Faster Algorithms for Isomer Network Generation

Thiagarajan, Dheivya; Mehta, Dinesh P.

doi:10.1021/acs.jcim.6b00128

Cited by 6 publications

(7 citation statements)

References 16 publications

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“…Isomer enumeration is a long-standing problem that is still under scrutiny [ 24 , 25 ]. Our intent here is not to provide the fastest enumeration algorithm but to demonstrate how RetroPath2.0 can perform that job once appropriate reaction rules are provided.…”

Section: Resultsmentioning

confidence: 99%

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Koch¹,

Duigou²,

Carbonell³

et al. 2017

J Cheminform

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Background: Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for. Results:Here, we showcase the use of the open source workflow RetroPath2.0. First, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. We then use this enumeration strategy to screen the chemical space around a set of monomers and predict their glass transition temperatures, as well as around aminoglycosides to search structures maximizing antibacterial activity. We also perform a screening around aminoglycosides with enzymatic reaction rules to ensure biosynthetic accessibility. We finally use our workflow on an E. coli model to complete E. coli metabolome, with novel molecules generated using promiscuous enzymatic reaction rules. These novel molecules are searched on the MS spectra of an E. coli cell lysate interfacing our workflow with OpenMS through the KNIME Analytics Platform. Conclusion:We provide an easy to use and modify, modular, and open-source workflow. We demonstrate its versatility through a variety of use cases including molecular structure enumeration, virtual screening in the chemical space, and metabolome completion. Because it is open source and freely available on MyExperiment.org, workflow community contributions should likely expand further the features of the tool, even beyond the use cases presented in the paper.

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Section: Resultsmentioning

confidence: 99%

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Koch¹,

Duigou²,

Carbonell³

et al. 2017

J Cheminform

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“…These results might be attributed to the similar structures of the two salt forms. The similar crystal structures and the comparable solubility property might suggest resembling biological activities of Sor.HCl and Reg.HCl [42].…”

Section: Discussionmentioning

confidence: 99%

Isomorphous Crystals Formed by the Similar Supramolecular Motifs in Sorafenib Hydrochloride and Regorafenib Hydrochloride Salts

et al. 2019

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Sorafenib and regorafenib (or fluoro-sorafenib) are multikinase inhibitors active in the treatment of various human cancers, but their solubilities are very poor. To improve their solubilities, in this study, sorafenib hydrochloride (Sor·HCl, I) and regorafenib hydrochloride (Reg·HCl, II) have been prepared and their crystal structures were characterized. Their solubility properties in water were evaluated. Intriguingly, they are isomorphous crystal structures with the same space group and the similar unit cell dimensions, which were caused by the similar supramolecular patterns resulted by the formation of N–H···Cl− hydrogen bond instead of hydrogen bond between the protonated pyridinium cation and counterion. Moreover, the solubility properties displayed identical profiles. It may be concluded that a similar crystal structure leads to a comparable solubility profile.

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“…Figure 2 Mathematica code used to generate tuples for substitution of benzene. A total of 5 6 or 15625 tuples were generated for halo-substituted benzenes. Duplicate entries are underlined using the same color.…”

Section: Generation Of Tuples For Substitution Sitesmentioning

confidence: 99%

“…Initial structures (Z-matrix or Cartesian coordinate) are important starting points for the in silico investigation of chemical species. Robust and exhaustive processes to generate chemical structures have been described previously in different contexts [1][2][3][4][5][6][7][8][9]. However, there are still no consistent onesize-fits-all standard for structural enumeration.…”

Section: Introductionmentioning

confidence: 99%

Z-Matrix template-based substitution approach for enumeration of 3D molecular structures

Lorpaiboon¹,

Limpanuparb

2021

Preprint

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The exhaustive enumeration of 3D chemical structures based on Z-matrix templates has recently been used in the quantum chemical investigation of constitutional isomers, diastereomers and rotamers. This simple yet powerful initial structure generation approach can apply beyond the investigation of compounds of identical formula by quantum chemical methods. This paper aims to provide a short description of the overall concept followed by a practical tutorial to the approach. · - The four steps required for Z-matrix template-based substitution are template construction, generation of tuples for substitution sites, removal of duplicate tuples and substitution on the template. · -The generated tuples can be used to create chemical identifiers to query compound properties from chemical databases. · - All of these steps are demonstrated in this paper by common model compounds and are very straightforward for an undergraduate audience to reproduce. A comparison of the approach in this tutorial and other options is also discussed.

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Faster Algorithms for Isomer Network Generation

Cited by 6 publications

References 16 publications

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Isomorphous Crystals Formed by the Similar Supramolecular Motifs in Sorafenib Hydrochloride and Regorafenib Hydrochloride Salts

Z-Matrix template-based substitution approach for enumeration of 3D molecular structures

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