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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 7548

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Prof. Dr. Brindusa Tiperciuc

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Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania
Interests: cancer therapy; anti-infective drugs; molecular mechanisms; drug synthesis; targeted therapies; bioactive heterocycle synthesis; docking and molecular modelling
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Dear Colleagues,

In recent decades, the emergence of new highly pathogenic strains of viruses and microorganisms, such as SARS-CoV-2, drug-resistant tuberculosis, and malaria (i.e., superbugs), has presented challenges that require an urgent response. The effective treatment of cancer is another important and unresolved problem. Tumors develop through genetic and epigenetic changes that modify fundamental cellular programs for growth and proliferation, followed by the natural selection of reprogrammed cells that best adapt to the constant fight against human immunity and chemotherapy drugs.

To address these issues, a number of breakthrough synthetic methodologies need to be developed which enable the efficient assembly of new molecules and make it possible to achieve the high variability of substituents necessary for studying structure–biological activity relationships.

This Special Issue aims to gather scientific articles devoted to the synthesis and study of the activity of previously unknown compounds, as well as fully synthetic papers that describe new effective approaches to known biologically active compounds, without further evaluation of the biological properties.

Prof. Dr. Brindusa Tiperciuc
Guest Editor

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Keywords

biological activity
nature-derived molecules
heterocyclic moieties
aromatic species
structural diversity
alkaloids
organic synthesis

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Related Special Issues

Synthesis of Bioactive Compounds in Molecules (11 articles)
Synthesis of Bioactive Compounds: Volume II in Molecules (18 articles)

Published Papers (10 papers)

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Research

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18 pages, 3251 KB

Open AccessArticle

Exploring the Synthesis, Anti-Inflammatory and Anti-Tumor Potential of 4-Maleimidylphenyl-Hydrazide Derivatives

by Francis Cloutier, Alexis Paquin, Maude Cloutier, Yassine Oufqir, Laurie Fortin, Julie Girouard, Heidar-Ali Tajmir-Riahi, Carlos Reyes-Moreno and Gervais Bérubé

Molecules 2025, 30(20), 4035; https://doi.org/10.3390/molecules30204035 - 10 Oct 2025

Viewed by 223

Abstract

The design of innovative compounds displaying anti-inflammatory activity in oncological context is a subject of great interest in drug development. It has been proved that a pro-inflammatory microenvironment which accelerates cancer growth and cellular differentiation is often present in malignant bladder tumor. In earlier work, we reported the synthesis of p-aminobenzoic acid derivatives that act as anti-inflammatory compounds able to inhibit the pro-inflammatory markers present in bladder cancer microenvironment. DAB-1 rapidly emerged as an effective lead candidate in this investigation, with its ability to shrink by 90% in 25 days the size of human bladder cancer tumors in an ectopic mouse model. This manuscript discloses the synthesis of 23 new hydrazide derivatives of DAB-1 and reports their in vitro and in vivo biological evaluation. It was discovered that most of the new compounds are essentially nontoxic against RAW 264.7 cells, as evaluated by an MTT assay. Anti-inflammatory activity of the new derivatives was investigated by evaluation of their impact on cellular nitric oxide production, measured by a Griess assay. Some compounds did significatively inhibit nitric oxide production much more effectively than the original DAB-1. Striking activity of 14, which is around four times more potent than DAB-1, promotes this derivative as new lead compound in this study. The study of these analogs reveals that a phenolic/anisole core is a key component to achieve high biological activity. Furthermore, mice models of acute inflammation and invasive BCa tumors were used to assess the in vivo impact of derivative 14, and it was found that this compound does reduce inflammation in these mice, possess similar anti-inflammatory activity but higher anti-tumoral activity compared to DAB-1 with no apparent signs of toxicity. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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28 pages, 5122 KB

Open AccessArticle

Major Components of Dittrichia viscosa (Asteraceae) as a Source of New Pesticides

by María José Segura-Navarro, José Francisco Quílez del Moral, María Fe Andrés, Félix Valcárcel, Azucena González-Coloma, Diego O. Molina Inzunza and Alejandro F. Barrero

Molecules 2025, 30(19), 3950; https://doi.org/10.3390/molecules30193950 - 1 Oct 2025

