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Heterocycles in Medicinal Chemistry III

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 17747

Special Issue Editor


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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
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Special Issue Information

Dear Colleagues,

We announce with great pleasure the third edition of “Heterocycles in Medicinal Chemistry III”.

Heteroatoms constitute a very common fragment of several active pharmaceutical ingredients, as well as excipients; from the point of view of significance, it is all the same if these are isosterically/bioisosterically replaced carbons/carbon substructures in aliphatic structures or real heterocycles. Many heterocyclic scaffolds can be considered as privilege structures. Most frequently, nitrogen heterocycles or various positional combinations of nitrogen atoms, sulphur, and oxygen can be found in five- or six-membered rings. According to statistics, more than 85% of all biologically active chemical entities contain a heterocycle. This fact reflects the central role of heterocycles in modern drug design. The application of heterocycles provides a useful tool for the modification of solubility, lipophilicity, polarity, and hydrogen bonding capacity of biologically active agents, which results in the optimization of the ADME/Tox properties of drugs or drug candidates. The increasing presence of various heterocycles in drugs is related to advances in synthetic methodologies, such as metal-catalyzed cross-coupling and hetero-coupling reactions, that allow rapid access to a wide variety of functionalized heterocycles. On the other hand, many heterocyclic lead compounds were isolated from natural resources, and their structures were subsequently simplified and modified by medicinal chemists. Thus, heterocycles have critical importance for medicinal chemists because using them can expand the available drug-like chemical space and drive more effective drug discovery programmes. Medicinal chemistry is “a chemistry-based discipline, also involving aspects of biological, medical and pharmaceutical sciences” and “concerned with the invention, discovery, design, identification, and preparation of biologically active compounds, the study of their metabolism, the interpretation of their mode of action at the molecular level and the construction of structure-activity relationships”, this Special Issue of Molecules titled “Heterocycles in Medicinal Chemistry” is devoted to the following research topics focused on heterocycles: (i) synthesis and analysis; (ii) natural compounds; (iii) carbohydrates; (iv) drug design; (v) in silico investigations; (vi) biological screening; (vii) chemical biology and biological chemistry; (vii) biomaterials; and, in general, other topics related to heterocycles.

Prof. Dr. Josef Jampilek
Guest Editor

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Keywords

  • drugs
  • heterocycles
  • pharmacophore
  • drug design
  • computer study
  • synthesis
  • analysis
  • natural compounds
  • carbohydrates
  • physicochemical properties
  • ADMET
  • biological screening
  • chemical biology
  • biological chemistry
  • biomaterials

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Published Papers (10 papers)

