Urban Care for Unpaid Caregivers: Community Voices in the Care Block Program, in Bogotá, Colombia.

The Care Block of Bogotá, Colombia, is an urban program that offers services for low-income unpaid caregivers. This study aimed to (i) characterize unpaid caregivers' subjective well-being, mental health symptoms, physical activity levels, and use of public spaces linked to the Care Block; (ii) identify caregivers' perceived built and social environment facilitators and barriers to accessing the Care Block facility; and (iii) document the community-led advocacy process to improve the Care Block program. The quantitative component included a subjective well-being and mental health symptoms survey, and the System for Observing Play and Recreation in Communities (SOPARC) instrument. The qualitative component included the Our Voice citizen science method augmented with portable virtual reality equipment to engage participants in advocacy for changes. Participants (median age of 53 years) dedicated a median of 13.8 h a day to unpaid caregiving, had an average subjective well-being score of 7.0, and 19.1% and 23.8% reported having depression and generalized anxiety symptoms respectively. Caregivers reported that the program fosters their perception of purpose, enjoyment, resilience, and cognitive and emotional awareness. SOPARC evaluation showed that most women engaged in moderate to vigorous physical activity. The caregivers highlighted education, physical activity services, and integration of facilities as facilitators to accessing the Care Block program. Poor quality and lack of sidewalks and roads, limited personal safety, and the risk of pedestrian-vehicle collisions were identified as barriers. Virtual Reality sparked compelling dialogue between participants and stakeholders, allowing stakeholders to reflect on an urban program facilitating unpaid care work.

Developing non-response weights to account for attrition-related bias in a longitudinal pregnancy cohort.

BACKGROUND: Prospective cohorts may be vulnerable to bias due to attrition. Inverse probability weights have been proposed as a method to help mitigate this bias. The current study used the "All Our Families" longitudinal pregnancy cohort of 3351 maternal-infant pairs and aimed to develop inverse probability weights using logistic regression models to predict study continuation versus drop-out from baseline to the three-year data collection wave. METHODS: Two methods of variable selection took place. One method was a knowledge-based a priori variable selection approach, while the second used Least Absolute Shrinkage and Selection Operator (LASSO). The ability of each model to predict continuing participation through discrimination and calibration for both approaches were evaluated by examining area under the receiver operating curve (AUROC) and calibration plots, respectively. Stabilized inverse probability weights were generated using predicted probabilities. Weight performance was assessed using standardized differences of baseline characteristics for those who continue in study and those that do not, with and without weights (unadjusted estimates). RESULTS: The a priori and LASSO variable selection method prediction models had good and fair discrimination with AUROC of 0.69 (95% Confidence Interval [CI]: 0.67-0.71) and 0.73 (95% CI: 0.71-0.75), respectively. Calibration plots and non-significant Hosmer-Lemeshow Goodness of Fit Tests indicated that both the a priori (p = 0.329) and LASSO model (p = 0.242) were well-calibrated. Unweighted results indicated large (> 10%) standardized differences in 15 demographic variables (range: 11 - 29%), when comparing those who continued in the study with those that did not. Weights derived from the a priori and LASSO models reduced standardized differences relative to unadjusted estimates, with the largest differences of 13% and 5%, respectively. Additionally, when applying the same LASSO variable selection method to develop weights in future data collection waves, standardized differences remained below 10% for each demographic variable. CONCLUSION: The LASSO variable selection approach produced robust weights that addressed non-response bias more than the knowledge-driven approach. These weights can be applied to analyses across multiple longitudinal waves of data collection to reduce bias.

Respirometric tests in a combined UASB-MBR system treating wastewater containing emerging contaminants at different OLRs and temperatures: Biokinetic analysis.

