Identification of low micromolar dual inhibitors for aldose reductase (ALR2) and poly (ADP-ribose) polymerase (PARP-1) using structure based design approach

Clinical studies have revealed that diabetic retinopathy is a multifactorial disorder. Moreover, studies also suggest that ALR2 and PARP-1 co-occur in retinal cells, making them appropriate targets for the treatment of diabetic retinopathy. To find the dual inhibitors of ALR2 and PARP-1, the structure based design was carried out in parallel for both the target proteins. A series of novel thiazolidine-2,4-dione (TZD) derivatives were therefore rationally designed, synthesized and their in vitro inhibitory activities against ALR2 and PARP-1 were evaluated. The experimental results showed that compounds 5b and 5f, with 2-chloro and 4-fluoro substitutions, showed biochemical activities in micromolar and submicromolar range (IC₅₀ 1.34–5.03 μM) against both the targeted enzymes. The structure-activity relationship elucidated for these novel inhibitors against both the enzymes provide new insight into the binding mode of the inhibitors to the active sites of enzymes. The positive results of the biochemical assay suggest that these compounds may be further optimized and utilized for the treatment of diabetic retinopathy.     

Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir

To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)–quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guanosine and its analog acyclovir in aqueous solution. The solvent effects were simulated by explicit inclusion of water molecules that model the relevant part of the first hydration shell around the solute. The position of these water molecules was estimated by carrying out a classical Metropolis Monte Carlo simulation of dilute water solutions of the guanosine (Gs) and acyclovir (ACV) and subsequently analyzing solute–solvent intermolecular interactions in the statistically-independent MC-generated configurations. The solvent-assisted proton transfer processes were further investigated using two different ab initio MP2 quantum chemical approaches. In the first one, potential energy surfaces of the ‘bare’ finite solute–solvent clusters containing Gs/ACV and four water molecules (MP2/6-31+G(d,p) level) were explored, while within the second approach, these clusters were embedded in ‘bulk’ solvent treated as polarizable continuum (C-PCM/MP2/6-31+G(d,p) level of theory). It was found that in the gas phase and in water solution, the most stable tautomer for guanosine and acyclovir is the 1H-2-amino-6-oxo form followed by the 2-amino-6-(sZ)-hydroxy form. The energy barriers of the water-assisted proton transfer reaction in guanosine and in acyclovir are found to be very similar – 11.74 kcal mol^?1 for guanosine and 11.16 kcal mol^?1 for acyclovir, and the respective rate constants (k = 1.5?×?10¹ s^?1, guanosine and k = 4.09?×?10¹ s^?1, acyclovir), are sufficiently large to generate the 2-amino-6-(sZ)-hydroxy tautomer. The analysis of the reaction profiles in both compounds shows that the proton transfer processes occur through the asynchronous concerted mechanism.     

基于元胞自动机的城市空间动态模拟

城市空间动态的模拟与预测可以为城市可持续发展规划与管理提供重要的参考依据。SLEUTH元胞自动机模型在城市空间模拟中较强的适用性和可移植性,该模型通过对历史数据的蒙特卡洛迭代自动寻找城市增长误差最小的参数组合,解决了传统元胞自动机模型中转换规则不易确定的问题。以武汉市为研究案例,运用SLEUTH模型进行了城市空间动态模拟与情景预测。2007年至2011年的城市空间模拟结果显示,模拟结果与实际历史数据可以获得良好的空间匹配度,Lee-Sallee形状指数均在0.6以上,显示SLEUTH元胞自动机模型经过本地化校正后具有较强的适用性和满意的模拟精度。进而,设置了现状趋势、基本保护、严格保护等3种情景对武汉2025年城市空间动态进行了预测,结果显示,各情景模式下城市居住用地均明显增长,农业用地、林地、水域等均有所减少;现状趋势情景和基本保护情景下农田、林地、水域减少的幅度较大,会加剧区域的生境破碎、耕地功能下降、水资源匮乏、湖滨湿地萎缩等生态问题,说明这两种情景不能有效满足城市生态系统健康和可持续发展的需要。严格保护情景下,城市居住用地扩张的程度得到了明显的控制,水域和林地得到了有效的保护,对于重要的自然生态系统组分保护及其服务能力维持可以起到显著作用。     

A comparison of the accuracy and precision of several open-water oxygen productivity techniques

Several methods for the estimation of the reaeration coefficient were compared by determining the ability of the methods to recover the correct K value from a computer-simulated stream oxygen record affected by a variety of non-ideal conditions. Noisy data and long observation intervals were not a serious problem for most methods. Saturating photosynthesis, fluctuating light intensity, afternoon depression and temperature variation caused failures by some methods but were well handled by others. Serious impairment of all methods occurred with low productivity or high K. In general, the best-performing methods were the modified hysteresis, nighttime regression, daytime regression, Odum and Hornberger-Kelly daytime methods.     

Conformation of ring single-stranded DNA measured by DNA origami structures

Measuring the mechanical properties of single-stranded DNA (ssDNA) is a complex challenge that has been addressed lately by different methods. We measured the persistence length of ring ssDNA using a combination of a special DNA origami structure, a self-avoiding ring polymer simulation model, and nonparametric estimation statistics. The method overcomes the complexities set forth by previously used methods. We designed the DNA origami nano structures and measured the ring ssDNA polymer conformations using atomic force microscopy. We then calculated their radius of gyration, which was used as a fitting parameter for finding the persistence length. As there is no simple formulation for the radius of gyration distribution, we developed a simulation program consisting of a self-avoiding ring polymer to fit the persistence length to the experimental data. ssDNA naturally forms stem-loops, which should be taken into account in fitting a model to the experimental measurement. To overcome that hurdle, we found the possible loops using minimal energy considerations and used them in our fitting procedure of the persistence length. Due to the statistical nature of the loops formation, we calculated the persistence length for different percentages of loops that are formed. In the range of 25–75% loop formation, we found the persistence length to be 1.9–4.4 nm, and for 50% loop formation we get a persistence length of 2.83 ± 0.63 nm. This estimation narrows the previously known persistence length and provides tools for finding the conformations of ssDNA.     

