Stereochemical analysis by simplex representation of molecules

Кузьмин, В. Е.; Chelombitko, V. A.; Yudanova, I. V.; Stel'makh, I. B.; Rublev, I. S.

doi:10.1007/bf02873658

Cited by 3 publications

(3 citation statements)

References 1 publication

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“…Therefore, to describe the SC, it is enough to use mutually unbound simplexes, which make up shorter sequences. The corresponding procedure is described below based on a simple example already mentioned [ 7 ].…”

Section: The Methodology Of Sirmsmentioning

confidence: 99%

Simplex representation of molecular structure as universal QSAR/QSPR tool

et al. 2021

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We review the development and application of the Simplex approach for the solution of various QSAR/QSPR problems. The general concept of the simplex method and its varieties are described. The advantages of utilizing this methodology, especially for the interpretation of QSAR/QSPR models, are presented in comparison to other fragmentary methods of molecular structure representation. The utility of SiRMS is demonstrated not only in the standard QSAR/QSPR applications, but also for mixtures, polymers, materials, and other complex systems. In addition to many different types of biological activity (antiviral, antimicrobial, antitumor, psychotropic, analgesic, etc.), toxicity and bioavailability, the review examines the simulation of important properties, such as water solubility, lipophilicity, as well as luminescence, and thermodynamic properties (melting and boiling temperatures, critical parameters, etc.). This review focuses on the stereochemical description of molecules within the simplex approach and details the possibilities of universal molecular stereo-analysis and stereochemical configuration description, along with stereo-isomerization mechanism and molecular fragment “topography” identification.

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Section: The Methodology Of Sirmsmentioning

confidence: 99%

Simplex representation of molecular structure as universal QSAR/QSPR tool

et al. 2021

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“…The simplex representation of molecular structure for biologically active substances allows unifying the description of spatial structure of compounds with saving of the complete stereochemical information [11][12][13]. It enables to determine easily common fragments of spatial structure both promoting given biological activity and interfering with it.…”

Section: D Qsar Approach Based On Simplex Representation Of Moleculmentioning

confidence: 99%

The analysis of structure-anticancer and antiviral activity relationships for macrocyclic pyridinophanes and their analogues on the basis of 4D QSAR models (simplex representation of molecular structure).

et al. 2002

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A new 4D-QSAR approach has been considered. For all investigated molecules the 3D structural models have been created and the set of conformers (fourth dimension) have been used. Each conformer is represented as a system of different simplexes (tetratomic fragments of fixed structure, chirality and symmetry).The investigation of influence of molecular structure of macrocyclic pyridinophanes, their analogues and certain other compounds on anticancer and antiviral (anti-influenza, antiherpes and antiadenovirus) activity has been carried out by means of the 4D-QSAR. Statistic characteristics for QSAR of PLS (partial least squares) models are satisfactory (R = 0.92-0.97; CVR = 0.

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“…Thus, HiT QSAR has been selected as a main research tool used in this work. Also, the Simplex representation of molecular structure that serves as a foundation of HiT QSAR has been originally developed as the method for stereochemical analysis and design of chemical structures [31]. Only later SiRMS has been successfully used as promising QSAR technique [9,13,14,32,33].…”

Section: Introductionmentioning

confidence: 99%

Consensus QSAR Modeling of Phosphor‐Containing Chiral AChE Inhibitors

et al. 2009

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In this article the Hierarchical QSAR technology (HiT QSAR) has been used for consensus QSAR modeling of Acetylcholinesterase (AChE) inhibition by various organophosphate compounds. Simplex representation of molecular structure (SiRMS) and Lattice model (LM) QSAR approaches have been used for descriptors generation. Statistical models have been obtained by partial least squares (PLS) method. Various chiral organophosphates represented by their (R)-and (S)-isomers, racemic mixtures and achiral structures have been investigated. Successful consensus model (R 2 ¼ 0.978) based on fourteen best QSAR models obtained using different QSAR approaches and training sets for several levels and methods of molecular structure representation (2.5D, double 2.5D, and 3D) has been used for the prediction of AChE inhibition of new compounds. In order to avoid chance correlations 1000 rounds of Y-scrambling were performed for each selected model. Leverage and ellipsoid Applicability domain (DA) approaches have been used for additional estimation of the quality of prognosis. Molecular fragments enhancing and interfering with inhibitory activity have been determined. It was revealed that atoms individuality and stereochemistry of chiral surroundings of the asymmetric atom of phosphorus play a vital role in AChE inhibition. Thus, (R)-isomers are always less active than the (S) isomers and the racemate. HiT QSAR proves to be a powerful tool for investigation of activity of stereo selective interactions and can be used in such subsequent studies.

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Stereochemical analysis by simplex representation of molecules

Cited by 3 publications

References 1 publication

Simplex representation of molecular structure as universal QSAR/QSPR tool

Simplex representation of molecular structure as universal QSAR/QSPR tool

The analysis of structure-anticancer and antiviral activity relationships for macrocyclic pyridinophanes and their analogues on the basis of 4D QSAR models (simplex representation of molecular structure).

Consensus QSAR Modeling of Phosphor‐Containing Chiral AChE Inhibitors

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