Шитяков Сергей Васильевич

Учебник, учебное пособие

Курс лекций по хемоинформатике

Учебник, учебное пособие

Autodock molecular docking in PyMOL for rational drug design: a tutorial

Статья

Afolabi S., Oyebamiji A., Akinola O., Adekunle D., Erazua E., Olaseinde A., Olanrewaju A., Ebenezer O., Kravtsov V., Skorb E., Shityakov S. Discovery of Polyphenolic Compounds from Mangifera indica as Potent Therapeutics for Strongyloides stercoralis Infection via Computer-aided Drug Design. Current Computer-Aided Drug Design. 2025. pp. in press.

Статья

Isakova A.M., Kutyrev M.A., Kudasheva A.S., Rogacheva E.V., Kraeva L.A., Shityakov S., Zhukov M.V., Ulasevich S.A., Skorb E.V. Fabrication of biocidal materials based on the molecular interactions of tetracycline and quercetin with hydroxyapatite via In Silico- and In vitro approaches. Heliyon. 2025. Vol. 11. No. 1. pp. e41064.

Статья

Shityakov S., Forster C., Skorb E. Comparative in silico analysis of CNS-active molecules targeting the blood–brain barrier choline transporter for Alzheimer’s disease therapy. In Silico Pharmacology. 2024. Vol. 12. pp. 71.

Статья

Isakova A.M., Skorb E.V., Shityakov S. NeuroClick: Advanced Software for Designing Blood-Brain Barrier-Permeable Drugs Using Click Reaction Simulations. Current Protocols. 2024. Vol. 4. No. 11. pp. e70050.

Статья

Dutta K., Kravtsov V., Oleynikova K., Ruzov A., Skorb E.V., Shityakov S. Analyzing the Effects of Single Nucleotide Polymorphisms on hnRNPA2/B1 Protein Stability and Function: Insights for Anticancer Therapeutic Design. ACS Omega. 2024. Vol. 9. No. 5. pp. 5485–5495.

Учебник, учебное пособие

NeuroClick: Advanced Software for Designing Blood-Brain Barrier-Permeable Drugs Using Click Reaction Simulation

Тезисы

Accessible and reliable machine learning models for the blood-brain barrier permeability assessment

Статья

Khalid H., Fareed M., Dandekar T., Shityakov S. Calcineurin and mTOR inhibitors in kidney transplantation: integrative metamodeling on transplant survival and kidney function. International Urology and Nephrology. 2024. Vol. 56. No. 4. pp. 1403-1414.

Статья

Fareed M.M., Khalid H., Khalid S., Shityakov S. Deciphering Molecular Mechanisms of Carbon Tetrachloride- Induced Hepatotoxicity: A Brief Systematic Review. Current Molecular Medicine. 2024. Vol. 24. No. 9. pp. 112-1134.

Статья

Isakova A.M., Kovalenko A.A., Skorb E.V., Shityakov S. NeuroClick: software for mimicking click reaction to generate drug-like molecules permeating the blood-brain barrier. Future Medicinal Chemistry. 2024. Vol. 16. No. 5. pp. 389-398.

Статья

Eirich P., Nesterov P., Shityakov S., Skorb E.V., Sander B., Broscheit J., Dandekar T., Jones N.G., Engstler M. The release of host-derived antibodies bound to the variant surface glycoprotein (VSG) of Trypanosoma brucei cannot be explained by pH-dependent conformational changes of the VSG dimer. Open Research Europe. 2024. Vol. 4. pp. 87.

Статья

Khalid H., Shityakov S., Forster C., Song Y. Exploring the Anticancer Properties of Azadirachta indica: In Silico and In Vitro Study of Its Phytochemicals against Hepatocellular Carcinoma. Journal of Molecular Structure. 2024. Vol. 1317. pp. 138962.