This research focuses on the application of respirometric techniques to provide new insights into the biokinetic behaviour of bacterial species developed in an Upflow Anaerobic Sludge Blanked -UASB reactor combined with a membrane bioreactor -MBR, treating urban wastewater with emerging contaminants frequently found in this kind of effluents. The lab-scale pilot plant was operated at different metabolic and operational conditions by limiting the organic loading rate- OLR of the influent. In a first stage, the MBR was performed with suspended biomass, while in a second stage bio-supports were introduced to operate coexisting suspended and fixed biomass. From the results of the microscopic monitoring of sludge, it was concluded that the decrease in OLR resulted in a greater disintegration of the floc structure, more dispersed growth, and a low presence of inter-floccular bonds. However, no effect of toxicity or inhibition of microorganisms caused by the presence of emerging contaminants -ECs was determined. Kinetic modelling was carried out to study the behaviour of the system. The results showed a slowing down of biomass degradative capacity at low OLR stages and operating at low temperatures of mixed liquor. In addition, a decrease in oxygen consumption was observed with decreasing biodegradable substrate, resulting in lower degradation of organic matter. Mean values of specific oxygen uptake rate and heterotrophic biomass yield at low OLR were SOUR end = 1.49 and 1.15 mg O2· g MLVSS-1 h-1 and YH,MLSSV end = 0.48 and 0.28 mg MLVSS· mg COD-1substrate at stage 1 (suspended biomass) and stage 2 (suspended and supported biomass), respectively. From the analysis of the endogenous decomposition constant (kd), a higher cell lysis was determined operating with suspended biomass (kd = 0.03 d-1) in comparison to the operation coexisting suspended and supported biomass (kd = 0.01 d-1). Heterotrophic biomass yield values (YH, MLVSS = 0.48 ± 0.06, 0.40 ± 0.01 and 0.29 ± 0.01 mg MLVSS· mg COD-1substrate at high, medium and low OLR) showed lower sludge production at low OLR due to the influence of substrate limitation on cell growth.

Soft-sensors application for automated feeding control in high-throughput mammalian cell cultures.

The ever-increasing demand for biopharmaceuticals has created the need for improving the overall productivity of culture processes. One such operational concept that is considered is fed-batch operations as opposed to batch operations. However, optimal fed-batch operations require complete knowledge of the cell culture to optimize the culture conditions and the nutrients feeding. For example, when using high-throughput small-scale bioreactors to test multiple clones that do not behave the same, depletion or overfeeding of some key components can occur if the feeding strategy is not individually optimized. Over the recent years, various solutions for real-time measuring of the main cell culture metabolites have been proposed. Still, the complexity in the implementation of these techniques has limited their use. Soft-sensors present an opportunity to overcome these limitations by indirectly estimating these variables in real-time. This manuscript details the development of a new soft-sensor-based fed-batch strategy to maintain substrate concentration (glucose and glutamine) at optimal levels in small-scale multiparallel Chinese Hamster Ovary Cells cultures. Two alternatives to the standard feeding strategy were tested: an OUR soft-sensor-based strategy for glucose and glutamine (Strategy 1) and a dual OUR for glutamine and CO2 /alkali addition for glucose soft-sensor strategy (Strategy 2). The results demonstrated the applicability of the OUR soft-sensor-based strategy to optimize glucose and glutamine feedings, which yielded a 21% increase in final viable cell density (VCD) and a 31% in erythropoietin titer compared with the reference one. However, CO2 /alkali addition soft-sensor suffered from insufficient data to relate alkali addition with glucose consumption. As a result, the culture was overfed with glucose resulting in a 4% increase on final VCD, but a 9% decrease in final titer compared with the Reference Strategy.

How do presentation age and CSF opening pressure level affect long-term prognosis of pseudotumor cerebri syndrome in children? Experience of a single tertiary clinic.

