Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein–ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate binders from nonbinders in virtual screening and to more accurately predict the ligand binding modes prior to the more computationally expensive FEP calculations of binding affinity.     

A novel palladium-mediated coupling approach to 2,3-disubstituted benzo(b)thiophenes and its application to the synthesis of tubulin binding agents

[structure: see text]. Flexible, convergent access to 2,3-disubstituted benzo[b]thiophenes has been developed. The most concise approach involves sequential coupling of o-bromoiodobenzenes with benzylmercaptan and zinc acetylides to give benzyl o-ethynylphenyl sulfides which react with iodine to give 3-iodobenzo[b]thiophenes in a 5-endo-dig iodocyclization. These iodides can be further elaborated using palladium-mediated coupling and/or metalation techniques. This method has been applied to the synthesis of some novel tubulin binding agents.     

Rail vs truck transport of biomass

This study analyzes the economics of transshipping biomass from truck to train in a North American setting. Transshipment will only be economic when the cost per unit distance of a second transportation mode is less than the original mode. There is an optimum number of transshipment terminals which is related to biomass yield. Transshipment incurs incremental fixed costs, and hence there is a minimum shipping distance for rail transport above which lower costs/km offset the incremental fixed costs. For transport by dedicated unit train with an optimum number of terminals, the minimum economic rail shipping distance for straw is 170 km, and for boreal forest harvest residue wood chips is 145 km. The minimum economic shipping distance for straw exceeds the biomass draw distance for economically sized centrally located power plants, and hence the prospects for rail transport are limited to cases in which traffic congestion from truck transport would otherwise preclude project development. Ideally, wood chip transport costs would be lowered by rail transshipment for an economically sized centrally located power plant, but in a specific case in Alberta, Canada, the layout of existing rail lines precludes a centrally located plant supplied by rail, whereas a more versatile road system enables it by truck. Hence for wood chips as well as straw the economic incentive for rail transport to centrally located processing plants is limited. Rail transshipment may still be preferred in cases in which road congestion precludes truck delivery, for example as result of community objections.     

Liquid membrane transport: a survey

The literature pertaining to facilitated transport and liquid membrane separations is reviewed and summarized, especially work reported since 1977. Liquid membranes of all geometries are discussed, including immobilized liquid membranes and liquid surfactant or emulsion liquid membranes. Emphasis is placed on facilitated, or carrier-mediated transport in both configurations although other mechanisms such as coupled-transport and transport due to solubility differences are discussed. Mathematical modeling and analytical solutions for facilitated transport models are summarized. The possibility of industrial application of liquid membrane technology is mentioned and the most important experimental techniques for liquid membrane research are discussed. Also, directions for future research are recommended.     

The proton shell closure at 14C

Data for the ¹⁴C(³He, d)¹⁵N and ¹⁴C(t, ⁴He)¹³B reactions are compared to DWBA calculations to measure the spectroscopic factors for $\text{p}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{and}\text{p}{}_{\mathrm{<mtext>3</mtext><mtext>2</mtext>}}$ proton transitions. Good fits are found for the stripping data, as well as to similar stripping data on ¹²C. These results lower the previous value for proton $\text{p}{}_{\mathrm{<mtext>3</mtext><mtext>2</mtext>}}$ hole strength in ¹⁴C by a factor of two, indicating that the neutron closure of the p-shell has provided a very good proton closed shell at ¹⁴C. Stripping results to low-lying positive parity states in ¹⁵N are interpreted within a Nilsson scheme, which reproduces the experimental results, but which requires a large deformation for the s-d orbitals.     

Development of a multicriteria assessment model for ranking biomass feedstock collection and transportation systems

This study details multicriteria assessment methodology that integrates economic, social, environmental, and technical factors in order to rank alternatives for biomass collection and transportation systems. Ranking of biomass collection systems is based on cost of delivered biomass, quality of biomass supplied, emissions during collection, energy input to the chain operations, and maturity of supply system technologies. The assessment methodology is used to evaluate alternatives for collecting 1.8×10⁶ dry t/yr based on assumptions made on performance of various assemblies of biomass collection systems is based on cost of delivered biomass, quality of biomass supplied, emissions during collection, energy input to the chain operations, and maturity of supply system technologies. The assessment methodology is used to evaluate alternatives for collecting 1.8×10⁶ dry t/yr based on assumptions made on performance of various assemblies of biomass collection systems. A proposed collection option using loafer/stacker was shown to be the best option followed by ensiling and baling. Ranking of biomass transport systems is based on cost of biomass transport, emissions during transport, traffic congestion, and maturity of different technologies. At a capacity of 4×10⁶ dry t/yr, rail transport was shown to be the best option, followed by truck transport and pipeline transport, respectively. These rankings depend highly on assumed maturity of technologies and scale of utilization. These may change if technologies such as loafing or ensiling (wet storage) methods are proved to be infeasible for large-scale collection systems.     

Cavity ring-down spectroscopy of the torsional motions of 1,4-bis(phenylethynyl)benzene

The torsional motions of jet-cooled 1,4-bis(phenylethynyl)benzene (BPEB), a prototype molecular wire, were studied using cavity ring-down spectroscopy in the first UV absorption band (316-321 nm). The torsional spectrum of 1,4-bis(phenylethynyl)-2,3,5,6-tetradeuteriobenzene was also recorded in the gas phase. Both spectra were successfully simulated using simple cosine potentials to describe the torsional motions. The ground-state barrier to rotation was estimated to be 220-235 cm(-1), which is similar to that of diphenylacetylene (tolane). Complementary DFT calculations were found to overestimate the torsional barrier.