Molecular docking studies of 1-(substituted phenyl)-3-(naphtha [1, 2-d] thiazol-2-yl) urea/thiourea derivatives with human adenosine A(2A) receptor

Computational assessment of the binding interactions of drugs is an important component of computer-aided drug design paradigms. In this perspective, a set of 30 1-(substituted phenyl)-3-(naphtha[1, 2-d] thiazol-2-yl) urea/thiourea derivatives showing antiparkinsonian activity were docked into inhibitor binding cavity of human adenosine A(2A) receptor (AA2AR) to understand their mode of binding interactions in silico. Lamarckian genetic algorithm methodology was employed for docking simulations using AutoDock 4.2 program. The results signify that the molecular docking approach is reliable and produces a good correlation coefficient (r(2) = 0.483) between docking score and antiparkinsonian activity (in terms of % reduction in catalepsy score). Potent antiparkinsonian agents carried methoxy group in the phenyl ring, exhibited both hydrophilic and lipophilic interactions with lower energy of binding at the AA(2A)R. These molecular docking analyses should, in our view, contribute for further development of selective AA(2A)R antagonists for the treatment of Parkinson's disease.     

Social transmission of physiological and behavioural responses to castration in suckling Merino lambs

In social species like sheep, social context can modify both physiological and behavioural responses to stressors and normal behavioural patterns. Presence of conspecifics can ameliorate responses to noxious stimuli, an effect termed social buffering, whereas the presence of a distressed conspecific can invoke a distress response in an observer animal not receiving a noxious organic insult, an effect termed social contagion. Furthermore, synchrony of normal behaviours can occur within a group. Here a range of social contexts were created by grouping suckling lambs undergoing knife, ring or sham castration treatments either homogeneously or heterogeneously by castration treatment in pens within an animal house. The impact of social grouping on cortisol, rectal temperature, pain avoidance behaviours, postural behaviours and synchrony of behaviour in the first 12 h following castration treatment was examined. Irrespective of castration treatment, lambs grouped homogeneously by castration treatment had higher cortisol concentrations across the four time points measured than lambs grouped heterogeneously. They also spent 1.9% more of the time in restless behaviour in the first 1 h following castration, and in the 12 h following castration spent 6.7% more of their time lying ventrally, 4.9% less time standing normally, 1.6% more time walking normally, and 4.9% less time in total standing postures. Interactions between social grouping and castration treatment were not significant for physiological variables, pain related behaviours or postures with the exception of lateral lying which was decreased in knife castrated lambs grouped heterogeneously with other castration treatments from 1.9% (homogeneous grouping) to 0.4% (heterogeneous group). Synchronisation of behaviour was seen for walking in lambs grouped heterogeneously by castration treatment and for feeding at the trough in lambs grouped homogenously by ring and sham castration treatments. Lying and standing respectively, were negatively synchronised (occurred less frequently than predicted by chance alone) in ring and knife castrated lambs grouped homogeneously. The results indicate that mixing lambs that received the three castration treatments within a pen modified the activity profile of the lambs but did not substantially modify the behavioural or physiological changes that are stigmatic of responses to the specific castration treatments. The social contexts contrasted in the study did not result in marked contagion or social buffering between lambs of the measured responses and did not confound comparison of castration treatments. None-the-less, the comparability of responses observed in castration treatment groups penned homogenously or heterogeneously might not necessarily occur in other classes of sheep or in other social contexts. The absence of social transmission of behavioural and physiological responses indicates that grouping non-castrated lambs with castrated lambs did not compromise the welfare of the non-castrated lambs when their mothers were present.     

Stress-induced changes in plasma concentrations of immunoreactive beta-endorphin and cortisol in response to routine surgical procedures in lambs

Following four different surgical procedures in lambs 3-5 weeks old, plasma immunoreactive beta-endorphin (beta-EP) and cortisol were assayed at 15 min and 24 h as determinants of post-operative stress. A threefold increase in mean plasma beta-EP levels occurred 15 min after tail docking, and a maximal eight- to tenfold increase occurred in response to castration and/or mulesing with tail docking. Significant increments in mean plasma cortisol levels followed these surgical procedures with the maximal response 15 min after mulesing plus castration with tail docking. The physiologically active 'free' cortisol in plasma represents about 25% of the cortisol, as measured, and the two are highly correlated. At 24 h, beta-EP levels in all treated groups were similar to controls, although a small elevation in cortisol levels was still present in the lambs subjected to mulesing. Ultrafiltration of plasma extracts showed that peak beta-EP levels contained about 40% immunoreactivity from low molecular weight species (mol. wt less than 10,000). By specific radioimmunoassay and reverse-phase high-performance liquid chromatography this comprised about 75% beta-EP1-31, the most potent analgesic endorphin, 10% beta-EP1-27, and 15% alpha-N-acetyl-beta-EP. Increased beta-EP1-31 levels may modulate post-operative pain in lambs.     

