Estimation of Acceptable Daily Intake Values based on Modeling and In Vivo Mutagenicity of NDSRIs of Fluoxetine, Duloxetine and Atomoxetine.

Nitrosamine drug substance related impurities or NDSRIs can be formed if an active pharmaceutical ingredient (API) has an intrinsic secondary amine that can undergo nitrosation. This is a concern as 1) nitrosamines are potentially highly potent carcinogens, 2) secondary amines in API are common, and 3) NDSRIs that might form from such secondary amines will be of unknown carcinogenic potency. Approaches for evaluating NDSRIs include read across, quantum mechanical modeling of reactivity, in vitro mutation data, and transgenic in vivo mutation data. These approaches were used here to assess NDSRIs that could potentially form from the drugs fluoxetine, duloxetine and atomoxetine. Based on a read across informed by modeling of physicochemical properties and mechanistic activation from quantum mechanical modeling, NDSRIs of fluoxetine, duloxetine, and atomoxetine were 10-100-fold less potent compared with highly potent nitrosamines such as NDMA or NDEA. While the NDSRIs were all confirmed to be mutagenic in vitro (Ames assay) and in vivo (TGR) studies, the latter data indicated that the potency of the mutation response was > 4400 ng/day for all compounds- an order of magnitude higher than published regulatory limits for these NDSRIs. The approaches described herein can be used qualitatively to better categorize NDSRIs with respect to potency and inform whether they are in the ICH M7R2-designated Cohort of Concern.

Nurse Practitioner Care, Scope of Practice, and End-of-Life Outcomes for Nursing Home Residents With Dementia.

Importance: Nursing home residents with Alzheimer disease and related dementias (ADRD) often receive burdensome care at the end of life. Nurse practitioners (NPs) provide an increasing share of primary care in nursing homes, but how NP care is associated with end-of-life outcomes for this population is unknown. Objectives: To examine the association of NP care with end-of-life outcomes for nursing home residents with ADRD and assess whether these associations differ according to state-level NP scope of practice regulations. Design, Setting, and Participants: This cohort study using fee-for-service Medicare claims included 334 618 US nursing home residents with ADRD who died between January 1, 2016, and December 31, 2018. Data were analyzed from April 6, 2015, to December 31, 2018. Exposures: Share of nursing home primary care visits by NPs, classified as minimal (<10% of visits), moderate (10%-50% of visits), and extensive (>50% of visits). State NP scope of practice regulations were classified as full vs restrictive in 2 domains: practice authority (authorization to practice and prescribe independently) and do-not-resuscitate (DNR) authority (authorization to sign DNR orders). Main Outcomes and Measures: Hospitalization within the last 30 days of life and death with hospice. Linear probability models with hospital referral region fixed effects controlling for resident characteristics, visit volume, and geographic factors were used to estimate whether the associations between NP care and outcomes varied across states with different scope of practice regulations. Results: Among 334 618 nursing home decedents (mean [SD] age at death, 86.6 [8.2] years; 69.3% female), 40.5% received minimal NP care, 21.4% received moderate NP care, and 38.0% received extensive NP care. Adjusted hospitalization rates were lower for residents with extensive NP care (31.6% [95% CI, 31.4%-31.9%]) vs minimal NP care (32.3% [95% CI, 32.1%-32.6%]), whereas adjusted hospice rates were higher for residents with extensive (55.6% [95% CI, 55.3%-55.9%]) vs minimal (53.6% [95% CI, 53.3%-53.8%]) NP care. However, there was significant variation by state scope of practice. For example, in full practice authority states, adjusted hospice rates were 2.88 percentage points higher (95% CI, 1.99-3.77; P < .001) for residents with extensive vs minimal NP care, but the difference between these same groups was 1.77 percentage points (95% CI, 1.32-2.23; P < .001) in restricted practice states. Hospitalization rates were 1.76 percentage points lower (95% CI, -2.52 to -1.00; P < .001) for decedents with extensive vs minimal NP care in full practice authority states, but the difference between these same groups in restricted practice states was only 0.43 percentage points (95% CI, -0.84 to -0.01; P < .04). Similar patterns were observed in analyses focused on DNR authority. Conclusions and Relevance: The findings of this cohort study suggest that NPs appear to be important care providers during the end-of-life period for many nursing home residents with ADRD and that regulations governing NP scope of practice may have implications for end-of-life hospitalizations and hospice use in this population.

