Pharmacophore modeling and virtual screening for designing potential 5-Lipoxygenase inhibitors

Inhibitors of the 5-Lipoxygenase (5-LOX) pathway have a therapeutic potential in a variety of inflammatory disorders such as asthma. In this study, chemical feature based pharmacophore models of inhibitors of 5-LOX have been developed with the aid of HipHop and HypoGen modules within Catalyst program package. The best quantitative pharmacophore model, Hypo1, which has the highest correlation coefficient (0.97), consists of two hydrogen-bond acceptors, one hydrophobic feature and one ring aromatic feature. Hypo1 was further validated by test set and cross validation method. The application of the model shows great success in predicting the activities of 65 known 5-LOX inhibitors in our test set with a correlation coefficient of 0.85 with a cross validation of 95% confidence level, proving that the model is reliable in identifying structurally diverse compounds for inhibitory activity against 5-LOX. Furthermore, Hypo1 was used as a 3D query for screening Maybridge and NCI databases within catalyst and also drug like compounds obtained from Enamine Ltd, which follow Lipinski’s rule of five. The hit compounds were subsequently subjected to filtering by docking and visualization, to identify the potential lead molecules. Finally 5 potential lead compounds, identified in the above process, were evaluated for their inhibitory activities. These studies resulted in the identification of two compounds with potent inhibition of 5-LOX activity with IC₅₀ of 14 μM and 35 μM, respectively. These studies thus validate the pharmacophore model generated and suggest the usefulness of the model in screening of various small molecule libraries and identification of potential lead compounds for 5-LOX inhibition.     

Optimization of Cd2+ removal by the cyanobacterium Synechocystis pevalekii using the response surface methodology

Response surface methodology (RSM) has been used to optimize the critical parameters responsible for higher Cd²⁺ removal by a unicellular cyanobacterium Synechocystis pevalekii. A three-level Box–Behnken factorial design was used to optimize pH, biomass and metal concentration for Cd²⁺ removal. A coefficient of determination (R²) value (0.99), model F-value (86.40) and its low p-value (F < 0.0001) along with lower value of coefficient of variation (5.61%) indicated the fitness of response surface quadratic model during the present study. At optimum pH (6.48), biomass concentration (0.25 mg protein ml^?1) and metal concentration (5 μg ml^?1) the model predicted 4.29 μg ml^?1 Cd²⁺ removal and experimentally, 4.27 μg ml^?1 Cd²⁺ removal was obtained.     

Pharmacophore-guided lead optimization: The rational design of a non-zinc coordinating,sub-micromolar inhibitor of the botulinum neurotoxin serotype a metalloprotease

Botulinum neurotoxins, responsible for the neuroparalytic syndrome botulism, are the deadliest of known biological toxins. The work described in this study was based on a three-zone pharmacophore model for botulinum neurotoxin serotype A light chain inhibition. Specifically, the pharmacophore defined a separation between the overlaps of several different, non-zinc(II)-coordinating small molecule chemotypes, enabling the design and synthesis of a new structural hybrid possessing a K_i = 600 nM (±100 nM).     

Design,synthesis and biological evaluation of new 2,3-diarylquinoline derivatives as selective cyclooxygenase-2 inhibitors

A new group of 2,3-diarylquinoline derivatives possessing a methylsulfonyl COX-2 pharmacophore at the para-position of the C-2 phenyl ring were synthesized and evaluated as selective COX-2 inhibitors. In vitro COX-1/COX-2 structure–activity relationships were determined by varying the substituents on the C-4 quinoline ring. Among the 2,3-diarylquinolines, 2-(4-(methylsulfonyl) phenyl)-3-phenylquinoline-4-carboxylic acid (8) exhibited the highest potency and selectivity for COX-2 inhibitory activity (COX-2 IC₅₀ = 0.07 μM; selectivity index = 687.1) that was more selective than the reference drug celecoxib (COX-2 IC₅₀ = 0.06 μM; selectivity index = 405). A molecular modeling study where 8 was docked in the binding site of COX-2 indicated that the p-MeSO₂ COX-2 pharmacophore group on the C-2 phenyl ring is oriented in the vicinity of the COX-2 secondary pocket (Arg⁵¹³, Phe⁵¹⁸ and Val⁵²³) and the carboxylic acid substituent can interact with Ser⁵³⁰. The structure activity data acquired indicate that the size and nature of the C-4 quinoline substituent are important for COX-2 inhibitory activity.     