Structure based prediction of functional sites with potential inhibitors to Nudix enzymes from disease causing microbes

The functional sites were predicted for Nudix enzymes from pathogenic microorganisms such as Streprococcus pneumonia (2B06) and Enterococcus faecalis (2AZW). Their structures are already determined, however, no data is reported about their functional sites, substrates and inhibitors. Therefore, we report prediction of functional sites in these Nudix enzymes via Geometric Invariant (GI) technique (Construct different geometries of peptides which remain unchanged). The GI method enumerated 2B06: RA57, EA58, EA61, EA62 and 2AZW: RA62, EA63, EA66, EA67 as putative functional sites in these Nudix enzymes. In addition, the substrate was predicted via Molecular docking (Docking of substrates against whole structure of Nudix enzymes). The substrate ADP-Ribose was docked with the Nudix enzymes, 2B06 (Docking energy -15.68 Kcal/mol) and 2AZW (Docking energy -10.86 Kcal/mol) with the higher affinity and the lower docking energy as compared to other substrates. The residues EA62 in 2B06 and RA62 in 2AZW make hydrogen bonds with the ADP-ribose. Furthermore, we screened 51 inhibitor compounds against structures of 2B06 and 2AZW. The inhibitor compounds AMPCPR and CID14258187 were docked well as compared to other compounds. The compound CID14258187 was also in agreement with Lipinski rule of 5 for drug likeness properties. Therefore, our findings of functional sites, substrates and inhibitors for these Nudix enzymes may help in structure based drug designing against Streprococcus pneumonia and Enterococcus faecalis.     

Extending the interval between second vaccination and slaughter: I. Effects on growth,scrotal size and stress responses of immunocastrated ram lambs

Immunocastration provides a less invasive means of castrating lambs. Considering increasing consumer awareness, the efficacy of this technique on commercial slaughter lambs needs to be further investigated and its effects on growth and stress responses need to be established. This study compared the growth rate, testes size and stress responses of immunocastrated lambs with that of lambs physically castrated with a Burdizzo clamp, as well as intact rams. A total of 40 Dohne Merino ram lambs (average live weight = 45.4±3.68 kg) were randomly allocated to the following four treatment groups: control (intact; R), Burdizzo-castrated (on day 2; B), immunocastrated with a 4-week (ICS4), or a 6-week (ICS6) interval between the second immunocastration vaccination and slaughter. Within the immunocastration treatments, the reaction to vaccination was assessed through injection site scoring, recording the local injection site surface temperature and assigning a walking score. The response to Burdizzo castration was assessed by scoring the reaction during the procedure, testes palpation reaction, walking gait and measuring testis temperature. Additional parameters recorded included BW, serum cortisol concentration, scrotal circumference and rectal temperature. Pain behaviours were described for the short-, medium- and long-term effects after the two methods of castration. Predominantly, tissue-hardening and bruising occurred at the injection sites of immunocastrates, but little effect was observed on walking comfort and no effect on injection site temperature or rectal temperatures. After Burdizzo castration, lambs spent more time in abnormal postures, and from day 3 (D3) to D8 of the trial, discomfort was observed during testes palpation and walking in B lambs. Serum cortisol concentrations were elevated in B lambs on D3 and D15, indicating physiological stress. Thus, immunocastration improved the welfare of castrated lambs as assessed by cortisol secretion, scrotal swelling and pain behaviours, without influencing growth rate.     

