Investigation of F508del CFTR unfolding and a search for stabilizing small molecules.

Mutation of phenylalanine at position 508 in the cystic fibrosis transmembrane conductance regulator (F508del CFTR) yields a protein unstable at physiological temperatures that is rapidly degraded in the cell. This mutation is present in about 90% of cystic fibrosis patients, hence there is great interest in compounds reversing its instability. We have previously reported the expression of the mutated protein at low temperature and its purification in detergent. Here we describe the use of the protein to screen compounds present in a library of Federal Drug Administration (FDA) - approved drugs and also in a small natural product library. The kinetics of unfolding of F508del CFTR at 37 °C were probed by the increase in solvent-exposed cysteine residues accessible to a fluorescent reporter molecule. This occurred in a bi-exponential manner with a major (≈60%) component of half-life around 5 min and a minor component of around 60 min. The faster kinetics match those observed for loss of channel activity of F508del CFTR in cells at 37 °C. Most compounds tested had no effect on the fluorescence increase, but some were identified that significantly slowed the kinetics. The general properties of these compounds, and any likely mechanisms for inducing stability in purified CFTR are discussed. These experimental data may be useful for artificial intelligence - aided design of CFTR-specific drugs and in the identification of stabilizing additives for membrane proteins (in general).

Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance.

ABCG2 is an important ATP-binding cassette transporter impacting the absorption and distribution of over 200 chemical toxins and drugs. ABCG2 also reduces the cellular accumulation of diverse chemotherapeutic agents. Acquired somatic mutations in the phylogenetically conserved amino acids of ABCG2 might provide unique insights into its molecular mechanisms of transport. Here, we identify a tumor-derived somatic mutation (Q393K) that occurs in a highly conserved amino acid across mammalian species. This ABCG2 mutant seems incapable of providing ABCG2-mediated drug resistance. This was perplexing because it is localized properly and retained interaction with substrates and nucleotides. Using a conformationally sensitive antibody, we show that this mutant appears "locked" in a non-functional conformation. Structural modeling and molecular dynamics simulations based on ABCG2 cryo-EM structures suggested that the Q393K interacts with the E446 to create a strong salt bridge. The salt bridge is proposed to stabilize the inward-facing conformation, resulting in an impaired transporter that lacks the flexibility to readily change conformation, thereby disrupting the necessary communication between substrate binding and transport.

Characterizing Trends in Chronic Superficial Venous Disease Treatment among Medicare Beneficiaries from 2010 to 2018.

This study describes trends in surgical versus endovascular interventions for treatment of chronic superficial venous disease (SVD) in the Medicare population. Medicare Part B data from 2010 to 2018 were obtained. Claims for SVD treatment were identified using Healthcare Common Procedure Coding System codes. Total percentage change in utilization rates and market share was determined for each provider group. Utilization of SVD treatments increased by 58%, mostly owing to growing utilization of endovascular treatments. There was a 66% decrease in surgical treatments. The utilization of ablation and sclerotherapy plateaued in 2016 and decreased in 2017-2018 with the advent of mechanochemical ablation, endovenous microfoam, and cyanoacrylate adhesive, respectively. Analysis showed that endovascular utilization increased across most specialties, with the largest growth seen in cardiology by 427%. Radiologists showed utilization growth of 125%, encompassing 11% of the market share. Endovascular treatment for SVD remains predominant, with increased utilization and concomitant decrease in surgical methods.

The net electrostatic potential and hydration of ABCG2 affect substrate transport.

