Special Issue on “Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products”

Natural medicines refer to products derived from nature that exhibit pharmacological properties [1]. Most of these substances are compounds generated through secondary metabolic processes in various organisms, including animals, plants, and microorganisms [2,3]. These products are crucial for safeguarding human health and for managing various diseases affecting individuals [4]. Numerous pharmaceuticals have been developed from natural substances and their derivatives; consequently, these natural compounds serve as vital resources in contemporary drug development [3]. The refinement of crude extracts from apple pomace presents a promising strategy for enhancing the concentration of beneficial antioxidants and anti-inflammatory phenolic compounds [5]. Yanhui Zhao [6] investigated the chemical properties of DSS and its protective role against CCl4-induced liver fibrosis, focusing particularly on its mechanisms related to antioxidative stress and anti-inflammatory effects. The significant bacterial inhibition rate of O. mascula extract indicates its potential as an antibacterial agent [7]. Terpenoids are naturally occurring metabolites that serve significant roles in numerous pharmaceutical applications [8]. The majority of commercially accessible terpenoids are derived from higher plants; however, the cost-effective and sustainable production of these compounds for pharmaceutical use remains a challenge. This is primarily due to their limited natural availability, difficulties associated with extraction and purification processes, and the high labor intensity involved in their production [9]. The emergence of antibiotic-resistant microbial pathogens presents a considerable threat to both global health and economic stability, thereby underscoring the urgent need to create novel pharmaceuticals and antimicrobial therapies [10]. Synthetic biology methodologies offer insights into various biosynthetic pathways and enable innovative metabolic engineering strategies aimed at enhancing probiotic strains [11]. However, due to increasing resistance to pathogenic microorganisms, drug production and quantity requirements have increased recently, and traditional methods of producing natural drugs are unable to meet these requirements. Sustainability and green development of production are becoming increasingly important. Synthetic biology represents a contemporary interdisciplinary field within life sciences and systems science that has developed in the twenty-first century, integrating traditional metabolic engineering with principles of systems biology. Recent advancements in synthetic biology have significantly encouraged research into natural products and medicines. Enhanced and modified organisms can consistently and effectively produce specific target compounds in high quantities. They are distinguished by their minimal carbon emissions, eco-friendliness, and cost efficiency. The exclusive dependence on conventional methods of discovery and separation, or intricate synthetic chemistry, to acquire a restricted array of natural drugs and their analogs is unnecessary. This is due to the potential for designing novel biosynthetic pathways that can yield various natural drugs and their analogs. The advancement of synthetic biology can potentially lead to a new era for exploring natural pharmaceuticals [12,13].

At present, the extraction of plant materials serves as the principal technique for producing natural pharmaceuticals derived from botanical sources. Nevertheless, conventional approaches to preparing these natural compounds, which depend on plant extraction, exhibit numerous constraints. Natural plant medicines are typically distinguished by their remarkably low concentrations within the host organism. For instance, approximately 3 kilograms of bark from a century-old Pacific yew tree may yield merely 300 milligrams of paclitaxel, representing about 0.01% of the bark’s dry weight [14]. The concentration of the active compound ginsenoside in ginseng that has been aged between 3 to 5 years constitutes approximately 2% of the root’s dry weight. Additionally, the levels of certain rare saponins, which possess significant medicinal properties, range from approximately 0.02% to 0.0009% by weight in the dried roots [15].

Plastid terminal oxidases (PTOXs) have great potential to maintain cellular redox homeostasis and regulate the efficiency of photosynthetic reactions. In Chlamydomonas reinhardtii, oxidative stress, induced by nutrient limitation and highlight intensity, triggers the biosynthesis and accumulation of astaxanthin due to PTOX activity. The ptox2 gene exhibited high resistance under intensive light stress. ptox1 acts as a positive regulator, while ptox2 functions as a negative regulator of accumulation biosynthesis in gene-silenced strains of C. reinhardtii and confirms the synergistic actions in maintaining the photosynthetic activity and redox balance under various environmental conditions [16].

Heba Hellany [17] investigated isolating and characterizing the antimicrobial activity of B. subtilis BSP1 metabolites against various pathogenic microorganisms. They found that their crude extract displayed antimicrobial properties against various bacterial and fungal isolates. 98.9% scavenging activity of DPPH at 30 mg/mL was observed.

Anwar [13] investigated the role of MYB transcriptional factors for C. reinhardtii in the biosynthesis of terpenoid compounds through recent advanced metabolic and genetic engineering approaches. Heterologous overexpression of SmMYB36 from Salvia miltiorrhiza into the genome of C. reinhardtii improved the synthesis of the medicinal compound squalene. qPCR assay indicated that MYB affected the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway-encoding genes in overexpressed lines, which subsequently triggered the downstream biosynthetic pathway of triterpenoids. The squalene contents were enhanced to about 90.20 µg/g through heterologous overexpression of MYB transcriptional factor in microalgae, suggesting potential novel understandings into the regulation mechanisms of C. reinhardtii triterpenoid metabolism through MYB TFs.

