Chemical Composition of Volatile and Extractive Components of Canary (Tenerife) Propolis.

The vegetation of the Canary Islands is characterized by a large number of endemic species confined to different altitudinal levels. It can be assumed that these circumstances determine the characteristic features of the chemical composition of local beekeeping products, including propolis. We report, for the first time, the chemical composition of propolis from Tenerife (Canary Islands). The volatile emissions of three propolis samples collected from different apiaries are represented by 162 C1-C20 compounds, of which 144 were identified using the HS-SPME/GC-MS technique. The main group of volatiles, consisting of 72 compounds, is formed by terpenoids, which account for 42-68% of the total ion current (TIC) of the chromatograms. The next most numerous groups are formed by C6-C17 alkanes and alkenes (6-32% TIC) and aliphatic C3-C11 carbonyl compounds (7-20% TIC). The volatile emissions also contain C1-C6 aliphatic acids and C2-C8 alcohols, as well as their esters. Peaks of 138 organic C3-C34 compounds were recorded in the chromatograms of the ether extracts of the studied propolis. Terpene compounds form the most numerous group, but their number and content in different samples is within very wide limits (9-63% TIC), which is probably due to the origin of the samples from apiaries located at different altitudes. A peculiarity of the chemical composition of the extractive substances is the almost complete absence of phenylcarboxylic acids and flavonoids, characteristic of Apis mellifera propolis from different regions of Eurasia and North America. Aromatic compounds of propolis from Tenerife are represented by a group of nine isomeric furofuranoid lignans, as well as alkyl- and alkenyl-substituted derivatives of salicylic acid and resorcinol.

Mechanisms of Nitrosamine Mutagenicity and Their Relationship to Rodent Carcinogenic Potency.

A thorough literature review was undertaken to understand how the pathways of N-nitrosamine transformation relate to mutagenic potential and carcinogenic potency in rodents. Empirical and computational evidence indicates that a common radical intermediate is created by CYP-mediated hydrogen abstraction at the α-carbon; it is responsible for both activation, leading to the formation of DNA-reactive diazonium species, and deactivation by denitrosation. There are competing sites of CYP metabolism (e.g., ß-carbon), and other reactive species can form following initial bioactivation, although these alternative pathways tend to decrease rather than enhance carcinogenic potency. The activation pathway, oxidative dealkylation, is a common reaction in drug metabolism and evidence indicates that the carbonyl byproduct, e.g., formaldehyde, does not contribute to the toxic properties of N-nitrosamines. Nitric oxide (NO), a side product of denitrosation, can similarly be discounted as an enhancer of N-nitrosamine toxicity based on carcinogenicity data for substances that act as NO-donors. However, not all N-nitrosamines are potent rodent carcinogens. In a significant number of cases, there is a potency overlap with non-N-nitrosamine carcinogens that are not in the Cohort of Concern (CoC; high-potency rodent carcinogens comprising aflatoxin-like-, N-nitroso-, and alkyl-azoxy compounds), while other N-nitrosamines are devoid of carcinogenic potential. In this context, mutagenicity is a useful surrogate for carcinogenicity, as proposed in the ICH M7 (R2) (2023) guidance. Thus, in the safety assessment and control of N-nitrosamines in medicines, it is important to understand those complementary attributes of mechanisms of mutagenicity and structure-activity relationships that translate to elevated potency versus those which are associated with a reduction in, or absence of, carcinogenic potency.

MELLODDY: Cross-pharma Federated Learning at Unprecedented Scale Unlocks Benefits in QSAR without Compromising Proprietary Information.