Mandibular biomechanics after marginal resection: Correspondences of simulated volumetric strain and skeletal resorption

Serious mandibular diseases such as tumor or osteonecrosis often require segmental or marginal mandibulectomy, the latter with improved outcome thanks to preserved mandibular continuity. Nevertheless, gradual osteolytic and/or osteosclerotic skeletal changes frequently indicate repetitive resections. Based on the fundamental adaptivity of bone to mechanical loads, the question arose whether resection-related anatomical alterations trigger relevant pathological skeletal adaptations. For a clinical case after mandibular box resection due to progressive osteoradionecrosis (ORN), routine biomechanical loading was simulated by finite element method, respecting pathology-related anatomy, tissue properties, and biting capacity. By 3D-visualization of the mandible’s pathological development from follow-up-CT’s over four years, remarkable correspondences of skeletal resorptions and increased unphysiological strain were revealed. Higher unphysiological load was correlated with more serious and earlier skeletal alterations. Three months post-operatively, serious buccal destruction at the distal resection corner occurred in correspondence with dominant tensile strain. At the resection, elevated strain caused by reduced alveolar height corresponded to skeletal compromise, observed 8–9 months post-operatively. ORN-related lesions, diagnosed before resection, entailed unphysiological strain coinciding with local skeletal alterations. Simulations with “healthy” instead of pathological tissue coefficients induced quantitative improvements of 25–33%, but without fundamental change. These results suggest a decisive contribution of resection-related biomechanical skeletal adaptations to this patient’s mandibular decline with hemimandibulectomy about 2.5 years after the first resection. However, mechanical stress concentrations in sharp angles as the distal resection corner and reduced stability due to decreased alveolar height generally bear the danger of pathological biomechanics and severe skeletal adaptations for patients after mandibular box resection.     

农田灌溉对印度区域气候的影响模拟

为满足人类对粮食的需求,全球灌溉农田面积迅速扩张,农田灌溉对区域气候的影响引起广泛地关注。利用区域环境系统集成模式(RIEMS2.0)和最新的土地利用变化资料,选取农田灌溉面积最大的印度区域作为研究区域,进行雨养农田和灌溉农田的对比试验,探讨农田灌溉对区域气候的影响。结果表明:(1)农田灌溉使得印度区域年平均气温降低1.4℃,年平均降水率增加0.35mm/d。农田灌溉对印度区域气候的影响存在明显的季节波动,季风前期及6月份该区域气候对下垫面变化的响应最为敏感;7-9月各气候要素变化较小。(2) 农田灌溉使得印度区域地表净辐射增加,且地表净辐射在潜热通量和感热通量之间的分配发生了较大的改变,潜热通量增加,感热通量减少;对地表起冷却作用;同时由于土壤湿度增加,蒸散作用增强,大气中水汽含量增加,潜热不稳定能量增加,导致对流性降水增加。     

生态位理论在张家界市主要旅游景区评价中的应用

选择张家界市5个主要旅游景区作为研究对象、50种影响旅游景区发展的资源状态作为评价指标, 通过指标逐级合并处理, 在3个指标级别(Ⅰ、Ⅱ、Ⅲ级)上分析了生态位宽度和生态位重叠. 结果表明: 张家界市旅游景区生态位宽度受指标级别的影响显著(F=10.278, P=0.006), 而采用相对生态位宽度则不受指标级别的影响, 说明在旅游景区开发潜力评价中, 相对生态位宽度比绝对生态位宽度更具合理性; 从Ⅲ级指标到Ⅰ级指标, 旅游景区生态位重叠度值有增大趋势, 表明指标级别的选择会影响旅游景区间实际生态位重叠的评价. 随着评价指标的逐步细化, 当观测到的Pianka指数和采用Monte Carlo模拟的Pianka指数的差值达到显著水平时, 该指标级别可作为评价指标细化的最低标准, 模拟的生态位重叠值可作为旅游景区竞争评价的重要参考.     

Molecular dynamics simulation of thionated hen egg white lysozyme

Understanding of the driving forces of protein folding is a complex challenge because different types of interactions play a varying role. To investigate the role of hydrogen bonding involving the backbone, the effect of thio substitutions in a protein, hen egg white lysozyme (HEWL), was investigated through molecular dynamics simulations of native as well as partly (only residues in loops) and fully thionated HEWL using the GROMOS 54A7 force field. The results of the three simulations show that the structural properties of fully thionated HEWL clearly differ from those of the native protein, while for partly thionated HEWL they only changed slightly compared with native HEWL. The analysis of the torsional-angle distributions and hydrogen bonds in the backbone suggests that the α-helical segments of native HEWL tend to show a propensity to convert to 3(10)-helical geometry in fully thionated HEWL. A comparison of the simulated quantities with experimental NMR data such as nuclear overhauser effect (NOE) atom-atom distance bounds and (3)J((H)(N)(H)(α))-couplings measured for native HEWL illustrates that the information content of these quantities with respect to the structural changes induced by thionation of the protein backbone is rather limited.     

Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein

With the development of de novo binders for protein targets from non‐related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single‐chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking “disembodied” amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein‐antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen‐based detection agents for typhoid diagnostics.