Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model.

BACKGROUND: During the maturation process, HIV capsid proteins self-assemble into polymorphic capsids. The strong polymorphism precludes high resolution structural characterization under in vivo conditions. In spite of the determination of structural models for various in vitro assemblies of HIV capsid proteins, the assembly mechanism is still not well-understood. METHODS: We report 3D simulations of HIV capsid proteins by a novel coarse grain model that captures the backbone of the rigid segments in the protein accurately. The effects of protein dynamics on assembly are emulated by a static ensemble of subunits in conformations derived from molecular dynamics simulation. RESULTS: We show that HIV capsid proteins robustly assemble into hexameric lattices in a range of conditions where trimers of dimeric subunits are the dominant oligomeric intermediates. Variations of hexameric lattice curvatures are observed in simulations with subunits of variable inter-domain orientations mimicking the conformation distribution in solution. Simulations with subunits based on pentameric structural models lead to assembly of sharp curved structures resembling the tips of authentic HIV capsids, along a distinct pathway populated by tetramers and pentamers with the characteristic quasi-equivalency of viral capsids. CONCLUSIONS: Our results suggest that the polymorphism assembly is triggered by the inter-domain dynamics of HIV capsid proteins in solution. The assembly of highly curved structures arises from proteins in conformation with a highly specific inter-domain orientation. SIGNIFICANCE: Our work proposes a mechanism of HIV capsid assembly based on available structural data, which can be readily verified. Our model can be applied to other large biomolecular assemblies.

Botulinum toxin for subacute/chronic neck pain.

BACKGROUND: Neck disorders are common, disabling and costly. Botulinum toxin (BoNT) intramuscular injections are often used with the intention of treating neck pain. OBJECTIVES: To systematically evaluate the literature on the treatment effectiveness of BoNT for neck pain, disability, global perceived effect and quality of life in adults with neck pain with or without associated cervicogenic headache, but excluding cervical radiculopathy and whiplash associated disorder. SEARCH STRATEGY: We searched CENTRAL, MEDLINE, AMED, Index to Chiropractic Literature, CINAHL, LILACS, and EMBASE from their origin to 20 September 2010. SELECTION CRITERIA: We included randomised and quasi-randomised controlled trials in which BoNT injections were used to treat subacute or chronic neck pain. DATA COLLECTION AND ANALYSIS: A minimum of two review authors independently selected articles, abstracted data, and assessed risk of bias, using the Cochrane Back Review Group criteria. In the absence of clinical heterogeneity, we calculated standardized mean differences (SMD) and relative risks, and performed meta-analyses using a random-effects model. The quality of the evidence and the strength of recommendations were assigned an overall grade for each outcome. MAIN RESULTS: We included nine trials (503 participants). Only BoNT type A (BoNT-A) was used in these studies.High quality evidence suggests there was little or no difference in pain between BoNT-A and saline injections at four weeks (five trials; 252 participants; SMD pooled -0.07 (95% confidence intervals (CI) -0.36 to 0.21)) and six months for chronic neck pain. Very low quality evidence indicated little or no difference in pain between BoNT-A combined with physiotherapeutic exercise and analgesics and saline injection with physiotherapeutic exercise and analgesics for patients with chronic neck pain at four weeks (two trials; 95 participants; SMD pooled 0.09 (95% CI -0.55 to 0.73)) and six months (one trial; 24 participants; SMD -0.56 (95% CI -1.39 to 0.27)). Very low quality evidence from one trial (32 participants) showed little or no difference between BoNT-A and placebo at four weeks (SMD 0.16 (95% CI -0.53 to 0.86)) and six months (SMD 0.00 (95% CI -0.69 to 0.69)) for chronic cervicogenic headache. Very low quality evidence from one trial (31 participants), showed a difference in global perceived effect favouring BoNT-A in chronic neck pain at four weeks (SMD -1.12 (95% CI: -1.89 to -0.36)). AUTHORS' CONCLUSIONS: Current evidence fails to confirm either a clinically important or a statistically significant benefit of BoNT-A injection for chronic neck pain associated with or without associated cervicogenic headache. Likewise, there was no benefit seen for disability and quality of life at four week and six months.

Alum with interleukin-12 augments immunity to a melanoma peptide vaccine: correlation with time to relapse in patients with resected high-risk disease.

PURPOSE: We attempted to augment immunity to melanoma antigens using interleukin-12 (IL-12) with aluminum hydroxide (alum) for sustained release or granulocyte macrophage colony-stimulating factor (GM-CSF) added to a multipeptide vaccine. EXPERIMENTAL DESIGN: Sixty patients with high-risk resected melanoma were randomized to receive melanoma peptides gp100(209-217) (210M), MART-1(26-35) (27L), and tyrosinase(368-376) (370D) with adjuvant Montanide ISA 51 and either IL-12 at 30 ng/kg with alum (group A), IL-12 at 100 ng/kg with alum (group B), or IL-12 at 30 ng/kg with 250 mug GM-CSF (group C). RESULTS: Three patients had stage IIC (5%), 50 had stage III (83%), and 7 had stage IV (12%) melanoma. Most toxicities were grade 1/2 and resolved rapidly. Significant toxicity included grade 3 colitis and visual changes and grade 3 headache resolving after stopping IL-12 but continuing peptide vaccine. A higher rate of post-vaccine 6-month immune response to gp100 and MART-1 was observed in group A (15 of 19) or B (19 of 20) that received IL-12 plus alum versus group C with IL-12/GM-CSF (4 of 21; P < 0.001). Post-vaccine enzyme-linked immunospot response rates to peptide analogues in group B were higher than group A (P = 0.031 for gp100 and P = 0.010 for MART-1); both were higher than group C (P < 0.001 for gp100 and P < 0.026 for MART-1). With a median of 24 months of follow-up, 23 patients have relapsed. Post-vaccine immune response to MART-1 was associated with relapse-free survival (P = 0.012). CONCLUSIONS: IL-12 with alum augmented an immune response to melanoma antigens compared with IL-12 with GM-CSF. Immune response was associated with time to relapse.