The effect of local or general anesthesia on the physiology and behavior of tail docked pigs

Tail docking of pigs is a routine procedure on farms to help control tail-biting behavior; however, docking can cause pain. The objective of this research was to evaluate the effect of local or general anesthesia on the physiology (experiment 1) and behavior (experiment 2) of tail docked pigs. Pigs were allocated to one of six treatment groups: (i) sham docking (CON); (ii) docking using conventional cutting (CUT) with side-cutting pliers; (iii) CUT docking plus local anesthesia injected immediately before docking (LA); (iv) CUT docking plus short-acting local anesthesia applied topically to the tail wound (SHORT); (v) CUT docking plus long-acting anesthesia applied topically to the tail wound (LONG) and (vi) CUT docking while the pig was anesthetized with carbon dioxide gas (CO(2)). In experiment 1, blood samples were collected from pigs (10 pigs per treatment) before and 30, 60 and 120 min after docking to measure leukocyte counts and percentages and cortisol concentrations. In experiment 2, the above treatments were repeated (10 pigs per treatment); the percentage of stress vocalizations were recorded during the administration of the treatments and behavior was recorded for up to 120 min after docking or handling. All pigs were weighed before and 24 h after docking and wound healing was recorded until weaning. The neutrophil/lymphocyte ratio was greater (P < 0.05) in CUT, LA, SHORT and LONG compared with CON pigs. At 30 min, cortisol concentrations were greater (P < 0.05) in CUT, LA, LONG and CO(2) compared with CON pigs. Cortisol concentrations did not differ (P > 0.05) between SHORT and CON pigs 30 min after docking. Cortisol concentrations did not differ (P > 0.05) among pigs given pain relief at the time of docking compared with pigs' docked without pain relief. Body weight change and wound scores did not differ (P > 0.05) among treatments. The percentage of stress vocalizations increased (P < 0.05) in CUT, SHORT and LONG, but not in CON, LA and CO(2) pigs in response to docking or handling. The percentage of time pigs spent lying without contact after docking tended to be greater (P = 0.06) in CUT pigs compared with all other docking treatments and CON pigs. In this study, none of the anesthesia treatments tested were effective at significantly changing the physiological or behavioral response to tail docking in pigs.     

Molecular docking studies on DMDP derivatives as human DHFR inhibitors

Molecular docking is routinely used for understanding drug‐receptor interaction in modern drug design. Here, we describe the docking of 2, 4-diamino-5-methyl-5-deazapteridine (DMDP) derivatives as inhibitors to human dihydrofolate reductase (DHFR). We docked 78 DMDP derivates collected from literature to DHFR and studied their specific interactions with DHFR. A new shape-based method, LigandFit, was used for docking DMDP derivatives into DHFR active sites. The result indicates that the molecular docking approach is reliable and produces a good correlation coefficient (r² = 0.499) for the 73 compounds between docking score and IC₅₀ values (Inhibitory Activity). The chloro substituted naphthyl ring of compound 63 makes significant hydrophobic contact with Leu 22, Phe 31 and Pro 61 of the DHFR active site leading to enhanced inhibition of the enzyme. The docked complexes provide better insights to design more potent DHFR inhibitors prior to their synthesis.     

GEMDOCK: a generic evolutionary method for molecular docking

We have developed an evolutionary approach for flexible ligand docking. This approval, GEMDOCK, uses a Generic Evolutionary Method for molecular DOCKing and an empirical scoring function. The former combines both discrete and continuous global search strategies with local search strategies to speed up convergence, whereas the latter results in rapid recognition of potential ligands. GEMDOCK was tested on a diverse data set of 100 protein-ligand complexes from the Protein Data Bank. In 79% of these complexes, the docked lowest energy ligand structures had root-mean-square derivations (RMSDs) below 2.0 A with respect to the corresponding crystal structures. The success rate increased to 85% if the structure water molecules were retained. We evaluated GEMDOCK on two cross-docking experiments in which each ligand of a protein ensemble was docked into each protein of the ensemble. Seventy-six percent of the docked structures had RMSDs below 2.0 A when the ligands were docked into foreign structures. We analyzed and validated GEMDOCK with respect to various search spaces and scoring functions, and found that if the scoring function was perfect, then the predicted accuracy was also essentially perfect. This study suggests that GEMDOCK is a useful tool for molecular recognition and may be used to systematically evaluate and thus improve scoring functions.     