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Research

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24 pages, 8064 KiB  
Article
Design and Synthesis of Novel 6-(Substituted phenyl)-[1,3]dioxolo[4′,5′:4,5]benzo[1,2-d]thiazole Compounds as Tyrosinase Inhibitors: In Vitro and In Vivo Insights
by Hyeon Seo Park, Hee Jin Jung, Hye Soo Park, Hye Jin Kim, Sang Gyun Noh, Yujin Park, Pusoon Chun, Hae Young Chung and Hyung Ryong Moon
Molecules 2025, 30(7), 1535; https://doi.org/10.3390/molecules30071535 - 30 Mar 2025
Viewed by 302
Abstract
The 2,4-dihydroxyphenyl group is commonly present in the chemical structures of potent tyrosinase inhibitors. Based on this observation, a series of 6-(substituted phenyl)-[1,3]dioxolo[4′,5′:4,5]benzo[1,2-d]thiazole compounds 113 were designed and synthesized as potential tyrosinase inhibitors. Among these, compounds 5 and 9 [...] Read more.
The 2,4-dihydroxyphenyl group is commonly present in the chemical structures of potent tyrosinase inhibitors. Based on this observation, a series of 6-(substituted phenyl)-[1,3]dioxolo[4′,5′:4,5]benzo[1,2-d]thiazole compounds 113 were designed and synthesized as potential tyrosinase inhibitors. Among these, compounds 5 and 9 strongly inhibited mushroom tyrosinase activity. Particularly, compound 9 exhibited nanomolar IC50 values regardless of the substrate used, whereas kojic acid yielded IC50 values of 15.99–26.18 μM. Kinetic studies on mushroom tyrosinase revealed that compounds 5 and 9 competitively inhibited tyrosinase activity, findings further corroborated by in silico docking analysis. In B16F10 cell-based experiments, both compounds effectively inhibited the cellular tyrosinase activity and melanin formation. These inhibitory effects were confirmed through in situ cellular tyrosinase activity assays. Compound 9 exhibited strong antioxidant activity by scavenging radicals, suggesting that its ability to reduce melanin production may be attributed to a combination of its antioxidant and tyrosinase inhibitory properties. Additionally, five compounds, including compound 5, demonstrated effective depigmentation activity in vivo in zebrafish embryos, and their depigmentation efficacy was similar to that of kojic acid, even at concentrations hundreds of times lower. These findings suggest that 6-(substituted phenyl)-[1,3]dioxolo[4′,5′:4,5]benzo[1,2-d]thiazole compounds may be promising anti-melanogenic agents. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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21 pages, 983 KiB  
Article
Synthesis, Characterization, and Antioxidant Activity Evaluation of New N-Methyl Substituted Thiazole-Derived Polyphenolic Compounds
by Alexandra Cătălina Cornea, Gabriel Marc, Ioana Ionuț, Cristina Moldovan, Anca Stana, Smaranda Dafina Oniga, Adrian Pîrnău, Laurian Vlase, Ilioara Oniga and Ovidiu Oniga
Molecules 2025, 30(6), 1345; https://doi.org/10.3390/molecules30061345 - 17 Mar 2025
Cited by 1 | Viewed by 471
Abstract
Reactive oxygen species play a significant role in various pathological conditions, driving the need for novel, potent antioxidants. While polyphenols are known for their antioxidant properties, their limited stability and bioavailability present challenges for therapeutic applications. To address these limitations, a series of [...] Read more.
Reactive oxygen species play a significant role in various pathological conditions, driving the need for novel, potent antioxidants. While polyphenols are known for their antioxidant properties, their limited stability and bioavailability present challenges for therapeutic applications. To address these limitations, a series of novel thiazolyl-polyphenolic compounds was synthesized via a multi-step synthetic route incorporating Hantzsch heterocyclization in the final step. The synthesized compounds 7ak were structurally characterized using spectroscopic techniques, including NMR, MS, and IR. In silico thermodynamic calculations, including HOMO–LUMO gap and bond dissociation enthalpy (BDE) calculations, revealed a promising antioxidant profile for these compounds and indicated that the substitution in position 2 of the thiazole ring does not substantially influence the antioxidant activity conferred by the catechol moiety in position 4. The antioxidant capacity of the synthesized