BACKGROUND: Diagnosis and treatment of pseudotumor cerebri syndrome in children is still a challenge for clinicians. The aim of this study is to reveal the influence of presentation age and CSF opening pressure on long-term prognosis of pseudotumor cerebri and share our clinical data of the very young age (≤ 5-year) group. METHOD: This retrospective study includes the patients followed by the Marmara University Pediatric Neurology Clinic between years 2012 and 2020 diagnosed with definite, probable, or suggestive pseudotumor cerebri syndrome according to modified Friedman criteria. Patients were classified into three groups according to presentation age: group 1: ≤ 5 years old; group 2: 6-10 years; and group 3 > 10 years old. CSF opening pressure was also categorized into three groups as CSF < 20 cmH20; CSF 20-30 cmH20; and CSF > 30 cmH20. RESULTS: One hundred three patients, 62.1% female (n = 64), were enrolled in the study. Group 1 consisted of 16 patients (60% male), group 2 consisted of 30 patients (63.3% female), and group 3 consisted of 57 patients (66.7% female). The mean CSF opening pressure did not differ between the three age groups in our study (p > 0.05). Treatment response was not correlated with CSF opening pressure. Papilledema presence and level of CSF opening pressure were independent of age (p > 0.05). CONCLUSIONS: Age at presentation and CSF opening pressure at diagnosis are not any predictive factors that influence long-term prognosis of pseudotumor cerebri syndrome in children. Evaluation and follow-up of children should be done in personalized approach.

Using citizen science to empower older adults to improve a food security initiative in Australia.

Food security is an increasing problem for older adults who are living longer and having to stretch their resources further. Initiatives such as subsidized community market days are increasingly important in bolstering food security amongst these groups but there have been few attempts to understand these initiatives from the perspective of community members. This exploratory study examined the utility of a novel citizen science approach to engage older adults in evaluating and improving a local food security initiative. Using the Our Voice methodology, citizen scientists recorded their perceptions of their local Market Day via photographs and audio narratives. Thirteen citizen scientists captured 127 photographs and 125 commentaries. Citizen scientists participated in workshops to discuss, code and synthesize their data, and used their findings to advocate for change. A number of improvements to the Market Day were made by key stakeholders on the basis of citizen scientist recommendations, including improving the processes for sourcing and storing food and changing the layout to improve access. This study demonstrates that citizen science is a useful and feasible approach to engaging community members in capturing data and advocating for change to ensure that local initiatives meet the needs of communities.

Systematic Review on Psychological Impacts and Mitigating Strategies of COVID-19: The Lesson Every One Shall Learn From the Our Time Pandemic.

Objective: The pandemic is expanding exponentially, burning, and threatening the world population regardless of differences. Cognizant of these, world nations make it their daily agenda and give due concern in preventing and intervening it. However, the prevention and intervention strategies are of more biological and less attention is given for the psychological impacts. So that this manuscript is intended to review the psychological impacts and mitigating strategies of COVID-19 in Ethiopia. Method: Out the 63 downloaded articles, 26 articles were selected by considering relatedness, reputable journal, and pattern of writing and reviewed. Results: Most reviewed studies reported negative psychological impacts including, boredom, loneliness, anger, violence and abuse, distress, low mood and irritability, anxiety, insomnia, hopelessness and worthless, and suicide. Other associated factors like poverty, fears of infection, duration of quarantine, lack of genuine and adequate information, lack of basic supplies, stigma, housing condition, and cultural issues potentially worsen the psychological impacts. Conclusion: Psychological intervention strategies like mobilizing volunteers and professionals, identifying vulnerable population, assuring psychological readiness, offering adequate and genuine information, providing adequate supplies, improving communication for those in quarantine, utilizing counseling platform and rehabilitation program are of the cures for psychological impacts of COVID-19.

Adverse childhood experiences are associated with illicit drug use among pregnant women with middle to high socioeconomic status: findings from the All Our Families Cohort.

BACKGROUND: Adverse childhood experiences (ACEs) are associated with illicit drug use among pregnant women who are socioeconomically vulnerable. While it is assumed that the impact of ACEs on illicit drug use in pregnancy is reduced among women with higher socioeconomic status (SES), this assumption is not well tested in the literature. The objective of this study was to examine the impact of maternal ACEs on illicit drug use in a community-based sample of pregnant women with middle to high SES. METHODS: This study is a secondary analysis of a prospective cohort study that collected data from 1660 women during and after pregnancy in Calgary, Canada between 2008 and 2011 using mailed surveys. Illicit drug use in pregnancy was self-reported by women at 34-36 weeks gestation. An established scale examined maternal ACEs before 18 years. Logistic regression models and 95% confidence intervals tested associations between maternal ACE scores and illicit drug use in pregnancy. RESULTS: Overall, 3.1% of women in this predominantly married, well-educated, middle and upper middle income sample reported illicit drug use in pregnancy. Women with 2-3 ACEs had more than a two-fold increase, and women with 4 or more ACEs had almost a four-fold increase in illicit drug use in pregnancy, relative to women with 0-1 ACEs after adjustment for confounders. Exposure to child abuse was more consistently associated with illicit drug use in pregnancy than exposure to household dysfunction in childhood. CONCLUSIONS: Maternal ACEs were common and associated with a moderate increase in the odds of illicit drug use in pregnancy among Canadian women with middle to high SES.

