Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach

Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. The inhibiting potency of 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been investigated by docking simulation against SARS-CoV-2 protein. The optimized geometry shows a planar structure between the chromone and the side chain. Differences in the geometries due to the substitution of the electronegative atom and intermolecular contacts due to the chromone and hydrazinecarbothioamide were analyzed. NBO analysis confirms the presence of two strong stable hydrogen bonded NH⋯O intermolecular interactions and two weak hydrogen bonded CH⋯O interactions. The red shift in NH stretching frequency exposed from IR substantiates the formation of NH⋯O intermolecular hydrogen bond and the blue shift in CH stretching frequency substantiates the formation of CH⋯O intermolecular hydrogen bond. Drug likeness, absorption, distribution, metabolism, excretion and toxicity property gives an idea about the pharmacokinetic properties of the title molecule. The binding energy of the nonbonding interaction with Histidine 41 and Cysteine 145, present a clear view that 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide can irreversibly interact with SARS-CoV-2 protease.

Quantum chemical insight into molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-19 molecule 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluorophenyl)acetamide - dimer

Novel antiviral active molecule 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl)acetamide has been synthesised and characterized by FT-IR and FT-Raman spectra. The equilibrium geometry, natural bond orbital calculations and vibrational assignments have been carried out using density functional B3LYP method with the 6-311G++(d,p) basis set. The complete vibrational assignments for all the vibrational modes have been supported by normal coordinate analysis, force constants and potential energy distributions. A detailed analysis of the intermolecular interactions has been performed based on the Hirshfeld surfaces. Drug likeness has been carried out based on Lipinski's rule and the absorption, distribution, metabolism, excretion and toxicity of the title molecule has been calculated. Antiviral potency of 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro-phenyl) acetamide has been investigated by docking against SARS-CoV-2 protein. The optimized geometry shows near-planarity between the phenyl ring and the pyrimidine ring. Differences in the geometries due to the substitution of the most electronegative fluorine atom and intermolecular contacts due to amino pyrimidine were analyzed. NBO analysis reveals the formation of two strong stable hydrogen bonded N-H···N intermolecular interactions and weak intramolecular interactions C-H···O and N-H···O. The Hirshfeld surfaces and consequently the 2D-fingerprint confirm the nature of intermolecular interactions and their quantitative contributions towards the crystal packing. The red shift in N-H stretching frequency exposed from IR substantiate the formation of N-H···N intermolecular hydrogen bond. Drug likeness and absorption, distribution, metabolism, excretion and toxicity properties analysis gives an idea about the pharmacokinetic properties of the title molecule. The binding energy -8.7 kcal/mol of the nonbonding interaction present a clear view that 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl) acetamide can irreversibly interact with SARS-CoV-2 protease.

Spectral Investigations, Molecular Interactions and Electrochemical Studies of (2R)-(-)2-(2,6-dimethylphenylaminocarbonyl)-1-methyl Piperidinium Chloride

Background:

Local anesthetics are widely used to decrease sensitivity to pain in specific regions of the body while performing medical tasks. Many studies have probed the mechanism of action of local anesthetics but still many questions remain. (2R - (-) 2 - (2, 6-dimethylphenylaminocarbonyl) - 1 – methyl piperidinium chloride (DAMP), is an extensively used amide-type local anesthetic.

Objective:

This study aims at revealing the various electrophysical and chemical properties of the title compound. This study will be useful for future research by pharmacologists.

Method:

Density Functional Theory (DFT) computations were executed using Gaussian’09 program package and were optimized with the B3LYP /6-311+G (d, p) basis set. Natural bond orbital (NBO) analysis was carried out with version 3.1. Normal Coordinate Analysis (NCA) was used to systematically calculate the harmonic vibrational wavenumbers. Molecular docking simulations were carried out to understand the pharmacokinetic behavior of the drug.

Results:

The presence of strong N-H…Cl intra molecular hydrogen bonding was evidently revealed from the FT-IR spectrum due to the shifting of NH stretching wavenumber. Stability of the molecule arising from hyper conjugative interactions exhibits the bioactivity of the molecule by natural bond orbital analysis. The title molecule binds to the inner pore and blocks voltage - gated sodium channels in peripheral neurons.