compounds was experimentally validated using a panel of six distinct assays: two radical scavenging assays (ABTS and DPPH) and four electron transfer-based assays (RP, TAC, FRAP, and CUPRAC). The in vitro evaluation demonstrated that compounds 7j and 7k exhibited significantly enhanced antioxidant activity compared to the established antioxidant standards, ascorbic acid and Trolox. These findings suggest that the strategic modifications in position 2 of the thiazole scaffold represent a promising direction for future research aimed at developing novel therapeutic agents with enhanced antioxidant properties. The present study is limited to the in vitro evaluation of compounds based on the N-methyl substituted thiazole scaffold, but future studies can include modifications such as changing the substituent on the thiazole nitrogen, the hydrazone linker or possible insertion of substituents in position 5 of thiazole ring of substituents with various electronic or physico-chemical properties. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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29 pages, 10314 KiB  
Article
Structure–Activity Relationship Studies of Tetracyclic Pyrrolocarbazoles Inhibiting Heterotetrameric Protein Kinase CK2
by Lukas Kröger, Sebastian Borgert, Miriam Lauwers, Michaela Steinkrüger, Joachim Jose, Markus Pietsch and Bernhard Wünsch
Molecules 2025, 30(1), 63; https://doi.org/10.3390/molecules30010063 - 27 Dec 2024
Viewed by 651
Abstract
The serine/threonine kinase CK2 (formerly known as casein kinase II) plays a crucial role in various CNS disorders and is highly expressed in various types of cancer. Therefore, inhibiting this key kinase could be promising for the treatment of these diseases. The CK2 [...] Read more.
The serine/threonine kinase CK2 (formerly known as casein kinase II) plays a crucial role in various CNS disorders and is highly expressed in various types of cancer. Therefore, inhibiting this key kinase could be promising for the treatment of these diseases. The CK2 holoenzyme is formed by the recruitment of two catalytically active CK2α and/or CK2α′ subunits by a regulatory CK2β dimer. Starting with the lead furocarbazole W16 (4) inhibiting the CK2α/CK2β interaction, analogous pyrrolocarbazoles were prepared and tested for their protein–protein interaction inhibition (PPII). The key step of the synthesis was a multicomponent Levy reaction of 2-(indolyl)acetate 6, benzaldehydes 7, and N-substituted maleimides 8. Targeted modifications were performed by the saponification of the tetracyclic ester 9a, followed by the coupling of the resulting acid 10 with diverse amines. The replacement of the O-atom of the lead furocarbazole 4 by an N-atom in pyrrolocarbazoles retained or even increased the inhibition of the CK2α/CK2β interaction. The large benzyloxazolidinyl moiety of 4 could be replaced by smaller N-substituents without the loss of the PPII. The introduction of larger substituents at the 2-position and/or at p-position of the phenyl moiety at the 10-position to increase the surface for the inhibition of the PPI did not enhance the inhibition of the CK2α/CK2β association. The strong inhibition of the CK2α/CK2β association by the histidine derivative (+)-20a (Ki = 6.1 µM) translated into a high inhibition of the kinase activity of the CK2 holoenzyme (CK2α2β2, IC50 = 2.5 µM). Thus, 20a represents a novel lead compound inhibiting CK2 via the inhibition of the association of the CK2α and Ck2β subunits. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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27 pages, 2618 KiB  
Article
Phosphine Oxide Indenoquinoline Derivatives: Synthesis and Biological Evaluation as Topoisomerase I Inhibitors and Antiproliferative Agents
by Alba Rodriguez-Paniagua, Cinzia Tesauro, Birgitta R. Knudsen, Maria Fuertes and Concepción Alonso
Molecules 2024, 29(24), 5992; https://doi.org/10.3390/molecules29245992 - 19 Dec 2024
Viewed by 680
Abstract
The synthesis of phosphorous indenoquinolines and their biological evaluation as topoisomerase 1 (TOP1) inhibitors and antiproliferative agents were performed. First, the preparation of new hybrid 5H-indeno[2,1-c]quinolines with a phosphine oxide group was performed by a two-step Povarov-type [4+2]-cycloaddition reaction [...] Read more.
