Molecular Framework of Mouse Endothelial Cell Dysfunction during Inflammation: A Proteomics Approach.

A key aspect of cytokine-induced changes as observed in sepsis is the dysregulated activation of endothelial cells (ECs), initiating a cascade of inflammatory signaling leading to leukocyte adhesion/migration and organ damage. The therapeutic targeting of ECs has been hampered by concerns regarding organ-specific EC heterogeneity and their response to inflammation. Using in vitro and in silico analysis, we present a comprehensive analysis of the proteomic changes in mouse lung, liver and kidney ECs following exposure to a clinically relevant cocktail of proinflammatory cytokines. Mouse lung, liver and kidney ECs were incubated with TNF-α/IL-1ß/IFN-γ for 4 or 24 h to model the cytokine-induced changes. Quantitative label-free global proteomics and bioinformatic analysis performed on the ECs provide a molecular framework for the EC response to inflammatory stimuli over time and organ-specific differences. Gene Ontology and PANTHER analysis suggest why some organs are more susceptible to inflammation early on, and show that, as inflammation progresses, some protein expression patterns become more uniform while additional organ-specific proteins are expressed. These findings provide an in-depth understanding of the molecular changes involved in the EC response to inflammation and can support the development of drugs targeting ECs within different organs. Data are available via ProteomeXchange (identifier PXD031804).

Natural-Product-Inspired Compounds as Countermeasures against the Liver Carcinogen Aflatoxin B1.

Aflatoxin B1 (AfB1) ranks among the most potent liver carcinogens known, and the accidental or intentional exposure of humans and livestock to this toxin remains a serious global threat. One protective measure that had been proposed is employing small-molecule therapeutics capable of mitigating the toxicity of AfB1; however, to date, these efforts have had little clinical success. To identify molecular scaffolds that reduce the toxicity of AfB1, we developed a cell-based high-throughput high-content imaging assay that enabled our team to test natural products (pure compounds, fractions, and extracts) for protection of monolayers and spheroids composed of HepG2 liver cells against AfB1. The spheroid assay showed notable potential for further development, as it afforded greater sensitivity of HepG2 cells to AfB1, which is believed to better mimic the in vivo response of hepatocytes to the toxin. One of the most bioactive compounds to arise from this investigation was alternariol-9-methyl ether (1, purified from an Alternaria sp. isolate), which inspired the synthesis and testing of several structurally related molecules. Based on these findings, it is proposed that several types of natural and synthetic polyarene molecules that have undergone oxidative functionalization (e.g., compounds containing 3-methoxyphenol moieties) are promising starting points for the development of new agents that protect against AfB1 toxicity.

Exploiting large-scale drug-protein interaction information for computational drug repurposing.

BACKGROUND: Despite increased investment in pharmaceutical research and development, fewer and fewer new drugs are entering the marketplace. This has prompted studies in repurposing existing drugs for use against diseases with unmet medical needs. A popular approach is to develop a classification model based on drugs with and without a desired therapeutic effect. For this approach to be statistically sound, it requires a large number of drugs in both classes. However, given few or no approved drugs for the diseases of highest medical urgency and interest, different strategies need to be investigated. RESULTS: We developed a computational method termed "drug-protein interaction-based repurposing" (DPIR) that is potentially applicable to diseases with very few approved drugs. The method, based on genome-wide drug-protein interaction information and Bayesian statistics, first identifies drug-protein interactions associated with a desired therapeutic effect. Then, it uses key drug-protein interactions to score other drugs for their potential to have the same therapeutic effect. CONCLUSIONS: Detailed cross-validation studies using United States Food and Drug Administration-approved drugs for hypertension, human immunodeficiency virus, and malaria indicated that DPIR provides robust predictions. It achieves high levels of enrichment of drugs approved for a disease even with models developed based on a single drug known to treat the disease. Analysis of our model predictions also indicated that the method is potentially useful for understanding molecular mechanisms of drug action and for identifying protein targets that may potentiate the desired therapeutic effects of other drugs (combination therapies).

Superior Mesenteric Artery (SMA) Syndrome With Enterocutaneous Fistula in a Young Woman: A Rare Association.

