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Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition
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Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 4467

Special Issue Editor

Dr. Wing-Leung Wong

E-Mail Website
Guest Editor
State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Kowloon 999077, Hong Kong
Interests: small-molecule inhibitors; biosensors; chemical biology; G-quadruplex structures; molecular design and synthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Many naturally occurring bioactive organic compounds, such as polyphenols, carotenoids, phytosterols, organic acids, omega-3 fatty acids, vitamins, nucleosides and nucleotides, and pentacyclic triterpenoids, have attracted attention because of their active biofunctions in the prevention of certain diseases. In recent years, both natural and synthetic or semi-synthetic bioactive organic compounds have been used in modern drug development as the compounds are a prolific source of important lead compounds and pharmacophores. These include anticancer and antimicrobial agents against drug-resistant bacteria, such as superbugs, antivirus agents, cardioprotective agents, and anti-inflammatory agents. To ensure pharmaceutical development to address modern health challenges, the molecular design, synthesis, and semi-synthesis of potentially bioactive compounds and systematic evaluation of their bioactivity, biotoxicity, and potential applications for pre-clinical trials are crucial. These multi-disciplinary investigations may integrate many areas of knowledge and expertise, including, but not limited to, molecular design and organic synthesis, chemical transformation and structure–activity relationship studies, bioactive compound library construction, high-throughput screening, drug-target identification, molecular simulation, in vitro and in vivo evaluations, and so on. Therefore, contributions from cross-disciplinary experts, such as synthetic chemists, medicinal chemists, phytochemists, biochemists, combinatorial chemists, analytical chemists, as well as other practitioners and engineers in related fields, are clearly highly important in supporting pharmaceutical development and advancement. This Special Issue aims to gather individual efforts to support new drug discoveries through the identification, synthesis, and evaluation of novel bioactive organic compounds that may provide positive impacts in various areas of human health.

Dr. Wing-Leung Wong
Guest Editor

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Keywords

  • bioactive compounds
  • bioactivity evaluation
  • drug discovery
  • medicinal chemistry
  • chemical biology
  • natural products
  • lead compounds and pharmacophores
  • molecular design and organic synthesis

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Related Special Issue

Published Papers (5 papers)