ABCG2 is a medically important ATP-binding cassette transporter with crucial roles in the absorption and distribution of chemically-diverse toxins and drugs, reducing the cellular accumulation of chemotherapeutic drugs to facilitate multidrug resistance in cancer. ABCG2's capacity to transport both hydrophilic and hydrophobic compounds is not well understood. Here we assess the molecular basis for substrate discrimination by the binding pocket. Substitution of a phylogenetically-conserved polar residue, N436, to alanine in the binding pocket of human ABCG2 permits only hydrophobic substrate transport, revealing the unique role of N436 as a discriminator. Molecular dynamics simulations show that this alanine substitution alters the electrostatic potential of the binding pocket favoring hydration of the transport pore. This change affects the contact with substrates and inhibitors, abrogating hydrophilic compound transport while retaining the transport of hydrophobic compounds. The N436 residue is also required for optimal transport inhibition of ABCG2, as many inhibitors are functionally impaired by this ABCG2 mutation. Overall, these findings have biomedical implications, broadly extending our understanding of substrate and inhibitor interactions.

Updated trends in percutaneous renal arteriography among radiologists and other specialties.

PURPOSE: Prior studies have demonstrated an overall decline in percutaneous renal artery angioplasty with and without stenting from 1988 to 2009. We evaluated the recent utilization trends in percutaneous renal arteriography (PTRA) among radiologists and non-radiologist providers from 2010 to 2018. METHODS: Data from the 2010-2018 nationwide Medicare Part B fee-for-service database were used to tabulate case volumes for PTRA. Annual utilization rates per 10,000 Medicare beneficiaries were calculated and aggregated based on physician specialty: radiologists, cardiologists, vascular surgeons, general surgeons, or others. RESULTS: From 2010 to 2018, the overall utilization rate of PTRA markedly declined (-72% change; from 15.5 to 4.3 cases per 10,000 Medicare beneficiaries). Proportionally, the cardiologist share of PTRA saw the greatest decline, falling from 74% market share in 2010 (11.4/15.5 cases) to only 36% market share in 2018 (1.6/4.3 cases). The market share of PTRA performed by radiologists grew from 12% market share in 2010 (1.9/15.5 cases) to 28% in 2018 (1.2/4.3 cases); despite this, the absolute number of PTRA performed by radiologists saw a smaller decline over this period (-34%; 1.9 to 1.2 cases). CONCLUSION: The total utilization rates of PTRA in the Medicare population has continued to decline from 2010 to 2018, likely due to clinical trials suggesting limited efficacy of angioplasty and stenting in the treatment of renovascular hypertension and other factors such as declining reimbursement. The overall and per-specialty rates continue to decline, reflecting an overarching trend away from procedural management of renovascular hypertension.

Pelvic Venous Disorders (PeVD).

Pelvic venous disorders (PeVDs) have replaced the concept of pelvic congestion syndrome encompassing venous origin chronic pelvic pain (VO-CPP) in women. The evaluation of women with VO-CPP includes the assessment for other causes of pelvic pain as well as imaging evaluation for pelvic varicosities measuring greater than 5 mm diameter, ovarian vein diameter, and flow direction, as well as iliac vein diameter and signs of compression. Proper identification of these patients can lead to high degrees of success eliminating chronic pelvic pain following ovarian vein embolization and/or iliac vein stenting. Strong encouragement is provided to use the symptoms, varices, pathophysiology classification for these patients and upcoming research studies on the specific symptoms of patients with VO-CPP will help elucidate patient selection for intervention. Additional future randomized controlled trials are also upcoming to evaluate for outcomes of ovarian vein embolization and iliac vein.

Virtual Drug Repositioning as a Tool to Identify Natural Small Molecules That Synergize with Lumacaftor in F508del-CFTR Binding and Rescuing.

Cystic fibrosis is a hereditary disease mainly caused by the deletion of the Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. Cystic fibrosis remains a potentially fatal disease, but it has become treatable as a chronic condition due to some CFTR-rescuing drugs that, when used in combination, increase in their therapeutic effect due to a synergic action. Also, dietary supplementation of natural compounds in combination with approved drugs could represent a promising strategy to further alleviate cystic fibrosis symptoms. On these bases, we screened by in silico drug repositioning 846 small synthetic or natural compounds from the AIFA database to evaluate their capacity to interact with the highly druggable lumacaftor binding site of F508del-CFTR. Among the identified hits, nicotinamide (NAM) was predicted to accommodate into the lumacaftor binding region of F508del-CFTR without competing against the drug but rather stabilizing its binding. The effective capacity of NAM to bind F508del-CFTR in a lumacaftor-uncompetitive manner was then validated experimentally by surface plasmon resonance analysis. Finally, the capacity of NAM to synergize with lumacaftor increasing its CFTR-rescuing activity was demonstrated in cell-based assays. This study suggests the possible identification of natural small molecules devoid of side effects and endowed with the capacity to synergize with drugs currently employed for the treatment of cystic fibrosis, which hopefully will increase the therapeutic efficacy with lower doses.

