Structural and functional conservation profiles of novel cathepsin L-like proteins identified in the Drosophila melanogaster genome

Cathepsin L is a cysteine protease which degrades connective tissue proteins including collagen, elastin, and fibronectin. In this study, five well-characterized cathepsin L proteins from different arthropods were used as query sequences for the Drosophila genome database. The search yielded 10 cathepsin L-like sequences, of which eight putatively represent novel cathepsin L-like proteins. To understand the phylogenetic relationship among these cathepsin L-like proteins, a phylogenetic tree was constructed based on their sequences. In addition, models of the tertiary structures of cathepsin L were constructed using homology modeling methods and subjected to molecular dynamics simulations to obtain reasonable structure to understand its dynamical behavior. Our findings demonstrate that all of the potential Drosophila cathepsin L-like proteins contain at least one cathepsin propeptide inhibitor domain. Multiple sequence alignment and homology models clearly highlight the conservation of active site residues, disulfide bonds, and amino acid residues critical for inhibitor binding. Furthermore, comparative modeling indicates that the sequence/structure/function profiles and active site architectures are conserved.     

Laboratory culture and evaluation of the tubeworm Ficopomatus enigmaticus for biofouling studies

Ficopomatus enigmaticus, a euryhaline tube-building polychaete worm with a subtropical to temperate distribution, is an increasingly problematic fouling organism. In this study, laboratory protocols for maintaining adult broodstock, destructive spawning, larval culture and a settlement bioassay were developed. The method routinely yielded approximately 200 larvae per spawning adult. The mean number of eggs released by females was 1517 and the mean number of spermatozoids per male was 4.425?×?10⁶. Fertilisation success, using an initial concentration of 2.5?×?10⁶ spermatozoids and 45?eggs?ml^?1, was 76% after a contact time of 60?min. The first cleavage occurred after 20?min and the trocophore larval stage was attained by 18?h. Metatrochophores were observed 4?d post-fertilisation and were competent to settle 1?day later. The proportion of larvae that settled after 48?h was surface-dependent: 10.24% on glass, 1.39% on polystyrene and 11.07% on a poly(dimethylsiloxane) elastomer. The presence of a biofilm on glass increased the rate of settlement 7-fold compared to clean glass.     

Excluded volume of hard cylinders of variable aspect ratio

In this article, we report expressions for the excluded volume, v _ex and second virial coefficient, B ₂, of hard cylinders as a function of their aspect ratio (𝒜 = L/D), where L and D are the length and diameter of the cylinder, respectively. These expressions are valid for aspect ratio values within the interval 0.001 < 𝒜 < 100, that covers from thin plates to long rods and reproduce Monte Carlo (MC) simulation values. We compare these results with Onsager's predictions and with reported values of hard bodies of similar geometry, as cut spheres (CS), hard spherocylinders (HSC) and linear tangent hard sphere chains (LTHSC). Simulation values for v _ex were obtained with an overlap algorithm that is also presented in detail. The obtained results can be applied in theoretical and computer simulation studies of discotic liquid crystals.     

The role of particle softness in determining the value of Poisson's ratio for soft sphere solids

The influence of particle softness on the Poisson's ratio of model solids has been investigated. We have used the repulsive inverse power potential (～r ^? n for particle separations, r) between the particles, which is conveniently characterised by one adjustable parameter, ? = 1/n. For large ?, the interaction is soft whereas in the ? → 0 limit the particles approach hard spheres. The pressure and elastic constants of the solid phase have been calculated at various densities with constant temperature molecular dynamics (MD) simulation for a range of the softness parameter in the range, n>12. Density-softness surfaces of these quantities were determined which revealed hitherto unrecorded trends in the behaviour of the elastic moduli and Poisson's ratio. It was found that the pressure and some elastic properties, e.g. the C₁₂ elastic constant and the bulk modulus, manifest a maximum value or ‘ridge’ on this surface. The height of the maximum increases with density and interaction steepness (small ?). The Poisson's ratio varies essentially linearly with softness and is relatively insensitive to density. However, at higher densities and for larger steepness a considerable lowering of the Poisson's ratio is observed. In order to identify possible mechanisms for reducing the value of Poisson's ratio, ν, the fluctuation and Born-Green contributions were analysed. Changes in the Poisson's ratio are mainly determined by the fluctuation contribution which can cause a considerable decrease as well as increase of its value.     

Simulation Study of Sorption of CO2 and N2 with Application to the Characterization of Carbon Adsorbents

Abstract

The Monte Carlo method was used in its grand ensemble variant (GCMC) in combination with CO₂ and N₂ experimental isotherm data at low (77 and 195.5 K) and ambient temperatures (298 and 308 K), in order to characterize microporous carbons and obtain the corresponding pore size distribution (PSD). In particular, the CO₂ and N₂ densities and the isosteric heats of adsorption inside single, slit shaped, graphitic pores of given width were found on the basis of GCMC for pre-defined temperatures and different relative pressures. In a further step, we determined the optimal PSD for which the best match is obtained between computed and measured isotherms. Comparisons were made between the PSDs found for the same carbon sample at low and ambient temperatures for different gases, and conclusions concerning the applicability of the method and the reliability of the resulting micropore size distributions were drawn.     

