The future of molecular dynamics simulations in drug discovery

Molecular dynamics simulations can now track rapid processes—those occurring in less than about a millisecond—at atomic resolution for many biologically relevant systems. These simulations appear poised to exert a significant impact on how new drugs are found, perhaps even transforming the very process of drug discovery. We predict here future results we can expect from, and enhancements we need to make in, molecular dynamics simulations over the coming 25 years, and in so doing set out several Grand Challenges for the field. In the context of the problems now facing the pharmaceutical industry, we ask how we can best address drug discovery needs of the next quarter century using molecular dynamics simulations, and we suggest some possible approaches

Swelling and shrinking kinetics of a lamellar gel phase

We investigate the swelling and shrinking of L_beta lamellar gel phases composed of surfactant and fatty alcohol after contact with aqueous poly(ethylene-glycol) solutions. The height change $\Delta h(t)$ is diffusion-like with a swelling coefficient, S: $\Delta h = S \sqrt{t}$. On increasing polymer concentration we observe sequentially slower swelling, absence of swelling, and finally shrinking of the lamellar phase. This behavior is summarized in a non-equilibrium diagram and the composition dependence of S quantitatively described by a generic model. We find a diffusion coefficient, the only free parameter, consistent with previous measurements.Comment: 3 pages, 4 figures to appear in Applied Physics Letter

A New History and Discussion of 180-Day Exclusivity

This is the third in a series of articles on 180-day exclusivity. The first article traced the history of 180-day exclusivity from 1984 through its amendment in 2003 and court cases in 2004. A second article, published by two of the authors in 2007, updated the earlier piece through the end of 2006 but was arranged by issue rather than in a chronology. This article, which includes a third author, provides a comprehensive resource on 180-day exclusivity for old abbreviated new drug applications (ANDAs) (but less detail in some places where the 2007 article may be referenced) and focuses more discussion on the new provisions as well as some policy and legal issues related to 180-day exclusivity

Delayed Insemination of Non-Estrual Beef Heifers in 7-day CO-Synch Timed Artificial Insemination

Reproductive performance in cattle is considered to be the most economically important trait and is essential for the success of an operation. In the last decade, timed artificial insemination (AI) in the beef cattle industry has increased in popularity due to the decreased amount of labor required for estrous detection. To increase the use of AI; however, cost and time inputs need to be further decreased. The objective of this study was to determine if fertility could be improved in beef heifers that are not expressing estrus before timed AI by delaying insemination

Post seismic response of repeating aftershocks

The recurrence intervals of repeating earthquakes on the San Andreas Fault in the Loma Prieta aftershock zone follow the characteristic 1/t decay of Omori's law. A model in which these earthquakes occur on isolated patches of the fault that fail in stick-slip with creep around them can explain this observation. In this model the recurrence interval is inversely proportional to the loading rate due to creep. Logarithmic velocity strengthening friction predicts 1/t decay in creep rate following the mainshock. The time dependence of recurrence is inconsistent with a simple viscous constitutive relationship, which predicts an exponential decay of loading rate. Thus, our observations imply postseismic slip at seismogenic depth under a power law rheology. The time dependence of postseismic deformation measured geodetically may be diagnostic of whether postseismic deformation is caused by creep or possible viscoelastic deformation at greater depths

Hedgehog Signalling in Androgen Independent Prostate Cancer

Objectives: Androgen-deprivation therapy effectively shrinks hormone-naïve prostate cancer, both in the prostate and at sites of distant metastasis. However prolonged androgen deprivation generally results in relapse and androgen-independent tumour growth, which is inevitably fatal. The molecular events that enable prostate cancer cells to proliferate in reduced androgen conditions are poorly understood. Here we investigate the role of Hedgehog signalling in androgen-independent prostate cancer (AIPC). Methods: Activity of the Hedgehog signalling pathway was analysed in cultured prostate cancer cells, and circulating prostate tumour cells were isolated from blood samples of patients with AIPC. Results: AIPC cells were derived through prolonged culture in reduced androgen conditions, modelling hormone therapy in patients, and expressed increased levels of Hedgehog signalling proteins. Exposure of cultured AIPC cells to cyclopamine, which inhibits Hedgehog signalling, resulted in inhibition of cancer cell growth. The expression of the Hedgehog receptor PTCH and the highly prostate cancer-specific gene DD3PCA3 was significantly higher in circulating prostate cancer cells isolated from patients with AIPC compared with samples prepared from normal individuals. There was an association between PTCH and DD3PCA3 expression and the length of androgen-ablation therapy. Conclusions: Our data are consistent with reports implicating overactivity of Hedgehog signalling in prostate cancer and suggest that Hedgehog signalling contributes to the androgen-independent growth of prostate cancer cells. As systemic anti-Hedgehog medicines are developed, the Hedgehog pathway will become a potential new therapeutic target in advanced prostate cancer.Peer reviewedFinal Accepted Versio