The synthesis of phosphorous indenoquinolines and their biological evaluation as topoisomerase 1 (TOP1) inhibitors and antiproliferative agents were performed. First, the preparation of new hybrid 5H-indeno[2,1-c]quinolines with a phosphine oxide group was performed by a two-step Povarov-type [4+2]-cycloaddition reaction between the corresponding phosphorated aldimines with indene in the presence of BF3·Et2O. Subsequent oxidation of the methylene present in the structure resulted in the corresponding indeno[2,1-c]quinolin-7-one phosphine oxides 10. The synthesized derivatives were evaluated as TOP1 inhibitors showing higher inhibition values than CPT at prolonged incubation times (5 min). Inhibition of TOP1 was even observed after 30 min of incubation. The cytotoxic activities of these compounds were also studied against different cancer cell lines and a non-cancerous cell line. While some compounds showed cytotoxicity against some cancerous cells, none of the compounds showed any cytotoxicity against the non-cancerous cell line, MRC-5, in contrast to CPT, which exhibits high toxicity against this cell line. These results represent a very interesting advance since the heterocyclic phosphine oxide derivatives have important properties as TOP1 inhibitors and show an interesting cytotoxicity against different cell lines. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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25 pages, 6703 KiB  
Article
Combining Fluconazole with Benzo[a]phenoxazine Derivatives as a Promising Strategy Against Fluconazole-Resistant Candida Species
by Maria Inês Pacheco, Bárbara Guimarães, Patrícia Pereira-Silva, Augusto Costa-Barbosa, M. Sameiro T. Gonçalves, Maria João Sousa and Paula Sampaio
Molecules 2024, 29(21), 5197; https://doi.org/10.3390/molecules29215197 - 2 Nov 2024
Viewed by 1478
Abstract
The rise in non-albicans Candida species, exhibiting unpredictable antifungal resistance, complicates treatment and contributes to the growing threat of invasive, life-threatening infections. This study evaluates the antifungal activity of four benzo[a]phenoxazine derivatives (C34, C35, A42, and [...] Read more.
The rise in non-albicans Candida species, exhibiting unpredictable antifungal resistance, complicates treatment and contributes to the growing threat of invasive, life-threatening infections. This study evaluates the antifungal activity of four benzo[a]phenoxazine derivatives (C34, C35, A42, and A44) against 14 Candida strains following EUCAST standards. Fluconazole interactions are analysed through fractional inhibitory concentration index (FICI) calculation and response surface analysis based on the Bliss model. Macrophage-like J774A.1 cells are used to assess Candida killing in the presence of synergistic compounds. The MIC values against the different strains vary, with C34 showing the strongest activity, followed by C35, while A42 has the highest MIC values, indicating lower efficacy. However, A42 demonstrates the best synergy with fluconazole against fluconazole-resistant Candida strains. Cytotoxicity assays reveal that the chloropropyl group present in C35 and A42 enhances cytocompatibility. Co-culture with macrophages shows significant yeast killing for C. albicans and C. auris when fluconazole and A42 are combined, requiring concentrations 4 and 16 times lower than their MIC values, enhancing antifungal activity. Given fluconazole’s fungistatic nature and the emergence of drug-resistant strains, benzo[a]phenoxazine derivatives’ ability to enhance fluconazole’s efficacy present a promising strategy to address antifungal resistance in critical pathogens. These findings align with global research priorities, offering new potential avenues for developing more effective antifungal therapies. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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22 pages, 4312 KiB  
Article
Design, Synthesis, and Anticancer and Antibacterial Activities of Quinoline-5-Sulfonamides
by Andrzej Zieba, Dominika Pindjakova, Malgorzata Latocha, Justyna Plonka-Czerw, Dariusz Kusmierz, Alois Cizek and Josef Jampilek
Molecules 2024, 29(17), 4044; https://doi.org/10.3390/molecules29174044 - 26 Aug 2024
Cited by 3 | Viewed by 1781
Abstract
