The increasing worldwide contamination of freshwater systems with thousands of industrial and natural chemical compounds is one of the key environmental problems facing humanity. Although most of these compounds are present at low concentrations, many of them raise considerable toxicological concerns, particularly when present as components of complex mixtures. Here we review three scientific challenges in addressing water-quality problems caused by such micropollutants. First, tools to assess the impact of these pollutants on aquatic life and human health must be further developed and refined. Second, cost-effective and appropriate remediation and water-treatment technologies must be explored and implemented. Third, usage and disposal strategies, coupled with the search for environmentally more benign products and processes, should aim to minimize introduction of critical pollutants into the aquatic environment.

https://science.sciencemag.org/content/sci/313/5790/1072.full.pdf

The Challenge of Micropollutants in Aquatic Systems

Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks–Chandler–Andersen like integral method). We showcase the effectiveness of the tool ...

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.

/pdf/water-analysis-emerging-contaminants-and-current-issues-4iaf1qar5i.pdf

Water Analysis: Emerging Contaminants and Current Issues

In the last few decades, pharmaceuticals, credited with saving millions of lives, have emerged as a new class of environmental contaminant. These compounds can have both chronic and acute harmful effects on natural flora and fauna. The presence of pharmaceutical contaminants in ground waters, surface waters (lakes, rivers, and streams), sea water, wastewater treatment plants (influents and effluents), soils, and sludges has been well doccumented. A range of methods including oxidation, photolysis, UV-degradation, nanofiltration, reverse osmosis, and adsorption has been used for their remediation from aqueous systems. Many methods have been commercially limited by toxic sludge generation, incomplete removal, high capital and operating costs, and the need for skilled operating and maintenance personnel. Adsorption technologies are a low-cost alternative, easily used in developing countries where there is a dearth of advanced technologies, skilled personnel, and available capital, and adsorption appears to be the most broadly feasible pharmaceutical removal method. Adsorption remediation methods are easily integrated with wastewater treatment plants (WWTPs). Herein, we have reviewed the literature (1990-2018) illustrating the rising environmental pharmaceutical contamination concerns as well as remediation efforts emphasizing adsorption.

Pharmaceuticals of Emerging Concern in Aquatic Systems: Chemistry, Occurrence, Effects, and Removal Methods.

Occurrences and removal of pharmaceuticals and personal care products (PPCPs) in drinking water and water/sewage treatment plants: A review

The bactericide triclosan and methyl triclosan, an environmental transformation product thereof, were detected in lakes and in a river in Switzerland at concentrations of up to 74 and 2 ng L(-1), respectively. Both compounds were emitted via wastewater treatment plants (WWTPs), with methyl triclosan probably being formed by biological methylation. A regional mass balance for a lake (Greifensee) indicated significant removal of triclosan by processes other than flushing. Laboratory experiments showed that triclosan in the dissociated form was rapidly decomposed in lake water when exposed to sunlight (half-life less than 1 h in August at 47 degrees latitude). Methyl triclosan and nondissociated triclosan, however, were relatively stable toward photodegradation. Modeling these experimental data for the situation of lake Greifensee indicated that photodegradation can account for the elimination of triclosan from the lake and suggested a seasonal dependence of the concentrations (lower in summer, higher in winter), consistent with observed concentrations. Although emissions of methyl triclosan from WWTPs were only approximately 2% relative to those of triclosan, its predicted concentration relative to triclosan in the epilimnion of the lake increases to 30% in summer. Passive sampling with semipermeable membrane devices (SPMDs) indicated the presence of methyl triclosan in lakes with inputs from anthropogenic sources but not in a remote mountain lake. Surprisingly, no parent triclosan was observed in the SPMDs from these lakes. Methyl triclosan appears to be preferentially accumulated in SPMDs under the conditions in these lakes, leading to concentrations comparable to those of persistent chlorinated organic pollutants.

Occurrence and environmental behavior of the bactericide triclosan and its methyl derivative in surface waters and in wastewater.

Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification ...

Postprocessing of docked protein-ligand complexes using implicit solvation models.

A new approach is presented for predicting ligand binding to proteins using hierarchical partial-least-squares regression to latent structures (Hi-PLS). Models were based on information from the 2002 release of the PDBbind database containing (after in-house refinement) high-resolution X-ray crystallography and binding affinity (Kd or Ki) data for 612 protein−ligand complexes. The complexes were characterized by four different descriptor blocks:  three-dimensional (3D) structural descriptors of the proteins, protein−ligand interactions according to the Validate scoring function, binding site surface areas, and ligand 2D and 3D descriptors. These descriptor blocks were used in Hi-PLS models, generated using both linear and nonlinear terms, to relate the characterizations to pKd/i. The results show that each of the four descriptor blocks contributed to the model, and the predictions of pKd/i of the internal test set gave a root-mean-square error of prediction (RMSEP) of 1.65. The data were further divided a...

Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein−Ligand Complexes

Increasingly powerful docking programs for analyzing and estimating the strength of protein-ligand interactions have been developed in recent decades, and they are now valuable tools in drug discovery. Software used to perform dockings relies on a number of parameters that affect various steps in the docking procedure. However, identifying the best choices of the settings for these parameters is often challenging. Therefore, the settings of the parameters are quite often left at their default values, even though scientists with long experience with a specific docking tool know that modifying certain parameters can improve the results. In the study presented here, we have used statistical experimental design and subsequent regression based on root-mean-square deviation values using partial least-square projections to latent structures (PLS) to scrutinize the effects of different parameters on the docking performance of two software packages: FRED and GOLD. Protein-ligand complexes with a high level of ligand diversity were selected from the PDBbind database for the study, using principal component analysis based on 1D and 2D descriptors, and space-filling design. The PLS models showed quantitative relationships between the docking parameters and the ability of the programs to reproduce the ligand crystallographic conformation. The PLS models also revealed which of the parameters and what parameter settings were important for the docking performance of the two programs. Furthermore, the variation in docking results obtained with specific parameter settings for different protein-ligand complexes in the diverse set examined indicates that there is great potential for optimizing the parameter settings for selected sets of proteins.

Anton Lindström

Papers

Occurrence and environmental behavior of the bactericide triclosan and its methyl derivative in surface waters and in wastewater.

Postprocessing of docked protein-ligand complexes using implicit solvation models.

Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein−Ligand Complexes

A Multivariate Approach to Investigate Docking Parameters' Effects on Docking Performance

Quantitative protein descriptors for secondary structure characterization and protein classification