Superior mesenteric artery (SMA) syndrome is also known as Wilkie's syndrome. Sometimes it is the cause of obstruction in the duodenum. In SMA syndrome, the acute angulation of the SMA against the abdominal aorta can prevent duodenal contents from draining into the jejunum (upper small intestine); hence inadequate intake of nutrition leads to weight loss and malnutrition. This is primarily attributed to the loss of intervening pad of mesenteric fat tissue due to various debilitating conditions. Abnormal connections between the intra-abdominal gastrointestinal tracts and skin over the abdomen are known as enterocutaneous fistulas (ECF).  In this case report, a 37-year-old woman with a history of chronic dull pain in the upper abdominal region over the last seven months, who also complained of bloating, infrequent vomiting, nausea, and upper abdominal fullness for the same amount of time, was seen in the emergency room. Her symptoms had deteriorated by the time she approached the hospital. Additionally, she reports having had a foul-smelling, purulent discharge for the past five years right below the umbilicus. Upon close investigation, it was determined to be feces, and it was later discovered to be a low-output enterocutaneous fistula. She describes having an exploratory laparotomy and adhesiolysis for an intra-abdominal abscess and an acute intestinal obstruction caused by adhesions. This case emphasizes the provocation given a diagnosis of SMA syndrome with enterocutaneous fistula and demands increased awareness of this entity. This will ameliorate early identification to reduce immaterial tests and irrelevant treatments.

A Prospective Comparative Study of the Functional Outcomes of Patellar Resurfacing Versus Non-resurfacing in Patients Undergoing Total Knee Arthroplasty.

Background and objective Total knee arthroplasty (TKA) is a highly successful surgical procedure. However, there is a lack of consensus about whether to resurface the patella or not. This study was aimed at evaluating the outcome of patellar resurfacing in terms of a decrease in the incidence of anterior knee pain after TKA and assessing whether patellar resurfacing is beneficial in improving functional outcomes. Materials and methods This prospective comparative study included 100 patients undergoing TKA who were randomly allotted to the patellar resurfacing or non-resurfacing group. Functional evaluation was done based on the Knee Society Score, and the pain was evaluated by the visual analogue scale (VAS) preoperatively and after one year. Results There was a significant improvement in the Knee Society scores as well as the pain scores in both groups postoperatively. The patellar resurfacing group showed statistically significant improvement as compared to the non-resurfacing group in the Knee Society clinical and functional scores as well as the VAS at the end of one year. Conclusion Patellar resurfacing during TKA provides better clinical and functional outcomes as well as more relief from anterior knee pain as compared to non-resurfacing of the patella.

QSAR classification model for antibacterial compounds and its use in virtual screening.

As novel and drug-resistant bacterial strains continue to present an emerging health threat, the development of new antibacterial agents is critical. This includes making improvements to existing antibacterial scaffolds as well as identifying novel ones. The aim of this study is to apply a Bayesian classification QSAR approach to rapidly screen chemical libraries for compounds predicted to have antibacterial activity. Toward this end we assembled a data set of 317 known antibacterial compounds as well as a second data set of diverse, well-validated, non-antibacterial compounds from 215 PubChem Bioassays against various bacterial species. We constructed a Bayesian classification model using structural fingerprints and physicochemical property descriptors and achieved an accuracy of 84% and precision of 86% on an independent test set in identifying antibacterial compounds. To demonstrate the practical applicability of the model in virtual screening, we screened an independent data set of ~200k compounds. The results show that the model can screen top hits of PubChem Bioassay actives with accuracy up to ~76%, representing a 1.5-2-fold enrichment. The top screened hits represented a mixture of both known antibacterial scaffolds as well as novel scaffolds. Our study suggests that a well-validated Bayesian classification QSAR approach could compliment other screening approaches in identifying novel and promising hits. The data sets used in constructing and validating this model have been made publicly available.

Exploring polypharmacology using a ROCS-based target fishing approach.