Structure modeling of novel DNA glycosylase enzyme from oral pathogen Streptococcus sanguinis

The novel 3-methyladenine DNA glycosylase enzyme from oral pathogen Streptococcus sanguinisin involves in DNA repair mechanisms and participates in base excision repair. Its 3D structure is still unknown which may be a potential drug target, therefore here we proposed its putative 3D structure by homology modeling approach. EsyPred3d software produced more precise modeled structure as compare to Swiss model software. The modeled structure was further verified by PROCHECK analysis and subjected to functional site prediction servers for active site residues prediction. The functional site was further validated by molecular docking approach with ligand EDA (3- [2- Deoxyribofuranosyl] - 3H- 1, 3, 4, 5A, 8-Pentaaza- Asindacene-5- monophosphate) from 1F4R. The EDR docked at the cavity of modeled structure of 3-methyladenine DNA glycosylase enzyme with highest Patchdock score of 3966 and lowest Autodock 4 docking energy of -10.30 Kcal/mol. The YA51, LA105, RA107 residues are surrounding the EDA and matching with ligand binding residues predicted by PROFUNC server.     

Homology model of human retinoic acid metabolising enzyme cytochrome P450 26A1 (CYP26A1): active site architecture and ligand binding

Homology models of cytochrome P450 RA1 (CYP26A1) were constructed using three human P450 structures, CYP2C8, CYP2C9 and CYP3A4 as templates for the model building. Using MOE software the lowest energy CYP26A1 model was then assessed for stereochemical quality and side chain environment. Further active site optimisation of the CYP26A1 model built using the CYP3A4 template was performed by molecular dynamics to generate a final CYP26A1 model. The natural substrate, all-trans-retinoic acid (atRA), and inhibitor R 15866, were docked into the model allowing further validation of the active site architecture. Using the docking studies structurally and functionally important residues were identified with subsequent characterisation of secondary structure. Multiple hydrophobic interactions, including the side chains of TRP112, PHE299, PHE222, PHE84, PHE374 and PRO371, are important for binding of atRA and R115866. Additional hydrogen bonding interactions were noted as follows: atRA-- C==O of the atRA carboxylate group and ARG86; R115866--benzothiazole nitrogen and the backbone NH of SER115.     

Optimal design of protein docking potentials: efficiency and limitations

Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s) upon binding. The major challenge is to define scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations. Using a linear programming technique, we derived protein docking potentials (PDPs) that comply with this requirement. We considered a set of 63 nonredundant complexes to this aim, and generated 400,000 putative docked complexes (decoys) based on shape complementarity criterion for each complex. The PDPs were required to yield for the native (correctly docked) structure a potential energy lower than those of all the nonnative (misdocked) structures. The energy constraints applied to all complexes led to ca. 25 million inequalities, the simultaneous solution of which yielded an optimal set of PDPs that discriminated the correctly docked (up to 4.0 A root-mean-square deviation from known complex structure) structure among the 85 top-ranking (0.02%) decoys in 59/63 examined bound-bound cases. The high performance of the potentials was further verified in jackknife tests and by ranking putative docked conformation submitted to CAPRI. In addition to their utility in identifying correctly folded complexes, the PDPs reveal biologically meaningful features that distinguish docking potentials from folding potentials.     

An evaluation of automated in silico ligand docking of amino acid ligands to Family C G-protein coupled receptors

Family C G-protein coupled receptors (GPCRs) consist of the metabotropic glutamate receptors (mGluRs), the calcium-sensing receptor (CaSR), the T1R taste receptors, the GABA(B) receptor, the V2R pheromone receptors, and several chemosensory receptors. A common feature of Family C receptors is the presence of an amino acid binding pocket. The objective of this study was to evaluate the ability of the automatic docking program FlexX to predict the favored amino acid ligand at several Family C GPCRs. The docking process was optimized using the crystal structure of mGluR1 and the 20 amino acids were docked into homology models of the CaSR, the 5.24 chemosensory receptor, and the GPRC6A amino acid receptor. Under optimized docking conditions, glutamate was docked in the binding pocket of mGluR1 with a root mean square deviation of 1.56 angstroms from the co-crystallized glutamate structure and was ranked as the best ligand with a significantly better FlexX score compared to all other amino acids. Ligand docking to a homology model of the 5.24 receptor gave generally correct predictions of the favored amino acids, while the results obtained with models of GPRC6A and the CaSR showed that some of the favored amino acids at these receptors were correctly predicted, while a few other top scoring amino acids appeared to be false positives. We conclude that with certain caveats, FlexX can be successfully used to predict preferred ligands at Family C GPCRs.     

