Discovery of novel anti-leishmanial agents targeting LdLip3 lipase

Leishmaniasis is a neglected tropical disease, caused by several species of Leishmania. Being an opportunistic lipid-scavenging pathogen, Leishmania relies extensively on lipid metabolism especially for host–pathogen interaction, utilizing host lipids for energy and virulence. The rational approach is to target lipid metabolism of the pathogen focusing lipid-catabolizing lipases. The LdLip3 lipase is considered as drug target as it is constitutively expressed in both promastigote and amastigote forms. Since the LdLip3 structure is not known, we modeled its three-dimensional structure to implement structure-based drug discovery approach. Similarity-based virtual screening was carried out to identify potential inhibitors utilizing NCI diversity set on ZINC database including natural products. Implementing computational and experimental approaches, four anti-leishmanial agents were discovered. The screened molecules ZINC01821375, ZINC04008765, ZINC06117316 and ZINC12653571 had anti-leishmanial activity with IC₅₀ (% viable promastigotes vs. concentration) of 5.2 ± 1.8 μM, 13.1 ± 2.6 μM, 9.4 ± 2.6 μM and 17.3 ± 3.1 μM, respectively. The molecules showed negligible toxicity toward mouse macrophages. Based on the contact footprinting analysis, new molecules were designed with better predicted free energy of binding than discovered anti-leishmanial agents. Further validation for the therapeutic utility of discovered molecules can be carried out by the research community to combat leishmaniasis.     

A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis,molecular docking,density functional and molecular dynamics simulation study

Deregulated epigenetic activity of Histone deacetylase 1 (HDAC1) in tumor development and carcinogenesis pronounces it as promising therapeutic target for cancer treatment. HDAC1 has recently captured the attention of researchers owing to its decisive role in multiple types of cancer. In the present study a multistep framework combining ligand based 3D-QSAR, molecular docking and Molecular Dynamics (MD) simulation studies were performed to explore potential compound with good HDAC1 binding affinity. Four different pharmacophore hypotheses Hypo1 (AADR), Hypo2 (AAAH), Hypo3 (AAAR) and Hypo4 (ADDR) were obtained. The hypothesis Hypo1 (AADR) with two hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatics ring (R) was selected to build 3D-QSAR model on the basis of statistical parameter. The pharmacophore hypothesis produced a statistically significant QSAR model, with co-efficient of correlation r² = 0.82 and cross validation correlation co-efficient q² = 0.70. External validation result displays high predictive power with r² (o) value of 0.88 and r² (m) value of 0.58 to carry out further in silico studies. Virtual screening result shows ZINC70450932 as the most promising lead where HDAC1 interacts with residues Asp99, His178, Tyr204, Phe205 and Leu271 forming seven hydrogen bonds. A high docking score (−11.17 kcal/mol) and lower docking energy −37.84 kcal/mol) displays the binding efficiency of the ligand. Binding free energy calculation was done using MM/GBSA to access affinity of ligands towards protein. Density Functional Theory was employed to explore electronic features of the ligands describing intramolcular charge transfer reaction. Molecular dynamics simulation studies at 50 ns display metal ion (Zn)-ligand interaction which is vital to inhibit the enzymatic activity of the protein.     

Expansion of the active site of the azoreductase from Shewanella oneidensis MR-1

Azoreductase from Shewanella oneidensis MR-1 (soAzoR) possesses great potential in cleaving azo bond of azo dyes during degradation progress. However, detailed information on interaction of soAzoR with either prosthetic group or substrate remains unavailable, mainly due to the absence of crystallization of soAzoR. In order to unravel these mechanisms, we firstly built the tertiary structure of soAzoR and then computationally predicted the binding mode of FMN, NADH and a model dye, methyl red (MR). Ten residues of soAzoR, which are predicted to participate in ligands binding, were separately substituted for either alanine or phenylalanine to confirm their function. The homologous modeling result reveals soAzoR employs a typical Rossmann fold. In terms of ligand binding modes, the isoalloxazine ring of FMN is stabilized in planar conformation by amino acids in the loop L6 and L9 region. NADH and MR is superposed against the isoalloxazine ring with an angle and the distance from C4 atom of NADH and azo bond of MR to N5 atom of FMN is 4.3 Å and 4.6 Å, respectively. The result of predicted interaction and enzyme kinetic analysis suggests that Asn96, Gly140 and Gly141 are crucial for FMN and MR binding; Tyr119 and Phe161 are more meaningful for NADH binding; Ser16 plays an important role in appropriately binding of both FMN and NADH.     

