The Influence of 150-Cavity Binders on the Dynamics of Influenza A Neuraminidases as Revealed by Molecular Dynamics Simulations and Combined Clustering

Neuraminidase inhibitors are the main pharmaceutical agents employed for treatments of influenza infections. The neuraminidase structures typically exhibit a 150-cavity, an exposed pocket that is adjacent to the catalytic site. This site offers promising additional contact points for improving potency of existing pharmaceuticals, as well as generating entirely new candidate inhibitors. Several inhibitors based on known compounds and designed to interact with 150-cavity residues have been reported. However, the dynamics of any of these inhibitors remains unstudied and their viability remains unknown. This work reports the outcome of long-term, all-atom molecular dynamics simulations of four such inhibitors, along with three standard inhibitors for comparison. Each is studied in complex with four representative neuraminidase structures, which are also simulated in the absence of ligands for comparison, resulting in a total simulation time of 9.6µs. Our results demonstrate that standard inhibitors characteristically reduce the mobility of these dynamic proteins, while the 150-binders do not, instead giving rise to many unique conformations. We further describe an improved RMSD-based clustering technique that isolates these conformations – the structures of which are provided to facilitate future molecular docking studies – and reveals their interdependence. We find that this approach confers many advantages over previously described techniques, and the implications for rational drug design are discussed

Imprinting: expanding the extra-pharmacological model of psychedelic drug action to incorporate delayed influences of sets and settings

BackgroundPsychedelic drug experiences are shaped by current-moment contextual factors, commonly categorized as internal (set) and external (setting). Potential influences of past environments, however, have received little attention.AimsTo investigate how previous environmental stimuli shaped the experiences of patients receiving ketamine for treatment-resistant depression (TRD), and develop the concept of “imprinting” to account for such time-lagged effects across diverse hallucinogenic drugs.MethodsRecordings of treatment sessions and phenomenological interviews from 26 participants of a clinical trial investigating serial intravenous ketamine infusions for TRD, conducted from January 2021 to August 2022, were retrospectively reviewed. A broad literature search was undertaken to identify potentially underrecognized examples of imprinting with both serotonergic and atypical psychedelics, as well as analogous cognitive processes and neural mechanisms.ResultsIn naturalistic single-subject experiments of a 28-year-old female and a 34-year-old male, subjective ketamine experiences were significantly altered by varying exposures to particular forms of digital media in the days preceding treatments. Higher levels of media exposure reduced the mystical/emotional qualities of subsequent psychedelic ketamine experiences, overpowering standard intention-setting practices and altering therapeutic outcomes. Qualitative data from 24 additional patients yielded eight further spontaneous reports of past environmental exposures manifesting as visual hallucinations during ketamine experiences. We identified similar examples of imprinting with diverse psychoactive drugs in past publications, including in the first-ever report of ketamine in human subjects, as well as analogous processes known to underly dreaming.Conclusions/interpretationPast environmental exposures can significantly influence the phenomenology and therapeutic outcomes of psychedelic experiences, yet are underrecognized and understudied. To facilitate future research, we propose expanding the contextual model of psychedelic drug actions to incorporate imprinting, a novel concept that may aid clinicians, patients, and researchers to better understand psychedelic drug effects.Clinical trial registrationClinicalTrials.gov, identifier NCT04701866

The Montreal model: an integrative biomedical-psychedelic approach to ketamine for severe treatment-resistant depression

BackgroundSubanesthetic ketamine has accumulated meta-analytic evidence for rapid antidepressant effects in treatment-resistant depression (TRD), resulting in both excitement and debate. Many unanswered questions surround ketamine’s mechanisms of action and its integration into real-world psychiatric care, resulting in diverse utilizations that variously resemble electroconvulsive therapy, conventional antidepressants, or serotonergic psychedelics. There is thus an unmet need for clinical approaches to ketamine that are tailored to its unique therapeutic properties.MethodsThis article presents the Montreal model, a comprehensive biopsychosocial approach to ketamine for severe TRD refined over 6 years in public healthcare settings. To contextualize its development, we review the evidence for ketamine as a biomedical and as a psychedelic treatment of depression, emphasizing each perspectives’ strengths, weaknesses, and distinct methods of utilization. We then describe the key clinical experiences and research findings that shaped the model’s various components, which are presented in detail.ResultsThe Montreal model, as implemented in a recent randomized clinical trial, aims to synergistically pair ketamine infusions with conventional and psychedelic biopsychosocial care. Ketamine is broadly conceptualized as a brief intervention that can produce windows of opportunity for enhanced psychiatric care, as well as powerful occasions for psychological growth. The model combines structured psychiatric care and concomitant psychotherapy with six ketamine infusions, administered with psychedelic-inspired nonpharmacological adjuncts including rolling preparative and integrative psychological support.DiscussionOur integrative model aims to bridge the biomedical-psychedelic divide to offer a feasible, flexible, and standardized approach to ketamine for TRD. Our learnings from developing and implementing this psychedelic-inspired model for severe, real-world patients in two academic hospitals may offer valuable insights for the ongoing roll-out of a range of psychedelic therapies. Further research is needed to assess the Montreal model’s effectiveness and hypothesized psychological mechanisms

