Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals

Polarization and charge transfer strongly characterize the ligand-receptor interaction when metal atoms are present, as for the Au(I)-biscarbene/DNA G-quadruplex complexes. In a previous work (J Comput Aided Mol Des2022, 36, 851-866) we used the ab initio FMO2 method at the RI-MP2/6-31G* level of theory with the PCM [1] solvation approach to calculate the binding energy (ΔEFMO) of two Au(I)-biscarbene derivatives, [Au(9-methylcaffein-8-ylidene)2]+ and [Au(1,3-dimethylbenzimidazole-2-ylidene)2]+, able to interact with DNA G-quadruplex motif. We found that ΔEFMO and ligand-receptor pair interaction energies (EINT) show very large negative values making the direct comparison with experimental data difficult and related this issue to the overestimation of the embedded charge transfer energy between fragments containing metal atoms. In this work, to improve the accuracy of the FMO method for predicting the binding affinity of metal-based ligands interacting with DNA G-quadruplex (Gq), we assess the effect of the following computational features: (i) the electron correlation, considering the Hartree-Fock (HF) and a post-HF method, namely RI-MP2; (ii) the two (FMO2) and three-body (FMO3) approaches; (iii) the basis set size (polarization functions and double-ζ vs. triple-ζ) and (iv) the embedding electrostatic potential (ESP). Moreover, the partial screening method was systematically adopted to simulate the solvent screening effect for each calculation. We found that the use of the ESP computed using the screened point charges for all atoms (ESP-SPTC) has a critical impact on the accuracy of both ΔEFMO and EINT, eliminating the overestimation of charge transfer energy and leading to energy values with magnitude comparable with typical experimental binding energies. With this computational approach, EINT values describe the binding efficiency of metal-based binders to DNA Gq more accurately than ΔEFMO. Therefore, to study the binding process of metal containing systems with the FMO method, the adoption of partial screening solvent method combined with ESP-SPCT should be considered. This computational protocol is suggested for FMO calculations on biological systems containing metals, especially when the adoption of the default ESP treatment leads to questionable results.

Towards a standardised cross-sectoral data access agreement template for research: a core set of principles for data access within trusted research environments

Introduction

Trusted Research Environments (TREs) are secure computing environments that provide access to data for approved researchers to use in studies that can save and improve lives. TREs rely on Data Access Agreements (DAAs) to bind researchers and their organisations to the terms and conditions of accessing the infrastructure and data use. However, DAAs can be overly lengthy, complex, and can contain outdated terms from historical data sharing agreements for physical exchange of data. This is often cited as a cause of significant delays to legal review and research projects starting.

Objectives

The aim was to develop a standardised DAA optimised for data science in TREs across the UK and framed around the 'Five Safes framework' for trustworthy data use. The DAA is underpinned by principles of data access in TREs, the development of which is described in this paper.

Methods

The Pan-UK Data Governance Steering Group of the UK Health Data Research Alliance led the development of a core set of data access principles. This was informed by a benchmarking exercise of DAAs used by established TREs and consultation with public members and stakeholders.

Results

We have defined a core set of principles for TRE data access that can be mapped to a common set of DAA terms for UK-based TREs. Flexibility will be ensured by including terms specific to TREs or specific data/data owners in customisable annexes. Public views obtained through public involvement and engagement (PIE) activities are also reported.

Conclusions

These principles provide the foundation for a standardised UK TRE DAA template, designed to support the growing ecosystem of TREs. By providing a familiar structure and terms, this template aims to build trust among data owners and the UK public and to provide clarity to researchers on their obligations to protect the data. Widespread adoption is intended to accelerate health data research by enabling faster approval of projects, ultimately enabling more timely and effective research.

Management of severe right lung cystic pulmonary interstitial emphysema in an infant at 24 weeks gestation with bedside selective left main stem bronchial intubation: Case report and review of the literature

Pulmonary interstitial emphysema (PIE) is a severe complication of mechanical ventilation in preterm infants. Selective bronchial intubation is a rarely used treatment strategy, as it is challenging, especially left main stem bronchial intubation. We report our experience in an infant at 24 weeks gestation with bedside left main stem bronchial intubation using flexible fiberoptic bronchoscopy. We also describe in detail the procedural details involved in the selective left main stem bronchial intubation including the helpful technique of gently bending the tip of the endotracheal tube to create "memory" to better direct the tube into the left main-stem bronchus while using the flexible fiberoptic bronchoscope. A review of the literature regarding selective bronchial intubation in newborn infants is presented. This case report and literature review suggest that bedside left main stem bronchial intubation using a flexible fiberoptic bronchoscope is a viable option to successfully manage even the most unstable extreme premature infant with unilateral right lung cystic PIE. This may potentially prevent a rare but necessary invasive surgical procedure like lobectomy or even death.

