Recent Advances in the Synthetic Biology of Natural Drugs

De Novo Artificial Biosynthesis of 3-Hydroxyphloretin in Escherichia coli

3-Hydroxyphloretin (3-OH phloretin), a dihydrochalcone compound containing a catechol moiety, is naturally present in apples and exhibits potent anti-adipogenic, anti-obesity, and anticancer activities. In this study, we developed a modular co-culture platform enabling the de novo biosynthesis of 3-OH phloretin from glucose in Escherichia coli. We demonstrated that 4-coumarate 3-hydroxylase (Sam5), derived from Saccharothrix espanaensis, efficiently catalyzes the hydroxylation of phloretin to 3-OH phloretin. The engineered co-culture system comprised two functional modules: an upstream module that converts l-tyrosine to phloretic acid through the expression of tyrosine ammonia-lyase and enoate reductase genes, and a downstream module that converts phloretic acid to 3-OH phloretin via the sequential action of 4-coumarate-CoA ligase, a mutated chalcone synthase, and Sam5. Using this system, we successfully achieved the de novo production of 3-OH phloretin at a titer of 4.69 mg/L from glucose. In parallel, the artificial biosynthetic pathway also yielded phloretic acid and 3-hydroxyphloretic acid (3-OH phloretic acid) at titers of 161.7 and 176.2 mg/L, respectively, in an engineered l-tyrosine-overproducing E. coli strain. To the best of our knowledge, this study represents the first successful establishment of an artificial biosynthetic route for the production of both 3-OH phloretic acid and 3-OH phloretin directly from glucose in E. coli. This platform lays the groundwork for the microbial production of valuable dihydrochalcone compounds and holds promise for further optimization toward industrial-scale applications.

Gut microbiome dynamics of patients on dialysis: implications for complications and treatment

The gut microbiome plays a significant role in dialysis. As disease progresses, the choice of dialysis method and dietary habits change, and the diversity and richness of the gut microbiome in patients on dialysis change as well. The uremic toxins produced exacerbate inflammatory responses and oxidative stress, leading to markedly different incidence rates of complications such as cardiovascular disease and dialysis-associated peritonitis among patients on dialysis. The intake of probiotics, prebiotics, synbiotics, and natural medicines during daily life can regulate the gut microbiome, reduce the production of uremic toxins in patients on dialysis. This review found that the occurrence of complications in dialysis patients is related to changes in the gut microbiome and the accumulation of uremic toxins. The use of probiotics, prebiotics, synbiotics, and natural medicines can improve these conditions and reduce the incidence of dialysis-related complications.

Discovery of Novel Multiangiogenic Agents Targeting VEGFR2, EphB4, FGFR-1, and TIE-2: Receptor-Based Pharmacophore Modeling, Virtual Screening, and Molecular Modeling Studies

The angiogenesis phenomenon is crucial for the formation of new blood vessels in cancer cells. The cancerous cells' progress hampers other healthy cells. The main objective of this study is to explore and decipher multimodal natural compounds against VEGFR2, EphB4, FGFR-1, and TIE-2 drug targets to arrest angiogenesis and progression. The receptor-based pharmacophore modeling of VEGFR2, EphB4, FGFR-1, and TIE-2 was developed and validated through enrichment parameters. Further, the validated hypothesis allowed for screening druglike natural product databases such as SuperNatural 3.0, COCONUT, and LOTUS. The common pharmacophoric featured natural compounds were assessed for binding affinities using absolute end-point methods. Finally, density functional theory has been studied to understand the chemical reactivity and stability of the protein complexes. Among all of the screened natural compounds, 17 natural compounds were found to align accurately against validated pharmacophore models having higher fitness scores and align scores. Taking reference drugs sorafenib (VEGFR2), NVP-BHG712 (EphB4), pemiganitib (FGFR-1), and DP1919 (TIE-2), three promising natural compounds CNP0003920, CNP0243075, and CNP0211397 were concluded based on their end-point binding energies, binding interactions, molecular dynamics, and optimal pharmacokinetic and toxicity profiles. The density functional theory (DFT) results suggested that the identified compounds bound with protein complexes are stable. Our findings can represent a promising starting point for developing multimodal analogues VEGFR2, EphB4, FGFR-1, and TIE-2 proteins.