Theoretical Study of the Mechanism of Ribosomal Peptide Bond Formation Using the ONIOM Method.

Peptide bond formation in living cells occurs at the peptidyl transferase center (PTC) of the large ribosomal subunit and involves the transfer of the peptidyl group from peptidyl-tRNA to aminoacyl-tRNA. Despite numerous kinetic and theoretical studies, many details of this reaction -such as whether it proceeds via a stepwise or concerted mechanism- remain unclear. In this study, we calculated the geometry and energy of the transition states and intermediates in peptide bond formation in the PTC environment using the ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) method. The calculations indicated that the energy of the transition states of stepwise mechanisms are lower than those of concerted mechanisms and suggested that the reaction involves a neutral tetrahedral intermediate that is stabilized through the hydrogen-bonding network in the PTC environment. The results will lead to a better understanding of the mechanism of peptidyl transfer reaction, and resolve fundamental questions of the steps and molecular intermediates involved in peptide bond formation in the ribosome.

Real-time biomonitoring of oxygen uptake rate and biochemical oxygen demand using a novel optical biogas respirometric system.

In response to the ever-increasing need for monitoring-based process control of wastewater treatment plants, an online applicable respirometer shows great promise for real-time measurement of oxygen uptake rate (OUR) and biochemical oxygen demand (BOD) measurements as a surrogate of the biodegradability of wastewater. Here, we have developed a photosensor-assisted real-time respirometric system equipped with bubble counting sensors for accurate measurement of microbial oxygen consumption in a bottle. This system can measure OUR and BOD in a bottle equipped with a tube containing NaOH solution to absorb carbon dioxide and supplied with continuous atmospheric oxygen to the bottle, which reliably supplies non-limiting dissolved oxygen (DO) for aerobic biodegradation even at high organic loads. These technical improvements allow a sensitive and rapid analytical tool offering real-time profiles of oxygen uptake rate as well as BOD measurements with an extended measurable range (0-420 mg O2/L), enabling significant reduction or elimination of dilution steps. The respirometric system was used to elucidate the biodegradable kinetics of domestic and swine wastewaters as a function of the type and concentration of organic matters, depending on source characteristics including rapidly or slowly oxidizable organic substances by bacteria. Compared with conventional and manometric BOD methods, our method is reliable and accurate.

Online monitoring of the cell-specific oxygen uptake rate with an in situ combi-sensor.

In a biotechnological process, standard monitored process variables are pH, partial oxygen pressure (pO2), and temperature. These process variables are important, but they do not give any information about the metabolic activity of the cell. The ISICOM is an in situ combi-sensor that is measuring the cell-specific oxygen uptake rate (qOUR) online. This variable allows a qualitative judgement of metabolic cell activity. The measuring principle of the ISICOM is based on a volume element enclosed into a small measuring chamber. Inside the measuring chamber, the pO2 and the scattered light is measured. Within a defined measuring interval, the chamber closes, and the oxygen supply for the cells is interrupted. The decreasing oxygen concentration is recorded by the pO2 optode. This measuring principle, known as the dynamic method, determines the oxygen uptake rate (OUR). Together with the scattered light signal, the cell concentration is estimated and the qOUR is available online. The design of the ISICOM is focused on functionality, sterility, long-term stability, and response time behavior so the sensor can be used in bioprocesses. With the ISICOM, measurement of online and in situ measurement of the OUR is possible. The OUR and qOUR online measurement of an animal cell batch cultivation is demonstrated, with maximum values of OUR = 2.5 mmol L-1 h-1 and a qOUR = 9.5 pmol cell-1 day-1. Information about limitation of the primary and secondary substrate is derived by the monitoring of the metabolic cell activity of bacteria and yeast cultivation processes. This sensor contributes to a higher process understanding by offering an online view on to the cell behavior. In the sense of process analytical technology (PAT), this important information is needed for bioprocesses to realize a knowledge base process control.