Modelling and simulation of continuous L (+) lactic acid production from sugarcane juice in membrane integrated hybrid-reactor system

Modelling and simulation was done for a two-stage membrane-integrated hybrid reactor system for continuous production of L (+) lactic acid under non-neutralizing conditions. The model captures microbial conversion of sugar cane juice to lactic acid under substrate–product inhibitions with downstream purification by nanofiltration. All the major phenomena and the governing parameters like fluid flow, feed dilution, substrate–product inhibitions, Donnan and steric effects during micro and nanofiltration for cell recycle, product separation and purification have been reflected in the modelling. The model describes a green, integrated continuous process of direct lactic acid production starting with a cheap, renewable carbon source. The highest lactic acid concentration achieved after the final stage of nanofiltration was 66.97 g/L at 13 kg/cm² operating pressure when the overall productivity reached 12.40 g/(L h). The developed model could successfully predict production, purification and transport of lactic acid through two stage membrane modules. Performance of the model was very good as indicated in the high overall correlation coefficient (R² > 0.980) and the low relative error (RE < 0.1).     

Investigation on the formation and kinetics of glucose-fed aerobic granular sludge

Aerobic granular sludge was cultivated in a glass sequencing batch reactor (SBR) with glucose synthetic wastewater. The spherical shaped granules were observed on 4th day with the mean diameter of 0.1 mm. With the increase of chemical oxygen demand (COD) concentration of the influent, aerobic granules grew matured, the size of which ranged from 1.2 to 1.9 mm. The aerobic granular sludge could sustain high organic loading rate (about 4.0 g COD L⁻¹ d⁻¹), with good settling ability (settling velocity 36 m/h) and high biomass concentration (MLSS 6.7 ±0.2 g/L). Experimental data indicated that the substrate utilization and biomass growth kinetics followed Monod's kinetics model approximately. The corresponding kinetic coefficients of maximum specific substrate utilization rate (k), half velocity coefficient (K_s), growth yield coefficient (Y) and decay coefficient (K_d) were 13.2 d⁻¹, 275.8 mg/L, 0.183–0.250 mg MLSS/mg COD and 0.023–0.075 d⁻¹, respectively, which made aerobic granules have short setup period, high rate of substrate utilization and little surplus sludge.     

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.     

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.     

An effective technique for the processing of saliva for the analysis of leptin and adiponectin

The recovery of protein from saliva has been extensively investigated as a method to monitor health. The aim of this study was to compare filtration and centrifugation as two methods of saliva processing necessary for determining the levels of salivary leptin and adiponectin. Thirty-seven healthy patients (median age of 45 years; range 35–73) participated in the study. Unstimulated whole saliva was collected by a drooling technique. An aliquot was filtered using a Millex-Millipore^® (0.45 μm PVDF Dura Pore membrane) syringe and a second aliquot was centrifuged at 15 000 × g for 15 min at 4 °C. Leptin and adiponectin levels were analyzed using an ELISA kit for serum (RayBio^®, GA, USA) with minor modifications. Leptin and adiponectin levels following the filtration technique yielded comparable results with those after centrifugation. Correlation was observed between filtered and centrifuged salivary leptin levels ((r = 0.9155; 95% CI 0.8362–0.9573; p < 0.0001) with concordance correlation coefficient k 0.9114 (95% CI 0.8332–0.9539)). Less correlation was observed for adiponectin ((r = 0.5718; 95% CI 0.3041–0.7558; p = 0.0002) with concordance correlation coefficient k 0.5586 (95% CI 0.2977–0.7419)). Using a Bland–Altman plot, similar measurements for both adipocytokines were observed with mean difference within a 95% CI, and interpreted as no systematic differences between the two processing techniques. This study showed that filtration is an alternative saliva processing technique to retrieve supernatant for protein analysis. Filtered saliva yielded leptin and adiponectin concentrations comparable with those obtained from centrifuged saliva.     

Isolation,spectroscopic characterization,X-ray,theoretical studies as well as in vitro cytotoxicity of Samarcandin

Samarcandin 1, a natural sesquiterpene-coumarin, was isolated as well as elucidated from F. assa-foetida which has significant effect in Iranian traditional medicine because of its medicinal attitudes. The crystal structure of samarcandin was determined by single-crystal X-ray structure analysis. It is orthorhombic, with unit cell parameters a = 10.8204 (5) Å, b = 12.9894 (7) Å, c = 15.2467 (9) Å, V = 2142.9 (2) Å³, space group P2₁2₁2₁ and four symmetry equivalent molecules in the unit cell. Samarcandin was isolated in order to study for its theoretical studies as well as its cellular toxicity as anti-cancer drug against two cancerous cells. In comparison with controls, our microscopic and MTT assay data showed that samarcandin suppresses cancer cell proliferation in a dose-dependent manner with IC₅₀ = 11 μM and 13 for AGS and WEHI-164 cell lines, respectively. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) of the structure was computed by three functional methods and 6-311++G⁷ standard basis set. The optimized molecular geometry and theoretical analysis agree closely to that obtained from the single crystal X-ray crystallography. To sum up, the good correlations between experimental and theoretical studies by UV, NMR, and IR spectra were found.     