ATP-Binding Cassette Transporters: Snap-on Complexes?

ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins in prokaryotic organisms. Much is now understood about the structure of these transporters and many reviews have been written on that subject. In contrast, less has been written on the assembly of ABC transporter complexes and this will be a major focus of this book chapter. The complexes are formed from two cytoplasmic subunits that are highly conserved (in terms of their primary and three-dimensional structures) across the whole family. These ATP-binding subunits give rise to the name of the family. They must assemble with two transmembrane subunits that will typically form the permease component of the transporter. The transmembrane subunits have been found to be surprisingly diverse in structure when the whole family is examined, with seven distinct folds identified so far. Hence nucleotide-binding subunits appear to have been bolted on to a variety of transmembrane platforms during evolution, leading to a greater variety in function. Furthermore, many importers within the family utilise a further external substrate-binding component to trap scarce substrates and deliver them to the correct permease components. In this chapter, we will discuss whether assembly of the various ABC transporter subunits occurs with high fidelity within the crowded cellular environment and whether promiscuity in assembly of transmembrane and cytoplasmic components can occur. We also discuss the new AlphaFold protein structure prediction tool which predicts a new type of transmembrane domain fold within the ABC transporters that is associated with cation exporters of bacteria and plants.

Structure of ABCB1/P-Glycoprotein in the Presence of the CFTR Potentiator Ivacaftor.

ABCB1/P-glycoprotein is an ATP binding cassette transporter that is involved in the clearance of xenobiotics, and it affects the disposition of many drugs in the body. Conformational flexibility of the protein within the membrane is an intrinsic part of its mechanism of action, but this has made structural studies challenging. Here, we have studied different conformations of P-glycoprotein simultaneously in the presence of ivacaftor, a known competitive inhibitor. In order to conduct this, we used high contrast cryo-electron microscopy imaging with a Volta phase plate. We associate the presence of ivacaftor with the appearance of an additional density in one of the conformational states detected. The additional density is in the central aqueous cavity and is associated with a wider separation of the two halves of the transporter in the inward-facing state. Conformational changes to the nucleotide-binding domains are also observed and may help to explain the stimulation of ATPase activity that occurs when transported substrate is bound in many ATP binding cassette transporters.

Kite-Shaped Molecules Block SARS-CoV-2 Cell Entry at a Post-Attachment Step.

Anti-viral small molecules are currently lacking for treating coronavirus infection. The long development timescales for such drugs are a major problem, but could be shortened by repurposing existing drugs. We therefore screened a small library of FDA-approved compounds for potential severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antivirals using a pseudovirus system that allows a sensitive read-out of infectivity. A group of structurally-related compounds, showing moderate inhibitory activity with IC50 values in the 2-5 µM range, were identified. Further studies demonstrated that these "kite-shaped" molecules were surprisingly specific for SARS-CoV-1 and SARS-CoV-2 and that they acted early in the entry steps of the viral infectious cycle, but did not affect virus attachment to the cells. Moreover, the compounds were able to prevent infection in both kidney- and lung-derived human cell lines. The structural homology of the hits allowed the production of a well-defined pharmacophore that was found to be highly accurate in predicting the anti-viral activity of the compounds in the screen. We discuss the prospects of repurposing these existing drugs for treating current and future coronavirus outbreaks.

Enrichment and Liquid Chromatography-Mass Spectrometry Analysis of Trastuzumab and Pertuzumab Using Affimer Reagents.

