Genome-Scale Metabolic Reconstruction, Non-Targeted LC-QTOF-MS Based Metabolomics Data, and Evaluation of Anticancer Activity of Cannabis sativa Leaf Extracts.

Over the past decades, Colombia has suffered complex social problems related to illicit crops, including forced displacement, violence, and environmental damage, among other consequences for vulnerable populations. Considerable effort has been made in the regulation of illicit crops, predominantly Cannabis sativa, leading to advances such as the legalization of medical cannabis and its derivatives, the improvement of crops, and leaving an open window to the development of scientific knowledge to explore alternative uses. It is estimated that C. sativa can produce approximately 750 specialized secondary metabolites. Some of the most relevant due to their anticancer properties, besides cannabinoids, are monoterpenes, sesquiterpenoids, triterpenoids, essential oils, flavonoids, and phenolic compounds. However, despite the increase in scientific research on the subject, it is necessary to study the primary and secondary metabolism of the plant and to identify key pathways that explore its great metabolic potential. For this purpose, a genome-scale metabolic reconstruction of C. sativa is described and contextualized using LC-QTOF-MS metabolic data obtained from the leaf extract from plants grown in the region of Pesca-Boyaca, Colombia under greenhouse conditions at the Clever Leaves facility. A compartmentalized model with 2101 reactions and 1314 metabolites highlights pathways associated with fatty acid biosynthesis, steroids, and amino acids, along with the metabolism of purine, pyrimidine, glucose, starch, and sucrose. Key metabolites were identified through metabolomic data, such as neurine, cannabisativine, cannflavin A, palmitoleic acid, cannabinoids, geranylhydroquinone, and steroids. They were analyzed and integrated into the reconstruction, and their potential applications are discussed. Cytotoxicity assays revealed high anticancer activity against gastric adenocarcinoma (AGS), melanoma cells (A375), and lung carcinoma cells (A549), combined with negligible impact against healthy human skin cells.

Enhancing Wound Healing: A Novel Topical Emulsion Combining CW49 Peptide and Lavender Essential Oil for Accelerated Regeneration and Antibacterial Protection.

Wound healing is a complex process involving blood cells, extracellular matrix, and parenchymal cells. Research on biomimetics in amphibian skin has identified the CW49 peptide from Odorrana grahami, which has been demonstrated to promote wound regeneration. Additionally, lavender essential oil exhibits anti-inflammatory and antibacterial activities. Given these considerations, we propose an innovative emulsion that combines the CW49 peptide with lavender oil. This novel formulation could serve as a potent topical treatment, potentially fostering the regeneration of damaged tissues and providing robust antibacterial protection for skin wounds. This study investigates the physicochemical properties, biocompatibility, and in vitro regenerative capacity of the active components and the emulsion. The results show that the emulsion possesses appropriate rheological characteristics for topical application. Both the CW49 peptide and lavender oil exhibit high viability in human keratinocytes, indicating their biocompatibility. The emulsion induces hemolysis and platelet aggregation, an expected behavior for such topical treatments. Furthermore, the lavender-oil emulsion demonstrates antibacterial activity against both Gram-positive and Gram-negative bacterial strains. Finally, the regenerative potential of the emulsion and its active components is confirmed in a 2D wound model using human keratinocytes. In conclusion, the formulated emulsion, which combines the CW49 peptide and lavender oil, shows great promise as a topical treatment for wound healing. Further research is needed to validate these findings in more advanced in vitro models and in vivo settings, potentially leading to improved wound-care management and novel therapeutic options for patients with skin injuries.

Multifunctional magnetoliposomes as drug delivery vehicles for the potential treatment of Parkinson's disease.

Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease. Therefore, development of novel technologies and strategies to treat PD is a global health priority. Current treatments include administration of Levodopa, monoamine oxidase inhibitors, catechol-O-methyltransferase inhibitors, and anticholinergic drugs. However, the effective release of these molecules, due to the limited bioavailability, is a major challenge for the treatment of PD. As a strategy to solve this challenge, in this study we developed a novel multifunctional magnetic and redox-stimuli responsive drug delivery system, based on the magnetite nanoparticles functionalized with the high-performance translocating protein OmpA and encapsulated into soy lecithin liposomes. The obtained multifunctional magnetoliposomes (MLPs) were tested in neuroblastoma, glioblastoma, primary human and rat astrocytes, blood brain barrier rat endothelial cells, primary mouse microvascular endothelial cells, and in a PD-induced cellular model. MLPs demonstrated excellent performance in biocompatibility assays, including hemocompatibility (hemolysis percentages below 1%), platelet aggregation, cytocompatibility (cell viability above 80% in all tested cell lines), mitochondrial membrane potential (non-observed alterations) and intracellular ROS production (negligible impact compared to controls). Additionally, the nanovehicles showed acceptable cell internalization (covered area close to 100% at 30 min and 4 h) and endosomal escape abilities (significant decrease in lysosomal colocalization after 4 h of exposure). Moreover, molecular dynamics simulations were employed to better understand the underlying translocating mechanism of the OmpA protein, showing key findings regarding specific interactions with phospholipids. Overall, the versatility and the notable in vitro performance of this novel nanovehicle make it a suitable and promising drug delivery technology for the potential treatment of PD.

Identification of Active Compounds against Melanoma Growth by Virtual Screening for Non-Classical Human DHFR Inhibitors.

Antifolates such as methotrexate (MTX) have been largely known as anticancer agents because of their role in blocking nucleic acid synthesis and cell proliferation. Their mechanism of action lies in their ability to inhibit enzymes involved in the folic acid cycle, especially human dihydrofolate reductase (hDHFR). However, most of them have a classical structure that has proven ineffective against melanoma, and, therefore, inhibitors with a non-classical lipophilic structure are increasingly becoming an attractive alternative to circumvent this clinical resistance. In this study, we conducted a protocol combining virtual screening (VS) and cell-based assays to identify new potential non-classical hDHFR inhibitors. Among 173 hit compounds identified (average logP = 3.68; average MW = 378.34 Da), two-herein, called C1 and C2-exhibited activity against melanoma cell lines B16 and A375 by MTT and Trypan-Blue assays. C1 showed cell growth arrest (39% and 56%) and C2 showed potent cytotoxic activity (77% and 51%) in a dose-dependent manner. The effects of C2 on A375 cell viability were greater than MTX (98% vs 60%) at equivalent concentrations and times. Our results indicate that the integrated in silico/in vitro approach provided a benchmark to identify novel promising non-classical DHFR inhibitors showing activity against melanoma cells.

Novel covalent and non-covalent complex-based pharmacophore models of SARS-CoV-2 main protease (Mpro) elucidated by microsecond MD simulations.

As the world enters its second year of the pandemic caused by SARS-CoV-2, intense efforts have been directed to develop an effective diagnosis, prevention, and treatment strategies. One promising drug target to design COVID-19 treatments is the SARS-CoV-2 Mpro. To date, a comparative understanding of Mpro dynamic stereoelectronic interactions with either covalent or non-covalent inhibitors (depending on their interaction with a pocket called S1' or oxyanion hole) has not been still achieved. In this study, we seek to fill this knowledge gap using a cascade in silico protocol of docking, molecular dynamics simulations, and MM/PBSA in order to elucidate pharmacophore models for both types of inhibitors. After docking and MD analysis, a set of complex-based pharmacophore models was elucidated for covalent and non-covalent categories making use of the residue bonding point feature. The highest ranked models exhibited ROC-AUC values of 0.93 and 0.73, respectively for each category. Interestingly, we observed that the active site region of Mpro protein-ligand complex undergoes large conformational changes, especially within the S2 and S4 subsites. The results reported in this article may be helpful in virtual screening (VS) campaigns to guide the design and discovery of novel small-molecule therapeutic agents against SARS-CoV-2 Mpro protein.

Hemp seeds: Nutritional value, associated bioactivities and the potential food applications in the Colombian context.

For many years, Colombia was one of the countries with the largest illegal cultivation of cannabis around the world. Currently, it is going through a period of transition with a new government law that recently allows the cultivation, transformation, and commercialization of such plant species. In this sense, the identification of strategies for the valorization of products or by-products from Cannabis sativa represent a great opportunity to improve the value chain of this crop. One of these products is hemp seeds, which are exceptionally nutritious and rich in healthy lipids (with high content of three polyunsaturated fatty acids: linoleic acid, alpha-linolenic acid, and gamma-linolenic acid), good quality protein, and several minerals. In addition, hemp seeds contain THC (tetrahydrocannabinol) or CBD (cannabidiol) in traces, molecules that are responsible for the psychoactive and therapeutic properties of cannabis. These low terpenophenolic contents make it more attractive for food applications. This fact, together with the constant search for proteins of vegetable origin and natural food ingredients, have aroused an important interest in the study of this biomass. Some bioactivities of phytochemical compounds (polyphenols and terpenoids, mainly) present in hemp seeds have provided antioxidant, antimicrobial, and anti-inflammatory properties. This review summarizes and discusses the context of hemp use in Latin-American and the new opportunities for hemp seeds culture in Colombia considering the valuable nutritional value, main functional bioactivities, and recent advances in food market applications of hemp seeds.

