Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization

A Structure-Activity Investigation of the Fungal Metabolite (-)-TAN-2483B: Inhibition of Bruton's Tyrosine Kinase

The natural product (-)-TAN-2483B is a fungal secondary metabolite which displays promising anti-cancer and immunomodulatory activity. Our previous syntheses of (-)-TAN-2483B and sidechain analogues uncovered inhibitory activity against Bruton's tyrosine kinase (Btk), an established drug target for various leukaemia and immunological diseases. A structure-based computational study using ensemble docking and molecular dynamics was performed to determine plausible binding modes for (-)-TAN-2483B and analogues in the Btk binding site. These hypotheses guided the design of new analogues which were synthesised and their inhibitory activities determined, providing insights into the structural determinants of the furopyranone scaffold that confer both activity and selectivity for Btk. These findings offer new perspectives for generating optimised (-)-TAN-2483B-based kinase inhibitors for the treatment of leukaemia and immunological diseases.

Constructing and validating a predictive nomogram for osteoporosis risk among Chinese single-center male population using the systemic immune-inflammation index

Osteoporosis (OP) is a bone metabolism disease that is associated with inflammatory pathological mechanism. Nonetheless, rare studies have investigated the diagnostic effectiveness of immune-inflammation index in the male population. Therefore, it is interesting to achieve early diagnosis of OP in male population based on the inflammatory makers from blood routine examination. We developed a prediction model based on a training dataset of 826 Chinese male patients through a retrospective study, and the data was collected from January 2022 to May 2023. All participants underwent the dual-energy X-ray absorptiometry (DXEA) and blood routine examination. Inflammatory markers such as systemic immune-inflammation index (SII) and platelet-to-lymphocyte ratio (PLR) was calculated and recorded. We utilized the least absolute shrinkage and selection operator (LASSO) regression model to optimize feature selection. Multivariable logistic regression analysis was applied to construct a predicting model incorporating the feature selected in the LASSO model. This predictive model was displayed as a nomogram. Receiver operating characteristic (ROC) curve, C-index, calibration curve, and clinical decision curve analysis (DCA) to evaluate model performance. Internal validation was test by the bootstrapping method. This study was approved by the Ethic Committee of the First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine (Ethic No. JY2023012) and conducted in accordance with the relevant guidelines and regulations. The predictive factors included in the prediction model were age, BMI, cardiovascular diseases, cerebrovascular diseases, neuropathy, thyroid diseases, fracture history, SII, PLR, C-reactive protein (CRP). The model displayed well discrimination with a C-index of 0.822 (95% confidence interval: 0.798-0.846) and good calibration. Internal validation showed a high C-index value of 0.805. Decision curve analysis (DCA) showed that when the threshold probability was between 3 and 76%, the nomogram had a good clinical value. This nomogram can effectively predict the incidence of OP in male population based on SII and PLR, which would help clinicians rapidly and conveniently diagnose OP with men in the future.

Establishment of a risk prediction model for bowel necrosis in patients with incarcerated inguinal hernia

INTRODUCTION

Incarceration occurred in approximately 5% to 15% of inguinal hernia patients, with around 15% of incarcerated cases progressing to intestinal necrosis, necessitating bowel resection surgery. Patients with intestinal necrosis had significantly higher mortality and complication rates compared to those without necrosis.The primary objective of this study was to design and validate a diagnostic model capable of predicting intestinal necrosis in patients with incarcerated groin hernias.

METHODS

We screened the clinical records of patients who underwent emergency surgery for incarcerated inguinal hernia between January 1, 2015, and December 31, 2022. To ensure balanced representation, the enrolled patients were randomly divided into a training set (n = 180) and a validation set (n = 76) using a 2:1 ratio. Logistic regression analysis was conducted using the rms package in R software, incorporating selected features from the LASSO regression model, to construct a predictive model.

RESULTS

Based on the results of the LASSO regression analysis, a multivariate logistic regression model was developed to establish the predictive model. The predictors included in the model were Abdominal effusion, Hernia Sac Effusion, and Procalcitonin. The area under the receiver operating characteristic (ROC) curve for the nomogram graph in the training set was 0.977 (95% CI = 0.957-0.992). In the validation set, the AUC for the nomogram graph was 0.970. Calibration curve and decision curve analysis (DCA) verified the accuracy and practicability of the nomogram graph in our study.

CONCLUSION

Bowel necrosis in patients with incarcerated inguinal hernia was influenced by multiple factors. The nomogram predictive model constructed in this study could be utilized to predict and differentiate whether incarcerated inguinal hernia patients were at risk of developing bowel necrosis.

A Novel Body Mass Index-Based Thromboembolic Risk Score for Overweight Patients with Nonvalvular Atrial Fibrillation

BACKGROUND

A novel risk prediction model appears to be urgently required to improve the assessment of thrombotic risk in overweight patients with nonvalvular atrial fibrillation (NVAF). We developed a novel body mass index (BMI)-based thromboembolic risk score (namely AB2S score) for these patients.

METHODS

A total of 952 overweight patients with NVAF were retrospectively enrolled in this study with a 12-month follow-up. The primary endpoint was 1-year systemic thromboembolism and the time to thrombosis (TTT). The candidate risk variables identified by logistic regression analysis were included in the final nomogram model to construct AB2S score. The measures of model fit were evaluated using area under the curve (AUC), C-statistic, and calibration curve. The performance comparison of the AB2S score to the CHADS2 and CHA2DS2-VASc score was performed in terms of the AUC and decision analysis curve (DAC).

RESULTS

The AB2S score was constructed using 7 candidate risk variables, including a 3-category BMI (25 to 30, 30 to 34, or ≥35 kg/m2). It yielded a c-index of 0.885 (95% CI, 0.814-0.954) and an AUC of 0.885 (95% CI, 0.815-0.955) for predicting 1-year systemic thromboembolism in patients with NVAF. Compared to the CHADS2 score and CHA2DS2-VASc score, the AB2S score had greater AUC and DAC values in predicting the thromboembolic risk and better risk stratification in TTT (P <.0001, P =.082, respectively).

CONCLUSION

Our results highlighted the importance of a BMI-based AB2S score in determining systemic thromboembolism risk in overweight patients with NVAF, which may aid in decision-making for these patients to balance the effectiveness of anticoagulation from the underlying thrombotic risk.

Nomogram for predicting bleeding events in nonvalvular atrial fibrillation patients receiving rivaroxaban: A retrospective study

Background and Aims

To construct a bleeding events prediction model of nonvalvular atrial fibrillation (NVAF) patients receiving rivaroxaban.

Methods

We conducted a retrospective cohort study in patients with NVAF who received rivaroxaban from June 2017 to March 2019. Demographic information and clinical characteristics were obtained from the electronic medical system. Univariate analysis was used to find the primary predictive factors of bleeding events in patients receiving rivaroxaban. Multiple analysis was conducted to screen the primary independent predictive factors selected from the univariate analysis. Finally, the independent influencing factors were applied to build a prediction model by using R software; then, a nomogram was established according to the selected variables visually, and the sensitivity and specificity of the model was evaluated.

Results

Twelve primary predictive factors were selected by univariate analysis from 46 variables, and multivariate analysis showed that older age, higher prothrombin time (PT) values, history of heart failure and stroke were independent risk factors of bleeding events. The area under curve (AUC) for this novel nomogram model was 0.828 (95% CI: 0.763-0.894). The mean AUC over 10-fold stratified cross-validation was 0.787, and subgroup analysis validation also showed a satisfied AUC. In addition, the decision curve analysis showed that the PT in combination with CHA2DS2-VASc and HASBLED was more practical and accurate for predicting bleeding events than using CHA2DS2-VASc and HASBLED alone.

Conclusions

PT in combination with CHA2DS2-VASc and HASBLED could be considered as a more practical and accurate method for predicting bleeding events in patients taking rivaroxaban.

