After nearly five decades "in the making", QSAR modeling has established itself as one of the major computational molecular modeling methodologies. As any mature research discipline, QSAR modeling can be characterized by a collection of well defined protocols and procedures that enable the expert application of the method for exploring and exploiting ever growing collections of biologically active chemical compounds. This review examines most critical QSAR modeling routines that we regard as best practices in the field. We discuss these procedures in the context of integrative predictive QSAR modeling workflow that is focused on achieving models of the highest statistical rigor and external predictive power. Specific elements of the workflow consist of data preparation including chemical structure (and when possible, associated biological data) curation, outlier detection, dataset balancing, and model validation. We especially emphasize procedures used to validate models, both internally and externally, as well as the need to define model applicability domains that should be used when models are employed for the prediction of external compounds or compound libraries. Finally, we present several examples of successful applications of QSAR models for virtual screening to identify experimentally confirmed hits.

Best Practices for QSAR Model Development, Validation, and Exploitation.

Solid dispersions as strategy to improve oral bioavailability of poor water soluble drugs.

Chem. Pharm. Bull.(オピニオン)

Cancer is one of the main causes of death worldwide. Despite the significant development of methods of cancer healing during the past decades, chemotherapy still remains the main method for cancer treatment. Depending on the mechanism of action, commonly used chemotherapeutic agents can be divided into several classes (antimetabolites, alkylating agents, mitotic spindle inhibitors, topoisomerase inhibitors, and others). Multidrug resistance (MDR) is responsible for over 90% of deaths in cancer patients receiving traditional chemotherapeutics or novel targeted drugs. The mechanisms of MDR include elevated metabolism of xenobiotics, enhanced efflux of drugs, growth factors, increased DNA repair capacity, and genetic factors (gene mutations, amplifications, and epigenetic alterations). Rapidly increasing numbers of biomedical studies are focused on designing chemotherapeutics that are able to evade or reverse MDR. The aim of this review is not only to demonstrate the latest data on the mechanisms of cellular resistance to anticancer agents currently used in clinical treatment but also to present the mechanisms of action of novel potential antitumor drugs which have been designed to overcome these resistance mechanisms. Better understanding of the mechanisms of MDR and targets of novel chemotherapy agents should provide guidance for future research concerning new effective strategies in cancer treatment.

Mechanisms of Multidrug Resistance in Cancer Chemotherapy.

Phenolic compounds constitute a group of secondary metabolites which have important functions in plants. Besides the beneficial effects on the plant host, phenolic metabolites (polyphenols) exhibit a series of biological properties that influence the human in a health-promoting manner. Evidence suggests that people can benefit from plant phenolics obtained either by the diet or through skin application, because they can alleviate symptoms and inhibit the development of various skin disorders. Due to their natural origin and low toxicity, phenolic compounds are a promising tool in eliminating the causes and effects of skin aging, skin diseases, and skin damage, including wounds and burns. Polyphenols also act protectively and help prevent or attenuate the progression of certain skin disorders, both embarrassing minor problems (e.g., wrinkles, acne) or serious, potentially life-threatening diseases such as cancer. This paper reviews the latest reports on the potential therapy of skin disorders through treatment with phenolic compounds, considering mostly a single specific compound or a combination of compounds in a plant extract.

The Potential of Plant Phenolics in Prevention and Therapy of Skin Disorders

In this chapter, we give an overview of the regulatory requirements for acute systemic toxicity information in the European Union, and we review the availability of structure-based computational models that are available and potentially useful in the assessment of acute systemic toxicity. The most recently published literature models for acute systemic toxicity are also discussed, and perspectives for future developments in this field are offered.

In silico models for acute systemic toxicity

Silymarin, the active constituent of Silybum marianum (milk thistle), and its main component, silybin, are products with well-known hepatoprotective, cytoprotective, antioxidant, and chemopreventative properties. Despite substantial in vitro and in vivo investigations of these flavonolignans, their mechanisms of action and potential toxic effects are not fully defined. In this study we explored important ADME/Tox properties and biochemical interactions of selected flavonolignans using in silico methods. A quantitative structure-activity relationship (QSAR) model based on data from a parallel artificial membrane permeability assay (PAMPA) was used to estimate bioavailability after oral administration. Toxic effects and metabolic transformations were predicted using the knowledge-based expert systems Derek Nexus and Meteor Nexus (Lhasa Ltd). Potential estrogenic activity of the studied silybin congeners was outlined. To address further the stereospecificity of this effect the stereoisomeric forms of silybin were docked into the ligand-binding domain of the human estrogen receptor alpha (ERa) (MOE software, CCG). According to our results both stereoisomers can be accommodated into the ERa active site, but different poses and interactions were observed for silybin A and silybin B.

https://journals.sagepub.com/doi/pdf/10.1177/1934578X1701200208

ADME/Tox Properties and Biochemical Interactions of Silybin Congeners: In silico Study.

Summary: This article provides an overview of the use of computational methods in chemicals hazard and risk assessment under the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) legislation. The key aspects of the REACH guidance on the assessment of chemicals are discussed that treat the possible stepwise (tiered) approach combining multiple computational methods in assessing chemicals. Several publicly accessible software tools for the computer-based estimation of chemical hazard, developed by the European Commission’s Joint Research Centre (JRC), are described.

The Use of Computational Methods for the Assessment of Chemicals in REACH

Oxidative stress is associated with the increased production of reactive oxygen species or with a significant decrease in the effectiveness of antioxidant enzymes and nonenzymatic defense. The penetration of oxygen and free radicals in the hydrophobic interior of biological membranes initiates radical disintegration of the hydrocarbon "tails" of the lipids. This process is known as "lipid peroxidation", and the accumulation of the oxidation products as peroxides and the aldehydes and acids derived from them are often used as a measure of oxidative stress levels. In total, 40 phenolic antioxidants were selected for a comparative study and analysis of their chain-breaking antioxidant activity, and thus as modulators of oxidative stress. This included natural and natural-like ortho-methoxy and ortho-hydroxy phenols, nine of them newly synthesized. Applied experimental and theoretical methods (bulk lipid autoxidation, chemiluminescence, in silico methods such as density functional theory (DFT) and quantitative structure-activity relationship ((Q)SAR) modeling) were used to clarify their structure-activity relationship. Kinetics of non-inhibited and inhibited lipid oxidation in close connection with inhibitor transformation under oxidative stress is considered. Special attention has been paid to chemical reactions resulting in the initiation of free radicals, a key stage of oxidative stress. Effects of substituents in the side chains and in the phenolic ring of hydroxylated phenols and biphenols, and the concentration were discussed.

Natural Chain-Breaking Antioxidants and Their Synthetic Analogs as Modulators of Oxidative Stress.

Development of new COSMOS oRepeatDose and non-cancer Threshold of Toxicological Concern (TTC) databases to support alternative testing methods for cosmetics related chemicals

Ivanka Tsakovska

Papers

In silico models for acute systemic toxicity

ADME/Tox Properties and Biochemical Interactions of Silybin Congeners: In silico Study.

The Use of Computational Methods for the Assessment of Chemicals in REACH

Natural Chain-Breaking Antioxidants and Their Synthetic Analogs as Modulators of Oxidative Stress.

Development of new COSMOS oRepeatDose and non-cancer Threshold of Toxicological Concern (TTC) databases to support alternative testing methods for cosmetics related chemicals