Navigating the challenges of engineering composite specialized metabolite pathways in plants

Plants are a valuable source of diverse specialized metabolites with numerous applications. However, these compounds are often produced in limited quantities, particularly under unfavorable ecological conditions. To achieve sufficient levels of target metabolites, alternative strategies such as pathway engineering in heterologous systems like microbes (e.g., bacteria and fungi) or cell-free systems can be employed. Another approach is plant engineering, which aims to either enhance the native production in the original plant or reconstruct the target pathway in a model plant system. Although increasing metabolite production in the native plant is a promising strategy, these source plants are often exotic and pose significant challenges for genetic manipulation. Effective pathway engineering requires comprehensive prior knowledge of the genes and enzymes involved, as well as the precursor, intermediate, branching, and final metabolites. Thus, a thorough elucidation of the biosynthetic pathway is closely linked to successful metabolic engineering in host or model systems. In this review, we highlight recent advances in strategies for biosynthetic pathway elucidation and metabolic engineering. We focus on efforts to engineer complex, multi-step pathways that require the expression of at least eight genes for transient and three genes for stable transformation. Reports on the engineering of complex pathways in stably transformed plants remain relatively scarce. We discuss the major hurdles in pathway elucidation and strategies for overcoming them, followed by an overview of achievements, challenges, and solutions in pathway reconstitution through metabolic engineering. Recent advances including computer-based predictions offer valuable platforms for the sustainable production of specialized metabolites in plants.

Application of 18β-glycyrrhetinic acid in the structural modification of natural products: a review

18β-Glycyrrhetinic acid (GA) is an oleane-type pentacyclic triterpene saponin obtained from glycyrrhizic acid by removing 2 glucuronic acid groups. GA and its analogues are active substances of glycyrrhiza aicd, with similar structure and important pharmacological effects such as anti-inflammatory, anti-diabetes, anti-tumor and anti-fibrosis. Although GA combined compounds are in the clinical trial stages, its application potential is severely restricted by its low bioavailability, water solubility and membrane permeability. In this article, synthetic methods and structure-activity relationships (SARs) of GA derivatives from 2018 to present are reviewed based on pharmacological activity. It is hoped that this review can provide reference for the future development of potential GA preclinical candidate compounds, and furnish ideas for the development of pentacyclic triterpenoid lead compounds.

Inhibition of Kinase Activity and In Vitro Downregulation of the Protein Kinases in Lung Cancer and Cervical Cancer Cell Lines and the Identified Known Anticancer Compounds of Ziziphus mucronata

Plants have long been used as sources of natural compounds with therapeutic benefits, providing molecules capable of inhibiting multiple kinases. Many medicinal plants are recognized for their anticancer properties and may offer ways to mitigate the adverse effects of conventional cancer treatments. In this study, the potential of Ziziphus mucronata methanol extract as a kinase inhibitor was assessed using the MTT assay, a universal kinase assay, and a human phosphokinase antibody array, along with a GC-MS analysis of volatile anticancer compounds. The MTT assay revealed strong cytotoxicity in A549 cells, with an IC50 of 31.25 µg/mL, while HeLa cells showed weaker cytotoxicity with an IC50 of 125 µg/mL. In comparison, paclitaxel exhibited potent inhibitory effects on A549 cells (IC50 of 31.25 µg/mL) and moderate inhibition on HeLa cells (IC50 of 65 µg/mL). Enzyme activity, measured by ADP production in the ADP-Glo assay, indicated that the extract inhibited protein kinase activity in both A549 and HeLa cells after 24 h of treatment. Additionally, the human phosphokinase antibody array, which includes 44 pre-spotted kinases, showed that the extract downregulated multiple phosphorylated kinases in both cell lines. Some of the affected kinases, such as TOR, Fyn, HcK, Fgr, STAT5b, PLC-γ1, p38α, ERK1/2, AMPKA, Akt1/2, GSK-3α/β, MSK1/2, CREB, RSK1/2/3, PLC-γ1, and STAT5a are critical regulators of various cellular processes, including apoptosis, differentiation, and proliferation. The findings of this study suggest that extract from Z. mucronata may have the capacity to regulate protein kinase activity, highlighting their significant potential as growth inhibitors for cancer cells.