Quantum Mechanical Assessment of Nitrosamine Potency.

Nitrosamines are in the cohort of concern (CoC) as determined by regulatory guidance. CoC compounds are considered highly potent carcinogens that need to be limited below the threshold of toxicological concern, 1.5 µg/day. Nitrosamines like NDMA and NDEA require strict control, while novel nitrosamine drug substance-related impurities (NDSRIs) may or may not be characterized as potent carcinogens. A risk assessment based on the structural features of NDSRIs is important in order to predict potency because they lack substance-specific carcinogenicity. Herein, we present a quantum mechanical (QM)-based analysis on structurally diverse sets of nitrosamines to better understand how structure influences the reactivity that could result in carcinogenicity. We describe the potency trend through activation energies corresponding to α-hydroxylation, aldehyde formation, diazonium intermediate formation, reaction with DNA base, and hydrolysis reactions, and other probable metabolic pathways associated with the carcinogenicity of nitrosamines. We evaluated activation energies for selected cases such as N-nitroso pyrrolidines, N-nitroso piperidines, N-nitroso piperazines, N-nitroso morpholines, N-nitroso thiomorpholine, N-methyl nitroso aromatic, fluorine-substituted nitrosamines, and substituted aliphatic nitrosamines. We compare these results to the recent framework of the carcinogenic potency characterization approach (CPCA) proposed by health authorities which is meant to give guidance on acceptable intakes (AI) for NDSRIs lacking substance-specific carcinogenicity data. We show examples where QM modeling and CPCA are aligned and examples where CPCA both underestimates and overestimates the AI. In cases where CPCA predicts high potency for NDSRIs, QM modeling can help better estimate an AI. Our results suggest that a combined mechanistic understanding of α-hydroxylation, aldehyde formation, hydrolysis, and reaction with DNA bases could help identify the structural features that underpin the potency of nitrosamines. We anticipate this work will be a valuable addition to the CPCA and provide a more analytical way to estimate AI for novel NDSRIs.

Toward Post-Hartree-Fock Accuracy for Protein-Ligand Affinities Using the Molecules-in-Molecules Fragmentation-Based Method.

The complexity and size of large molecular systems, such as protein-ligand complexes, pose computational challenges for accurate post-Hartree-Fock calculations. This study delivers a thorough benchmarking of the Molecules-in-Molecules (MIM) method, presenting a clear and accessible strategy for layer/theory selections in post-Hartree-Fock computations on substantial molecular systems, notably protein-ligand complexes. An approach is articulated, enabling augmented computational efficiency by strategically canceling out common subsystem energy terms between complexes and proteins within the supermolecular equation. Employing DLPNO-based post-Hartree-Fock methods in conjunction with the three-layer MIM method (MIM3), this study demonstrates the achievement of protein-ligand binding energies with remarkable accuracy (errors <1 kcal mol-1), while significantly reducing computational costs. Furthermore, noteworthy correlations between theoretically computed interaction energies and their experimental equivalents were observed, with R2 values of approximately 0.90 and 0.78 for CDK2 and BZT-ITK sets, respectively, thus validating the efficacy of the MIM method in calculating binding energies. By highlighting the crucial role of diffuse or small Pople-style basis sets in the middle layer for reducing energy errors, this work provides valuable insights and practical methodologies for interaction energy computations in large molecular complexes and opens avenues for their application across a diverse range of molecular systems.

Functional and Radiological Outcome of Short Same Segment Instrumentation in Thoracolumbar Burst fracture.

