A Computational Physics-based Approach to Predict Unbound Brain-to-Plasma Partition Coefficient, Kp,uu.

The blood-brain barrier (BBB) plays a critical role in preventing harmful endogenous and exogenous substances from penetrating the brain. Optimal brain penetration of small-molecule central nervous system (CNS) drugs is characterized by a high unbound brain/plasma ratio (Kp,uu). While various medicinal chemistry strategies and in silico models have been reported to improve BBB penetration, they have limited application in predicting Kp,uu directly. We describe a physics-based computational approach, a quantum mechanics (QM)-based energy of solvation (E-sol), to predict Kp,uu. Prospective application of this method in internal CNS drug discovery programs highlights the utility and accuracy of this new method, which showed a categorical accuracy of 79% and an R2 of 0.61 from a linear regression model.

Diagnostic validity of the MINI-KID disorder classifications in specialized child and adolescent psychiatric outpatient clinics in Sweden.

BACKGROUND: Missing diagnostic information often results poor accuracy of the clinical diagnostic decision process. The Mini International Neuropsychiatric Interview for Children and Adolescents (MINI-KID) is a short standardized diagnostic interview and covers a rather broad range of diagnoses applicable to children and adolescents. MINI-KID disorder classifications have shown test-retest reliability and validity comparable to other standardized diagnostic interviews and is claimed to be a useful tool for diagnostic screening in Child and Adolescent Psychiatric care. The concordance between the Swedish language version of the MINI-KID Interview and LEAD (Longitudinal, Expert, All Data) research diagnoses was studied in secondary child and adolescent psychiatric outpatient care. METHODS: MINI-KID interviews were performed for 101 patients, boys n = 50, girls n = 51, aged 4 to 18 years. The duration of the interview was on average 46 min, the child/adolescent participating together with the parent(s) in most cases. The seven most prevalent diagnoses were included in the analyses. RESULTS: The average overall percent agreement (OPA) between MINI-KID and LEAD was 79.5%, the average percent positive agreement (PPA) 35.4 and the average percent negative agreement (NPA) 92.7. OPA was highest for Obsessive-Compulsive Disorder (OCD) (0.89), Tic disorders (0.88) and Pervasive developmental disorders (0.81). There were similar results in diagnostic agreement comparing the two versions: the standard MINI-KID and MINI-KID for parents. The specific screening questions in MINI-KID resulted in additional preliminary diagnoses compared with the regular initial clinical assessment. CONCLUSIONS: Overall, there was an acceptable agreement between MINI-KID disorder classifications and research diagnoses according to LEAD. The standardized interview MINI-KID could be considered as a tool with the possibility to give valuable information in the diagnostic process in child and adolescent care which is similar to the setting in the present study.

Relationship Between Cervical, Thoracic, and Lumbar Spinal Alignments in Automotive Seated Posture.

The purpose of this study was to investigate the relationship between cervical, thoracic, and lumbar spinal alignments in one automotive occupant seated posture. An image dataset of the spinal column in the automotive seated posture, previously acquired by an upright open magnetic resonance imaging (MRI) system, was re-analyzed in this study. Spinal alignments were presented by the geometrical centers of the vertebral bodies extracted from the image data. Cervical, thoracic, and lumbar spinal alignments were analyzed separately with multidimensional scaling (MDS). Based on distribution maps of cervical, thoracic, and lumbar spinal alignments created by MDS, representative spinal alignment patterns of the cervical, thoracic, and lumbar spines and the relationship between cervical, thoracic, and lumbar spinal alignments were investigated. As a result, this study found a correlation between cervical and thoracic spinal alignments in an automotive occupant seated posture. According to representative spinal alignment patterns illustrated by the distribution map of spinal alignments, subjects who had kyphotic cervical spinal alignment tended to have less kyphotic thoracic spinal alignment, while subjects who had lordotic cervical spinal alignment tended to have more kyphotic thoracic spinal alignment. For lumbar spinal alignments, no prominent relationship was found between cervical and thoracic spinal alignment in the seated condition of this study.