External L5–S1 joint moments when lifting wire mesh screen used to prevent rock falls in underground mines

Bolting large sheets of wire mesh screen (WMS) to the roof of underground mines prevents injuries due to rock falls. However, WMS can be heavy and awkward to lift and transport, and may result in significant spinal loading. Accordingly, six male subjects (mean age = 45.8 years + 7.5 SD) were recruited to lift WMS in a laboratory investigation of the biomechanical demands. Biomechanical modeling was used to estimate external moments about L5–S1 for sixteen lifting tasks, using two sizes of WMS. Full-size WMS involved a two-person lift, while half-size WMS involved a one-person lift. Lifts were performed under 168 cm and 213 cm vertical space. Restriction in vertical space increased the maximum L5–S1 extensor moment from 254 to 274 Nm and right lateral bending moment from 195 to 251 Nm. Lifting full sheets of screen (as opposed to half sheets) resulted in an average 33 Nm increase in L5–S1 extensor moment. The L5–S1 extensor moment was increased by an average of 44 Nm (18%) when lifting screens positioned flat on the floor compared to an upright position.

Relevance to industry

Large flexible materials are commonly lifted in industrial work environments, and may involve the efforts of two or more workers. The current study examines the low back loading associated with lifting large flexible screens and presents recommendations to reduce spine loading.     

Potent inhibitors precise to S1′ loop of MMP-13, a crucial target for osteoarthritis

Matrix metalloproteinase-13 (MMP-13) is the primary MMP involved in cartilage degradation through its particular ability to cleave type-II collagen. This protein is expressed by chondrocytes and synovial cells in human osteoarthritis and rheumatoid arthritis; hence, it is an attractive target for the treatment of arthritic diseases. Currently available inhibitors lack specificity for metalloproteinase because of a common Zn binding site in MMPs; thus, there is a need to identify selective MMP-13 inhibitors for osteoarthritis therapy. Because selectivity is the major concern, both ligand-based and protein-based pharmacophore methodologies were used to identity potent and selective MMP-13 inhibitors. Different hypotheses were validated, and the best hypothesis was used to screen Zinc (natural and chemical) databases to seek novel scaffolds as MMP-13 inhibitors. The identified hits were validated using different strategies, such as Glide Standard precision, extra precision, E-model energies and receiver operating curve (ROC). In addition, potent inhibitors were selected based on two criteria: a similar binding mode as that of the active site PB3 crystal ligand and crucial amino acid interactions that are catalytically important for the function of MMP-13. The candidate potent inhibitors ZINC 02535232, ZINC 08399795, ZINC 12419118 and ZINC 00624580 nearly reproduced the H-bond interactions formed in the crystal structure of 1XUC with reasonable RMSD values exhibiting a novel interaction pattern that was not previously observed in MMP-13 inhibitors. The identified potent hits with diverse chemical scaffolds may be useful in designing new MMP-13 inhibitors.     

Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity

Podophyllotoxin and its analogues have important therapeutic value in the treatment of cancer, due to their ability to induce apoptosis in cancer cells in a proliferation-independent manner. These ligands bind to colchicine binding site of tubulin near the α- and β-tubulin interface and interfere with tubulin polymerization. The binding free energies of podophyllotoxin-based inhibitors of tubulin were computed using a linear interaction energy (LIE) method with a surface generalized Born (SGB) continuum solvation model. A training set of 76 podophyllotoxin analogues was used to build a binding affinity model for estimating the free energy of binding for 36 inhibitors (test set) with diverse structural modifications. The average root mean square error (RMSE) between the experimental and predicted binding free energy values was 0.56 kcal/mol which is comparable to the level of accuracy achieved by the most accurate methods, such as free energy perturbation (FEP) or thermodynamic integration (TI). The squared correlation coefficient between experimental and SGB–LIE estimates for the free energy for the test set compounds is also significant (R² = 0.733). On the basis of the analysis of the binding energy, we propose that the three-dimensional conformation of the A, B, C and D rings is important for interaction with tubulin. On the basis of this insight, 12 analogues of varying ring modification were taken, tested with LIE methodology and then validated with their experimental potencies of tubulin polymerization inhibition. Low levels of RMSE for the majority of inhibitors establish the structure-based LIE method as an efficient tool for generating more potent and specific inhibitors of tubulin by testing rationally designed lead compounds based on podophyllotoxin derivatization.     

