Monte-Carlo method-based QSAR model to discover phytochemical urease inhibitors using SMILES and GRAPH descriptors

We developed a Monte-Carlo method based QSAR model to predict urease inhibiting potency of molecules using SMILES and GRAPH descriptors on an existing diverse database of urease inhibitors. The QSAR model satisfies all the statistical parameters required for acceptance as a good model. The model is applied to identify urease inhibitors among the wide range of compounds in the phytochemical database, NPACT, as a test case. We combine the ligand-based and structure-based drug discovery methods to improve the accuracy of the prediction. The method predicts pIC50 and estimates docking score of compounds in the database. The method may be applied to any other database or compounds designed in silico to discover novel drugs targeting urease.

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Monte-Carlo Method Based QSAR Model to Discover Phytochemical Urease Inhibitors Using SMILES and GRAPH Descriptors

10.26434/chemrxiv.12948587.v1 ◽

2020 ◽

Author(s):

Kumar Sambhav Chopdar ◽

Ganesh Chandra Dash ◽

Pranab Kishor Mohapatra ◽

Binata Nayak ◽

Mukesh Kumar Raval

Keyword(s):

Monte Carlo ◽

Drug Discovery ◽

Monte Carlo Method ◽

In Silico ◽

Qsar Model ◽

Test Case ◽

Urease Inhibitors ◽

Statistical Parameters ◽

Novel Drugs ◽

Wide Range

We developed a Monte-Carlo method based QSAR model to predict urease inhibiting potency of molecules using SMILES and GRAPH descriptors on an existing diverse database of urease inhibitors. The QSAR model satisfies all the statistical parameters required for acceptance as a good model. The model is applied to identify urease inhibitors among the wide range of compounds in the phytochemical database, NPACT, as a test case. We combine the ligand-based and structure-based drug discovery methods to improve the accuracy of the prediction. The method predicts pIC50 and estimates docking score of compounds in the database. The method may be applied to any other database or compounds designed in silico to discover novel drugs targeting urease.

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Monte Carlo Method Based QSAR Studies of Mer Kinase Inhibitors in Compliance with OECD Principles

Drug Research ◽

10.1055/s-0043-119288 ◽

2017 ◽

Vol 68 (04) ◽

pp. 189-195 ◽

Cited By ~ 18

Author(s):

Parvin Kumar ◽

Ashwani Kumar

Keyword(s):

Monte Carlo ◽

Monte Carlo Method ◽

Kinase Inhibitors ◽

Structural Characteristics ◽

Predictive Ability ◽

Qsar Model ◽

Correlation Technique ◽

Qsar Studies ◽

Oecd Principles ◽

Qsar Models

AbstractMonte Carlo method based QSAR studies for inhibitors of Mer kinase, a potential novel target for cancer treatment, has been carried out using balance of correlation technique. The data was divided into three random and dissimilar splits and hybrid optimal descriptors derived from SMILES and hydrogen filled graphs based notations were used for construction of QSAR models. The generated models have good fitting ability, robustness, generalizability and internal predictive ability. The external predictive ability has been tested using multiple criteria and described models exhibited good performance in all of these tests. The values of R2, Q2, R2 test, Q2 test, R2 m and ∆R2 m for the best model are 0.9502, 0.9388, 0.9469, 0.9083, 0.7534 and 0.0894 respectively. Also, the structural characteristics responsible for enhancement and reduction of activity have been extracted. Further, the agreement with the OECD rules for QSAR model has been discussed.

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Building up a QSAR model for toxicity toward Tetrahymena pyriformis by the Monte Carlo method: A case of benzene derivatives

Environmental Toxicology and Pharmacology ◽

10.1016/j.etap.2016.01.010 ◽

2016 ◽

Vol 42 ◽

pp. 135-145 ◽

Cited By ~ 17

Author(s):

Alla P. Toropova ◽

Terry W. Schultz ◽

Andrey A. Toropov

Keyword(s):

Monte Carlo ◽

Monte Carlo Method ◽

Tetrahymena Pyriformis ◽

Qsar Model ◽

Benzene Derivatives ◽

The Monte Carlo Method

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Building up QSAR model for toxicity of psychotropic drugs by the Monte Carlo method

Structural Chemistry ◽

10.1007/s11224-013-0380-4 ◽

2013 ◽

Vol 25 (4) ◽

pp. 1067-1073 ◽

Cited By ~ 5

Author(s):

Andrea Gissi ◽

Andrey A. Toropov ◽

Alla P. Toropova ◽

Orazio Nicolotti ◽

Angelo Carotti ◽

...

Keyword(s):

Monte Carlo ◽

Monte Carlo Method ◽

Psychotropic Drugs ◽

Qsar Model ◽

The Monte Carlo Method

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Outbursts of comet Schwassmann-Wachmann 1, and the cloud of interplanetary boulders

International Astronomical Union Colloquium ◽

10.1017/s0252921100034035 ◽

1974 ◽

Vol 22 ◽

pp. 307 ◽

Cited By ~ 3

Author(s):

Zdenek Sekanina

Keyword(s):

Monte Carlo ◽

Monte Carlo Method ◽

Interplanetary Space ◽

Porous Matrix ◽

Maximum Diameter ◽

Expansion Velocity ◽

Solid Constituent ◽

Meteoric Material ◽

Periodic Comet

AbstractIt is suggested that the outbursts of Periodic Comet Schwassmann-Wachmann 1 are triggered by impacts of interplanetary boulders on the surface of the comet’s nucleus. The existence of a cloud of such boulders in interplanetary space was predicted by Harwit (1967). We have used the hypothesis to calculate the characteristics of the outbursts – such as their mean rate, optically important dimensions of ejected debris, expansion velocity of the ejecta, maximum diameter of the expanding cloud before it fades out, and the magnitude of the accompanying orbital impulse – and found them reasonably consistent with observations, if the solid constituent of the comet is assumed in the form of a porous matrix of lowstrength meteoric material. A Monte Carlo method was applied to simulate the distributions of impacts, their directions and impact velocities.

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Structures and crystallization of vacuum-deposited amorphous Se and Sb films

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100173832 ◽

1990 ◽

Vol 48 (4) ◽

pp. 140-141

Author(s):

Makoto Shiojiri ◽

Toshiyuki Isshiki ◽

Tetsuya Fudaba ◽

Yoshihiro Hirota

Keyword(s):

Monte Carlo ◽

Electron Microscope ◽

Monte Carlo Method ◽

Computer Program ◽

Radial Distribution ◽

Film Formation ◽

Amorphous State ◽

Two Dimensional ◽

Amorphous Films ◽

Binding Condition

In hexagonal Se crystal each atom is covalently bound to two others to form an endless spiral chain, and in Sb crystal each atom to three others to form an extended puckered sheet. Such chains and sheets may be regarded as one- and two- dimensional molecules, respectively. In this paper we investigate the structures in amorphous state of these elements and the crystallization.HRTEM and ED images of vacuum-deposited amorphous Se and Sb films were taken with a JEM-200CX electron microscope (Cs=1.2 mm). The structure models of amorphous films were constructed on a computer by Monte Carlo method. Generated atoms were subsequently deposited on a space of 2 nm×2 nm as they fulfiled the binding condition, to form a film 5 nm thick (Fig. 1a-1c). An improvement on a previous computer program has been made as to realize the actual film formation. Radial distribution fuction (RDF) curves, ED intensities and HRTEM images for the constructed structure models were calculated, and compared with the observed ones.

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