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First report on pesticide sub-chronic and chronic toxicities against dogs using QSAR and chemical read-across SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-23 A. Kumar, P.K. Ojha, K. Roy
Excessive use of chemicals is the outcome of the industrialization of agricultural sectors which leads to disturbance of ecological balance. Various agrochemicals are widely used in agricultural fi...
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Quantitative structure-property relationship modelling on autoignition temperature: evaluation and comparative analysis SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-19 J. Chen, L. Zhu, J. Wang
The autoignition temperature (AIT) serves as a crucial indicator for assessing the potential hazards associated with a chemical substance. In order to gain deeper insights into model performance an...
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Ligand and structure-based discovery of phosphorus-containing compounds as potential metalloproteinase inhibitors SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-21 Y. Cañizares-Carmenate, Y. Perera-Sardiña, Y. Marrero-Ponce, R. Díaz-Amador, F. Torrens, J.A. Castillo-Garit
In this study, a methodology is proposed, combining ligand- and structure-based virtual screening tools, for the identification of phosphorus-containing compounds as inhibitors of zinc metalloprote...
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Docking and other computing tools in drug design against SARS-CoV-2 SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-14 A.V. Sulimov, I.S. Ilin, A.S. Tashchilova, O.A. Kondakova, D.C. Kutov, V.B. Sulimov
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular ...
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Exploring crucial structural attributes of quinolinyl methoxyphenyl sulphonyl-based hydroxamate derivatives as ADAM17 inhibitors through classification-dependent molecular modelling approaches SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-12 T.B. Samoi, S. Banerjee, B. Ghosh, T. Jha, N. Adhikari
A Disintegrin and Metalloproteinase 17 (ADAM17), a Zn2+-dependent metalloenzyme of the adamalysin family of the metzincin superfamily, is associated with various pathophysiological conditions inclu...
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Development of terpenoid repellents against Aedes albopictus: a combined study of biological activity evaluation and computational modelling SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-07 J. Wang, X. Feng, W. Yuan, J. Zhang, S. Zhu, L. Xu, H. Li, J. Song, X. Rao, S. Liao, Z. Wang, H. Si
To explore novel terpenoid repellents, 22 candidate terpenoid derivatives were synthesized and tested for their electroantennogram (EAG) responses and repellent activities against Aedes albopictus....
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Correction SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-06
Published in SAR and QSAR in Environmental Research (Vol. 35, No. 2, 2024)
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Development of a standardized methodology for transfer learning with QSAR models: a purely data-driven approach for source task selection SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-05 L. Melo, L. Scotti, M.T. Scotti
Transfer learning is a machine learning technique that works well with chemical endpoints, with several papers confirming its efficiency. Although effective, because the choice of source/assistant ...
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Steroidal hydrazones as antimicrobial agents: biological evaluation and molecular docking studies SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-02-05 M. Merlani, N. Nadaraia, N. Barbakadze, L. Amiranashvili, M. Kakhabrishvili, A. Petrou, T. Carević, J. Glamočlija, A. Geronikaki
Most of pharmaceutical agents display several or even many biological activities. It is obvious that testing even one compound for thousands of biological activities is a practically not reasonable...
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Ligand-based virtual screening and biological evaluation of inhibitors of Mycobacterium tuberculosis H37Rv SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-01-29 P.V. Pogodin, E.G. Salina, V.V. Semenov, M.M. Raihstat, D.S. Druzhilovskiy, D.A. Filimonov, V.V. Poroikov
Novel antimycobacterial compounds are needed to expand the existing toolbox of therapeutic agents, which sometimes fail to be effective. In our study we extracted, filtered, and aggregated the dive...
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Descriptor generation from Morgan fingerprint using persistent homology SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-01-29 T. Ehiro
In cheminformatics, molecular fingerprints (FPs) are used in various tasks such as regression and classification. However, predictive models often underutilize Morgan FP for regression and related ...
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q-RASTR modelling for prediction of diverse toxic chemicals towards T. pyriformis SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-01-29 V. Ghosh, A. Bhattacharjee, A. Kumar, P.K. Ojha
A series of diverse organic compounds impose serious detrimental effects on the health of living organisms and the environment. Determination of the structural aspects of compounds that impart toxi...