Polypharmacology has emerged as a new theme in drug discovery. In this paper, we studied polypharmacology using a ligand-based target fishing (LBTF) protocol. To implement the protocol, we first generated a chemogenomic database that links individual protein targets with a specified set of drugs or target representatives. Target profiles were then generated for a given query molecule by computing maximal shape/chemistry overlap between the query molecule and the drug sets assigned to each protein target. The overlap was computed using the program ROCS (Rapid Overlay of Chemical Structures). We validated this approach using the Directory of Useful Decoys (DUD). DUD contains 2950 active compounds, each with 36 property-matched decoys, against 40 protein targets. We chose a set of known drugs to represent each DUD target, and we carried out ligand-based virtual screens using data sets of DUD actives seeded into DUD decoys for each target. We computed Receiver Operator Characteristic (ROC) curves and associated area under the curve (AUC) values. For the majority of targets studied, the AUC values were significantly better than for the case of a random selection of compounds. In a second test, the method successfully identified off-targets for drugs such as rimantadine, propranolol, and domperidone that were consistent with those identified by recent experiments. The results from our ROCS-based target fishing approach are promising and have potential application in drug repurposing for single and multiple targets, identifying targets for orphan compounds, and adverse effect prediction.

Evaluating Drug Deposition Patterns from Turbuhaler® in Healthy and Diseased Lung Models of Preschool Children.

The efficacy of pediatric oral drug delivery using dry powder inhalers, such as Turbuhaler®, is dependent on the age and health of the test subjects. The available clinical data for these studies is scant and rarely provide correlations between the health condition and the regional lung deposition. In particular, the data and the correlations for pre-school children are minimal. Deposition simulations were performed using the newly developed Quasi-3D whole lung model to analyze the effect of health conditions on the regional lung deposition from the Turbuhaler® in 3-year-old children. The healthy lung model was created from CT scan data. Cystic-fibrosis models were created by uniformly constricting the airways to various degrees. The simulated drug deposition outcomes were validated against the available experimental data. The results show that, while the dose deposited in the lungs exhibits minor variations, the Peripheral:Central (P/C) ratio is strongly affected by both the health condition and the inflow variations. The above ratio is reduced by ~30% for the severely diseased case, compared to its healthy counterpart, for the same inhalation profile. This indicates that lower doses reach the peripheral lung, in pediatric cystic-fibrosis subjects, thus requiring a larger therapeutic dose.

Molecular Subtypes As Emerging Predictors of Clinicopathological Response to Neoadjuvant Chemotherapy (NACT) in Locally Advanced Breast Cancer (LABC): A Single-Centre Experience in Western India.

INTRODUCTION: Locally advanced breast cancer (LABC) is a subset of breast cancer characterized by the most advanced breast tumours in the absence of distant metastasis. Treatment of LABC has evolved from a single modality treatment to multimodality management. Neoadjuvant chemotherapy (NACT) is increasingly being used to treat patients with LABC. This study assessed tumour response after NACT using clinical changes, Response Evaluation Criteria in Solid Tumors (RECIST) criteria and pathological report. METHODOLOGY: This study was a prospective as well as retrospective observational study carried out in the department of general surgery, Dr. Sampurnanand Medical College, Jodhpur. All the patients admitted with stage III (IIIA, IIIB, IIIC) were included in the study after obtaining approval from the institutional ethical committee. Clinical response was assessed by RECIST criteria (clinical complete response (cCR), clinical partial response (cPR), clinical progressive disease (cPD), and clinical stable disease (cSD)) and pathological response by histopathological report (pCR). Response of various molecular subtypes was noted. RESULTS: Among 31 patients included in the study, cCR observed in 22.58% cases, cPR observed in 61.29% cases while cPD and cSD seen in 3.22% and 12.90% cases, respectively. Pathological complete response (pCR) observed in 19.35% cases. Favourable response seen with human epidermal growth factor receptor 2 (HER2) overexpression (cCR = 50%, pCR = 37.50%) followed by triple negative (cCR = 25%, pCR = 25%) molecular subtypes. CONCLUSIONS: It can be concluded that molecular subtype determination helps in deciding treatment protocol in patients with LABC with HER2 overexpression and triple-negative breast cancers having a better clinicopathological response to NACT than luminal subtypes. NACT results in downstaging of tumours, thus, help in achieving surgically clear margins and elimination of micrometastases which decreases the recurrence rates and morbidity/mortality of patients.