Development of Potential Multi-Target Inhibitors for Human Cholinesterases and Beta-Secretase 1: A Computational Approach

Alzheimer's disease causes chronic neurodegeneration and is the leading cause of dementia in the world. The causes of this disease are not fully understood but seem to involve two essential cerebral pathways: cholinergic and amyloid. The simultaneous inhibition of AChE, BuChE, and BACE-1, essential enzymes involved in those pathways, is a promising therapeutic approach to treat the symptoms and, hopefully, also halt the disease progression. This study sought to identify triple enzymatic inhibitors based on stereo-electronic requirements deduced from molecular modeling of AChE, BuChE, and BACE-1 active sites. A pharmacophore model was built, displaying four hydrophobic centers, three hydrogen bond acceptors, and one positively charged nitrogen, and used to prioritize molecules found in virtual libraries. Compounds showing adequate overlapping rates with the pharmacophore were subjected to molecular docking against the three enzymes and those with an adequate docking score (n = 12) were evaluated for physicochemical and toxicological parameters and commercial availability. The structure exhibiting the greatest inhibitory potential against all three enzymes was subjected to molecular dynamics simulations (100 ns) to assess the stability of the inhibitor-enzyme systems. The results of this in silico approach indicate ZINC1733 can be a potential multi-target inhibitor of AChE, BuChE, and BACE-1, and future enzymatic assays are planned to validate those results.

Establishment of a risk prediction model for suicide attempts in first-episode and drug naïve patients with major depressive disorder

BACKGROUND

Suicide is common in patients with major depressive disorder (MDD) and has serious consequences for individuals and families. This study aims to establish a risk prediction model for suicide attempts in MDD patients to make the detection of suicide risk more accurate and effective.

METHODS

A cross-sectional survey, clinical examination, and biochemical indicator tests were performed on 1718 first-episode and drug naïve patients with major depressive disorder. We used Machine Learning to establish a risk prediction model for suicide attempts in FEDN patients with MDD.

RESULTS

Five predictors were identified by LASSO regression analysis from a total of 20 variables studied, namely psychotic symptoms, anxiety symptoms, thyroid peroxidase antibodies (ATPO), total cholesterol (TC), and high-density lipoprotein-cholesterol (HDL-C). The model constructed using the five predictors displayed moderate predictive ability, with an area under the ROC of 0.771 in the training set and 0.720 in the validation set. The DCA curve showed that the nomogram could be applied clinically if the risk threshold was between 22 % and 60 %. The risk threshold was found to be between 20 % and 60 % in external validation.

CONCLUSION

Introducing psychotic symptoms, anxiety symptoms, ATPO, TC, and HDL-C to the risk nomogram increased its usefulness for predicting suicide risk in patients with MDD. It may be useful in clinical decision-making or in discussions with patients, especially in crisis interventions.

Benchmarking different docking protocols for predicting the binding poses of ligands complexed with cyclooxygenase enzymes and screening chemical libraries

Introduction

Non-steroidal anti-inflammatory drugs (NSAIDs) constitute an important class of pharmaceuticals acting on cyclooxygenase COX-1 and COX-2 enzymes. Due to their numerous severe side effects, it is necessary to search for new selective, safe, and effective anti-inflammatory drugs. In silico design of novel therapeutics plays an important role in nowadays drug discovery pipelines. In most cases, the design strategies require the use of molecular docking calculations. The docking procedure may require case-specific condition for a successful result. Additionally, many different docking programs are available, which highlights the importance of identifying the most proper docking method and condition for a given problem.

Methods

In the current work, the performances of five popular molecular docking programs, namely, GOLD, AutoDock, FlexX, Molegro Virtual Docker (MVD) and Glide to predict the binding mode of co- crystallized inhibitors in the structures of known complexes available for cyclooxygenases were evaluated. Furthermore, the best performers, Glide, AutoDock, GOLD and FlexX, were further evaluated in docking-based virtual screening of libraries consisted of active ligands and decoy molecules for cyclooxygenase enzymes and the obtained docking scores were assessed by receiver operating characteristics (ROC) analysis.

Results

The results of docking experiments indicated that Glide program outperformed other docking programs by correctly predicting the binding poses (RMSD less than 2 Å) of all studied co-crystallized ligands of COX-1 and COX-2 enzymes (i.e., the performance was 100%). However, the performances of the other studied docking methods for correctly predicting the binding poses of the ligands were between 59% to 82%. Virtual screening results treated by ROC analysis revealed that all tested methods are useful tools for classification and enrichment of molecules targeting COX enzymes. The obtained AUCs range between 0.61-0.92 with enrichment factors of 8 - 40 folds.

Conclusion

The obtained results support the importance of choosing appropriate docking method for predicting ligand-receptor binding modes, and provide specific information about docking calculations on COXs ligands.

Establishment of hypertension risk nomograms based on physical fitness parameters for men and women: a cross-sectional study

Objective

This study aims to establish hypertension risk nomograms for Chinese male and female adults, respectively.

Method

A series of questionnaire surveys, physical assessments, and biochemical indicator tests were performed on 18,367 adult participants in China. The optimization of variable selection was conducted by running cyclic coordinate descent with 10-fold cross-validation through the least absolute shrinkage and selection operator (LASSO) regression. The nomograms were built by including the predictors selected through multivariable logistic regression. Calibration plots, receiver operating characteristic curves (ROC), decision curve analysis (DCA), clinical impact curves (CIC), and net reduction curve plots (NRC) were used to validate the models.

Results

Out of a total of 18 variables, 5 predictors-namely age, body mass index, waistline, hipline, and resting heart rate-were identified for the hypertension risk predictive model for men with an area under the ROC of 0.693 in the training set and 0.707 in the validation set. Seven predictors-namely age, body mass index, body weight, cardiovascular disease history, waistline, resting heart rate, and daily activity level-were identified for the hypertension risk predictive model for women with an area under the ROC of 0.720 in the training set and 0.748 in the validation set. The nomograms for both men and women were externally well-validated.

Conclusion

Gender differences may induce heterogeneity in hypertension risk prediction between men and women. Besides basic demographic and anthropometric parameters, information related to the functional status of the cardiovascular system and physical activity appears to be necessary.

Multimodal data-driven prognostic model for predicting new-onset ST-elevation myocardial infarction following emergency percutaneous coronary intervention

OBJECTIVES

We developed a nomogram model derived from inflammatory indices, clinical data, and imaging data to predict in-hospital major adverse cardiac and cerebrovascular events (MACCEs) following emergency percutaneous coronary intervention (PCI) in patients with new-onset ST-elevation myocardial infarction (STEMI).

METHODS

Patients with new-onset STEMI admitted between June 2020 and November 2022 were retrospectively reviewed. Data pertaining to coronary angiograms, clinical data, biochemical indices, and in-hospital clinical outcomes were derived from electronic medical records. Lasso regression model was employed to screen risk factors and construct a prediction model.

RESULTS

Overall, 547 patients with new-onset STEMI who underwent PCI were included and assigned to the training cohort (n = 384) and independent verification cohort (n = 163). Six clinical features (age, diabetes mellitus, current smoking, hyperuricemia, neutrophil-to-lymphocyte ratio, and Gensini score) were selected by LASSO regression to construct a nomogram to predict the risk of in-hospital MACCEs. The area-under-the-curve (AUC) values for in-hospital MACCEs risk in the training and independent verification cohorts were 0.921 (95% CI 0.881-0.961) and 0.898 (95% CI 0.821-0.976), respectively. It was adequately calibrated in both training cohort and independent verification cohorts, and predictions were correlated with actual outcomes. Decision curve analysis demonstrated that the nomogram was capable of predicting in-hospital MACCEs with good clinical benefit.

CONCLUSIONS

Our prediction nomogram based on multi-modal data (inflammatory indices, clinical and imaging data) reliably predicted in-hospital MACCEs in new-onset STEMI patients with emergency PCI. This prediction nomogram can enable individualized treatment strategies.

A Nomogram for Predicting Surgical Timing in Neonates with Necrotizing Enterocolitis

OBJECTIVE

To explore the surgical risk variables in patients with necrotizing enterocolitis (NEC) and develop a nomogram model for predicting the surgical intervention timing of NEC.

METHODS

Infants diagnosed with NEC were enrolled in our study. We gathered information from clinical data, laboratory examinations, and radiological manifestations. Using LASSO (least absolute shrinkage and selection operator) regression analysis and multivariate logistic regression analysis, a clinical prediction model based on the logistic nomogram was developed. The performance of the nomogram model was evaluated using the receiver operating characteristic (ROC) curve, calibration curves, and decision curve analysis (DCA).

