Surfactant for the treatment of respiratory distress syndrome in very low birth weight infants at a level 2 hospital: A descriptive retrospective cohort study - safety and efficacy.

Respiratory distress syndrome (RDS) is common and is a leading cause of death in pre-term infants. The purpose of our study is to describe the demographics and incidence of adverse events in very low birth weight (VLBW) pre-term infants with RDS treated with surfactant at George, a level 2 Hospital in the Western Cape Province of South Africa. This was a retrospective observational study. We conducted an electronic folder review of infants with a birth weight of 800-1200 g treated during the study period 2017-2019 at George Regional Hospital. Outborn infants and those with congenital abnormalities were excluded. The total number of patients included in the study was 66. The mortality rate was 25.8% (17/66). The incidence of bronchopulmonary dysplasia was 6% (4/66). Our study showed that the outcomes of VLBW infants treated with surfactant at level 2 hospitals are comparable to South African central hospitals.

Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces.

Molecular recognition between peptides and metal oxide surfaces is a fundamental process in biomineralization, self-assembly, and biocompatibility. Yet, the underlying driving forces and dominant mechanisms remain unclear, bringing obstacles to understand and control this process. To elucidate the mechanism of peptide/surface recognition, specifically the role of serine phosphorylation, we employed molecular dynamics simulation and metadynamics-enhanced sampling to study five artificial peptides, DDD, DSS, DpSpS, DpSpSGKK, and DpSKGpSK, interacting with two surfaces: rutile TiO2 and quartz SiO2. On both surfaces, we observe that phosphorylation increases the binding energy. However, the interfacial peptide conformation reveals a distinct binding mechanism on each surface. We also study the impact of peptide sequence to binding free energy and interfacial conformation on both surfaces, specifically the impact on the behavior of phosphorylated serine. Finally, the results are discussed in context of prior studies investigating the role of serine phosphorylation in peptide binding to silica.

Unmet needs of high-risk mothers reduce success of antiretroviral treatment in HIV-infected infants.

In the era of effective prevention of mother-to-child transmission of HIV, the same psychosocioeconomic factors that predispose to mother-to-child transmission also substantially increase the likelihood of antiretroviral therapy failure in infected infants. For HIV-infected infants to benefit from early infant diagnosis and treatment initiation, into which much funding and effort is now invested, it is vital that these unmet needs of high-risk mothers are urgently attended to. From an ongoing study of early infant diagnosis and treatment following in utero transmission in KwaZulu-Natal, South Africa, we describe four cases to highlight these challenges facing transmitting mothers that contribute to treatment failure in their infants.

Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation.

Many proteins exhibit strong binding affinities to surfaces, with binding energies much greater than thermal fluctuations. When modelling these protein-surface systems with classical molecular dynamics (MD) simulations, the large forces that exist at the protein/surface interface generally confine the system to a single free energy minimum. Exploring the full conformational space of the protein, especially finding other stable structures, becomes prohibitively expensive. Coupling MD simulations with metadynamics (enhanced sampling) has fast become a common method for sampling the adsorption of such proteins. In this paper, we compare three different flavors of metadynamics, specifically well-tempered, parallel-bias, and parallel-tempering in the well-tempered ensemble, to exhaustively sample the conformational surface-binding landscape of model peptide GGKGG. We investigate the effect of mobile ions and ion charge, as well as the choice of collective variable (CV), on the binding free energy of the peptide. We make the case for explicitly biasing ions to sample the true binding free energy of biomolecules when the ion concentration is high and the binding free energies of the solute and ions are similar. We also make the case for choosing CVs that apply bias to all atoms of the solute to speed up calculations and obtain the maximum possible amount of information about the system.

Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations.