Active biomass estimation based on ASM1 and on-line OUR measurements for partial nitrification processes in sequencing batch reactors.

The main challenge for partial nitrification is to reach stable nitrite accumulation, which strongly depends on the nitrite-oxidizing bacteria (NOB) growth in the reactor. The on-line estimation of active biomass may enhance the decision-making process to maintain a high nitrite accumulation in the reactor. In this work, we propose an active biomass estimator based on ASM1 and on-line oxygen uptake rate measurements (OUR-E) in a sequencing batch reactor. In order to validate the OUR-E, two operating scenarios were applied during 200 days of operation: unfavorable (sludge retention time (SRT) = 40 d, pH = 7.6, dissolved oxygen (DO) = 2 mg/L) and favorable for partial nitrification (SRT = 10 d, pH = 8.5, DO = 2 mg/L). Furthermore, a second estimation method based on off-line measurements of N-species concentrations (Nsp-E) was implemented to evaluate the performance of the OUR-E. The OUR-E was able to predict a reduction in the NOB active fraction from 10.3% to 1.6% with nitrite accumulation over 80% when we shifted the operating scenario. Although both estimators predicted similar results, the OUR-E showed a better prediction quality than the Nsp-E, according to Theil's coefficient of inequality.

The Influence of COD Fraction Forms and Molecules Size on Hydrolysis Process Developed by Comparative OUR Studies in Activated Sludge Modelling.

The activated sludge models (ASMs) commonly used by the International Water Association (IWA) task group are based on chemical oxygen demand (COD) fractionations. However, the proper evaluation of COD fractions, which is crucial for modelling and especially oxygen uptake rate (OUR) predictions, is still under debate. The biodegradation of particulate COD is initiated by the hydrolysis process, which is an integral part of an ASM. This concept has remained in use for over 30 years. The aim of this study was to verify an alternative, more complex, modified (Activated Sludge Model No 2d) ASM2d for modelling the OUR variations and novel procedure for the estimation of a particulate COD fraction through the implementation of the GPS-X software (Hydromantis Environmental Software Solutions, Inc., Hamilton, ON, Canada) in advanced computer simulations. In comparison to the original ASM2d, the modified model more accurately predicted the OUR behavior of real settled wastewater (SWW) samples and SWW after coagulation-flocculation (C-F). The mean absolute relative deviations (MARDs) in OUR were 11.3-29.5% and 18.9-45.8% (original ASM2d) vs. 9.7-15.8% and 11.8-30.3% (modified ASM2d) for the SWW and the C-F samples, respectively. Moreover, the impact of the COD fraction forms and molecules size on the hydrolysis process rate was developed by integrated OUR batch tests in activated sludge modelling.

New developments in online OUR monitoring and its application to animal cell cultures.

The increasing demand for biopharmaceuticals produced in mammalian cells has driven the industry to enhance the productivity of bioprocesses through intensification of culture process. Fed-batch and perfusion culturing strategies are considered the most attractive choices, but the application of these processes requires the availability of reliable online measuring systems for the estimation of cell density and metabolic activity. This manuscript reviews the methods (and the devices used) for monitoring of the oxygen consumption, also known as oxygen uptake rate (OUR), since it is a straightforward parameter to estimate viable cell density and the physiological state of cells. Furthermore, as oxygen plays an important role in the cell metabolism, OUR has also been very useful to estimate nutrient consumption, especially the carbon (glucose and glutamine) and nitrogen (glutamine) sources. Three different methods for the measurement of OUR have been developed up to date, being the dynamic method the golden standard, even though DO and pH perturbations generated in the culture during each measurement. For this, many efforts have been focused in developing non-invasive methods, such as global mass balance or stationary liquid mass balance. The low oxygen consumption rates by the cells and the high accuracy required for oxygen concentration measurement in the gas streams (inlet and outlet) have limited the applicability of the global mass balance methodology in mammalian cell cultures. In contrast, stationary liquid mass balance has successfully been implemented showing very similar OUR profiles compared with those obtained with the dynamic method. The huge amount of studies published in the last years evidence that OUR have become a reliable alternative for the monitoring and control of high cell density culturing strategies with very high productivities.

