3D-QSAR and molecular modeling studies on 2,3-dideoxy hexenopyranosid-4-uloses as anti-tubercular agents targeting alpha-mannosidase

Ligand-based and structure-based methods were applied in combination to exploit the physicochemical properties of 2,3-dideoxy hex-2-enopyranosid-4-uloses against Mycobacterium tuberculosis H37Rv. Statistically valid 3D-QSAR models with good correlation and predictive power were obtained with CoMFA steric and electrostatic fields (r² = 0.797, q² = 0.589) and CoMSIA with combined steric, electrostatic, hydrophobic and hydrogen bond acceptor fields (r² = 0.867, q² = 0.570) based on training set of 33 molecules with predictive r² of 0.808 and 0.890 for CoMFA and CoMSIA respectively. The results illustrate the requirement of optimal alkyl chain length at C-1 position and acceptor groups along hydroxy methyl substituent of C-6 to enhance the anti-tubercular activity of the 2,3-dideoxy hex-2-enopyranosid-4-uloses while any substitution at C-3 position exert diminishing effect on anti-tubercular activity of these enulosides. Further, homology modeling of M. tuberculosis alpha-mannosidase followed by molecular docking and molecular dynamics simulations on co-complexed models were performed to gain insight into the rationale for binding affinity of selected inhibitors with the target of interest. The comprehensive information obtained from this study will help to better understand the structural basis of biological activity of this class of molecules and guide further design of more potent analogues as anti-tubercular agents.     

3D-QSAR (CoMFA,CoMSIA), molecular docking and molecular dynamics simulations study of 6-aryl-5-cyano-pyrimidine derivatives to explore the structure requirements of LSD1 inhibitors

Recently, Histone Lysine Specific Demethylase 1 (LSD1) was regarded as a promising anticancer target for the novel drug discovery. And several small molecules as LSD1 inhibitors in different structures have been reported. In this work, we carried out a molecular modeling study on the 6-aryl-5-cyano-pyrimidine fragment LSD1 inhibitors using three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking and molecular dynamics simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to generate 3D-QSAR models. The results show that the best CoMFA model has q² = 0.802, r²_ncv = 0.979, and the best CoMSIA model has q² = 0.799, r²_ncv = 0.982. The electrostatic, hydrophobic and H-bond donor fields play important roles in the models. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. Molecular dynamics simulations results reveal that the complex of the ligand and the receptor protein are stable at 300 K. All the results can provide us more useful information for our further drug design.     

Low-mass molecular dynamics simulation for configurational sampling enhancement: More evidence and theoretical explanation

It has been reported recently that classical, isothermal–isobaric molecular dynamics (NTP MD) simulations at a time step of 1.00 fs of the standard-mass time (Δt=1.00 fs^smt) and a temperature of ≤340 K using uniformly reduced atomic masses by tenfold offers better configurational sampling than standard-mass NTP MD simulations at the same time step. However, it has long been reported that atomic masses can also be increased to improve configurational sampling because higher atomic masses permit the use of a longer time step. It is worth investigating whether standard-mass NTP MD simulations at Δt=2.00 or 3.16 fs^smt can offer better or comparable configurational sampling than low-mass NTP MD simulations at Δt=1.00 fs^smt. This article reports folding simulations of two β-hairpins showing that the configurational sampling efficiency of NTP MD simulations using atomic masses uniformly reduced by tenfold at Δt=1.00 fs^smt is statistically equivalent to and better than those using standard masses at Δt=3.16 and 2.00 fs^smt, respectively. The results confirm that, relative to those using standard masses at routine Δt=2.00 fs^smt, the low-mass NTP MD simulations at Δt=1.00 fs^smt are a simple and generic technique to enhance configurational sampling at temperatures of ≤340 K.     

Design of the influenza virus inhibitors targeting the PA endonuclease using 3D-QSAR modeling,side-chain hopping,and docking

With the emergence of drug resistance and the structural determination of the PA N-terminal domain (PA_N), influenza endonucleases have become an attractive target for antiviral therapies for influenza infection. Here, we combined 3D-QSAR with side-chain hopping and molecular docking to produce novel structures as endonuclease inhibitors. First, a new molecular library was generated with side-chain hopping on an existing template molecule, L-742001, using an in-house fragment library that targets bivalent-cation-binding proteins. Then, the best 3D-QSAR model (AAAHR.500), with q² = 0.76 and r² = 0.97 from phase modeling, was constructed from 23 endonuclease inhibitors and validated with 17 test compounds. The AAAHR.500 model was then used to select effective candidates from the new molecular library. Combining 3D-QSAR with docking using Glide and Autodock, 13 compounds were considered the most likely candidate inhibitors. Docking studies showed that the binding modes of these compounds were consistent with the crystal structures of known inhibitors. These compounds could serve as potential endonuclease inhibitors for further biological activity tests.     

