Targeting Dynamical Binding Processes in the Design of Non-Antibiotic Anti-Adhesives by Molecular Simulation-The Example of FimH

The artificial neural network selects saccharides from natural sources a promise for potential FimH inhibitor to prevent UTI infections

The major challenge in the development of affordable medicines from natural sources is the unavailability of logical protocols to explain their mechanism of action in biological targets. FimH (Type 1 fimbrin with D-mannose specific adhesion property), a lectin on E. coli cell surface is a promising target to combat the urinary tract infection (UTI). The present study aimed at predicting the inhibitory capacity of saccharides on FimH. As mannosides are considered FimH inhibitors, the readily accessible saccharides from the PubChem collection were utilized. The artificial neural networks (ANN)-based machine learning algorithm Self-organizing map (SOM) has been successfully employed in predicting active molecules as they could discover relationships through self-organization for the ligand-based virtual screening. Docking was used for the structure-based virtual screening and molecular dynamic simulation for validation. The result revealed that the predicted molecules malonyl hexose and mannosyl glucosyl glycerate exhibit exactly similar binding interactions and better docking scores as that of the reference bioassay active, heptyl mannose. The pharmacokinetic profile matches that of the selected bioflavonoids (quercetin malonyl hexose, kaempferol malonyl hexose) and has better values than the control drug bioflavonoid, monoxerutin. Thus, these two molecules can effectively inhibit type 1 fimbrial adhesin, as antibiotics against E. coli and can be explored as a prophylactic against UTIs. Moreover, this investigation can pave the way to the exploration of the potential benefits of plant-based treatments.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00212-5.

Glycomimetics for the inhibition and modulation of lectins

Carbohydrates are essential mediators of many processes in health and disease. They regulate self-/non-self- discrimination, are key elements of cellular communication, cancer, infection and inflammation, and determine protein folding, function and life-times. Moreover, they are integral to the cellular envelope for microorganisms and participate in biofilm formation. These diverse functions of carbohydrates are mediated by carbohydrate-binding proteins, lectins, and the more the knowledge about the biology of these proteins is advancing, the more interfering with carbohydrate recognition becomes a viable option for the development of novel therapeutics. In this respect, small molecules mimicking this recognition process become more and more available either as tools for fostering our basic understanding of glycobiology or as therapeutics. In this review, we outline the general design principles of glycomimetic inhibitors (Section 2). This section is then followed by highlighting three approaches to interfere with lectin function, i.e. with carbohydrate-derived glycomimetics (Section 3.1), novel glycomimetic scaffolds (Section 3.2) and allosteric modulators (Section 3.3). We summarize recent advances in design and application of glycomimetics for various classes of lectins of mammalian, viral and bacterial origin. Besides highlighting design principles in general, we showcase defined cases in which glycomimetics have been advanced to clinical trials or marketed. Additionally, emerging applications of glycomimetics for targeted protein degradation and targeted delivery purposes are reviewed in Section 4.

Insightful Improvement in the Design of Potent Uropathogenic E. coli FimH Antagonists

Selective antiadhesion antagonists of Uropathogenic Escherichia coli (UPEC) type-1 Fimbrial adhesin (FimH) are attractive alternatives for antibiotic therapies and prophylaxes against acute or recurrent urinary tract infections (UTIs) caused by UPECs. A rational small library of FimH antagonists based on previously described C-linked allyl α-D-mannopyranoside was synthesized using Heck cross-coupling reaction using a series of iodoaryl derivatives. This work reports two new members of FimH antagonist amongst the above family with sub nanomolar affinity. The resulting hydrophobic aglycones, including constrained alkene and aryl groups, were designed to provide additional favorable binding interactions with the so-called FimH "tyrosine gate". The newly synthesized C-linked glycomimetic antagonists, having a hydrolytically stable anomeric linkage, exhibited improved binding when compared to previously published analogs, as demonstrated by affinity measurement through interactions by FimH lectin. The crystal structure of FimH co-crystallized with one of the nanomolar antagonists revealed the binding mode of this inhibitor into the active site of the tyrosine gate. In addition, selected mannopyranoside constructs neither affected bacterial growth or cell viability nor interfered with antibiotic activity. C-linked mannoside antagonists were effective in decreasing bacterial adhesion to human bladder epithelial cells (HTB-9). Therefore, these molecules constituted additional therapeutic candidates' worth further development in the search for potent anti-adhesive drugs against infections caused by UPEC.