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BC CLC-Pred: a freely available web-application for quantitative and qualitative predictions of substance cytotoxicity in relation to human breast cancer cell lines SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2024-01-29 A.A. Lagunin, A.S. Sezganova, E.S. Muraviova, A.V. Rudik, D.A. Filimonov
In silico prediction of cell line cytotoxicity considerably decreases time and financial costs during drug development of new antineoplastic agents. (Q)SAR models for the prediction of drug-like co...
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Evaluation of QSAR models for predicting mutagenicity: outcome of the Second Ames/QSAR international challenge project SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-12-04 A. Furuhama, A. Kitazawa, J. Yao, C.E. Matos dos Santos, J. Rathman, C. Yang, J.V. Ribeiro, K. Cross, G. Myatt, G. Raitano, E. Benfenati, N. Jeliazkova, R. Saiakhov, S. Chakravarti, R.S. Foster, C. Bossa, C. Laura Battistelli, R. Benigni, T. Sawada, H. Wasada, T. Hashimoto, M. Wu, R. Barzilay, P.R. Daga, R.D. Clark, J. Mestres, A. Montero, E. Gregori-Puigjané, P. Petkov, H. Ivanova, O. Mekenyan, S
Quantitative structure−activity relationship (QSAR) models are powerful in silico tools for predicting the mutagenicity of unstable compounds, impurities and metabolites that are difficult to exami...
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Exploring marine-derived compounds for MET signalling pathway inhibition in cancer: integrating virtual screening, ADME profiling and molecular dynamics investigations SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-12-04 A.A. Alzain, F.A. Elbadwi, S.G.A. Mohamed, K.S.A. Kushk, R.I. Bafarhan, S.A. Alswiri, S.N. Khushaim, H.G.A. Hussein, M.Y.A. Abuhajras, G.A. Mohamed, S.R.M. Ibrahim
The MET signalling pathway regulates fundamental cellular processes such as growth, division, and survival. While essential for normal cell function, dysregulation of this pathway can contribute to...
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Prioritizing pharmaceutically active compounds (PhACs) based on occurrence-persistency-mobility-toxicity (OPMT) criteria: an application to the Brazilian scenario SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-12-04 V. Roveri, L. Lopes Guimarães, A.T. Correia
A study of Quantitative Structure Activity Relationship (QSAR) was performed to assess the possible adverse effects of 25 pharmaceuticals commonly found in the Brazilian water compartments and to e...
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Computational explorations of the interaction between laccase and bisphenol A: influence of surfactant and different organic solvents SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-12-04 Y. Li, L. Chen, J. Li, B. Zhao, T. Jing, R. Wang
Bisphenol A (BPA), as an environmental endocrine disruptor can cause damage to the reproductive, nervous and immune systems. Laccase can be used to degrade BPA. However, laccase is easily deactivat...
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QSAR assessment of aquatic toxicity potential of diverse agrochemicals SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-21 A. Nath, P.K. Ojha, K. Roy
The fast-increasing number of commercially produced chemicals challenges the experimental ecotoxicity assessment methods, which are costly, time-consuming, and dependent on the sacrifice of animals...
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Metrics for estimating vapour pressure deviation from ideality in binary mixtures SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-21 A.K.D. Celsie, J.M. Parnis, T.N. Brown
A novel method is introduced for estimating the degree of interactions occurring between two different compounds in a binary mixture resulting in deviations from ideality as predicted by Raoult’s l...
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Exploring molecular interactions of potential inhibitors against the spleen tyrosine kinase implicated in autoimmune disorders via virtual screening and molecular dynamics simulations SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-21 S. Samanta, M.F. Sk, S. Koirala, P. Kar
The spleen tyrosine kinase (Syk) plays a pivotal role in immune cells’ signal transduction mechanism. While fostamatinib, an FDA-approved Syk inhibitor, is currently used to treat immune thrombocyt...
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Discovery of dual-target natural inhibitors of meprins α and β metalloproteases for inflammation regulation: pharmacophore modelling, molecular docking, ADME prediction, and molecular dynamics studies SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-21 L. Eltaib, A.A. Alzain
Meprins, zinc-dependent metalloproteinases belonging to the metzincin family, have been associated with various inflammatory diseases due to their abnormal expression and activity. In this study, w...
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Quantitative structure-property relationship modelling for predicting retention indices of essential oils based on an improved horse herd optimization algorithm SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-03 A.M. Alharthi, D.H. Kadir, A.M. Al-Fakih, Z.Y. Algamal, N.A. Al-Thanoon, M.K. Qasim
The horse herd optimization algorithm (HOA), one of the more contemporary metaheuristic algorithms, has demonstrated superior performance in a number of challenging optimization tasks. In the prese...