Classical MD and metadynamics simulations on back-pocket binders of CDK2 and VEGFR2: a guidepost to design novel small-molecule dual inhibitors.

Cyclin-Dependent Kinase 2 (CDK2) and Vascular-Endothelial Growth Factor Receptor 2 (VEGFR2) are promising targets for the design of novel inhibitors in anticancer therapeutics. In a recent work, our group designed a set of potential dual inhibitors predicted to occupy an allosteric back pocket near the active site of both enzymes, but their dynamic and unbinding behavior was unclear. Here, we used molecular dynamics (MD) and metadynamics (meta-D) simulations to study two of these virtual candidates (herein called IQ2 and IQ3). Their binding mode was predicted to be similar to that observed in LQ5 and BAX, well-known back-pocket binders of CDK2 and VEGFR2, respectively, including H-bonding with critical residues such as Leu83/Cys113 and Asp145/Asp190 (but excepting H-bonding with Glu51/Glu111) in CDK2/VEGFR2, correspondingly. Likewise, while LQ5 and BAX unbound through the allosteric channel as expected for type-IIA inhibitors, IQ2 and IQ3 unbound via the ATP channel (except for CDK2-IQ2) as expected for type-I½A inhibitors. Interestingly, a C-C single/double bond difference between IQ2/IQ3, respectively, resulted associated with differences in the AS/T loop flexibility observed for CDK2. These insights will help developing scaffold modifications during an optimization stage, serving as a starting point to develop dual kinase inhibitors in challenging biological targets with a promising anticancer potential.Communicated by Ramaswamy H. Sarma.

Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products.

Cyclin-Dependent Kinase 2 (CDK2) and Vascular Endothelial Growth Factor Receptor (VEGFR2) have largely been considered as attractive targets for developing anticancer agents. However, there is no dual inhibitor commercially available in the market that interacts simultaneously with the allosteric back pocket of these enzymes. We applied a combined computational strategy that started with the generation of two overlapping pharmacophore models of both kinases at 'inactive' conformation. Next, several virtual libraries of natural products, including the databases TCM (Traditional Chinese Medicine), UEFS (Universidade Estadual de Feira de Santana), NuBBE (Nuclei of Bioassays, Biosynthesis, and Ecophysiology of Natural Products) and AfroDb (African Medicinal Plants Database) were deconstructed using a non-extensive version of the approach RECAP (retrosynthetic combinatorial analysis procedure). These natural-product-derived fragments (NPDFs) were screened and merged into drug-sized compounds, which were filtered by Lipinski's Rule-of-five (Ro5) and docking. As a result, two pharmacophore models, namely Hypo1 and Hypo2, were developed with an accuracy of 0.94 and 0.84, respectively. Deconstruction of natural products produced a set of 16655 unique non-extensive NPDFs that were screened against both pharmacophore models. Finally, after merging, Ro5-filtering and docking, we obtained a set of 20 hit compounds predicted to be diverse, developable, synthesizable and potent. The computational strategy proved successful to find virtual candidates of kinase inhibitors and therefore contributes to the identification of innovative multi-target compounds with potential anticancer activity. Communicated by Ramaswamy H. Sarma.

Insights into the behavior of six rationally designed peptides based on Escherichia coli's OmpA at the water-dodecane interface.