Regulation of synaptic vesicle docking by different classes of macromolecules in active zone material

The docking of synaptic vesicles at active zones on the presynaptic plasma membrane of axon terminals is essential for their fusion with the membrane and exocytosis of their neurotransmitter to mediate synaptic impulse transmission. Dense networks of macromolecules, called active zone material, (AZM) are attached to the presynaptic membrane next to docked vesicles. Electron tomography has shown that some AZM macromolecules are connected to docked vesicles, leading to the suggestion that AZM is somehow involved in the docking process. We used electron tomography on the simply arranged active zones at frog neuromuscular junctions to characterize the connections of AZM to docked synaptic vesicles and to search for the establishment of such connections during vesicle docking. We show that each docked vesicle is connected to 10-15 AZM macromolecules, which fall into four classes based on several criteria including their position relative to the presynaptic membrane. In activated axon terminals fixed during replacement of docked vesicles by previously undocked vesicles, undocked vesicles near vacated docking sites on the presynaptic membrane have connections to the same classes of AZM macromolecules that are connected to docked vesicles in resting terminals. The number of classes and the total number of macromolecules to which the undocked vesicles are connected are inversely proportional to the vesicles' distance from the presynaptic membrane. We conclude that vesicle movement toward and maintenance at docking sites on the presynaptic membrane are directed by an orderly succession of stable interactions between the vesicles and distinct classes of AZM macromolecules positioned at different distances from the membrane. Establishing the number, arrangement and sequence of association of AZM macromolecules involved in vesicle docking provides an anatomical basis for testing and extending concepts of docking mechanisms provided by biochemistry.     

Ability of ram introduction to induce LH secretion, estrus and ovulation in fall-born ewe lambs during anestrus.

The ability of ram introduction (RI) and progesterone pre-treatment to induce increases in LH secretion and ovulation, and the ability of progesterone pre-treatment with or without estrogen to induce estrus and ovulation in fall-born ewe lambs during seasonal anestrus was investigated. In early July, lambs of mixed breeds (41.8+/-0.6 kg and 250.7+/-1.3 days of age) were assigned to receive no treatment (C, n=7), to be introduced to rams (7:1 ewe:ram ratio; R, n=7), to be treated with progesterone (a used CIDR device) for 5 days (P, n=5), to be treated with progesterone and introduced to rams at CIDR removal (PR, n=11), or to receive the latter treatment plus an injection of estradiol benzoate (25 microg, E2beta i.m.) 24 h after CIDR withdrawal/RI (PER, n=11). Blood samples were collected from all lambs every 4h for 60 h beginning at RI/CIDR withdrawal (0 h), to characterize the LH surge profile and in groups R and C every 15 min for 8 h between 12 and 20 h for determination of LH pulse frequencies. Ultrasonographic examinations of the ovaries were conducted at 0, 36 and 60 h. In ram-exposed groups lambs were also observed for raddle marks every 4h from 0 to 60 h. The LH pulse frequency (pulses/8 h) was higher in group R (P<0.01; 7.7+/- 0.5) than group C lambs (2.7+/- 0.8). More lambs in groups exposed to rams than in the C or P groups showed an LH surge (P<0.05; 0, 100, 0, 72.7 and 100%, for C, R, P, PR and PER groups, respectively). Time from RI/CIDR removal to initiation of the LH surge was greater in lambs in the PR (43.5+/- 3.8h) than in the R (32.6+/- 4.6h; P=0.08) or PER (33+/- 1.2h; P<0.01). Diameter of the largest follicle at 0 h (3.2+/- 0.2mm) was not different among groups. Growth rate of the largest follicle between 0 and 36 h was greater (P<0.05) in RI than in C or P groups. Diameter of the largest follicle at 36 h was larger (P<0.05) in lambs in R (5.6+/- 0.2mm) and PR (5.1+/- 0.5mm) than C (4.0+/- 0.6mm) or P (3.8+/- 0.4mm) groups, and in R than PER (4.3+/- 0.4mm) treatment groups. Only lambs in the RI groups ovulated. Among RI groups the percentage of lambs ovulating was greater in the R (P<0.05; 85.7%) than PR (33.3%) groups with an intermediate response observed in lambs in treatment group PER (71.4%). The estrous response in progesterone pre-treated groups was greater (P<0.05) in lambs also treated with estrogen (PER; 81.8%), than in lambs introduced to rams alone (PR; 45.5%). In conclusion, ram introduction by itself, but not progesterone treatment alone, induces increases in LH pulse frequency, follicular development, and ovulation in fall-born ewe lambs during seasonal anestrus, further, P4 pre-treatment and RI when combined with E2 results in a high estrous response.     

