A reactogenic "placebo" and the ethics of informed consent in Gardasil HPV vaccine clinical trials: A case study from Denmark.

BACKGROUND: Medical ethics guidelines require of clinical trial investigators and sponsors to inform prospective trial participants of all known and potential risks associated with investigational medical products, and to obtain their free informed consent. These guidelines also require that clinical research be so designed as to minimize harms and maximize benefits. OBJECTIVE: To examine Merck's scientific rationale for using a reactogenic aluminum-containing "placebo" in Gardasil HPV vaccine pre-licensure clinical trials. METHODS: We examined the informed consent form and the recruitment brochure for the FUTURE II Gardasil vaccine trial conducted in Denmark; and we interviewed several FUTURE II trial participants and their treating physicians. We also reviewed regulatory documentation related to Gardasil vaccine approval process and the guidelines on evaluation of adjuvants used in human vaccines. RESULTS: It was found that the vaccine manufacturer Merck made several inaccurate statements to trial participants that compromised their right to informed consent. First, even though the study protocol listed safety testing as one of the study's primary objectives, the recruitment brochure emphasized that FUTURE II was not a safety study, and that the vaccine had already been proven safe. Second, the advertising material for the trial and the informed consent forms stated that the placebo was saline or an inactive substance, when, in fact, it contained Merck's proprietary highly reactogenic aluminum adjuvant which does not appear to have been properly evaluated for safety. Several trial participants experienced chronic disabling symptoms, including some randomized to the adjuvant "placebo" group. CONCLUSION: In our view, the administration of a reactive placebo in Gardasil clinical trials was without any possible benefit, needlessly exposed study subjects to risks, and was therefore a violation of medical ethics. The routine use of aluminum adjuvants as "placebos" in vaccine clinical trials is inappropriate as it hinders the discovery of vaccine-related safety signals.

Screening of Big Pharma's Library against Various in-house Biological Targets.

Open innovation initiatives provide opportunities for collaboration and sharing of knowledge and experience between industry, academia, and government institutions. Through open innovation, Merck is offering a Mini Library of 80 carefully selected compounds from previous research and development projects to a broader scientific community for testing in academic drug discovery projects. These compounds are predominantly drug-like and cover a broad range of molecular targets. They could potentially interact with other enzymes, receptors, transporters, and ion channels of interest. The Mini Library was tested on seven in-house enzymes (bacterial MurA, MurC ligase, and DdlB enzyme, human MAO-A/B, human BChE, and murine AChE), and several hits were identified. A follow-up series of structural analogues provided by Merck gave a more detailed insight into the accessibility and the quality of the hit compounds. For example, sartan derivatives were moderate inhibitors of MurC, whereas bisarylureas were potent, selective, nanomolar inhibitors of hMAO-B. Importantly, 3-n-butyl-substituted indoles were identified as low nanomolar selective inhibitors of hBChE. All in all, the hit derivatives provide new starting points for the further exploration of the chemical space of high-quality enzyme inhibitors.

Variation in secondary metabolites in a unique set of tomato accessions collected in Turkey.

In this study, 50 tomato landraces grown in Turkey were investigated in terms of their secondary metabolite profiles. Each accession was planted in 2016 and 2017 in 3 replicates in an open field. In this study, color, pH and brix of the fruit samples were measured and an unbiased LCMS-based metabolomics approach was applied. Based on Principal Components Analysis (PCA) and Hierarchical Cluster Analysis (HCA) of the relative abundance levels of >250 metabolites, it could be concluded that fruit size was the most influential to the biochemical composition, rather than the geographical origin of accessions. Results indicated substantial biodiversity in various metabolites generally regarded as key to fruit quality aspects, including sugars; phenolic compounds like phenylpropanoids and flavonoids; alkaloids and glycosides of flavour-related volatile compounds. The phytochemical data provides insight into which Turkish accessions might be most promising as starting materials for the tomato processing and breeding industries.