Comparison of computational approaches for predicting the effects of missense mutations on p53 function

We applied our recently developed kinetic computational mutagenesis (KCM) approach [L.T. Chong, W.C. Swope, J.W. Pitera, V.S. Pande, Kinetic computational alanine scanning: application to p53 oligomerization, J. Mol. Biol. 357 (3) (2006) 1039–1049] along with the MM-GBSA approach [J. Srinivasan, T.E. Cheatham 3rd, P. Cieplak, P.A. Kollman, D.A. Case, Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices, J. Am. Chem. Soc. 120 (37) (1998) 9401–9409; P.A. Kollman, I. Massova, C.M. Reyes, B. Kuhn, S. Huo, L.T. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, T.E. Cheatham 3rd., Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models, Acc. Chem. Res. 33 (12) (2000) 889–897] to evaluate the effects of all possible missense mutations on dimerization of the oligomerization domain (residues 326–355) of tumor suppressor p53. The true positive and true negative rates for KCM are comparable (within 5%) to those of MM-GBSA, although MM-GBSA is much less computationally intensive when it is applied to a single energy-minimized configuration per mutant dimer. The potential advantage of KCM is that it can be used to directly examine the kinetic effects of mutations.     

Voltammetric sensor for amoxicillin determination in human urine using polyglutamic acid/glutaraldehyde film

A voltammetric sensor for determination of amoxicillin (AMX) was developed based on a glutaraldehyde cross-linked polyglutamic acid modified glassy carbon electrode. The proposed method is based on pre-concentration of AMX by cathodic accumulation as its oxidative product before being determined indirectly at potential as low as +0.23 V by square wave voltammetry. Linear response range, sensitivity and limit of detection were 2.0–25.0, 1.06 and 0.9.2 μmol L⁻¹, respectively, for AMX in 0.1 mol L⁻¹ acetate buffer pH 5.2, pre-accumulation time of 60 s and accumulation potential of +1.0 V. It was demonstrated that the glassy carbon electrode modified with PGA/GLU could be used for AMX determination in human urine without any separation step.     

Structural and electrical properties of mixed oxides of manganese and vanadium: A new semiconductor oxide thermistor material

Binary oxides of manganese and vanadium have been synthesized by solid state sintering, in which the mass ratio of the individual components Mn₂O₃ and VO₂ have been varied from 90:10 to 5:95. The bulk ceramic samples were characterized by X-ray diffraction and scanning electron microscopy with energy dispersive X-ray analysis. The initial compositions either rich in Mn₂O₃ or in equi-proportion by mass with VO₂ yield β-Mn₂V₂O₇ or a new crystalline form of Mn₂V₂O₇, with unit cell parameters: a = 7.73091 Å, b = 6.640788 Å, c = 6.70779 Å α = γ = 90° and β = 98.7086° which is designated as γ-Mn₂V₂O₇. The compositions, richer in VO₂ produce MnV₂O₆ co-existing with V₂O₅ the proportion of which increases with increase in VO₂. The surface microanalysis shows a spherical-granular morphology in Mn₂V₂O₇ structure and plate/rod-like structures co-existing with granular morphology in case of MnV₂O₆ together with V₂O₅. The electrical parameters of the negative temperature coefficient thermistors were determined. Depending on the constituent oxide composition, the NTC thermistors showed room temperature resistivity in the range of 6.52 × 10² to 6.1 × 10⁶ Ω-cm. The thermistor constant and activation energy are in the range of 0.12–0.458 eV and 1393–4801 K, respectively.     

Modeling of high-affinity binding of the novel atrial anti-arrhythmic agent, vernakalant, to Kv1.5 channels

Vernakalant (RSD1235) is an investigational drug that converts atrial fibrillation rapidly and safely in patients intravenously [Roy et al., J. Am. Coll. Cardiol. 44 (2004) 2355–2361; Roy et al., Circulation 117 (2008) 1518–1525] and maintains sinus rhythm when given orally [Savelieva et al., Europace 10 (2008) 647–665]. Here, modeling using AutoDock4 allowed exploration of potential binding modes of vernakalant to the open-state of the Kv1.5 channel structure. Point mutations were made in the channel model based on earlier patch-clamp studies [Eldstrom et al., Mol. Pharmacol. 72 (2007) 1522–1534] and the docking simulations re-run to evaluate the ability of the docking software to predict changes in drug–channel interactions. Each AutoDock run predicted a binding conformation with an associated value for free energy of binding (FEB) in kcal/mol and an estimated inhibitory concentration (K_i). The most favored conformation had a FEB of −7.12 kcal/mol and a predicted K_i of 6.08 μM (the IC50 for vernakalant is 13.8 μM; [Eldstrom et al., Mol. Pharmacol. 72 (2007) 1522–1534]). This conformation makes contact with all four T480 residues and appears to be clearly positioned to block the channel pore.     

