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The human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus in the human genome and is activated and expressed in many cancers and amyotrophic lateral sclerosis. We present the immature HERV-K capsid structure at 3.2 Å resolution determined from native virus-like particles using cryo-electron tomography and subtomogram averaging. The structure shows a hexamer unit oligomerized through a 6-helix bundle, which is stabilized by a small molecule analogous to IP6 in immature HIV-1 capsid. The HERV-K immature lattice is assembled via highly conserved dimer and trimer interfaces, as detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the linker between the N-terminal and the C-terminal domains of CA occurs during HERV-K maturation. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time., (© 2023. Springer Nature Limited.)

Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine., (© 2023. The Author(s).)

Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.

Transmission electron microscopy (TEM) has a multitude of uses in biomedical imaging due to its ability to discern ultrastructure morphology at the nanometer scale. Through its ability to directly visualize virus particles, TEM has for several decades been an invaluable tool in the virologist's toolbox. As applied to HIV-1 research, TEM is critical to evaluate activities of inhibitors that block the maturation and morphogenesis steps of the virus lifecycle. However, both the preparation and analysis of TEM micrographs requires time consuming manual labor. Through the dedicated use of computer vision frameworks and machine learning techniques, we have developed a convolutional neural network backbone of a two-stage Region Based Convolutional Neural Network (RCNN) capable of identifying, segmenting and classifying HIV-1 virions at different stages of maturation and morphogenesis. Our results outperformed common RCNN backbones, achieving 80.0% mean Average Precision on a diverse set of micrographs comprising different experimental samples and magnifications. We expect that this tool will be of interest to a broad range of researchers., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Author(s).)

Objective: To develop/validate an instrument to measure health-related quality of life (HRQoL) in patients with psoriatic arthritis (PsA), for use in clinical studies., Methods: An item pool of 35 items was generated following standardized procedures. Item reduction was performed using clinimetric and psychometric approaches after administration to 66 patients with PsA. The resulting instrument, the VITACORA-19, consists of 19 items. Its validity content, internal consistency, test-retest reliability, known groups/convergent validity, and sensitivity to change were tested in a longitudinal and multicenter study conducted in 10 hospitals in Spain, with 323 patients who also completed the EuroQol 5-dimensional questionnaire (EQ-5D) and a health status transition item. There were 3 study groups: group A (n = 209, patients with PsA), group B (n = 71, patients with arthritis without psoriatic aspect, patients with arthrosis, and patients with dermatitis), and group C (n = 43, healthy controls)., Results: The questionnaire was considered easy/very easy to answer by 94.7% of the patients with PsA. The factorial analysis clearly identified only 1 factor. Cronbach's alpha coefficient and interclass correlation coefficients exceeded 0.90. Statistically significant differences (p < 0.001) were observed between groups: subjects from group C had better HRQoL, followed by group B, and finally group A had the worst HRQoL. The VITACORA-19 scores showed significant correlations (p < 0.001) to PsA disease activity, EQ-5D, and perceived health state, scoring the patients with better health state higher. The minimum important difference was established as an 8-point change in the global score., Conclusion: The Spanish-developed VITACORA-19, designed to measure HRQoL in patients with PsA, has good validity, reliability, and sensitivity to change.

Objective: To investigate the influence of both clinical and pharmacokinetic factors as determinants of response to tiludronate in Paget's bone disease (PBD)., Patients and Methods: Twenty six PBD patients with serum alkaline phosphatase (SAP) levels at least twice the normal upper limit were enrolled. The sample included 17 (65%) men and 9 (35%) women whose mean age (SD) was 60.3 (9.8) (range: 38-76). Each patient received 400 mg/day of tiludronate, per os, for 90 (6) days. The SAP variations were considered as the main parameter of response. Plasma concentrations of tiludronate were assayed using the HPLC method with UV detection; the maximum and minimum (Cmin) concentration, as well as the area under a concentration-time curve were calculated. Multivariate regression analysis was performed to assess the influence on tiludronate effect., Results: Mean (SD) percent reduction of SAP from the initial values ranged from 30.5 (13.9) at the end of the first month of drug intake to a nadir of 76.1 (8.8) achieved 6 months after the treatment was stopped. Serum SAP activity fell to normal range in 7 (27%) patients at the end of the therapy period, in 17 (65%) three months later, and in 18 (69%) one year thereafter. One year after the treatment ended only one patient had evidence of relapse. Final multivariate regression model showed that the percent reduction of SAP increases by 11.9 percent points per Cmin tiludronate unit and by 0.006 points per basal SAP unit, and decreases by 0.52 per year of age. Out of 13 patients with bone pain, 9 (69%) experienced relief within the second and third months of treatment. No clinical or laboratory severe side effects were seen and only five patients (19%) had mild adverse events., Conclusions: These results confirm that tiludronate leads to a marked suppression of PDB clinical and biochemical activity. Cmin of tiludronate in plasma is the best predictor of biochemical response.

To identify animal-related factors associated with Paget's disease of bone (osteitis deformans), we conducted a case-control study in two geographical areas of Spain characterized by different socioeconomic profiles. The analysis presented here is based on 149 cases and 150 controls, frequency matched by sex, age, study area, and place of residence in youth (urban/rural). From a logistic regression analysis, we found that contact with bovine cattle [odds ratio (OR) = 2.14; 95% confidence interval (CI) = 1.16-3.94], consumption of meat traceable to sick livestock (OR = 2.70; 95% CI = 0.98-7.43), and frequent consumption during youth of brains (OR = 1.77; 95% CI = 1.05-2.98) and other viscera increased the risk for Paget's disease of bone. Contact with bovine cattle and consumption during youth of bovid viscera exhibited a dose-response effect as regards length of exposure and frequency of consumption, respectively. A life-style shared with dogs showed itself to be differentially linked to the disease in one study area. Overall, our results support the hypothesis that various animal species are carriers of etiologic agents of Paget's disease of bone.

The cause of Paget's disease of bone (PDB) is unknown. In an attempt to ascertain the proportion of familial cases and evaluate the influence of genetic factors on the occurrence of the disease, a study was undertaken based on 35 PDB patients from our Unit. Their families were investigated, with the participation of a total of 128 first-degree relatives. Fourteen (40%) of these 35 index cases had at least one other first-degree relative affected with PDB and were defined as "familial." The remaining 21 (60%) were considered "sporadic." The frequency of males in the familial cases (79%) was significantly higher than among the sporadics (29%; p < or = 0.01). Mean age at diagnosis (63.1 +/- 12.6 vs. 71.3 +/- 8.7; p < or = 0.02), proportion of polyostotic cases (85.7% vs. 52.4%, p < or = 0.05), and mean number of involved bones per patient (4.36 +/- 2.50 vs. 2.33 +/- 1.93, p < or = 0.01) differ significantly in the familial and sporadic groups. The disease appears to be transmitted via both paternal and maternal sides, and pedigree analysis suggested an autosomal dominant inheritance or multifactorial mechanism. Apart from green-and-blue eye color, which was clearly associated with familial grouping (OR 6.25, 95% CI 1.15-37.16, p < or = 0.01), crude analysis on several genetically based traits and environmental variables revealed no other significant differences between the groups. The adjusted odds ratio estimated for green-and-blue eye color was 2.92 (95% CI 0.38-22.74).(ABSTRACT TRUNCATED AT 250 WORDS)