Ligand-based CoMFA and CoMSIA studies on chromone derivatives as radical scavengers

The antioxidant activity for a series of chromone compounds, evaluated by DPPH free radical scavenging assay, were subjected to 3D-QSAR studies using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). All 48 chromone derivatives were geometry optimized by AM1 and HF/6-31G^* calculations. The CoMFA and CoMSIA results were compared between different alignment strategies. The best CoMFA model obtained from HF/6-31G^* optimization with field fit alignment gave cross-validated r² (q²) = 0.821, noncross-validated r² = 0.987, S = 0.095, and F = 388.255. The best CoMSIA model derived from AM1 optimized structures and superimposition alignment gave q² = 0.876, noncross-validated r² = 0.976, S = 0.129, and F = 208.073, including electrostatic, hydrophobic, hydrogen bond donor and acceptor fields. The contour maps provide the fruitful structure–radical scavenging activity relationships which are useful for designing new compounds with higher activity.     

3D-QSAR and docking studies of pentacycloundecylamines at the sigma-1 (σ1) receptor

Pentacycloundecylamine (PCU) derived compounds have been shown to be promising lead structures for the development of novel drug candidates aimed at a variety of neurodegenerative and psychiatric diseases. Here we show for the first time a 3D quantitative structure–activity relationship (3D-QSAR) for a series of aza-PCU-derived compounds with activity at the sigma-1 (σ₁) receptor. A comparative molecular field analysis (CoMFA) model was developed with a partial least squares cross validated (q²) regression value of 0.6, and a non-cross validated r² of 0.9. The CoMFA model was effective at predicting the sigma-1 activities of a test set with an r² >0.7. We also describe here the docking of the PCU-derived compounds into a homology model of the sigma-1 (σ₁) receptor, which was developed to gain insight into binding of these cage compounds to the receptor. Based on docking studies we evaluated in a [³H]pentazocine binding assay an oxa-PCU, NGP1-01 (IC₅₀ = 1.78 μM) and its phenethyl derivative (IC₅₀ = 1.54 μM). Results from these studies can be used to develop new compounds with specific affinity for the sigma-1(σ₁) receptor.     

3D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulators

Positive allosteric modulation of the metabotropic glutamate receptor subtype 5 was studied by conducting a comparative molecular field analysis on 118 benzoxazepine derivatives. The model with the best predictive ability retained significant cross-validated correlation coefficients of q² = 0.58 (r² = 0.81) yielding a standard error of 0.20 in pEC₅₀ for this class of compounds. The subsequent contour maps highlight the structural features pertinent to the bioactivity values of benzoxazepines.     

In silico study of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanones derivatives as CCR1 antagonist: Homology modeling,docking and 3D-QSAR approach

C–C chemokine receptor type 1 (CCR1) is a chemokine receptor with seven transmembrane helices and it belongs to the G-Protein Coupled receptor (GPCR) family. It plays an important role in rheumatoid arthritis, organ transplant rejection, Alzheimer’s disease and also causes inflammation. Because of its role in disease processes, CCR1 is considered to be an important drug target. In the present study, we have performed three dimensional Quantitative Structure activity relationship (3D-QSAR) studies on a series of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanone derivatives targeting CCR1. Homology modeling of CCR1 was performed based on a template structure (4EA3) which has a high sequence identity and resolution. The highest active molecule was docked into this model. Ligand-based and Receptor-based quantitative structure–activity relationship (QSAR) study was performed and CoMFA models with reasonable statistics was developed for both ligand-based (q² = 0.606; r² = 0.968) and receptor-guided (q² = 0.640; r² = 0.932) alignment methods. Contour map analyses identified favorable regions for high affinity binding. The docking results highlighted the important active site residues. Tyr113 was found to interact with the ligand through hydrogen bonding. This residue has been considered responsible for anchoring ligands inside the active site. Our results could also be helpful to understand the inhibitory mechanism of 1-(4-Phenylpiperazin-1-yl)-2-(1H-pyrazol-1-yl) ethanone derivatives thereby to design more effective ligands in the future.     

