Building and deploying a cyberinfrastructure for the data-driven design of chemical systems and the exploration of chemical space

Abstract

The use of modern data science has recently emerged as a promising new path to tackling the complex challenges involved in the creation of next-generation chemistry and materials. However, despite the appeal of this potentially transformative development, the chemistry community has yet to incorporate it as a central tool in every-day work. Our research program is designed to enable and advance this emerging research approach. It is centred around the creation of a software ecosystem that brings together physics-based modelling, high-throughput in silico screening and data analytics (i.e. the use of machine learning and informatics for the validation, mining and modelling of chemical data). This cyberinfrastructure is devised to offer a comprehensive set of data science techniques and tools as well as a general-purpose scope to make it as versatile and widely applicable as possible. It also emphasises user-friendliness to make it accessible to the community at large. It thus provides the means for the large-scale exploration of chemical space and for a better understanding of the hidden mechanisms that determine the properties of complex chemical systems. Such insights can dramatically accelerate, streamline and ultimately transform the way chemical research is conducted. Aside from serving as a production-level tool, our cyberinfrastructure is also designed to facilitate and assess methodological innovation. Both the software and method development work are driven by concrete molecular design problems, which also allow us to assess the efficacy of the overall cyberinfrastructure.     

Influence of extracellular pH on the cytotoxicity, cellular accumulation, and DNA interaction of novel pH-sensitive 2-aminoalcoholatoplatinum(II) complexes

Extracellular acidity is a frequent pathophysiological condition of solid tumors offering possibilities for improving the tumor selectivity of molecular therapy. This might be accomplished by prodrugs with low systemic toxicity, attaining their full antitumor potency only under acidic conditions, such as bis(2-aminoalcoholato-κ²N,O)platinum(II) complexes that are activated by protonation of alcoholato oxygen, resulting in cleavage of platinum–oxygen bonds. In this work, we examined whether the pH dependency of such compounds is reflected in differential biological activity in vitro. In particular, the pH dependence of cytotoxicity, cellular accumulation, DNA platination, GMP binding, effects on DNA secondary structure, cell cycle alterations, and induction of apoptosis was investigated. Enhanced cytotoxicity of five of these complexes in non-small-cell lung cancer (A549) and colon carcinoma (HT-29) cells at pH 6.0 in comparison with pH 7.4 was confirmed: 50 % growth inhibition concentrations ranged from 42 to 214 μM in A549 cells and from 35 to 87 μM in HT-29 cells at pH 7.4 and decreased at pH 6.0 to 11–50 and 7.3–25 μM, respectively. The effects induced by all five pH-sensitive compounds involve increased 5′-GMP binding, cellular accumulation, and DNA platination as well as stronger effects on DNA secondary structure at pH 6.0 than at pH 7.4. As exemplified by treatment of A549 cells with a 2-amino-4-methyl-1-pentanolato complex, induction of apoptosis is enhanced at pH 6.5. These results confirm the increased reactivity and in vitro activity of these compounds under slightly acidic conditions, encouraging further evaluation of ring-closed aminoalcoholatoplatinum(II) derivatives in solid tumors in vivo.     

Extraction and determination of opium alkaloids in urine samples using dispersive liquid-liquid microextraction followed by high-performance liquid chromatography

A simple, rapid and sensitive method based on dispersive liquid-liquid microextraction (DLLME) combined with high-performance liquid chromatography-ultraviolet detection (HPLC-UV) was used to determine opium alkaloids in urine samples. Some effective parameters on extraction were studied and optimized. Under the optimum conditions, enrichment factors and recoveries for different opiates are in the range of 63.0-104.5 and 31.5-52.2%, respectively. The calibration graphs are linear in the range of 0.50-500 μg L(-1) and limit of detections (LODs) are in the range of 0.2-10 μg L(-1). The relative standard deviations (RSDs) for 200 μg L(-1) of morphine, codeine and thebaine, 5.0 μg L(-1) of papaverine and 10.0 μg L(-1) of noscapine in diluted urine sample are in the range of 2.8-6.1% (n=7). The relative recoveries of urine samples spiked with alkaloids are 84.3-106.0%. The obtained results show that DLLME combined with HPLC-UV is a fast and simple method for the determination of opium alkaloids in urine samples.     

Host preference by Allothrombium pulvinum (Acari: Trombidiidae) larvae on aphids: Macrosiphum rosae,Aphis gossypii and Hyalopterus amygdali (Homoptera: Aphididae)

In this study aphid-plant association and its effect on host preference of parasitic Allothrombium pulvinum larvae was examined with multiple-choice tests. Host species selection, host size selection and superparasitism with mite larvae were studied with two-choice tests. Three aphid species were used: Macrosiphum rosae, Aphis gossypii and Hyalopterus amygdali. In multiple-choice tests, larvae of A. pulvinum showed no significant preference for any aphid-plant association when given M. rosae on rose, A. gossypii on cucumber and H. amygdali on apricot simultaneously. Two-choice tests showed that larval mites preferred H. amygdali to A. gossypii, but had no preference when offered a choice between A. gossypii and M. rosae or between H. amygdali and M. rosae. In host size selection and superparasitism tests, significantly more mites selected the larger host (M. rosae). Furthermore, parasitised H. amygdali were preferred to unparasitised ones. This revised version was published online in July 2006 with corrections to the Cover Date.     

Serum Trace Element Levels in Febrile Convulsion

Febrile convulsion is the most common disorder in childhood with good prognosis. There are different hypotheses about neurotransmitters and trace element changes in biological fluids which can have a role in pathogenesis of febrile convulsion. In this study, serum selenium, zinc, and copper were measured by atomic absorption spectrometry in the children with febrile convulsion (n?=?30) and in the control group (n?=?30). The age and sex of the subjects were registered. Selenium and zinc were found to be significantly lower in febrile convulsion cases than in the control group (p?<?0.0001 and p?<?0.0001, respectively). There was no significant difference in the value of copper between the two groups (p?=?0.16). While selenium and zinc levels were 44.92?±?10.93 μg/l and 66.13?±?18.97 μg/dl in febrile convulsion, they were found to be 62.98?±?9.80 μg/l and 107.87?±?28.79 μg/dl in healthy children. Meanwhile, copper levels were 146.40?±?23.51 μg/dl in the patients and 137.63?±?24.19 μg/dl in the control group, respectively. This study shows that selenium and zinc play an important role in the pathogenesis of febrile convulsion.