Childhood cognitive skills trajectories and suicide by mid-adulthood:an investigation of the 1958 British Birth Cohort

International audienceBackground : Poor cognitive abilities and low intellectual quotient (IQ) are associated with an increased risk of suicide attempts and suicide mortality. However, knowledge of how this association develops across the life-course is limited. Our study aims to establish whether individuals who died by suicide by mid-adulthood are distinguishable by their child-to-adolescence cognitive trajectories.Methods : Participants were from the 1958 British Birth Cohort and were assessed for academic performance at ages 7, 11, and 16 and intelligence at 11 years. Suicides occurring by September 2012 were identified from linked national death certificates. We compared mean mathematics and reading abilities and rate of change across 7–16 years for individuals who died by suicide v. those still alive, with and without adjustment for potential early-life confounding factors. Analyses were based on 14 505 participants.Results : Fifty-five participants (48 males) had died by suicide by age 54 years. While males who died by suicide did not differ from participants still alive in reading scores at age 7 [effect size (g) = −0.04, p = 0.759], their reading scores had a less steep improvement up to age 16 compared to other participants. Adjustments for early-life confounding factors explained these differences. A similar pattern was observed for mathematics scores. There was no difference between individuals who died by suicide v. participants still alive on intelligence at 11 years.Conclusions : While no differences in tests of academic performance and IQ were observed, individuals who died by suicide had a less steep improvement in reading abilities over time compared to same-age peers

Probing Hyperconjugation Experimentally with the Conformational Deuterium Isotope Effect

Hyperconjugation underlies many chemical phenomena of fundamental and practical importance. Owing to a great deal of interest in the anomeric effect, anomeric-like hyperconjugative effects have been thoroughly investigated in oxygen-containing systems. However, such interactions in the second- and third-row chalcogens are less well-understood and have generated some controversy. Here, we show that the conformational deuterium isotope effect, in combination with Saunders’ isotopic perturbation method, permits sensitive and direct experimental probing of the conformational equilibria in dioxane, dithiane, and diselenane analogues by variable-temperature, dynamic NMR spectroscopy. We find that the magnitude of the conformational deuterium isotope effect is 252.1, 28.3, and 7.1 J/mol (±10%) for the oxygen, sulfur, and selenium analogues, respectively. These results reveal the periodic trend for hyperconjugation in the chalcogens, which reflect a decreasing n_<i>x</i>→σ_C–H(D) interaction throughout the period, as supported by IR spectroscopy and in agreement with DFT calculations and a natural bond order analysis

N2-1 alternate enzyme poses.

<p>Shown are the C1, C3, C8 of N2 with L1 of <b>3</b>. The color scheme is identical to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059873#pone-0059873-g005" target="_blank">Figure 5</a>.</p

N1₀₉-6 shows a significant loop-opening effect.

<p>Shown is C3, C7 and C9 of N1₀₉ and L1 and L2 of <b>6</b>. C1 is included for reference, though not occupied. The color scheme is identical to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059873#pone-0059873-g005" target="_blank">Figure 5</a>.</p

N1₀₉-3 dominant pose and its destabilization.

<p>Shown is C1, C15, C25 and C28 of N1₀₉ and L1 and L5 of <b>3</b>. The color scheme is identical to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059873#pone-0059873-g005" target="_blank">Figure 5</a>.</p

N2–5 facilitating R152 moving into the active site center.

<p>Shown is C1 and C5 of N2 and L1, L3, and L4 of <b>5</b>. The color scheme is identical to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059873#pone-0059873-g005" target="_blank">Figure 5</a>.</p