A synthetic combinatorial strategy for developing alpha-conotoxin analogs as potent alpha7 nicotinic acetylcholine receptor antagonists.

alpha-Conotoxins are peptide neurotoxins isolated from venomous cone snails that display exquisite selectivity for different subtypes of nicotinic acetylcholine receptors (nAChR). They are valuable research tools that have profound implications in the discovery of new drugs for a myriad of neuropharmacological conditions. They are characterized by a conserved two-disulfide bond framework, which gives rise to two intervening loops of extensively mutated amino acids that determine their selectivity for different nAChR subtypes. We have used a multistep synthetic combinatorial approach using alpha-conotoxin ImI to develop potent and selective alpha(7) nAChR antagonists. A positional scan synthetic combinatorial library was constructed based on the three residues of the n-loop of alpha-conotoxin ImI to give a total of 10,648 possible combinations that were screened for functional activity in an alpha(7) nAChR Fluo-4/Ca2+ assay, allowing amino acids that confer antagonistic activity for this receptor to be identified. A second series of individual alpha-conotoxin analogs based on the combinations of defined active amino acid residues from positional scan synthetic combinatorial library screening data were synthesized. Several analogs exhibited significantly improved antagonist activity for the alpha(7) nAChR compared with WT-ImI. Binding interactions between the analogs and the alpha(7) nAChR were explored using a homology model of the amino-terminal domain based on a crystal structure of an acetylcholine-binding protein. Finally, a third series of refined analogs was synthesized based on modeling studies, which led to several analogs with refined pharmacological properties. Of the 96 individual alpha-conotoxin analogs synthesized, three displayed > or =10-fold increases in antagonist potency compared with WT-ImI.

Immediate rehabilitation of a rheumatoid arthritis patient with single-piece implants.

INTRODUCTION AND IMPORTANCE: The aim of this article is to report the long-term outcome of full mouth rehabilitation with single piece, smooth surface implants following immediate loading protocol on a patient suffering with RA and severe unilateral condylar resorption. CASE PRESENTATION: Here, we present a challenging case of a patient suffering from Rheumatoid Arthritis who was stabilized and completed successfully with a 4 year follow-up period. Prosthetic management optimized the inter-occlusal relationship to maintain both function and esthetic integrity. Single piece implants are designed to engage and take support from the cortical bone low in metabolic activities thus promoting the force transmission through apical threads that are engaged in the cortical bone. DISCUSSION: Rheumatoid Arthritis [RA] is an auto-immune inflammatory condition in which the inflamed and hypertrophic synovial membrane grows into the articulation surfaces. The Temporomandibular Joints [TM] are frequently involved in rheumatoid arthritis. According to the literature on RA, due to frequent periodontitis, decreased salivary secretion, medication, as well as decrease in bone regenerative potential, RA is often considered as a relative contraindication in the use of implants. Atrophic jaws and cases with comorbidities like osteoporosis, diabetes, rheumatoid arthritis, periodontally infected cases are restored with high success by single piece smooth surface. CONCLUSION: To the best of our knowledge, this may be the first case of immediate functional loading by bi-cortical single piece implants.

A quasi-3D model of the whole lung: airway extension to the tracheobronchial limit using the constrained constructive optimization and alveolar modeling, using a sac-trumpet model.

Existing computational models used for simulating the flow and species transport in the human airways are zero-dimensional (0D) compartmental, three-dimensional (3D) computational fluid dynamics (CFD), or the recently developed quasi-3D (Q3D) models. Unlike compartmental models, the full CFD and Q3D models are physiologically and anatomically consistent in the mouth and the upper airways, since the starting point of these models is the mouth-lung surface geometry, typically created from computed tomography (CT) scans. However, the current resolution of CT scans limits the airway detection between the 3rd-4th and 7th-9th generations. Consequently, CFD and the Q3D models developed using these scans are generally limited to these generations. In this study, we developed a method to extend the conducting airways from the end of the truncated Q3D lung to the tracheobronchial (TB) limit. We grew the lung generations within the closed lung lobes using the modified constrained constructive optimization, creating an aerodynamically optimized network aiming to produce equal pressure at the distal ends of the terminal segments. This resulted in a TB volume and lateral area of ∼165 cc and ∼2000 cm2, respectively. We created a "sac-trumpet" model at each of the TB outlets to represent the alveoli. The volumes of the airways and the individual alveolar generations match the anatomical values by design: with the functional residual capacity at 2611 cc. Lateral surface areas were scaled to match the physiological values. These generated Q3D whole lung models can be efficiently used for conducting multiple breathing cycles of drug transport and deposition simulations.