Federated multipartner machine learning has been touted as an appealing and efficient method to increase the effective training data volume and thereby the predictivity of models, particularly when the generation of training data is resource-intensive. In the landmark MELLODDY project, indeed, each of ten pharmaceutical companies realized aggregated improvements on its own classification or regression models through federated learning. To this end, they leveraged a novel implementation extending multitask learning across partners, on a platform audited for privacy and security. The experiments involved an unprecedented cross-pharma data set of 2.6+ billion confidential experimental activity data points, documenting 21+ million physical small molecules and 40+ thousand assays in on-target and secondary pharmacodynamics and pharmacokinetics. Appropriate complementary metrics were developed to evaluate the predictive performance in the federated setting. In addition to predictive performance increases in labeled space, the results point toward an extended applicability domain in federated learning. Increases in collective training data volume, including by means of auxiliary data resulting from single concentration high-throughput and imaging assays, continued to boost predictive performance, albeit with a saturating return. Markedly higher improvements were observed for the pharmacokinetics and safety panel assay-based task subsets.

Generation of two induced pluripotent stem cell lines from psoriatic patient with cardiovascular comorbidity.

Psoriasis (Ps) is a chronic, inflammatory skin disease characterized by thickened, red and scaly plaques. Systemic inflammation associated with psoriasis results in an increased risk of death due to the development of psoriasis-associated comorbidities such as cardiovascular disease (CVD) and metabolic syndrome. Although the cardiometabolic features in psoriasis are clinically well described, the underlying molecular mechanisms linking these comorbidities remain poorly understood. Generation of induced pluripotent stem cells (hiPSCs) from peripheral blood mononuclear cells (PBMCs) and skin fibroblasts (SFs) of psoriatic patients provides a novel approach to investigate the pathway by which cutaneous inflammation promotes CV complications in this disorder.

Psychosocial Consequences of Hand Eczema-A Prospective Cross-Sectional Study.

BACKGROUND: Hand eczema (HE) is a chronic inflammatory disease with a high prevalence, negatively influencing patients' quality of life (QoL). It may also affect patients' psychological status. The aim of this study was to assess and characterize the psychological burden of HE, its influence on patients' QoL, and the presence and severity of anxiety and depressive disorders in HE patients. METHODS: The study group consisted of 100 adult HE individuals. To assess the severity of the disease, two instruments were used: the Investigator Global Assessment for Chronic Hand Eczema (IGA-CHE) scale and the Hand Eczema Severity Index (HECSI). Assessment of patients' quality of life (QoL) was obtained with the use of the DLQI tool. Patient Health Questionnaire-9 (PHQ-9) and Generalized Anxiety Disorder-7 (GAD-7) questionnaires were employed to assess depression and anxiety, respectively, as well as a modified version of the Hospital Anxiety and Depression Scale (HADS-M). RESULTS: The mean DLQI value for the whole group reached 11.62 ± 6.35 points (13.27 ± 6.67 points in females and 9.15 ± 4.95 points in males; p = 0.023). A decrease in QoL correlated positively with the severity of the disease and the severity of itch and pain. In 17 patients (17%), a possible diagnosis of depressive disorder was found. Patients scoring higher results on the PHQ-9 and HADS-M depression (D) questionnaires reported greater intensity of the itch (r = 0.363, p < 0.001, and r = 0.237, p = 0.017, respectively) and the pain (r = 0.445, p < 0.001, and r = 0.287, p = 0.004, respectively). The anxiety disorder might possibly be diagnosed in 25% of patients (n = 25). This study revealed a positive correlation between the severity of the anxiety symptoms, measured with the use of both GAD-7 and HADS-M anxiety (A) tools, and the intensity of the pain (r = 0.248, p = 0.013, and r = 0.342, p = 0.001, respectively). The severity of depressive and anxiety symptoms correlated positively with the severity of the disease. CONCLUSIONS: The psychosocial burden of HE is an undeniable phenomenon. The disorder influences patients' QoL and may cause mental disturbances such as depression and anxiety disorders.

Prevalence and Characteristics of Itch and Pain in Patients Suffering from Chronic Hand Eczema.

