Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments

Karaboga, A.S.; Petronin, F.; Marchetti, G.; Souchet, M.; Maigret, B.
(2013) J. Mol. Graph. Model., 41, 20-30

Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes.

Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets.

Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods.

Recent trends and future prospects in computational GPCR drug discovery: from virtual screening to polypharmacology

Carrieri, A.; Pérez-Nueno, V. I.; Lentini, G.;Ritchie, D.W.
(2013) Current Topics in Medicinal Chemistry., 13(9),1069-97

Extending virtual screening approaches to deal with multi-target drug design and polypharmacology is an increasingly important aspect in drug design. In light of this, the concept of accessible chemical space and its exploration should be reviewed. The great advantages of re-using drugs with safe pharmacological profiles with favourable pharmacokinetic properties highlights drug repositioning as a valid alternative to rational drug design, massive drug development efforts, and high-throughput screening, especially when supported by in silico techniques. Here, we discuss some of the advantages of multi-target approaches, and we review some significant examples of their application in the last decade to that well known class of pharmaceutical targets, the G-protein coupled receptors.

Recent Trends and Applications in 3D Virtual Screening

Ghemtio, L.; Pérez-Nueno, V. I.; Leroux, V.; Asses, Y.; Souchet, M.; Mavridis, L.; Ritchie, D.W.
(2012) Combinatorial Chemistry & High Throughput Screening., 15,749-769

Virtual screening (VS) is becoming an increasingly important approach for identifying and selecting biologically active molecules against specific pharmaceutically relevant targets. Compared to conventional high throughput screening techniques, in silico screening is fast and inexpensive, and is increasing in popularity in early-stage drug discovery endeavours. This paper reviews and discusses recent trends and developments in three-dimensional (3D) receptor-based and ligand-based VS methodologies. First, we describe the concept of accessible chemical space and its exploration. We then describe 3D structural ligand-based VS techniques, hybrid approaches, and new approaches to exploit additional knowledge that can now be found in large chemogenomic databases. We also briefly discuss some potential issues relating to pharmacokinetics, toxicity profiling, target identification and validation, inverse docking, scaffold-hopping and drug re-purposing. We propose that the best way to advance the state of the art in 3D VS is to integrate complementary strategies in a single drug discovery pipeline, rather than to focus only on theoretical or computational improvements of individual techniques. Two recent 3D VS case studies concerning the LXR-β receptor and the CCR5/CXCR4 HIV co-receptors are presented as examples which implement some of the complementary methods and strategies that are reviewed here.

Detecting Drug Promiscuity using Gaussian Ensemble Screening

Pérez-Nueno, V. I.; Venkatraman, V.; Mavridis, L.; Ritchie, D.W.
(2012) J. Chem. Inf. Model., 52,1948-1961

Polypharmacology describes the binding of a ligand to multiple protein targets (a promiscuous ligand) or multiple diverse ligands binding to a given target (a promiscuous target). Pharmaceutical companies are discovering increasing numbers of both promiscuous drugs and drug targets. Hence, polypharmacology is now recognized as an important aspect of drug design. Here, we describe a new and fast way to predict polypharmacological relationships between drug classes quantitatively, which we call Gaussian Ensemble Screening (GES). This approach represents a cluster of molecules with similar spherical harmonic surface shapes as a Gaussian distribution with respect to a selected center molecule. Calculating the Gaussian overlap between pairs of such clusters allows the similarity between drug classes to be calculated analytically without requiring thousands of bootstrap comparisons, as in current promiscuity prediction approaches. We find that such cluster similarity scores also follow a Gaussian distribution. Hence, a cluster similarity score may be transformed into a probability value, or “p-value”, in order to quantify the relationships between drug classes. We present results obtained when using the GES approach to predict relationships between drug classes in a subset of the MDL Drug Data Report (MDDR) database. Our results indicate that GES is a useful way to study polypharmacology relationships, and it could provide a novel way to propose new targets for drug repositioning.

Identifying and characterizing promiscuous targets: Implications for virtual screening

Pérez-Nueno, V. I.; Ritchie, D.W.
(2012) Expert Opinion On Drug Discovery.,7,1-17

Introduction: Ligand-based shape matching approaches have become established as important and popular virtual screening (VS) techniques. However, despite their relative success, the question of how to best choose the initial query compounds and their conformations remains largely unsolved. This issue gains importance when dealing with promiscuous targets, that is, proteins that bind multiple ligand scaffold families in one or more binding site. Conventional shape matching VS approaches assume that there is only one binding mode for a given protein target. This may be true for some targets, but it is certainly not true in all cases. Several recent studies have shown that some protein targets bind to different ligands in different ways.

Areas covered: The authors discuss the concept of promiscuity in the context of virtual drug screening, and present and analyze several examples of promiscuous targets. The article also reports on the impact of the query conformation on the performance of shape-based VS and the potential to improve VS performance by using consensus shape clustering techniques.

Expert opinion: The notion of polypharmacology is becoming highly relevant in drug discovery. Understanding and exploiting promiscuity present challenges and opportunities for drug discovery endeavors. The examples of promiscuity presented here suggest that promiscuous targets and ligands are much more common than previously assumed, and this should be taken into account in practical VS protocols. Although some progress has been made, there is a need to develop more sophisticated computational techniques and protocols that can identify and characterize promiscuous targets on a genomic scale.

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