RESULTS

A surgical intervention risk nomogram based on hypothermia, absent bowel sounds, WBC > 20 × 10⁹/L or < 5 × 10⁹/L, CRP > 50 mg/L, pneumatosis intestinalis, and ascites was practical, had a moderate predictive value (AUC > 0.8), improved calibration, and enhanced clinical benefit.

CONCLUSIONS

This simple and reliable clinical prediction nomogram model can help physicians evaluate children with NEC in a fast and effective manner, enabling the early identification and diagnosis of children at risk for surgery. It offers clinical revolutionary value for the development of medical or surgical treatment plans for children with NEC.

Virtual Screening Strategy to Identify Retinoic Acid-Related Orphan Receptor γt Modulators

Molecular docking is a key method used in virtual screening (VS) campaigns to identify small-molecule ligands for drug discovery targets. While docking provides a tangible way to understand and predict the protein-ligand complex formation, the docking algorithms are often unable to separate active ligands from inactive molecules in practical VS usage. Here, a novel docking and shape-focused pharmacophore VS protocol is demonstrated for facilitating effective hit discovery using retinoic acid receptor-related orphan receptor gamma t (RORγt) as a case study. RORγt is a prospective target for treating inflammatory diseases such as psoriasis and multiple sclerosis. First, a commercial molecular database was flexibly docked. Second, the alternative docking poses were rescored against the shape/electrostatic potential of negative image-based (NIB) models that mirror the target's binding cavity. The compositions of the NIB models were optimized via iterative trimming and benchmarking using a greedy search-driven algorithm or brute force NIB optimization. Third, a pharmacophore point-based filtering was performed to focus the hit identification on the known RORγt activity hotspots. Fourth, free energy binding affinity evaluation was performed on the remaining molecules. Finally, twenty-eight compounds were selected for in vitro testing and eight compounds were determined to be low μM range RORγt inhibitors, thereby showing that the introduced VS protocol generated an effective hit rate of ~29%.

Discovery of octahydropyrrolo [3,2-b] pyridin derivative as a highly selective Type I inhibitor of FGFR3 over VEGFR2 by high-throughput virtual screening

Although the aberrant activity of fibroblast growth factor receptor 3 (FGFR3) is implicated in various cancers, the reported kinase inhibitors of FGFR3 tend to cause side effects resulting from the inhibitory activity on vascular endothelial growth factor receptor 2 (VEGFR2). Therefore, it is necessary to find a novel high-selective inhibitor of FGFR3 over VEGFR2 from the small-molecule compound database. In this study, integrated virtual screening protocols were established to screen for selective inhibitors of FGFR3 over VEGFR2 in Drugbank and Asinex databases by combining three-dimensional pharmacophore model, molecular docking, molecular dynamics (MD) simulation, and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations. Finally, it is found that Asinex-5082, as an octahydropyrrolo[3,2-b] pyridin derivative, has larger binding free energy with FGFR3 (-39.3 kcal/mol) than reference drug Erdafitinib (-29.9 kcal/mol), while cannot bind with VEGFR2, resulting in considerable inhibitory selectivity. This is because Asinex-5082, unlike Erdafitinib, has not m-dimethoxybenzene with large steric hindrance, thus can enter the larger ATP-binding pocket of FGFR3 with DFG-in conformation to form hydrophobic interaction with residues Met529, Ile539, and Tyr557 as well as hydrogen bond with Ala558. On the other hand, due to the fact that the benzodioxane and N-heterocyclic rings are connected by carbonyl (C=O), Asinex-5082 cannot rotate freely so as to enter the smaller ATP binding pocket of VEGFR2 on the DFG-out conformation. The lead molecule Asinex-5082 may facilitate the rational design and development of novel selective inhibitors of FGFR3 over VEGFR2 as anticancer drugs.

Protein Homology Modeling for Effective Drug Design

The effective drug design, especially for combating the multi-drug-resistant bacterial pathogens, requires more and more sophisticated procedures to obtain novel lead-like compounds. New classes of enzymes should be explored, especially those that help bacteria overcome existing treatments. The homology modeling is useful in obtaining the models of new enzymes; however, the active sites of them are sometimes present in closed conformations in the crystal structures, not suitable for drug design purposes. In such difficult cases, the combination of homology modeling, molecular dynamics simulations, and fragment screening can give satisfactory results.

Prediction of major adverse cardiovascular events in patients with acute coronary syndrome: Development and validation of a non-invasive nomogram model based on autonomic nervous system assessment

BACKGROUND

Disruption of the autonomic nervous system (ANS) can lead to acute coronary syndrome (ACS). We developed a nomogram model using heart rate variability (HRV) and other data to predict major adverse cardiovascular events (MACEs) following emergency coronary angiography in patients with ACS.

METHODS

ACS patients admitted from January 2018 to June 2020 were examined. Holter monitors were used to collect HRV data for 24 h. Coronary angiograms, clinical data, and MACEs were recorded. A nomogram was developed using the results of Cox regression analysis.

RESULTS

There were 439 patients in a development cohort and 241 in a validation cohort, and the mean follow-up time was 22.80 months. The nomogram considered low-frequency/high-frequency ratio, age, diabetes, previous myocardial infarction, and current smoking. The area-under-the-curve (AUC) values for 1-year MACE-free survival were 0.790 (95% CI: 0.702-0.877) in the development cohort and 0.894 (95% CI: 0.820-0.967) in the external validation cohort. The AUCs for 2-year MACE-free survival were 0.802 (95% CI: 0.739-0.866) in the development cohort and 0.798 (95% CI: 0.693-0.902) in the external validation cohort. Development and validation were adequately calibrated and their predictions correlated with the observed outcome. Decision curve analysis (DCA) showed the model had good discriminative ability in predicting MACEs.

CONCLUSION

Our validated nomogram was based on non-invasive ANS assessment and traditional risk factors, and indicated reliable prediction of MACEs in patients with ACS. This approach has potential for use as a method for non-invasive monitoring of health that enables provision of individualized treatment strategies.

Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening

Human carbonic anhydrase VII (hCA VII) constitutes a promising molecular target for the treatment of epileptic seizures and other central nervous system disorders due to its almost exclusive expression in neurons. Achieving isoform selectivity is one of the main challenges for the discovery of new hCA inhibitors, since nonspecific inhibition may lead to tolerance and side effects. In the present work, we report the development of a molecular docking protocol based on AutoDock4_Zn for the search of new hCA VII inhibitors by virtual screening. The docking protocol was applied to the screening of two sets of compounds: a ZINC15 subset of sulfur-containing structures and an in-house library consisting of synthetic and commercial candidates (including approved drugs). Five compounds were selected from the first screening campaign and three from the second one, and they were tested in vitro against the enzyme. Among the eight selected structures, four showed K_i values in the low nanomolar range. These confirmed hits include three approved drugs: meloxicam, piroxicam, and nitrofurantoin, which also showed good selectivity for hCA VII versus hCA II.

Identification of Potential Insect Growth Inhibitor against Aedes aegypti: A Bioinformatics Approach

Aedes aegypti is the main vector that transmits viral diseases such as dengue, hemorrhagic dengue, urban yellow fever, zika, and chikungunya. Worldwide, many cases of dengue have been reported in recent years, showing significant growth. The best way to manage diseases transmitted by Aedes aegypti is to control the vector with insecticides, which have already been shown to be toxic to humans; moreover, insects have developed resistance. Thus, the development of new insecticides is considered an emergency. One way to achieve this goal is to apply computational methods based on ligands and target information. In this study, sixteen compounds with acceptable insecticidal activities, with 100% larvicidal activity at low concentrations (2.0 to 0.001 mg·L−1), were selected from the literature. These compounds were used to build up and validate pharmacophore models. Pharmacophore model 6 (AUC = 0.78; BEDROC = 0.6) was used to filter 4793 compounds from the subset of lead-like compounds from the ZINC database; 4142 compounds (dG < 0 kcal/mol) were then aligned to the active site of the juvenile hormone receptor Aedes aegypti (PDB: 5V13), 2240 compounds (LE < −0.40 kcal/mol) were prioritized for molecular docking from the construction of a chitin deacetylase model of Aedes aegypti by the homology modeling of the Bombyx mori species (PDB: 5ZNT), which aligned 1959 compounds (dG < 0 kcal/mol), and 20 compounds (LE < −0.4 kcal/mol) were predicted for pharmacokinetic and toxicological prediction in silico (Preadmet, SwissADMET, and eMolTox programs). Finally, the theoretical routes of compounds M01, M02, M03, M04, and M05 were proposed. Compounds M01−M05 were selected, showing significant differences in pharmacokinetic and toxicological parameters in relation to positive controls and interaction with catalytic residues among key protein sites reported in the literature. For this reason, the molecules investigated here are dual inhibitors of the enzymes chitin synthase and juvenile hormonal protein from insects and humans, characterizing them as potential insecticides against the Aedes aegypti mosquito.