Open Abdomen Therapy with Vacuum and Mesh Mediated Fascial Traction After Aortic Repair: an International Multicentre Study.

OBJECTIVES: Open abdomen therapy may be necessary to prevent or treat abdominal compartment syndrome (ACS). The aim of the study was to analyse the primary delayed fascial closure (PDFC) rate and complications after open abdomen therapy with vacuum and mesh mediated fascial traction (VACM) after aortic repair and to compare outcomes between those treated with open abdomen after primary versus secondary operation. METHODS: This was a retrospective cohort, multicentre study in Sweden, Finland, and Norway, including consecutive patients treated with open abdomen and VACM after aortic repair at six vascular centres in 2006-2015. The primary endpoint was PDFC rate. RESULTS: Among 191 patients, 155 were men. The median age was 71 years (IQR 66-76). Ruptured abdominal aortic aneurysm (RAAA) occurred in 69.1%. Endovascular/hybrid and open repairs were performed in 49 and 142 patients, respectively. The indications for open abdomen were inability to close the abdomen (62%) at primary operation and ACS (80%) at secondary operation. Duration of open abdomen was 11 days (IQR 7-16) in 157 patients alive at open abdomen termination. The PDFC rate was 91.8%. Open abdomen initiated at primary (N=103), compared with secondary operation (N=88), was associated with less severe initial open abdomen status (p=.006), less intestinal ischaemia (p=.002), shorter duration of open abdomen (p=.007), and less renal replacement therapy (RRT, p<.001). In hospital mortality was 39.3%, and after entero-atmospheric fistula (N=9) was 88.9%. Seven developed graft infection within 6 months, 1 year mortality was 28.6%. Intestinal ischaemia (OR 3.71, 95% CI 1.55-8.91), RRT (OR 3.62, 95% CI 1.72-7.65), and age (OR 1.12, 95% CI 1.06-1.12), were independent factors associated with in hospital mortality, but not open abdomen initiated at primary versus secondary operation. CONCLUSIONS: VACM was associated with a high PDFC rate after prolonged open abdomen therapy following aortic repair. Patient outcomes seemed better when open abdomen was initiated at primary, compared with secondary operation but a selection effect is possible.

A Female Ligamentous Cervical Spine Finite Element Model Validated for Physiological Loads.

Mathematical cervical spine models allow for studying of impact loading that can cause whiplash associated disorders (WAD). However, existing models only cover the male anthropometry, despite the female population being at a higher risk of sustaining WAD in automotive rear-end impacts. The aim of this study is to develop and validate a ligamentous cervical spine intended for biomechanical research on the effect of automotive impacts. A female model has the potential to aid the design of better protection systems as well as improve understanding of injury mechanisms causing WAD. A finite element (FE) mesh was created from surface data of the cervical vertebrae of a 26-year old female (stature 167 cm, weight 59 kg). Soft tissues were generated from the skeletal geometry and anatomical literature descriptions. Ligaments were modeled with nonlinear elastic orthotropic membrane elements, intervertebral disks as composites of nonlinear elastic bulk elements, and orthotropic anulus fibrosus fiber layers, while cortical and trabecular bones were modeled as isotropic plastic-elastic. The model has geometrical features representative of the female cervical spine-the largest average difference compared with published anthropometric female data was the vertebral body depth being 3.4% shorter for the model. The majority the cervical segments compare well with respect to biomechanical data at physiological loads, with the best match for flexion-extension loads and less biofidelity for axial rotation. An average female FE ligamentous cervical spine model was developed and validated with respect to physiological loading. In flexion-extension simulations with the developed female model and an existing average male cervical spine model, a greater range of motion (ROM) was found in the female model.

Potency prediction of ß-secretase (BACE-1) inhibitors using density functional methods.