Towards chemically accurate QM/MM simulations on GPUs.

Computational chemistry simulations are extensively used to model natural phenomena. To maintain performance similar to molecular mechanics, but achieve comparable accuracy to quantum mechanical calculations, many researchers are using hybrid QM/MM methods. In this article we evaluate our GPU-accelerated ONIOM implementation by measurements on the crambin and HIV integrase proteins with different size QM model systems. We demonstrate that by using a larger QM region, a better energy accuracy can be achieved at the expense of simulation time. This trade-off is important to consider for the researcher running QM/MM calculations. Furthermore, we show that the ONIOM energy monotonically approaches the pure quantum mechanical energy of the whole system. The experiments are made feasible by utilizing the cutting-edge BrianQC quantum chemistry module for Hartree-Fock level SCF and our GPU-accelerated MMFF94 force field implementation for molecular mechanics calculations.

Validation Study of QSAR/DNN Models Using the Competition Datasets.

Since the QSAR/DNN model showed predominant predictive performance over other conventional methods in the Kaggle QSAR competition, many artificial neural network (ANN) methods have been applied to drug and material discovery. Appearance of artificial intelligence (AI), which is combined various general purpose ANN platforms with large-scale open access chemical databases, has attracting great interest and expectation in a wide range of molecular sciences. In this study, we investigate various DNN settings in order to reach a high-level of predictive performance comparable to the champion team of the competition, even with a general purpose ANN platform, and introduce the Meister setting for constructing a good QSAR/DNNs model. Here, we have used the most commonly available DNN model and constructed many QSAR/DNN models trained with various DNN settings by using the 15 datasets employed in the competition. As a result, it was confirmed that we can constructed the QSAR/DNN model that shows the same level of R2 performance as the champion team. The difference from the DNN setting recommended by the champion team was to reduce the mini-batch size. We have also explained that the R2 performance of each target depends on the molecular activity type, which is related to the complexity of biological mechanisms and chemical processes observed in molecular activity measurements.

Freezing of Stallion Semen: In Vitro Evaluation of Motility and Acrosin Activity in Sperm Cells Cryopreserved Using Different Semen Extenders.

The work described here aimed to verify the efficiency of different extenders for cryopreservation of equine semen using sperm motility and acrosin activity as spermatic parameters. The semen was fractioned into two equal parts and resuspended in an 11% lactose solution in a 1:1 proportion, where it remained for 20 minutes at room temperature. The semen was centrifuged at 600 g for 10 minutes, and after the second centrifugation, each pellet received the freezing extender (Merck or Zorlesco) and was loaded into 4 mL straws. Each straw was placed in liquid nitrogen vapor steam for 15 minutes and further immersion in liquid nitrogen at -196°C for long-term storage. After thawing, semen samples were initially evaluated for sperm motility, both total and progressive, and acrosin activity. Moreover, semen was incubated at 37°C and further assessed at 60 and 120 minutes in a thermoresistance test (TRT) for sperm motility and acrosin activity. Immediately after thawing, both progressive and total motility, and acrosin activity were lower (p < 0.05) in thawed semen than in fresh semen. During the TRT, total sperm motility and acrosin activity after 60 minutes were lower (p < 0.05) than those obtained after thawing. Similarly, total sperm motility and acrosin activity were lower (p < 0.05) after 120 minutes than at 60 minutes of the TRT. The analysis of motility and acrosin activity allowed the conclusion that both extenders have a similar capacity to preserve the integrity of sperm cells subject to freezing and thawing.

The Recipe for Corporate Longevity: From the Perspective of "Managing Innovation".