BACKGROUND: Hand eczema (HE) is a frequent chronic inflammatory dermatosis. Itch and pain are considered two of the most common and burdensome symptoms of the disease. Yet, the data related to these symptoms are still limited. The aim of this study was to evaluate characteristics of itch and pain in adults suffering from HE. METHODS: The study group comprised 100 adult HE patients. An original questionnaire designed by the authors was used to survey the patients. It included questions regarding demographic characteristics such as the duration of the disease, exacerbation count, past diagnostics and treatment, as well as atopic predispositions. Additionally, the itch and pain intensity (numerical rating scale-NRS) during '3 days prior to the study' and the 'entire disease' period was implemented. The clinical assessment of the disease severity was performed according to two specific measurement instruments: Investigator Global Assessment for Chronic Hand Eczema (IGA-CHE) scale and Hand Eczema Severity Index (HECSI). To assess patient quality of life (QoL), the DLQI tool was used and to determine the level of stigmatization and for its impact on patients' life the 6-Item Stigmatization Scale (6-ISS) was employed. RESULTS: Within the period of 3 days prior to the examination, itch was reported by 81.0% of patients (n = 81), whereas 53.0% (n = 53) of them experienced pain. Both symptoms were reported more frequently in females (itch: p = 0.022; pain: p = 0.033). When sexes were compared, females reached higher scores in both IGA-CHE and HECSI. Itch and pain intensity correlated positively with disease severity. The intensity of itch and pain significantly influences HE patients' QoL. A positive correlation between the 6-ISS score and the intensity of itch in the 'last 3 days' period was revealed (r = 0.221; p = 0.027). CONCLUSIONS: Itch and pain are common symptoms in HE patients, significantly contributing to the feeling of stigmatization. Providing characteristics of itch and pain may improve HE management. Symptom-decreasing treatment would definitely have a positive influence on patients' well-being.

Chemical Composition and Antimicrobial Properties of Honey Bee Venom.

Due to its great medical and pharmaceutical importance, honey bee venom is considered to be well characterized both chemically and in terms of biomedical activity. However, this study shows that our knowledge of the composition and antimicrobial properties of Apis mellifera venom is incomplete. In this work, the composition of volatile and extractive components of dry and fresh bee venom (BV) was determined by GC-MS, as well as antimicrobial activity against seven types of pathogenic microorganisms. One-hundred and forty-nine organic C1-C19 compounds of different classes were found in the volatile secretions of the studied BV samples. One-hundred and fifty-two organic C2-C36 compounds were registered in ether extracts, and 201 compounds were identified in methanol extracts. More than half of these compounds are new to BV. In microbiological tests involving four species of pathogenic Gram-positive and two species of Gram-negative bacteria, as well as one species of pathogenic fungi, the values of the minimum inhibitory concentration (MIC) and minimum bactericidal/fungicidal concentration (MBC/MFC) were determined for samples of dry BV, as well as ether and methanol extracts from it. Gram-positive bacteria show the greatest sensitivity to the action of all tested drugs. The minimum MIC values for Gram-positive bacteria in the range of 0.12-7.63 ng mL-1 were recorded for whole BV, while for the methanol extract they were 0.49-125 ng mL-1. The ether extracts had a weaker effect on the tested bacteria (MIC values 31.25-500 ng mL-1). Interestingly, Escherichia coli was more sensitive (MIC 7.63-500 ng mL-1) to the action of bee venom compared to Pseudomonas aeruginosa (MIC ≥ 500 ng mL-1). The results of the tests carried out indicate that the antimicrobial effect of BV is associated with the presence of not only peptides, such as melittin, but also low molecular weight metabolites.

Topical and systemic JAK inhibitors in hand eczema - a narrative review.

INTRODUCTION: Hand eczema is a chronic inflammatory skin disease characterized by significant prevalence and impact on patients' Quality of Life (QoL). Because of its complex and diverse clinical picture, HE management requires patient-specific treatment which may constitute a challenge. First described in the 1990s, Janus kinase inhibitors (JAK inhibitors) state a group of modern therapeuticals, which exhibit good bioavailability and are well tolerated by patients in both - topical and systemic - routes of administration. They are an immunomodulating small molecules, impacting JAKs' enzymatic activity. AREAS COVERED: This review provides a summary of available data concerning JAK inhibitors' use in HE patients, regarding also clinical trials for the HE treatment. EXPERT OPINION: Recent studies are introducing JAK inhibitors as an alternative for other topical and systemic therapies in HE patients. Treatment targeting specific immune pathways enables precise management and extends range of potential therapeutic options. Despite early promising results, future studies need to evaluate JAK inhibitors' safety, potential risks and benefits resulting from the treatment, as well as impact of the therapy on patients' QoL.