SCORCH: Improving structure-based virtual screening with machine learning classifiers, data augmentation, and uncertainty estimation

INTRODUCTION

The discovery of a new drug is a costly and lengthy endeavour. The computational prediction of which small molecules can bind to a protein target can accelerate this process if the predictions are fast and accurate enough. Recent machine-learning scoring functions re-evaluate the output of molecular docking to achieve more accurate predictions. However, previous scoring functions were trained on crystalised protein-ligand complexes and datasets of decoys. The limited availability of crystal structures and biases in the decoy datasets can lower the performance of scoring functions.

OBJECTIVES

To address key limitations of previous scoring functions and thus improve the predictive performance of structure-based virtual screening.

METHODS

A novel machine-learning scoring function was created, named SCORCH (Scoring COnsensus for RMSD-based Classification of Hits). To develop SCORCH, training data is augmented by considering multiple ligand poses and labelling poses based on their RMSD from the native pose. Decoy bias is addressed by generating property-matched decoys for each ligand and using the same methodology for preparing and docking decoys and ligands. A consensus of 3 different machine learning approaches is also used to improve performance.

RESULTS

We find that multi-pose augmentation in SCORCH improves its docking power and screening power on independent benchmark datasets. SCORCH outperforms an equivalent scoring function trained on single poses, with a 1% enrichment factor (EF) of 13.78 vs. 10.86 on 18 DEKOIS 2.0 targets and a mean native pose rank of 5.9 vs 30.4 on CSAR 2014. Additionally, SCORCH outperforms widely used scoring functions in virtual screening and pose prediction on independent benchmark datasets.

CONCLUSION

By rationally addressing key limitations of previous scoring functions, SCORCH improves the performance of virtual screening. SCORCH also provides an estimate of its uncertainty, which can help reduce the cost and time required for drug discovery.

Ligand-Enhanced Negative Images Optimized for Docking Rescoring

Despite the pivotal role of molecular docking in modern drug discovery, the default docking scoring functions often fail to recognize active ligands in virtual screening campaigns. Negative image-based rescoring improves docking enrichment by comparing the shape/electrostatic potential (ESP) of the flexible docking poses against the target protein’s inverted cavity volume. By optimizing these negative image-based (NIB) models using a greedy search, the docking rescoring yield can be improved massively and consistently. Here, a fundamental modification is implemented to this shape-focused pharmacophore modelling approach—actual ligand 3D coordinates are incorporated into the NIB models for the optimization. This hybrid approach, labelled as ligand-enhanced brute-force negative image-based optimization (LBR-NiB), takes the best from both worlds, i.e., the all-roundedness of the NIB models and the difficult to emulate atomic arrangements of actual protein-bound small-molecule ligands. Thorough benchmarking, focused on proinflammatory targets, shows that the LBR-NiB routinely improves the docking enrichment over prior iterations of the R-NiB methodology. This boost can be massive, if the added ligand information provides truly essential binding information that was lacking or completely missing from the cavity-based NIB model. On a practical level, the results indicate that the LBR-NiB typically works well when the added ligand 3D data originates from a high-quality source, such as X-ray crystallography, and, yet, the NIB model compositions can also sometimes be improved by fusing into them, for example, with flexibly docked solvent molecules. In short, the study demonstrates that the protein-bound ligands can be used to improve the shape/ESP features of the negative images for effective docking rescoring use in virtual screening.

Novel Insights into the Predictors of Obstructive Sleep Apnea Syndrome in Patients with Chronic Coronary Syndrome: Development of a Predicting Model

Background

Obstructive sleep apnea syndrome (OSAS) is common in patients with chronic coronary syndrome (CCS); however, a predictive model of OSAS in patients with CCS remains rarely reported. The study aimed to construct a novel nomogram scoring system to predict OSAS comorbidity in patients with CCS.

Methods

Consecutive CCS patients scheduled for sleep monitoring at our hospital from January 2019 to September 2020 were enrolled in the current study. Coronary CT angiography or coronary angiography was used for the diagnosis of CCS, and clinical characteristics of the patients were collected. Significant predictors for OSAS in patients with moderate/severe CCS were estimated via logistic regression analysis, and a clinical nomogram was constructed. A calibration plot, examining discrimination (Harrell's concordance index) and decision curve analysis (DCA), was applied to validate the nomogram's predictive performance. Internal validity of the predictive model was assessed using bootstrapping (1000 replications).

Results

The nomograms were constructed based on available clinical variables from 527 patients which were significantly associated with moderate/severe OSAS in patients with CCS, including body mass index, impaired glucose tolerance, hypertension, diabetes mellitus, nonalcoholic fatty liver disease, and routine laboratory indices such as neutrophil to lymphocyte ratio, platelet-to-lymphocyte ratio, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol. The C-index (0.793) and AUC (0.771, 95% CI: 0.731–0.811) demonstrated a favorable discriminative ability of the nomogram. Moreover, calibration plots revealed consistency between moderate/severe OSAS predicted by the nomogram and validated by the results of sleep monitoring. Clinically, DCA showed that the nomogram had good discriminative ability to predict moderate/severe OSAS in patients with CCS.

Conclusions

The risk nomogram constructed via the routinely available clinical variables in patients with CCS showed satisfying discriminative ability to predict comorbid moderate/severe OSAS, which may be useful for identification of high-risk patients with OSAS in patients with CCS.

Virtual screening of natural products against 5-enolpyruvylshikimate-3-phosphate synthase using the Anagreen herbicide-like natural compound library

The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a reaction involved in the production of amino acids essential for plant growth and survival. EPSPS is the main target of glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor concerning phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. In the present study, we introduce a natural compound library, named Anagreen, which is a compendium of herbicide-like compounds obtained from different natural product databases. Herein, we combined the structure- and ligand-based virtual screening strategies to explore Anagreen against EPSPS using the structure of glyphosate complexed with a T102I/P106S mutant of EPSPS from Eleusine indica (EiEPSPS) as a starting point. First, ligand-based pharmacophore screening was performed to select compounds with a similar pharmacophore to glyphosate. Then, structure-based pharmacophore modeling was applied to build a model which represents the molecular features of glyphosate. Then, consensus docking was performed to rank the best poses of the natural compounds against the PEP binding site, and then molecular dynamics simulations were performed to analyze the stability of EPSPS complexed with the selected ligands. Finally, we have investigated the binding affinity of the complexes using free energy calculations. The selected hit compound, namely AG332841, showed a stable conformation and binding affinity to the EPSPS structure and showed no structural similarity to the already known weed EPSPS inhibitors. Our computational study aims to clarify the inhibition of the mutant EiEPSPS, which is resistant to glyphosate, and identify new potential herbicides from natural products.

Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA

The recent availability of large numbers of GPCR crystal structures has provided an unprecedented opportunity to evaluate their performance in virtual screening protocols using established benchmarking datasets. In this study, we evaluated the ability of MM/GBSA in consensus scoring-based virtual screening enrichment together with nine classical scoring functions, using the GPCR-Bench dataset consisting of 24 GPCR crystal structures and 254,646 actives and decoys. While the performance of consensus scoring was modest overall, combinations which included MM/GBSA performed relatively well compared to combinations of classical scoring functions. Combinations of MM/GBSA and good-performing scoring functions provided the highest proportion of improvements, with improvements observed in 32% and 19% of all combinations across all targets at the EF_1% and EF_5% levels respectively. Combinations of MM/GBSA and poor-performing scoring functions still outperformed classical scoring functions, with improvements observed in 26% and 17% of all combinations at the EF_1% and EF_5% levels. In comparison, only 14-22% and 6-11% of combinations of classical scoring functions produced improvements at EF_1% and EF_5% respectively. Efforts to improve performance by increasing the number of scoring functions in consensus scoring to three were mostly ineffective. We also observed that consensus scoring performed better for individual scoring functions possessing initially low enrichment factors, potentially implying their benefits are more relevant in such scenarios. Overall, this study demonstrated the first implementation of MM/GBSA in consensus scoring using the GPCR-Bench dataset and could provide a valuable benchmark of the performance of MM/GBSA in comparison to classical scoring functions in consensus scoring for GPCRs.

