Per Aspera Ad Astra : Application of Simplex Qsar Approach in Antiviral Research
Abstract
This review explores the application of the Simplex representation of molecular structure (SiRMS) QSAR approach in antiviral research. We provide an introduction to and description of SiRMS, its application in antiviral research and future directions of development of the Simplex approach and the whole QSAR field. In the Simplex approach every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality and symmetry). The main advantages of SiRMS are consideration of the different physical-chemical properties of atoms, high adequacy and good interpretability of models obtained and clear procedures for molecular design. The reliability of developed QSAR models as predictive virtual screening tools and their ability to serve as the basis of directed drug design was validated by subsequent synthetic and biological experiments. The SiRMS approach is realized as the complex of the computer program 'HiT QSAR', which is available on request.
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Self-citationAlves, V. M., Bobrowski, T., Melo-Filho, C. C., Korn, D., Auerbach, S. S., Schmitt, C., Muratov, E. N., & Tropsha, A. (2020) · Molecular Informatics · doi:10.1002/minf.202000113 · Cited by 95 · see citing works
Self-citationChen, C., Tanaka, K., Kotera, M., & Funatsu, K. (2020) · Journal of Cheminformatics · doi:10.1186/s13321-020-0417-9 · Cited by 93 · see citing works
Pred-Skin: A Web Portal for Accurate Prediction of Human Skin Sensitizers
Borba, J. V. V. B., Braga, R. C., Alves, V. M., Muratov, E. N., Kleinstreuer, N., Tropsha, A., & Andrade, C. H. (2020) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.0c00186 · Cited by 87 · see citing works
Self-citationInterpretation of QSAR Models Based on Random Forest Methods
Kuz’min, V. Е., Полищук, П. Г., Artemenko, A. G., & Andronati, S. A. (2011) · Molecular Informatics · doi:10.1002/minf.201000173 · Cited by 84 · see citing works
Self-citationAlves, V. M., Muratov, E. N., Fourches, D., Strickland, J. A., Kleinstreuer, N., Andrade, C. H., & Tropsha, A. (2015) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2014.12.013 · Cited by 83 · see citing works
Self-citationQSAR Modeling of Tox21 Challenge Stress Response and Nuclear Receptor Signaling Toxicity Assays
Capuzzi, S. J., Politi, R., Isayev, O., Farag, S., & Tropsha, A. (2016) · Frontiers in Environmental Science · doi:10.3389/fenvs.2016.00003 · Cited by 79 · see citing works
QSAR Modeling and Prediction of Drug–Drug Interactions
Zakharov, A. V., Varlamova, E. V., Lagunin, A. A., Dmitriev, A. V., Muratov, E. N., Fourches, D., Kuz’min, V. Е., Poroikov, V., Tropsha, A., & Nicklaus, M. C. (2015) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.5b00762 · Cited by 77 · see citing works
Self-citationUniversal Approach for Structural Interpretation of QSAR/QSPR Models
Polishchuk, P. G., Kuz'min, V. E., Artemenko, A. G., & Muratov, E. N. (2013) · Molecular Informatics · doi:10.1002/minf.201300029 · Cited by 76 · see citing works
Self-citationAlves, V. M., Muratov, E. N., Zakharov, A. V., MURATOV, N. N., Andrade, C. H., & Tropsha, A. (2017) · Food and Chemical Toxicology · doi:10.1016/j.fct.2017.04.008 · Cited by 75 · see citing works
Self-citationOprisiu, I., Varlamova, E. V., Muratov, E. N., Artemenko, A. G., Marcou, G., Полищук, П. Г., Kuz’min, V. Е., & Varnek, A. A. (2012) · Molecular Informatics · doi:10.1002/minf.201200006 · Cited by 69 · see citing works
Self-citationComputational approaches for skin sensitization prediction
Wilm, A., Kühnl, J., & Kirchmair, J. (2018) · Critical Reviews in Toxicology · doi:10.1080/10408444.2018.1528207 · Cited by 64 · see citing works
Cheminformatics-driven discovery of polymeric micelle formulations for poorly soluble drugs