Tinea Gladiatorum: Epidemiology, Clinical Aspects, and Management.

Tinea gladiatorum (TG) is a fungal skin infection that occurs among wrestlers and other contact sport athletes with a varied prevalence rate. The most common causative factor responsible as well for local outbreaks of the infection is an anthropophilic dermatophyte species-Trichophyton tonsurans (T. tonsurans). The purpose of this study was to gather current data about TG, including epidemiology, possible diagnosing methods, clinical features, treatment approaches, and potential prevention techniques. We also performed a systematic review of studies describing TG incidence. The prevalence of the disease varied from 2.4% up to 100%. That wide range of variability forces medical practitioners to update knowledge about TG and points to the fact that it still may be a diagnostic and therapeutic challenge. Spreading awareness among athletes and trainers is one of the most important preventive steps.

Splitting chemical structure data sets for federated privacy-preserving machine learning.

With the increase in applications of machine learning methods in drug design and related fields, the challenge of designing sound test sets becomes more and more prominent. The goal of this challenge is to have a realistic split of chemical structures (compounds) between training, validation and test set such that the performance on the test set is meaningful to infer the performance in a prospective application. This challenge is by its own very interesting and relevant, but is even more complex in a federated machine learning approach where multiple partners jointly train a model under privacy-preserving conditions where chemical structures must not be shared between the different participating parties. In this work we discuss three methods which provide a splitting of a data set and are applicable in a federated privacy-preserving setting, namely: a. locality-sensitive hashing (LSH), b. sphere exclusion clustering, c. scaffold-based binning (scaffold network). For evaluation of these splitting methods we consider the following quality criteria (compared to random splitting): bias in prediction performance, classification label and data imbalance, similarity distance between the test and training set compounds. The main findings of the paper are a. both sphere exclusion clustering and scaffold-based binning result in high quality splitting of the data sets, b. in terms of compute costs sphere exclusion clustering is very expensive in the case of federated privacy-preserving setting.

Don't Overweight Weights: Evaluation of Weighting Strategies for Multi-Task Bioactivity Classification Models.

Machine learning models predicting the bioactivity of chemical compounds belong nowadays to the standard tools of cheminformaticians and computational medicinal chemists. Multi-task and federated learning are promising machine learning approaches that allow privacy-preserving usage of large amounts of data from diverse sources, which is crucial for achieving good generalization and high-performance results. Using large, real world data sets from six pharmaceutical companies, here we investigate different strategies for averaging weighted task loss functions to train multi-task bioactivity classification models. The weighting strategies shall be suitable for federated learning and ensure that learning efforts are well distributed even if data are diverse. Comparing several approaches using weights that depend on the number of sub-tasks per assay, task size, and class balance, respectively, we find that a simple sub-task weighting approach leads to robust model performance for all investigated data sets and is especially suited for federated learning.

Cat Allergy as a Source Intensification of Atopic Dermatitis in Adult Patients.

Atopic dermatitis (AD) is characterized by exacerbations and remissions of eczematous skin, underlain by impaired skin barrier and aberrant Th2-type and Th-22 cytokine production. A number of allergens, in particular contact with fur animals, may aggravate the disease. This study seeks to define the influence of having a regular contact with a pet cat at home on the severity of symptoms and signs of AD. We addressed the issue using the SCORing Atopic Dermatitis (SCORAD) and visual analog (VAS) scores to assess the intensity of pruritus and by measuring the blood content of specific IgE and IL-4, IL-13, and IL-22 cytokines. The study group consisted of 47 adult patients suffering from AD since childhood, 18 of whom declared having regular contact with a cat and the remaining 29 who denied it. There also was a control group consisted of 16 healthy volunteers with no AD signs. The SCORAD and VAS scores were significantly higher in patients in contact with a cat than in those without it (median SCORAD 61.0 vs. 50.4 and VAS 9.0 vs. 4.0 points, respectively). The sIgE of a majority of patients (94.4%) in contact with a cat was in Class V-VI, compared with just a few patients (3.4%) with no such contact, having sIgE in the same classes (p < 0.001). Significant correlations were revealed between SCORAD and VAS scores and the class level of serum sIgE value. In addition, IL-22 was a single elevated cytokine, only in the patients in contact with a cat, and it correlated with pruritus severity. The results of the study underline the need to beware of the cat fur allergen, and they stress forethought and caution in acquiring and keeping a pet cat by patients suffering from AD.