A series of new unique acetylene derivatives of 8-hydroxy- and 8-methoxyquinoline- 5-sulfonamide 3af and 6af were prepared by reactions of 8-hydroxy- and 8-methoxyquinoline- 5-sulfonyl chlorides with acetylene derivatives of amine. A series of new hybrid systems containing quinoline and [...] Read more.
A series of new unique acetylene derivatives of 8-hydroxy- and 8-methoxyquinoline- 5-sulfonamide 3af and 6af were prepared by reactions of 8-hydroxy- and 8-methoxyquinoline- 5-sulfonyl chlorides with acetylene derivatives of amine. A series of new hybrid systems containing quinoline and 1,2,3-triazole systems 7ah were obtained by reactions of acetylene derivatives of quinoline-5-sulfonamide 6ad with organic azides. The structures of the obtained compounds were confirmed by 1H and 13C NMR spectroscopy and HR-MS spectrometry. The obtained quinoline derivatives 3af and 6af and 1,2,3-triazole derivatives 7ah were tested for their anticancer and antimicrobial activity. Human amelanotic melanoma cells (C-32), human breast adenocarcinoma cells (MDA-MB-231), and human lung adenocarcinoma cells (A549) were selected as tested cancer lines, while cytotoxicity was investigated on normal human dermal fibroblasts (HFF-1). All the compounds were also tested against reference strains Staphylococcus aureus ATCC 29213 and Enterococcus faecalis ATCC 29212 and representatives of multidrug-resistant clinical isolates of methicillin-resistant S. aureus (MRSA) and vancomycin-resistant E. faecalis. Only the acetylene derivatives of 8-hydroxyquinoline-5-sulfonamide 3af were shown to be biologically active, and 8-hydroxy-N-methyl-N-(prop-2-yn-1-yl)quinoline-5-sulfonamide (3c) showed the highest activity against all three cancer lines and MRSA isolates. Its efficacies were comparable to those of cisplatin/doxorubicin and oxacillin/ciprofloxacin. In the non-cancer HFF-1 line, the compound showed no toxicity up to an IC50 of 100 µM. In additional tests, compound 3c decreased the expression of H3, increased the transcriptional activity of cell cycle regulators (P53 and P21 proteins), and altered the expression of BCL-2 and BAX genes in all cancer lines. The unsubstituted phenolic group at position 8 of the quinoline is the key structural fragment necessary for biological activity. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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26 pages, 3339 KiB  
Article
Novel Quinazoline Derivatives as Highly Effective A2A Adenosine Receptor Antagonists
by Amélie Laversin, Robin Dufossez, Raphaël Bolteau, Romain Duroux, Séverine Ravez, Sergio Hernandez-Tapia, Martin Fossart, Mathilde Coevoet, Maxime Liberelle, Saïd Yous, Nicolas Lebègue and Patricia Melnyk
Molecules 2024, 29(16), 3847; https://doi.org/10.3390/molecules29163847 - 14 Aug 2024
Cited by 1 | Viewed by 1574
Abstract
The adenosine A2A receptor (A2AR) has been identified as a therapeutic target for treating neurodegenerative diseases and cancer. In recent years, we have highlighted the 2-aminoquinazoline heterocycle as an promising scaffold for designing new A2AR antagonists, exemplified by [...] Read more.
The adenosine A2A receptor (A2AR) has been identified as a therapeutic target for treating neurodegenerative diseases and cancer. In recent years, we have highlighted the 2-aminoquinazoline heterocycle as an promising scaffold for designing new A2AR antagonists, exemplified by 6-bromo-4-(furan-2-yl)quinazolin-2-amine 1 (Ki (hA2AR) = 20 nM). Here, we report the synthesis of new 2-aminoquinazoline derivatives with substitutions at the C6- and C7-positions, and the introduction of aminoalkyl chains containing tertiary amines at the C2-position to enhance antagonist activity and solubility properties. Compound 5m showed a high affinity for hA2AR with a Ki value of 5 nM and demonstrated antagonist activity with an IC50 of 6 µM in a cyclic AMP assay. Introducing aminopentylpiperidine and 4-[(piperidin-1-yl)methyl]aniline substituents maintained the binding affinities (9x, Ki = 21 nM; 10d, Ki = 15 nM) and functional antagonist activities (9x, IC50 = 9 µM; 10d, IC50 = 5 µM) of the synthesized compounds while improving solubility. This study provides insights into the future development of A2AR antagonists for therapeutic applications. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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Review

