Exploring the biological promiscuity of high-throughput screening hits through DFT calculations Ramona Curpa ˘n a,⇑,  , Sorin Avram a,  , Robert Vianello b , Cristian Bologa c a Department of Computational Chemistry, Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul, Timisoara 300223, Romania b Quantum Organic Chemistry Group, Ru - der Boškovic ´ Institute, Bijenic ˇka cesta 54, Zagreb HR-10000, Croatia c Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA article info Article history: Received 3 December 2013 Revised 20 February 2014 Accepted 28 February 2014 Available online 12 March 2014 Keywords: Frequent hitters Biological promiscuity HTS Chemical reactivity descriptors DFT abstract The goal of this study is the understanding of biologically promiscuous compounds (frequent hitters) in HTS outcomes through their chemical behavior estimated via reactivity descriptors. Chemical reactivity is often an undesirable property due to the lack in biological selectivity of compounds comprised in HTS libraries. In this study the reactivity indexes have been computed within the DFT formalism, at different levels of theory, for two classes of representative compounds compiled from PubChem database, one comprising frequent hitters and the second one comprising rare hitters (biologically more selective compounds). We found that frequent hitters exert increased reactivity, mainly due to their electrophilic character, compared to the more selective class of compounds. Ó 2014 Elsevier Ltd. All rights reserved. 1. Introduction The optimization of small molecule libraries design has yielded improvements in the success rate of high-throughput screening (HTS) campaigns, 1 but retrospective analysis of hit lists have emphasized new sources of false active compounds, 2 assay interference, 3 reactive moieties, 4,5 oxidation potential, 6 formal molecular charge, 7 high degree of flexibility 8 and/or liability to degradation and precipitation. 9 The development of these concepts and methodologies has lead to a significant evolution of HTS and currently, it represents the favorite technology employed in the discovery of new potentially active compounds against specific tar- gets and/or biological system of interest in both pharmaceutical industry and academia. 1,10–12 Although, a handful of methods and concepts have been devel- oped for the compound libraries design, assay adaptation and hit structures selection, the key challenge of HTS campaigns has continued to be the reduction of false hits or false-positive compounds. Some known common categories are: aggregators, which mimic the effects of binding via aggregation; 13 compounds which absorb light and interfere with the assay; compound which act through a redox mechanism under the biological testing condi- tions; 14 electrophilic reactive molecules which form covalent bonds with cysteine, threonine and/or serine residues of target proteins or react with biological nucleophiles under the assay con- ditions. 5 These compound classes act via specific mechanisms, which are influenced by the biological target type, assay conditions and the physico-chemical properties of the tested compounds. These aspects have to be taken into account during the develop- ment of the assays. For example, documented aggregators may not exhibit aggregator behavior under different assay conditions (different reactives, pH, temperature, etc.) or a compound that acts via a redox mechanism against a specific target may lose this behavior when a different protein is involved. 15 On the other hand, a recent study of 1070 marketed drugs which monitors the occur- rence of moieties described in the literature as ‘undesirable’ for HTS compound libraries, has revealed that 26% of the set contains at least one of such moieties. 16 When it comes to the most fre- quently observed fragments from the compiled drugs set, the same study has shown that electrophilic reactive groups, particularly ali- phatic esters, were the most abundant type representing 55% of the total. Also, the analysis of the FDA approved drugs from the HTS era (post 2000, when the first drugs resulted from HTS have emerged on the market) has pointed out a decrease of the percentage of undesirable fragments. Approximately 30% of drugs approved by http://dx.doi.org/10.1016/j.bmc.2014.02.055 0968-0896/Ó 2014 Elsevier Ltd. All rights reserved. Abbreviations: FHs, set of frequent hitters; RHs, set of rare hitters; l, chemical potential; v, electronegativity; g, hardness; x, electrophilicity index; IP, ionization potential; EA, electron affinity; HOMO, highest occupied molecular orbital; LUMO, lowest unoccupied molecular orbital. ⇑ Corresponding author. Tel.: +40 256 491818; fax: +40 256 491824. E-mail address: rcurpan@acad-icht.tm.edu.ro (R. Curpa ˘n).   These authors contributed equally to the work. Bioorganic & Medicinal Chemistry 22 (2014) 2461–2468 Contents lists available at ScienceDirect Bioorganic & Medicinal Chemistry journal homepage: www.elsevier.com/locate/bmc