Discovery and Optimization of Ergosterol Peroxide Derivatives as Novel Glutaminase 1 Inhibitors for the Treatment of Triple-Negative Breast Cancer

In this study, novel ergosterol peroxide (EP) derivatives were synthesized and evaluated to assess their antiproliferative activity against four human cancer cell lines (A549, HepG2, MCF-7, and MDA-MB-231). Compound 3g exhibited the most potent antiproliferative activity, with an IC50 value of 3.20 µM against MDA-MB-231. This value was 5.4-fold higher than that of the parental EP. Bioassay optimization further identified 3g as a novel glutaminase 1 (GLS1) inhibitor (IC50 = 3.77 µM). In MDA-MB-231 cells, 3g reduced the cellular glutamate levels by blocking the glutamine hydrolysis pathway, which triggered reactive oxygen species production and induced caspase-dependent apoptosis. Molecular docking indicated that 3g interacts with the reaction site of the variable binding pocket by forming multiple interactions with GLS1. In a mouse model of breast cancer, 3g showed remarkable therapeutic effects at a dose of 50 mg/kg, with no apparent toxicity. Based on these results, 3g could be further evaluated as a novel GLS1 inhibitor for triple-negative breast cancer (TNBC) therapy.

Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12.1C

Previous studies have reported the functional role, biochemical features and synthesis pathway of podophyllotoxin (PTOX) in plants. In this study, we employed combined morphological and molecular techniques to identify an endophytic fungus and extract PTOX derivatives. Based on the analysis of ITS sequences and the phylogenetic tree, the isolate was classified as Penicillium herquei HGN12.1C, with a sequence identity of 98.58%. Morphologically, the HGN12.1C strain exhibits white colonies, short-branched mycelia and densely packed hyphae. Using PacBio sequencing at an average read depth of 195×, we obtained a high-quality genome for the HGN12.1C strain, which is 34.9 Mb in size, containing eight chromosomes, one mitochondrial genome and a GC content of 46.5%. Genome analysis revealed 10 genes potentially involved in PTOX biosynthesis. These genes include VdtD, Pinoresinollariciresinol reductase (PLR), Secoisolariciresinol dehydrogenase (SDH), CYP719A23, CYP71BE54, O-methyltransferase 1 (OMT1), O-methyltransferase 3 (OMT3), 2-ODD, CYP71CU and CYP82D61. Notably, the VdtD gene in fungi shares functional similarities with the DIR gene found in plants. Additionally, we identified peltatin, a PTOX derivative, in the HGN12.1C extract. Docking analysis suggests a potential role for the 2-ODD enzyme in converting yatein to deoxypodophyllotoxin. These findings offer invaluable insights into the synthesis mechanism of PTOX in fungi, shedding light on the relationship between host plants and endophytes.

Progress and prospect: Biosynthesis of plant natural products based on plant chassis

Plant-derived natural products are a specific class of active substances with numerous applications in the medical, energy, and industrial fields. Many of these substances are in high demand and have become the fundamental materials for various purposes. Recently, the use of synthetic biology to produce plant-derived natural products has become a significant trend. Plant chassis, in particular, offer unique advantages over microbial chassis in terms of cell structure, product affinity, safety, and storage. The development of the plant hairy root tissue culture system has accelerated the commercialization and industrialization of synthetic biology in the production of plant-derived natural products. This paper will present recent progress in the synthesis of various plant natural products using plant chassis, organized by the types of different structures. Additionally, we will summarize the four primary types of plant chassis used for synthesizing natural products from plant sources and review the enabling technologies that have contributed to the development of synthetic biology in recent years. Finally, we will present the role of isolated and combined use of different optimization strategies in breaking the upper limit of natural product production in plant chassis. This review aims to provide practical references for synthetic biologists and highlight the great commercial potential of plant chassis biosynthesis, such as hairy roots.

Overview of Caffeine Effects on Human Health and Emerging Delivery Strategies

Caffeine is a naturally occurring alkaloid found in various plants. It acts as a stimulant, antioxidant, anti-inflammatory, and even an aid in pain management, and is found in several over-the-counter medications. This naturally derived bioactive compound is the best-known ingredient in coffee and other beverages, such as tea, soft drinks, and energy drinks, and is widely consumed worldwide. Therefore, it is extremely important to research the effects of this substance on the human body. With this in mind, caffeine and its derivatives have been extensively studied to evaluate its ability to prevent diseases and exert anti-aging and neuroprotective effects. This review is intended to provide an overview of caffeine's effects on cancer and cardiovascular, immunological, inflammatory, and neurological diseases, among others. The heavily researched area of caffeine in sports will also be discussed. Finally, recent advances in the development of novel nanocarrier-based formulations, to enhance the bioavailability of caffeine and its beneficial effects will be discussed.