BACKGROUND: Thoracolumbar region is important biomechanics transition zone in which rigid thoracic and flexible lumbar spine meet. This area is highly vulnerable to traumatic spinal fracture.Among all spine fracture, compression type is most common and managed conservatively. Thoracolumbar spine fracture can be associated with neurological deficit, spinal instability. The optimal treatment for these injuries is still controversy and subject for research. METHODS: This retrospective study included 30 patients with single level thoracolumbar fracture.All the patients clinical and radiological parameters were evaluated preoperative, post-operative and 1 year follow up. Clinical parameters were included Visual analogue score, Oswestry disability index. Radiologic measurement were regional kyphotic angle by cobb's method and anterior vertebral body height loss (Mumford' santerior body compression equation method) in X-ray. All the data were analysed in SPSS version 20. RESULTS: A total of 30 patients were included in this study,19 were male.The mean age of the patients were 40.8±13.The main cause of injury was fall from height,26 patients. The most common level of fracture vertebra was L1,11 patients.The mean difference of preop and postop kyphosis was 11.70±50 with P<0.05.The mean difference of preop Oswestry disability index and postop Oswestry disability index score was 30.7±7.6 with T score 22(P<0.05).The preop and postop Visual analogue score score also improved ,mean difference was 2.8±1(P<0.05). CONCLUSIONS: Short segment instrumentation with placement of pedicle screw at fracture vertebra is one option in the treatment of thoracolumbar burst fracture.

Advanced practice clinician care and end-of-life outcomes for community- and nursing home-dwelling Medicare beneficiaries with dementia.

INTRODUCTION: Older adults with Alzheimer's disease and related dementias (ADRD) often face burdensome end-of-life care transfers. Advanced practice clinicians (APCs)-which include nurse practitioners and physician assistants-increasingly provide primary care to this population. To fill current gaps in the literature, we measured the association between APC involvement in end-of-life care versus hospice utilization and hospitalization for older adults with ADRD. METHODS: Using Medicare data, we identified nursing home- (N=517,490) and community-dwelling (N=322,461) beneficiaries with ADRD who died between 2016 and 2018. We employed propensity score-weighted regression methods to examine the association between different levels of APC care during their final 9 months of life versus hospice utilization and hospitalization during their final month. RESULTS: For both nursing home- and community-dwelling beneficiaries, higher APC care involvement associated with lower hospitalization rates and higher hospice rates. DISCUSSION: APCs are an important group of providers delivering end-of-life primary care to individuals with ADRD. HIGHLIGHTS: For both nursing home- and community-dwelling Medicare beneficiaries with ADRD, adjusted hospitalization rates were lower and hospice rates were higher for individuals with higher proportions of APC care involvement during their final 9 months of life. Associations between APC care involvement and both adjusted hospitalization rates and adjusted hospice rates persisted when accounting for primary care visit volume.

A bioinspired cobalt catalyst based on a tripodal imidazole/pyridine platform capable of water reduction and oxidation.

The prototypical drug carrier [CoII(L1)Cl]PF6 (1), where L1 is a tripodal amine bound to pyridine and methyl-imidazoles, had its electrocatalytic water splitting activity studied under different pH conditions. This species contains a high-spin 3d7 CoII metal center, and is capable of generating both H2 from water reduction and O2 from water oxidation. Turnover numbers reach 390 after 3 h for water reduction. Initial water oxidation activity is molecular, with TONs of 71 at pH 7 and 103 at pH 11.5. The results reveal that species 1 can undergo several redox transformations, including reduction to the 3d8 CoI species that precedes a LS3d6 hydride for water reduction, as well as nominal CoIVO and CoIII-OOH species required for water oxidation. Post-catalytic analyses confirm the molecular nature of reduction and support initial molecular activity for oxidation.

Prevalence and risk factors for functional iron deficiency in children with chronic kidney disease.