Conclusion:

A detailed molecular picture of DAMP and its interactions were obtained by modeling analysis, IR, Raman, and UV-Vis spectroscopy. The geometrical parameters agree well with the XRD data. NBO analysis indicates the bioactivity of the molecule. The HOMO-LUMO energy gap indicates the possibility of intramolecular charge transfer of the molecule. From the ligand docking studies it is concluded that the title molecule binds to the inner pore and blocks voltage - gated sodium channels in peripheral neurons.

First Measurement of Differential Charged Current Quasielasticlike ν_{μ}-Argon Scattering Cross Sections with the MicroBooNE Detector

We report on the first measurement of flux-integrated single differential cross sections for charged-current (CC) muon neutrino (ν_{μ}) scattering on argon with a muon and a proton in the final state, ^{40}Ar (ν_{μ},μp)X. The measurement was carried out using the Booster Neutrino Beam at Fermi National Accelerator Laboratory and the MicroBooNE liquid argon time projection chamber detector with an exposure of 4.59×10^{19} protons on target. Events are selected to enhance the contribution of CC quasielastic (CCQE) interactions. The data are reported in terms of a total cross section as well as single differential cross sections in final state muon and proton kinematics. We measure the integrated per-nucleus CCQE-like cross section (i.e., for interactions leading to a muon, one proton, and no pions above detection threshold) of (4.93±0.76_{stat}±1.29_{sys})×10^{-38}  cm^{2}, in good agreement with theoretical calculations. The single differential cross sections are also in overall good agreement with theoretical predictions, except at very forward muon scattering angles that correspond to low-momentum-transfer events.

Improved Limits on Millicharged Particles Using the ArgoNeuT Experiment at Fermilab

A search for millicharged particles, a simple extension of the standard model, has been performed with the ArgoNeuT detector exposed to the Neutrinos at the Main Injector beam at Fermilab. The ArgoNeuT liquid argon time projection chamber detector enables a search for millicharged particles through the detection of visible electron recoils. We search for an event signature with two soft hits (MeV-scale energy depositions) aligned with the upstream target. For an exposure of the detector of 1.0×10^{20} protons on target, one candidate event has been observed, compatible with the expected background. This search is sensitive to millicharged particles with charges between 10^{-3}e and 10^{-1}e and with masses in the range from 0.1 to 3 GeV. This measurement provides leading constraints on millicharged particles in this large unexplored parameter space region.

Safety of hospital discharge before return of bowel function after elective colorectal surgery

BACKGROUND

Ileus is common after colorectal surgery and is associated with an increased risk of postoperative complications. Identifying features of normal bowel recovery and the appropriateness for hospital discharge is challenging. This study explored the safety of hospital discharge before the return of bowel function.

METHODS

A prospective, multicentre cohort study was undertaken across an international collaborative network. Adult patients undergoing elective colorectal resection between January and April 2018 were included. The main outcome of interest was readmission to hospital within 30 days of surgery. The impact of discharge timing according to the return of bowel function was explored using multivariable regression analysis. Other outcomes were postoperative complications within 30 days of surgery, measured using the Clavien-Dindo classification system.

RESULTS

A total of 3288 patients were included in the analysis, of whom 301 (9·2 per cent) were discharged before the return of bowel function. The median duration of hospital stay for patients discharged before and after return of bowel function was 5 (i.q.r. 4-7) and 7 (6-8) days respectively (P < 0·001). There were no significant differences in rates of readmission between these groups (6·6 versus 8·0 per cent; P = 0·499), and this remained the case after multivariable adjustment for baseline differences (odds ratio 0·90, 95 per cent c.i. 0·55 to 1·46; P = 0·659). Rates of postoperative complications were also similar in those discharged before versus after return of bowel function (minor: 34·7 versus 39·5 per cent; major 3·3 versus 3·4 per cent; P = 0·110).

CONCLUSION

Discharge before return of bowel function after elective colorectal surgery appears to be safe in appropriately selected patients.

Safety and efficacy of non-steroidal anti-inflammatory drugs to reduce ileus after colorectal surgery

BACKGROUND

Ileus is common after elective colorectal surgery, and is associated with increased adverse events and prolonged hospital stay. The aim was to assess the role of non-steroidal anti-inflammatory drugs (NSAIDs) for reducing ileus after surgery.

METHODS

A prospective multicentre cohort study was delivered by an international, student- and trainee-led collaborative group. Adult patients undergoing elective colorectal resection between January and April 2018 were included. The primary outcome was time to gastrointestinal recovery, measured using a composite measure of bowel function and tolerance to oral intake. The impact of NSAIDs was explored using Cox regression analyses, including the results of a centre-specific survey of compliance to enhanced recovery principles. Secondary safety outcomes included anastomotic leak rate and acute kidney injury.