Functional characterization of four mono-terpene synthases (TPSs) provided insight into the biosynthesis of volatile monoterpenes in the medicinal herb Blumea balsamifera

Blumea balsamifera, a wooden plant belonging to the family Asteraceae, is a medicinal herb with anticancer, antiviral, and multiple pharmacological effects, which are believed to be caused by its essential oil. The essential oil from B. balsamifera is comprised of mono- and sesqui-terpenes as the majority. Unfortunately, this plant has been facing the challenge of resource shortage, which could be effectively alleviated by biological engineering. Therefore, the identification of key elements involved in the biosynthesis of active ingredients becomes an indispensable prerequisite. In this study, candidate genes encoding monoterpene synthase were screened by transcriptome sequencing combined with metabolomics profiling in the roots, stems, and leaves of B. balsamifera. Then, these candidates were successfully cloned and verified by heterologous expression and in vitro enzyme activity assays. As a result, six candidate BbTPS genes were isolated from B. balsamifera, of which three encoded single-product monoterpene synthases and one encoded a multi-product monoterpene synthase. Among them, BbTPS1, BbTPS3, and BbTPS4 could catalyze the formation of D-limonene, α-phellandrene, and L-borneol, respectively. Meanwhile, BbTPS5 functioned in catalyzing GPP into terpinol, β-phellandrene, β-myrcene, D-limonene, and 2-carene in vitro. In general, our results provided important elements for the synthetic biology of volatile terpenes in B. balsamifera, which laid a foundation for subsequent heterologous production of these terpenoids through metabolic engineering and increasing their yield, as well as promoting sustainable development and utilization of B. balsamifera.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01306-8.

Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development

The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.

Breynia cernua: Chemical Profiling of Volatile Compounds in the Stem Extract and Its Antioxidant, Antibacterial, Antiplasmodial and Anticancer Activity In Vitro and In Silico

Breynia cernua has been used as an alternative medicine for wounds, smallpox, cervical cancer, and breast cancer. This plant is a potential source of new plant-derived drugs to cure numerous diseases for its multiple therapeutic functions. An in vitro study revealed that the methanol extract of B. cernua (stem) exhibits antioxidant activity according to DPPH and SOD methods, with IC₅₀ values of 33 and 8.13 ppm, respectively. The extract also exerts antibacterial activity against Staphylococcus aureus with minimum bactericidal concentration of 1875 ppm. Further analysis revealed that the extract with a concentration of 1-2 ppm protects erythrocytes from the ring formation stage of Plasmodium falciparum, while the extract with a concentration of 1600 ppm induced apoptosis in the MCF-7 breast cancer cell line. GC-MS analysis showed 45 bioactive compounds consisting of cyclic, alkyl halide, organosulfur, and organoarsenic compounds. Virtual screening via a blind docking approach was conducted to analyze the binding affinity of each metabolite against various target proteins. The results unveiled that two compounds, namely, N-[β-hydroxy-β-[4-[1-adamantyl-6,8-dichloro]quinolyl]ethyl]piperidine and 1,3-phenylene, bis(3-phenylpropenoate), demonstrated the best binding score toward four tested proteins with a binding affinity varying from -8.3 to -10.8 kcal/mol. Site-specific docking analysis showed that the two compounds showed similar binding energy with native ligands. This finding indicated that the two phenolic compounds could be novel antioxidant, antibacterial, antiplasmodial, and anticancer drugs. A thorough analysis by monitoring drug likeness and pharmacokinetics revealed that almost all the identified compounds can be considered as drugs, and they have good solubility, oral bioavailability, and synthetic accessibility. Altogether, the in vitro and in silico analysis suggested that the extract of B. cernua (stem) contains various compounds that might be correlated with its bioactivities.