INTRODUCTION: Anemia in chronic kidney disease (CKD) is multifactorial. The presence of functional iron deficiency (FID), whereby, there is a block in the transport of iron from macrophage to erythroid marrow is one possible etiology. In this study, we aim to assess the prevalence and risk factors of FID in pediatric CKD. METHODS: A cross-sectional study was performed from March to December 2018, after obtaining Institute Ethical Clearance. Children aged ≤ 12 years with CKD, with or without iron supplementation who consented were enrolled. Patients on erythropoietin or on maintenance dialysis were excluded. Details of patients and diseases characteristics were recorded. Various laboratory parameters including complete blood count, red blood cell indices, hypochromic RBC, reticulocyte hemoglobin content, and serum ferritin were measured. Appropriate statistical tests were applied. RESULTS: Out of 174 children, 127 (73%) had structural kidney disease as an etiology of CKD, and 110 (63%) had anemia. Prevalence of anemia was 44%, 43%, 74%, 64% and 92% in CKD stage 1, 2, 3, 4 and 5, respectively. Absolute iron deficiency was found in 66 (38%) even when some children were already on iron supplementation. FID was seen in 44 (25%) and on multivariate analysis, lower estimated glomerular filtration rate and mineral bone disease are associated risk factors. CONCLUSION: FID is present in one-fourth of our CKD cohort. It should be considered when the response to adequate measures of improving hemoglobin level fails. More studies are required to know its impact on short-term and long-term patient-related outcomes such as quality of life and mortality.

Socioeconomic risk factors of hypertension and blood pressure among persons aged 15-49 in Nepal: a cross-sectional study.

OBJECTIVES: This study estimated the prevalence of hypertension, in accordance with the American College of Cardiology and American Heart Association's 2017 guidelines, and examined the association between various socioeconomic factors and systolic blood pressure (SBP), diastolic blood pressure (DBP) and hypertension. SETTING AND DESIGN: We used nationally representative data from the 2016 Nepal Demographic and Health Survey. Multivariate analysis was used to study the association of hypertension with socioeconomic factors: logistic regression was used for hypertension and linear regression was used for DBP and SBP. PARTICIPANTS: Our sample consisted of 9827 adults between the ages of 15 and 49 years. RESULTS: The prevalence of hypertension was 36%. The mean DBP and SBP were 76.4 and 111.5, respectively. Janjatis (adjusted OR (AOR): 1.34, CI: 1.12 to 1.59), Other Terai castes (AOR: 1.38, CI: 1.03 to 1.84), Muslim and other ethnicities (AOR: 1.64, CI: 1.15 to 2.33) and Dalits (AOR: 1.26, CI: 1.00 to 1.58) had higher odds of hypertension. Individuals employed in professional, technical and managerial professions collectively (AOR: 1.62; CI: 1.18 to 2.21) also had higher odds of hypertension. Moderately food insecure household had lower odds of hypertension (AOR: 0.84; CI: 0.72 to 0.99) compared with households with no issue of food insecurity. Results were similar for SBP and DBP. When stratified by sex, there were differences mainly in terms of occupation and ethnicity. CONCLUSION: There are substantial disparities in hypertension prevalence in Nepal. These disparities extend across ethnic groups, occupational status and food security status. Differences also persist across different provinces. As hypertension continues to be increasingly more significant, more research is needed to better understand the disparities and gradients that exist across various socioeconomic factors.

Comparative assessment of QM-based and MM-based models for prediction of protein-ligand binding affinity trends.

Methods which accurately predict protein-ligand binding strengths are critical for drug discovery. In the last two decades, advances in chemical modelling have enabled steadily accelerating progress in the discovery and optimization of structure-based drug design. Most computational methods currently used in this context are based on molecular mechanics force fields that often have deficiencies in describing the quantum mechanical (QM) aspects of molecular binding. In this study, we show the competitiveness of our QM-based Molecules-in-Molecules (MIM) fragmentation method for characterizing binding energy trends for seven different datasets of protein-ligand complexes. By using molecular fragmentation, the MIM method allows for accelerated QM calculations. We demonstrate that for classes of structurally similar ligands bound to a common receptor, MIM provides excellent correlation to experiment, surpassing the more popular Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) methods. The MIM method offers a relatively simple, well-defined protocol by which binding trends can be ascertained at the QM level and is suggested as a promising option for lead optimization in structure-based drug design.