The regulatory mechanisms of post-transcription are mainly regulated by alternative splicing (AS). It has a perspective role in plants in response to abiotic stresses. Xingcai Yang [18] described the mechanisms of alternative splicing (AS) in C. reinhardtii in response to starvation of nitrogen. The researcher in this study has performed a broad and systematic analysis of AS events under nitrogen starvation with different time intervals (0 h, 10 m, 30 m, 1 h, 6 h, 8 h, 24 h, and 48 h) using SAR and rMATS tools. A total of 5806 AS events in 3500 genes were identified. The genes associated with the AS event under nitrogen starvation were generally entangled in spliceosome and transporter and enriched in the citrate cycle and fatty acid degradation pathways. The outcomes of this study suggested valuable information for post-transcriptional regulation mechanisms and the significant potential role of nitrogen starvation response in C. reinhardtii.

Asadullah Khan [19] endeavored to remove mitochondrial DNA (mtDNA) in Chlamydomonas, aiming to create cells analogous to rho⁺ or rho⁻ cells, which are characterized by a complete or partial absence of mtDNA. They successfully produced cells with partially eliminated mitochondrial DNA, referred to as crm- cells, which resulted in the inactivation of mitochondrial function. The qPCR technique was employed to quantify the mitochondrial DNA (mtDNA) copy number, as well as to analyze the specific rrnL6 gene for the identification of mitochondria. A decrease in the mitochondrial copy number resulted in an increased expression of AOX1, UCP1, PGRL1, and ICL1, suggesting a disruption in the balance of ATP and NADPH between the mitochondria and chloroplasts. This research provides a foundation for the subsequent utilization of cells with partially removed mitochondrial DNA to investigate various pathways related to the dependence of mitochondria and chloroplasts on the modulation of ATP and NADPH levels.

Esophageal cancer (ESCA) ranks as the sixth most prevalent malignancy globally, largely attributable to the significant mortality rates associated with this disease. Baculoviral IAP repeat-containing protein 3 (BIRC3) serves as a primary inhibitor of apoptosis across various types of malignancies. Qiulan Luo [20] examined the BIRC3’s function in ESCA cells. BIRC3 was identified as being highly expressed in ESCA cells through analyses conducted using TNMplot and GEPIA2. Proinflammatory cytokines TNFα and IL-1β have been demonstrated to enhance the expression of BIRC3 in ESCA cells. The quantitative RT-PCR assay demonstrated a significant induction of BIRC3 across all examined ESCA cell lines. The observed promotive effects were obstructed upon the inhibition of NF-κB function by the Bay 11-7082, suggesting that the regulation of the BIRC3 gene expression occurs through the NF-κB transcriptional pathway in esophageal cancer (ESCA). The results from this study suggest that BIRC3 could play a significant role in the prevention and treatment of esophageal cancer.

Akebia trifoliata (A. trifoliata) is a vital fruit crop known for its medicinal properties. It also contains significant bioactive compounds. There is limited research concerning the bacteriostatic properties of A. trifoliata, and the mechanisms by which A. trifoliata exerts its antibacterial effects remain largely unexplored. Therefore, Jing Chen [21] investigated the bacteriostatic activity and antibacterial mechanism of A. trifoliata using the UHPLC-TOF-MS/MS approaches. EEPA demonstrated both bacteriostatic and bactericidal properties against all tested Gram-positive and Gram-negative bacteria, with inhibition zone diameters (IZDs) varying from 13.80 ± 0.79 mm to 17.00 ± 0.58 mm. Conversely, both antibiotics, kanamycin sulfate and ampicillin sodium salt, demonstrated significantly greater antimicrobial efficacy against Gram-positive bacteria compared to Gram-negative bacteria. Furthermore, the principal antimicrobial action involved the enhancement of cellular content leakage, modification of cell morphology, and disruption of the internal cellular architecture. It was determined that the presence of both hydroxide and methyl groups plays a significant role in their antibacterial efficacy. The results indicate that EEPA demonstrates considerable antimicrobial efficacy against S. aureus, E. coli, B. subtilis, and P. aeruginosa, suggesting its potential as a natural antibacterial agent.

Conclusions

The papers presented in this Special Issue focus on the advancement of pharmacological application, chemical characterization, and novel synthetic biological approaches for natural compounds and their potential application in the pharmaceutical and industrial era. For the first time, heterologous overexpression of MYB transcriptional factors in C. reinhardtii for the production of pharmaceutical compounds was characterized, which further explored the new era for heterologous overexpression systems. There is limited research concerning the bacteriostatic properties of A. trifoliata, and the mechanisms by which A. trifoliata exerts its antibacterial effects remain largely unexplored. Removed mitochondrial DNA provides a foundation for the subsequent utilization of cells with partially removed mitochondrial DNA to investigate various pathways related to the dependence of mitochondria and chloroplasts on the modulation of ATP and NADPH levels. The majority of commercially accessible terpenoids are derived from higher plants; however, the cost-effective and sustainable production of these compounds for pharmaceutical use remains a challenge. Conventional methods for extracting plant materials necessitate the separation of minute active components from substantial volumes of plant resources. This process generates significant waste and inflicts considerable harm on wild plant populations, potentially endangering certain species. Biosynthesis of natural pharmaceuticals, including artemisinin, paclitaxel, tanshinones, breviscapine, noscapine, and thebaine, illustrates the application of advancements in synthetic biology to the production of natural plant-derived compounds.