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Priority list of potential endocrine-disrupting chemicals in food chemical contaminants: a docking study and in vitro/epidemiological evidence integration SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-03 J. Ren, T. Jin, R. Li, Y.Y. Zhong, Y.X. Xuan, Y.L. Wang, W. Yao, S.L. Yu, J.T. Yuan
Diet is an important exposure route of endocrine-disrupting chemicals (EDCs), but many unfiltered potential EDCs remain in food. The in silico prediction of EDCs is a popular method for preliminary...
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Correction SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-03
Published in SAR and QSAR in Environmental Research (Vol. 34, No. 10, 2023)
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Assessing structural insights into in-house arylsulfonyl L-(+) glutamine MMP-2 inhibitors as promising anticancer agents through structure-based computational modelling approaches SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-03 S.K. Baidya, S. Banerjee, B. Ghosh, T. Jha, N. Adhikari
MMP-2 is potentially contributing to several cancer progressions including leukaemias. Therefore, considering MMP-2 as a promising target, novel anticancer compounds may be designed. Here, 32 in-ho...
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Modelling enzyme inhibition toxicity of ionic liquid from molecular structure via convolutional neural network model SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-11-03 R. Zhang, Y. Chen, D. Fan, T. Liu, Z. Ma, Y. Dai, Y. Wang, Z. Zhu
Deep learning (DL) methods further promote the development of quantitative structure–activity/property relationship (QSAR/QSPR) models by dealing with complex relationships between data. An acetylc...
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QSPR models to predict the physical hazards of mixtures: a state of art SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-09-14 G. Fayet, P. Rotureau
ABSTRACT Physical hazards of chemical mixtures, associated for example with their fire or explosion risks, are generally characterized using experimental tools. These tests can be expensive, complex, long to perform and even dangerous for operators. Therefore, for several years and especially with the implementation of the REACH regulation, predictive methods like quantitative structure-property relationships
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Exploring the Traditional Chinese Medicine (TCM) database chemical space to target I7L protease from monkeypox virus using molecular screening and simulation approaches SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-09-07 A. Khan, M. Shahab, F. Nasir, Y. Waheed, A. Alshammari, A. Mohammad, G. Zichen, R. Li, D.Q. Wei
ABSTRACT In the current study, we used molecular screening and simulation approaches to target I7L protease from monkeypox virus (mpox) from the Traditional Chinese Medicines (TCM) database. Using molecular screening, only four hits TCM27763, TCM33057, TCM34450 and TCM31564 demonstrated better pharmacological potential than TTP6171 (control). Binding of these molecules targeted Trp168, Asn171, Arg196
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Optimal selection of learning data for highly accurate QSAR prediction of chemical biodegradability: a machine learning-based approach SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-09-07 K. Takeda, K. Takeuchi, Y. Sakuratani, K. Kimbara
ABSTRACT Prior to the manufacture of new chemicals, regulations mandate a thorough review of the chemicals under risk management. This review involves evaluating their effects on the environment and human health. To assess these effects, a review report that conforms to the OECD Test Guidelines must be submitted to the regulatory body. One of the essential components of the report is an assessment
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What is the ecotoxicity of a given chemical for a given aquatic species? Predicting interactions between species and chemicals using recommender system techniques SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-09-06 M. Viljanen, J. Minnema, P.N.H. Wassenaar, E. Rorije, W. Peijnenburg
Ecotoxicological safety assessment of chemicals requires toxicity data on multiple species, despite the general desire of minimizing animal testing. Predictive models, specifically machine learning...