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Research

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18 pages, 3269 KiB  
Article
Exploring the Mutated Kinases for Chemoenzymatic Synthesis of N4-Modified Cytidine Monophosphates
by Martyna Koplūnaitė, Kamilė Butkutė, Jonita Stankevičiūtė and Rolandas Meškys
Molecules 2024, 29(16), 3767; https://doi.org/10.3390/molecules29163767 - 9 Aug 2024
Viewed by 524
Abstract
Nucleosides, nucleotides, and their analogues are an important class of molecules that are used as substrates in research of enzymes and nucleic acid, or as antiviral and antineoplastic agents. Nucleoside phosphorylation is usually achieved with chemical methods; however, enzymatic phosphorylation is a viable [...] Read more.
Nucleosides, nucleotides, and their analogues are an important class of molecules that are used as substrates in research of enzymes and nucleic acid, or as antiviral and antineoplastic agents. Nucleoside phosphorylation is usually achieved with chemical methods; however, enzymatic phosphorylation is a viable alternative. Here, we present a chemoenzymatic synthesis of modified cytidine monophosphates, where a chemical synthesis of novel N4-modified cytidines is followed by an enzymatic phosphorylation of the nucleosides by nucleoside kinases. To enlarge the substrate scope, multiple mutant variants of Drosophila melanogaster deoxynucleoside kinase (DmdNK) (EC:2.7.1.145) and Bacillus subtilis deoxycytidine kinase (BsdCK) (EC:2.7.1.74) have been created and tested. It has been determined that certain point mutations in the active sites of the kinases alter their substrate specificities noticeably and allow phosphorylation of compounds that had been otherwise not phosphorylated by the wild-type DmdNK or BsdCK. Full article
(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)
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14 pages, 2570 KiB  
Article
Cytotoxicity and Chemotaxonomic Significance of Saponins from Wild and Cultured Asparagus Shoots
by Tarik Chileh-Chelh, Rosalía López-Ruiz, Ana M. García-Cervantes, Ignacio Rodríguez-García, Miguel A. Rincón-Cervera, Mohamed Ezzaitouni and José L. Guil-Guerrero
Molecules 2024, 29(14), 3367; https://doi.org/10.3390/molecules29143367 - 18 Jul 2024
Viewed by 820
Abstract
The shoots of Asparagus L. are consumed worldwide, although most species belonging to this genus have a restricted range, and several taxa remain unstudied. In this work, a total of four taxa from different locations were scrutinized and compared with cultivated A. [...] Read more.
The shoots of Asparagus L. are consumed worldwide, although most species belonging to this genus have a restricted range, and several taxa remain unstudied. In this work, a total of four taxa from different locations were scrutinized and compared with cultivated A. officinalis. All shoots were screened for saponins via LC-MS, and in vitro antiproliferative activities against the HT-29 colorectal cancer cell line were assessed via the MTT assay. The total saponins (TS) contained in the crude extracts ranged from 710.0 (A. officinalis) to 1258.6 mg/100 g dw (A. acutifolius). The richness of the compounds detected in this work stands out; a total of 47 saponins have been detected and quantified in the edible parts (shoots) of five taxa of Asparagus. The structure of all the saponins found present skeletons of the furostane and spirostane type. In turn, the structures with a furostane skeleton are divided into unsaturated and dioxygenated types, both in the 20–22 position. The sum of dioscin and derivatives varied largely among the studied taxa, reaching the following percentages of TS: 27.11 (A. officinalis), 18.96 (A. aphyllus), 5.37 (A. acutifolius), and 0.59 (A. albus); while in A. horridus, this compound remains undetected. Aspachiosde A, D, and M varied largely among samples, while a total of seven aspaspirostanosides were characterized in the analyzed species. The hierarchical cluster analysis of the saponin profiles clearly separated the various taxa and demonstrated that the taxonomic position is more important than the place from which the samples were acquired. Thus, saponin profiles have chemotaxonomic significance in Asparagus taxa. The MTT assay showed dose- and time-dependent inhibitory effects of all saponins extracts on HT-29 cancer cells, and the strongest cell growth inhibition was exercised by A. albus and A. acutifolius (GI50 of 125 and 175 µg/mL). This work constitutes a whole approach to evaluating the saponins from the shoots of different Asparagus taxa and provides arguments for using them as functional foods. Full article
(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)
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22 pages, 11265 KiB  
Article
Design, Synthesis, and Biological Evaluation of the Quorum-Sensing Inhibitors of Pseudomonas aeruginosa PAO1
by Xinlin Yan, Shi Hou, Cheng Xing, Yuanyuan Zhang, Jiajia Chang, Junhai Xiao and Feng Lin
Molecules 2024, 29(10), 2211; https://doi.org/10.3390/molecules29102211 - 8 May 2024
Viewed by 992
Abstract
Due to the resistance of Gram-negative bacteria Pseudomonas aeruginosa PAO1 to most clinically relevant antimicrobials, the use of traditional antibiotic treatments in hospitals is challenging. The formation of biofilms, which is regulated by the quorum-sensing (QS) system of Pseudomonas aeruginosa (PA), is an [...] Read more.
Due to the resistance of Gram-negative bacteria Pseudomonas aeruginosa PAO1 to most clinically relevant antimicrobials, the use of traditional antibiotic treatments in hospitals is challenging. The formation of biofilms, which is regulated by the quorum-sensing (QS) system of Pseudomonas aeruginosa (PA), is an important cause of drug resistance. There are three main QS systems in P. aeruginosa: the las system, the rhl system, and the pqs system. The inhibitors of the las system are the most studied. Previously, the compound AOZ-1 was found to have a certain inhibitory effect on the las system when screened. In this study, twenty-four compounds were designed and synthesized by modifying the Linker and Rings of AOZ-1. Using C. violaceum CV026 as a reporter strain, this study first assessed the inhibitory effects of new compounds against QS, and their SAR was investigated. Then, based on the SAR analysis of compound AOZ-1 derivatives, the parent core of AOZ-1 was replaced to explore the structural diversity. Then, nine new compounds were designed and synthesized with a new nucleus core component of 3-amino-tetrahydro-l,3-oxazin-2-one. The compound Y-31 (IC50 = 91.55 ± 3.35 µM) was found to inhibit the QS of C. violaceum CV026. Its inhibitory effect on C. violaceum CV026 was better than that of compound AOZ-1 (IC50 > 200 µM). Furthermore, biofilm formation is one of the important causes of Pseudomonas aeruginosa PAO1 resistance. In this study, it was found that compound Y-31, with a new nucleus core component of 3-amino-tetrahydro-l,3-oxazin-2-one, had the highest biofilm inhibition rate (40.44%). The compound Y-31 has a certain inhibitory effect on the production of PAO1 virulence factors (pyocyanin, rhamnolipid, and elastase) and swarming. When the concentration of compound Y-31 was 162.5 µM, the inhibition rates of pyocyanin, rhamnolipid, and elastase were 22.48%, 6.13%, and 22.67%, respectively. In vivo, the lifetime of wildtype Caenorhabditis elegans N2 infected with P. aeruginosa PAO1 was markedly extended by the new parent nucleus Y-31. This study also performed cytotoxicity experiments and in vivo pharmacokinetics experiments on the compound Y-31. In conclusion, this study identified a compound, Y-31, with a new nucleus core component of 3-amino-tetrahydro-l,3-oxazin-2-one, which is a potential agent for treating P. aeruginosa PAO1 that is resistant to antibiotics and offers a way to discover novel antibacterial medications. Full article
(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)
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Review

