A novel Golgi mannosidase inhibitor: Molecular design,synthesis, enzyme inhibition,and inhibition of spheroid formation

Effective chemotherapy for solid cancers is challenging due to a limitation in permeation that prevents anticancer drugs from reaching the center of the tumor, therefore unable to limit cancer cell growth. To circumvent this issue, we planned to apply the drugs directly at the center by first collapsing the outer structure. For this, we focused on cell–cell communication (CCC) between N-glycans and proteins at the tumor cell surface. Mature N-glycans establish CCC; however, CCC is hindered when numerous immature N-glycans are present at the cell surface. Inhibition of Golgi mannosidases (GMs) results in the transport of immature N-glycans to the cell surface. This can be employed to disrupt CCC. Here, we describe the molecular design and synthesis of an improved GM inhibitor with a non-sugar mimic scaffold that was screened from a compound library. The synthesized compounds were tested for enzyme inhibition ability and inhibition of spheroid formation using cell-based methods. Most of the compounds designed and synthesized exhibited GM inhibition at the cellular level. Of those, AR524 had higher inhibitory activity than a known GM inhibitor, kifunensine. Moreover, AR524 inhibited spheroid formation of human malignant cells at low concentration (10 µM), based on the disruption of CCC by GM inhibition.     

Monte Carlo replica‐exchange based ensemble docking of protein conformations

A replica‐exchange Monte Carlo (REMC) ensemble docking approach has been developed that allows efficient exploration of protein–protein docking geometries. In addition to Monte Carlo steps in translation and orientation of binding partners, possible conformational changes upon binding are included based on Monte Carlo selection of protein conformations stored as ordered pregenerated conformational ensembles. The conformational ensembles of each binding partner protein were generated by three different approaches starting from the unbound partner protein structure with a range spanning a root mean square deviation of 1–2.5 Å with respect to the unbound structure. Because MC sampling is performed to select appropriate partner conformations on the fly the approach is not limited by the number of conformations in the ensemble compared to ensemble docking of each conformer pair in ensemble cross docking. Although only a fraction of generated conformers was in closer agreement with the bound structure the REMC ensemble docking approach achieved improved docking results compared to REMC docking with only the unbound partner structures or using docking energy minimization methods. The approach has significant potential for further improvement in combination with more realistic structural ensembles and better docking scoring functions. Proteins 2017; 85:924–937. © 2016 Wiley Periodicals, Inc.     

Sampling Schemes for Studying Growth of Children

Efficiency of linked cross-sectional scheme has been compared with pure longitudinal schemes for generalised estimation of norm relaxing the condition of constancy of variances. The relevant theory of estimation has been developed and the expression for the optimum estimators alongwith their variances have been derived. The percentage gain in efficiency has been calculated. It has been observed that for higher values of Q, percentage gain in efficiency of proposed scheme over cross-sectional is very high.     

Spectral resolution of cardio-circulatory variations in men measured by autorhythmometry over 2 years

An analogue of the periodogram method for unequally spaced data is presented with a view to resolving the frequency structure of the observations. The algorithm is explicitly based on the sequential least squares procedure. In particular, the key concept is that the with-in-plot spectral analysis can be augmented by the between-plot information to make inferences about common characteristics. It is also shown how the between-plot random variations can be incorporated into the multiple harmonic regression model. A detailed spectral analysis investigates the periodic fluctuations in four cardio-circulatory variables, measured by autorhythmometric observation by eight men at rest and extending over a time span of 2 years. The spectral curves show the existence of circadian and circaseptan rhythmicities. The amplitude modulation of the dian rhythm by circaseptan variation is assimilated with the rhythmicity of work during the week. The blood-pressure variables situate their maximum annual peak in the winter period. These quasi-periodic fluctuations appear to be related to the amount of physical activity performed in time by the subjects.     