Electromyographic and mechanomyographic responses across repeated maximal isometric and concentric muscle actions of the leg extensors

The purpose of the present study was to examine the patterns of responses for torque, electromyographic (EMG) amplitude, EMG mean power frequency (MPF), mechanomyographic (MMG) amplitude, and MMG MPF across 30 repeated maximal isometric (ISO) and concentric (CON) muscle actions of the leg extensors. Twelve female subjects (21.1 ± 1.4 yrs; 63.3 ± 7.4 kg) performed ISO and CON fatigue protocols with EMG and MMG signals recorded from the vastus lateralis. The relationships for torque, EMG amplitude, EMG MPF, MMG amplitude, and MMG MPF versus repetition number were examined using polynomial regression. The results indicated there were decreases (p < 0.05) across the ISO muscle actions for torque (r² = 0.95), EMG amplitude (R² = 0.44), EMG MPF (r² = 0.62), and MMG MPF (r² = 0.48), but no change in MMG amplitude (r² = 0.07). In addition, there were decreases across the CON muscle actions for torque (R² = 0.97), EMG amplitude (R² = 0.46), EMG MPF (R² = 0.86), MMG amplitude (R² = 0.44), and MMG MPF (R² = 0.80). Thus, the current findings suggested that the mechanisms of fatigue and motor control strategies used to modulate torque production were similar between maximal ISO and CON muscle actions.     

3D-QSAR studies of 1,2-diaryl-1H-benzimidazole derivatives as JNK3 inhibitors with protective effects in neuronal cells

JNKs (c-Jun N-terminal kinases) have the potential to serve as a therapeutic target for various inflammatory, vascular, neurodegenerative, metabolic and oncological diseases. In particular, ATP-competitive JNK3 inhibitors act as neuroprotective agents. Here we introduce 1,2-diaryl-1H-benzimidazole derivatives as selective JNK3 inhibitors from among our in-house compounds and describe our elucidation of their SAR using 3D-QSAR models. A predictive CoMFA model (q² = 0.795, r² = 0.931) and a CoMSIA model (q² = 0.700, r² = 0.937) were used to describe the non-linearly combined affinity of each functional group in the inhibitors.     

Effect of essential oils,such as raspberry ketone and its derivatives,on antiandrogenic activity based on in vitro reporter gene assay

The effect of essential oils, such as raspberry ketone, on androgen (AR) receptor was investigated using a MDA-kb2 human breast cancer cell line for predicting potential AR activity. Among them, eugenol had the highest AR antagonistic activity with its IC₅₀ value of 19 μM. Raspberry ketone, which has threefold higher anti-obese activity than that of capsaicin, also had AR antagonist activity with its IC₅₀ value of 252 μM. Based on these findings, a more precise CoMFA model was proposed as follows: pIC₅₀ [log (1/IC₅₀)] = 3.77 + [CoMFA field terms] (n = 39, s = 0.249, r² = 0.834, s_cv = 0.507, q² = 0.311 (three components).     

Forest biomass and volume estimation using airborne LiDAR in a cool-temperate forest of northern Hokkaido,Japan

Trees are recognized as a carbon reservoir, and precise and convenient methods for forest biomass estimation are required for adequate carbon management. Airborne light detection and ranging (LiDAR) is considered to be one of the solutions for large-scale forest biomass evaluation. To clarify the relationship between mean canopy height determined by airborne LiDAR and forest timber volume and biomass of cool-temperate forests in northern Hokkaido, Japan, we conducted LiDAR observations covering the total area of the Teshio Experimental Forest (225 km²) of Hokkaido University and compared the results with ground surveys and previous studies. Timber volume and aboveground tree carbon content of the studied forest stands ranged from 101.43 to 480.40 m³ ha^–1 and from 30.78 to 180.54 MgC ha^–1, respectively. The LiDAR mean canopy height explained the variation among stands well (volume: r² = 0.80, RMSE = 55.04 m³ ha^–1; aboveground tree carbon content: r² = 0.78, RMSE = 19.10 MgC ha^–1) when one simple linear regression equation was used for all types (hardwood, coniferous, and mixed) of forest stands. The determination of a regression equation for each forest type did not improve the prediction power for hardwood (volume: r² = 0.84, RMSE = 62.66 m³ ha^–1; aboveground tree carbon content: r² = 0.76, RMSE = 27.05 MgC ha^–1) or coniferous forests (volume: r² = 0.75, RMSE = 51.07 m³ ha^–1; aboveground tree carbon content: r² = 0.58, RMSE = 19.00 MgC ha^–1). Thus, the combined regression equation that includes three forest types appears to be adequate for practical application to large-scale forest biomass estimation.     