The elephant is in the room-a metaphorical idiom for an obvious problem or risk that nobody wants to discuss. This abstract is not intended to be a summary, to reveal major findings, or unveil conclusions. On the contrary, it is aimed to provoke curiosity as to the question of corporate survival. Is there any recipe to be followed for companies to achieve this? The answer comes neither from the modest and traditional study rooms of philosophers nor the recent fact-based studies from the offices (and well-paid opinions) of business consultants. The Archimedean point from which we can objectively explore the subject of corporate survival does not exist. Instead we offer seven analogies (or metaphors) as intellectual platforms where new perspectives can be considered. Innovation obviously plays a major role in corporate survival-yet, by its nature all innovation is messy. In order to reduce entropy, this abstract reveals some keywords in alphabetical order starting from A, such as ambidexterity, architecture, and ant colonies, moving on to B, such as, (mental) boxes and biodiversity. For obvious reasons, C plays a major role-sufficiently that we have already revealed curiosity as one part of the answer-treading over to D (Darwin, DNA, and discontinuity), followed by E (earthquakes and evolution). As a final warning signal in order to manage the expectation: It is not the intention of this article to give a comprehensive overview about the rich and complex history of Merck KGaA, Darmstadt, Germany. Indeed, only the final chapter will provide reference to this company: Before the curtains will finally close, an epilogue will start in which one of the protagonists of the 350-year journey of the company-Emanuel Merck-will appear on the stage and "let history speak for itself". Still curious?

Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer's disease.

Alzheimer's disease (AD) is one of the most significant neurodegenerative disorders and its symptoms mostly appear in aged people. Catechol-o-methyltransferase (COMT) is one of the known target enzymes responsible for AD. With the use of 23 known inhibitors of COMT, a query has been generated and validated by screening against the database of 1500 decoys to obtain the GH score and enrichment value. The crucial features of the known inhibitors were evaluated by the online ZINC Pharmer to identify new leads from a ZINC database. Five hundred hits were retrieved from ZINC Pharmer and by ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering by using FAF-Drug-3 and 36 molecules were considered for molecular docking. From the COMT inhibitors, opicapone, fenoldopam, and quercetin were selected, while ZINC63625100_413 ZINC39411941_412, ZINC63234426_254, ZINC63637968_451, and ZINC64019452_303 were chosen for the molecular dynamics simulation analysis having high binding affinity and structural recognition. This study identified the potential COMT inhibitors through pharmacophore-based inhibitor screening leading to a more complete understanding of molecular-level interactions.

Odanacatib, a Cathepsin K Cysteine Protease Inhibitor, Kills Hookworm In Vivo.

Hookworm infection is chief among soil-transmitted helminthiases (STHs) for the chronic morbidly inflicted. Deworming via mass drug administration (MDA) programs most often employs single doses of benzimidazole drugs to which resistance is a constant threat. To discover new drugs, we employ a hamster model of hookworm infection with Ancylostoma ceylanicum and use albendazole (ABZ; 10 mg/kg orally) as the gold standard therapy. We previously showed that a single oral 100 mg/kg dose of the cathepsin cysteine protease (CP) inhibitor, K11777, offers near cure of infection that is associated with a 95% reduction in the parasite's resident CP activity. We confirm these findings here and demonstrate that odanacatib (ODN), Merck's cathepsin K inhibitor and post-clinical Phase III drug candidate for treatment of osteoporosis, decreases worm burden by 73% at the same dose with a 51% reduction in the parasite's CP activity. Unlike K11777, ODN is a modest inhibitor of both mammalian cathepsin B and the predominant cathepsin B-like activity measureable in hookworm extracts. ODN's somewhat unexpected efficacy, therefore, may be due to its excellent pharmacokinetic (PK) profile which allows for sustained plasma exposure and, possibly, sufficient perturbation of hookworm cathepsin B activity to be detrimental to survival. Accordingly, identifying a CP inhibitor(s) that combines the inhibition potency of K11777 and the PK attributes of ODN could lead to a drug that is effective at a lower dose. Achieving this would potentially provide an alternative or back-up to the current anti-hookworm drug, albendazole.

Medicine patent pool--pharma philanthropy or PR?