Structural and functional characterization of the FimH adhesin of uropathogenic Escherichia coli and its novel applications

Type 1 fimbriae are responsible for bacterial pathogenicity and biofilm production, which are important virulence factors in uropathogenic Escherichia coli strains. Many articles are published on fimH, but each examined a specific aspect of this protein. The current review study aimed at focusing on structure and conformational changes and describing efforts to use this protein in novel potential treatments for urinary tract infections, typing methods, and expression systems. The current study was the first review that briefly and effectively examined issues related to fimH adhesin.

Synthesis of regioisomeric maltose-based Man/Glc glycoclusters to control glycoligand presentation in 3D space

The investigation of carbohydrate recognition in a natural environment suffers from the complexity of overlapping functional effects such as multivalency and heteromultivalency effects. Another key factor in carbohydrate recognition is the presentation mode of glycoligands in three-dimensional (3D) space. In order to trace out the effect of 3D ligand presentation, we utilized an oligosaccharide model to precisely control the spatial relation between a mannose ligand (Man) and a glucose moiety (Glc). A disaccharide (maltose) served as a scaffold to alternately conjugate Man and Glc at position 6 and 6' of a synthetic maltoside, resulting in a pair of regioisomeric heterobivalent glycoclusters. The biological effect of this specific structural tuning was tested in a native system employing mannose-specific adhesion of live E. coli cells. Indeed, the variable 3D presentation of the Man ligand resulted in a 2-fold difference between the regioisomeric heterobivalent glycoclusters as inhibitors of bacterial adhesion. This can be considered a remarkable effect, which could be interpreted by computer-aided modelling of the complexes between the bacterial lectin and the synthetic regioisomeric glycoligands.

Recent development in the design of small 'drug-like' and nanoscale glycomimetics against Escherichia coli infections

Glycoconjugates are involved in several pathological processes. Glycomimetics that can favorably emulate complex carbohydrate structures, while competing with natural ligands as inhibitors, are gaining considerable attention owing to their improved hydrolytic stability, binding affinity, and pharmacokinetic (PK) properties. Of particular interest are the families of α-d-mannopyranoside analogs, which can be used as inhibitors against adherent invasive Escherichia coli infections. Bacterial resistance to modern antibiotics triggers the search for new alternative antibacterial strategies that are less susceptible to acquiring resistance. In this review, we highlight recent progress in the chemical syntheses of this family of compounds, one of which having reached clinical trials against Crohn's disease (CD).

Discovery of a species-specific novel antifungal compound against Fusarium graminearum through an integrated molecular modeling strategy

BACKGROUND

The cyanoacrylate fungicide phenamacril targeting fungal myosin I has been widely used for controlling Fusarium head blight (FHB) of wheat caused by the pathogenic fungus Fusarium graminearum worldwide. Therefore, there is great interest in the discovery and development of novel FgMyo1 inhibitors through structure-based drug design for the treatment of FHB.

RESULTS

In this study, the binding mechanism of phenamacril with FgMyo1 was predicted by an integrated molecular modeling strategy. The predicted key phenamacril-binding residues of FgMyo1 were further experimentally validated by point mutagenesis and phenamacril sensitivity assessment. Four novel key residues responsible for phenamacril binding were identified, highlighting the reliability of the theoretical predictions. The subsequent optimization of phenamacril derivatives led to the discovery of a novel compound (10) which shows better activity than phenamacril against conidial germination of F. graminearum, but not against other fungal species. Moreover, 10 also inhibits conidial germination of phenamacril-resistant strains effectively. Further experiments illustrated that application of 10 could dramatically inhibit deoxynivalenol biosynthesis.

CONCLUSION

Overall, our results further optimize and develop the binding model of phenamacril-myosin I. Furthermore, 10 was found and has the potential to be developed as a species-specific fungicide for management of FHB. © 2020 Society of Chemical Industry.

