Deploying Microbial Synthesis for Halogenating and Diversifying Medicinal Alkaloid Scaffolds

Can biotechnology lead the way toward a sustainable pharmaceutical industry?

The impact-intensive and rapidly growing pharmaceutical industry must ensure its sustainability. This study reveals that environmental sustainability assessments have been conducted for only around 0.2% of pharmaceuticals, environmental impacts have significant variations among the assessed products, and different impact categories have not been consistently studied. Highly varied impacts require assessing more products to understand the industry's sustainability status. Reporting all impact categories will be crucial, especially when comparing production technologies. Biological production of (semi)synthetic pharmaceuticals could reduce their environmental costs, though the high impacts of biologically produced monoclonal antibodies should also be optimized. Considering the sustainability potential of biopharmaceuticals from economic, environmental, and social perspectives, collaboratively guiding their immense market growth would lead to the industry's sustainability transition.

A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules

Halogen-containing molecules are ubiquitous in modern society and present unique chemical possibilities. As a whole, de novo fermentation and synthetic pathway construction for these molecules remain relatively underexplored and could unlock molecules with exciting new applications in industries ranging from textiles to agrochemicals to pharmaceuticals. Here, we report a mix-and-match co-culture platform to de novo generate a large array of halogenated tryptophan derivatives in Escherichia coli from glucose. First, we engineer E. coli to produce between 300 and 700 mg/L of six different halogenated tryptophan precursors. Second, we harness the native promiscuity of multiple downstream enzymes to access unexplored regions of metabolism. Finally, through modular co-culture fermentations, we demonstrate a plug-and-play bioproduction platform, culminating in the generation of 26 distinct halogenated molecules produced de novo including precursors to prodrugs 4-chloro- and 4-bromo-kynurenine and new-to-nature halogenated beta carbolines.

Algal blooms in the ocean: hot spots for chemically mediated microbial interactions

The cycling of major nutrients in the ocean is affected by large-scale phytoplankton blooms, which are hot spots of microbial life. Diverse microbial interactions regulate bloom dynamics. At the single-cell level, interactions between microorganisms are mediated by small molecules in the chemical crosstalk that determines the type of interaction, ranging from mutualism to pathogenicity. Algae interact with viruses, bacteria, parasites, grazers and other algae to modulate algal cell fate, and these interactions are dependent on the environmental context. Recent advances in mass spectrometry and single-cell technologies have led to the discovery of a growing number of infochemicals - metabolites that convey information - revealing the ability of algal cells to govern biotic interactions in the ocean. The diversity of infochemicals seems to account for the specificity in cellular response during microbial communication. Given the immense impact of algal blooms on biogeochemical cycles and climate regulation, a major challenge is to elucidate how microscale interactions control the fate of carbon and the recycling of major elements in the ocean. In this Review, we discuss microbial interactions and the role of infochemicals in algal blooms. We further explore factors that can impact microbial interactions and the available tools to decipher them in the natural environment.

On Demand Synthesis of C3-N1' Bisindoles by a Formal Umpolung Strategy: First Total Synthesis of (±)-Rivularin A

In this work, a straightforward synthesis of C3-N1' bisindolines is achieved by a formal umpolung strategy. The protocols were tolerant of a wide variety of substituents on the indole and indoline ring. In addition, the C3-N1' bisindolines could be converted to C3-N1' indole-indolines and C3-N1'-bisindoles. Also, we have successfully synthesized (±)-rivularin A through a biomimetic late-stage tribromination as a key step.

Naturally Occurring Organohalogen Compounds-A Comprehensive Review

The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.

Discovery of Novel c-Jun N-Terminal Kinase 1 Inhibitors from Natural Products: Integrating Artificial Intelligence with Structure-Based Virtual Screening and Biological Evaluation

c-Jun N-terminal kinase 1 (JNK1) is currently considered a critical therapeutic target for type-2 diabetes. In recent years, there has been a great interest in naturopathic molecules, and the discovery of active ingredients from natural products for specific targets has received increasing attention. Based on the above background, this research aims to combine emerging Artificial Intelligence technologies with traditional Computer-Aided Drug Design methods to find natural products with JNK1 inhibitory activity. First, we constructed three machine learning models (Support Vector Machine, Random Forest, and Artificial Neural Network) and performed model fusion based on Voting and Stacking strategies. The integrated models with better performance (AUC of 0.906 and 0.908, respectively) were then employed for the virtual screening of 4112 natural products in the ZINC database. After further drug-likeness filtering, we calculated the binding free energy of 22 screened compounds using molecular docking and performed a consensus analysis of the two methodologies. Subsequently, we identified the three most promising candidates (Lariciresinol, Tricin, and 4′-Demethylepipodophyllotoxin) according to the obtained probability values and relevant reports, while their binding characteristics were preliminarily explored by molecular dynamics simulations. Finally, we performed in vitro biological validation of these three compounds, and the results showed that Tricin exhibited an acceptable inhibitory activity against JNK1 (IC₅₀ = 17.68 μM). This natural product can be used as a template molecule for the design of novel JNK1 inhibitors.