Scoring potency is a main challenge for structure based drug design. Inductive effects of subtle variations in the ligand are not possible to accurately predict by classical computational chemistry methods. In this study, the problem of predicting potency of ligands with electronic variations participating in key interactions with the protein was addressed. The potency was predicted for a large set of cyclic amidine and guanidine cores extracted from ß-secretase (BACE-1) inhibitors. All cores were of similar size and had equal interaction motifs but were diverse with respect to electronic substitutions. A density functional theory approach, in combination with a representation of the active site of a protein using only key residues, was shown to be predictive. This computational approach was used to guide and support drug design, within the time frame of a normal drug discovery design cycle.

Quantifying rider posture variability in powered two- and three-wheelers for safety assessment.

OBJECTIVE: Injury outcomes for powered two- and three-wheeler (PTW) riders are influenced by the rider posture. To enable analysis of PTW rider accidents and development of protection systems, detailed whole-body posture data is needed. Therefore, the aim of this study is to fill this gap by providing collections of average male whole-body postures, including subpopulation variability, for different PTW types. This will enable future studies to explore the influence of PTW rider posture variation and to support safety system development. METHODS: 3D photometric measurements of 51 anatomical landmarks were recorded on 20 (50th percentile male) volunteers in their preferred riding postures across three PTW types (naked, scooter, and touring). Following an outlier removal process, a principal component analysis (PCA) was performed to calculate average postures and principal components (PCs), to describe the observed posture variation, for each PTW. The visualization of the PCs was facilitated through kinematic linkage representations, connecting anatomical landmarks and estimated joint centers to form segments and characteristic joint angles. RESULTS: The first seven PCs explained 80% of the variance in posture for each of the three PTWs. Across PTWs, these PCs frequently described combinations of postural features including variation in fore-aft seat positions, pelvic tilt, spinal curvature, head position, and extremity flexion-extension. Analysis revealed distinct differences in average postures across the three PTWs, on average, 10 ± 9° for the characteristic joint angles within a min-to-max range between the three PTWs. However, for all three PTWs, the variability between volunteers in characteristic joint angles on the same PTW were on average more than twice as large within a ± 2 SD range (26 ± 11°). CONCLUSIONS: The results suggest that PTW rider posture variation must be addressed by involving simultaneous adjustments of multiple body parts, as described by each of the first seven PCs, as a direct consequence of the human body interconnectedness. Furthermore, the study's findings challenge conventional assumptions that the relative distance between PTWs' handlebar, seat, and foot support predominantly influences rider postures. Instead, the research demonstrates that individual variability has a substantial influence on rider posture and should be considered in PTW safety development.

Characterization of a ligand binding site in the human transient receptor potential ankyrin 1 pore.

The pharmacology and regulation of Transient Receptor Potential Ankyrin 1 (TRPA1) ion channel activity is intricate due to the physiological function as an integrator of multiple chemical, mechanical, and temperature stimuli as well as differences in species pharmacology. In this study, we describe and compare the current inhibition efficacy of human TRPA1 on three different TRPA1 antagonists. We used a homology model of TRPA1 based on Kv1.2 to select pore vestibule residues available for interaction with ligands entering the vestibule. Site-directed mutation constructs were expressed in Xenopus oocytes and their functionality and pharmacology assessed to support and improve our homology model. Based on the functional pharmacology results we propose an antagonist-binding site in the vestibule of the TRPA1 ion channel. We use the results to describe the proposed intravestibular ligand-binding site in TRPA1 in detail. Based on the single site substitutions, we designed a human TRPA1 receptor by substituting several residues in the vestibule and adjacent regions from the rat receptor to address and explain observed species pharmacology differences. In parallel, the lack of effect on HC-030031 inhibition by the vestibule substitutions suggests that this molecule interacts with TRPA1 via a binding site not situated in the vestibule.

Bioactivation of sitaxentan in liver microsomes, hepatocytes, and expressed human P450s with characterization of the glutathione conjugate by liquid chromatography tandem mass spectrometry.

