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Ouabane M, Zaki K, Tabti K, Alaqarbeh M, Sbai A, Sekkate C, Bouachrine M, Lakhlifi T. Molecular toxicity of nitrobenzene derivatives to tetrahymena pyriformis based on SMILES descriptors using Monte Carlo, docking, and MD simulations. Comput Biol Med 2024; 169:107880. [PMID: 38211383 DOI: 10.1016/j.compbiomed.2023.107880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
It is challenging to model the toxicity of nitroaromatic compounds due to limited experimental data. Nitrobenzene derivatives are commonly used in industry and can lead to environmental contamination. Extensive research, including several QSPR studies, has been conducted to understand their toxicity. Predictive QSPR models can help improve chemical safety, but their limitations must be considered, and the molecular factors affecting toxicity should be carefully investigated. The latest QSPR methods, molecular modeling techniques, machine learning algorithms, and computational chemistry tools are essential for developing accurate and robust models. In this work, we used these methods to study a series of fifty compounds derived from nitrobenzene. The Monte Carlo approach was used for QSPR modeling by applying the SMILES molecular structure representation and optimal molecular descriptors. The correlation ideality index (CII) and correlation contradiction index (CCI) were further introduced as validation parameters to estimate the developed models' predictive ability. The statistical quality of the CII models was better than those without CII. The best QSPR model with the following statistical parameters (Split-3): (R2 = 0.968, CCC = 0.984, IIC = 0.861, CII = 0.979, Q2 = 0.954, QF12 = 0.946, QF22 = 0.938, QF32 = 0.947, Rm2 = 0.878, RMSE = 0.187, MAE = 0.151, FTraining = 390, FInvisible = 218, FCalibration = 240, RTest2 = 0.905) was selected to generate the studied promoters with increasing and decreasing activity.
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Affiliation(s)
- Mohamed Ouabane
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco; Chemistry-Biology Applied to the Environment URL CNRT 13, Chemistry Department, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Khadija Zaki
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Marwa Alaqarbeh
- Basic Science Department, Prince Al Hussein Bin Abdullah II Academy for Civil Protection, Al-Balqa Applied University, Al-Salt, 19117, Jordan
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Chakib Sekkate
- Chemistry-Biology Applied to the Environment URL CNRT 13, Chemistry Department, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco; Higher School of Technology-Khenifra (EST-Khenifra), University of Sultan Moulay Slimane, PB 170, Khenifra, 54000, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco.
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Prakash Nirmal N, Singh Rajput M, Bhojraj Rathod N, Mudgil P, Pati S, Bono G, Nalinanon S, Li L, Maqsood S. Structural characteristic and molecular docking simulation of fish protein-derived peptides: Recent updates on antioxidant, anti-hypertensive and anti-diabetic peptides. Food Chem 2023; 405:134737. [DOI: 10.1016/j.foodchem.2022.134737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/30/2022] [Accepted: 10/22/2022] [Indexed: 11/25/2022]
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Achary PGR, Toropova AP, Toropov AA. Prediction of the self‐accelerating decomposition temperature of organic peroxides. PROCESS SAFETY PROGRESS 2020. [DOI: 10.1002/prs.12189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Patnala Ganga Raju Achary
- Department of Chemistry Institute of Technical Education and Research (ITER), Siksha 'O' Anusandhan deemed to be University Bhubaneswar Odisha India
| | - Alla P. Toropova
- Department of Environmental Health Science, Laboratory of Environmental Chemistry and Toxicology Istituto di Ricerche Farmacologiche Mario Negri IRCCS Milan Italy
| | - Andrey A. Toropov
- Department of Environmental Health Science, Laboratory of Environmental Chemistry and Toxicology Istituto di Ricerche Farmacologiche Mario Negri IRCCS Milan Italy
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Toropova AP, Toropov AA. Application of the Monte Carlo Method for the Prediction of Behavior of Peptides. Curr Protein Pept Sci 2019; 20:1151-1157. [DOI: 10.2174/1389203720666190123163907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022]
Abstract
Prediction of physicochemical and biochemical behavior of peptides is an important and attractive
task of the modern natural sciences, since these substances have a key role in life processes. The
Monte Carlo technique is a possible way to solve the above task. The Monte Carlo method is a tool with
different applications relative to the study of peptides: (i) analysis of the 3D configurations (conformers);
(ii) establishment of quantitative structure – property / activity relationships (QSPRs/QSARs); and (iii)
development of databases on the biopolymers. Current ideas related to application of the Monte Carlo
technique for studying peptides and biopolymers have been discussed in this review.