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Discovery of dual-target natural antimalarial agents against DHODH and PMT of Plasmodium falciparum: pharmacophore modelling, molecular docking, quantum mechanics, and molecular dynamics simulations SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-09-04 E.M. Elamin, S.E. Eshage, S.M. Mohmmode, R.M. Mukhtar, M. Mahjoub, E. Sadelin, T.H. Shoaib, A. Edris, E.M. Elshamly, A.A. Makki, A. Ashour, A.E. Sherif, W. Osman, S.R.M. Ibrahim, G.A. Mohamed, A.A. Alzain
ABSTRACT Malaria is a lethal disease that claims thousands of lives worldwide annually. The objective of this study was to identify new natural compounds that can target two P. falciparum enzymes; P. falciparum Dihydroorotate dehydrogenase (PfDHODH) and P. falciparum phosphoethanolamine methyltransferase (PfPMT). To accomplish this, e-pharmacophore modelling and molecular docking were employed against
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Machine learning-based models for accessing thermal conductivity of liquids at different temperature conditions SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-08-29 R. Moreno Jimenez, B. Creton, S. Marre
ABSTRACT Combating global warming-related climate change demands prompt actions to reduce greenhouse gas emissions, particularly carbon dioxide. Biomass-based biofuels represent a promising alternative fossil energy source. To convert biomass into energy, numerous conversion processes are performed at high pressure and temperature conditions, and the design and dimensioning of such processes requires
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3D-QSAR-based design, synthesis and biological evaluation of 2,4-disubstituted quinoline derivatives as antimalarial agents SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-08-31 V.K. Vyas, S. Bhati, M. Sharma, P. Gehlot, N. Patel, S. Dalai
ABSTRACT 2,4-Disubstituted quinoline derivatives were designed based on a 3D-QSAR study, synthesized and evaluated for antimalarial activity. A large dataset of 178 quinoline derivatives was used to perform a 3D-QSAR study using CoMFA and CoMSIA models. PLS analysis provided statistically validated results for CoMFA (r2ncv = 0.969, q2 = 0.677, r2cv = 0.682) and CoMSIA (r2ncv = 0.962, q2 = 0.741, r2cv = 0
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Pteridine reductase (PTR1): initial structure-activity relationships studies of potential leishmanicidal arylindole derivatives compounds SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-08-22 J.V. Silva, S. Sueyoshi, T.J. Snape, S. Lal, J. Giarolla
ABSTRACT Leishmaniasis is a public health concern, especially in Brazil and India. The drugs available for therapy are old, cause toxicity and have reports of resistance. Therefore, this paper aimed to carry out initial structure-activity relationships (applying molecular docking and dynamic simulations) of arylindole scaffolds against the pteridine reductase (PTR1), which is essential target for the
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Predicting cytotoxicity of engineered nanoparticles using regularized regression models: an in silico approach SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-08-08 A. Valeriano, F. Bondaug, I. Ebardo, P. Almonte, M.A. Sabugaa, J.R. Bagnol, M.J. Latayada, J.M. Macalalag, B.D. Paradero, M. Mayes, M. Balanay, A. Alguno, R. Capangpangan
ABSTRACT The widespread application of engineered nanoparticles (NPs) in various industries has demonstrated their effectiveness over the years. However, modifications to NPs’ physicochemical properties can lead to toxicological effects. Therefore, understanding the toxicity behaviour of NPs is crucial. In this paper, regularized regression models, such as ridge, LASSO, and elastic net, were constructed
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HDAC6 detector: online application for evaluating compounds as potential histone deacetylase 6 inhibitors SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-08-11 O.V. Tinkov, V.Y. Grigorev, L.D. Grigoreva, V.N. Osipov, A.V. Kolotaev, D.S. Khachatryan
ABSTRACT The HDAC6 (histone deacetylase 6) enzyme plays a key role in many biological processes, including cell division, apoptosis, and immune response. To date, HDAC6 inhibitors are being developed as effective drugs for the treatment of various diseases. In this work, adequate QSAR models of HDAC6 inhibitors are proposed. They are integrated into the developed application HDAC6 Detector, which is
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Synthesis, biological evaluation and in silico studies of novel thiadiazole-hydrazone derivatives for carbonic anhydrase inhibitory and anticancer activities SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-08-04 H.E. Bostancı, U.A. Çevik, R. Kapavarapu, Y.C. Güldiken, Z.D.Ş. Inan, Ö.Ö. Güler, T.K. Uysal, A. Uytun, F.N. Çetin, Y. Özkay, Z.A. Kaplancıklı
ABSTRACT Thiadiazole and hydrazone derivatives (5a–5i) were synthesized and their chemical structures were verified and described by 1H NMR, 13C NMR, and HRMS spectra. Three cancer cell lines (MCF-7, MDA, and HT-29) and one healthy cell line (L929) were used to test the cytotoxicity activity of synthesized compounds as well as their inhibitory activity against carbonic anhydrase I, II and IX isoenzymes