Wither health science librarianship? Many questions, many options.

The 2019 virtual issue of the Health Information and Libraries Journal (HILJ) is published to link to the 2019 EAHIL Workshop taking place in Basel, Switzerland on 17-20 June 2019. The workshop is structured around six topics: (i) Roadmap of our Profession; (ii) Technology Uptake; (iii) Ecology of Scholarly Communications; (iv) Impact + Assessment; (v) Benchmarking + Advocacy; (vi) Evidence-Based Practice. These themes have been used to compile this virtual issue, which contains published articles selected from HILJ from the March 2019 issue through to June 2017. The virtual issue mirrors the format of a regular issue of HILJ, namely a review article, five original articles and articles from our three regular features: 'Dissertations into Practice', 'International Perspectives and Initiatives' and 'Teaching and Learning in Action'. The authors come from the UK, Canada, Australia, Italy, Iran and Belgium. All articles included in this virtual issue are available free online.

The evaluation of COD fractionation and modeling as a key factor for appropriate optimization and monitoring of modern cost-effective activated sludge systems.

A study was conducted to characterize the raw wastewater entering a modern cost effective municipal WWTP in Poland using two approaches; 1) a combination of modeling and carbonaceous oxygen demand (COD) fractionation using respirometric test coupled with model estimation (RT-ME) and 2) flocculation/filtration COD fractionation method combined with BOD measurements (FF-BOD). It was observed that the particulate fractions of COD obtained using FF-BOD method was higher than those estimated by RT-ME approach. Contrary to the above, the values of inert soluble fraction evaluated by FF-BOD method was significantly lower than RT-ME approach (2.4% and 3.9% respectively). Furthermore, the values for low colloidal and particulate fractions as well as soluble inert fractions were different than expected from a typical municipal wastewater. These observations suggest that even at low load (10% of the total wastewater treatment inflow), the industrial wastewater composition can significantly affect the characteristics of municipal wastewater which could also affect the performance and accuracy of respirometric tests. Therefore, in such cases, comparison of the respirometric tests with flocculation/filtration COD/BOD measurements are recommended. Oxygen uptake rate profile with settled wastewater and/or after coagulation-flocculation, however, could still be recommended as a "rapid" control method for monitoring/optimising modern cost-effective wastewater treatment plants.

Tuning of activated sludge in winter based on respirogram profiles under standard and site temperatures.

Respirograms of activated sludge OURTx and OUR20x were measured under site (T) and standard (20°C) temperatures, respectively, and the predicted standard temperature respirogram OUR20x,cal was also calculated using the Arrhenius equation. These respirogram profiles reveal more information than effluent quality. A decrease of OUR20x is a critical alarm signal for the loss of pollutant removal capacity, and a sudden increase of the predicted value OUR20x,cal is an alarm signal for the unrecoverable deterioration of biomass. The sign of OUR20x-OUR20x,cal can be used for selection of tuning strategies. For example, a negative value of OUR20x-OUR20x,cal indicates that doubling biomass is difficult, thus strategies such as extending the reaction time with limited available biomass is preferred. The findings in this study elucidated the respiration profile of activated sludge under changes of temperature and can be effectively used for the stable operation of Wastewater Treatment Plants under cold temperatures and seasonal variations.

Cutaneous afferent innervation of the human foot sole: what can we learn from single-unit recordings?

Cutaneous afferents convey exteroceptive information about the interaction of the body with the environment and proprioceptive information about body position and orientation. Four classes of low-threshold mechanoreceptor afferents innervate the foot sole and transmit feedback that facilitates the conscious and reflexive control of standing balance. Experimental manipulation of cutaneous feedback has been shown to alter the control of gait and standing balance. This has led to a growing interest in the design of intervention strategies that enhance cutaneous feedback and improve postural control. The advent of single-unit microneurography has allowed the firing and receptive field characteristics of foot sole cutaneous afferents to be investigated. In this review, we consolidate the available cutaneous afferent microneurographic recordings from the foot sole and provide an analysis of the firing threshold, and receptive field distribution and density of these cutaneous afferents. This work enhances the understanding of the foot sole as a sensory structure and provides a foundation for the continued development of sensory augmentation insoles and other tactile enhancement interventions.