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Affiliation(s)
- Alla P. Toropova
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milano, Italy
| | - Andrey A. Toropov
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milano, Italy
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Hare SR, Bratholm LA, Glowacki DR, Carpenter BK. Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices. Chem Sci 2019; 10:9954-9968. [PMID: 32055352 PMCID: PMC6991188 DOI: 10.1039/c9sc02742d] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/23/2019] [Indexed: 01/22/2023] Open
Abstract
Most chemical transformations (reactions or conformational changes) that are of interest to researchers have many degrees of freedom, usually too many to visualize without reducing the dimensionality of the system to include only the most important atomic motions. In this article, we describe a method of using Principal Component Analysis (PCA) for analyzing a series of molecular geometries (e.g., a reaction pathway or molecular dynamics trajectory) and determining the reduced dimensional space that captures the most structural variance in the fewest dimensions. The software written to carry out this method is called PathReducer, which permits (1) visualizing the geometries in a reduced dimensional space, (2) determining the axes that make up the reduced dimensional space, and (3) projecting the series of geometries into the low-dimensional space for visualization. We investigated two options to represent molecular structures within PathReducer: aligned Cartesian coordinates and matrices of interatomic distances. We found that interatomic distance matrices better captured non-linear motions in a smaller number of dimensions. To demonstrate the utility of PathReducer, we have carried out a number of applications where we have projected molecular dynamics trajectories into a reduced dimensional space defined by an intrinsic reaction coordinate. The visualizations provided by this analysis show that dynamic paths can differ greatly from the minimum energy pathway on a potential energy surface. Viewing intrinsic reaction coordinates and trajectories in this way provides a quick way to gather qualitative information about the pathways trajectories take relative to a minimum energy path. Given that the outputs from PCA are linear combinations of the input molecular structure coordinates (i.e., Cartesian coordinates or interatomic distances), they can be easily transferred to other types of calculations that require the definition of a reduced dimensional space (e.g., biased molecular dynamics simulations).
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Affiliation(s)
- Stephanie R Hare
- University of Bristol School of Chemistry , Cantock's Close , Bristol , UK BS8 1TS
- University of Bristol School of Mathematics , University Walk , Bristol , UK BS8 1TW
| | - Lars A Bratholm
- University of Bristol School of Chemistry , Cantock's Close , Bristol , UK BS8 1TS
- University of Bristol School of Mathematics , University Walk , Bristol , UK BS8 1TW
| | - David R Glowacki
- University of Bristol School of Chemistry , Cantock's Close , Bristol , UK BS8 1TS
- University of Bristol School of Computer Science , Merchant Venturers Building, Woodland Road , Bristol , UK BS8 1UB
| | - Barry K Carpenter
- Cardiff University School of Chemistry , Main Building, Park Place , Cardiff , UK CF10 3AT .