Impacts of community-based care program on health care utilization and cost.

OBJECTIVES: A variety of care coordination and delivery models have been used to address the social and medical needs of high-need, high-cost patient populations. However, the evidence on the effectiveness of such models is far from clear. The purpose of this study is to determine whether the Community Health Team (CHT) program, a community-based care management program in Rhode Island, had impacts on health care utilization and cost. STUDY DESIGN: We used data from 2014 to 2018 to evaluate the effects of the CHT program on health care utilization and cost. Our analytical sample consisted of a total of 12,830 patients, with 2282 in the intervention group and 10,548 in the matched comparison group. METHODS: We used a combination of propensity score-matched difference-in-differences framework and generalized linear models. RESULTS: The program led to an overall decrease in hospitalizations (incidence rate ratio [IRR], 0.89; P = .028) and inpatient costs (IRR, 0.79; P = .024). This translates into a reduction of 7 hospitalizations per 1000 people per month and a reduction of inpatient cost of $289 per person per month. Impacts varied considerably across subgroups. For patients with 1 to 2 encounters with the program, there was a significant decrease in emergency department visits, hospitalizations, inpatient cost, outpatient cost, professional cost, and total cost. Although no significant impacts were observed for patients with 3 to 5 encounters with the program, patients with more than 6 encounters with the program saw an increase in pharmacy cost and total cost. CONCLUSIONS: There is a need for a tailored approach to addressing patients' needs in primary care.

Orthopedic Implant Removal in the Department of Orthopedics of a Tertiary Care Centre of Nepal: A Descriptive Cross-sectional Study.

INTRODUCTION: Implant removal surgery is one of the common surgical procedures done in orthopedics. Studies report that a major portion of orthopedic surgeries carried out in different institutions comprises implant removal procedures. This can be challenging in limited manpower and infrastructure availability scenarios, like in developing countries like Nepal. This study aims to study the prevalence of orthopedic implant removal procedures carried out among overall surgical procedures in the orthopedic department of a tertiary care center in Nepal. METHODS: A descriptive cross-sectional study was performed on the medical records of the department of orthopedics of a tertiary care center after approval from the institutional review committee. The data included records from the starting of 2018 to the end of 2019. Data related to the number of implant removal procedures, types of implants, indications, fracture sites, anesthesia use, gender and age distribution were studied. Statistical Package for Social Sciences version 20 was used to study descriptive data. RESULTS: Out of 2557 orthopedic operations carried out in the study duration, 458 (17.91%) of implant removal procedures were done in the department. The most common age group was the young adult age group, 255 (55.68%). Medium-sized implants were the commonly removed ones, 337 (73.58%). Elective procedures were the most common indication, 369 (80.57%). CONCLUSIONS: Implant removal procedures cover a major fraction of overall orthopedic operations carried out by the department, most of which are elective procedures. In limited-resource settings, this can be challenging, and a proper evaluation with counseling could be done before implant removal surgery.

Unusual Presentation of Extruded Disc: A Case Report.

A 38-year male presented with severe low back pain radiating towards right lower limb which was progressively increasing with decrease in motor power of the ipsilateral ankle dorsiflexion and toe extension. Magnetic Resonance study with gadolinium suggested dorsal epidural migration of the extruded disc at L4-L5 level compressing the thecal sac, which mimics the differential diagnosis epidural abscess, epidural hematoma, synovial cyst and extradural space-occupying lesion. Open lumbar discectomy was done, and the large, herniated disc was found dorsal to the thecal sac adhering dura mater, which was removed meticulously and the patient was symptomatically better postoperatively. The power of his lower limb gradually increased by physiotherapy in subsequent follow-up.