Effect of potassium fertilizer on the growth, physiological parameters, and water status of Brassica juncea cultivars under different irrigation regimes.

Abiotic stress, especially a lack of water, can significantly reduce crop yields. In this study, we evaluated the physiological and biochemical effects of potassium sulfate (K2SO4) fertilizer and varied irrigation regimes on the economically significant oilseed crop, Brassica juncea L, under open field conditions. Two cultivars (RH-725 and RH-749) of B. juncea were used in a randomized complete block design experiment with three replicates. Irrigation regimes consisted of a control (double irrigation: once at the 50% flowering and another at 50% fruiting stages), early irrigation (at 50% flowering only), late irrigation (at 50% fruiting only) and stress (no irrigation). The K2SO4 applications were: control (K0, no fertilization); K1, 10 kg ha-1; and K2, 20 kg ha-1. We measured growth via fresh and dry plant weight, plant height, root length, and leaf area. All the growth parameters were higher in RH-749. The physiological attributes, including the membrane stability index and relative water content, were higher at the 50% flowering stage in RH-749. The amount of antioxidant enzymes (catalase (CAT), guaiacol peroxidase (POX), ascorbate peroxidase (APX), and superoxide dismutase (SOD)) was enhanced when both plants were fertilized during water stress. All of these enzymes had higher activity in RH-749. The total chlorophyll content and photosynthesis rate were considerably higher in RH-749, which leaked fewer electrolytes and maintained a less destructive osmotic potential under limited water conditions. The results indicated that it is water-stress tolerant when given a high concentration of K2SO4, which alleviated the adverse effects of water stress on growth and physiology.

Root Trait Variation in Lentil (Lens culinaris Medikus) Germplasm under Drought Stress.

Drought is the most critical environmental factor across the continents affecting food security. Roots are the prime organs for water and nutrient uptake. Fine tuning between water uptake, efficient use and loss determines the genotypic response to water limitations. Targeted breeding for root system architecture needs to be explored to improve water use efficiency in legumes. Hence, the present study was designed to explore root system architecture in lentil germplasm in response to drought. A set of 119 lentil (Lens culinaris Medik.) genotypes was screened in controlled conditions to assess the variability in root traits in relation to drought tolerance at seedling stage. We reported significant variation for different root traits in lentil germplasm. Total root length, surface area, root volume and root diameter were correlated to the survival and growth under drought. Among the studied genotypes, the stress tolerance index varied 0.19-1.0 for survival and 0.09-0.90 for biomass. Based on seedling survival and biomass under control and drought conditions, 11 drought tolerant genotypes were identified, which may be investigated further at a physiological and molecular level for the identification of the genes involved in drought tolerance. Identified lines may also be utilised in a lentil breeding program.

Novel and selective DNA methyltransferase inhibitors: Docking-based virtual screening and experimental evaluation.

The DNA methyltransferase (DNMT) enzyme family consists of four members with diverse functions and represents one of the most promising targets for the development of novel anticancer drugs. However, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects that have been developed several decades ago. In this work, we conducted a virtual screening of more than 65,000 lead-like compounds selected from the National Cancer Institute collection using a multistep docking approach with a previously validated homology model of the catalytic domain of human DNMT1. Experimental evaluation of top-ranked molecules led to the discovery of novel small molecule DNMT1 inhibitors. Virtual screening hits were further evaluated for DNMT3B inhibition revealing several compounds with selectivity towards DNMT1. These are the first small molecules reported with biochemical selectivity towards an individual DNMT enzyme capable of binding in the same pocket as the native substrate cytosine, and are promising candidates for further rational optimization and development as anticancer drugs. The availability of enzyme-selective inhibitors will also be of great significance for understanding the role of individual DNMT enzymes in epigenetic regulation.

Alginate-encapsulation of shoot tips of jojoba [Simmondsia chinensis (Link) Schneider] for germplasm exchange and distribution.