Effect of ligand congeniality on energy transfer reaction between photo-excited tris(bipyridine)ruthenium(II) and chromate(III) complexes in aqueous solutions

Energy-transfer rate-constants from photo-excited [Ru(N–N)₃]²⁺ (N–N = 2,2′-bipyridine (bpy), 4,4′-dimethyl-2,2′-bipyridine (4dmb), 5,5′-dimethyl-2,2′-bipyridine (5dmb)) to [Cr(O–O)₃]³⁻ (O–O²⁻ = ox²⁻ ((COO⁻)₂), mal²⁻ (CH₂(COO⁻)₂)) and [Cr(CN)₆]³⁻ in encounter complexes were evaluated in aqueous solutions containing alkali metal ion. The rate constant depends on the molecular size of the ruthenium(II) complex: 1.8 × 10⁸ s⁻¹ for [Ru(bpy)₃]²⁺ (molecular radius, r = 5.8 Å), 1.4 × 10⁸ s⁻¹ for [Ru(5dmb)₃]²⁺ (r = 6.1 Å) and 0.96 × 10⁸ s⁻¹ for [Ru(4dmb)₃]²⁺ (r = 6.7 Å) in the system of [Ru(N–N)₃]²⁺–[Cr(ox)₃]³⁻ in aqueous solution. However, the rate constant is much more sensitive to the chromate(III) complex than to ruthenium(II) complex; 1.8 × 10⁸ s⁻¹ and 0.43 × 10⁸ s⁻¹ for [Cr(ox)₃]³⁻ (r = 4.0 Å) and [Cr(mal)₃]³⁻ (r = 4.2 Å) in the [Ru(bpy)₃]²⁺–[Cr(O–O)₃]³⁻ systems, respectively. We conclude that the congeniality between the donor’s and acceptor’s ligands in encounter complex plays an important role in energy transfer in aqueous solution.     

The Quételet index revisited in children and adults

BackgroundThe body mass index (BMI) is based on the original concept that body weight increases as a function of height squared. As an indicator of obesity the modern BMI assumption postulates that adiposity also increases as a function of height in states of positive energy balance.ObjectiveTo evaluate the BMI concept across different adiposity magnitudes, in both children and adults.MethodsWe studied 975 individuals who underwent anthropometric evaluation: 474 children and 501 adults. Tetrapolar bioimpedance analysis was used to assess body fat and lean mass.ResultsBMI significantly correlated with percentage of body fat (%BF; children: r = 0.893; adults: r = 0.878) and with total fat mass (children: r = 0.967; adults: r = 0.953). In children, body weight, fat mass, %BF and waist circumference progressively increased as a function of height squared. In adults body weight increased as a function of height squared, but %BF actually decreased with increasing height both in men (r = −0.406; p < 0.001) and women (r = −0.413; p < 0.001). Most of the BMI variance in adults was explained by a positive correlation of total lean mass with height squared (r² = 0.709), and by a negative correlation of BMI with total fat mass (r = −0.193).ConclusionsBody weight increases as a function of height squared. However, adiposity progressively increases as a function of height only in children. BMI is not an ideal indicator of obesity in adults since it is significantly influenced by the lean mass, even in obese individuals.     

Oxadiazole-diarylpyrazole 4-carboxamides as cannabinoid CB1 receptor ligands

Cannabinoid CB-1 receptors have been the focus of extensive studies since the first clinical results of rimonabant (SR141716) for the treatment of obesity and obesity-related metabolic disorders were reported in 2001. To further evaluate the properties of CB receptors, we have designed and efficiently prepared a series of oxadiazole-diarylpyrazole 4-carboxamides. Six of the new compounds which displayed high in vitro CB1 binding affinities were assayed for binding to CB2 receptor. Noticeably, 5-(4-bromophenyl)-3-(5-tert-butyl-1,3,4-oxadiazol-2-yl)-1-(2,4-dichlorophenyl)-N-phenyl-1H-pyrazole-4-carboxamide (12q) and 5-(4-bromophenyl)-3-(5-tert-butyl-1,3,4-oxadiazol-2-yl)-1-(2,4-dichlorophenyl)-N-(pyridin-2-yl)-1H-pyrazole-4-carboxamide (12r) demonstrated good binding affinity and decent selectivity for CB1 receptor (IC₅₀ = 1.35 nM, CB2/CB1 = 286 for 12q; IC₅₀ = 1.46 nM, CB2/CB1 = 256 for 12r).     