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Novel molecular hybrid geometric-harmonic-Zagreb degree based descriptors and their efficacy in QSPR studies of polycyclic aromatic hydrocarbons SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-08-04 M. Arockiaraj, D. Paul, J. Clement, S. Tigga, K. Jacob, K. Balasubramanian
ABSTRACT The physicochemical characteristics of polycyclic aromatic compounds critical to environmental modelling such as octanol partition coefficients, solubility, lipophilicity, polarity and several equilibrium constants are functions of their underlying molecular structures, prompting the development of mathematical models to predict such characteristics for which experimental results are difficult
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Predictive profiling of gram-negative antibiotics in CagA oncoprotein inactivation: a molecular dynamics simulation approach SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-07-18 N. Varshney, D. Kashyap, S.K. Behra, V. Saini, A. Chaurasia, S. Kumar, H.C. Jha
ABSTRACT Gastric cancer (GC) is the fifth most prevalent form of cancer worldwide. CagA - positive Helicobacter pylori infects more than 60% of the human population. Moreover, chronic infection of CagA-positive H. pylori can directly affect GC incidence. In the current study, we have repurposed FDA-approved antibiotics that are viable alternatives to current regimens and can potentially be used as
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Design and experimental validation of the oxazole and thiazole derivatives as potential antivirals against of human cytomegalovirus SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-07-10 V. Kovalishyn, O. Severin, M. Kachaeva, I. Semenyuta, K.A. Keith, E.A. Harden, C.B. Hartline, S.H. James, L. Metelytsia, V. Brovarets
ABSTRACT QSAR studies of a set of previously synthesized azole derivatives tested against human cytomegalovirus (HCMV) were performed using the OCHEM web platform. The predictive ability of the classification models has a balanced accuracy (BA) of 73–79%. The validation of the models using an external test set proved that the models can be used to predict the activity of newly designed compounds with
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Utilizing machine learning techniques to predict the blood-brain barrier permeability of compounds detected using LCQTOF-MS in Malaysian Kelulut honey SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-07-06 R. Edros, T.W. Feng, R.H. Dong
ABSTRACT Current in silico modelling techniques, such as molecular dynamics, typically focus on compounds with the highest concentration from chromatographic analyses for bioactivity screening. Consequently, they reduce the need for labour-intensive in vitro studies but limit the utilization of extensive chromatographic data and molecular diversity for compound classification. Compound permeability
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Molecular docking-based interaction studies on imidazo[1,2-a] pyridine ethers and squaramides as anti-tubercular agents SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-06-27 S. Ahmed, A.E. Prabahar, A.K. Saxena
ABSTRACT Development of new anti-tubercular agents is required in the wake of resistance to the existing and newly approved drugs through novel-validated targets like ATP synthase, etc. The major limitation of poor correlation between docking scores and biological activity by SBDD was overcome by a novel approach of quantitatively correlating the interactions of different amino acid residues present
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Understanding mechanism governing the inflammatory potential of metal oxide nanoparticles using periodic table-based descriptors: a nano-QSAR approach SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-06-23 J. Roy, K. Roy
ABSTRACT Metal oxide nanoparticles (MeOxNPs) can be made safer by understanding the interaction between the immune system and nanoparticles. A nano-quantitative structure–activity relationship (nano-QSAR) model can be used to evaluate nanoparticle risk quickly and conveniently. The present work attempts to develop nano-QSAR models to determine the inflammatory potential of MeOxNPs based on the THP-1
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Hybrid descriptors–conjoint indices: a case study on imidazole-thiourea containing glutaminyl cyclase inhibitors for design of novel anti-Alzheimer’s candidates SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-06-01 K. Bagri, A. Kapoor, P. Kumar, A. Kumar
ABSTRACT Clinical studies show that the pyroglutamate alteration of amyloid-β (Aβ) catalysed by metalloenzyme glutaminyl cyclase results in the formation of the more neurotoxic pGlu-Aβ, and inhibition of glutaminyl cyclase can bring down the load of pGlu-Aβ in the brain and reduces Alzheimer’s disease pathology with improvement in cognition. The present study involves the identification of activity-modulating
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Functionally substituted 2-aminothiazoles as antimicrobial agents: in vitro and in silico evaluation SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-05-30 A. Petrou, V. Kartsev, A. Geronikaki, J. Glamočlija, A. Ciric, M. Sokovic