Merck recently signed an agreement with The Medicines Patent Pool (MPP) to license intellectual property relating to pediatric formulations of its integrase HIV drug, raltegravir (Ral) (the 'Agreement'). The Agreement is alleged to clear the way for cheaper formulations for use in developing and some middle income countries and allows for the development of novel pediatric formulations of Ral as well as novel combinations. Merck's license is royalty free and under the terms of the Agreement, manufacturers anywhere in the world who meet the quality assurance criteria, can manufacture and sell pediatric versions of the drug in the licensed countries under the agreed conditions without paying a royalty to Merck. The Agreement covers at least 92 countries and MPP reports that 98.1% of children with HIV in the developing world live in the included countries. The Agreement has been criticized as a public relations exercise. The article asks if the criticism is justified and explores several aspects of the Agreement in addressing the question.

Intussusception following rotavirus vaccination in the Valencia Region, Spain.

Studies have shown high intussusception rates in Spain. We performed a hospital-based retrospective observational study of the intussusception risk following rotavirus vaccinations among infants in Valencia, a region of Spain with an annual birth cohort of approximately 48,000 children, during 2007-2011, using a self-controlled case series design. We performed medical record review of all cases using Brighton Collaboration's case definition and assessed the positive predictive value (PPV) of the intussusception diagnosis code. Among 151 hospitalized cases discharged as intussusception, we confirmed 136 as Brighton Collaboration's Levels 1 or 2, resulting in a PPV of 93% (95% CI: 87%-96%). Three confirmed cases occurred within days 1-7 following the first rotavirus vaccination. The incidence rate ratio was 9.0 (95% CI: 0.9-86.5) (crude) and 4.7 (95% CI:0.3-74.1)(age adjusted). In this first study in Europe, the intussusception risk point estimate was comparable to other studies, although results were not statistically significant, maybe due to limited power. The high PPV found will facilitate implementation of a larger study without requiring medical record review. Our finding of very few vaccinated cases despite a thorough 5-year investigation in a country that, according to previous studies, may have a large background rate of intussusception is reassuring and should contribute to deliberations about the need to include rotavirus vaccines in the official Spanish calendars.

Evaluation of safety and immunogenicity of a quadrivalent human papillomavirus vaccine in healthy females between 9 and 26 years of age in Sub-Saharan Africa.

Due to sporadic and not easily accessible cervical cancer screening, human papillomavirus (HPV)-related cervical cancer is a leading cause of cancer death in Sub-Saharan African women. This study was designed to assess the safety and immunogenicity of a quadrivalent human papillomavirus (qHPV) vaccine in sub-Saharan African women. This seven month, double-blind study enrolled 250 healthy, human immunodeficiency virus (HIV)-uninfected females ages 9-26 residing in Ghana, Kenya, and Senegal. Thirty females ages 13-15 and 120 females ages 16-26 received qHPV vaccine. In addition, 100 females ages 9-12 y were randomized in a 4:1 ratio to receive either qHPV vaccine (n = 80) or placebo (n = 20 ). The primary immunogenicity hypothesis was that an acceptable percentage of subjects who received the qHPV vaccine seroconvert to HPV6/11/16/18 at 4 weeks post-dose 3, defined as the lower bound of the corresponding 95% confidence interval (CI) exceeding 90%. The primary safety objective was to demonstrate that qHPV vaccine was generally well tolerated when administered in a 3-dose regimen. The pre-specified statistical criterion for the primary immunogenicity hypothesis was met: the lower bound of the 95% exact binomial CI on the seroconversion rate was at least 98% for each vaccine HPV type and all subjects seroconverted by 4 weeks post-dose 3. Across vaccination groups, the most common adverse events (AE) were at the injection site, including pain, swelling, and erythema. No subject discontinued study medication due to an AE and no serious AEs were reported. There were no deaths. This study demonstrated that qHPV vaccination of sub-Saharan African women was highly immunogenic and generally well tolerated.

A new technique to make transparent teeth without decalcifying: description of the methodology and micro-hardness assessment.