Enhanced H2S sensing characteristics of SnO2 nanowires functionalized with CuO

The CuO-functionalized SnO₂ nanowire (NW) sensors were fabricated by depositing a slurry containing SnO₂ NWs on a polydimethylsiloxane (PDMS)-guided substrate and subsequently dropping Cu nitrate aqueous solution. The CuO coating increased the gas responses to 20 ppm H₂S up to 74-fold. The R_a/R_g value of the CuO-doped SnO₂ NWs to 20 ppm H₂S was as high as 809 at 300 °C, while the cross-gas responses to 5 ppm NO₂, 100 ppm CO, 200 ppm C₂H₅OH, and 100 ppm C₃H₈ were negligibly low (1.5–4.0). Moreover, the 90% response times to H₂S were as short as 1–2 s at 300–400 °C. The selective detection of H₂S and enhancement of the gas response were attributed to the uniform distribution of the sensitizer (CuO) on the surface of the less agglomerated network of the SnO₂ NWs.     

Thermodynamic analysis of the interaction between 3-aminophenylboronic acid and monosaccharides for development of biosensor

The special interaction between 3-aminophenylboronic acid and monosaccharides, particularly glucose, fructose and galactose, has been investigated and used for the development of electrochemical and surface plasmon resonance (SPR) based saccharide sensors. The binding constants and thermodynamic parameters of interaction such as free energy of binding (ΔG), enthalpy (ΔH) and entropy (ΔS) were determined for the first time using isothermal titration calorimetry revealed the enthalpic and entropic contributions to the free energies of binding. Effects of pH and buffer on the binding constants (k) between 3-aminophenylboronic acid and monosaccharides were also examined. The binding constant of fructose was found to be six times higher than glucose and four times higher than galactose at pH 11, leading the specific detection of fructose. SPR and potentiometric calibration for fructose were linear in the concentration range of 10–120 mM and 8–84 mM, respectively. Limit of detection of the SPR and potentiometric method were found to be as 8.9 mM and 1.4 mM, respectively.     

Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study

Dengue virus is a major issue of tropical and sub-tropical regions. Dengue virus has been the cause behind the major alarming epidemics in the history with mass causalities from the decades. Unavailability of on-shelf drugs for the prevention of further proliferation of virus inside the human body results in immense number of deaths each year. This issue necessitates the design of novel anti-dengue drug. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of dengue virus. Therefore, approximately eighteen million compounds from the ZINC database have been virtually screened against nonstructural protein 3 (NS3). The incremental construction algorithm of Glide docking program has been used with its features high throughput virtual screening (HTVS), standard precision (SP), extra precision (XP) and in combination of Prime module, induced fit docking (IFD) approach has also been applied. Five top-ranked compounds were then selected from the IFD results with better predicted binding energies with the catalytic triad residues (His51, Asp75, and Ser135) that may act as potential inhibitors for the underlying target protease enzyme. The top-ranked compounds ZINC95518765, ZINC44921800, ZINC71917414, ZINC39500661, ZINC36681949 have shown the predicted binding energies of −7.55, −7.36, −8.04, −8.41, −9.18 kcal/mol, respectively, forming binding interactions with three catalytically important amino acids. Top-docking poses of compounds are then used in molecular dynamics (MD) simulations. In computational studies, our proposed compounds confirm promising results against all the four serotypes of dengue virus, strengthening the opportunity of these compounds to work as potential on-shelf drugs against dengue virus. Further experimentation on the proposed compounds can result in development of strong inhibitors.     

A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors

Decrease in sphingosine 1-phosphate (S1P) concentration induces migration of pathogenic T cells to the blood stream, disrupts the CNS and it is implicated in multiple sclerosis (MS), a progressive inflammatory disorder of the central nervous system (CNS), and Alzheimer’s disease (AD). A promising treatment alternative for MS and AD is inhibition of the activity of the microsomal enzyme sphingosine 1-phosphate lyase (S1PL), which degrades intracellular S1P. This report describes an integrated systematic approach comprising virtual screening, molecular docking, substructure search and molecular dynamics simulation to discover novel S1PL inhibitors. Virtual screening of the ZINC database via ligand-based and structure-based pharmacophore models yielded 10000 hits. After molecular docking, common substructures of the top ranking hits were identified. The ligand binding poses were optimized by induced fit docking. MD simulations were performed on the complex structures to determine the stability of the S1PL-ligand complex and to calculate the binding free energy. Selectivity of the selected molecules was examined by docking them to hERG and cytochrome P450 receptors. As a final outcome, 15 compounds from different chemotypes were proposed as potential S1PL inhibitors. These molecules may guide future medicinal chemistry efforts in the discovery of new compounds against the destructive action of pathogenic T cells.     

Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity

Podophyllotoxin and its analogues have important therapeutic value in the treatment of cancer, due to their ability to induce apoptosis in cancer cells in a proliferation-independent manner. These ligands bind to colchicine binding site of tubulin near the α- and β-tubulin interface and interfere with tubulin polymerization. The binding free energies of podophyllotoxin-based inhibitors of tubulin were computed using a linear interaction energy (LIE) method with a surface generalized Born (SGB) continuum solvation model. A training set of 76 podophyllotoxin analogues was used to build a binding affinity model for estimating the free energy of binding for 36 inhibitors (test set) with diverse structural modifications. The average root mean square error (RMSE) between the experimental and predicted binding free energy values was 0.56 kcal/mol which is comparable to the level of accuracy achieved by the most accurate methods, such as free energy perturbation (FEP) or thermodynamic integration (TI). The squared correlation coefficient between experimental and SGB–LIE estimates for the free energy for the test set compounds is also significant (R² = 0.733). On the basis of the analysis of the binding energy, we propose that the three-dimensional conformation of the A, B, C and D rings is important for interaction with tubulin. On the basis of this insight, 12 analogues of varying ring modification were taken, tested with LIE methodology and then validated with their experimental potencies of tubulin polymerization inhibition. Low levels of RMSE for the majority of inhibitors establish the structure-based LIE method as an efficient tool for generating more potent and specific inhibitors of tubulin by testing rationally designed lead compounds based on podophyllotoxin derivatization.     

Amperometric phenol biosensor based on polyaniline

The catechol biosensor is constructed by cross-linking between polyphenol oxidase (PPO) and polyaniline (PANI) using glutaraldehyde as a cross-linking agent. The PANI, which is electrochemically synthesized in a solution containing ionic liquid, 1-ethyl-3-methylimidazolium ethyl sulfate, possesses good electroactivity and high conductivity above pH 6. In the presence of catechol as a substrate, the biosensor exhibits a linear range from 0.2 to 80 μmol dm⁻³. The maximum response current (I_max) and the Michaelis–Menten constant (k^′_m) are 9.44 μA and 117 μmol dm⁻³, respectively. The effects of pH and operating potential are also explored to optimize measurement conditions. The activation energy (E_a) of the PPO catalytic reaction is 30.23 kJ mol⁻¹ in the B–R buffer. Electrochemical impedance spectroscopy (EIS), UV–vis and SEM are used to characterize the PANI–PPO biosensor. The biosensor exhibits good long-term stability.     

Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking,molecular dynamics and MM/PBSA studies

Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔG_bind, −16.83 and −10.99 kcal mol⁻¹) are comparable to that of current commercial drug oseltamivir (−23.62 kcal mol⁻¹). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs.     

Graphics processing unit‐accelerated bounding for branch‐and‐bound applied to a permutation problem using data access optimization

Branch‐and‐bound (B&B) algorithms are attractive methods for solving to optimality combinatorial optimization problems using an implicit enumeration of a dynamically built tree‐based search space. Nevertheless, they are time‐consuming when dealing with large problem instances. Therefore, pruning tree nodes (subproblems) is traditionally used as a powerful mechanism to reduce the size of the explored search space. Pruning requires to perform the bounding operation, which consists of applying a lower bound function to the subproblems generated during the exploration process. Preliminary experiments performed on the Flow‐Shop scheduling problem (FSP) have shown that the bounding operation consumes over 98% of the execution time of the B&B algorithm. In this paper, we investigate the use of graphics processing unit (GPU) computing as a major complementary way to speed up the search. We revisit the design and implementation of the parallel bounding model on GPU accelerators. The proposed approach enables data access optimization. Extensive experiments have been carried out on well‐known FSP benchmarks using an Nvidia Tesla C2050 GPU card. Compared to a CPU‐based single core execution using an Intel Core i7‐970 processor without GPU, speedups higher than 100 times faster are achieved for large problem instances. At an equivalent peak performance, GPU‐accelerated B&B is twice faster than its multi‐core counterpart. Copyright © 2013 John Wiley & Sons, Ltd.