Climatic dependency of soil organic carbon isotopic composition along the S–N Transect from 34°N to 52°N in central-east Asia

We explored the relationships between surface-soil (1–20 cm) organic carbon isotopic signatures and associated climatic factors in central-east Asia in an attempt to develop transfer functions that can be used to retrieve the paleoclimatic information stored in the thick eolian–paleosol sequences within the area. Our analysis shows that the negative correlation between the surface-soil organic δ¹³C values and the mean annual precipitation is robust (R² = 0.453; n = 196; p < 0.05) and the negative correlation with the growing-season (April–September) precipitation is more significant (R² = 0.4966; n = 196; p < 0.05). Our study further shows that the positive correlation between the surface-soil organic δ¹³C values and mean growing-season aridity is most significant (R² = 0.5805; n = 196; p < 0.05). We have smoothed both the organic δ¹³C values and the mean growing-season aridity values using a 3-point moving-window average-filter method in an attempt to remove some of random errors and found that the positive correlation between the two is further increased (R² =  0.7784; n =  192; p < 0.05). These robust linear relationships demonstrate their value in reconstructing paleoclimate changes in the study area. The documented climatic dependency of the surface-soil carbon isotopic composition in the study area might have resulted both from the humidity-related isotopic enrichment processes of the dominant C₃ plants (stomatal conductance and photosynthetic discrimination) and from the aridity-related abundance of C₄ plants (mainly Chenopodiaceae species) along the S–N bioclimatic gradient.     

Highly potent tyrosinase inhibitor,neorauflavane from Campylotropis hirtella and inhibitory mechanism with molecular docking

Tyrosinase inhibition may be a means to alleviate not only skin hyperpigmentation but also neurodegeneration associated with Parkinson’s disease. In the course of metabolite analysis from tyrosinase inhibitory methanol extract (80% inhibition at 20 μg/ml) of Campylotropis hirtella, we isolated fourteen phenolic compounds, among which neorauflavane 3 emerged as a lead structure for tyrosinase inhibition. Neorauflavane 3 inhibited tyrosinase monophenolase activity with an IC₅₀ of 30 nM. Thus this compound is 400-fold more active than kojic acid. It also inhibited diphenolase (IC₅₀ = 500 nM), significantly. Another potent inhibitor 1 (IC₅₀ = 2.9 μM) was found to be the most abundant metabolite in C. hirtella. In kinetic studies, compounds 3 showed competitive inhibitory behavior against both monophenolase and diphenolase. It manifested simple reversible slow-binding inhibition against monophenolase with the following kinetic parameters: K_i^app = 1.48 nM, k₃ = 0.0033 nM⁻¹ min⁻¹ and k₄ = 0.0049 min⁻¹. Neorauflavane 3 efficiently reduced melanin content in B16 melanoma cells with 12.95 μM of IC₅₀. To develop a pharmacophore model, we explored the binding mode of neuroflavane 3 in the active site of tyrosinase. Docking results show that resorcinol motif of B-ring and methoxy group in A-ring play crucial roles in the binding the enzyme.     

Direct in vivo interaction of the antibiotic primycin with the plasma membrane of Candida albicans: An EPR study