Viewed by 288

Abstract

Ilicic acid, nerolidol, and 9-hydroxynerolidol are major components of the aerial parts of Dittrichia viscosa. These components were selectively isolated in multigram quantities and used as lead compounds to generate diversity in the search for new natural-product-derived pesticides. A total of 29 derivatives of these three molecules—some of which are known natural products—were generated by subjecting these natural products to different transformations. In order to explore potential applications in sustainable biocontrol, some of the compounds generated were evaluated for plant protection potential against insect pests (Spodoptera littoralis, Myzus persicae, Rhopalosiphum padi), against the nematode Meloidogyne javanica, and for their phytotoxic effects on ryegrass (Lolium perenne) and lettuce (Lactuca sativa). Additionally, their effects against the tick Hyalomma lusitanicum have been tested. Compound 11 was found to be antifeedant against S. littoralis and nematicidal. Compounds 3a and 8 were potent antifeedants against R. padi. None of the tested compounds significantly inhibited lettuce growth, and compounds 17, 3, and 3a even promoted root development. Conversely, compounds 3, 4, 11, 17, and 21a exhibited strong herbicidal activity on ryegrass. In larvicidal assays against H. lusitanicum, compounds 3, 3a, 11, 17, 29, and 33 were active, with compound 29 being six times more active than the positive control nootkatone. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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21 pages, 3591 KB

Open AccessArticle

Synthesis, Clastogenic and Cytotoxic Potential, and In Vivo Antitumor Activity of a Novel N-Mustard Based on Indole-3-carboxylic Acid Derivative

by Marina Filimonova, Olga Soldatova, Anna Shitova, Valentina Surinova, Vitaly Rybachuk, Alexander Kosachenko, Kirill Nikolaev, Daria Filatova, Ekaterina Prosovskaya, Sergey Ivanov, Petr Shegay, Andrey Kaprin and Alexander Filimonov

Molecules 2025, 30(18), 3710; https://doi.org/10.3390/molecules30183710 - 12 Sep 2025

Viewed by 565

Abstract

Compound T1089—a novel nitrogen mustard based on an indole-3-carboxylic acid derivative (ICAD)—has been synthesized. The ICAD used as the basis for T1089 is a TLR agonist capable of activating an antitumor immune response. This study describes the synthesis method and presents the results of preliminary investigations of this compound. This research included an assessment of acute toxicity in mice, in vivo clastogenic activity evaluated via the bone marrow chromosome aberration (BMCA) test in mice, in vitro cytotoxicity determined by the MTT assay against human lung carcinoma A549 cells, and in vivo antitumor effects (ATEs) in models of conventional chemotherapy (CCT) of solid tumors in mice. The bifunctional alkylating agent cyclophosphamide (CPA) was used as a reference drug. Toxicological studies revealed that T1089 belongs to toxicity class III (moderately toxic), with acute toxicity values (LD₁₆ and LD₅₀) in mice following intraperitoneal (i.p.) administration being 191 and 202 mg/kg, respectively. The alkylating activity and clastogenic potential of T1089 were demonstrated by its effects in the BMCA test, which were comparable to those of CPA. A single i.p. administration of CPA and T1089 at a dose of 0.064 mmol/kg induced similar stimulation of structural mutagenesis associated with DNA strand breaks. The frequency of karyocytes with aberrations increased 20-fold compared to the control, primarily due to a rise in chromatid breaks and fragments, and to a lesser extent, due to an increase in exchange-type aberrations. In vitro cytotoxicity studies indicated differences in the mechanisms of alkylating activity between CPA and T1089. According to the MTT assay, the cytotoxic effects of CPA were observed only at concentrations exceeding 2 mM (IC₅₀ = 4.2 ± 0.3 mM), corresponding to lethal in vivo doses, which is expected since the formation of CPA’s alkylating metabolite requires hepatic microsomal enzymes. In contrast, significant cytotoxic effects of T1089 were observed at much lower concentrations (15–50 μM, IC₅₀ = 33.4 ± 1.3 μM), corresponding to safe in vivo doses. Differences were also observed in the in vivo ATEs of CPA and T1089 in the Ehrlich solid carcinoma (ESC) CCT model. Following seven i.p. administrations at 48 h intervals (33 mg/kg), both compounds exhibited increasing toxicity, manifested as cumulative body weight loss in treated mice. However, despite the aggressive CCT regimen, ESC showed low sensitivity to CPA. The ATE of CPA developed slowly, reaching a significant level only after four injections, and even after seven administrations, tumor inhibition (TI) did not exceed 30%. In contrast, ESC was significantly more sensitive to T1089 under the same CCT conditions. The ATE of T1089 exhibited a cumulative pattern but developed more rapidly and to a greater extent. A significant antitumor effect was observed after just two injections, with maximal efficacy (TI = 53%) achieved after four injections and sustained until the end of the observation period. A high ATE of T1089 was also observed in the B-16 melanoma CCT model. Following six i.p. administrations at 48 h intervals (28 mg/kg), T1089 treatment was associated with minimal toxicity. Despite this mild CCT regimen, melanoma exhibited high sensitivity to T1089. Maximal ATE (TI = 56%) was achieved after two injections, and subsequent administrations maintained a consistently high efficacy (TI = 52–55%) until the end of the study. In summary, preliminary findings demonstrate that T1089 possesses alkylating activity characteristic of bifunctional agents, accompanied by high in vitro cytotoxicity and in vivo ATEs in CCT models (at high doses). Given that the ICAD used as the basis for T1089 is a TLR agonist capable of stimulating antitumor immunity, T1089 can be considered a dual-action alkylating agent with combined antitumor effects. These results justify further investigation of T1089 in conventional and metronomic chemotherapy regimens, particularly in combination with immune checkpoint inhibitors and antitumor vaccines. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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16 pages, 2782 KB