Interpreting the structural mechanism of action for MT7 and human muscarinic acetylcholine receptor 1 complex by modeling protein–protein interaction

MT7 is a selective human muscarinic acetylcholine receptor 1 (hM1) allosteric binder with subnanomolar affinity. Understanding the binding mode of hM1–MT7 will give insights to discover small molecular ligand for hM1. MT7 is a peptide, and hM1 is a G-protein-coupled membrane receptor. Therefore, we have employed homology modeling, protein–protein docking, explicit membrane molecular dynamics (MD) simulations, and molecular mechanic/Poisson-Boltzmann surface area energy decomposition analysis approaches to reveal the hM1–MT7 binding mode. The binding mode is consistent with the experimental data. We have discovered that the binding mode consists of three interaction regions in five residue interaction clusters. By analyzing the cluster representative structures, the cluster residues form an interaction network, which shows a multiple-point-to-site binding mode. Hydrogen binding statistical analysis reveals that E170 (hM1) and R34 (MT7) are both locked in electrostatic cages with counter charges, respectively. This is confirmed by the dynamic distances calculation between these residues, and biological mutant experiments.     

Computational screening of fatty acid synthase inhibitors against thioesterase domain

Thioesterase (TE) domain of fatty acid synthase (FAS) is an attractive therapeutic target for design and development of anticancer drugs. In this present work, we search for the potential FAS inhibitors of TE domain from the ZINC database based on similarity search using three natural compounds as templates, including flavonoids, terpenoids, and phenylpropanoids. Molecular docking was used to predict the interaction energy of each screened ligand compared to the reference compound, which is methyl γ-linolenylfluorophosphonate (MGLFP). Based on this computational technique, rosmarinic acid and its eight analogs were observed as a new series of potential FAS inhibitors, which showed a stronger binding affinity than MGLFP. Afterward, nine docked complexes were studied by molecular dynamics simulations for investigating protein–ligand interactions and binding free energies using MM-PB(GB)SA, MM-3DRISM-KH, and QM/MM-GBSA methods. The binding free energy calculation indicated that the ZINC85948835 (R34) displayed the strongest binding efficiency against the TE domain of FAS. There are eight residues (S2308, I2250, E2251, Y2347, Y2351, F2370, L2427, and E2431) mainly contributed for the R34 binding. Moreover, R34 could directly form hydrogen bonds with S2308, which is one of the catalytic triad of TE domain. Therefore, our finding suggested that R34 could be a potential candidate as a novel FAS-TE inhibitor for further drug design.     

Theoretical Design,Chemical Synthesis and Footprinting Analysis of a Novel Peptide Derivative of the Intercalator 7-H Pyridocarbazole Targeted Towards the Major Groove of DNA

Abstract

In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen of the ring by a protonated β-alanyl-ethyl chain. We have investigated two alternative means of intercalation of the chromophore: first, into the (pur-pur) sequences, d(CpG)₂ and d(CpA)·d(TpG); second, into the (pur-pyr) sequences, d(GpC)₂and d(GpT)·d(ApC). For the first intercalative mode, the best bound triplet sequences are d(ACG)·d(CGT) and d(ACA) d(TGT), namely with an adenine immediately upstream from the intercalation site. In these complexes, the chromophore has its concave side in the major groove, its long axis nearly colinear with the mean long axis of the two base pairs of the intercalation site, and a bidentate H-bonded configuration occurs which involves the C=0 and NH groups of the D-Asn side chain and HN₆ and N₇ (resp.) of the adenine base upstream. One alkylammonium proton is H-bonded to N₇ of the guanine of the intercalation site, on the strand opposite to the one bearing the adenine. In the second intercalative mode, the chromophore's concave site now faces one DNA strand, and both alkylammonium protons are involved in H-bonds with N₇ and O₆ of the 3′ guanine on the same strand. The peptide's complexes with sequences having A, G, or C upstream of this guanine were computed to be energetically competitive with those with the best (pyr-pur) triplets. This provides a rare example of energetically favourable drug intercalation in-between (pur-pyr) sequences as compared to the standard (pyr-pur) ones. The synthesis of this compound was performed, and a series of footprinting experiments undertaken on a total of approximately 300 nucleotides. These experiments were consistent with the inferences from the theoretical computations.     

Multicomplex-based pharmacophore modeling in conjunction with multi-target docking and molecular dynamics simulations for the identification of PfDHFR inhibitors

Abstract

Plasmodium falciparum dihydrofolate reductase enzyme (PfDHFR) is counted as one of the attractive and validated antimalarial drug targets. However, the point mutations in the active site of wild-type PfDHFR have developed resistance against the well-known antifolates. Therefore, there is a dire need for the development of inhibitors that can inhibit both wild-type and mutant-type DHFR enzyme. In the present contribution, we have constructed the common feature pharmacophore models from the available PfDHFR. A representative hypothesis was prioritized and then employed for the screening of natural product library to search for the molecules with complementary features responsible for the inhibition. The screened candidates were processed via drug-likeness filters and molecular docking studies. The docking was carried out on the wild-type PfDHFR (3QGT); double-mutant PfDHFR (3UM5 and 1J3J) and quadruple-mutant PfDHFR (1J3K) enzymes. A total of eight common hits were obtained from the docking calculations that could be the potential inhibitors for both wild and mutant type DHFR enzymes. Eventually, the stability of these candidates with the selected proteins was evaluated via molecular dynamics simulations. Except for SPECS14, all the prioritized candidates were found to be stable throughout the simulation run. Overall, the strategy employed in the present work resulted in the retrieval of seven candidates that may show inhibitory activity against PfDHFR and could be further exploited as a scaffold to develop novel antimalarials.

Communicated by Ramaswamy H. Sarma