics/molecular mechanics (QM/MM) methods to systematically elucidate these mechanisms at the atomic level. Our calculations reveal that the hydroxylation of γBB proceeds via a classical three-step mechanism in the quintet state, with hydrogen atom abstraction as the rate-determining step. Remarkably, substitution of the C4 methylene group in γBB with an amino group in THP redirects the reaction pathway, as the lone pair electrons on the adjacent nitrogen atom render N-N bond cleavage kinetically favored over hydroxyl rebound, thereby blocking carnitine synthesis. Through systematic evaluation of possible rearrangement pathways, we rule out the previously proposed direct 1,2-H migration and suggest a revised mechanism featuring imine-mediated hydrogen transfer, hydroxyl rebound preceding C-C bond formation, and final radical coupling. This work provides a detailed atomic-level understanding of both the catalytic and inhibitory mechanisms of BBOX, revealing how substrate electronic effects dictate reaction outcomes. The elucidated mechanistic insights offer a theoretical foundation for understanding the catalytic versatility of the αKG-dependent dioxygenase family and provide valuable guidance for the rational design of novel BBOX inhibitors. Full article
(This article belongs to the Special Issue The Application of Molecular Modeling in Chemistry Science)
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16 pages, 2302 KB  
Article
Integrated Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Simulations Accelerate the Discovery of Novel PDE1 Inhibitors with Potential for the Treatment of Idiopathic Pulmonary Fibrosis
by Xin-Lin Cai, Zhao-Hang Xue, Shu-Jin He, Wei-Hao Luo, Run-Duo Liu, Qian Zhou and Chen Zhang
Molecules 2026, 31(10), 1731; https://doi.org/10.3390/molecules31101731 - 19 May 2026
Viewed by 443
Abstract
Phosphodiesterase-1 (PDE1) represents an attractive target for the treatment of idiopathic pulmonary fibrosis (IPF). However, the limited chemical diversity of current PDE1 inhibitors has hindered the development of potential anti-IPF drugs, primarily due to an ambiguous understanding of interactions between inhibitors and PDE1. [...] Read more.
Phosphodiesterase-1 (PDE1) represents an attractive target for the treatment of idiopathic pulmonary fibrosis (IPF). However, the limited chemical diversity of current PDE1 inhibitors has hindered the development of potential anti-IPF drugs, primarily due to an ambiguous understanding of interactions between inhibitors and PDE1. Herein, we report an integrated virtual screening strategy containing pharmacophore modeling, molecular docking, and molecular dynamics simulations, which markedly accelerated the discovery of novel PDE1 inhibitors. Enzymatic assays identified eleven active compounds with moderate inhibition from twenty-six purchased candidates, encompassing nine distinct scaffold types. Notably, 6484-0008 and 6484-0032 exhibited more than 50% inhibition at a concentration of 1 μM. Hydrogen bond analysis and residue-based energy decompositions revealed key recognition mechanisms involving crucial residues Gln421, His373, and Phe424, as well as the unique Thr271 in the flexible H-loop region, providing insights for the rational design of inhibitors with enhanced potency. Full article
(This article belongs to the Special Issue The Application of Molecular Modeling in Chemistry Science)
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