The thermodynamics of prediction

A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an implicit model of the environmental variables. The system's state retains information about past environmental fluctuations, and a fraction of this information is predictive of future ones. The remaining nonpredictive information reflects model complexity that does not improve predictive power, and thus represents the ineffectiveness of the model. We expose the fundamental equivalence between this model inefficiency and thermodynamic inefficiency, measured by dissipation. Our results hold arbitrarily far from thermodynamic equilibrium and are applicable to a wide range of systems, including biomolecular machines. They highlight a profound connection between the effective use of information and efficient thermodynamic operation: any system constructed to keep memory about its environment and to operate with maximal energetic efficiency has to be predictive.Comment: 5 pages, 1 figur

Attenuation of lung graft reperfusion injury by a nitric oxide donor

AbstractObjective: One of the primary features of ischemia-reperfusion injury is reduced production of protective autocoids, such as nitric oxide, by dysfunctional endothelium. Administration of a nitric oxide donor during reperfusion of lung grafts may therefore be beneficial through modulation of vascular tone and leukocyte and platelet function. Methods: Rat lung grafts were flushed with University of Wisconsin solution and reperfused for 1 hour in an ex vivo model incorporating a support animal. Group I grafts (n = 6) were reperfused immediately after explantation, group II (n = 6) and III (n = 5) grafts after 24 hours of storage at 4° C. In group III, glyceryl trinitrate, a nitric oxide donor, was administered during the first 10 minutes of reperfusion at a rate of 200 μg/min. In an additional group (n = 5), 200 μg/min hydralazine was administered instead, to assess the effect of vasodilation alone. Results: Graft function in group II deteriorated compared with that in group I, with significant reduction of graft effluent oxygen tension and blood flow and elevation of pulmonary artery pressure, peak airway pressure, and wet/dry weight ratio. In contrast, in group III, glyceryl trinitrate treatment improved graft function to baseline levels in all these parameters. Administration of hydralazine, meanwhile, produced mixed results with only two out of five grafts functioning at control levels. Conclusions: In this model, administration of glyceryl trinitrate to supplement the nitric oxide pathway in the early phase of reperfusion has a sustained beneficial effect on lung graft function after 24-hour hypothermic storage, probably through mechanisms beyond vasodilation alone. (J Thorac Cardiovasc Surg 1997;113:327-34

Architecture and Membrane Interactions of the EGF Receptor

SummaryDimerization-driven activation of the intracellular kinase domains of the epidermal growth factor receptor (EGFR) upon extracellular ligand binding is crucial to cellular pathways regulating proliferation, migration, and differentiation. Inactive EGFR can exist as both monomers and dimers, suggesting that the mechanism regulating EGFR activity may be subtle. The membrane itself may play a role but creates substantial difficulties for structural studies. Our molecular dynamics simulations of membrane-embedded EGFR suggest that, in ligand-bound dimers, the extracellular domains assume conformations favoring dimerization of the transmembrane helices near their N termini, dimerization of the juxtamembrane segments, and formation of asymmetric (active) kinase dimers. In ligand-free dimers, by holding apart the N termini of the transmembrane helices, the extracellular domains instead favor C-terminal dimerization of the transmembrane helices, juxtamembrane segment dissociation and membrane burial, and formation of symmetric (inactive) kinase dimers. Electrostatic interactions of EGFR’s intracellular module with the membrane are critical in maintaining this coupling