Trastuzumab and pertuzumab are monoclonal antibodies used in the treatment of human epidermal growth factor receptor-2 (HER2)-positive breast cancer. Therapeutic proteins may undergo chemical modifications that may affect the results of bioanalytical assays, as well as their therapeutic efficacy. Modifications may arise during production and storage, as well as after administration to patients. Studying in vivo biotransformation of monoclonal, therapeutic antibodies requires their enrichment from plasma to discriminate them from endogenous antibodies, as well as from other plasma proteins. To this end, we screened Affimer reagents for selectivity toward trastuzumab or pertuzumab. Affimer reagents are alternative binding proteins possessing two variable binding loops that are based on the human protease inhibitor stefin A or phytocystatin protein scaffolds. Affimer reagents were selected from an extensive library by phage display. The four best-performing binders for each therapeutic antibody were prioritized using a microtiter plate-based approach combined with liquid chromatography-mass spectrometry (LC-MS) in the selected reaction monitoring (SRM) mode. These Affimer reagents were immobilized via engineered 6-His or Cys tags to Ni2+- or maleimide beads, respectively. Recovery values of 70% and higher were obtained for both trastuzumab and pertuzumab when spiked at 100, 150, and 200 µg/mL concentrations in human plasma followed by trypsin digestion in the presence of 0.5% sodium deoxycholate and 10 mM dithiothreitol (DTT). Notably, the maleimide beads showed undetectable unspecific binding to endogenous immunoglobulin G (IgGs) or other plasma proteins when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The enrichment method was applied to samples from stress tests of the antibodies at 37 °C to mimic in vivo conditions.

Radiologists and Clinical Trials: Part 1 The Truth About Reader Disagreements.

The debate over human visual perception and how medical images should be interpreted have persisted since X-rays were the only imaging technique available. Concerns over rates of disagreement between expert image readers are associated with much of the clinical research and at times driven by the belief that any image endpoint variability is problematic. The deeper understanding of the reasons, value, and risk of disagreement are somewhat siloed, leading, at times, to costly and risky approaches, especially in clinical trials. Although artificial intelligence promises some relief from mistakes, its routine application for assessing tumors within cancer trials is still an aspiration. Our consortium of international experts in medical imaging for drug development research, the Pharma Imaging Network for Therapeutics and Diagnostics (PINTAD), tapped the collective knowledge of its members to ground expectations, summarize common reasons for reader discordance, identify what factors can be controlled and which actions are likely to be effective in reducing discordance. Reinforced by an exhaustive literature review, our work defines the forces that shape reader variability. This review article aims to produce a singular authoritative resource outlining reader performance's practical realities within cancer trials, whether they occur within a clinical or an independent central review.

Radiologists and Clinical Trials: Part 2: Practical Statistical Methods for Understanding and Monitoring Independent Reader Performance.

Though many clinical trials rely on medical image evaluations for primary or key secondary endpoints, the methods to monitor reader performance are all too often mired in the legacy use of adjudication rates. If misused, this simple metric can be misleading and sometimes entirely contradictory. Furthermore, attempts to overcome the limitations of adjudication rates using de novo or ad hoc methods often ignore well-established research conducted over the last half-century and can lead to inaccurate conclusions or variable interpretations. Underperforming readers can be missed, expert readers retrained, or worse, replaced. This paper aims to standardize reader performance evaluations using proven statistical methods. Additionally, these methods will describe how to discriminate between scenarios of concern and normal medical interpretation variability. Statistical methods are provided for inter-reader and intra-reader variability and bias, including the adjudicator's bias. Finally, we have compiled guidelines for calculating correct sample sizes, considerations for intra-reader memory recall, and applying alternative designs for independent readers.

Imaging approach to COVID-19 associated pulmonary embolism.