Sitaxentan is a selective endothelin-A receptor antagonist that was marketed as Thelin in several European countries and Canada for pulmonary arterial hypertension. Sitaxentan was undergoing further clinical trials in the United States but due to four deaths and one case of liver transplantation from severe liver toxicity that appeared to be idiosyncratic in nature, it was withdrawn worldwide in December, 2010. Sitaxentan contains a 1,3-benzodioxole ring that undergoes enzymatic demethyleneation to an ortho-catechol metabolite that can further oxidize to a reactive ortho-quinone metabolite. Here, we report the detection and mass spectral characterization of a glutathione conjugate of this sitaxentan quinone reactive metabolite that was trapped in vitro using mouse, rat, dog, and human liver microsomes supplemented with NADPH and glutathione and that was also observed in rat and human hepatocytes. Using human liver microsomes, we also demonstrated that P450 3A4 undergoes time-dependent inhibition. Density functional calculations on the catechol metabolite of sitaxentan indicated that the reaction leading to the quinone was thermodynamically favorable with an enthalpy change of -6.3 kcal/mol. Using density functional methodology, we modeled the attack of glutathione on the quinone with an S-methyl thiolate anion which allowed us to predict, based on the difference in transition state energies, that the 2-position on the phenyl ring was more likely than the 5-position as the site of glutathione conjugation. Overall, our results demonstrated that sitaxentan is capable of facile formation of a reactive ortho-quinone metabolite capable of reacting with glutathione and may rationalize the idiosyncratic nature of the hepatotoxicity that led to its withdrawal.

Utilizing the σ-complex stability for quantifying reactivity in nucleophilic substitution of aromatic fluorides.

A computational approach using density functional theory to compute the energies of the possible σ-complex reaction intermediates, the "σ-complex approach", has been shown to be very useful in predicting regioselectivity, in electrophilic as well as nucleophilic aromatic substitution. In this article we give a short overview of the background for these investigations and the general requirements for predictive reactivity models for the pharmaceutical industry. We also present new results regarding the reaction rates and regioselectivities in nucleophilic substitution of fluorinated aromatics. They were rationalized by investigating linear correlations between experimental rate constants (k) from the literature with a theoretical quantity, which we call the sigma stability (SS). The SS is the energy change associated with formation of the intermediate σ-complex by attachment of the nucleophile to the aromatic ring. The correlations, which include both neutral (NH3) and anionic (MeO(-)) nucleophiles are quite satisfactory (r = 0.93 to r = 0.99), and SS is thus useful for quantifying both global (substrate) and local (positional) reactivity in SNAr reactions of fluorinated aromatic substrates. A mechanistic analysis shows that the geometric structure of the σ-complex resembles the rate-limiting transition state and that this provides a rationale for the observed correlations between the SS and the reaction rate.

How much does the injury risk between average female and average male anthropometry differ? - A simulation study with open source tools for virtual crash safety assessments.

Differences in injury risk between females and males are often reported in field data analysis. The aim of this study was to investigate the differences in kinematics and injury risks between average female and male anthropometry in two exemplary use cases. A simulation study comprising the newly introduced VIVA+ human body models (HBM) was performed for two use cases. The first use case relates to whiplash associated disorders sustained in rear impacts and the second to femur fractures in pedestrians impacted by passenger cars as field data indicates that females have higher injury risk compared to males in these scenarios. Detailed seat models and a generic vehicle exterior were used to simulate crash scenarios close to those currently tested in consumer information tests. In the evaluations with one of the vehicle seats and one car shape the injury risks were equal for both models. However, the risk of the average female HBM for whiplash associated disorders was 1.5 times higher compared to the average male HBM for the rear impacts in the other seat and 10 times higher for proximal femur fractures in the pedestrian impacts for one of the two evaluated vehicle shapes.. Further work is needed to fully understand trends observed in the field and to derive appropriate countermeasures, which can be performed with the open source tools introduced in the current study.

2-thioxanthines are mechanism-based inactivators of myeloperoxidase that block oxidative stress during inflammation.