Development and Validation of a Model That Predicts the Risk of Diabetic Nephropathy in Type 2 Diabetes Mellitus Patients: A Cross-Sectional Study

Purpose

To develop a nomogram model that predicts the risk of diabetic nephropathy (DN) incidence in type 2 diabetes mellitus (T2DM) patients.

Methods

We collect information from electronic medical record systems. The data were split into a training set (n=521) containing 73.8% of patients and a validation set (n=185) holding the remaining 26.2% of patients based on the date of data collection. Stepwise and multivariable logistic regression analyses were used to screen out DN risk factors. A predictive model including selected risk factors was developed by logistic regression analysis. The results of binary logistic regression are presented through forest plots and nomogram. Lastly, the c-index, calibration plots, and receiver operating characteristic (ROC) curves were used to assess the accuracy of the nomogram in internal and external validation. The clinical benefit of the model was evaluated by decision curve analysis.

Results

Predictors included serum creatinine (Scr), hypertension, glycosylated hemoglobin A1c (HbA1c), blood urea nitrogen (BUN), body mass index (BMI), triglycerides (TG), and Diabetic peripheral neuropathy (DPN). Harrell’s C-indexes were 0.773 (95% CI:0.726–0.821) and 0.758 (95% CI:0.679–0.837) in the training and validation sets, respectively. Decision curve analysis (DCA) demonstrated that the novel nomogram was clinically valuable.

Conclusion

Our simple nomogram with seven factors may help clinicians predict the risk of DN incidence in patients with T2DM.

Optimization of Cavity-Based Negative Images to Boost Docking Enrichment in Virtual Screening

Molecular docking is a key in silico method used routinely in modern drug discovery projects. Although docking provides high-quality ligand binding predictions, it regularly fails to separate the active compounds from the inactive ones. In negative image-based rescoring (R-NiB), the shape/electrostatic potential (ESP) of docking poses is compared to the negative image of the protein's ligand binding cavity. While R-NiB often improves the docking yield considerably, the cavity-based models do not reach their full potential without expert editing. Accordingly, a greedy search-driven methodology, brute force negative image-based optimization (BR-NiB), is presented for optimizing the models via iterative editing and benchmarking. Thorough and unbiased training, testing and stringent validation with a multitude of drug targets, and alternative docking software show that BR-NiB ensures excellent docking efficacy. BR-NiB can be considered as a new type of shape-focused pharmacophore modeling, where the optimized models contain only the most vital cavity information needed for effectively filtering docked actives from the inactive or decoy compounds. Finally, the BR-NiB code for performing the automated optimization is provided free-of-charge under MIT license via GitHub (https://github.com/jvlehtonen/brutenib) for boosting the success rates of docking-based virtual screening campaigns.

Evaluation of Docking Machine Learning and Molecular Dynamics Methodologies for DNA-Ligand Systems

DNA is a molecular target for the treatment of several diseases, including cancer, but there are few docking methodologies exploring the interactions between nucleic acids with DNA intercalating agents. Different docking methodologies, such as AutoDock Vina, DOCK 6, and Consensus, implemented into Molecular Architect (MolAr), were evaluated for their ability to analyze those interactions, considering visual inspection, redocking, and ROC curve. Ligands were refined by Parametric Method 7 (PM7), and ligands and decoys were docked into the minor DNA groove (PDB code: 1VZK). As a result, the area under the ROC curve (AUC-ROC) was 0.98, 0.88, and 0.99 for AutoDock Vina, DOCK 6, and Consensus methodologies, respectively. In addition, we proposed a machine learning model to determine the experimental ∆T_m value, which found a 0.84 R² score. Finally, the selected ligands mono imidazole lexitropsin (42), netropsin (45), and N,N′-(1H-pyrrole-2,5-diyldi-4,1-phenylene)dibenzenecarboximidamide (51) were submitted to Molecular Dynamic Simulations (MD) through NAMD software to evaluate their equilibrium binding pose into the groove. In conclusion, the use of MolAr improves the docking results obtained with other methodologies, is a suitable methodology to use in the DNA system and was proven to be a valuable tool to estimate the ∆T_m experimental values of DNA intercalating agents.

Novel nomogram for predicting the 3-year incidence risk of osteoporosis in a Chinese male population

OBJECTIVE

To establish a rapid, cost-effective, accurate, and acceptable osteoporosis (OP) screening model for the Chinese male population (age ≥ 40 years) based on data mining technology.

MATERIALS AND METHODS

This was a 3-year retrospective cohort study, which belonged to the sub-cohort of the Chinese Reaction Study. The research period was from March 2011 to December 2014. A total of 1834 subjects who did not have OP at the baseline and completed a 3-year follow-up were included in this study. All subjects underwent quantitative ultrasound examinations for calcaneus at the baseline and follow-ups that lasted for 3 years. We utilized the least absolute shrinkage and selection operator (LASSO) regression model to select feature variables. The characteristic variables selected in the LASSO regression were analyzed by multivariable logistic regression (MLR) to construct the predictive model. This predictive model was displayed through a nomogram. We used the receiver operating characteristic (ROC) curve, C-index, calibration curve, and clinical decision curve analysis (DCA) to evaluate model performance and the bootstrapping validation to internally validate the model.

RESULTS

The predictive factors included in the prediction model were age, neck circumference, waist-to-height ratio, BMI, triglyceride, impaired fasting glucose, dyslipidemia, osteopenia, smoking history, and strenuous exercise. The area under the ROC (AUC) curve of the risk nomogram was 0.882 (95% CI, 0.858-0.907), exhibiting good predictive ability and performance. The C-index for the risk nomogram was 0.882 in the prediction model, which presented good refinement. In addition, the nomogram calibration curve indicated that the prediction model was consistent. The DCA showed that when the threshold probability was between 1 and 100%, the nomogram had a good clinical application value. More importantly, the internally verified C-index of the nomogram was still very high, at 0.870.

CONCLUSIONS

This novel nomogram can effectively predict the 3-year incidence risk of OP in the male population. It also helps clinicians to identify groups at high risk of OP early and formulate personalized intervention measures.

Ensemble learning application to discover new trypanothione synthetase inhibitors

Trypanosomatid-caused diseases are among the neglected infectious diseases with the highest disease burden, affecting about 27 million people worldwide and, in particular, socio-economically vulnerable populations. Trypanothione synthetase (TryS) is considered one of the most attractive drug targets within the thiol-polyamine metabolism of typanosomatids, being unique, essential and druggable. Here, we have compiled a dataset of 401 T. brucei TryS inhibitors that includes compounds with inhibitory data reported in the literature, but also in-house acquired data. QSAR classifiers were derived and validated from such dataset, using publicly available and open-source software, thus assuring the portability of the obtained models. The performance and robustness of the resulting models were substantially improved through ensemble learning. The performance of the individual models and the model ensembles was further assessed through retrospective virtual screening campaigns. At last, as an application example, the chosen model-ensemble has been applied in a prospective virtual screening campaign on DrugBank 5.1.6 compound library. All the in-house scripts used in this study are available on request, whereas the dataset has been included as supplementary material.

Combination of consensus and ensemble docking strategies for the discovery of human dihydroorotate dehydrogenase inhibitors

The inconsistencies in the performance of the virtual screening (VS) process, depending on the used software and structural conformation of the protein, is a challenging issue in the drug design and discovery field. Varying performance, especially in terms of early recognition of the potential hit compounds, negatively affects the whole process and leads to unnecessary waste of the time and resources. Appropriate application of the ensemble docking and consensus-scoring approaches can significantly increase reliability of the VS results. Dihydroorotate dehydrogenase (DHODH) is a key enzyme in the pyrimidine biosynthesis pathway. It is considered as a valuable therapeutic target in cancer, autoimmune and viral diseases. Based on the conducted benchmark study and analysis of the effect of different combinations of the applied methods and approaches, here we suggested a structure-based virtual screening (SBVS) workflow that can be used to increase the reliability of VS.