Intestinal microbiota characteristics of mice treated with Folium senna decoction gavage combined with restraint and tail pinch stress

To investigate the characteristics of the intestinal microbiota of mice treated with Folium senna decoction gavage combined with restraint and tail pinch stress. Ten healthy male Kunming mice were chosen and randomly divided into control group and model group, with five mice in each group. Mice in the control group were raised regularly, while mice in the model group were treated by feeding with Folium senna decoction, restraint in a constraint tube and tail pinch with a clip for 7 days. Intestinal contents from the jejunum to ileum were collected, and DNA was extracted from each mouse. The characteristics of the intestinal microbial species were analysed by PacBio Sequel-based 16S rRNA sequencing. Result showed that alpha diversity indices in the model group were higher than those in the control group, and the Simpson index differed significantly (P < 0.05). Based on the composition and abundances of species, there were differences between the control group and model group at the species level, but these differences were not significant (P > 0.05). In the control group, Candidatus arthromitus sp. SFB-mouse and Lactobacillus johnsonii were the dominant species. In the model group, Staphylococcus lentus, Lactobacillus johnsonii, Candidatus arthromitus sp. SFB-mouse and Lactobacillus murinus were included. Furthermore, LEfSe analysis showed that the relative abundances of Escherichia sp. BBDP27, Helicobacter ganmani, Bacteroides vulgatus and Lactobacillus intestinalis in the model group were higher than those in the control group (P < 0.05 or P < 0.01). In conclusion, Folium senna decoction gavage combined with restraint and tail pinch stress increased the intestinal microbiota diversity. Strains associated with intestinal diseases, including Bacteroides vulgatus, Helicobacter ganmani, Staphylococcus lentus and Lactobacillus murinus, were significantly enriched, while strains beneficial to health, such as Candidatus arthromitus sp. SFB-mouse and Lactobacillus johnsonii, were significantly depleted.

Strategies for discovery of new molecular targets for anti-infective drugs

Multidrug resistant bacterial pathogens as causative agents of infectious disease are a primary public health concern. Clinical efficacy of antimicrobial chemotherapy toward bacterial infection has been compromised in cases where causative agents are resistant to multiple structurally distinct antimicrobial agents. Modification of extant antimicrobial agents that exploit conventional bacterial targets have been developed since the advent of the antimicrobial era. This approach, while successful in certain cases, nonetheless suffers overall from the costs of development and rapid emergence of bacterial variants with confounding resistances to modified agents. Thus, additional strategies toward discovery of new molecular targets have been developed based on bioinformatics analyses and comparative genomics. These and other strategies meant to identify new molecular targets represent promising avenues for reducing emergence of bacterial infections. This short review considers these strategies for discovery of new molecular targets within bacterial pathogens.

A Novel Integrated Way for Deciphering the Glycan Code for the FimH Lectin

The fimbrial lectin FimH from uro- and enteropathogenic Escherichia coli binds with nanomolar affinity to oligomannose glycans exposing Manα1,3Man dimannosides at their non-reducing end, but only with micromolar affinities to Manα1,2Man dimannosides. These two dimannoses play a significantly distinct role in infection by E. coli. Manα1,2Man has been described early on as shielding the (Manα1,3Man) glycan that is more relevant to strong bacterial adhesion and invasion. We quantified the binding of the two dimannoses (Manα1,2Man and Manα1,3Man to FimH using ELLSA and isothermal microcalorimetry and calculated probabilities of binding modes using molecular dynamics simulations. Our experimentally and computationally determined binding energies confirm a higher affinity of FimH towards the dimannose Manα1,3Man. Manα1,2Man displays a much lower binding enthalpy combined with a high entropic gain. Most remarkably, our molecular dynamics simulations indicate that Manα1,2Man cannot easily take its major conformer from water into the FimH binding site and that FimH is interacting with two very different conformers of Manα1,2Man that occupy 42% and 28% respectively of conformational space. The finding that Manα1,2Man binding to FimH is unstable agrees with the earlier suggestion that E. coli may use the Manα1,2Man epitope for transient tethering along cell surfaces in order to enhance dispersion of the infection.