Alves, V. M., Hwang, D., Muratov, E., Sokolsky-Papkov, M., Varlamova, E., Vinod, N., Lim, C., Andrade, C. H., Tropsha, A., & Kabanov, A. (2019) · Science Advances · doi:10.1126/sciadv.aav9784 · Cited by 56 · see citing works
Self-citationConsensus of classification trees for skin sensitisation hazard prediction
Asturiol, D., Casati, S., & Worth, A. P. (2016) · Toxicology in Vitro · doi:10.1016/j.tiv.2016.07.014 · Cited by 56 · see citing works
Artemenko, A. G., Muratov, E. N., Kuz’min, V. Е., MURATOV, N. N., Varlamova, E. V., Kuz’mina, A. V., Gorb, L., Golius, A., Hill, F. C., Leszczyński, J., et al. (2011) · SAR and QSAR in environmental research · doi:10.1080/1062936x.2011.569950 · Cited by 55 · see citing works
Self-citationAlves, V. M., Golbraikh, A., Capuzzi, S. J., Liu, K., Lam, W. I., Korn, D., Pozefsky, D., Andrade, C. H., Muratov, E. N., & Tropsha, A. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00124 · Cited by 53 · see citing works
Self-citationA Perspective and a New Integrated Computational Strategy for Skin Sensitization Assessment
Alves, V. M., Capuzzi, S. J., Braga, R. C., Borba, J. V. V. B., Silva, A. C., Luechtefeld, T., Härtung, T., Andrade, C. H., Muratov, E. N., & Tropsha, A. (2018) · ACS Sustainable Chemistry & Engineering · doi:10.1021/acssuschemeng.7b04220 · Cited by 51 · see citing works
Self-citationSimplex representation of molecular structure as universal QSAR/QSPR tool
Kuz’min, V. Е., Artemenko, A. G., Ognichenko, L. N., Hromov, A. I., Kosinskaya, A. P., Stelmakh, S. I., Sessions, Z. L., & Muratov, E. N. (2021) · Structural Chemistry · doi:10.1007/s11224-021-01793-z · Cited by 46 · see citing works
Self-citationTan, H., Wu, J., Zhang, R., Zhang, C., Li, W., Chen, Q., Zhang, X., Yu, H., & Shi, W. F. (2022) · Environmental Science & Technology · doi:10.1021/acs.est.2c02242 · Cited by 39 · see citing works
Computer-Aided Discovery and Characterization of Novel Ebola Virus Inhibitors
Capuzzi, S. J., Sun, W., Muratov, E. N., Martínez-Romero, C., He, S., Zhu, W., Li, H., Tawa, G., Fisher, E. G., Xu, M., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b00035 · Cited by 35 · see citing works
Self-citationSaagar–A New, Extensible Set of Molecular Substructures for QSAR/QSPR and Read-Across Predictions
Sedykh, A., Shah, R., Kleinstreuer, N., Auerbach, S. S., & Gombar, V. K. (2020) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.0c00464 · Cited by 33 · see citing works
In Silico Chemogenomics Drug Repositioning Strategies for Neglected Tropical Diseases
Andrade, C. H., Neves, B. J., Melo-Filho, C. C., Rodrigues, J., Silva, D. C., Braga, R. C., & Cravo, P. (2018) · Current Medicinal Chemistry · doi:10.2174/0929867325666180309114824 · Cited by 29 · see citing works
Jiang, J., Duan, W., Wei, Q., Zhao, X., Ni, L., Pan, Y. L., & Shu, C. (2020) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2020.112471 · Cited by 25 · see citing works
Design, Virtual Screening, and Synthesis of Antagonists of αIIbβ3 as Antiplatelet Agents
Полищук, П. Г., Samoylenko, G. V., Khristova, T. M., Krysko, O. L., Кабанова, Т. А., Kabanov, V. M., Kornylov, A. Y., Klimchuk, O., Langer, T., Andronati, S. A., et al. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b00865 · Cited by 23 · see citing works
Self-citationModern approaches to accelerate discovery of new antischistosomal drugs
Neves, B. J., Muratov, E. N., Machado, R. B., Andrade, C. H., & Cravo, P. (2016) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2016.1178230 · Cited by 23 · see citing works
Self-citationQSAR analysis of poliovirus inhibition by dual combinations of antivirals
Muratov, E. N., Varlamova, E. V., Artemenko, A. G., Полищук, П. Г., Nikolaeva–Glomb, L., Galabov, A. S., & Kuz’min, V. Е. (2013) · Structural Chemistry · doi:10.1007/s11224-012-0195-8 · Cited by 21 · see citing works
Self-citationPredicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches
Fourches, D., Muratov, E. N., Ding, F., Dokholyan, N. V., & Tropsha, A. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400216q · Cited by 21 · see citing works
Self-citationPrediction of the flash points of binary biodiesel mixtures from molecular structures
Yao, J., Qi, R., Pan, Y., He, H., Fan, Y., Jiang, J., & Jiang, J. (2020) · Journal of Loss Prevention in the Process Industries · doi:10.1016/j.jlp.2020.104137 · Cited by 19 · see citing works
Qsar Analysis of [(Biphenyloxy)Propyl]Isoxazoles: Agents Against Coxsackievirus B3
Muratov, E. N., Varlamova, E. V., Artemenko, A. G., Khristova, T., Kuz’min, V. Е., Makarov, V., Riabova, O., Wutzler, P., & Schmidtke, M. (2010) · Future Medicinal Chemistry · doi:10.4155/fmc.10.278 · Cited by 19 · see citing works
Self-citationDreher, J., Scheiber, J., Stiefl, N., & Baumann, K. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00419 · Cited by 18 · see citing works
Egorova, A., Bogner, E., Novoselova, E., Zorn, K. M., Ekins, S., & Makarov, V. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.113014 · Cited by 18 · see citing works
Self-citationThompson, C. G., Sedykh, A., Nicol, M. R., Muratov, E. N., Fourches, D., Tropsha, A., & Kashuba, A. D. M. (2014) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2013.0254 · Cited by 17 · see citing works
Self-citationA novel method for predicting the flash points of binary mixtures from molecular structures
Cao, W., Pan, Y., Liu, Y., & Jiang, J. (2020) · Safety Science · doi:10.1016/j.ssci.2020.104680 · Cited by 16 · see citing works
Efficient design of peptide-binding polymers using active learning approaches
Rakhimbekova, A., Lopukhov, A. V., Klyachko, N. L., Kabanov, A. V., Madzhidov, T., & Tropsha, A. (2022) · Journal of Controlled Release · doi:10.1016/j.jconrel.2022.11.023 · Cited by 14 · see citing works
Shen, S., Pan, Y. L., Ji, X., Ni, Y., & Jiang, J. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20092084 · Cited by 14 · see citing works
Ognichenko, L. N., Kuz’min, V. Е., Gorb, L., Hill, F. C., Artemenko, A. G., Polischuk, P. G., & Leszczyński, J. (2012) · Molecular Informatics · doi:10.1002/minf.201100102 · Cited by 12 · see citing works
Self-citationQSPR modeling of critical properties of organic binary mixtures
Mokshyna, O., Полищук, П. Г., Недоступ, В. И., & Kuz’min, V. Е. (2016) · Russian Journal of Organic Chemistry · doi:10.1134/s1070428016010024 · Cited by 9 · see citing works
Self-citationDrug design of new 5-HT6R antagonists aided by artificial neural networks
da Silva, A. P., Chiari, L. P. A., Guimarães, A. R., Honorio, K. M., & da Silva, A. B. F. (2021) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2021.107844 · Cited by 8 · see citing works
Silva, L. D. M. E., Lorenzo, V. P., Lopes, W. S., Scotti, L., & Scotti, M. T. (2019) · Molecular Informatics · doi:10.1002/minf.201800156 · Cited by 7 · see citing works
Using Molecular Fingerprints as Descriptors in Toxicity Prediction: A Survey
Mahmoud, R. S., & Yousef, A. H. (2019) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm47256.2019.8982990 · Cited by 7 · see citing works
Korn, D., Pervitsky, V., Bobrowski, T., Alves, V. M., Schmitt, C., Bizon, C., Baker, N., Chirkova, R. Y., Cherkasov, A. R., Muratov, E. N., et al. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01285 · Cited by 6 · see citing works
Self-citationQSAR Analysis of Poliovirus Inhibition By Dual Combinations of Antivirals
Muratov, E. N., Varlamova, E. V., Kuz’min, V. Е., Artemenko, A. G., Nikolaeva–Glomb, L., & Galabov, A. S. (2010) · Antiviral Research · doi:10.1016/j.antiviral.2010.02.456 · Cited by 5 · see citing works
Self-citationNew Advances in QSPR/QSAR Analysis of Nitrocompounds: Solubility, Lipophilicity, and Toxicity