Open AccessArticle

Photochemically Assisted Synthesis of Thienobenzotriazole-Based Dual Cholinesterase Inhibitors

by Antonija Jelčić, Stanislava Talić, Ilijana Odak, Paula Pongrac, Dora Štefok and Irena Škorić

Molecules 2025, 30(16), 3439; https://doi.org/10.3390/molecules30163439 - 20 Aug 2025

Viewed by 749

Abstract

Background: It has been shown previously that thienobenzo-1,2,3-triazoles exhibit very good selective inhibition toward butyrylcholinesterase (BChE), while the same derivatives converted into salts also display inhibitory activity against acetylcholinesterase (AChE), enzymes relevant to Alzheimer’s disease therapy. They show even better BChE inhibition potential than neutral analogs. Methods: This study presents the synthesis and biological evaluation of a novel series of charged thienobenzo-1,2,3-triazolinium salts (1–17) as inhibitors of AChE and BChE. The basic skeleton of the targeted compounds was synthesized via a photochemical method and subsequently converted into corresponding bromide salts. Their structures were confirmed using NMR and HRMS analyses. Results: In vitro testing showed that all synthesized compounds exhibit moderate to strong BChE inhibition and, to a lesser extent, AChE inhibition. Compounds 8 and 11 emerged as the most potent AChE inhibitors (IC₅₀ ~ 2.6–3.2 µM), while compounds 1, 2, and 8 demonstrated excellent and selective BChE inhibition (IC₅₀ ~ 0.3–0.4 µM), outperforming the reference drug galantamine. Anti-inflammatory evaluation revealed limited activity, with compound 17 slightly reducing LPS-induced TNF-α production at the highest tested concentration. Conclusions: These findings highlight the role of the electric charge and substituent type in modulating biological activity and confirm the therapeutic potential of these molecules as dual cholinesterase inhibitors for further development in neurodegenerative disease treatment. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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19 pages, 6614 KB

Open AccessArticle

Synthesis, Structure and Cytoprotective Activity of New Derivatives of 4-Aryl-3-Aminopyridin-2(1H)-One

by Zarina Shulgau, Irina Palamarchuk, Egor Dezhko, Shynggys Sergazy, Assel Urazbayeva, Yuliya Safarova, Alexander Gulyayev, Yuri Gatilov and Ivan Kulakov

Molecules 2025, 30(16), 3331; https://doi.org/10.3390/molecules30163331 - 9 Aug 2025