Biomimetic silica formation, a process that is largely driven by proteins, has garnered considerable interest in recent years due to its role in the development of new biotechnologies. However, much remains unknown of the molecular-scale mechanisms underlying the binding of proteins to biomineral surfaces such as silica, or even of the key residue-level interactions between such proteins and surfaces. In this study, we employ molecular dynamics (MD) simulations to study the binding of R5-a 19-residue segment of a native silaffin peptide used for in vitro silica formation-to a silica surface. The metadynamics enhanced sampling method is used to converge the binding behavior of R5 on silica at both neutral (pH 7.5) and acidic (pH 5) conditions. The results show fundamental differences in the mechanism of binding between the two cases, providing unique insight into the pH-dependent ability of R5 and native silaffin to precipitate silica. We also study the effect of phosphorylation of serine residues in R5 on both the binding free energy to silica and the interfacial conformation of the peptide. Results indicate that phosphorylation drastically decreases the binding free energy and changes the structure of silica-adsorbed R5 through the introduction of charge and steric repulsion. New mechanistic insights from this work could inform rational design of new biomaterials and biotechnologies.

Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids.

The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). Enzymatic studies revealed that [BMIM][Cl] inactivates E1 in a biphasic manner that involves rapid, reversible inhibition, followed by slow, irreversible deactivation. Backbone NMR signals of the 40.5 kDa E1 were assigned by triple resonance NMR methods, enabling monitoring of residue-specific perturbations. 1H-15N NMR titration experiments revealed that [BMIM][Cl] binds reversibly to the E1 active site, indicating that reversible deactivation is due to competitive inhibition of substrate binding. Prolonged incubation with [BMIM][Cl] led to substantial global changes in the 1H-15N heteronuclear single quantum coherence NMR and CD spectra of E1 indicative of protein denaturation. Notably, weak interactions between [BMIM][Cl] and residues at the termini of several helices were also observed, which, together with MD simulations, suggest that E1 denaturation is promoted by [BMIM][Cl]-induced destabilization of helix capping structures. In addition to identifying determinants of E1 inactivation, our findings establish a molecular framework for engineering cellulases with improved IL compatibility.

Elucidating sequence and solvent specific design targets to protect and stabilize enzymes for biocatalysis in ionic liquids.

For many different frameworks, the structure, function, and dynamics of an enzyme is largely determined by the nature of its interactions with the surrounding host environment, thus a molecular level understanding of enzyme/host interactions is essential to the design of new processes and applications. Ionic liquid (IL) solvents are a popular class of solvents in which to study enzyme behavior, yet it is still not possible to predict how a given enzyme will behave in a given IL solvent. Furthermore, a dearth of experimental data with which to evaluate simulation force fields has prevented the full integration of experimental and computational techniques to gain a complete picture of enzyme/IL interactions. Utilizing recently published crystallographic data of an enzyme in complex with an IL, this study aims to validate the use of current molecular force fields for studying enzyme/IL interactions, and to provide new mechanistic insight into enzyme stabilization in IL solvents. Classical molecular dynamics (MD) simulations have been performed on both the folded and unfolded state of Bacillus subtilis lipase A and a quadruple-mutant version of lipase A, in solutions of aqueous 1-butyl-3-methylimidazolium chloride. Results show classical MD simulations can predict the preferred surface binding locations of IL cations as well as reductions in IL anion binding to mutated surface residues with high accuracy. The results also point to a mechanistic difference between IL binding to the folded and unfolded state of an enzyme, which we call the "counter-ion effect". These findings could have important implications for future rational design efforts to stabilize enzymes in non-conventional media.

Using Molecular Simulation to Study Biocatalysis in Ionic Liquids.

The practice of computational biocatalysis in ionic liquids (ILs) is still in its infancy, and thus best simulation practices are still developing. Herein, we examine the computational and experimental literature to date featuring systems of enzymes in aqueous and neat ILs. The many different approaches taken to parameterize ILs and set up simulations of enzymes in ILs are discussed, and common analysis techniques are reviewed. We also shed light on potential drawbacks and limitations to simulating enzymes in ILs, which include a lack of experimental data with which to validate computational models and inadequate sampling arising from the slow dynamics of many ILs that can lead to inaccurate descriptions of transport and equilibrium thermodynamic properties. A small case study illustrates the effects of scaling IL partial charges, which is a common practice in the field, on the conformational transitions of alanine dipeptide. The degree of charge scaling has a significant effect on the transition times between states of the biomolecule and highlights the importance of carefully setting up systems of enzymes in ILs. Finally, we discuss means to overcome these challenges and briefly consider possible new directions for the field.