Improving virtual screening results with MM/GBSA and MM/PBSA rescoring

Virtual screening (VS) based on molecular docking is one of the most useful methods in computer-aided drug design. By allowing to identify computationally putative ligands binding to the proteins of interest, VS dramatically reduces the time and expense of the development of novel therapeutics. Among the limitations of the VS approaches is the low accuracy of scoring functions implemented in docking methods for assessing binding affinity. Many such scoring functions are developed for rapid, high-throughput evaluation of binding energy of multiple conformations generated by a searching algorithm. The methods for more rigorous calculation of binding affinity calculation are generally time-consuming. Even so, in many studies more accurate methods were used for rescoring of the final poses and false-positive hits evaluation. We performed VS for three benchmark sets and used energy minimization with MM/PB(GB)SA methods (molecular mechanics energies combined with the Poisson-Boltzmann or generalized Born and surface area) to rescore binding affinities. The comparison of the area under the curve (AUC), enrichment factor (EF), and Boltzmann-enhanced discrimination of receiver operating characteristics (BEDROC) showed essential improvements in the binding energy prediction after the rescoring. Finally, we provide a program for minimization and rescoring VS results based on freely available AmberTools. The code requires just the final binding poses of the ligand as the input and can be used with any docking program.

Structure-based design of small molecule and peptide inhibitors for selective targeting of ROCK1: an integrative computational approach

Rho-associated, coiled-coil-containing protein kinase (ROCK1) regulates cell contraction, morphology, and motility by phosphorylating its downstream targets. ROCK1 is a proven target for many pathological conditions like cancer, atherosclerosis, glaucoma, neuro-degeneration, etc. Though many kinase inhibitors are available, there is a dearth of studies on repurposing approved drugs and novel peptide inhibitors that could potentially target ROCK1. Hence, in this study, an extensive integration of open-source pipelines was employed to probe the potential inhibitors (ligand/peptide) for targeting ROCK1. To start with, a systematic enrichment analysis was performed to delineate the most optimal ROCK1 crystal structure that can be harnessed for drug design. A comparative analysis of conformational flexibility between monomeric and dimeric forms was also performed to prioritize the optimal assembly for structural studies. Subsequently, Virtual screening of FDA-approved drugs in Drugbank was performed using POAP pipeline. Further, the top hits were probed for binding affinity, crucial interaction fingerprints, and complex stability during MD simulation. In parallel, a combinatorial tetrapeptide library was also virtually screened against ROCK1 using the PepVis pipeline. Following which, all these shortlisted inhibitors (compounds/peptides) were subjected to Kinomerun analysis to infer other potential kinase targets. Finally, Polydatin and conivaptan were prioritized as the most potential repurposable inhibitors, and WWWF, WWVW as potential inhibitory peptides for targeting ROCK1. The prioritized inhibitors are highly promising for use in therapeutics, as these are resultants of the multilevel stringent filtration process. The computational strategies implemented in this study could potentially serve as a scaffold towards selective inhibitor design for other kinases.Communicated by Ramaswamy H. Sarma.

New machine learning and physics-based scoring functions for drug discovery

Scoring functions are essential for modern in silico drug discovery. However, the accurate prediction of binding affinity by scoring functions remains a challenging task. The performance of scoring functions is very heterogeneous across different target classes. Scoring functions based on precise physics-based descriptors better representing protein–ligand recognition process are strongly needed. We developed a set of new empirical scoring functions, named DockTScore, by explicitly accounting for physics-based terms combined with machine learning. Target-specific scoring functions were developed for two important drug targets, proteases and protein–protein interactions, representing an original class of molecules for drug discovery. Multiple linear regression (MLR), support vector machine and random forest algorithms were employed to derive general and target-specific scoring functions involving optimized MMFF94S force-field terms, solvation and lipophilic interactions terms, and an improved term accounting for ligand torsional entropy contribution to ligand binding. DockTScore scoring functions demonstrated to be competitive with the current best-evaluated scoring functions in terms of binding energy prediction and ranking on four DUD-E datasets and will be useful for in silico drug design for diverse proteins as well as for specific targets such as proteases and protein–protein interactions. Currently, the MLR DockTScore is available at www.dockthor.lncc.br.

A recursive molecular docking coupled with energy-based pose-rescoring and MD simulations to identify hsGC βH-NOX allosteric modulators for cardiovascular dysfunctions

Modulating the activity of human soluble guanylate cyclase (hsGC) through allosteric regulation of the βH-NOX domain has been considered as an immediate treatment for cardiovascular disorder (CVDs). Currently available βH-NOX domain-specific agonists including cinaciguat are unable to deal with the conundrum raised due to oxidative stress in the case of CVDs and their associated comorbidities. Therefore, the idea of investigating novel compounds for allosteric regulation of hsGC activation has been rekindled to circumvent CVDs. Current study aims to identify novel βH-NOX domain-specific compounds that can selectively turn on sGC functions by modulating the conformational dynamics of the target protein. Through a comprehensive computational drug-discovery approach, we first executed a target-based performance assessment of multiple docking (PLANTS, QVina, LeDock, Vinardo, Smina) scoring functions based on multiple performance metrices. QVina showed the highest capability of selecting true-positive ligands over false positives thus, used to screen 4.8 million ZINC15 compounds against βH-NOX domain. The docked ligands were further probed in terms of contact footprint and pose reassessment through clustering analysis and PLANTS docking, respectively. Subsequently, energy-based AMBER rescoring of top 100 low-energy complexes, per-residue energy decomposition analysis, and ADME-Tox analysis yielded the top three compounds i.e. ZINC000098973660, ZINC001354120371, and ZINC000096022607. The impact of three selected ligands on the internal structural dynamics of the βH-NOX domain was also investigated through molecular dynamics simulations. The study revealed potential electrostatic interactions for better conformational dialogue between βH-NOX domain and allosteric ligands that are critical for the activation of hsGC as compared to the reference compound.

Property-Unmatched Decoys in Docking Benchmarks

Enrichment of ligands versus property-matched decoys is widely used to test and optimize docking library screens. However, the unconstrained optimization of enrichment alone can mislead, leading to false confidence in prospective performance. This can arise by over-optimizing for enrichment against property-matched decoys, without considering the full spectrum of molecules to be found in a true large library screen. Adding decoys representing charge extrema helps mitigate over-optimizing for electrostatic interactions. Adding decoys that represent the overall characteristics of the library to be docked allows one to sample molecules not represented by ligands and property-matched decoys but that one will encounter in a prospective screen. An optimized version of the DUD-E set (DUDE-Z), as well as Extrema and sets representing broad features of the library (Goldilocks), is developed here. We also explore the variability that one can encounter in enrichment calculations and how that can temper one's confidence in small enrichment differences. The new tools and new decoy sets are freely available at http://tldr.docking.org and http://dudez.docking.org.

Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening

Molecular docking produces often lackluster results in real-life virtual screening assays that aim to discover novel drug candidates or hit compounds. The problem lies in the inability of the default docking scoring to properly estimate the Gibbs free energy of binding, which impairs the recognition of the best binding poses and the separation of active ligands from inactive compounds. Negative image-based rescoring (R-NiB) provides both effective and efficient way for re-ranking the outputted flexible docking poses to improve the virtual screening yield. Importantly, R-NiB has been shown to work with multiple genuine drug targets and six popular docking algorithms using demanding benchmark test sets. The effectiveness of the R-NiB methodology relies on the shape/electrostatics similarity between the target protein's ligand-binding cavity and the docked ligand poses. In this chapter, the R-NiB method is described with practical usability in mind.

The structure-based virtual screening of non-benzofuran inhibitors against M. tuberculosis Pks13-TE for anti-tuberculosis phenotypic discovery

Structure-based virtual screening against M. tuberculosis Pks13-TE was performed for anti-tuberculosis phenotypic discovery.