RESULTS

A total of 4164 patients were included, with a median age of 68 (i.q.r. 57-75) years (54·9 per cent men). Some 1153 (27·7 per cent) received NSAIDs on postoperative days 1-3, of whom 1061 (92·0 per cent) received non-selective cyclo-oxygenase inhibitors. After adjustment for baseline differences, the mean time to gastrointestinal recovery did not differ significantly between patients who received NSAIDs and those who did not (4·6 versus 4·8 days; hazard ratio 1·04, 95 per cent c.i. 0·96 to 1·12; P = 0·360). There were no significant differences in anastomotic leak rate (5·4 versus 4·6 per cent; P = 0·349) or acute kidney injury (14·3 versus 13·8 per cent; P = 0·666) between the groups. Significantly fewer patients receiving NSAIDs required strong opioid analgesia (35·3 versus 56·7 per cent; P < 0·001).

CONCLUSION

NSAIDs did not reduce the time for gastrointestinal recovery after colorectal surgery, but they were safe and associated with reduced postoperative opioid requirement.

First Measurement of Inclusive Muon Neutrino Charged Current Differential Cross Sections on Argon at E_{ν}∼0.8 GeV with the MicroBooNE Detector

We report the first measurement of the double-differential and total muon neutrino charged current inclusive cross sections on argon at a mean neutrino energy of 0.8 GeV. Data were collected using the MicroBooNE liquid argon time projection chamber located in the Fermilab Booster neutrino beam and correspond to 1.6×10^{20} protons on target of exposure. The measured differential cross sections are presented as a function of muon momentum, using multiple Coulomb scattering as a momentum measurement technique, and the muon angle with respect to the beam direction. We compare the measured cross sections to multiple neutrino event generators and find better agreement with those containing more complete treatment of quasielastic scattering processes at low Q^{2}. The total flux integrated cross section is measured to be 0.693±0.010(stat)±0.165(syst)×10^{-38}  cm^{2}.

OS12.6 Intracranial GBM PDX Mutations Induced by Temozolomide Treatment

BACKGROUND

Temozolomide (TMZ) is routinely used in the post-surgical treatment of patients with newly diagnosed glioblastoma (GBM). Nearly all GBM recur following TMZ treatment, and there is an increasing body of data that detail TMZ-associated mutations in recurrent GBM. In vivo models of recurrent GBM are scarce in comparison to models of treatment-naïve GBM.

MATERIAL AND METHODS

Mice with intracranial treatment naïve GBM patient derived xenograft (PDX) were treated with radiotherapy (RT) only, TMZ only, or RT + TMZ. Tumors were monitored for recovery from treatment by bioluminescence imaging (BLI), and upon animal subject decline due to growing tumor, subjects were euthanized, with viable intracranial tumor dissected and used to establish subcutaneous tumor in new animal hosts that received no treatment. Subcutaneous tumors were sequentially passaged through two additional animal hosts. DNA was extracted from third passage subcutaneous tumors and subjected to full exome sequencing. PDX exome sequence data were examined for genes with nonsynonymous frameshift and nonsense variants (mutations).

RESULTS

Exome sequence analysis showed striking differences between PDX receiving RT only vs. TMZ with or without RT. Most notable is the substantially greater incidence of G-C to A-T transition mutations in TMZ-treated PDX, which are a signature of TMZ treatment. All TMZ-treated PDX also showed substantially more genes being mutated than PDX receiving RT only: one cycle RT only = 88; one cycle TMZ only = 339; one cycle of concurrent RT + TMZ = 531; one cycle of concurrent RT + TMZ followed by two additional cycles of TMZ only = 1502. The PDX subjected to multiple cycles of TMZ treatment prior to establishment as a subcutaneous tumor has shown stable resistance to TMZ treatment in subsequent experiments. Importantly, TMZ-treated PDX had mutations in LTBP4, MSH6, and PREX1 genes that are enriched in patient GBM following recurrence after initial TMZ treatment (Nat Genet 2016;48:768–76); these genes were not mutated in PDX receiving RT only.