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21 pages, 3794 KiB  
Review
Heterocyclic Antidepressants with Antimicrobial and Fungicide Activity
by Darya Zolotareva, Alexey Zazybin, Yelizaveta Belyankova, Sarah Bayazit, Anuar Dauletbakov, Tulegen Seilkhanov, Ulan Kemelbekov and Murat Aydemir
Molecules 2025, 30(5), 1102; https://doi.org/10.3390/molecules30051102 - 27 Feb 2025
Viewed by 469
Abstract
In this review, the presence of antimicrobial and fungicidal activity in heterocyclic antidepressants was investigated. The already proven connection between the intestinal microbiome and mental health prompted the idea of whether these drugs disrupt the normal intestinal microflora. In addition, there is a [...] Read more.
In this review, the presence of antimicrobial and fungicidal activity in heterocyclic antidepressants was investigated. The already proven connection between the intestinal microbiome and mental health prompted the idea of whether these drugs disrupt the normal intestinal microflora. In addition, there is a serious problem of increasing resistance of microorganisms to antibiotics. In this article, we found that almost all of the antidepressants considered (except moclobemide, haloperidol, and doxepin) have antimicrobial activity and can suppress the growth of not only pathogenic microorganisms but also the growth of bacteria that directly affect mental health (such as Lactobacillus, Lactococcus, Streptococcus, Enterococcus, and Bifidobacterium). Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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49 pages, 7930 KiB  
Review
Indole Derivatives: A Versatile Scaffold in Modern Drug Discovery—An Updated Review on Their Multifaceted Therapeutic Applications (2020–2024)
by Xingyou Mo, Devendra Pratap Rao, Kirandeep Kaur, Roket Hassan, Ahmed S. Abdel-Samea, Sara Mahmoud Farhan, Stefan Bräse and Hamada Hashem
Molecules 2024, 29(19), 4770; https://doi.org/10.3390/molecules29194770 - 9 Oct 2024
Cited by 9 | Viewed by 6919
Abstract
Indole derivatives have become an important class of compounds in medicinal chemistry, recognized for their wide-ranging biological activities and therapeutic potential. This review provides a comprehensive overview of recent advances in the evaluation of indole-based compounds in the last five years, highlighting their [...] Read more.
Indole derivatives have become an important class of compounds in medicinal chemistry, recognized for their wide-ranging biological activities and therapeutic potential. This review provides a comprehensive overview of recent advances in the evaluation of indole-based compounds in the last five years, highlighting their roles in cancer treatment, infectious disease management, anti-inflammatory therapies, metabolic disorder interventions, and neurodegenerative disease management. Indole derivatives have shown significant efficacy in targeting diverse biological pathways, making them valuable scaffolds in designing new drugs. Notably, these compounds have demonstrated the ability to combat drug-resistant cancer cells and pathogens, a significant breakthrough in the field, and offer promising therapeutic options for chronic diseases such as diabetes and hypertension. By summarizing recent key findings and exploring the underlying biological mechanisms, this review underscores the potential of indole derivatives in addressing major healthcare challenges, thereby instilling hope and optimism in the field of modern medicine. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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31 pages, 6810 KiB  
Review
Synthetic Approaches, Properties, and Applications of Acylals in Preparative and Medicinal Chemistry
by Tobias Keydel and Andreas Link
Molecules 2024, 29(18), 4451; https://doi.org/10.3390/molecules29184451 - 19 Sep 2024
Cited by 1 | Viewed by 2689
Abstract
Diesters of geminal diols (R-CH(O-CO-R′)2, RR′C(OCOR″)2, etc. with R = H, aryl or alkyl) are termed acylals according to IUPAC recommendations (Rule P-65.6.3.6 Acylals) if the acids involved are carboxylic acids. Similar condensation products can be obtained from various [...] Read more.
Diesters of geminal diols (R-CH(O-CO-R′)2, RR′C(OCOR″)2, etc. with R = H, aryl or alkyl) are termed acylals according to IUPAC recommendations (Rule P-65.6.3.6 Acylals) if the acids involved are carboxylic acids. Similar condensation products can be obtained from various other acidic structures as well, but these related “non-classical acylals”, as one might call them, differ in various aspects from classical acylals and will not be discussed in this article. Carboxylic acid diesters of geminal diols play a prominent role in organic chemistry, not only in their application as protective groups for aldehydes and ketones but also as precursors in the total synthesis of natural compounds and in a variety of organic reactions. What is more, acylals are useful as a key structural motif in clinically validated prodrug approaches. In this review, we summarise the syntheses and chemical properties of such classical acylals and show what potentially under-explored possibilities exist in the field of drug design, especially prodrugs, and classify this functional group in medicinal chemistry. Full article
(This article belongs to the Special Issue Heterocycles in Medicinal Chemistry III)
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