The Escherichia coli's membrane protein OmpA has been identified as a potential biosurfactant due to their amphiphilic nature, and their capacity to stabilize emulsions of dodecane in water. In this study, the influence of surfactant type, concentration, preservation time and droplet size on the crystallization of n-dodecane and water, in oil-in-water emulsions stabilized with six rationally designed Escherichia coli's OmpA-based peptides was investigated. A differential scanning calorimetry (DSC) protocol was established using emulsions stabilized with Tween 20® and Tween 80®. A relationship between the surfactant concentration and the crystallization temperatures of n-dodecane and water was observed, where the crystallization temperatures seem to be dependent on the preservation time. A deconvolution analysis shows that the peak morphology possibly depends on the interactions at the interface because the enthalpic contributions of each Gaussian peak remained similar in emulsions stabilized with the same peptide. Adsorption results show that the main driver for adsorption and thus stabilization of emulsions is polar interactions (e.g. H-bonding) through the hydrophilic parts of the peptides. Those peptides with a preponderance of polar interaction groups distribution (i.e. NH2, COOH, imidazole) showed the highest interfacial activity under favorable pH conditions. This suggests that custom-made peptides whose hydrophilic/hydrophobic regions can be fine-tuned depending on the application can be easily produced with the additional advantage of their biodegradable nature.

Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains' pathogenicity level.

The Helicobacter pylori cytotoxin-associated gene A (CagA) is known for causing gastroduodenal diseases, such as atrophic gastritis and peptic ulcerations. Furthermore Helicobacter pylori CagA positive strains has been reported as one of the main risk factors for gastric cancer (Parsonnet et al., 1997). Structural variations in the CagA structure can alter its affinity with the host proteins, inducing differences in the pathogenicity of H. pylori. CagA N-terminal region is characterized for be conserved among all H. pylori strains since the C-terminal region is characterized by an intrinsically disorder behavior. We generated complete structural models of CagA using different conformations of the C-terminal region for two H. pylori strains. These models contain the same EPIYA (ABC1C2) motifs but different level of pathogenicity: gastric cancer and duodenal ulcer. Using these structural models we evaluated the pathogenicity level of the H. pylori strain, based on the affinity of the interaction with SHP-2 and Grb2 receptors and on the number of interactions with the EPIYA motif. We found that the main differences in the interaction was due to the contributions of certain types of energies from each strain and not from the total energy of the molecule. Specifically, the electrostatic energy, helix dipole energy, Wander Waals clashes, torsional clash, backbone clash and cis bond energy allowed a separation between severe and mild pathology for the interaction of only CagA with SHP2.

Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.

BACKGROUND: The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like Clostridium butyricum. However, despite the increasing role of Clostridium butyricum as a bio-production platform, its metabolism remains poorly modeled. RESULTS: We reconstructed iCbu641, the first genome-scale metabolic (GSM) model of a PDO producer Clostridium strain, which included 641 genes, 365 enzymes, 891 reactions, and 701 metabolites. We found an enzyme expression prediction of nearly 84% after comparison of proteomic data with flux distribution estimation using flux balance analysis (FBA). The remaining 16% corresponded to enzymes directionally coupled to growth, according to flux coupling findings (FCF). The fermentation data validation also revealed different phenotype states that depended on culture media conditions; for example, Clostridium maximizes its biomass yield per enzyme usage under glycerol limitation. By contrast, under glycerol excess conditions, Clostridium grows sub-optimally, maximizing biomass yield while minimizing both enzyme usage and ATP production. We further evaluated perturbations in the GSM model through enzyme deletions and variations in biomass composition. The GSM predictions showed no significant increase in PDO production, suggesting a robustness to perturbations in the GSM model. We used the experimental results to predict that co-fermentation was a better alternative than iCbu641 perturbations for improving PDO yields. CONCLUSIONS: The agreement between the predicted and experimental values allows the use of the GSM model constructed for the PDO-producing Clostridium strain to propose new scenarios for PDO production, such as dynamic simulations, thereby reducing the time and costs associated with experimentation.

Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations.

BACKGROUND: Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. RESULTS: A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. CONCLUSION: Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

Peptides design based on transmembrane Escherichia coli's OmpA protein through molecular dynamics simulations in water-dodecane interfaces.