Discovery of simplified N2-substituted pyrazolo[3,4-d]pyrimidine derivatives as novel adenosine receptor antagonists: Efficient synthetic approaches,biological evaluations and molecular docking studies

In the present study, a molecular simplification approach was employed to design novel bicyclic pyrazolo[3,4-d]pyrimidine (PP) derivatives from tricyclic pyrazolo[4,3-e]-1,2,4-triazolo-[1,5-c]pyrimidines (PTP) as promising human A₃ adenosine receptor (hA₃AR) antagonists. All the target compounds were synthesized using novel and efficient synthetic schemes and the structure–activity relationship studies of these PPs were explored through the synthesis of a series of PTP analogues with various substituents. Substituents with different lipophilicity and steric hindrance (e.g., alkyl and aryl–alkyl) functions were introduced at N² position of the pyrazole ring, while acyl groups with different electronic properties were introduced at C⁶ position of the bicyclic nucleus to probe both electronic and positional effects. Most of the synthesized derivatives of the PP series presented good affinity at the hA₃AR, as indicated by the low micromolar range of K_i values and among them, compound 63 with N² neopentyl substituents showed most potent hA₃AR affinity with K_i value of 0.9 μM and high selectivity (hA₁AR/hA₃AR = >111 & hA_2AAR/hA₃AR = >111) towards other adenosine receptor subtypes. Interestingly, small isopropyl groups at N² position displayed high affinity at another receptor subtype (hA_2AAR, e.g., compound 55, with K_i hA_2AAR = 0.8 μM), while they were less favorable at the hA₃AR. Molecular docking analysis was also performed to predict the possible binding mode of target compounds inside the hA₃AR and hA_2AAR. Overall, PP derivatives represent promising starting points for new AR antagonists.     

Circulating levels of irisin in patients with anorexia nervosa and different stages of obesity – Correlation with body mass index

Irisin was recently identified as cleavage product of fibronectin type III domain containing 5 (FNDC5) and shown to increase energy expenditure in mice and humans and therefore was discussed as potential treatment option in obesity. However, the regulation of irisin under conditions of severely altered body weight such as anorexia nervosa and obesity remains to be investigated. We analyzed circulating irisin levels over a broad spectrum of body weight in 40 patients with anorexia nervosa (mean body mass index, BMI 12.6 ± 0.7 kg/m²), normal weight controls (22.6 ± 0.9 kg/m²) and obese patients with BMI of 30–40 (36.9 ± 1.2 kg/m²), 40–50 (44.9 ± 1.1 kg/m²) and >50 (70.1 ± 2.7 kg/m², n = 8/group). Correlation analyses were performed between irisin and different body indices, parameters of body composition and hormones involved in various homeostatic processes. Obese patients showed higher circulating irisin levels compared to normal weight and anorexic patients (p < 0.05) resulting in a correlation of irisin with body weight (r = 0.47, p < 0.01) and BMI (r = 0.50, p < 0.001). Plasma irisin was also positively correlated with fat mass (r = 0.48, p < 0.01), body cell mass (r = 0.45, p < 0.01) and fat free mass (r = 0.40, p < 0.05). Insulin levels were positively correlated with irisin (r = 0.45, p < 0.01), whereas circulating ghrelin, cortisol, thyroid-stimulating hormone or C-reactive protein were not (p > 0.05). These data indicate that circulating irisin is affected under conditions of altered BMI with highest levels in severely obese patients. The increase of irisin under conditions of obesity may indicate a physiological function to improve glucose tolerance which is often impaired in obese subjects.     

Determination of prediction equations for estimating body weight of Zulu (Nguni) sheep

Data on linear body measurements (LBM) of 403 sheep collected in three areas of KwaZulu-Natal were utilized to develop a prediction equation for live body weight of Zulu sheep. Data were collected on live weight (LW), heart girth (HG), wither height (WH) and scrotum circumference (SC) on sheep of all ages. The age of sheep was estimated by dentition. The analysis of variance showed that age and sex were important factors contributing to variation in LW of Zulu sheep. Phenotypic correlation coefficients and regression equations of LW on HG, WH and SC were computed within different age groups (milk set of teeth, one pair, two pairs and the three and four pairs of incisors). Low correlation coefficients (r = 0.21–0.48) between LW, HG and WH were found among the pregnant ewes. The relationship between LBM and LW was stronger (r = 0.66–0.86) for males than among females (r = 0.42–0.75). The cubic polynomial of HG was the best fit (R² = 0.76) for the live weight prediction of young sheep with milk set of teeth. The combination of HG and WH produced the best fit for the two tooth and above males and non-pregnant females. The LW prediction equations for pregnant females were not reliable (R² = 0.05–0.26). The SC was more precise (R² = 0.61–0.80) when estimating the live weight of young males (<15–22-month-old) than of the older rams (R² = 0.23–0.56). It was concluded that LW of Zulu sheep can be reasonably estimated using the HG and WH. A table could be constructed for the farmers to estimate the LW of their animals.