Data Sources for Understanding the Social Determinants of Health: Examples from Two Middle-Income Countries: the 3-D Commission.

The expansion in the scope, scale, and sources of data on the wider social determinants of health (SDH) in the last decades could bridge gaps in information available for decision-making. However, challenges remain in making data widely available, accessible, and useful towards improving population health. While traditional, government-supported data sources and comparable data are most often used to characterize social determinants, there are still capacity and management constraints on data availability and use. Conversely, privately held data may not be shared. This study reviews and discusses the nature, sources, and uses of data on SDH, with illustrations from two middle-income countries: Kenya and the Philippines. The review highlights opportunities presented by new data sources, including the use of big data technologies, to capture data on social determinants that can be useful to inform population health. We conducted a search between October 2010 and September 2020 for grey and scientific publications on social determinants using a search strategy in PubMed and a manual snowball search. We assessed data sources and the data environment in both Kenya and the Philippines. We found limited evidence of the use of new sources of data to study the wider SDH, as most of the studies available used traditional sources. There was also no evidence of qualitative big data being used. Kenya has more publications using new data sources, except on the labor determinant, than the Philippines. The Philippines has a more consistent distribution of the use of new data sources across the HEALTHY determinants than Kenya, where there is greater variation of the number of publications across determinants. The results suggest that both countries use limited SDH data from new data sources. This limited use could be due to a number of factors including the absence of standardized indicators of SDH, inadequate trust and acceptability of data collection methods, and limited infrastructure to pool, analyze, and translate data.

Use of Data to Understand the Social Determinants of Depression in Two Middle-Income Countries: the 3-D Commission.

Depression accounts for a large share of the global disease burden, with an estimated 264 million people globally suffering from depression. Despite being one of the most common kinds of mental health (MH) disorders, much about depression remains unknown. There are limited data about depression, in terms of its occurrence, distribution, and wider social determinants. This work examined the use of novel data sources for assessing the scope and social determinants of depression, with a view to informing the reduction of the global burden of depression.This study focused on new and traditional sources of data on depression and its social determinants in two middle-income countries (LMICs), namely, Brazil and India. We identified data sources using a combination of a targeted PubMed search, Google search, expert consultations, and snowball sampling of the relevant literature published between October 2010 and September 2020. Our search focused on data sources on the following HEALTHY subset of determinants: healthcare (H), education (E), access to healthy choices (A), labor/employment (L), transportation (T), housing (H), and income (Y).Despite the emergence of a variety of data sources, their use in the study of depression and its HEALTHY determinants in India and Brazil are still limited. Survey-based data are still the most widely used source. In instances where new data sources are used, the most commonly used data sources include social media (twitter data in particular), geographic information systems/global positioning systems (GIS/GPS), mobile phone, and satellite imagery. Often, the new data sources are used in conjunction with traditional sources of data. In Brazil, the limited use of new data sources to study depression and its HEALTHY determinants may be linked to (a) the government's outsized role in coordinating healthcare delivery and controlling the data system, thus limiting innovation that may be expected from the private sector; (b) the government routinely collecting data on depression and other MH disorders (and therefore, does not see the need for other data sources); and (c) insufficient prioritization of MH as a whole. In India, the limited use of new data sources to study depression and its HEALTHY determinants could be a function of (a) the lack of appropriate regulation and incentives to encourage data sharing by and within the private sector, (b) absence of purposeful data collection at subnational levels, and (c) inadequate prioritization of MH. There is a continuing gap in the collection and analysis of data on depression, possibly reflecting the limited priority accorded to mental health as a whole. The relatively limited use of data to inform our understanding of the HEALTHY determinants of depression suggests a substantial need for support of independent research using new data sources. Finally, there is a need to revisit the universal health coverage (UHC) frameworks, as these frameworks currently do not include depression and other mental health-related indicators so as to enable tracking of progress (or lack thereof) on such indicators.