CONCLUSION

Our study results support the following: 1) Intracranial GBM PDX treated with TMZ develop a global genomic treatment signature, as well as specific mutations that are observed in recurrent patient GBMs; 2) Mutations detected in TMZ-treated intracranial tumors are stable, persisting after repeated subcutaneous passages without further treatment; 3) Paired naïve and TMZ-treated GBM PDX will facilitate studies aimed at increasing our understanding of TMZ resistance, and help identify new therapies for more effective treatment of recurrent GBM.

Search for Sterile Neutrinos in MINOS and MINOS+ Using a Two-Detector Fit

A search for mixing between active neutrinos and light sterile neutrinos has been performed by looking for muon neutrino disappearance in two detectors at baselines of 1.04 and 735 km, using a combined MINOS and MINOS+ exposure of 16.36×10^{20} protons on target. A simultaneous fit to the charged-current muon neutrino and neutral-current neutrino energy spectra in the two detectors yields no evidence for sterile neutrino mixing using a 3+1 model. The most stringent limit to date is set on the mixing parameter sin^{2}θ_{24} for most values of the sterile neutrino mass splitting Δm_{41}^{2}>10^{-4}  eV^{2}.

Abstract P6-03-01: Development of patient-derived xenograft tumor model with organ-specific metastatic potential for evaluation of new therapeutics for hormone receptor-positive advanced breast cancer

Background: Breast cancer (BC) is a heterogeneous disease with most common metastatic sites of liver, lung, brain, and bone. Endocrine resistance in hormone receptor-positive (HR+) advanced BC (ABC) cancer is a clinical challenge. ESR1 mutations are a key mechanism in acquired resistance, primarily occurs after exposure to endocrine therapy such as aromatase inhibitors but also selective estrogen modulators and degraders (i.e. Tamoxifen and Fulvestrant). Circulating tumor cells (CTCs) enumeration is a prognostic biomarker in ABC but the relation between the onset of ESR1 mutations and CTCs status is still unclear. Aim of this project is to define the clinical behavior of ESR1 mutated ABC in terms of metastasizing potential, through CTC enumeration and pattern; and to establish ESR1 mutated HR+ ABC PDX models able to recapitulate these characteristics.

Methods: CTCs and circulating tumor DNA (ctDNA) were characterized in 55 HR+ ABC patients. ESR1 mutations status from 55 patient plasma cell-free DNA were generated using Guardant Next Generation Sequencing. Samples were also examined for numbers of CTCs by CellSearch. Association of ESR1 mutations with sites of distant organ metastasis and with CTC enumeration was analyzed by Chi square test and Kruskal–Wallis test, respectively. In preclinical model development, six samples of pleural effusion-derived tumor cells from Stage IV HR+ ABC patients were collected to establish HR+ ABC with ESR1 mutation PDX tumor model and its derived 3D organoid/spheroid cultures

Results: ESR1 mutations were identified in 10 out of 55 patients (4 Y537S variant and 3 D538G variant, 4 other variants, 1 patient with both variants). In 55 patients, 72 visceral vs 27 bone metastatic incidences were observed; the data indicated 9 observed vs 4.5 expected in ESR1 mutated and 16 observed vs 20.5 expected in wild type (WT) (P=0.003) for liver metastasis; 10 observed vs 7.1 expected in ESR1 mutated and 29 observed vs 31.9 expected in WT (P=0.026) for bone metastasis. Further liver metastasis analysis of individual hot spot mutation site indicated 4 observed vs 1.8 expected in Y537S and 21 observed vs 23.2 expected in WT (P=0.037); and 3 observed vs 1.4 expected in D538G and 22 observed vs 23.6 expected in wild type (P=0.088). The analysis of correlation/distribution between CTCs numbers and ESR1 mutated suggested CTCs median of 13 (IQR 7-49) in ESR1 mutated and 0 (IQR 0-4) in WT HR+ patients (P=0.0044). Four ABC PDX tumor models were developed in immunodeficient NSG female mice demonstrated by pathology to have highly heterogeneous characteristics and metastatic features of the origin patient tumor, in particular, breast fat pad xenografted PDX tumor can result in metastasis to liver and lung tissue. In addition, two patient 3D tumor organoid/spheroid cultures were successfully established.

Conclusions: ESR1 mutated ABC is associated with more aggressive (Stage IV) clinical behavior demonstrated by association with visceral metastases and CTCs detection. ESR1-mutated PDX models recapitulate aggressive features of the disease and can be used for preclinical testing of novel agents in endocrine resistant disease.