Harmonizing biosynthesis with post-ingestive modifications to understand the ecological functions of plant natural products

Covering: up to 2022The recent dramatic advances in our understanding of the biosynthetic pathways that produce diverse bouquets of plant-derived natural products have far surpassed our understanding of the function of these compounds for plants: how they influence a plant's Darwinian fitness in nature. Our understanding of their mechanisms, the life-processes targeted by these compounds, is similarly poorly resolved. Many plant specialized metabolites (PSMs) are further modified after ingestion by herbivores, and these post-ingestive modifications are frequently essential for PSM function. Here we summarize the biosynthesis and functional mechanisms of 17-hydroxygeranyllinalool diterpene glycosides in the ecological model plant Nicotiana attenuata, and summarize the post-ingestive modifications known from other two-component PSMs. We propose that parallel comparisons of plant natural product biosynthetic pathways and insect post-ingestive metabolism of the same plant tissues ("frassomics") will facilitate the often-elusive identification of the molecular targets of these effective chemical defenses, contribute to elucidations of post-ingestive metabolite interactions in insect guts, and predicate the rapid evolutions of resistance against insecticides inspired by PSMs. We highlight the value of conducting these parallel investigations at the level of the entire metabolome so as to include the multiple interacting pathways in both natural product biosynthesis as well as their post-ingestive processing. We introduce the concept of frass metabolite QTL (fmQTL) analysis that integrates powerful forward genetic approaches with frassomics, and suggest that insect-guided high-throughput forward- and reverse-genetics approaches in natural habitats will advance our understanding of PSM biosynthesis and function.

Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process

The conventional drug discovery approach is an expensive and time-consuming process, but its limitations have been overcome with the help of mathematical modeling and computational drug design approaches. Previously, finding a small molecular candidate as a drug against a disease was very costly and required a long time to screen a compound against a specific target. The development of novel targets and small molecular candidates against different diseases including emerging and reemerging diseases remains a major concern and necessitates the development of novel therapeutic targets as well as drug candidates as early as possible. In this regard, computational and mathematical modeling approaches for drug development are advantageous due to their fastest predictive ability and cost-effectiveness features. Computer-aided drug design (CADD) techniques utilize different computer programs as well as mathematics formulas to comprehend the interaction of a target and drugs. Traditional methods to determine small-molecule candidates as a drug have several limitations, but CADD utilizes novel methods that require little time and accurately predict a compound against a specific disease with minimal cost. Therefore, this review aims to provide a brief insight into the mathematical modeling and computational approaches for identifying a novel target and small molecular candidates for curing a specific disease. The comprehensive review mainly focuses on biological target prediction, structure-based and ligand-based drug design methods, molecular docking, virtual screening, pharmacophore modeling, quantitative structure-activity relationship (QSAR) models, molecular dynamics simulation, and MM-GBSA/MM-PBSA approaches along with valuable database resources and tools for identifying novel targets and therapeutics against a disease. This review will help researchers in a way that may open the road for the development of effective drugs and preventative measures against a disease in the future as early as possible.

Recent progress in strategies for steroid production in yeasts

As essential structural molecules of fungal cell membrane, ergosterol is not only an important component of fungal growth and stress-resistance but also a key precursor for manufacturing steroid drugs of pharmaceutical or agricultural significance. So far, ergosterol biosynthesis in yeast has been elucidated elaborately, and efforts have been made to increase ergosterol production through regulation of ergosterol metabolism and storage. Furthermore, the same intermediates shared by yeasts and animals or plants make the construction of heterologous sterol pathways in yeast a promising approach to synthesize valuable steroids, such as phytosteroids and animal steroid hormones. During these challenging processes, several obstacles have arisen and been combated with great endeavors. This paper reviews recent research progress of yeast metabolic engineering for improving the production of ergosterol and heterologous steroids. The remaining tactics are also discussed.

Research Progress of Natural Small-Molecule Compounds Related to Tumor Differentiation

Tumor differentiation is a therapeutic strategy aimed at reactivating the endogenous differentiation program of cancer cells and inducing cancer cells to mature and differentiate into other types of cells. It has been found that a variety of natural small-molecule drugs can induce tumor cell differentiation both in vitro and in vivo. Relevant molecules involved in the differentiation process may be potential therapeutic targets for tumor cells. Compared with synthetic drugs, natural small-molecule antitumor compounds have the characteristics of wide sources, structural diversity and low toxicity. In addition, natural drugs with structural modification and transformation have relatively concentrated targets and enhanced efficacy. Therefore, using natural small-molecule compounds to induce malignant cell differentiation represents a more targeted and potential low-toxicity means of tumor treatment. In this review, we focus on natural small-molecule compounds that induce differentiation of myeloid leukemia cells, osteoblasts and other malignant cells into functional cells by regulating signaling pathways and the expression of specific genes. We provide a reference for the subsequent development of natural small molecules for antitumor applications and promote the development of differentiation therapy.