Development and experimental validation of 3D QSAR models for the screening of thyroid peroxidase inhibitors using integrated methods of computational chemistry.

The intricate network of glands and organs that makes up the endocrine system. Hormones are used to regulate and synchronize the nervous and physiological systems. The agents which perturbate an endocrine system are called endocrine disruptors and they can eventually affect cellular proliferation and differentiation in target tissues. A subclass of endocrine disruptors known as thyroid disruptors (TDs) or thyroid disrupting chemicals (TDCs) influence the hypothalamo-pituitary-thyroid axis or directly interfere with thyroid function by binding to thyroid hormone receptors. Thyroid hormone levels in circulation are now included in more test guidelines (OECD TG 441, 407, 408, 414, 421/422, 443/416). Although these might be adequate to recognize thyroid adversity, they are unable to explain the underlying mechanism of action. Thyroid peroxidase (TPO) and sodium iodide symporter (NIS), two proteins essential in the biosynthesis of thyroid hormones, are well-accepted molecular targets for inhibition. The screening of a large number of molecules using high throughput screening (HTS) requires a minimum quantity of sample, cost, and time consuming. Whereas 3-dimensional quantitative structure-activity relationship (3D-QSAR) analysis can screen the TDCs before synthesizing a compound. In the present study, the human TPO (hTPO) and NIS (hNIS) structures were modelled using homology modeling and the quality of the structures was validated satisfactorily using MD simulation for 100ns. Further, 190 human TPO inhibitors with IC50 were curated from Comptox and docked with the modelled structure of TPO using D238, H239 and D240 centric grid. The binding conformation of a molecule with low binding energy was used as a reference and the rest other molecules were aligned after generating the possible conformers. The activity-stratified partition was performed for aligned molecules and training set (139), test set (51) were defined. The machine learning models such as k Nearest Neighbor (kNN) and Random Forest (RF) models were built and validated using external experimental dataset containing 10 molecules. Among the 10 molecules, all 10 molecules were identified as TPO inhibitors and demonstrated 100 % accuracy qualitatively. To confirm the selective TPO inhibition all 10 molecules were docked with the modelled structure of hNIS and the results have demonstrated the selective TPO inhibition.

GEANT4 based simulation study of converter and direct target design and optimization of target for 99Mo production using 30 MeV electron linear accelerator.

A 30 MeV, 5-10 kW beam power electron linac is under development at SAMEER for radio-isotope production. An enriched 100Mo target will be irradiated to produce 99Mo which will be eluted to give 99mTc. Two approaches of 100Mo target irradiation -converter and direct are studied using GEANT4 simulations. The main aim of this study is to optimize the 100Mo target geometry for maximum yield. It is observed that direct target irradiation gives better activity as compared to converter target approach.

In vitro assays for characterization of distinct multiple catalytic activities of thyroid peroxidase using LC-MS/MS.

A diverse set of environmental contaminants have raised a concern about their potential adverse effects on endocrine signaling. Robust and widely accepted battery of in vitro assays is available to assess the disruption of androgenic and estrogenic pathways. However, such definitive systems to investigate effects on the disruption of thyroid pathways by the xenobiotics are not yet well established. One of the major "Molecular Initiating Events" (MIEs) in thyroid disruption involves targeting of thyroid peroxidase (TPO), a key enzyme involved in thyroid hormone synthesis. TPO catalyzes mono- and diiodination of L-Tyrosine (L-Tyr) to generate 3-Iodo-l-tyrosine (MIT) and 3,5-Diiodo-l-tyrosine (DIT), respectively, followed by the coupling of iodinated tyrosine rings to generate thyroid hormones, 3,3'5-Triiodo-l-thyronine (T3) and Levothyroxine (T4). We sought to develop a robust, sensitive, and rapid in vitro assay systems to evaluate the effects of test chemicals on the multiple catalytic activities of thyroid peroxidase. Simple in vitro assays were designed to study TPO mediated distinct reactions using a single LC-MS/MS method. Herein, we describe a battery of assays to investigate the iodination of L-Tyr to MIT and DIT, MIT to DIT as well as, T3 to T4 catalyzed by rat thyroid TPO. Importantly, two sequential reactions involving mono- and diiodination of L-Tyr could be analyzed in a single assay. The assay that monitors in vitro conversion of DIT to T4 was developed to study the coupling of tyrosine rings. Enzyme kinetics studies revealed distinct characteristics of multiple reactions catalyzed by TPO. Further, the known TPO inhibitors were used to assess their potency towards individual TPO substrates and reactions. The resultant half maximum inhibitory concentration (IC50) values highlighted differential targeting of TPO catalyzed reactions by the same inhibitor. Overall results underscore the need to develop more nuanced approaches that account for distinct multiple catalytic activities of TPO.

