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Density Functional Theory for Rational Drug Design and the Prediction of Natural Compounds’ Bioactivity

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

Deadline for manuscript submissions: closed (31 August 2024) | Viewed by 3647

Special Issue Editor

Dr. Ana Amić

E-Mail Website
Guest Editor
Department of Chemistry, Josip Juraj Strossmayer University of Osijek, Ulica Cara Hadrijana 8A, 31000 Osijek, Croatia
Interests: computational chemistry; mechanisms of antioxidant activity; antiradical potential of polyphenolic compounds; DFT; molecular simulations; molecular docking; cheminformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Natural compounds have attracted increasing attention over the years for their capacity to assist in various diseases due to their antioxidant, anticancer, anti-inflammatory, antiviral, antibacterial, and other effects. Hence, extensive research has been carried out on natural compounds and their effects on the human body and health. With the development of computational chemistry, various computational methods and approaches have been employed for this purpose, for example, DFT.

Density functional theory (DFT) plays an important role in the study of natural compounds and the development of novel drugs. Theoretical calculations help in understanding the electronic characteristics of compounds and their reactivity, as well as elucidating the underlying mechanisms of their activity (for example, antioxidant activity). DFT is also used in drug design and can provide useful information and predictions of adsorption sites, adsorption energies, interactions between drug molecules and natural compounds or enzymes, etc. Hence, DFT calculations can significantly help in the design of drugs and the study of their activity and interactions.

This Special Issue is dedicated to collecting the latest DFT studies on natural compounds and novel drug design. We invite authors to submit original research or review articles on topics including DFT studies on various natural compounds, the design and characterization of novel drugs, the interactions between drugs and various natural compounds, and the reactions of natural compounds or drugs with biomolecules.

Dr. Ana Amić
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. 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

  • natural compounds
  • density functional theory (DFT)
  • drug design
  • theoretical computation
  • molecular docking

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Published Papers (2 papers)

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Research

25 pages, 5977 KiB  
Article
Theoretical Study of Antioxidant and Prooxidant Potency of Protocatechuic Aldehyde
by Ana Amić, Denisa Mastiľák Cagardová and Žiko Milanović
Int. J. Mol. Sci. 2025, 26(1), 404; https://doi.org/10.3390/ijms26010404 - 5 Jan 2025
Cited by 2 | Viewed by 1042
Abstract
In this study, the antioxidant and prooxidant potency of protocatechuic aldehyde (PCA) was evaluated using density functional theory (DFT). The potency of direct scavenging of hydroperoxyl (HOO•) and lipid peroxyl radicals (modeled by vinyl peroxyl, H2C=CHOO•) involved [...] Read more.
In this study, the antioxidant and prooxidant potency of protocatechuic aldehyde (PCA) was evaluated using density functional theory (DFT). The potency of direct scavenging of hydroperoxyl (HOO•) and lipid peroxyl radicals (modeled by vinyl peroxyl, H2C=CHOO•) involved in lipid peroxidation was estimated. The repair of oxidative damage in biomolecules (lipids, proteins and nucleic acids) and the prooxidant ability of PCA phenoxyl radicals were considered. The repairing potency of PCA was investigated for damaged tryptophan, cysteine, leucine, DNA base guanine and linolenic acid. The thermodynamics and kinetics of the single electron transfer (SET) and formal hydrogen atom transfer (fHAT) mechanisms underlying the studied processes were investigated under physiological conditions in aqueous and lipid environments using the SMD/M06-2X/6-311++G(d,p) level of theory. Sequestration of catalytic Fe2+ and Fe3+ ions by PCA, which prevents HO• production via Fenton-like reactions, was modeled. Molecular docking was used to study the inhibitory capability of PCA against xanthine oxidase (XO), one of the enzymes producing reactive oxygen species. The attained results show that PCA has the capability to scavenge lipid peroxyl radicals, repair damaged tryptophan, leucine and guanine, chelate catalytic iron ions and inhibit XO. Thus, PCA could be considered a possible multifunctional antioxidant. Full article
(This article belongs to the Special Issue Density Functional Theory for Rational Drug Design and the Prediction of Natural Compounds’ Bioactivity)
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18 pages, 6790 KiB  
Article
Correlation between Molecular Docking and the Stabilizing Interaction of HOMO-LUMO: Spirostans in CHK1 and CHK2, an In Silico Cancer Approach
by Antonio Rosales-López, Guiee N. López-Castillo, Jesús Sandoval-Ramírez, Joel L. Terán and Alan Carrasco-Carballo
Int. J. Mol. Sci. 2024, 25(16), 8588; https://doi.org/10.3390/ijms25168588 - 6 Aug 2024
Cited by 5 | Viewed by 1393
Abstract
Checkpoint kinases 1 and 2 (CHK1 and CHK2) are enzymes that are involved in the control of DNA damage. At the present time, these enzymes are some of the most important targets in the fight against cancer since their inhibition produces cytotoxic effects [...] Read more.
Checkpoint kinases 1 and 2 (CHK1 and CHK2) are enzymes that are involved in the control of DNA damage. At the present time, these enzymes are some of the most important targets in the fight against cancer since their inhibition produces cytotoxic effects in carcinogenic cells. This paper proposes the use of spirostans (Sp), natural compounds, as possible inhibitors of the enzymes CHK1 and CHK2 from an in silico analysis of a database of 155 molecules (S5). Bioinformatics studies of molecular docking were able to discriminate between 13 possible CHK1 inhibitors, 13 CHK2 inhibitors and 1 dual inhibitor for both enzymes. The administration, distribution, metabolism, excretion and toxicity (ADMETx) studies allowed a prediction of the distribution and metabolism of the potential inhibitors in the body, as well as determining the excretion routes and the appropriate administration route. The best inhibition candidates were discriminated by comparing the enzyme-substrate interactions from 2D diagrams and molecular docking. Specific inhibition candidates were obtained, in addition to studying the dual inhibitor candidate and observing their stability in dynamic molecular studies. In addition, Highest Occupied Molecular Orbital—Lowest Unoccupied Molecular Orbital (HOMO-LUMO) interactions were analyzed to study the stability of interactions between the selected enzymes and spirostans resulting in the predominant gaps from HOMOCHKs to LUMOSp (Highest Occupied Molecular Orbital of CHKs—Lowest Unoccupied Molecular Orbital of spirostan). In brief, this study presents the selection inhibitors of CHK1 and CHK2 as a potential treatment for cancer using a combination of molecular docking and dynamics, ADMETx predictons, and HOMO-LUMO calculation for selection. Full article
(This article belongs to the Special Issue Density Functional Theory for Rational Drug Design and the Prediction of Natural Compounds’ Bioactivity)
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