Mating behavior, serum testosterone and semen characteristics in vasectomized and short scrotum rams

Ten similar rams were either vasectomized (VAS) or altered by securing the testes near the abdomen using elastrator bands (short scrotum, SS). Semen characteristics (electroejaculation) were similar (P>0.10) between groups before treatment and ejaculate volumes remained relatively constant (P>0.10) throughout the trial. Remaining sperm cells were nonmotile and 95% abnormal by 6 days after vasectomy. By 12 days after surgery, ejaculates contained no cells. Two SS rams had detectable sperm numbers at 12 days after treatment, but 95% were abnormal and all but 1% were nonmotile. Ejaculates collected 3 months after surgery were similar between treatments, in that all existing cells were nonmotile and abnormal. Partial spermatogenic function was regained in SS rams 15 months after treatment as indicated by the presence of low concentrations of motile sperm. Three and 15 months after treatment, sexual activity was estimated by exposing rams to a group of four estrous ewes. During the 15-minute exposure, VAS males exhibited more (P<0.10) nonmating sexual approaches than did SS animals during the first year. However, nonmating approaches and incomplete and completed matings were similar (P>0.10) between VAS and SS rams during the second year. No treatment differences in serum testosterone were observed before, during or after either libido trial. Shortening the scrotum of 6-month-old ram lambs has little effect on libido or testosterone when compared with VAS rams. However, the SS method of alteration does not result in complete sterility as indicated by the presence of motile spermatozoa in ejaculates 15 months after SS treatment.     

Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities

A computational docking strategy using multiple conformations of the target protein is discussed and evaluated. A series of low molecular weight, competitive, nonpeptide protein tyrosine phosphatase inhibitors are considered for which the x-ray crystallographic structures in complex with protein tyrosine phosphatase 1B (PTP1B) are known. To obtain a quantitative measure of the impact of conformational changes induced by the inhibitors, these were docked to the active site region of various structures of PTP1B using the docking program FlexX. Firstly, the inhibitors were docked to a PTP1B crystal structure cocrystallized with a hexapeptide. The estimated binding energies for various docking modes as well as the RMS differences between the docked compounds and the crystallographic structure were calculated. In this scenario the estimated binding energies were not predictive inasmuch as docking modes with low estimated binding energies corresponded to relatively large RMS differences when aligned with the corresponding crystal structure. Secondly, the inhibitors were docked to their parent protein structures in which they were cocrystallized. In this case, there was a good correlation between low predicted binding energy and a correct docking mode. Thirdly, to improve the predictability of the docking procedure in the general case, where only a single target protein structure is known, we evaluate an approach which takes possible protein side-chain conformational changes into account. Here, side chains exposed to the active site were considered in their allowed rotamer conformations and protein models containing all possible combinations of side-chain rotamers were generated. To evaluate which of these modeled active sites is the most likely binding site conformation for a certain inhibitor, the inhibitors were docked against all active site models. The receptor rotamer model corresponding to the lowest estimated binding energy is taken as the top candidate. Using this protocol, correct inhibitor binding modes could successfully be discriminated from proposed incorrect binding modes. Moreover, the ranking of the estimated ligand binding energies was in good agreement with experimentally observed binding affinities.     

Docking simulation with a purine nucleoside specific homology model of deoxycytidine kinase, a target enzyme for anticancer and antiviral therapy

5'-Phosphorylation, catalyzed by human deoxycytidine kinase (dCK), is a crucial step in the metabolic activation of anticancer and antiviral nucleoside antimetabolites, such as cytarabine (AraC), gemcitabine, cladribine (CdA), and lamivudine. Recently, crystal structures of dCK (dCKc) with various pyrimidine nucleosides as substrates have been reported. However, there is no crystal structure of dCK with a bound purine nucleoside, although purines are good substrates for dCK. We have developed a model of dCK (dCKm) specific for purine nucleosides based on the crystal structure of purine nucleoside bound deoxyguanosine kinase (dGKc) as the template. dCKm is essential for computer aided molecular design (CAMD) of novel anticancer and antiviral drugs that are based on purine nucleosides since these did not bind to dCKc in our docking experiments. The active site of dCKm was larger than that of dCKc and the amino acid (aa) residues of dCKm and dCKc, in particular Y86, Q97, D133, R104, R128, and E197, were not in identical positions. Comparative docking simulations of deoxycytidine (dC), cytidine (Cyd), AraC, CdA, deoxyadenosine (dA), and deoxyguanosine (dG) with dCKm and dCKc were carried out using the FlexX docking program. Only dC (pyrimidine nucleoside) docked into the active site of dCKc but not the purine nucleosides dG and dA. As expected, the active site of dCKm appeared to be more adapted to bind purine nucleosides than the pyrimidine nucleosides. While water molecules were essential for docking experiments using dCKc, the absence of water molecules in dCKm did not affect the ability to correctly dock various purine nucleosides.     