Strong Electrostatic Interactions Lead to Entropically Favorable Binding of Peptides to Charged Surfaces.

Thermodynamic analyses can provide key insights into the origins of protein self-assembly on surfaces, protein function, and protein stability. However, obtaining quantitative measurements of thermodynamic observables from unbiased classical simulations of peptide or protein adsorption is challenging because of sampling limitations brought on by strong biomolecule/surface binding forces as well as time scale limitations. We used the parallel tempering metadynamics in the well-tempered ensemble (PTMetaD-WTE) enhanced sampling method to study the adsorption behavior and thermodynamics of several explicitly solvated model peptide adsorption systems, providing new molecular-level insight into the biomolecule adsorption process. Specifically studied were peptides LKα14 and LKß15 and trpcage miniprotein adsorbing onto a charged, hydrophilic self-assembled monolayer surface functionalized with a carboxylic acid/carboxylate headgroup and a neutral, hydrophobic methyl-terminated self-assembled monolayer surface. Binding free energies were calculated as a function of temperature for each system and decomposed into their respective energetic and entropic contributions. We investigated how specific interfacial features such as peptide/surface electrostatic interactions and surface-bound ion content affect the thermodynamic landscape of adsorption and lead to differences in surface-bound conformations of the peptides. Results show that upon adsorption to the charged surface, configurational entropy gains of the released solvent molecules dominate the configurational entropy losses of the bound peptide. This behavior leads to an apparent increase in overall system entropy upon binding and therefore to the surprising and seemingly nonphysical result of an apparent increased binding free energy at elevated temperatures. Opposite effects and conclusions are found for the neutral surface. Additional simulations demonstrate that by adjusting the ionic strength of the solution, results that show the expected physical behavior, i.e., peptide binding strength that decreases with increasing temperature or is independent of temperature altogether, can be recovered on the charged surface. On the basis of this analysis, an overall free energy for the entire thermodynamic cycle for peptide adsorption on charged surfaces is constructed and validated with independent simulations.

Lytic Polysaccharide Monooxygenases ScLPMO10B and ScLPMO10C Are Stable in Ionic Liquids As Determined by Molecular Simulations.

Lytic polysaccharide monooxygenases (LPMOs) are a newly discovered family of enzymes proposed to work synergistically with cellulases and aid in the decomposition of cellulose for the creation of environmentally friendly fuels and chemicals. To our knowledge, evaluation of the stability of LPMOs in ionic liquid (IL) solvents at relevant biomass processing conditions has not been explored. Herein, molecular dynamics simulations of ScLPMO10B and ScLPMO10C in three ILs at 10 and 20 wt% in water and in pure water have been performed. Enzyme stability was predicted to be high on the basis of structural and dynamic analyses we performed. We used the simulations to identify key areas that deviate from the crystal structures as a starting place for surface charge modifications to increase stability in ILs. Results show that, in general, both enzymes have a high degree of stability across the range of IL solutions tested. For each enzyme, two regions were identified that showed notable deviations from the crystal structure. In addition to providing a basis for future rational design efforts, this work represents a first step toward engineering LPMOs to function efficiently in enzyme cocktails for use in industrial biomass processing applications with ILs.

The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids.

We have applied molecular dynamics to calculate thermodynamic and transport properties of a set of 19 room-temperature ionic liquids. Since accurately simulating the thermophysical properties of solvents strongly depends upon the force field of choice, we tested the accuracy of the general AMBER force field, without refinement, for the case of ionic liquids. Electrostatic point charges were developed using ab initio calculations and a charge scaling factor of 0.8 to more accurately predict dynamic properties. The density, heat capacity, molar enthalpy of vaporization, self-diffusivity, and shear viscosity of the ionic liquids were computed and compared to experimentally available data, and good agreement across a wide range of cation and anion types was observed. Results show that, for a wide range of ionic liquids, the general AMBER force field, with no tuning of parameters, can reproduce a variety of thermodynamic and transport properties with similar accuracy to that of other published, often IL-specific, force fields.