Evaluating the impact of integrated behavioral health intervention: Evidence from Rhode Island.

ABSTRACT: There has been a historic separation between systems that address behavioral health problems and the medical care system that addresses other health issues. Integration of the 2 has the potential to improve care.The aim of this study was to evaluate the impact of Integrated Behavioral Health program on health care utilization and costs.Claims data between 2015 and 2018 from Rhode Island's All Payers Claims Database representing 42,936 continuously enrolled unique patients.Retrospective study based on propensity score-matched difference-in-differences framework.Utilization (emergency department visits, office visits, and hospitalizations) and costs (total, inpatient, outpatient, professional, and pharmacy).Integrated Behavioral Health intervention in Rhode Island was associated with reduction in healthcare utilization. Emergency department visits reduced by 6.4 per 1000 people per month and office visits reduced by 29.8 per 1000 people per month, corresponding to a reduction of 7% and 6%, respectively. No statistically significant association was observed between the intervention and hospitalizations. The evidence was mixed for cost outcomes, with negative association recorded between the intervention and the likelihood of incurring non-zero cost but no significant association was observed between the intervention and the level of costs. This relationship held true for most of the cost measures considered.Integrated Behavioral Health intervention in Rhode Island was associated with significant reductions in emergency department visits and office visits, with no effects on hospitalizations. In terms of the cost outcomes, we found evidence that the intervention negatively affected the likelihood of incurring any non-zero costs but did not affect the level of costs.

Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method.

We have developed an efficient protocol using our two-layer Molecules-in-Molecules (MIM2) fragmentation-based quantum chemical method for the prediction of NMR chemical shifts of large biomolecules. To investigate the performance of our fragmentation approach and demonstrate its applicability, MIM-NMR calculations are first calibrated on a test set of six proteins. The MIM2-NMR method yields a mean absolute deviation (MAD) from unfragmented full molecule calculations of 0.01 ppm for 1H and 0.06 ppm for 13C chemical shifts. Thus, the errors from fragmentation are only about 3% of our target accuracy of ∼0.3 ppm for 1H and 2-3 ppm for 13C chemical shifts. To compare with experimental chemical shifts, a standard protocol is first derived using two smaller proteins 2LHY (176 atoms) and 2LI1 (146 atoms) for obtaining an appropriate protein structure for NMR chemical shift calculations. The effect of the solvent environment on the calculated NMR chemical shifts is incorporated through implicit, explicit, or explicit-implicit solvation models. The expensive first solvation shell calculations are replaced by a micro-solvation model in which only the immediate interaction between the protein and the explicit solvation environment is considered. A single explicit water molecule for each amine and amide proton is found to be sufficient to yield accurate results for 1H chemical shifts. The 1H and 13C NMR chemical shifts calculated using our protocol give excellent agreement with experiments for two larger proteins, 2MC5 (the helical part with 265 atoms) and 3UMK (33 residue slice with 547 atoms). Overall, our target accuracy of ∼0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for the larger proteins. The proposed MIM-NMR method is accurate and computationally cost-effective and should be applicable to study a wide range of large proteins.

Electrosynthesis of a Biaurone by Controlled Dimerization of Flavone: Mechanistic Insight and Large-Scale Application.