Structure-activity relationship study on the 6-membered heteroaromatic ring system of diphenylpyrazine-type prostacyclin receptor agonists

A series of prostacyclin receptor agonists was prepared by modifying the central heteroaromatic ring of lead compound 2, and a docking study was performed to investigate their structure-activity relationships by using a homology-modeled structure of the prostacyclin receptor. Compound 2 and its derivatives could be docked to the prostacyclin receptor in two ways depending on the position of the nitrogen atom within the heteroaromatic ring. Furthermore, hydrogen bonding between the nitrogen atom in the heteroaromatic ring and the hydroxyl group of Ser20 or Tyr75 of the receptor appears to be important for the potent expression of biological activity.     

Molecular docking of balanol to dynamics snapshots of protein kinase A

Even if the structure of a receptor has been determined experimentally, it may not be a conformation to which a ligand would bind when induced fit effects are significant. Molecular docking using such a receptor structure may thus fail to recognize a ligand to which the receptor can bind with reasonable affinity. Here, we examine one way to alleviate this problem by using an ensemble of receptor conformations generated from a molecular dynamics simulation for molecular docking. Two molecular dynamics simulations were conducted to generate snapshots for protein kinase A: one with the ligand bound, the other without. The ligand, balanol, was then docked to conformations of the receptors presented by these trajectories. The Lamarckian genetic algorithm in Autodock [Goodsell et al. J Mol Recognit 1996;9(1):1-5; Morris et al. J Comput Chem 1998;19(14):1639-1662] was used in the docking. Three ligand models were used: rigid, flexible, and flexible with torsional potentials. When the snapshots were taken from the molecular dynamics simulation of the protein-ligand complex, the correct docking structure could be recovered easily by the docking algorithm in all cases. This was an easier case for challenging the docking algorithm because, by using the structure of the protein in a protein-ligand complex, one essentially assumed that the protein already had a pocket to which the ligand can fit well. However, when the snapshots were taken from the ligand-free protein simulation, which is more useful for a practical application when the structure of the protein-ligand complex is not known, several clusters of structures were found. Of the 10 docking runs for each snapshot, at least one structure was close to the correctly docked structure when the flexible-ligand models were used. We found that a useful way to identify the correctly docked structure was to locate the structure that appeared most frequently as the lowest energy structure in the docking experiments to different snapshots.     

Comparison of neural histomorphology in tail tips from pigs docked using clippers or cautery iron

Tail docking of pigs is commonly performed to reduce the incidence of unwanted tail-biting behaviour. Two docking methods are commonly used: blunt trauma cutting (i.e. using side clippers), or cutting and concurrent cauterisation using a hot cautery iron. A potential consequence of tail amputation is the development of neuromas at the docking site. Neuromas have been linked to neuropathic pain, which can influence the longer-term welfare of affected individuals. To determine whether method of tail docking influences the extent of neuroma formation, 75 pigs were allocated to one of three treatments at birth: tail docked using clippers; tail docked using cautery iron; tail left intact. Tail docking was performed at 2 days of age and pigs were kept under conventional conditions until slaughter at 21 weeks of age. Tails were removed following slaughter and subjected to histological examination. Nerve histomorphology was scored according to the following scale: 1=discrete well-organised nerve bundles; 2=moderate neural proliferation and disorganisation affecting more than half of the circumference of the tail; 3=marked neural proliferation to form almost continuous disorganised bundles or non-continuous enlarged bundles compressing the surrounding connective tissue. Scores of 2 or 3 indicated neuroma formation. Scores were higher in docked pigs than undocked pigs (P<0.001), but did not differ between pigs docked using clippers and those docked using cautery (P=0.23). The results indicate that tail docking using either clippers or cautery results in neuroma formation, thus having the potential to affect long-term pig welfare.