Статья

Qasmi M., Fareed M., Ali H., Khan Z., Shityakov S. Integrative multi-target analysis of Urtica dioica for gout arthritis treatment: a network pharmacology and clustering approach. In Silico Pharmacology. 2024. Vol. 12. pp. 88.

Статья

Siddiqui S., Adli D., Nugraha W., Yudhistira B., Lavrentev F.V., Shityakov S., Feng X., Nagdalian A., Ibrahim S. Social, Ethical, Environmental, Economic and Technological aspects of Rabbit Meat Production - A Critical Review. Heliyon. 2024. Vol. 10. No. 8. pp. e29635.

Статья

Ashikhmina M.S., Zenkin A.M., Pantiukhin I.S., Litvak I.G., Nesterov P., Datta K., Shityakov S., Nosonovsky M., Korablev-Dyson M.A., Orlova O.Y., Ulasevich S.A., Skorb E.V. Uncovering the taste features: applying machine learning and molecular docking approaches to predict umami taste intensity of peptides. Food Bioscience. 2024. Vol. 62. pp. 105358.

Статья

Ashikhmina M.S., Ostrokhishko A.A., Dyagil D.A., Nesterov P., Barkov A.V., Vinokurov V.A., Dutta K., Orlova O.Y., Iakovchenko N.V., Shityakov S., Ulasevich S.A., Skorb E.V. Impact of drying methods on ergosterol content and cholesterol-lowering activity of Ganoderma lucidum. Food Bioscience. 2024. Vol. 60. pp. 104350.

Статья

Siddiqui S.A., Karim I., Shahiya C., Shityakov S., Nugraha W., Kasza G. A critical review of consumer responsibility in promoting sustainable cocoa production. Current Research in Food Science. 2024. Vol. 9. pp. 100818.

Статья

Ajayi I.I., Fatoki T.H., Alonge A.S., Balogun T.C., Nwagwe O.R., Moge G.M., Shityakov S. In Silico ADME, Molecular Targets, Docking and Molecular Dynamics Simulation of Key Phytoconstituents of Lobelia inflata. Journal of Computational Biophysics and Chemistry. 2024. Vol. 23. No. 10. pp. 1359-1373.

Статья

Siddiqui S.A., Alvi T., Biswas A., Shityakov S., Gusinskaia T., Lavrentev F., Dutta K., Khan M., Stephen J., Radhakrishnan M. Food gels: principles, interaction mechanisms and its microstructure. Critical Reviews in Food Science and Nutrition. 2023. Vol. 63. No. 33. pp. 12530-12551.

Статья

Tamaian R., Porozov Y., Shityakov S. Exhaustive in silico design and screening of novel antipsychotic compounds with improved pharmacodynamics and blood-brain barrier permeation properties. Journal of Biomolecular Structure and Dynamics. 2023. Vol. 41. No. 24. pp. 14849-14870.

Статья

Kovalenko A.A., Porozov Y.B., Skorb E.V., Shityakov S. Using novel click chemistry algorithm to design D3R inhibitors as blood-brain barrier permeants. Future Medicinal Chemistry. 2023. Vol. 15. No. 11. pp. 923-935.

Статья

Nagai M., Shityakov S., Smetak M., Hunkler H.J., Bar C., Schlegel N., Thum T., Forster C. Blood Biomarkers in Takotsubo Syndrome Point to an Emerging Role for Inflammaging in Endothelial Pathophysiology. Biomolecules. 2023. Vol. 13. No. 6. pp. 995.

Статья

Iwaloye O., Ottu P.O., Olawale F., Babalola O.O., Elekofehinti O.O., Kikiowo B., Adegboyega A.E., Ogbonna H.N., Adeboboye C.F., Folorunso I., Fakayode A.E., Akinjiyan M.O., Onikanni S.A., Shityakov S. Computer-aided drug design in anti-cancer drug discovery: What have we learnt and what is the way forward?. Informatics in Medicine Unlocked. 2023. Vol. 41. pp. 101332.