Monte Carlo Processing on a Chip (MCoaC)-preliminary experiments toward the realization of optimal-hardware for TOPAS/Geant4 to drive discovery.

Amongst the scientific frameworks powered by the Monte Carlo (MC) toolkit Geant4 (Agostinelli et al., 2003), the TOPAS (Tool for Particle Simulation) (Perl et al., 2012) is one. TOPAS focuses on providing ease of use, and has significant implementation in the radiation oncology space at present. TOPAS functionality extends across the full capacity of Geant4, is freely available to non-profit users, and is being extended into radiobiology via TOPAS-nBIO (Ramos-Mendez et al., 2018). A current "grand problem" in cancer therapy is to convert the dose of treatment from physical dose to biological dose, optimized ultimately to the individual context of administration of treatment. Biology MC calculations are some of the most complex and require significant computational resources. In order to enhance TOPAS's ability to become a critical tool to explore the definition and application of biological dose in radiation therapy, we chose to explore the use of Field Programmable Gate Array (FPGA) chips to speedup the Geant4 calculations at the heart of TOPAS, because this approach called "Reconfigurable Computing" (RC), has proven able to produce significant (around 90x) (Sajish et al., 2012) speed increases in scientific computing. Here, we describe initial steps to port Geant4 and TOPAS to be used on FPGA. We provide performance analysis of the current TOPAS/Geant4 code from an RC implementation perspective. Baseline benchmarks are presented. Achievable performance figures of the subsections of the code on optimal hardware are presented; Aspects of practical implementation of "Monte Carlo on a chip" are also discussed.

Comparison of in chemico skin sensitization methods and development of an in chemico skin photosensitization assay.

Chemical substances that induce an allergic response in skin upon contact are called skin allergens or sensitizers, while chemical substances that elicit an allergic response only in presence of light are called photoallergens or photo sensitizers. The Direct Peptide Reactivity Assay (DPRA, OECD N° 442C, 2015) and the Amino Acid Derivative Reactivity Assay (ADRA) are in chemico assays used to discriminate between allergens and non-allergens. The DPRA and the ADRA, respectively, monitor the depletion of model peptides and modified amino acids induced by crosslinking with test chemicals. In the current study we compared these two assays and analyzed their suitability to predict skin sensitization potential of several chemical substances.  In order to study the combined effect of a chemical compound and UV light, we modified DPRA (photo-DPRA) as well as ADRA (photo-ADRA) by introduction of a photo-irradiation parameter. Analysis using photo-DPRA and photo-ADRA correctly distinguished known photoallergens from non-photoallergens. Upon irradiation, photoallergens selectively showed higher depletion of model peptides or modified amino acids. Thus, photo-DPRA and/or photo-ADRA can serve as non-animal in vitro methods for the identification and assessment of photoallergens/ photosensitizers.

Pandemic influenza A(H1N1) 2009 outbreak in a residential school at Panchgani, Maharashtra, India.

BACKGROUND & OBJECTIVES: An outbreak of influenza was investigated between June 24 and July 30, 2009 in a residential school at Panchgani, Maharashtra, India. The objectives were to determine the aetiology, study the clinical features in the affected individuals and, important epidemiological and environmental factors. The nature of public health response and effectiveness of the control measures were also evaluated. METHODS: Real time reverse transcriptase polymerase chain reaction was performed on throat swabs collected from 82 suspected cases to determine the influenza types (A or B) and sub-types [pandemic (H1N1) 2009, as well as seasonal influenza H1N1, H3N2]. Haemagglutination inhibition assay was performed on serum samples collected from entire school population (N=415) to detect antibodies for pandemic (H1N1) 2009, seasonal H1N1, H3N2 and influenza B/Yamagata and B/Victoria lineages. Antibody titres>or=10 for pandemic (H1N1) 2009 and >or=20 for seasonal influenza A and B were considered as positive for these viruses. RESULTS: Clinical attack rate for influenza-like illness was 71.1 per cent (295/415). The attack rate for pandemic (H1N1) 2009 cases was 42.4 per cent (176/415). Throat swabs were collected from 82 cases, of which pandemic (H1N1) 2009 virus was detected in 15 (18.3%), influenza type A in (6) 7.4 per cent and influenza type B only in one case. A serosurvey carried out showed haemagglutination inhibition antibodies to pandemic (H1N1) 2009 in 52 per cent (216) subjects in the school and 9 per cent (22) in the community. INTERPRETATION & CONCLUSION: Our findings confirmed an outbreak of pandemic (H1N1) 2009 due to local transmission among students in a residential school at Panchgani, Maharashtra, India.