Live-Cell Cardiac-Specific High-Throughput Screening Platform for Drug-Like Molecules that Enhance Ca2+ Transport

We engineered a concatenated fluorescent biosensor and dual-wavelength fluorescence lifetime (FLT) detection, to perform high-throughput screening (HTS) in living cells for discovery of potential heart-failure drugs. Heart failure is correlated with insufficient activity of the sarcoplasmic reticulum Ca-pump (SERCA2a), often due to excessive inhibition by phospholamban (PLB), a small transmembrane protein. We sought to discover small molecules that restore SERCA2a activity by disrupting this inhibitory interaction between PLB and SERCA2a. Our approach was to fluorescently tag the two proteins and measure fluorescence resonance energy transfer (FRET) to detect changes in binding or structure of the complex. To optimize sensitivity to these changes, we engineered a biosensor that concatenates the two fluorescently labeled proteins on a single polypeptide chain. This SERCA2a-PLB FRET biosensor construct is functionally active and effective for HTS. By implementing 2-wavelength FLT detection at extremely high speed during primary HTS, we culled fluorescent compounds as false-positive Hits. In pilot screens, we identified Hits that alter the SERCA2a-PLB interaction, and a newly developed secondary calcium uptake assay revealed both activators and inhibitors of Ca-transport. We are implementing this approach for large-scale screens to discover new drug-like modulators of SERCA2a-PLB interactions for heart failure therapeutic development.

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, sensors, and transporters. Protein-protein interactions (PPIs) are a key part of their function. There are more than 645,000 reported disease-relevant PPIs in the human interactome, but drugs have been developed for only 2% of these targets. The advances in PPI-focused drug discovery are highly dependent on the availability of structural data and accurate computational tools for analysis of this data. Quantum mechanical approaches are often too expensive computationally, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed and the ability to reveal key interactions that would otherwise be hard to detect. FMO provides essential information for PPI drug discovery, namely, identification of key interactions formed between residues of two proteins, including their strength (in kcal/mol) and their chemical nature (electrostatic or hydrophobic). In this chapter, we have demonstrated how three different FMO-based approaches (pair interaction energy analysis (PIE analysis), subsystem analysis (SA) and analysis of protein residue networks (PRNs)) have been applied to study PPI in three protein-protein complexes.

Beyond cognitive measures: Empirical evidence supporting holistic medical school admissions practices and professional identity formation

This article was migrated. The article was marked as recommended. Background: Medical schools seek admissions methods that identify applicants who hold promise to become physicians who will navigate and shape the future medical landscape. The focus on traditional cognitive measures for admission has prompted calls for holistic admissions review during the past five years. Yet, empirical evidence linking selection measures to holistic admissions practices has not been fully established, including their relationship with professional identity formation over time. A non-cognitive admissions situational judgment screening test (CASPer) measuring personal and professional characteristics was added to the University of Illinois College of Medicine admissions process two years ago, as we implemented a new curriculum that emphasizes professional identity development. Purpose: This study examined associations among admissions measures (Medical College Admission Test [MCAT], grade point average [GPA], interview, and CASPer), and their predictive relationships with curricular measures of professional identity formation (Professional Identity Essay [PIE]) and moral reasoning (Defining Issues Test [DIT2]). Methods: Data were taken from two entering cohorts ( n = 596; entering class of 2017 and 2018 across 3 regional sites). Correlations and regression analyses were used to examine associations between admissions and professional identity measures. Results: CASPer and in-person admissions interview ratings had significant positive correlations, suggesting that CASPer can contribute to effective screening processes. In addition, CASPer demonstrated statistically significant positive relationships with professional identity (CASPer and PIE, r=.10, p<.05) and a measure of moral reasoning (CASPer and DIT2 type indicator, r=.09, p<.05). Association between CASPer and PIE remained consistent, even after controlling for MCAT, interview, and GPA. Conclusion: Our institutional focus on professional identity formation has provided new ways to conceptualize students' readiness for medical school - demonstrated academic rigor as well as signs of professionalism, ethics, and motivation. Non-academic factors measured in situational judgment tests may promote better alignment of admissions practices and desired educational outcomes.