Viewed by 629

Abstract

As a continuation of our research on the synthesis and study of biological properties of new derivatives of 3-aminopyridin-2(1H)-ones, we investigated the Leuckart–Wallach and Eschweiler–Clarke reactions with selected 3-aminopyridin-2(1H)-ones and 3-(arylmethyl)pyridin-2(1H)-ones. It was found that under the conditions of the Leuckart–Wallach reaction with aromatic aldehydes in formic acid, mainly formamides of the indicated 3-aminopyridones are formed. The Eschweiler–Clarke reaction of 3-aminopyridin-2(1H)-ones and 3-(arylmethyl)pyridin-2(1H)-ones with an aqueous solution of formaldehyde result in the formation of tertiary N–benzyl(methyl)amino)-pyridin-2(1H)-ones in almost quantitative yield. The 3-aminopyridin-2(1H)-ones derivatives synthesized by us were used for the biological screening of cytoprotective activity in the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) test to determine the viability of fibroblast cells isolated from the NIH/Swiss mouse embryo (NIH/3T3, Gibco). It was found that many of the studied compounds under the conditions of our experiment exhibited significant cytoprotective effects, thereby enhancing cell survival. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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11 pages, 1040 KB

Open AccessArticle

A Concise Asymmetric Synthesis of Sex Pheromone of Euproctis pseudoconspersa (Strand) and Its Enantiomer

by Biyu An, Shengli Liu, Jianan Wang, Dan Liu, Qinghua Bian and Jiangchun Zhong

Molecules 2025, 30(12), 2494; https://doi.org/10.3390/molecules30122494 - 6 Jun 2025

Viewed by 631

Abstract

The tea tussock moth, Euproctis pseudoconspersa (Strand), is a serious pest, and its sex pheromone is (R)-10,14-dimethylpentadecyl isobutyrate. A new and concise asymmetric synthesis of the sex pheromone and its enantiomer was accomplished. The chiral methyl of the pheromone was introduced by Evans’s template, while the extension of the carbon chain was achieved through Li₂CuCl₄-catalyzed coupling of chiral tosylate with Grignard reagent. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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19 pages, 974 KB

Open AccessArticle

Design, Synthesis and Antiplasmodial Activities of a Library of Fluorine-Based 3-Benzylmenadiones

by Matthieu Roignant, Jimmy Richard, Maxime Donzel, Matthias Rottmann, Pascal Mäser and Elisabeth Davioud-Charvet

Molecules 2025, 30(11), 2446; https://doi.org/10.3390/molecules30112446 - 3 Jun 2025

Viewed by 786

Abstract

Plasmodione is a potent early antiplasmodial compound. A metabolic study on mice treated with plasmodione revealed that 6-hydroxy–plasmodione was the main metabolite eliminated in the urine of treated mice. To block the metabolic pathway in the host, the introduction of fluorine at C-6 of the 3-benzylmenadione core was applied and showed potent antiplasmodial activity similar to that of the plasmodione analogue in vitro. In this work, a library of 38 6-fluoro-3-benzylmenadione analogues (a series) was constructed by incorporating structurally diverse groups in place of the 4-(trifluoromethyl) substituent present in the antiplasmodial plasmodione, via three synthetic routes. All new compounds were tested against the P. falciparum NF54 strain and for cytotoxicity with the rat L6 line. With a fluorine atom at C-6, A-a-21 was revealed to be the only compound from the a series, superior to the 6-H- analogue from the b series, with an IC₅₀ value of 70 nM versus 200 nM. Then, five other fluorine-based 3-benzylmenadiones, in which the fluorine was introduced in various positions of the 3-benzylmenadione core, were synthetized to assist our understanding of the impact of fluorine on antiplasmodial potencies in vitro; in particular, the aim here was to compare the effects of human serum and P. berghei species in these drug screens. This was also conducted in vivo with the P. berghei-infected mouse model. In the P. berghei species assay, PD and the 4′-fluoro-3′-trifluoromethyl-benzylmenadione A-b-9 exhibited a similar antiplasmodial behavior toward P. falciparum versus P. berghei. In the human serum versus Albumax assays, only the 6-fluoro–plasmodione showed a lower shift factor between Albumax assays and human serum conditions, suggesting a lower protein binding for the 6-F-PD compared to plasmodione or A-b-9. In vivo, 6-fluoro–plasmodione proved to be the most potent 3-benzylmenadione, reducing parasitemia by 50% after oral administration at 50 mg/kg. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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18 pages, 1984 KB

Open AccessArticle

Discovery of MAGL Inhibition by Lophine Derivatives: An Unexpected Finding from Chemiluminescent Assay Development

by Roberta Ottria, Silvana Casati, Ornella Xynomilakis, Aleksandar Veselinović and Pierangela Ciuffreda

Molecules 2025, 30(7), 1605; https://doi.org/10.3390/molecules30071605 - 3 Apr 2025