The electrochemistry of flavone (1) has been carefully investigated at glassy carbon cathodes in dimethylformamide containing 0.10 M tetra-n-butylammonium tetrafluoroborate as supporting electrolyte. In this medium, a cyclic voltammogram for a reduction of 1 exhibits a reversible cathodic process (Epc = -1.58 V and Epa = -1.47 V vs SHE) that is followed by an irreversible cathodic peak (Epc = -2.17 V vs SHE). When water (5.0 M) is introduced into the medium, the first peak for 1 becomes irreversible (Epc = -1.56 V vs SHE), and the second (irreversible) peak shifts to -2.07 V vs SHE. Bulk electrolyses of 1 at -1.60 V vs SHE afford flavanone, 2'-hydroxychalcone, 2'-hydroxy-3-phenylpropionate, and two new compounds, namely (Z)-1,6-bis(2-hydroxyphenyl)-3,4-diphenylhex-3-ene-1,6-dione (D1) and (Z)-2,2'-(1,2-diphenylethene-1,2-bis(benzofuran-3(2H))-one) (D2), obtained in significant amounts, that were characterized by means of 1H and 13C NMR spectrometry as well as single-crystal X-ray diffraction. Along with the above findings, we have proposed a mechanism for the electroreduction of 1, which has been further corroborated by our quantum mechanical study.

Quantum Mechanical Investigation of Three-Dimensional Activity Cliffs Using the Molecules-in-Molecules Fragmentation-Based Method.

The concept of activity cliff (AC) (i.e., a small structural modification resulting in a substantial bioactivity change) is widely encountered in medicinal chemistry during compound design. Whereas the study of ACs is of high interest as it provides a wealth of opportunities for effective drug design, its practical application in the actual drug development process has been difficult because of significant computational challenges. To provide some understanding of the ACs, we have carried out a rigorous quantum-mechanical investigation of the electronic interactions of a wide range of ACs (205 cliffs formed by 261 protein-ligand complexes covering 37 different receptor types) using multilayer molecules-in-molecules (MIM) fragmentation-based methodology. The MIM methodology enables performing accurate high-level quantum mechanical (QM) calculations at a substantially lower computational cost, while allowing for a quantitative decomposition of the protein-ligand binding energy into the contributions from individual residues, solvation, and entropy. Our investigation in this study is mainly focused on whether the QM binding energy calculation can correctly identify the higher potency cliff partner for a given ligand pair having a sufficiently high activity difference. We have also analyzed the effect of including crystal water molecules as a part of the receptor as well as the impact of ligand desolvation energy on the correct identification of the more potent ligand in a cliff pair. Our analysis reveals that, in the majority of the cases, the AC prediction could be significantly improved by carefully identifying the critical crystal water molecules, whereas the contribution from the ligand desolvation also remains essential. Additionally, we have exploited the residue-specific interaction energies provided by MIM to identify the key residues and interaction hot-spots that are responsible for the experimentally observed drastic activity changes. The results show that our MIM fragmentation-based protocol provides comprehensive interaction energy profiles that can be employed to understand the distinctiveness of ligand modifications, for potential applications in structure-based drug design.

G4 accuracy at DFT cost: unlocking accurate redox potentials for organic molecules using systematic error cancellation.

The redox potential is a powerful thermodynamic and kinetic tool used to predict numerous chemical and biochemical mechanisms. However, despite the improving predictive power of density functional theory (DFT), chemically accurate theoretical redox potentials are often difficult to achieve with DFT. For example, calculated redox potentials are sensitive to density functional choice and often fall short of the desired accuracy. Thus, ranges of errors for computed redox potentials between different density functionals can become quite large. The current study presents a cost-effective protocol that utilizes effective error cancellation schemes in order to accurately predict the redox potentials of a wide range of organic molecules. This computational protocol, called CBH-Redox, is an extension of the connectivity-based hierarchy (CBH) method, and produces thermochemical data with near-G4 accuracy. Herein, we test the CBH-Redox protocol against both experimental and G4 reference values and compare these results to DFT alone. Considering 46 C, O, N, F, Cl, and S atom-containing molecules, when using the CBH-Redox correction scheme, the MAEs for all eight density functionals tested are within the 0.09 V target accuracy versus both experiment and G4. Moreover, CBH-Redox achieves an impressive accuracy, with a MAE of 0.05 V or below when compared to G4 for six of the eight density functionals tested. In addition, when the CBH correction is applied, the error range across all functionals tested decreases from 0.12 V to about 0.05 V versus G4, and from 0.13 V to 0.04 V versus experiment.