Diaphanisation and other in vitro endodontic models (i.e., plastic blocks, micro-CT reconstruction, computerised models) do not recreate real root canal working conditions: a more realistic endodontic model is essential for testing endodontic devices and teaching purposes. The aim of this study was to describe a new technique to construct transparent teeth without decalcifying and evaluate the micro-hardness of so treated teeth. Thirty freshly extracted teeth were randomly divided into three groups as follows: 10 non-treated teeth (4 molars, 3 premolars, 3 incisors; control group - G1), 10 teeth were diaphanised (4 molars, 4 premolars, 2 incisors - G2) and 10 teeth were treated with the new proposed technique (2 molars, 6 premolars, 2 incisors - G3). Vickers hardness tester (MHT-4 and AxioVision microscope, Carl Zeiss, 37030 Gottingen, Germany - load=50 g, dwell time=20s, slope=5, 50× magnification) was used to determine microhardness (Vickers Hardness Number - VHN). Statistical analysis was performed using the Intercooled Stata 8.0 software (Stata Corporation, College Station, TX, USA). Only groups 1 and 3 could be tested for hardness because diaphanised teeth were too tender and elastic. Differences in enamel VHN were observed between G1 (mean 304.29; DS=10.44; range 283-321) and G3 (mean 318.51; DS=14.36; range 295.5-339.2) - (p<0.05); differences in dentine VHN were observed between G1 (mean 74.73; DS=6.62; range 63.9-88.1) and G3 (mean 64.54; DS=5.55; range 51.2-72.3) - (p<0.05). G3 teeth presented a slightly lower VHN compared to G1, probably due to some little structural differences among groups, and were dramatically harder than the diaphanised teeth. The described technique, thus, can be considered ideal for testing endodontic instruments and for teaching purposes.

Immunogenicity assessment of HPV16/18 vaccine using the glutathione S-transferase L1 multiplex serology assay.

The glutathione S-transferase (GST)-L1 multiplex serology assay has favorable properties for use in clinical trials and epidemiologic studies, including low cost, high throughput capacity, and low serum volume requirement. Therefore, we evaluated the GST-L1 assay as a measure of HPV16/18 vaccine immunogenicity. Our study population included 65 women selected from the Costa Rica Vaccine Trial who received the bivalent HPV16/18 virus-like particle (VLP) vaccine at the recommended 0/1/6-month schedule. We tested replicate serum samples from months 0/1/12 (i.e., after 0/1/3 doses) by GST-L1 and 3 other commonly used serology assays, VLP-ELISA, SEAP-NA, and cLIA. We calculated the percentage of women seropositive by GST-L1 by time point and HPV type (14 HPV types), and compared GST-L1 to other assays using Spearman rank correlation coefficients. After 1 vaccine dose, seropositivity by GST-L1 was 40% each for HPV16 and HPV18, increasing to 100% and 98%, respectively, after 3 doses. Seropositivity after 3 doses ranged from 32% to 69% for HPV types 31/33/45, for which partial vaccine efficacy is reported, though increases also occurred for types with no evidence for cross-protection (e.g., HPV77). GST-L1 correlated best after 3 doses with VLP-ELISA (HPV16 and HPV18 each ρ = 0.72) and SEAP-NA (HPV16 ρ = 0.65, HPV18 ρ = 0.71) (all P < 0.001); correlation was lower with cLIA. The GST-L1 is suitable for evaluating HPV16/18 vaccine immunogenicity after 3 vaccine doses, although in contrast to other assays it may classify some samples as HPV16/18 seronegative. The assay's utility is limited for lower antibody levels such as after receipt of 1 dose.

Localization and characterization of val-opsin isoform-expressing cells in the brain of adult zebrafish.