The knowledge of issues associated with topical corticosteroids using in patients with atopic dermatitis.

Atopic dermatitis (AD) is the most common inflammatory dermatitis, always accompanied by the pruritus. First line treatment comprise of topical steroids, however, there is a particular concern among patients with atopic dermatitis - "steroid phobia", which results in lack of efficacy of the therapy. Steroid phobia arises usually from insufficient knowledge of these drugs. AIM: The aim of the study was to evaluate the knowledge of topical corticosteroids (TCS) and familiarity with so called safe therapy methods among atopic dermatitis patients. MATERIALS AND METHODS: In the study participated 143 adult patients with AD diagnosis made by a specialist dermatologist-venereologist and allergist in accordance with Hanifin and Rajka's diagnostic criteria. Patients filled anonymously authorial survey which included questions concerning disease duration, severity of pruritus, frequency of skin lubrication, understanding of topical steroid therapy and practical aspects of safe TCS application. RESULTS: Correct answers responding incidence to questions related to TCS diminished with the patients age, while on the other hand, it increased statistically significantly with the level of education. What responders were afraid of most frequently were the skin atrophy (56,6%), cataract (52,4%) and teleangiectasias (44,8%), in opposite to neoplasms (16,8%) and obesity (22,4%). Concerns were dependent to the treating physician- patients under the care of dermatologists more often were worried about the skin atrophy, teleangiectasias and cataract. Among participating patients just 3,5% of them (5 patients) knew the finger tip unit term, whereas the majority (56%) had been informed about safe TCS therapy methods. Amidst respondents who answered questions about TCS correctly statistically significantly lower pruritus intensity was observed. CONCLUSIONS: Results of our study indicate on necessity of taking action to improve cooperation between patients and doctors insofar as topical therapy of atopic dermatitis.

Mechanism of the Dual Activities of Human CYP17A1 and Binding to Anti-Prostate Cancer Drug Abiraterone Revealed by a Novel V366M Mutation Causing 17,20 Lyase Deficiency.

The CYP17A1 gene regulates sex steroid biosynthesis in humans through 17α-hydroxylase/17,20 lyase activities and is a target of anti-prostate cancer drug abiraterone. In a 46, XY patient with female external genitalia, together with a loss of function mutation S441P, we identified a novel missense mutation V366M at the catalytic center of CYP17A1 which preferentially impaired 17,20 lyase activity. Kinetic experiments with bacterially expressed proteins revealed that V366M mutant enzyme can bind and metabolize pregnenolone to 17OH-pregnenolone, but 17OH-pregnenolone binding and conversion to dehydroepiandrosterone (DHEA) was impaired, explaining the patient’s steroid profile. Abiraterone could not bind and inhibit the 17α-hydroxylase activity of the CYP17A1-V366M mutant. Molecular dynamics (MD) simulations showed that V366M creates a “one-way valve” and suggests a mechanism for dual activities of human CYP17A1 where, after the conversion of pregnenolone to 17OH-pregnenolone, the product exits the active site and re-enters for conversion to dehydroepiandrosterone. The V366M mutant also explained the effectiveness of the anti-prostate cancer drug abiraterone as a potent inhibitor of CYP17A1 by binding tightly at the active site in the WT enzyme. The V366M is the first human mutation to be described at the active site of CYP17A1 that causes isolated 17,20 lyase deficiency. Knowledge about the specificity of CYP17A1 activities is of importance for the development of treatments for polycystic ovary syndrome and inhibitors for prostate cancer therapy.