Cited by 1 | Viewed by 779

Abstract

The inhibitory effects of two novel lophine derivatives were unexpectedly discovered during the development of a chemiluminescent monoacylglycerol lipase (MAGL) assay. The proposed lophine derivatives were found to exhibit concentration-dependent inhibitory effects on MAGL with the octanoic and palmitic acid esters of 2-(4-hydroxyphenyl)-4,5-diphenylimidazole showing the strongest activity. Reversibility assays using a fluorometric method confirmed that these compounds interact with MAGL in a stable, irreversible manner. To further investigate their mode of interaction, docking studies were performed, supporting the hypothesis that compounds 3 and 4 may act as competitive and irreversible inhibitors. Lophine derivatives were initially designed and synthesized as potential chemiluminescence pro-enhancers. However, assay optimization revealed no signal production upon MAGL hydrolysis, precluding their use as chemiluminescent probes. These findings suggest that lophine is a promising candidate for the development of MAGL inhibitors, although further optimization is needed to enhance binding affinity and selectivity. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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27 pages, 6210 KB

Open AccessArticle

Synthetic Epoxyeicosatrienoic Acid Mimics Protect Mesangial Cells from Sorafenib-Induced Cell Death

by Marcus de Bourg, Abhishek Mishra, Rawand S. Mohammad, Christophe Morisseau, Bruce D. Hammock, John D. Imig and Anders Vik

Molecules 2025, 30(7), 1445; https://doi.org/10.3390/molecules30071445 - 24 Mar 2025

Cited by 1 | Viewed by 1022

Abstract

Nineteen potential mimics of 8,9-epoxyeicosatrienoic acid (8,9-EET), a natural bioactive oxylipin, were synthesized and evaluated for their ability to protect renal mesangial cells against sorafenib-induced cell death in a water-soluble tetrazolium (WST-8) assay. All compounds were also evaluated as inhibitors of soluble epoxide hydrolase. As expected of a potent pan-kinase inhibitor the drug sorafenib caused a significant decrease in cell viability in HRMCs. Several analogs containing amide and oxamide groups in place of the epoxide showed efficacy in reducing sorafenib induced human renal mesangial cell (HRMC) death. Oxamide containing analogs proved particularly effective, with the most promising analog increasing cell viability five-fold over control at 1 µM. These analogs, containing an oxamide group as a bioisostere for the epoxide in 8,9-EET, did not display significant inhibitory activity towards soluble epoxide hydrolase. This preliminary structure–activity relationship analysis reveals the oxamide group as a promising bioisostere for the epoxide in the 8,9-position of the fatty acid chain, producing protective effects against sorafenib-induced cell death in HRMCs. Collectively, these findings demonstrate the potential for using epoxide mimics and particularly oxamides as 8,9-EET analogs as bioisosteres of the corresponding epoxide in a therapeutic strategy against sorafenib-induced glomerular nephrotoxicity. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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Open AccessFeature PaperReview

Tetracyclic Bis-Piperidine Alkaloids: Structures, Bioinspired Synthesis, Synthesis, and Bioactivities

by Stan Iridio Gómez, Esveidy Isabel Oceguera Nava, Abbas Dadawalla, Dennis Ashong, Guanglin Chen and Qiao-Hong Chen

Molecules 2025, 30(14), 2907; https://doi.org/10.3390/molecules30142907 - 9 Jul 2025

Viewed by 1242

Abstract

Tetracyclic bis-piperidine alkaloids (TcBPAs) are structurally complex natural products primarily isolated from marine sponges of the order Haplosclerida. Distinguished by their intricate architecture, TcBPAs feature two central piperidine units linked by dual macrocyclic rings. These unique structural motifs contribute significantly to their biological activities. For example, TcBPAs exhibit antiproliferative activities at low micromolar concentrations across various cancer cell lines, including leukemia, melanoma, breast, colon, fibrosarcoma, and glioblastoma. Despite this promising therapeutic profile, the structural intricacy of TcBPAs has posed considerable challenges to the development of efficient synthetic methodologies, thereby limiting comprehensive exploration and potential clinical advancement. This review highlights recent progress and persisting challenges in the synthesis, structural analysis, and biological evaluation of TcBPAs, underscoring their therapeutic potential in anticancer drug discovery. Full article

(This article belongs to the Special Issue Synthesis of Bioactive Compounds, 3rd Edition)

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