The novel coronavirus disease-2019 (COVID-19) illness and deaths, caused by the severe acute respiratory syndrome coronavirus-2, continue to increase. Multiple reports highlight the thromboembolic complications, such as pulmonary embolism (PE), in COVID-19. Imaging plays an essential role in the diagnosis and management of COVID-19 patients with PE. There continues to be a rapid evolution of knowledge related to COVID-19 associated PE. This review summarises the current understanding of prevalence, pathophysiology, role of diagnostic imaging modalities, and management, including catheter-directed therapy for COVID-19 associated PE. It also describes infection control considerations for the radiology department while providing care for patients with COVID-19 associated PE.

ATP binding cassette importers in eukaryotic organisms.

ATP-binding cassette (ABC) transporters are ubiquitous across all realms of life. Dogma suggests that bacterial ABC transporters include both importers and exporters, whilst eukaryotic members of this family are solely exporters, implying that ABC import function was lost during evolution. This view is being challenged, for example energy-coupling factor (ECF)-type ABC importers appear to fulfil important roles in both algae and plants where they form the ABCI sub-family. Herein we discuss whether bacterial Type I and Type II ABC importers also made the transition into extant eukaryotes. Various studies suggest that Type I importers exist in algae and the liverwort family of primitive non-vascular plants, but not in higher plants. The existence of eukaryotic Type II importers is also supported: a transmembrane protein homologous to vitamin B12 import system transmembrane protein (BtuC), hemin transport system transmembrane protein (HmuU) and high-affinity zinc uptake system membrane protein (ZnuB) is present in the Cyanophora paradoxa genome. This protein has homologs within the genomes of red algae. Furthermore, its candidate nucleotide-binding domain (NBD) shows closest similarity to other bacterial Type II importer NBDs such as BtuD. Functional studies suggest that Type I importers have roles in maintaining sulphate levels in the chloroplast, whilst Type II importers probably act as importers of Mn2+ or Zn2+ , as inferred by comparisons with bacterial homologs. Possible explanations for the presence of these transporters in simple plants, but not in other eukaryotic organisms, are considered. In order to utilise the existing nomenclature for eukaryotic ABC proteins, we propose that eukaryotic Type I and II importers be classified as ABCJ and ABCK transporters, respectively.

Supporting contaminated sites management with Multiple Criteria Decision Analysis: Demonstration of a regulation-consistent approach.

This study proposes a set of key decision-making features of the contaminated site remediation process to assist in selecting the most appropriate decision support method(s). Using a case study consistent with the requirements of the U.S. regulation for contaminated sites management, this article shows that suitable Multiple Criteria Decision Analysis methods can be selected based on a dynamic and evolving problem structuring. The selected methods belong to the family of PROMETHEE methods and can provide ranking recommendations of the considered alternatives using variable structures of the criteria, evaluation of the alternatives and exploitation of the preference model. It was found that in order to support a quick and up-to-date application of powerful decision support techniques in the process of remediation of contaminated sites, decision analysts and stakeholders should interact and co-develop the process. This research also displays how such interactions can guarantee a transparent and traceable decision recommendation so that stakeholders can better understand why some alternatives perform comprehensively better than others when a multitude of inputs is used in the decision-making process.

Five Steps to Leading Your Team in the Virtual COVID-19 Workplace.

The emergence of COVID-19 has presented employees and employers new challenges as many employees and managers were forced to work in a remote environment for the first time. For many reasons, managing virtual teams is different than managing employees in a traditional face-to-face office environment. Although many managers have been learning how to lead their virtual teams over the last several months, we offer five steps for leaders to follow for how to maximize the effectiveness of a remote workplace. By taking specific actions and ensuring the organization has a culture to support their virtual workforce, leaders can improve the performance output and engagement of their teams. The five steps are: first establish and explain the new reality; second, establish and maintain a culture of trust; third, upgrade leadership communication tools and techniques to better inform virtual employees; fourth, encourage shared leadership among team members; and fifth, to create and periodically perform alignment audits to ensure virtual employees are aligned with the organization's cultural values including its commitment to mission. All these steps start with the realization that managing a team is going to be different when the members are dispersed, and new leadership strategies, communication routines and tools are required.