Individualistic responses of forest herb traits to environmental change

• Intraspecific trait variation (ITV; i.e. variability in mean and/or distribution of plant attribute values within species) can occur in response to multiple drivers. Environmental change and land‐use legacies could directly alter trait values within species but could also affect them indirectly through changes in vegetation cover. Increasing variability in environmental conditions could lead to more ITV, but responses might differ among species. Disentangling these drivers on ITV is necessary to accurately predict plant community responses to global change.
• We planted herb communities into forest soils with and without a recent history of agriculture. Soils were collected across temperate European regions, while the 15 selected herb species had different colonizing abilities and affinities to forest habitat. These mesocosms (384) were exposed to two‐level full‐factorial treatments of warming, nitrogen addition and illumination. We measured plant height and specific leaf area (SLA).
• For the majority of species, mean plant height increased as vegetation cover increased in response to light addition, warming and agricultural legacy. The coefficient of variation (CV) for height was larger in fast‐colonizing species. Mean SLA for vernal species increased with warming, while light addition generally decreased mean SLA for shade‐tolerant species. Interactions between treatments were not important predictors.
• Environmental change treatments influenced ITV, either via increasing vegetation cover or by affecting trait values directly. Species’ ITV was individualistic, i.e. species responded to different single resource and condition manipulations that benefited their growth in the short term. These individual responses could be important for altered community organization after a prolonged period.

     

Soybean aeroallergen around the port of New Orleans: A potential cause of asthma

There have been reported epidemics of severe asthma in Barcelona, Spain, linked to a 10 kDa low molecular mass (LMM) allergen from soybean hulls that became airborne during unloading of ships. As a preliminary probe of the potential for dispersion of this allergen in USA cities, four automated air samplers were placed around a grain elevator in New Orleans and operated continuously from May to October 1990. The allergen was extracted from the filters and immunochemically assayed for soybean aeroallergen. On 31 separate days, the airborne allergen concentration in at least one of the samples was over 10000 U/m³ similar to those observed in Barcelona on some epidemic days. Areas North and East of the elevator were most affected. Serologie studies showed that of 50 asthmatics from New Orleans who were participants in an unrelated clinical study 4 or 8% demonstrated elevated titers of IgE antibody to LMM soybean allergen. Only 1 of 475 control sera (half of which were also asthmatic) obtained elsewhere in the US was positive for LMM soybean IgE antibody. Based on the findings in this study, there is a great possibility that on some days there is enough soybean allergen in the air and a sufficient frequency of soybean aeroallergen RAST positive asthmatics in New Orleans to warrant further investigation of the contribution of soybean aeroallergen to asthma around the port of New Orleans.Supported by NIAID # A121255. Mayo Clinic and Foundation and Minnesota Lung Association.     

A comparison of direct and indirect methods for measuring leaf and surface areas of individual bushes

Indirect estimates of leaf area from measurements with three commercially available instruments (DEMON, LAI-2000 and Sunfleck Ceptometer) were compared with directly measured areas of individual Retama sphaerocarpa bushes. The three indirect methods gave good estimates of the total surface area of individual bushes. For the DEMON, the method of log-linear averaging of transmitted radiation gave estimates closer to directly measured surface area than the method of averaging transmission linearly. For the LAI-2000, estimated surface area index multiplied by canopy projected area gave the best agreement with directly measured values. For measurements with the Sunfleck Ceptometer, values of surface area estimated from the transmission of photosynthetic quantum flux density, without correcting for diffuse radiation, gave the best agreement with directly measured values. Surface areas estimated by the three instruments were not significantly different from directly measured total (leaf + branch + stem) surface areas. Leaf surface area could be calculated from estimated total surface area minus directly measured branch surface area. Measured branch surface area was linearly related to canopy projected area.     

Frustration‐guided motion planning reveals conformational transitions in proteins

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics‐inspired motion planning procedure called dCC‐RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non‐native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC‐RRT to examine how collective, small‐scale motions of four side‐chains in the active site of cyclophilin A propagate through the protein. dCC‐RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non‐canonical capsid binding site 25 Å away, rationalizing NMR and multi‐temperature crystallography experiments. In all, dCC‐RRT can reveal detailed, all‐atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/ .