The direct interaction of the antibiotic primycin with the plasma membrane was investigated by employing the well-characterized ergosterol-producing, amphotericin B-sensitive parental Candida albicans strain 33erg⁺ and its ergosterol-less amphotericin B-resistant plasma membrane mutant erg-2. The growth inhibition concentration in shaken liquid medium was 64 μg ml^?1 for 33erg⁺ and 128 μg ml^?1 for erg-2, suggesting that the plasma membrane composition influences the mode of action of primycin. To determine the primycin-induced changes in the plasma membrane dynamic, electron paramagnetic resonance (EPR) spectroscopy methods were used, the spin-labeled fatty acid 5-(4,4-dimethyloxazolidine-N-oxyl)stearic acid) being applied for the in vivo measurements. The phase transition temperatures of untreated strain 33erg⁺ and its mutant erg-2 were 12.5 °C and 11 °C, respectively. After 128 μg ml^?1 primycin treatment, these values increased to 17.5 °C and 16 °C, revealing a significant reduction in the phospholipid flexibility. Saturation transfer EPR measurements demonstrated that, the rotational correlation times of the spin label molecule for the control samples of 33erg⁺ and erg-2 were 60 ns and 100 ns. These correlation times gradually decreased on the addition of increasing primycin concentrations, reaching 8 μs and 1 μs. The results indicate the plasma membrane “rigidizing” effect of primycin, a feature that may stem from its ability to undergo complex formation with membrane constituent fatty acid molecules, causing alterations in the structures of phospholipids in the hydrophobic surface near the fatty acid chain region.     

Investigation on the properties and kinetics of glucose-fed aerobic granular sludge

Aerobic granulation is a process in which suspended biomass aggregate and form discrete well-defined granules in aerobic systems. To investigate the properties and kinetics of aerobic granular sludge, aerobic granules were cultivated with glucose synthetic wastewater in a series of sequencing batch reactors (SBR). The spherical shaped granules were observed on 8th day with the mean diameter of 0.1 mm. With the organic loading rate (OLR) being increased to 4.0 g COD L⁻¹ d⁻¹, aerobic granules grew matured with spherical shape. The size of granules ranged from 1.2 to 1.8 mm, and the corresponding settling velocity of individual granule was 24.2–36.4 m h⁻¹. The oxygen utilization rate (OUR) of mature granules was 41.90 g O₂ kg MLSS⁻¹ h⁻¹, which was two times higher than that of activated sludge (18.32 g O₂ kg MLSS⁻¹ h⁻¹). The experimental data indicated that the substrate utilization and biomass growth kinetics generally followed Monod's kinetics model. The corresponding kinetic coefficients of k (maximum specific substrate utilization rate), K_s (half velocity coefficient), Y (growth yield coefficient) and K_d (decay coefficient) were determined as follows, k_c = 23.65 d⁻¹, K_c = 3367.05 mg L⁻¹, K_N = 0.038 d⁻¹, K_N = 29.65 mg L⁻¹, Y = 0.1927–0.2022 mg MMLS (mg COD)⁻¹ and K_d = 0.00845–0.0135 d⁻¹, respectively. Those properties of aerobic granules made aerobic granules system had a short setup period, high substrate utilization rate and low sludge production.     

Synthesis and SAR of 99mTc/Re-labeled small molecule prostate specific membrane antigen inhibitors with novel polar chelates

Prostate specific membrane antigen (PSMA) is recognized as an attractive molecular target for the development of radiopharmaceuticals to image and potentially treat metastatic prostate cancer. A series of novel ^99mTc/Re-tricarbonyl radiolabeled PSMA inhibitors were therefore synthesized by the attachment of glutamate-urea-lysine (Glu-urea-Lys) and glutamate-urea-glutamate (Glu-urea-Glu) pharmacophore to single amino acid chelate (SAAC) where the SAAC ligand was either bis(pyridin-2-ylmethyl)amino (DPA), bis((1-methyl-1H-imidazol-2-yl)methyl)amino (NMI), bis((1-(carboxymethyl)-1H-imidazol-2-yl)methyl)amino (CIM) or bis((1-(2-(bis(carboxymethyl)amino)-2-oxoethyl)-1H-imidazol-2-yl)methyl)amino (TIM). The in vitro binding affinity of the rhenium complexes was evaluated using PSMA-expressing human prostate cancer LNCaP cells. IC₅₀ values ranged from 3.8 ± 2 to >2000 nM. A linker between the SAAC chelate and pharmacophore was required for high affinity binding. However, extending the length of the linker did not substantially improve binding. PSMA binding was also influenced by the nature of the SAAC chelate. One of the most potent compounds, 23b (IC₅₀ = 4.8 ± 2.7 nM), was radiolabeled with technetium tricarbonyl ({^99mTc(CO)₃}⁺) to afford the {^99mTc(CO)₃}⁺ complex in excellent yield and high purity. This effort has led to the identification of a diverse series of promising high affinity {^99mTc(CO)₃}⁺ radiolabeled PSMA inhibitors.     