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Quantitative sequence-activity modeling of ACE peptide originated from milk using ACC-QTMS amino acid indices. Amino Acids 2019; 51:1209-1220. [PMID: 31321559 DOI: 10.1007/s00726-019-02761-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/05/2019] [Indexed: 01/06/2023]
Abstract
Up to now, numerous peptides/hydrolysates derived from casein and whey protein have shown angiotensin-I-converting enzyme (ACE) inhibitory. In this research, quantum topological molecular similarity (QTMS) indices of amino acids were utilized in quantitative sequence-activity modeling (QSAM) to predict the activity of a set of milk-driven peptides with ACE inhibition. Since the derived peptides have not the same number of residues, we overcame this issue by auto cross covariance (ACC) methodology. Then, some QSAMs were built to predict the pIC50 value of ACE peptides derived from Bovine Casein and Whey. The model established an acceptable relationship between the selected variables and the pIC50 of the peptides. To estimate the performance of the developed models, casein and whey proteins from human, goat, bovine and sheep were virtually broken by trypsin and chymotrypsin enzymes and the ACE activity of the resultant virtual peptides were predicted and some new ACE peptides were proposed.
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Variable selection in multivariate calibration based on clustering of variable concept. Anal Chim Acta 2015; 902:70-81. [PMID: 26703255 DOI: 10.1016/j.aca.2015.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/31/2015] [Accepted: 11/04/2015] [Indexed: 11/22/2022]
Abstract
Recently we have proposed a new variable selection algorithm, based on clustering of variable concept (CLoVA) in classification problem. With the same idea, this new concept has been applied to a regression problem and then the obtained results have been compared with conventional variable selection strategies for PLS. The basic idea behind the clustering of variable is that, the instrument channels are clustered into different clusters via clustering algorithms. Then, the spectral data of each cluster are subjected to PLS regression. Different real data sets (Cargill corn, Biscuit dough, ACE QSAR, Soy, and Tablet) have been used to evaluate the influence of the clustering of variables on the prediction performances of PLS. Almost in the all cases, the statistical parameter especially in prediction error shows the superiority of CLoVA-PLS respect to other variable selection strategies. Finally the synergy clustering of variable (sCLoVA-PLS), which is used the combination of cluster, has been proposed as an efficient and modification of CLoVA algorithm. The obtained statistical parameter indicates that variable clustering can split useful part from redundant ones, and then based on informative cluster; stable model can be reached.
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Quantitative sequence–activity modeling of antimicrobial hexapeptides using a segmented principal component strategy: an approach to describe and predict activities of peptide drugs containing l/d and unnatural residues. Amino Acids 2014; 47:125-34. [DOI: 10.1007/s00726-014-1850-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/03/2014] [Indexed: 12/20/2022]
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Dai Z, Wang L, Chen Y, Wang H, Bai L, Yuan Z. A pipeline for improved QSAR analysis of peptides: physiochemical property parameter selection via BMSF, near-neighbor sample selection via semivariogram, and weighted SVR regression and prediction. Amino Acids 2014; 46:1105-19. [PMID: 24468929 DOI: 10.1007/s00726-014-1667-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/03/2014] [Indexed: 12/21/2022]
Abstract
In this paper, we present a pipeline to perform improved QSAR analysis of peptides. The modeling involves a double selection procedure that first performs feature selection and then conducts sample selection before the final regression analysis. Five hundred and thirty-one physicochemical property parameters of amino acids were used as descriptors to characterize the structure of peptides. These high-dimensional descriptors then go through a feature selection process given by the binary matrix shuffling filter (BMSF) to obtain a set of important low-dimensional features. Each descriptor that passes the BMSF filtering also receives a weight defined through its contribution to reduce the estimation error. These selected features served as the predictors for subsequent sample selection and modeling. Based on the weighted Euclidean distances between samples, a common range was determined with high-dimensional semivariogram and then used as a threshold to select the near-neighbor samples from the training set. For each sample to be predicted, the QSAR model was established using SVR with the weighted, selected features based on the exclusive set of near-neighbor training samples. Prediction was conducted for each test sample accordingly. The performances of this pipeline are tested with the QSAR analysis of angiotensin-converting enzyme inhibitors and HLA-A*0201 data sets. Improved prediction accuracy was obtained in both applications. This pipeline can optimize the QSAR modeling from both the feature selection and sample selection perspectives. This leads to improved accuracy over single selection methods. We expect this pipeline to have extensive application prospect in the field of regression prediction.
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Affiliation(s)
- Zhijun Dai
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Changsha, China,
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