ABSTRACT Nine new functionally substituted derivatives of 2-aminothiazole were evaluated for antimicrobial activity using microdilution method against the panel of eight bacterial and eight fungal strains. Evaluation of antibacterial activity revealed that compounds are potent antibacterial agents, more active than ampicillin and streptomycin except of some compounds against B. cereus and En. cloacae
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Selection of optimal validation methods for quantitative structure–activity relationships and applicability domain SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-05-25 K. Héberger
ABSTRACT This brief literature survey groups the (numerical) validation methods and emphasizes the contradictions and confusion considering bias, variance and predictive performance. A multicriteria decision-making analysis has been made using the sum of absolute ranking differences (SRD), illustrated with five case studies (seven examples). SRD was applied to compare external and cross-validation
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MDM-Pred: a freely available web application for predicting the metabolism of drug-like compounds by the gut microbiota SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-05-25 A.S. Kolodnitsky, N.S. Ionov, A.V. Rudik, A.A. Lagunin, D.A. Filimonov, V.V. Poroikov
ABSTRACT The human gut microbiota (HGM) comprises a complex population of microorganisms that significantly affect human health, including their influence on xenobiotics metabolism. Many pharmaceuticals are taken orally and thus come into contact with HGM, which can metabolize them. Therefore, it is necessary to evaluate the effect of HGM on the fate of pharmaceuticals in the organism. We have collected
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Exploration of structural alerts and fingerprints for novel anticancer therapeutics: a robust classification-QSAR dependent structural analysis of drug-like MMP-9 inhibitors SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-05-12 S. Banerjee, S.K. Baidya, B. Ghosh, T. Jha, N. Adhikari
ABSTRACT Among various matrix metalloproteinases (MMPs), overexpression of MMP9 has been established as a key player in a variety of cancers. Therefore, MMP9 has emerged as a promising biomolecule that may be targeted to design potent inhibitors as novel anticancer therapeutics. In this study, a large database containing 1,123 drug-like MMP-9 inhibitors was considered for robust classification-dependent
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QSAR classification model for diverse series of antifungal agents based on binary coyote optimization algorithm SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-05-09 A.M. Al-Fakih, M.K. Qasim, Z.Y. Algamal, A.M. Alharthi, M.H. Zainal-Abidin
ABSTRACT One of the recently developed metaheuristic algorithms, the coyote optimization algorithm (COA), has shown to perform better in a number of difficult optimization tasks. The binary form, BCOA, is used in this study as a solution to the descriptor selection issue in classifying diverse antifungal series. Z-shape transfer functions (ZTF) are evaluated to verify their efficiency in improving
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Development of binary classification models for grouping hydroxylated polychlorinated biphenyls into active and inactive thyroid hormone receptor agonists SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-05-04 L.K. Akinola, A. Uzairu, G.A. Shallangwa, S.E. Abechi
ABSTRACT Some adverse effects of hydroxylated polychlorinated biphenyls (OH-PCBs) in humans are presumed to be initiated via thyroid hormone receptor (TR) binding. Due to the trial-and-error approach adopted for OH-PCB selection in previous studies, experiments designed to test the TR binding hypothesis mostly utilized inactive OH-PCBs, leading to considerable waste of time, effort and other material
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A QSAR study to predict the survival motor neuron promoter activity of candidate diaminoquinazoline derivatives for the potential treatment of spinal muscular atrophy SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-04-26 G. Sabuncu Gürses, S.S. Erdem, M.T. Saçan
ABSTRACT Spinal Muscular Atrophy is a genetic neuromuscular disease that leads to muscle weakness and atrophy and it is characterized by the loss of α-motor neurons in the spinal cord’s anterior horn cells. The disease appears due to low levels of the survival motor neuron protein. There are continuing clinical trials for the treatment of Spinal Muscular Atrophy. Quinazoline–based compounds are promising
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Design of 2-amino-6-methyl-pyrimidine benzoic acids as ATP competitive casein kinase-2 (CK2) inhibitors using structure- and fragment-based design, docking and molecular dynamic simulation studies SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-04-13 S. Patel, S. Patel, K. Tulsian, P. Kumar, V.K. Vyas, M. Ghate
ABSTRACT Overexpression of casein kinase-2 (CK2) has been implicated in several carcinomas, mainly lung, prostate and acute myeloid leukaemia. The smaller nucleotide pocket compared to related kinases provides a great opportunity to discover newer ATP-competitive CK2 inhibitors. In this study, we have employed an integrated structure- and fragment-based design strategy to design 2-amino-6-methyl-pyrimidine