Citation Format: Qiang W, Zhong Z, Gerratana L, Zhang Y, Zhang Q, Gursel D, Wei J-J, Bleher R, James C, O'Halloran T, Cristofanilli M. Development of patient-derived xenograft tumor model with organ-specific metastatic potential for evaluation of new therapeutics for hormone receptor-positive advanced breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-03-01.

Ultra-short term HRV features as surrogates of short term HRV: a case study on mental stress detection in real life

Background

This paper suggests a method to assess the extent to which ultra-short Heart Rate Variability (HRV) features (less than 5 min) can be considered as valid surrogates of short HRV features (nominally 5 min). Short term HRV analysis has been widely investigated for mental stress assessment, whereas the validity of ultra-short HRV features remains unclear. Therefore, this study proposes a method to explore the extent to which HRV excerpts can be shortened without losing their ability to automatically detect mental stress.

Methods

ECGs were acquired from 42 healthy subjects during a university examination and resting condition. 23 features were extracted from HRV excerpts of different lengths (i.e., 30 s, 1 min, 2 min, 3 min, and 5 min). Significant differences between rest and stress phases were investigated using non-parametric statistical tests at different time-scales. Features extracted from each ultra-short length were compared with the standard short HRV features, assumed as the benchmark, via Spearman’s rank correlation analysis and Bland-Altman plots during rest and stress phases. Using data-driven machine learning approaches, a model aiming to detect mental stress was trained, validated and tested using short HRV features, and assessed on the ultra-short HRV features.

Results

Six out of 23 ultra-short HRV features (MeanNN, StdNN, MeanHR, StdHR, HF, and SD2) displayed consistency across all of the excerpt lengths (i.e., from 5 to 1 min) and 3 out of those 6 ultra-short HRV features (MeanNN, StdHR, and HF) achieved good performance (accuracy above 88%) when employed in a well-dimensioned automatic classifier.

Conclusion

This study concluded that 6 ultra-short HRV features are valid surrogates of short HRV features for mental stress investigation.

Electronic supplementary material

The online version of this article (10.1186/s12911-019-0742-y) contains supplementary material, which is available to authorized users.

Iodine contrast agents do not influence Platelet-Rich Plasma function at an early time point in vitro

BACKGROUND

Iodine contrast agents (ICAs) are routinely used by radiologists to help guide intra-articular infiltrations. The aim of this study was to assess the in vitro effects of ICA on platelet function of human autologous Platelet-Rich Plasma (PRP).

METHODS

One hundred thirty-seven consecutive patients with symptomatic femoral-patellar osteoarthritis were included. All were addressed to our institution for a fluoroscopy-guided intra-articular PRP infiltration of the pathological femoral-patellar joint. For each patient, 500 μl of PRP were sampled before intra-articular injection. First, PRP samples were mixed with 50 μl of 2 widely used ICA: Visipaque270® (Iodixanol, n = 58) and Iopamiron200® (Iopamidol, n = 69). PRP concentration ([PRP]) was measured at different delays of incubation (t = 0, 5, 10, 15, 20 and 30 min) enabling to calculate PRP ratio (defined as [PRP](t)/[PRP](0mn)) at each delay, for each mixture, in order to quantitatively assess the influence of ICA on PRP ratio. Second, the PRP samples of 10 additional patients were mixed with Visipaque270®, Visipaque270®, Iopamiron200® and phosphate buffer saline (PBS: control solution) in order to qualitatively assess the influence of ICA on platelet aggregation, using ADP, Collagen, Arachidonic acid and TRAP tests. The surface expression of human P-selectin, a marker of α-granule release, in the PRP + Visipaque270® and PRP + Iopamiron200® mixtures was finally compared. Repeated-measures ANOVA, classical 2-way ANOVA and Wilcoxon matched-pairs test were used to study the influence of ICA on PRP quality.

RESULTS

There was no significant change in PRP ratio during the first 30mn of incubation (p = 0.991) whatever the ICA (p = 0.926). Whatever the aggregation test, there was no significant difference in the percentage of platelet aggregation between PRP + PBS, PRP + Visipaque270® and PRP + Iopamiron200® (p = 0.998), nor between PRP + PBS and PRP + Visipaque320® (p = 0.470). Finally, there was no significant difference in P-selectin expression between the PRP + Visipaque270® and PRP + Iopamiron200® mixtures (p = 0.500).

CONCLUSION

At early delays of incubation, Visipaque® and Iopamiron®, which are two widely used ICA for intra-articular infiltrations, did not influence the in vitro platelet function nor the quality of PRP.