Ognichenko, L. N., Kuz’min, V. Е., Gorb, L., Muratov, E. N., Artemenko, A. G., Kovdienko, N. A., Полищук, П. Г., Hill, F. C., & Leszczyński, J. (2012) · Springer eBooks · doi:10.1007/978-94-007-0923-2_8 · Cited by 4 · see citing works
Self-citationTinkov, O. V., Muratov, E. N., Artemenko, A. G., & Кузьмин, В. Е. (2013) · Pharmaceutical Chemistry Journal · doi:10.1007/s11094-013-0974-6 · Cited by 4 · see citing works
Self-citationStructure-dependent incorporation of terpenes into amphiphilic Poly(2-oxazoline) micelles
Palchak, L., Kozlov, S., Melo-Filho, C. C., Tropsha, A., & Kabanov, A. V. (2026) · Biomedical Microdevices · doi:10.1007/s10544-026-00823-z · Cited by 3 · see citing works
Golovenko, N. Y., Borysiuk, I., Kulinskiy, М. А., Полищук, П. Г., Muratov, E. N., & Kuz’min, V. Е. (2014) · Challenges and advances in computational chemistry and physics · doi:10.1007/978-94-017-9257-8_14 · Cited by 3 · see citing works
Self-citationГридина, Т. Л., Федчук, А. С., Basok, S. S., Artemenko, A. G., Ognichenko, L. N., Шитикова, Л. И., Lutsyuk, A. F., Грузевский, А. A., & Kuz’min, V. Е. (2019) · Chemistry of Heterocyclic Compounds · doi:10.1007/s10593-019-02479-5 · Cited by 3 · see citing works
Self-citationZhao, G. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/w4vm-f755 · Cited by 2 · see citing works
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Louis, B., & Agrawal, V. K. (2022) · Polycyclic aromatic compounds · doi:10.1080/10406638.2022.2038215 · Cited by 1 · see citing works
Alves, V. D. M. (2014) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) · Cited by 1 · see citing works
Capuzzi, S. J. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/bs3n-4f22
Chen, C.-H., Tanaka, K., Kotera, M., & 船津, 公. (2020) · Figshare · doi:10.6084/m9.figshare.12050823
Wu, W., Chen, H., Liu, Z., Yan, W., Wu, D., Chen, J., Liu, J., & Xing, Z. (2026) · iScience · doi:10.1016/j.isci.2026.115393
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- Authors
- Muratov, E. N., Artemenko, A. G., Varlamova, E. V., Polischuk, P. G., Lozitsky, V. P., Fedchuk, A. S., Lozitska, R. L., Gridina, T. L., Koroleva, L. S., Sil’nikov, V. N., Galabov, A. S., Makarov, V. A., Riabova, O. B., Wutzler, P., Schmidtke, M., & Kuz’min, V. E.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- National Academy of Sciences of Ukraine (UA)
- I.I. Mechnikov Ukrainian Anti-Plague Research Institute, Odessa, Ukraine, Cerkovnaya 2/4, Odessa65003, Ukraine
- Laboratory of Organic Synthesis, Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, Novosibirsk, 630090Russia
- Bulgarian Academy of Sciences (BG)
- A N Bach Institute of Biochemistry (RU)
- Jena University Hospital (DE)
- Laboratory of Theoretical Chemistry, Department of Molecular Structure, A.V. Bogatsky Physical Chemical Institute National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa65080, Ukraine
- ORCID
- Venue
- Future Medicinal Chemistry
- Publisher
- Informa UK Limited
- Published
- 2010-07
- Volume
- 2
- Issue
- 7
- Pages
- 1205-1226
- ISSN
- 1756-8919 (ISSN-L)
- 1756-8927
- OpenAlex
- W2021389393
- Cited by
- 64
- References
- 92
- Citations by year
- 2026: 2 · 2022: 3 · 2021: 3 · 2020: 11 · 2019: 7 · 2018: 6 · 2017: 5 · 2016: 5 · 2015: 4 · 2014: 4 · 2013: 5 · 2012: 4
- FWCI
- 0.38
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Future Medicinal Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- President of Ukraine (GP/F11/0115)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Mathematics › Geometry and Topology › Graph theory and applications
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- SIRM, antiviral agents, QSAR models, virtual screening, molecular design, antiviral drug discovery
- MeSH terms
- Animals, Antiviral Agents, Humans, Models, Biological, Models, Molecular, Virus Diseases, Drug Design, Quantitative Structure-Activity Relationship
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