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Prediction of soil ecotoxicity against Folsomia candida using acute and chronic endpoints. SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-04-01 R Paul,J Roy,K Roy
Soil invertebrates serve as great biological indicators of soil quality. However, there are very few in silico models developed so far on the soil toxicity of chemicals against soil invertebrates due to paucity of data. In this study, three available soil ecotoxicity data (pLC50, pLOEL and pNOEL) against the soil invertebrate Folsomia candida were collected from the ECOTOX database (cfpub.epa.gov/ecotox)
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Synthesis, antiproliferative and 4D-QSAR studies of thiadiazole derivatives bearing acrylamide moiety as EGFR inhibitors. SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-04-01 B Y Cai,T S Zhao,D G Qin,G G Tu
As a target for clinical anti-cancer treatment, epidermal growth factor receptor (EGFR) exhibits its over-expression on various tumour cells and is associated with the development of a variety of human cancers. Herein, we described the synthesis, antiproliferative activity assay and 4D-QSAR studies of thiadiazole derivatives bearing acrylamide moiety as EGFR inhibitors. Compared with Gefitinib, some
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A multiple linear regression approach to the estimation of carboxylic acid ester and lactone alkaline hydrolysis rate constants SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-03-23 J. Lazare, C. Tebes-Stevens, E.J. Weber
ABSTRACT Pesticides, pharmaceuticals, and other organic contaminants often undergo hydrolysis when released into the environment; therefore, measured or estimated hydrolysis rates are needed to assess their environmental persistence. An intuitive multiple linear regression (MLR) approach was used to develop robust QSARs for predicting base-catalyzed rate constants of carboxylic acid esters (CAEs) and
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Study of two combined series of triketones with HPPD inhibitory activity by molecular modelling SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-03-23 L.R. Capucho, E.F.F. da Cunha, M.P. Freitas
ABSTRACT Triketones are suitable compounds for 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibition and are important compounds for eliminating agricultural weeds. We report herein quantitative structure-activity relationship (QSAR) modelling and docking studies for a series of triketone-quinoline hybrids and 2-(aryloxyacetyl)cyclohexane-1,3-diones with the aim of proposing new chemical candidates
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Turning down PI3K/AKT/mTOR signalling pathway by natural products: an in silico multi-target approach SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-02-28 N. Abd Emoniem, R.M. Mukhtar, H. Ghaboosh, E.M. Elshamly, M.A. Mohamed, T. Elsaman, A.A. Alzain
ABSTRACT The PI3K/AKT/mTOR pathway is a significant target for cancer drug discovery. Many efforts have focused on discovering new inhibitors against key kinase proteins involved in this pathway for cancer treatment. PI3K/mTOR dual inhibitors, such as PKI-179, have been reported to be more effective than agents that act only on a single protein target. The present computational study aimed to discover
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Energy decomposition and waterswapping analysis to investigate the SNP associated DPD mediated 5-FU resistance SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-02-13 H. Verma, J. Doshi, G. Narendra, B. Raju, P.K. Singh, O. Silakari
5-fluorouracil is an essential component of systemic chemotherapy for colon, breast, head, and neck cancer patients. However, tumoral overexpression of the dihydropyrimidine dehydrogenase has rende...
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Binding modes of GDP, GTP and GNP to NRAS deciphered by using Gaussian accelerated molecular dynamics simulations SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-02-10 H.Y. Bao, W. Wang, H.B. Sun, J.Z. Chen
ABSTRACT Probing binding modes of GDP, GTP and GNP to NRAS are of significance for understanding the regulation mechanism on the activity of RAS proteins. Four separate Gaussian accelerated molecular dynamics (GaMD) simulations were performed on the apo, GDP-, GTP- and GNP-bound NRAS. Dynamics analyses suggest that binding of three ligands highly affects conformational states of the switch domains
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Two QSAR models for predicting the toxicity of chemicals towards Tetrahymena pyriformis based on topological-norm descriptors and spatial-norm descriptors SAR QSAR Environ. Res. (IF 3.0) Pub Date : 2023-02-07 Q. Jia, S. Wang, M. Yu, Q. Wang, F. Yan
ABSTRACT Quantitative structure-activity relationship (QSAR) is important for safe, rapid and effective risk assessment of chemicals. In this study, two QSAR models were established with 1230 chemicals to predict toxicity towards Tetrahymena pyriformis using multiple linear regression (MLR) method. The topological(T)-QSAR model was developed by using topological-norm descriptors generated from the