Shoot tips excised from in vitro proliferated shoots derived from nodal explants of jojoba [Simmondsia chinensis (Link) Schneider] were encapsulated in calcium alginate beads for germplasm exchange and distribution. A gelling matrix of 3 % sodium alginate and 100 mM calcium chloride was found most suitable for formation of ideal calcium alginate beads. Best response for shoot sprouting from encapsulated shoot tips was recorded on 0.8 % agar-solidified full-strength MS medium. Rooting was induced upon transfer of sprouted shoots to 0.8 % agar-solidified MS medium containing 1 mg l(-1) IBA. About 70 % of encapsulated shoot tips were rooted and converted into plantlets. Plants regenerated from encapsulated shoot tips were acclimatized successfully. The present encapsulation approach could also be applied as an alternative method of propagation of desirable elite genotype of jojoba.

Discovery of a novel protein kinase B inhibitor by structure-based virtual screening.

Protein kinase B (PKB/AKT) is a promising and attractive therapeutic target in anticancer drug development. Herein, we report the findings of virtual screening for novel ATP-competitive inhibitors of AKT-2 using 2D- and 3D-similarity searching and sequential molecular docking with two crystal structures of AKT-2. Our multistep approach led to the identification of a low micromolar AKT-2 inhibitor (IC(50)=1.5 microM) with a novel scaffold. The experimentally validated inhibitor represents the starting point for an optimization program.

A Quasi-3D compartmental multi-scale approach to detect and quantify diseased regional lung constriction using spirometry data.

Spirometry is a widely used pulmonary function test to detect the airflow limitations associated with various obstructive lung diseases, such as asthma, chronic obstructive pulmonary disease, and even obesity-related complications. These conditions arise due to the change in the airway resistance, alveolar compliance, and inductance values. Currently, zero-dimensional compartmental models are commonly used for calibrating these resistance, compliance, and inductance values, ie, solving the inverse spirometry problem. However, zero-dimensional compartments cannot capture the flow physics or the spatial geometry effects, thereby generating a low fidelity prediction of the diseased lung. Computational fluid dynamics (CFD) models offer higher fidelity solutions but may be impractical for certain applications due to the duration of these simulations. Recently, a novel, fast-running, and robust Quasi-3D (Q3D) wire model for simulating the airflow in the human lung airway was developed by CFD Research Corporation. This Q3D method preserved the 3D spatial nature of the airways and was favorably validated against CFD solutions. In the present study, the Q3D compartmental multi-scale combination is further improved to predict regional lung constriction of diseased lungs using spirometry data. The Q3D mesh is resolved up to the eighth lung airway generation. The remainder of the airways and the alveoli sections are modeled using a compartmental approach. The Q3D geometry is then split into different spatial sections, and the resistance values in these regions are obtained using parameter inversion. Finally, the airway diameter values are then reduced to create the actual diseased lung model, corresponding to these resistance values. This diseased lung model can be used for patient-specific drug deposition predictions and the subsequent optimization of the orally inhaled drug products.

A compartment-quasi-3D multiscale approach for drug absorption, transport, and retention in the human lungs.

Most current models used for modeling the pulmonary drug absorption, transport, and retention are 0D compartmental models where the airways are generally split into the airways and alveolar sections. Such block models deliver low fidelity solutions and the spatial lung drug concentrations cannot be obtained. Other approaches use high fidelity CFD models with limited capabilities due to their exorbitant computational cost. Recently, we presented a novel, fast-running and robust quasi-3D (Q3D) model for modeling the pulmonary airflow. This Q3D method preserved the 3D lung geometry, delivered extremely accurate solutions, and was 25 000 times faster in comparison to the CFD methods. In this paper, we present a Q3D-compartment multiscale combination to model the pulmonary drug absorption, transport, and retention. The initial deposition is obtained from CFD simulations. The lung absorption compartment model of Yu and Rosania is adapted to this multiscale format. The lung is modeled in the Q3D format till the eighth airway generation. The remainder of the lung along with the systemic circulation and elimination processes was modeled using compartments. The Q3D model is further adapted, by allowing for various heterogeneous annular lung layers. This allows us to model the drug transport across the layers and along the lung. Using this multiscale model, the spatiotemporal drug concentrations in the different lung layers and the temporal concentration in the plasma are obtained. The concentration profile in the plasma was found to be better aligned with the experimental findings in comparison with compartmental model for the standard test cases. Thus, this multiscale model can be used to optimize the target-specific drug delivery and increase the localized bioavailability, thereby facilitating applications from the bench to bedside for various patient/lung-disease variations.