Myeloperoxidase (MPO) is a prime candidate for promoting oxidative stress during inflammation. This abundant enzyme of neutrophils uses hydrogen peroxide to oxidize chloride to highly reactive and toxic chlorine bleach. We have identified 2-thioxanthines as potent mechanism-based inactivators of MPO. Mass spectrometry and x-ray crystal structures revealed that these inhibitors become covalently attached to the heme prosthetic groups of the enzyme. We propose a mechanism whereby 2-thioxanthines are oxidized, and their incipient free radicals react with the heme groups of the enzyme before they can exit the active site. 2-Thioxanthines inhibited MPO in plasma and decreased protein chlorination in a mouse model of peritonitis. They slowed but did not prevent neutrophils from killing bacteria and were poor inhibitors of thyroid peroxidase. Our study shows that MPO is susceptible to the free radicals it generates, and this Achilles' heel of the enzyme can be exploited to block oxidative stress during inflammation.

Predicting regioselectivity in nucleophilic aromatic substitution.

We have investigated practical and computationally efficient methods for the quantitative prediction of regioisomer distribution in kinetically controlled nucleophilic aromatic substitution reactions. One of the methods is based on calculating the relative stabilities of the isomeric σ-complex intermediates using DFT. We show that predictions from this method can be used quantitatively both for anionic nucleophiles with F(-) as leaving group, as well as for neutral nucleophiles with HF as leaving group. The σ-complex approach failed when the leaving group was Cl/HCl or Br/HBr, both for anionic and neutral nucleophiles, because of difficulties in finding relevant σ-complex structures. An approach where we assumed a concerted substitution step and used such transition state structures gave quantitatively useful results. Our results are consistent with other theoretical works, where a stable σ-complex has been identified in some cases, whereas others have been indicated to proceed via a concerted substitution step.

Discovery of novel pyrrolopyridazine scaffolds as transient receptor potential vanilloid (TRPV1) antagonists.

A novel indolizine class of compounds was identified as TRPV1 antagonist from an HTS campaign. However, this indolizine class proved to be unstable and reacted readily with glutathione when exposed to light and oxygen. Reactivity was reduced by the introduction of a nitrogen atom alpha to the indolizine nitrogen. The pyrrolopyridazine core obtained proved to be inert to the action of light and oxygen. The synthesis route followed the one used for the indolizine compounds, and the potency and ADMET profile proved to be similar.

Potent and orally efficacious benzothiazole amides as TRPV1 antagonists.

Benzothiazole amides were identified as TRPV1 antagonists from high throughput screening using recombinant human TRPV1 receptor and structure-activity relationships were explored to pinpoint key pharmacophore interactions. By increasing aqueous solubility, through the attachment of polar groups to the benzothiazole core, and enhancing metabolic stability, by blocking metabolic sites, the drug-like properties and pharmokinetic profiles of benzothiazole compounds were sufficiently optimized such that their therapeutic potential could be verified in rat pharmacological models of pain.

A pragmatic approach using first-principle methods to address site of metabolism with implications for reactive metabolite formation.

A majority of xenobiotics are metabolized by cytochrome P450 (CYP) enzymes. The discovery of drug candidates with low propensity to form reactive metabolites and low clearance can be facilitated by understanding CYP-mediated xenobiotic metabolism. Being able to predict the sites where reactive metabolites form is beneficial in drug design to produce drug candidates free of reactive metabolite issues. Herein, we report a pragmatic protocol using first-principle density functional theory (DFT) calculations for predicting sites of epoxidation and hydroxylation of aromatic substrates mediated by CYP. The method is based on the relative stabilities of the CYP-substrate intermediates or the substrate epoxides. Consequently, it concerns mainly the electronic reactivity of the substrates. Comparing to the experimental findings, the presented protocol gave excellent first-ranked epoxidation site predictions of 83%, and when the test was extended to CYP-mediated sites of aromatic hydroxylation, satisfactory results were also obtained (73%). This indicates that our assumptions are valid and also implies that the intrinsic reactivities of the substrates are in general more important than their binding poses in proteins, although the protocol may benefit from the addition of docking information.

Imidazopyridine-based inhibitors of glycogen synthase kinase 3: synthesis and evaluation of amide isostere replacements of the carboxamide scaffold.