Recent research efforts have focused on the production of environmentally nonthreatening products, including identifying biosurfactants that can replace conventional surfactants. In order to utilize biosurfactants in different industries such as cosmetic, food or petroleum, it is necessary to understand the underpinnings behind the interactions that could take place for biosurfactants which display potential for interface activity. This work aimed to use molecular dynamics simulations to understand the interactions of rationally obtained peptide sequences from the original sequence of the OmpA gene in Escherichia coli, based on the free energy change (ΔG) during peptide insertion at the water-dodecane interface. Seventeen OmpA-based peptide sequences were selected and analyzed based on their hydropathy index profiles. We found that free energy change due to Columbic interactions and SASA (ΔGCoul/SASA), total free energy change and MW (ΔG/MW), and free energy change due to Coulombic and van der Waals interactions (ΔGCoul/ΔGvdW) ratios could provide a better understating in the contribution of the free energy decrease at the interface. The results indicated that the peptide sequences GKNHDTGVSPVFA and THENQLGAGAFG display biosurfactant potential based on low ΔG per square nanometer, high ΔGCoul/ΔGvdW ratio, clearly defined moieties along its hydrophobic surface and sequence, and the presence of charged residues in the polar head. Clearly defined moieties and SASA were determinant for electrostatic interactions between oil-water interfaces. Experimental validations exhibited that the emulsions prepared remained stable between 3 and 27h, respectively. Even though the peptide GKNHDTGVSPVFA displays strong interactions at the interface, stabilization times showed that the peptide THENQLGAGAFG exhibited the best performance suggesting that the stability can be better described by kinetic rather than thermodynamic criteria once the emulsion is formed.

Fagoterapia, alternativa para el control de las infecciones bacterianas. Perspectivas en Colombia / Phage-therapy, an alternative to control bacterial infections. Perspectives in Colombia / Fagoterapia, alternativa para o controle das infeccóes bacterianas. Perspectivas na Colombia

La capacidad de las bacterias para adquirir resistencia a agentes antimicrobianos ha reducido el número de antibióticos efectivos para combatir infecciones bacterianas. De otro lado, existen bacterias contaminantes de alimentos, que no pueden controlarse con antibióticos por tratarse de productos de consumo humano, lo que se traduce en pérdidas económicas y riesgos para la salud. Si a esto se suma la falta de desarrollo de nuevos antibióticos, es evidente que se requiere desarrollar otras estrategias para el tratamiento y control de las bacterias. Los bacteriófagos (fagos), virus que infectan bacterias, se proponen como uno de estos tratamientos alternativos en una estrategia conocida como fagoterapia. Diversos estudios han evaluado y demostrado su efectividad contra bacterias patógenas y ya existen empresas privadas que desarrollan productos basados en cocteles de fagos para controlar algunas infecciones bacterianas. En Colombia no existen antecedentes del uso de fagos pero estos representan una gran oportunidad para el aprovechamiento de la diversidad de la microbiota nativa. En este artículo presentamos las perspectivas de uso de la fagoterapia en Colombia como tratamiento de infecciones bacterianas.

Bacteria easily acquire resistance to antimicrobial agents and this reduces the number of effective antibiotics available to treat bacterial infections. Food contamination by bacteria also generates important economic losses and health risks. Products for human consumption must be free of antibiotics used in clinical treatments, and the control of bacteria with antimicrobials is strictly regulated; however, there is a lack of development of new antibiotics. As a result, the development of new antimicrobial strategies is vital. Viruses that infect bacteria called bacteriophages (phages) have been proposed as an alternative treatment in an approach known as phage-therapy. Several studies have evaluated and demonstrated their effectiveness against pathogenic bacteria; currently, there are private companies dedicated to the development of new products based on phage cocktails, to control some bacterial infections. In Colombia, there is no previous information about the use of phages, but phage-therapy represents a great opportunity to use the diversity of the native microbiota. In this review, we present the perspectives for phage-therapy in Colombia as a treatment against bacterial infections.

A capacidade das bactérias para adquirir resistencia a agentes antimicrobianos tem levado a que o número de antibióticos efetivos para combater infectes bacterianas em humanos seja cada vez menor. Nos alimentos se reportam bactérias causantes de contaminares que representam grandes perdas económicas e riscos para a saúde; estas bactérias nao podem ser tratadas com antibióticos por tratar-se de produtos para consumo humano. Tendo em conta a situado, e a falta de novos antibióticos, precisa-se do desenvolvimento de novas estratégias para o tratamento e controle das bactérias. Os bacteriófagos (fagos), vírus que infectam bactérias, propoem-se como um destes tratamentos alternativos, numa estratégia conhecida como fagoterapia. Diversos estudos tem demostrada a efetividade contra bactérias patógenas e já existem empresas privadas desenvolvendo produtos baseados em coqueteis de fagos, para controlar algumas infectes bacterianas. Na Colombia nao existe antecedente do uso de fagos, mas este apresenta uma grande oportunidade para o aproveitamento da diversidade da microbiota nativa. Nesta revisao apresentamos as perspectivas para a fagoterapia na Colombia como tratamento alternativo contra infectes bacterianas.

Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022).

The cross-species bacterial communication signal autoinducer 2 (AI-2), produced by the purified enzymes Pfs (nucleosidase) and LuxS (terminal synthase) from S-adenosylhomocysteine, directly increased Escherichia coli biofilm mass 30-fold. Continuous-flow cells coupled with confocal microscopy corroborated these results by showing the addition of AI-2 significantly increased both biofilm mass and thickness and reduced the interstitial space between microcolonies. As expected, the addition of AI-2 to cells which lack the ability to transport AI-2 (lsr null mutant) failed to stimulate biofilm formation. Since the addition of AI-2 increased cell motility through enhanced transcription of five motility genes, we propose that AI-2 stimulates biofilm formation and alters its architecture by stimulating flagellar motion and motility. It was also found that the uncharacterized protein B3022 regulates this AI-2-mediated motility and biofilm phenotype through the two-component motility regulatory system QseBC. Deletion of b3022 abolished motility, which was restored by expressing b3022 in trans. Deletion of b3022 also decreased biofilm formation significantly, relative to the wild-type strain in three media (46 to 74%) in 96-well plates, as well as decreased biomass (8-fold) and substratum coverage (19-fold) in continuous-flow cells with minimal medium (growth rate not altered and biofilm restored by expressing b3022 in trans). Deleting b3022 changed the wild-type biofilm architecture from a thick (54-mum) complex structure to one that contained only a few microcolonies. B3022 positively regulates expression of qseBC, flhD, fliA, and motA, since deleting b3022 decreased their transcription by 61-, 25-, 2.4-, and 18-fold, respectively. Transcriptome analysis also revealed that B3022 induces crl (26-fold) and flhCD (8- to 27-fold). Adding AI-2 (6.4 muM) increased biofilm formation of wild-type K-12 MG1655 but not that of the isogenic b3022, qseBC, fliA, and motA mutants. Adding AI-2 also increased motA transcription for the wild-type strain but did not stimulate motA transcription for the b3022 and qseB mutants. Together, these results indicate AI-2 induces biofilm formation in E. coli through B3022, which then regulates QseBC and motility; hence, b3022 has been renamed the motility quorum-sensing regulator gene (the mqsR gene).

Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid.

After 13,000 samples of compounds purified from plants were screened, a new biofilm inhibitor, ursolic acid, has been discovered and identified. Using both 96-well microtiter plates and a continuous flow chamber with COMSTAT analysis, 10 microg of ursolic acid/ml inhibited Escherichia coli biofilm formation 6- to 20-fold when added upon inoculation and when added to a 24-h biofilm; however, ursolic acid was not toxic to E. coli, Pseudomonas aeruginosa, Vibrio harveyi, and hepatocytes. Similarly, 10 microg of ursolic acid/ml inhibited biofilm formation by >87% for P. aeruginosa in both complex and minimal medium and by 57% for V. harveyi in minimal medium. To investigate the mechanism of this nontoxic inhibition on a global genetic basis, DNA microarrays were used to study the gene expression profiles of E. coli K-12 grown with or without ursolic acid. Ursolic acid at 10 and 30 microg/ml induced significantly (P < 0.05) 32 and 61 genes, respectively, and 19 genes were consistently induced. The consistently induced genes have functions for chemotaxis and mobility (cheA, tap, tar, and motAB), heat shock response (hslSTV and mopAB), and unknown functions (such as b1566 and yrfHI). There were 31 and 17 genes repressed by 10 and 30 microg of ursolic acid/ml, respectively, and 12 genes were consistently repressed that have functions in cysteine synthesis (cysK) and sulfur metabolism (cysD), as well as unknown functions (such as hdeAB and yhaDFG). Ursolic acid inhibited biofilms without interfering with quorum sensing, as shown with the V. harveyi AI-1 and AI-2 reporter systems. As predicted by the differential gene expression, deleting motAB counteracts ursolic acid inhibition (the paralyzed cells no longer become too motile). Based on the differential gene expression, it was also discovered that sulfur metabolism (through cysB) affects biofilm formation (in the absence of ursolic acid).