The price of flexibility - a case study on septanoses as pyranose mimetics.

Seven-membered ring mimetics of mannose were studied as ligands for the mannose-specific bacterial lectin FimH, which plays an essential role in the first step of urinary tract infections (UTI). A competitive binding assay and isothermal titration calorimetry (ITC) experiments indicated an approximately ten-fold lower affinity for the seven-membered ring mannose mimetic 2-O-n-heptyl-1,6-anhydro-d-glycero-d-galactitol (7) compared to n-heptyl α-d-mannopyranoside (2), resulting exclusively from a loss of conformational entropy. Investigations by solution NMR, X-ray crystallography, and molecular modeling revealed that 7 establishes a superimposable H-bond network compared to mannoside 2, but at the price of a high entropic penalty due to the loss of its pronounced conformational flexibility. These results underscore the importance of having access to the complete thermodynamic profile of a molecular interaction to "rescue" ligands from entropic penalties with an otherwise perfect fit to the protein binding site.

Mutation of Tyr137 of the universal Escherichia coli fimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding.

The most prevalent diseases manifested by Escherichia coli are acute and recurrent bladder infections and chronic inflammatory bowel diseases such as Crohn's disease. E. coli clinical isolates express the FimH adhesin, which consists of a mannose-specific lectin domain connected via a pilin domain to the tip of type 1 pili. Although the isolated FimH lectin domain has affinities in the nanomolar range for all high-mannosidic glycans, differentiation between these glycans is based on their capacity to form predominantly hydrophobic interactions within the tyrosine gate at the entrance to the binding pocket. In this study, novel crystal structures of tyrosine-gate mutants of FimH, ligand-free or in complex with heptyl α-d-O-mannopyranoside or 4-biphenyl α-d-O-mannopyranoside, are combined with quantum-mechanical calculations and molecular-dynamics simulations. In the Y48A FimH crystal structure, a large increase in the dynamics of the alkyl chain of heptyl α-d-O-mannopyranoside attempts to compensate for the absence of the aromatic ring; however, the highly energetic and stringent mannose-binding pocket of wild-type FimH is largely maintained. The Y137A mutation, on the other hand, is the most detrimental to FimH affinity and specificity: (i) in the absence of ligand the FimH C-terminal residue Thr158 intrudes into the mannose-binding pocket and (ii) ethylenediaminetetraacetic acid interacts strongly with Glu50, Thr53 and Asn136, in spite of multiple dialysis and purification steps. Upon mutation, pre-ligand-binding relaxation of the backbone dihedral angles at position 137 in the tyrosine gate and their coupling to Tyr48 via the interiorly located Ile52 form the basis of the loss of affinity of the FimH adhesin in the Y137A mutant.

Vitamin D-Dependent Rickets Type 1 Caused by Mutations in CYP27B1 Affecting Protein Interactions With Adrenodoxin.

CONTEXT: CYP27B1 converts 25-hydroxyvitamin D3 to active 1,25-dihydroxyvitamin D3, playing a vital role in calcium homeostasis and bone growth. Vitamin D-dependent rickets type 1 (VDDR-1) is a rare autosomal recessive disorder caused by mutations in CYP27B1. OBJECTIVE: The objective of the study was an enzymatic and structural analysis of mutations in a patient with calcipenic rickets. Design, Setting, Patient, and Intervention: Two siblings presented with calcipenic rickets and normal 1,25-dihydroxyvitamin D3 levels. CYP27B1 gene analysis showed compound heterozygous mutations confirming VDDR-1. We studied wild-type CYP27B1 and mutations H441Y and R459L by computational homology modeling, molecular dynamics simulations, and functional studies using a luciferase assay. The patients were successfully treated with calcitriol. MAIN OUTCOME: The main outcomes of the study were novel mutations leading to a severe loss of CYP27B1 activities for metabolism of 25-hydroxyvitamin D3. RESULTS: Mitochondrial cytochrome P450s require adrenodoxin (FDX1) and adrenodoxin reductase. We created models of CYP27B1-FDX1 complex, which revealed negative effects of mutations H441Y and R459L. Upon structural analysis, near-identical folds, protein contact areas, and orientations of heme/iron-sulfur cluster suggested that both mutations may destabilize the CYP27B1-FDX1 complex by negating directional interactions with adrenodoxin. This system is highly sensitive to small local changes modulating the binding/dissociation of adrenodoxin, and electron-transporting efficiency might change with mutations at the surface. Functional assays confirmed this hypothesis and showed severe loss of activity of CYP27B1 by both mutations. CONCLUSIONS: This is the first report of mutations in CYP27B1 causing VDDR-1 by affecting protein-protein interactions with FDX1 that results in reduced CYP27B1 activities. Detailed characterization of mutations in CYP27B1 is required for understanding the novel molecular mechanisms causing VDDR-1.

Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology.

Carbohydrates play a key role in a variety of physiological and pathological processes and, hence, represent a rich source for the development of novel therapeutic agents. Being able to predict binding mode and binding affinity is an essential, yet lacking, aspect of the structure-based design of carbohydrate-based ligands. We assembled a diverse data set comprising 273 carbohydrate-protein crystal structures with known binding affinity and evaluated the prediction accuracy of a large collection of well-established scoring and free-energy functions, as well as combinations thereof. Unfortunately, the tested functions were not capable of reproducing binding affinities in the studied complexes. To simplify the complex free-energy surface of carbohydrate-protein systems, we classified the studied proteins according to the topology and solvent exposure of the carbohydrate-binding site into five distinct categories. A free-energy model based on the proposed classification scheme reproduced binding affinities in the carbohydrate data set with an r(2) of 0.71 and root-mean-squared-error of 1.25 kcal/mol (N = 236). The improvement in model performance underlines the significance of the differences in the local micro-environments of carbohydrate-binding sites and demonstrates the usefulness of calibrating free-energy functions individually according to binding-site topology and solvent exposure.

A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences.

In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry and the knowledge of how to handle the complex underlying protocols, however, might keep medicinal chemists from routinely using in silico technologies. Our objective is to encourage those researchers to exploit existing modeling technologies more frequently through easy-to-use graphical user interfaces. In this account, we present two innovative tools (which we are prepared to share with academic institutions) facilitating computational tasks commonly utilized in drug discovery and development: (1) the VirtualDesignLab estimates the binding affinity of small molecules by simulating and quantifying their binding to the three-dimensional structure of a target protein; and (2) the MD Client launches molecular dynamics simulations aimed at exploring the time-dependent stability of ligand-protein complexes and provides residue-based interaction energies. This allows medicinal chemists to identify sites of potential improvement in their candidate molecule. As a case study, we present the application of our tools towards the design of novel antagonists for the FimH adhesin.

FimH antagonists: structure-activity and structure-property relationships for biphenyl α-D-mannopyranosides.

Urinary tract infections (UTIs) are caused primarily by uropathogenic Escherichia coli (UPEC), which encode filamentous surface-adhesive organelles called type 1 pili. FimH is located at the tips of these pili. The initial attachment of UPEC to host cells is mediated by the interaction of the carbohydrate recognition domain (CRD) of FimH with oligomannosides on urothelial cells. Blocking these lectins with carbohydrates or analogues thereof prevents bacterial adhesion to host cells and therefore offers a potential therapeutic approach for prevention and/or treatment of UTIs. Although numerous FimH antagonists have been developed so far, few of them meet the requirement for clinical application due to poor pharmacokinetics. Additionally, the binding mode of an antagonist to the CRD of FimH can switch from an in-docking mode to an out-docking mode, depending on the structure of the antagonist. In this communication, biphenyl α-D-mannosides were modified to improve their binding affinity, to explore their binding mode, and to optimize their pharmacokinetic properties. The inhibitory potential of the FimH antagonists was measured in a cell-free competitive binding assay, a cell-based flow cytometry assay, and by isothermal titration calorimetry. Furthermore, pharmacokinetic properties such as log D, solubility, and membrane permeation were analyzed. As a result, a structure-activity and structure-property relationships were established for a series of biphenyl α-D-mannosides.