In this study, we explored the effect of bioisostere replacement in a series of glycogen synthase kinase 3 (GSK3) inhibitors based on the imidazopyridine core. The synthesis and biological evaluation of a number of novel sulfonamide, 1,2,4-oxadiazole, and thiazole derivates as amide bioisosteres, as well as a computational rationalization of the obtained results are reported.

Finite element human body models with active reflexive muscles suitable for sex based whiplash injury prediction.

Previous research has not produced a satisfactory resource to study reflexive muscle activity for investigating potentially injurious whiplash motions. Various experimental and computational studies are available, but none provided a comprehensive biomechanical representation of human response during rear impacts. Three objectives were addressed in the current study to develop female and male finite element human body models with active reflexive neck muscles: 1) eliminate the buckling in the lower cervical spine of the model observed in earlier active muscle controller implementations, 2) evaluate and quantify the influence of the individual features of muscle activity, and 3) evaluate and select the best model configuration that can be used for whiplash injury predictions. The current study used an open-source finite element model of the human body for injury assessment representing an average 50th percentile female anthropometry, together with the derivative 50th percentile male morphed model. Based on the head-neck kinematics and CORelation and Analyis (CORA) tool for evaluation, models with active muscle controller and parallel damping elements showed improved head-neck kinematics agreement with the volunteers over the passive models. It was concluded that this model configuration would be the most suitable for gender-based whiplash injury prediction when different impact severities are to be studied.

Discovery of a Novel Class of d-Amino Acid Oxidase Inhibitors Using the Schrödinger Computational Platform.

d-Serine is a coagonist of the N-methyl d-aspartate (NMDA) receptor, a key excitatory neurotransmitter receptor. In the brain, d-serine is synthesized from its l-isomer by serine racemase and is metabolized by the D-amino acid oxidase (DAO, DAAO). Many studies have linked decreased d-serine concentration and/or increased DAO expression and enzyme activity to NMDA dysfunction and schizophrenia. Thus, it is feasible to employ DAO inhibitors for the treatment of schizophrenia and other indications. Powered by the Schrödinger computational modeling platform, we initiated a research program to identify novel DAO inhibitors with the best-in-class properties. The program execution leveraged an hDAO FEP+ model to prospectively predict compound potency. A new class of DAO inhibitors with desirable properties has been discovered from this endeavor. Our modeling technology on this program has not only enhanced the efficiency of structure-activity relationship development but also helped to identify a previously unexplored subpocket for further optimization.

Design and Evaluation of the Initial 50th Percentile Female Prototype Rear Impact Dummy, BioRID P50F - Indications for the Need of an Additional Dummy Size.

The objective of this study was to present the design of a prototype rear impact crash test dummy, representing a 50th percentile female, and compare its performance to volunteer response data. The intention was to develop a first crude prototype as a first step toward a future biofidelic 50th percentile female rear impact dummy. The current rear impact crash test dummy, BioRID II, represents a 50th percentile male, which may limit the assessment and development of whiplash protection systems with regard to female occupants. Introduction of this new dummy size will facilitate evaluation of seat and head restraint (HR) responses in both the average sized female and male in rear impacts. A 50th percentile female rear impact prototype dummy, the BioRID P50F, was developed from modified body segments originating from the BioRID II. The mass and rough dimensions of the BioRID P50F is representative of a 50th percentile female. The prototype dummy was evaluated against low severity rear impact sled tests comprising six female volunteers closely resembling a 50th percentile female with regard to stature and mass. The head/neck response of the BioRID P50F prototype resembled the female volunteer response corridors. The stiffness of the thoracic and lumbar spinal joints remained the same as the average sized male BioRID II, and therefore likely stiffer than joints of an average female. Consequently, the peak rearward angular displacement of the head and T1, and the rearward displacement of the T1, were lesser for the BioRID P50F in comparison to the female volunteers. The biofidelity of the BioRID P50F prototype thus has some limitations. Based on a seat response comparison between the BioRID P50F and the BioRID II, it can be concluded that the male BioRID II is an insufficient representation of the average female in the assessment of the dynamic seat response and effectiveness of whiplash protection systems.