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).

Кузьмин, В. Е.; Artemenko, Anatoly G.; Lozitsky, V.; Muratov, Eugene; Fedtchouk, Alla S.; Dyachenko, Natalia S.; Nosach, L N; Gridina, T.; Shitikova, Larisa I.; Mudrik, Liubov M.; Mescheriakov, Aleksey K.; Chelombitko, V. A.; Zheltvay, A. I.; Eynde, Jean Jacques Vanden

doi:10.18388/abp.2002_3832

Cited by 36 publications

(16 citation statements)

References 9 publications

(12 reference statements)

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“…The efficiency of this technique can be easily explained by the fact that nearly the same predictions obtained by different and independent methods (either statistical and descriptors generation) are more reliable than singular prediction made by even the best fitted and predictable model. Therefore, to increase "structure-property" relationships adequacy we used PLS method, also known as projection to latent structures method [20], which was successfully applied for solving of a great number of QSAR/QSPR tasks, for example [21][22][23][24][25][26]. Quality of "structure-property" relationships obtained by this method is noticeably higher, than for MLR models.…”

Section: Resultsmentioning

confidence: 99%

QSPR Analysis of Peroxidase Substrates Reactivity

Romanovskaya¹,

Кузьмин²,

Oseychuk³

et al. 2009

ChChT

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Quantitative structure-property relationship (QSPR) analysis of phenol derivatives reactivity in the horseradish peroxidase catalyzed oxidative reactions was carried out. The statistic models, which describe the substituted phenols reactivity (Кm-1, Vmax) quite adequately, were obtained by multiple linear regression and partial least squares (PLS) methods. The electronic parameters of molecules, their lipophylicity, molecular refraction, and form parameters were used as descriptors for molecular structure. The obtained models allow to predict the reactivity of the new phenolic substrates with satisfactory reliability.

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Section: Resultsmentioning

confidence: 99%

QSPR Analysis of Peroxidase Substrates Reactivity

Romanovskaya¹,

Кузьмин²,

Oseychuk³

et al. 2009

ChChT

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show abstract

“…A novel 4D-QSAR approach based on the simplex representation of molecular structures (SiRMS) has been implemented in order to overcome the superimposition ambiguity for non-congeneric (heterogeneous) set of compounds—in this case the topological representation is not a limitation [ 74 ]. Structural topography (topology and stereochemical configuration) is encoded by a system of different simplexes defined as (un)bounded ‘tetraatomic fragments of fixed constitution, chirality and symmetry’ [ 75 ]. The overall number

of all available simplexes for M -atomic structure is specified according to

formula.…”

Section: 4d-qsar Dialects: Towards ‘Magic Bullet’mentioning

confidence: 99%

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

Bąk

2021

IJMS

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A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.

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“…Our first work [ 14 ] that used simplex descriptors in QSAR studies of antiviral and antitumor activity was published in 2002. Based on 3D simplexes, 4D-QSAR models were built for 63 compounds, including macrocyclic pyridinophanes and their acyclic analogs, synthetic nucleosides, and a number of well-known antiviral drugs (ambenum, deiteforin, etc.).…”

Section: Qsar Models Based On Simplex Descriptorsmentioning

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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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).

Cited by 36 publications

References 9 publications

QSPR Analysis of Peroxidase Substrates Reactivity

QSPR Analysis of Peroxidase Substrates Reactivity

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

Simplex representation of molecular structure as universal QSAR/QSPR tool

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