Antibiofilm and Antimicrobial Activities of Chloroindoles Against Uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) is a nosocomial pathogen associated with urinary tract infections and expresses several virulence factors that cause recurring infections and cystitis of the bladder, which can lead to pyelonephritis. UPEC uses different types of extracellular appendages like fimbriae and pili that aid colonization and adherence to bladder epithelium and can form persistent biofilm-like bacterial communities that aid its survival after the deployment of host immune responses. We investigated the antibiofilm, antimicrobial, and antivirulence properties of three indole derivatives namely, 4-chloroindole, 5-chloroindole, and 5-chloro 2-methyl indole. All the three chloroindoles had MICs of 75 μg/ml and inhibited biofilm formation by an average of 67% at 20 μg/ml. In addition, they inhibited swarming and swimming motilities, which are essential for dissemination from bacterial communities and colonization, reduced cell surface hydrophobicity, and inhibited indole production and curli formation. Gene expression analysis showed all three chloroindoles significantly downregulated the expressions of virulence genes associated with adhesion, stress regulation, and toxin production. A 3D-QSAR analysis revealed substitutions at the fourth and fifth positions of the indole moiety favored antimicrobial activity. Furthermore, these chloroindoles potently inhibited biofilm formation in other nosocomial pathogens and polymicrobial consortia.

Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19

The present global COVID-19 pandemic caused by the noble pleomorphic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a vulnerable situation in the global healthcare and economy. In this pandemic situation, researchers all around the world are trying their level best to find suitable therapeutics from various sources to combat against the SARS-CoV-2. To date, numerous bioactive compounds from different sources have been tested to control many viral diseases. However, microbial metabolites are advantageous for drug development over metabolites from other sources. We herein retrieved and reviewed literatures from PubMed, Scopus and Google relevant to antiviral microbial metabolites by searching with the keywords "antiviral microbial metabolites," "microbial metabolite against virus," "microorganism with antiviral activity," "antiviral medicine from microbial metabolite," "antiviral bacterial metabolites," "antiviral fungal metabolites," "antiviral metabolites from microscopic algae' and so on. For the same purpose, the keywords "microbial metabolites against COVID-19 and SARS-CoV-2" and "plant metabolites against COVID-19 and SARS-CoV-2" were used. Only the full text literatures available in English and pertinent to the topic have been included and those which are not available as full text in English and pertinent to antiviral or anti-SARS-CoV-2 activity were excluded. In this review, we have accumulated microbial metabolites that can be used as antiviral agents against a broad range of viruses including SARS-CoV-2. Based on this concept, we have included 330 antiviral microbial metabolites so far available to date in the data bases and were previously isolated from fungi, bacteria and microalgae. The microbial source, chemical nature, targeted viruses, mechanism of actions and IC50/EC50 values of these metabolites are discussed although mechanisms of actions of many of them are not yet elucidated. Among these antiviral microbial metabolites, some compounds might be very potential against many other viruses including coronaviruses. However, these potential microbial metabolites need further research to be developed as effective antiviral drugs. This paper may provide the scientific community with the possible secret of microbial metabolites that could be an effective source of novel antiviral drugs to fight against many viruses including SARS-CoV-2 as well as the future viral pandemics.

Engineering Saccharomyces cerevisiae to produce plant benzylisoquinoline alkaloids

Benzylisoquinoline alkaloids (BIAs) are a diverse family of plant natural products with extensive pharmacological properties, but the yield of BIAs from plant is limited. The understanding of BIA biosynthetic mechanism in plant and the development of synthetic biology enable the possibility to produce BIAs through microbial fermentation, as an alternative to agriculture-based supply chains. In this review, we discussed the engineering strategies to synthesize BIAs in Saccharomyces cerevisiae (yeast) and improve BIA production level, including heterologous pathway reconstruction, enzyme engineering, expression regulation, host engineering and fermentation engineering. We also highlight recent metabolic engineering advances in the production of BIAs in yeast.

Metabolic engineering for plant natural products biosynthesis: new procedures, concrete achievements and remaining limits

Microorganisms and plants represent major sources of natural compounds with a plethora of bioactive properties. Among these, plant natural products (PNPs) remain indispensable to human health. With few exceptions, PNP-based pharmaceuticals come from plant specialized metabolisms and display a structure far too complex for a profitable production by total chemical synthesis. Accordingly, their industrial processes of supply are still mostly based on the extraction of final products or precursors directly from plant materials. This implies that particular contexts (e.g. pandemics, climate changes) and natural resource overexploitation are main drivers for the high production cost and recurrent supply shortages. Recently, biotechnological manufacturing alternatives gave rise to a multitude of benchmark studies implementing the production of important PNPs in various heterologous hosts. Here, we spotlight unprecedented advancements in the field of metabolic engineering dedicated to the heterologous production of a prominent series of PNPs that were achieved during the year 2020. We also discuss how the knowledge accumulated in recent years could pave the way for a broader manufacturing palette of natural products from a wide range of natural resources.

Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products

Natural products are continually explored in the development of new bioactive compounds with industrial applications, attracting the attention of scientific research efforts due to their pharmacophore-like structures, pharmacokinetic properties, and unique chemical space. The systematic search for natural sources to obtain valuable molecules to develop products with commercial value and industrial purposes remains the most challenging task in bioprospecting. Virtual screening strategies have innovated the discovery of novel bioactive molecules assessing in silico large compound libraries, favoring the analysis of their chemical space, pharmacodynamics, and their pharmacokinetic properties, thus leading to the reduction of financial efforts, infrastructure, and time involved in the process of discovering new chemical entities. Herein, we discuss the computational approaches and methods developed to explore the chemo-structural diversity of natural products, focusing on the main paradigms involved in the discovery and screening of bioactive compounds from natural sources, placing particular emphasis on artificial intelligence, cheminformatics methods, and big data analyses.