Negative Image-Based Screening: Rigid Docking Using Cavity Information

Rational drug discovery relies heavily on molecular docking-based virtual screening, which samples flexibly the ligand binding poses against the target protein's structure. The upside of flexible docking is that the geometries of the generated docking poses are adjusted to match the residue alignment inside the target protein's ligand-binding pocket. The downside is that the flexible docking requires plenty of computing resources and, regardless, acquiring a decent level of enrichment typically demands further rescoring or post-processing. Negative image-based screening is a rigid docking technique that is ultrafast and computationally light but also effective as proven by vast benchmarking and screening experiments. In the NIB screening, the target protein cavity's shape/electrostatics is aligned and compared against ab initio-generated ligand 3D conformers. In this chapter, the NIB methodology is explained at the practical level and both its weaknesses and strengths are discussed candidly.

Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets

Fatty acid binding proteins (FABPs) are small intracellular proteins that reversibly bind fatty acids and other hydrophobic ligands. In cestodes, due to their inability to synthesise fatty acids and cholesterol de novo, FABPs, together with other lipid binding proteins, have been proposed as essential, involved in the trafficking and delivery of such lipophilic metabolites. Pharmacological agents that modify specific parasite FABP function may provide control of lipid signalling pathways, inflammatory responses and metabolic regulation that could be of crucial importance for the parasite development and survival. Echinococcus multilocularis and Echinococcus granulosus are, respectively, the causative agents of alveolar and cystic echinococcosis (or hydatidosis). These diseases are included in the World Health Organization's list of priority neglected tropical diseases. Here, we explore the potential of FABPs from cestodes as drug targets. To this end, we have applied a target repurposing approach to identify novel inhibitors of Echinococcus spp. FABPs. An ensemble of computational models was developed and applied in a virtual screening campaign of DrugBank library. 21 hits belonging to the applicability domain of the ensemble models were identified, and 3 of the hits were assayed against purified E. multilocularis FABP, experimentally confirming the model's predictions. Noteworthy, this is to our best knowledge the first report on isolation and purification of such four FABP, for which initial structural and functional characterization is reported here.

Establishment of a Risk Prediction Model for Non-alcoholic Fatty Liver Disease in Type 2 Diabetes

INTRODUCTION

Non-alcoholic fatty liver disease (NAFLD) is becoming more prevalent in patients with type 2 diabetes mellitus (T2DM) and can contribute to serious liver damage in this patient population. The aim of this study was to develop a risk nomogram for NAFLD in a Chinese population with T2DM.

METHODS

A questionnaire survey, physical examination and biochemical indicator testing were performed on 874 patients with T2DM, and the collected data were used to evaluate the risk to develop NAFLD in T2DM patients. The least absolute shrinkage and selection operator (LASSO) regression analysis method was used to optimize variable selection by running cyclic coordinate descent with k-fold (tenfold in this case) cross-validation. Multivariable logistic regression analysis was applied to build a predictive model by introducing the predictors selected from the LASSO regression analysis. The nomogram was developed based on the selected variables visually. A calibration plot, receiver operating characteristic curve (ROC) and decision curve analysis (DCA) were used to validate the model, with further assessment by external validation.

RESULTS

A total of nine predictors, namely sex, age, total cholesterol (TC), body mass index (BMI), waistline, diastolic blood pressure (DBP), serum uric acid (SUA), course of disease and high-density lipoprotein-cholesterol (HDL-C), were identified by LASSO regression analysis from a total of 24 variables studied. The model constructed using these nine predictors displayed medium prediction ability, with an area under the ROC of 0.848 in the training set and 0.809 in the validation set. The DCA curve showed that the nomogram could be applied clinically if the risk threshold was between 48 and 91%, which was found to be between 44 and 82% in the external validation.

CONCLUSION

Introducing sex, age, TC, BMI, waistline, DBP, SUA, course of disease and HDL-C into the risk nomogram increased its usefulness for predicting NAFLD risk in patients with T2DM.

The impact of compound library size on the performance of scoring functions for structure-based virtual screening

Larger training datasets have been shown to improve the accuracy of machine learning (ML)-based scoring functions (SFs) for structure-based virtual screening (SBVS). In addition, massive test sets for SBVS, known as ultra-large compound libraries, have been demonstrated to enable the fast discovery of selective drug leads with low-nanomolar potency. This proof-of-concept was carried out on two targets using a single docking tool along with its SF. It is thus unclear whether this high level of performance would generalise to other targets, docking tools and SFs. We found that screening a larger compound library results in more potent actives being identified in all six additional targets using a different docking tool along with its classical SF. Furthermore, we established that a way to improve the potency of the retrieved molecules further is to rank them with more accurate ML-based SFs (we found this to be true in four of the six targets; the difference was not significant in the remaining two targets). A 3-fold increase in average hit rate across targets was also achieved by the ML-based SFs. Lastly, we observed that classical and ML-based SFs often find different actives, which supports using both types of SFs on those targets.

QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping

An affinity fingerprint is the vector consisting of compound’s affinity or potency against the reference panel of protein targets. Here, we present the QAFFP fingerprint, 440 elements long in silico QSAR-based affinity fingerprint, components of which are predicted by Random Forest regression models trained on bioactivity data from the ChEMBL database. Both real-valued (rv-QAFFP) and binary (b-QAFFP) versions of the QAFFP fingerprint were implemented and their performance in similarity searching, biological activity classification and scaffold hopping was assessed and compared to that of the 1024 bits long Morgan2 fingerprint (the RDKit implementation of the ECFP4 fingerprint). In both similarity searching and biological activity classification, the QAFFP fingerprint yields retrieval rates, measured by AUC (~ 0.65 and ~ 0.70 for similarity searching depending on data sets, and ~ 0.85 for classification) and EF5 (~ 4.67 and ~ 5.82 for similarity searching depending on data sets, and ~ 2.10 for classification), comparable to that of the Morgan2 fingerprint (similarity searching AUC of ~ 0.57 and ~ 0.66, and EF5 of ~ 4.09 and ~ 6.41, depending on data sets, classification AUC of ~ 0.87, and EF5 of ~ 2.16). However, the QAFFP fingerprint outperforms the Morgan2 fingerprint in scaffold hopping as it is able to retrieve 1146 out of existing 1749 scaffolds, while the Morgan2 fingerprint reveals only 864 scaffolds.

Identification of novel antiplasmodial compound by hierarquical virtual screening and in vitro assays

Malaria is an infectious disease caused by protozoa of the genus Plasmodium spp. with approximately 219 million cases in 2017. P. falciparum is main responsible for the most severe form of the disease, cerebral malaria. Despite of public health impacts, chemotherapy against malaria is still limited due to the emergence of drug resistance cases used in monotherapy and combination therapies. Thus, the development of new antimalarial drugs becomes emergency. One way of achieve this goal is to explore essential and/or unique therapeutic targets of the parasite, or at least sufficiently different to ensure selective inhibition. Enoil-ACP reductase (ENR) is a NADH-dependent enzyme responsible for the limiting step of the type II fatty acid biosynthetic pathway (FAS II). Thus, pharmacophore and docking based virtual screening were applied to prioritize molecules for in vitro assays against P. falciparum W2 strain. The application of successive filters at OOCC database (n = 618) resulted in the identification of one molecule (13) (EC₅₀ = 0.098 ± 0.021 μM) with similar biological activity to artemether. The molecule 13 is a typical drug repurposing case due to previous other approved therapeutic uses on Chinese medicine as a non-specific cholinergic antagonist, thus it could be accelerated the drug development process. Additionally, molecular dynamics studies were used to confirm stability of the molecular interactions identified by molecular docking. Thus, representative structures of P. falciparum ENR can be used in a study to propose new derivatives for evaluation of biological activity in vitro and in vivo. Communicated by Ramaswamy H. Sarma.