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30 pages, 21279 KiB  
Review
Squirting Cucumber, Ecballium elaterium (L.) A. Ritch: An Update of Its Chemical and Pharmacological Profile
by Attilio Anzano, Bruna de Falco, Laura Grauso and Virginia Lanzotti
Molecules 2024, 29(18), 4377; https://doi.org/10.3390/molecules29184377 (registering DOI) - 14 Sep 2024
Abstract
Ecballium elaterium, also known as squirting cucumber, is a plant which is widespread in temperate regions of Europe, Africa and Asia. The plant is considered to be one of the oldest used drugs. In the last decades, E. elaterium has been widely [...] Read more.
Ecballium elaterium, also known as squirting cucumber, is a plant which is widespread in temperate regions of Europe, Africa and Asia. The plant is considered to be one of the oldest used drugs. In the last decades, E. elaterium has been widely studied as a source of triterpene metabolites named cucurbitacins, often found as glycosylated derivatives, used by the plant as defensive agents. Such metabolites exhibit several biological activities, including cytotoxic, anti-inflammatory, and anti-cancer. Interestingly, the bioactive properties of E. elaterium extracts have been investigated in dozens of studies, especially by testing the apolar fractions, including the essential oils, extracted from leaves and fruits. The purpose of this review is to provide an overview of the chemical profile of different parts of the plants (leaves, flowers, and seeds) analyzing the methods used for structure elucidation and identification of single metabolites. The pharmacological studies on the isolated compounds are also reported, to highlight their potential as good candidates for drug discovery. Full article
(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)
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17 pages, 1488 KiB  
Review
Development of Potential Therapeutic Agents from Black Elderberries (the Fruits of Sambucus nigra L.)
by Yulin Ren, Gunnar Meyer, Andrew T. Anderson, Kaitlyn M. Lauber, Judith C. Gallucci, Gary Gao and Alan Douglas Kinghorn
Molecules 2024, 29(13), 2971; https://doi.org/10.3390/molecules29132971 - 22 Jun 2024
Viewed by 1330
Abstract
Elderberry (Sambucus nigra L.) is a widespread deciduous shrub, of which the fruits (elderberries) are used in the food industry to produce different types of dietary supplement products. These berries have been found to show multiple bioactivities, including antidiabetic, anti-infective, antineoplastic, anti-obesity, [...] Read more.
Elderberry (Sambucus nigra L.) is a widespread deciduous shrub, of which the fruits (elderberries) are used in the food industry to produce different types of dietary supplement products. These berries have been found to show multiple bioactivities, including antidiabetic, anti-infective, antineoplastic, anti-obesity, and antioxidant activities. An elderberry extract product, Sambucol®, has also been used clinically for the treatment of viral respiratory infections. As the major components, phenolic compounds, such as simple phenolic acids, anthocyanins and other flavonoids, and tannins, show promising pharmacological effects that could account for the bioactivities observed for elderberries. Based on these components, salicylic acid and its acetate derivative, aspirin, have long been used for the treatment of different disorders. Dapagliflozin, an FDA-approved antidiabetic drug, has been developed based on the conclusions obtained from a structure–activity relationship study for a simple hydrolyzable tannin, β-pentagalloylglucoside (β-PGG). Thus, the present review focuses on the development of therapeutic agents from elderberries and their small-molecule secondary metabolites. It is hoped that this contribution will support future investigations on elderberries. Full article
(This article belongs to the Special Issue Exploring Bioactive Organic Compounds for Drug Discovery, 2nd Edition)
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