An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant.

The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less activity towards the protease. A mutation and insertion designated L38L↑N↑L PR was recently reported from subtype of C-SA HIV-1. An integrated two-layered ONIOM (QM:MM) method was employed in this study to examine the binding affinities of the nine HIV PR inhibitors against this mutant. The computed binding free energies as well as experimental data revealed a reduced inhibitory activity towards the L38L↑N↑L PR in comparison with subtype C-SA HIV-1 PR. This observation suggests that the insertion and mutations significantly affect the binding affinities or characteristics of the HIV PIs and/or parent PR. The same trend for the computational binding free energies was observed for eight of the nine inhibitors with respect to the experimental binding free energies. The outcome of this study shows that ONIOM method can be used as a reliable computational approach to rationalize lead compounds against specific targets. The nature of the intermolecular interactions in terms of the host-guest hydrogen bond interactions is discussed using the atoms in molecules (AIM) analysis. Natural bond orbital analysis was also used to determine the extent of charge transfer between the QM region of the L38L↑N↑L PR enzyme and FDA approved drugs. AIM analysis showed that the interaction between the QM region of the L38L↑N↑L PR and FDA approved drugs are electrostatic dominant, the bond stability computed from the NBO analysis supports the results from the AIM application. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide information that will aid in the design of much improved HIV-1 PR antiviral drugs.

Molecular insight on the non-covalent interactions between carbapenems and L,D-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study.

Tuberculosis remains a dreadful disease that has claimed many human lives worldwide and elimination of the causative agent Mycobacterium tuberculosis also remains elusive. Multidrug-resistant TB is rapidly increasing worldwide; therefore, there is an urgent need for improving the current antibiotics and novel drug targets to successfully curb the TB burden. L,D-Transpeptidase 2 is an essential protein in Mtb that is responsible for virulence and growth during the chronic stage of the disease. Both D,D- and L,D-transpeptidases are inhibited concurrently to eradicate the bacterium. It was recently discovered that classic penicillins only inhibit D,D-transpeptidases, while L,D-transpeptidases are blocked by carbapenems. This has contributed to drug resistance and persistence of tuberculosis. Herein, a hybrid two-layered ONIOM (B3LYP/6-31G+(d): AMBER) model was used to extensively investigate the binding interactions of LdtMt2 complexed with four carbapenems (biapenem, imipenem, meropenem, and tebipenem) to ascertain molecular insight of the drug-enzyme complexation event. In the studied complexes, the carbapenems together with catalytic triad active site residues of LdtMt2 (His187, Ser188 and Cys205) were treated at with QM [B3LYP/6-31+G(d)], while the remaining part of the complexes were treated at MM level (AMBER force field). The resulting Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) for all complexes showed that the carbapenems exhibit reasonable binding interactions towards LdtMt2. Increasing the number of amino acid residues that form hydrogen bond interactions in the QM layer showed significant impact in binding interaction energy differences and the stabilities of the carbapenems inside the active pocket of LdtMt2. The theoretical binding free energies obtained in this study reflect the same trend of the experimental  observations. The electrostatic, hydrogen bonding and Van der Waals interactions between the carbapenems and LdtMt2 were also assessed. To further examine the nature of intermolecular interactions for carbapenem-LdtMt2 complexes, AIM and NBO analysis were performed for the QM region (carbapenems and the active residues of LdtMt2) of the complexes. These analyses revealed that the hydrogen bond interactions and charge transfer from the bonding to anti-bonding orbitals between catalytic residues of the enzyme and selected ligands enhances the binding and stability of carbapenem-LdtMt2 complexes. The two-layered ONIOM (B3LYP/6-31+G(d): Amber) model was used to evaluate the efficacy of FDA approved carbapenems antibiotics towards LdtMt2.