Structure-Based Virtual Screening: From Classical to Artificial Intelligence

The drug development process is a major challenge in the pharmaceutical industry since it takes a substantial amount of time and money to move through all the phases of developing of a new drug. One extensively used method to minimize the cost and time for the drug development process is computer-aided drug design (CADD). CADD allows better focusing on experiments, which can reduce the time and cost involved in researching new drugs. In this context, structure-based virtual screening (SBVS) is robust and useful and is one of the most promising in silico techniques for drug design. SBVS attempts to predict the best interaction mode between two molecules to form a stable complex, and it uses scoring functions to estimate the force of non-covalent interactions between a ligand and molecular target. Thus, scoring functions are the main reason for the success or failure of SBVS software. Many software programs are used to perform SBVS, and since they use different algorithms, it is possible to obtain different results from different software using the same input. In the last decade, a new technique of SBVS called consensus virtual screening (CVS) has been used in some studies to increase the accuracy of SBVS and to reduce the false positives obtained in these experiments. An indispensable condition to be able to utilize SBVS is the availability of a 3D structure of the target protein. Some virtual databases, such as the Protein Data Bank, have been created to store the 3D structures of molecules. However, sometimes it is not possible to experimentally obtain the 3D structure. In this situation, the homology modeling methodology allows the prediction of the 3D structure of a protein from its amino acid sequence. This review presents an overview of the challenges involved in the use of CADD to perform SBVS, the areas where CADD tools support SBVS, a comparison between the most commonly used tools, and the techniques currently used in an attempt to reduce the time and cost in the drug development process. Finally, the final considerations demonstrate the importance of using SBVS in the drug development process.

Molecular Architect: A User-Friendly Workflow for Virtual Screening

Computer-assisted drug design (CADD) methods have greatly contributed to the development of new drugs. Among CADD methodologies, virtual screening (VS) can enrich the compound collection with molecules that have the desired physicochemical and pharmacophoric characteristics that are needed to become drugs. Many free tools are available for this purpose, but they are difficult to use and do not have a graphical user interface. Furthermore, several free tools must be used to carry out the entire VS process, requiring the user to process the results of one software program so that they can be used in another program, adding a potential source of human error. Moreover, some software programs require knowledge of advanced computational skills, such as programming languages. This context has motivated us to develop Molecular Architect (MolAr). MolAr is a workflow with a simple and intuitive interface that acts in an integrated and automated form to perform the entire VS process, from protein preparation (homology modeling and protonation state) to virtual screening. MolAr carries out VS through AutoDock Vina, DOCK 6, or a consensus of the two. Two case studies were conducted to demonstrate the performance of MolAr. In the first study, the feasibility of using MolAr for DNA-ligand systems was assessed. Both AutoDock Vina and DOCK 6 showed good results in performing VS in DNA-ligand systems. However, the use of consensus virtual screening was able to enrich the results. According to the area under the ROC curve and the enrichment factors, consensus VS was better able to predict the positions of the active ligands. The second case study was performed on 8 targets from the DUD-E database and 10 active ligands for each target. The results demonstrated that using the final ligand conformation provided by AutoDock Vina as an input for DOCK 6 improved the DOCK 6 ROC curves by up to 42% in VS. These case studies demonstrated that MolAr is capable conducting the VS process and is an easy-to-use and effective tool. MolAr is available for download free of charge at http: //www.drugdiscovery.com.br/software/.

Nomogram-Based Prediction of the Risk of Diabetic Retinopathy: A Retrospective Study

OBJECTIVES

This study is aimed at developing a risk nomogram of diabetic retinopathy (DR) in a Chinese population with type 2 diabetes mellitus (T2DM).

METHODS

A questionnaire survey, biochemical indicator examination, and physical examination were performed on 4170 T2DM patients, and the collected data were used to evaluate the DR risk in T2DM patients. By operating R software, firstly, the least absolute shrinkage and selection operator (LASSO) regression analysis was used to optimize variable selection by running cyclic coordinate descent with 10 times K cross-validation. Secondly, multivariable logistic regression analysis was applied to build a predicting model introducing the predictors selected from the LASSO regression analysis. The nomogram was developed based on the selected variables visually. Thirdly, calibration plot, receiver operating characteristic (ROC) curve, and decision curve analysis were used to validate the model, and further assessment was running by external validation.

RESULTS

Seven predictors were selected by LASSO from 19 variables, including age, course of disease, postprandial blood glucose (PBG), glycosylated haemoglobin A1c (HbA1c), uric creatinine (UCR), urinary microalbumin (UMA), and systolic blood pressure (SBP). The model built by these 7 predictors displayed medium prediction ability with the area under the ROC curve of 0.700 in the training set and 0.715 in the validation set. The decision curve analysis curve showed that the nomogram could be applied clinically if the risk threshold is between 21% and 57% and 21%-51% in external validation.

CONCLUSION

Introducing age, course of disease, PBG, HbA1c, UCR, UMA, and SBP, the risk nomogram is useful for prediction of DR risk in T2DM individuals.

Nomogram for the Risk of Diabetic Nephropathy or Diabetic Retinopathy Among Patients with Type 2 Diabetes Mellitus Based on Questionnaire and Biochemical Indicators: A Cross-Sectional Study

PURPOSE

This study aimed to develop a diabetic nephropathy (DN) or diabetic retinopathy (DR) incidence risk nomogram in China's population with type 2 diabetes mellitus (T2DM) based on a community-based sample.

METHODS

We carried out questionnaire evaluations, physical examinations and biochemical tests among 4219 T2DM patients in Shanghai. According to the incidence of DN and DR, 4219 patients in our study were divided into groups of T2DM patients with DN or DR, patients with both, and patients without any complications. We successively used least absolute shrinkage and selection operator regression analysis and logistic regression analysis to optimize the feature selection for DN and DR. To ensure the accuracy of the results, we carried out multivariable logistic regression analysis of the above significant risk factors on the sample data for both DN and DR. The selected features were included to establish a prediction model. The C-index, calibration plot, curve analysis and internal validation were used to validate the distinction, calibration, and clinical practicality of the model.

RESULTS

The predictors in the prediction model included disease course, body mass index (BMI), total triglycerides (TGs), systolic blood pressure (SBP), postprandial blood glucose (PBG), haemoglobin A1C (HbA1c) and blood urea nitrogen (BUN). The model displayed moderate predictive power with a C-index of 0.807 and an area under the receiver operating characteristic curve of 0.807. In internal verification, the C-index reached 0.804. The risk threshold was 16-75% according to the analysis of the decision curve, and the nomogram could be applied in clinical practice.

CONCLUSION

This DN or DR incidence risk nomogram incorporating disease course, BMI, TGs, SBP, PBG, HbA1c and BUN can be used to predict DN or DR incidence risk in T2DM patients. The research team has developed an online app based on a clinical prediction model incorporating risk factors for rapid and simple prediction.

Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined

Extensive usage of molecular docking for computer-aided drug discovery resulted in development of numerous programs with versatile scoring and posing algorithms. Selection of the docking program among these vast number of options is central to the outcome of drug discovery. To this end, comparative assessment studies of docking offer valuable insights into the selection of the optimal tool. Despite the availability of various docking assessment studies, the performance difference of docking programs has not been well addressed on metalloproteins which comprise a substantial portion of the human proteome and have been increasingly targeted for treatment of a wide variety of diseases. This study reports comparative assessment of seven docking programs on a diverse metalloprotein set which was compiled for this study. The refined set of the PDBbind (2017) was screened to gather 710 complexes with metal ion(s) closely located to the ligands (<4 Å). The redundancy was eliminated by clustering and overall 213 complexes were compiled as the nonredundant metalloprotein subset of the PDBbind refined. The scoring, ranking, and posing powers of seven noncommercial docking programs, namely, AutoDock4, AutoDock4_Zn, AutoDock Vina, Quick Vina 2, LeDock, PLANTS, and UCSF DOCK6, were comprehensively evaluated on this nonredundant set. Results indicated that PLANTS (80%) followed by LeDock (77%), QVina (76%), and Vina (73%) had the most accurate posing algorithms while AutoDock4 (48%) and DOCK6 (56%) were the least successful in posing. Contrary to their moderate-to-high level of posing success, none of the programs was successful in scoring or ranking of the binding affinities (r² ≈ 0). Screening power was further evaluated by using active-decoy ligand sets for a large compilation of metalloprotein targets. PLANTS stood out among other programs to be able to enrich the active ligand for every target, underscoring its robustness for screening of metalloprotein inhibitors. This study provides useful information for drug discovery studies targeting metalloproteins.