Certara’s Best of Blogs 2016

A selection of short essays from our blog, written to empower our customers with modeling and simulation (M&S) and regulatory writing solutions in order to help them solve the toughest drug development problems. Certara staff contributions range in topic from pharmacometrics to systems biology to the growing importance of regulatory writing and sharing clinical trial results.

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Multistep Reaction Based De Novo Drug Design: Generating Synthetically Feasible Design Ideas

We describe a “multistep reaction driven” evolutionary algorithm approach to de novo molecular design. Structures generated by the approach include a proposed synthesis path intended to aid the chemist in assessing the synthetic feasibility of the ideas that are generated. The methodology is independent of how the design ideas are scored, allowing multicriteria drug design […]

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Man vs. Machine

Drug discovery teams often face roadblocks in their projects due to gaps between computer-aided drug design (CADD) and the medicinal chemistry lab. Thus, CADD scientists frequently identify promising ideas only to find that the medicinal chemists are unable to synthesize them.

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A Time-Saving Discovery Workflow

Chemists at a large chemical company improved their discovery hit rate fivefold by combining Muse molecular discovery platform with custom database search. A large chemical company initially turned to Muse® as part of a proprietary compound purchasing workflow. Then the company found a new way to leverage Muse to dramatically accelerate the discovery of new […]

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Finding Novel Ideas Through Both Ligand- and Target-based Discovery

Certara’s Muse Invent and a custom scoring function helped chemists differing needs to achieve faster discovery of innovative, realistic leads Discovery chemists at a large life sciences company needed to improve both speed and novelty in their generation of fresh ideas. When Certara® scientific consultants demonstrated the Muse® Invent™ molecular design workflow, they saw an […]

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R-group template CoMFA combines benefits of “ad hoc” and topomer alignments using 3D-QSAR for lead optimization

Template CoMFA methodologies extend topomer CoMFA by allowing user-designated templates, for example the experimental receptor-bound conformation of a prototypical ligand, to help determine the alignment of training and test set structures for 3D-QSAR. The algorithms that generate its new structural modality, template-constrained topomers, are described.

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Rethinking 3D-QSAR

The average error of pIC50 prediction reported for 140 structures in make-and-test applications of topomer CoMFA by four discovery organizations is 0.5. This remarkable accuracy can be understood to result from a topomer pose’s goal of generating field differences only at lattice intersections adjacent to intended structural change.

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Virtual screening for R-groups, including predicted pIC50 contributions, within large structural databases, using Topomer CoMFA

Multiple R-groups (monovalent fragments) are implicitly accessible within most of the molecular structures that populate large structural databases. R-group searching would desirably consider pIC50 contribution forecasts as well as ligand similarities or docking scores. However, R-group searching, with or without pIC50 forecasts, is currently not practical. The most prevalent and reliable source of pIC50 predictions, […]

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Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis

A novel procedure is proposed for 3D-QSAR analysis. The composition of 16 published QSAR datasets has been examined using Quantitative Series Enrichment Analysis (QSEA). The procedure is based on topomer technologies. A heatmap display in combination with topomer CoMFA and a novel series trajectory analysis revealed critical information for the assembly of structures into meaningful […]

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A structure-guided approach for protein pocket modeling and affinity prediction

Binding affinity prediction is frequently addressed using computational models constructed solely with molecular structure and activity data. We present a hybrid structure-guided strategy that combines molecular similarity, docking, and multiple-instance learning such that information from protein structures can be used to inform models of structure–activity relationships. The Surflex-QMOD approach has been shown to produce accurate […]

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Template CoMFA: The 3D-QSAR Grail?

Template CoMFA, a novel alignment methodology for training or test set structures in 3D-QSAR, is introduced. Its two most significant advantages are its complete automation and its ability to derive a single combined model from multiple structural series affecting a biological target. Its only two inputs are one or more “template” structures having 3D coordinates […]

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Angiotensin II pseudopeptides containing 1,3,5-trisubstituted benzene scaffolds with high AT2 receptor affinity

Two 1,3,5-trisubstituted aromatic scaffolds intended to serve as γ-turn mimetics have been synthesized and incorporated in five pseudopeptide analogues of angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe), replacing Val-Tyr-Ile, Val-Tyr, or Tyr-Ile. All the tested compounds exhibited nanomolar affinity for the AT2 receptor with the best compound (3) having a KI of 1.85 nM. Four pseudopeptides were AT2 selective, […]

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3D QSAR Studies on Substituted Benzimidazole Derivatives as Angiotensin II-AT1 Receptor Antagonist.

This study investigated 3D quantitative structure-activity relationships (QSAR) for a range of substituted benzimidazole derivatives as AngII-AT1 receptor antagonists by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices (CoMSIA). The alignment strategy was used for these compounds by means of Distill function defined in SYBYL X 1.2. The best CoMFA and CoMSIA models […]

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Binding Conformation of 2-Oxoamide Inhibitors to Group IVA Cytosolic Phospholipase A2 Determined by Molecular Docking Combined with Molecular Dynamics

The Group IVA cytosolic phospholipase A2 (GIVA cPLA2) plays a central role in inflammation. Long chain 2-oxoamides constitute a class of potent GIVA cPLA2 inhibitors that exhibit potent in vivo anti-inflammatory and analgesic activity. We have now gained insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA2 active site through a combination of […]

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