Biosorption kinetics and isotherm studies of Acid Red 57 by dried Cephalosporium aphidicola cells from aqueous solutions

Equilibrium, kinetics and thermodynamic studies on the removal of Acid Red 57 (AR57) by biosorption onto dried Cephalosporium aphidicola (C. aphidicola) cells have been investigated in a batch system with respect to pH, contact time and temperature. The results showed that the equilibrium time was attained within 40 min and the maximum biosorption capacity of AR57 dye onto C. aphidicola cells was 2.08 × 10⁻⁴ mol g⁻¹ or 109.41 mg g⁻¹ obtained after contact with 0.4 g dm⁻³ biosorbent concentration, pH₀ of 1 and at a temperature of 20 °C. The pseudo-second-order kinetic model was observed to provide the best correlation of the experimental data among the kinetic models studied. Biosorption isotherm models were developed and the Langmuir, Freundlich and Dubinin–Radushkevich (D–R) isotherm models were conformed well to the experimental data. The changes of free energy, enthalpy and entropy of biosorption were also evaluated for the biosorption of AR57 dye onto C. aphidicola cells.     

Development of a microfluidic device for determination of cell osmotic behavior and membrane transport properties

An understanding of cell osmotic behavior and membrane transport properties is indispensable for cryobiology research and development of cell-type-specific, optimal cryopreservation conditions. A microfluidic perfusion system is developed here to measure the kinetic changes of cell volume under various extracellular conditions, in order to determine cell osmotic behavior and membrane transport properties. The system is fabricated using soft lithography and is comprised of microfluidic channels and a perfusion chamber for trapping cells. During experiments, rat basophilic leukemia (RBL-1 line) cells were injected into the inlet of the device, allowed to flow downstream, and were trapped within a perfusion chamber. The fluid continues to flow to the outlet due to suction produced by a Hamilton Syringe. Two sets of experiments have been performed: the cells were perfused by (1) hypertonic solutions with different concentrations of non-permeating solutes and (2) solutions containing a permeating cryoprotective agent (CPA), dimethylsulfoxide (Me₂SO), plus non-permeating solute (sodium chloride (NaCl)), respectively. From experiment (1), cell osmotically inactive volume (V_b) and the permeability coefficient of water (L_p) for RBL cells are determined to be 41% [n = 18, correlation coefficient (r²) of 0.903] of original/isotonic volume, and 0.32 ± 0.05 μm/min/atm (n = 8, r² > 0.963), respectively, for room temperature (22 °C). From experiment (2), the permeability coefficient of water (L_p) and of Me₂SO (P_s) for RBL cells are 0.38 ± 0.09 μm/min/atm and (0.49 ± 0.13) × 10⁻³ cm/min (n = 5, r² > 0.86), respectively. We conclude that this device enables us to: (1) readily monitor the changes of extracellular conditions by perfusing single or a group of cells with prepared media; (2) confine cells (or a cell) within a monolayer chamber, which prevents imaging ambiguity, such as cells overlapping or moving out of the focus plane; (3) study individual cell osmotic response and determine cell membrane transport properties; and (4) reduce labor requirements for its disposability and ensure low manufacturing costs.     

Application of seaweeds for the removal of lead from aqueous solution

Ten different seaweed species were compared on the basis of lead uptake at different pH conditions. The brown seaweed, Turbinaria conoides, exhibited maximum lead uptake (at pH 4.5) and hence was selected for further studies. Sorption isotherms, obtained at different pH (4–5) and temperature (25–35 °C) conditions were fitted using Langmuir and Sips models. According to the Langmuir model, the maximum lead uptake of 439.4 mg/g was obtained at optimum pH (4.5) and temperature (30 °C). The Sips model better described the sorption isotherms with high correlation coefficients at all conditions examined. Various thermodynamic parameters such as ΔG°, ΔH° and ΔS° were calculated indicating that the present system was a spontaneous and endothermic process. Through potentiometric titrations, number of binding sites (carboxyl groups) and pK₁ were determined as 4.1 mmol/g and 4.4, respectively. The influence of co-ions (Na⁺, K⁺, Mg²⁺ and Ca²⁺) on lead uptake was well pronounced in the case of divalent ions compared to monovalent ions. The solution of 0.1 M HCl successfully eluted all lead ions from lead-loaded T. conoides biomass. The regeneration experiments revealed that the alga could be successfully reused for five cycles without any loss in lead biosorption capacity. A glass column (2 cm i.d. and 35 cm height) was used to study the continuous lead biosorption performance of T. conoides. At 25 cm (bed height), 5 ml/min (flow rate) and 100 mg/l (initial lead concentration), T. conoides exhibited lead uptake of 220.1 mg/g. The column was successfully eluted using 0.1 M HCl, with elution efficiency of 99.7%.     

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.