In addition to vision, light information is used to regulate a range of animal physiology. Such nonimage-forming functions of light are mediated by nonvisual photoreceptors expressed in distinct neurons in the retina and the brain in most vertebrates. A nonvisual photoreceptor vertebrate ancient long opsin (VAL-opsin) possesses two functional isoforms in the zebrafish, encoded by valopa and valopb, which has received little attention. To delineate the neurochemical identities of valop cells and to test for colocalization of the valop isoforms, we used in situ hybridization to characterize the expression of the valop genes along with that of neurotransmitters and a neuropeptide known to be present at the sites of valop expression. Double labeling showed that the thalamic valop population coexpresses valopa and valopb. All the thalamic valop cells overlapped with a GABAergic cell mass that continues from the anterior nucleus to the intercalated thalamic nucleus. A novel valopa cell population found in the superior raphe was serotonergic in nature. A valopb cell population in the Edinger-Westphal nucleus was identified as containing thyrotropin-releasing hormone. Valopb cells localized in the hindbrain intermediate reticular formation were noncholinergic in nature (nonmotorneurons). Thus, the presence of valop cell populations in different brain regions with coexpression of neurotransmitters and neuropeptides and the colocalization of valop isoforms in the thalamic cell population indicate regulatory and functional complexity of VAL-opsin in the brain of the zebrafish.

Assessment of HPV 16 and HPV 18 antibody responses by pseudovirus neutralization, Merck cLIA and Merck total IgG LIA immunoassays in a reduced dosage quadrivalent HPV vaccine trial.

We assessed HPV 16 and 18 antibody responses of female subjects enrolled in a 2- vs. 3-dose quadrivalent HPV (Q-HPV) vaccine trial (ClinicalTrials.gov NCT00501137) using the Merck competitive Luminex (cLIA) and total IgG Luminex (TIgG) immunoassays, and a pseudovirus neutralizing antibody (PsV NAb) assay. Subjects were enrolled in one of three groups: (1) 9-13yr, 2 doses of Q-HPV at 0, 6 months (n=259); (2) 9-13yr, 3 doses at 0, 2, 6 months (n=260); and (3) 16-26yr, 3 doses at 0, 2, 6 months (n=305). Sera were collected from all subjects at baseline, months 7 and 24, and from half the subjects at months 18 and 36. High correlation was observed between all three assays. At month 36, HPV 16 antibodies remained detectable in all subjects by all assays, whereas 86.4%, 99.6% and 100% of subjects respectively were HPV 18 cLIA, TIgG and PsV NAb (partial neutralization endpoint) seropositive. The proportion seropositive for HPV 18 by cLIA at 36 months was not significantly different for 2-dose girls vs. 3-dose adults (85.9% vs. 79.4%; p=0.51), whereas the proportion for 3-dose girls was significantly higher than for 3-dose adults (95.3% vs. 79.4%; p<0.01). The HPV 18 seropositive proportions by the TIgG and PsV NAb (partial neutralization endpoint) assays were the same for all subjects. High baseline HPV 16 and HPV 18 seropositivity was observed for the TIgG assay and it is unclear if all the detected TIgG antibodies are type-specific and/or neutralizing. For the PsV NAb assay, 90% and partial neutralization geometric mean titres were consistently 2-8-fold higher than for 100% neutralization, which enabled detection of HPV 18 NAb in subjects who lost detectable cLIA antibodies over time. We conclude that the PsV NAb assay is more sensitive than the cLIA, and likely more specific than the TIgG assay.

Staphylococcus aureus Infections After Elective Cardiothoracic Surgery: Observations From an International Randomized Placebo-Controlled Trial of an Investigational S aureus Vaccine.