What monomeric nucleotide binding domains can teach us about dimeric ABC proteins.

The classic conceptualization of ATP binding cassette (ABC) transporter function is an ATP-dependent conformational change coupled to transport of a substrate across a biological membrane via the transmembrane domains (TMDs). The binding of two ATP molecules within the transporter's two nucleotide binding domains (NBDs) induces their dimerization. Despite retaining the ability to bind nucleotides, isolated NBDs frequently fail to dimerize. ABC proteins without a TMD, for example ABCE and ABCF, have NBDs tethered via elaborate linkers, further supporting that NBD dimerization does not readily occur for isolated NBDs. Intriguingly, even in full-length transporters, the NBD-dimerized, outward-facing state is not as frequently observed as might be expected. This leads to questions regarding what drives NBD interaction and the role of the TMDs or linkers. Understanding the NBD-nucleotide interaction and the subsequent NBD dimerization is thus pivotal for understanding ABC transporter activity in general. Here, we hope to provide new insights into ABC protein function by discussing the perplexing issue of (missing) NBD dimerization in isolation and in the context of full-length ABC proteins.

Geophysical Assessment of a Proposed Landfill Site in Fredericktown, Missouri.

In cooperation with the U.S. Environmental Protection Agency (EPA), the U.S. Geological Survey (USGS) collected numerous types of geophysical data at a site in Fredericktown, Missouri, in June 2018. Various geophysical surveys were collectively used to help evaluate the overall suitability of the site for use as a mine waste-soil and sediment repository, and to evaluate the suite of geophysical methods for rapid collection and preliminary assessment of sites with shallow sediments. Land-based geophysical methods, which included frequency-domain electromagnetic induction (FDEM), electrical resistivity tomography (ERT), horizontal-to-vertical spectral ratio passive seismic (HVSR), and shear-wave refraction, were used to determine the depths to crystalline bedrock and characterize the overlying unconsolidated sediments (or regolith). Water-borne FDEM profiles and forward-looking infrared (FLIR) thermal image surveys were conducted along the Fredericktown City Lake shoreline to identify locations of potential interactions between groundwater and surface water. Sediment temperature profilers were installed at two locations along the shoreline to characterize shallow unconsolidated sediment thermal properties and support the interpretation of the other geophysical surveys. Geophysical reconnaissance methods including the FDEM and HVSR methods, were used to rapidly evaluate the vertical and lateral extent of overburden, or unconsolidated sediments, overlying the bedrock at the site. The results of these methods were compared to reference geophysical methods of ERT and shear-wave refraction surveys that have greater accuracy and are more labor intensive and time-consuming. A goal of the project was the evaluation of the validity and reliability of this suite of reconnaissance geophysical methods as a means by which shallow (less than 3 meters (m)) sediments can be rapidly assessed. Two orthogonal ERT survey profiles, which used 28 electrodes spaced 1 m apart in dipole-dipole and combined Wenner-Schlumberger configurations, were collected to determine the subsurface resistivity. The results were inverted to produce electrical resistivity profiles that were compared to the FDEM and HVSR survey results. The FDEM data were collected along cleared paths through the proposed disposal cell locations. The data were inverted to generate depth-dependent estimates of electrical conductivity along the transects. An analysis of the depth of investigation (DOI) indicated the FDEM imaged to depths of about 3 m below land surface. The ERT, FDEM, and HVSR indicated the depth to crystalline bedrock was approximately 1.5 m below land surface with shallower and deeper areas. Results from this investigation indicate this suite of methods will likely perform well at sites with shallow depths to bedrock and strong conductivity and acoustic impedance contrasts, where the FDEM and HVSR methods can provide estimates of the depth to bedrock, and ERT and shear-wave refraction surveys might not be worth the added time and expense.

Structural and functional diversity calls for a new classification of ABC transporters.

Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP-binding cassette in the nucleotide-binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that is based on structural homology in the TMDs.