Immunodynamics: a cancer immunotherapy trials network review of immune monitoring in immuno-oncology clinical trials.

The efficacy of PD-1/PD-L1 targeted therapies in addition to anti-CTLA-4 solidifies immunotherapy as a modality to add to the anticancer arsenal. Despite raising the bar of clinical efficacy, immunologically targeted agents raise new challenges to conventional drug development paradigms by highlighting the limited relevance of assessing standard pharmacokinetics (PK) and pharmacodynamics (PD). Specifically, systemic and intratumoral immune effects have not consistently correlated with standard relationships between systemic dose, toxicity, and efficacy for cytotoxic therapies. Hence, PK and PD paradigms remain inadequate to guide the selection of doses and schedules, both starting and recommended Phase 2 for immunotherapies. The promise of harnessing the immune response against cancer must also be considered in light of unique and potentially serious toxicities. Refining immune endpoints to better inform clinical trial design represents a high priority challenge. The Cancer Immunotherapy Trials Network investigators review the immunodynamic effects of specific classes of immunotherapeutic agents to focus immune assessment modalities and sites, both systemic and importantly intratumoral, which are critical to the success of the rapidly growing field of immuno-oncology.

Construction of a novel coarse grain model for simulations of HIV capsid assembly to capture the backbone structure and inter-domain motions in solution.

We show the construction of a novel coarse grain model for simulations of HIV capsid assembly based on four structural models of HIV capsid proteins: isolated hexamer 3H47.pdb, tubular assembly 3J34.pdb, isolated pentamer 3P05.pdb and C-terminus dimer 2KOD.pdb. The data demonstrates the derivation of inter-domain motions from all atom Molecular Dynamics simulations and comparison with the motions derived from the analysis of solution NMR results defined in 2M8L.pdb. Snapshots from a representative Monte Carlo simulation with 128 dimeric subunit proteins based on 3J34.pdb are shown in addition to the quantitative analysis of its assembly pathway. Movies of the assembly process are compiled with snapshots of representative simulations of four structural models. The methods and data in this article were utilized in Qiao et al. (in press) [1] to probe the mechanism of polymorphism and curvature control of HIV capsid assembly.

Powered ankle-foot prosthesis for the improvement of amputee ambulation.

This paper presents the mechanical design, control scheme, and clinical evaluation of a novel, motorized ankle-foot prosthesis, called MIT Powered Ankle-Foot Prosthesis. Unlike a conventional passive-elastic ankle-foot prosthesis, this prosthesis can provide active mechanical power during the stance period of walking. The basic architecture of the prosthesis is a unidirectional spring, configured in parallel with a force-controllable actuator with series elasticity. With this architecture, the anklefoot prosthesis matches the size and weight of the human ankle, and is also capable of delivering high mechanical power and torque observed in normal human walking. We also propose a biomimetic control scheme that allows the prosthesis to mimic the normal human ankle behavior during walking. To evaluate the performance of the prosthesis, we measured the rate of oxygen consumption of three unilateral transtibial amputees walking at self-selected speeds to estimate the metabolic walking economy. We find that the powered prosthesis improves amputee metabolic economy from 7% to 20% compared to the conventional passive-elastic prostheses (Flex-Foot Ceterus and Freedom Innovations Sierra), even though the powered system is twofold heavier than the conventional devices. This result highlights the benefit of performing net positive work at the ankle joint to amputee ambulation and also suggests a new direction for further advancement of an ankle-foot prosthesis.

Phase I clinical trial of weekly docetaxel and exisulind, a novel inducer of apoptosis.

BACKGROUND: The objective of this phase I study was to determine the maximal tolerated dose (MTD) of the combination of weekly docetaxel and exisulind in patients with advanced solid tumors. PATIENTS AND METHODS: Patients with advanced or refractory solid tumors were treated with intravenous weekly docetaxel with daily oral exisulind. The following dose levels (docetaxel/exisulind) were explored: 30-mg/m2/200 mg po bid, 35/200, 35/250 and 40/250. Docetaxel was administered weekly for 6 weeks followed by 2 weeks off, and exisulind was taken twice daily. Each cycle was 8 weeks. RESULTS: Eighteen patients were enrolled in the study. All of them had received prior systemic therapy. Most patients had either melanoma or carcinomas of the upper gastrointestinal tract. A total of 31 cycles of therapy were administered. DLTs were grade 3 diarrhea, anorexia and fatigue and grade 3 cutaneous toxicity at dose level 4 (40/250). Myelosuppression was mild. Fatigue and gastrointestinal toxicity (anorexia, dyspepsia, nausea, abdominal pain and diarrhea) represented the most common toxicities. However, grade 3 and grade 4 toxicities were uncommon. There were no treatment related deaths. No objective responses were observed and five patients achieved stable disease. CONCLUSIONS: The recommended dose for phase II studies is weekly docetaxel 35 mg/m2 for 6 weeks followed by 2 weeks off in combination with oral exisulind 250 mg po bid. This combination is feasible and well-tolerated at these doses.