BACKGROUND: An unmet need to prevent Staphylococcus aureus (SA) infections after cardiothoracic surgery persists despite current practices. Cost-effective implementation of preventive strategies requires contemporary knowledge about modifiable risk factors. METHODS: From 2007 to 2011, an international, double-blind, randomized placebo-controlled trial of a novel SA vaccine (V710) was conducted in 7664 adults scheduled for median sternotomy at 164 sites. We analyzed SA infections developing up to 360 days postoperatively in 3832 placebo recipients. RESULTS: Coronary artery bypass grafting was performed in 80.8% (3096 of 3832) of placebo recipients. The overall incidence of any postoperative SA infection was 3.1% (120 of 3832). Invasive SA infections (including bacteremia and deep sternal-wound infections) developed in 1.0%. Methicillin-resistant SA (MRSA) accounted for 19% (23 of 120) of SA infections, with 57% (13 of 23) of the MRSA infections occurring in diabetic patients. All-cause mortality was 4.1% (153 of 3712) in patients without SA infection, 7.2% (7 of 97) in methicillin-susceptible SA (MSSA) infections, and 17.3% (4 of 23) in MRSA infections (P < .01). Staphylococcus aureus nasal carriage was detected preoperatively in 18.3% (701 of 3096) patients, including 1.6% colonized with MRSA. Postoperative SA infections occurred in 7.0% (49 of 701) of colonized patients versus 2.3% (71 of 3131) of patients without colonization (relative risk = 3.1 [95% confidence interval, 2.2-4.4]). CONCLUSIONS: In this large international cohort of patients undergoing cardiac surgery and observed prospectively, invasive postoperative SA infections occurred in 1% of adult patients despite modern perioperative management. The attributable mortality rates were 3% for MSSA and 13% for MRSA infections. Preoperative nasal colonization with SA increased the risk of postoperative infection threefold. The utility of strategies to reduce this incidence warrants continued investigation.

Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery.

Computational conformational sampling underpins much of molecular modeling and design in pharmaceutical work. The sampling of smaller drug-like compounds has been an active area of research. However, few studies have tested in details the sampling of larger more flexible compounds, which are also relevant to drug discovery, including therapeutic peptides, macrocycles, and inhibitors of protein-protein interactions. Here, we investigate extensively mainstream conformational sampling methods on three carefully curated compound sets, namely the 'Drug-like', larger 'Flexible', and 'Macrocycle' compounds. These test molecules are chemically diverse with reliable X-ray protein-bound bioactive structures. The compared sampling methods include Stochastic Search and the recent LowModeMD from MOE, all the low-mode based approaches from MacroModel, and MD/LLMOD recently developed for macrocycles. In addition to default settings, key parameters of the sampling protocols were explored. The performance of the computational protocols was assessed via (i) the reproduction of the X-ray bioactive structures, (ii) the size, coverage and diversity of the output conformational ensembles, (iii) the compactness/extendedness of the conformers, and (iv) the ability to locate the global energy minimum. The influence of the stochastic nature of the searches on the results was also examined. Much better results were obtained by adopting search parameters enhanced over the default settings, while maintaining computational tractability. In MOE, the recent LowModeMD emerged as the method of choice. Mixed torsional/low-mode from MacroModel performed as well as LowModeMD, and MD/LLMOD performed well for macrocycles. The low-mode based approaches yielded very encouraging results with the flexible and macrocycle sets. Thus, one can productively tackle the computational conformational search of larger flexible compounds for drug discovery, including macrocycles.

Interaction of Carthamus tinctorius lignan arctigenin with the binding site of tryptophan-degrading enzyme indoleamine 2,3-dioxygenase.

Mediterranean Carthamus tinctorius (Safflower) is used for treatment of inflammatory conditions and neuropsychiatric disorders. Recently C. tinctorius lignans arctigenin and trachelogenin but not matairesinol were described to interfere with the activity of tryptophan-degrading enzyme indoleamine 2,3-dioxygenase (IDO) in peripheral blood mononuclear cells in vitro. We examined a potential direct influence of compounds on IDO enzyme activity applying computational calculations based on 3D geometry of the compounds. The interaction pattern analysis and force field-based minimization was performed within LigandScout 3.03, the docking simulation with MOE 2011.10 using the X-ray crystal structure of IDO. Results confirm the possibility of an intense interaction of arctigenin and trachelogenin with the binding site of the enzyme, while matairesinol had no such effect.