Examination of the biological safety of a drug derived from mammalian organs.

In order to assess the safety of a biological drug, a variety of factors have to be examined and then brought into an overall context considering the specific aspects of each individual product. Quoting Trasylol, the aprotinin (CAS 9087-70-1) drug extracted from bovine lungs as an example for such an approach, the complete procedure is discussed. The rationale of a safety concept, its implementation including safety related validation studies, and the combinatorial evaluation of results from these validations with underlying specificities for manufacture allow for an overall safety assessment. Validation of the removal/inactivation capacity of the manufacturing process for bovine spongiform encephalopathy (BSE) and various viruses showed high reduction potentials. These results constitute the cornerstone for the conclusion that Trasylol is safe with regard to BSE and viruses.

Treatment of chronic relapsing inflammatory demyelinating polyneuropathy by cyclosporin A and plasma exchange. A case report.

A patient with chronic relapsing inflammatory demyelinating polyneuropathy was successfully treated with plasma exchanges and cyclosporin A (CsA). Dynamometric measurements of hand force during the time of CsA treatment showed a highly significant correlation between hand force and CsA blood levels. The largest influence of CsA on hand force occurred 11-13 days after CsA uptake.

The problem of compliance in rheumatic fever.

During a 12-month period 115 patients defaulted from a rheumatic fever clinic, so a study was undertaken to identify factors related to non-compliance by comparing defaulters with a group of 50 regular attenders. Those defaulting were significantly more likely to be coloured, male, and over 12 years old. They lived 10-99 km from the hospital, were on several drugs and despite more frequent appointments, usually had a record of poor attendance. The severity of the underlying heart disease and use of parenteral penicillin did not affect compliance. Since the use of regular penicillin prophylaxis for the secondary prevention of rheumatic fever is an essential step in reducing the prevalence of rheumatic heart disease, rheumatic fever clinics should be structured to address the needs of adolescents. Furthermore, the use of neighbourhood clinics for routine therapy between visits to a rheumatic fever clinic is essential to improve compliance.

Valve replacement in children.

The performance of the St. Jude prosthetic valve is reviewed in 81 patients aged 3 to 15 years. All 66 mitral (2 re-replacements), 8 aortic and 9 double valve replacements between February 1979 and August 1984 are included. The early mortality was 3.7% and actuarial analysis shows a 90% event free survival up to 5 years. Anticoagulant therapy was used in most patients, but comparison between groups receiving warfarin or aspirin or no therapy reveals no differences in the complication rate. The valve is well suited for use in children since the early degeneration seen with heterograft valves does not occur, and anticoagulation is not essential.

Model for individual substitution of immunoglobulins after membrane plasma separation.

Patients who undergo extensive plasma exchanges using albumin replacement may be more susceptible to infection because they develop significant hypogammaglobulinemia. Substitution of IgG in these patients could be beneficial. A model to calculate the individual amount of IgG required is described. The course of IgG during chronic intermittent membrane plasma separation (MPS) therapy was simulated using an one-pool model. Three modes of substitution were considered for their efficacy: infusion after MPS infusion after discarding an equivalent plasma quantity after termination of MPS, and plasma exchange at the end of MPS against an IgG solution. Mode B was shown to be most economical and was subsequently used to check the validity of the substitution model in a prospective test. The difference between predicted and measured IgG levels was 5% both for simulations from one MPS to the next and for the long-term prediction. The data prove that replacement of IgG after plasma separation is practicable. The substitution model allows to fix in advance any plasma limit value for indication and target of the substitution therapy. Thus it permits to give therapeutic recommendations for individual IgG substitution therapy of secondary antibody deficiency after MPS.