Статья

Dutta K., Shityakov S., Maruyama F. DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions. Scientific Reports. 2023. Vol. 13. No. 1. pp. 8701.

Статья

Shityakov S., Kravtsov V., Skorb E.V., Nosonovsky M. Ergodicity Breaking and Self-Destruction of Cancer Cells by Induced Genome Chaos. Entropy. 2023. Vol. 26. No. 1. pp. 37.

Статья

Wilhelms B., Broscheit J., Shityakov S. Chemical Analysis and Molecular Modelling of Cyclodextrin-Formulated Propofol and Its Sodium Salt to Improve Drug Solubility, Stability and Pharmacokinetics (Cytogenotoxicity). Pharmaceuticals. 2023. Vol. 16. No. 5. pp. 667.

Статья

Olofinsan K., Olawale F., Karigidi K., Shityakov S., Iwaloye O. Probing the bioactive compounds of Kigelia africana as novel inhibitors of TNF-alpha converting enzyme using HPLC/GCMS analysis, FTIR and molecular modelling. Journal of Biomolecular Structure and Dynamics. 2023. Vol. 41. No. 22. pp. 12838-12862.

Статья

Shityakov S., Aglikov A.S., Skorb E.V., Nosonovsky M. Voronoi Entropy as a Ligand Molecular Descriptor of Protein–Ligand Interactions. ACS Omega. 2023. Vol. 8. No. 48. pp. 46190-46196.

Статья

Aliev T., Belyaev V.E., Pomytkina A.V., Nesterov P., Shityakov S., Sadovnichii R., Novikov A.S., Orlova O.Y., Masalovich M.S., Skorb E.V. Electrochemical Sensor to Detect Antibiotics in Milk Based on Machine Learning Algorithms. ACS Applied Materials and Interfaces. 2023. Vol. 15. No. 44. pp. 52010-52020.

Статья

Muravev A.A., Voloshina A.D., Sapunova A.S., Gabdrakhmanova F.B., Lenina O.A., Petrov K.A., Shityakov S., Skorb E.V., Solovieva S.E., Antipin I.S. Calix[4]arene–pyrazole conjugates as potential cancer therapeutics. Bioorganic Chemistry. 2023. Vol. 139. pp. 106742.

Статья

Olawale F., Iwaloye O., Folorunso I., Shityakov S. In silico High-Throughput Screening of ZINC Database of Natural Compounds to Identify Novel Histone Deacetylase Inhibitors. Journal of Computational Biophysics and Chemistry. 2023. Vol. 22. No. 1. pp. 11-30.

Статья

Shityakov S., Skorb E., Nosonovsky M. Folding–unfolding asymmetry and a RetroFold computational algorithm. Royal Society Open Science. 2023. Vol. 10. No. 5. pp. 221594.

Статья

Tamer T., Zhou H., Hassan M., Abu-Serie M.M., Shityakov S., Elbayomi S.M., Mohy-Eldin M., Zhang Y., Cheang T. Synthesis and physicochemical properties of an aromatic chitosan derivative: In vitro antibacterial, antioxidant, and anticancer evaluations, and in silico studies. International Journal of Biological Macromolecules. 2023. Vol. 240. pp. 124339.

Статья

Fareed M.M., Ullah S., Qasmi M., Shityakov S. The Role of Vitamins in DNA Methylation as Dietary Supplements or Neutraceuticals: A Systematic Review. Current Molecular Medicine. 2023. Vol. 23. No. 10. pp. 1012-1027.

Статья

Masalovich M., Aliev T., Beliaev V.E., Pomytkina A.V., Nesterov P., Shityakov S., Sadovnichii R., Novikov A., Orlova O., Skorb E. The development of an electrochemical sensor for antibiotics in milk based on machine learning algorithms. arXiv.org [база препринтов]. 2022. Vol. arXiv:2212.04422. No. 0. pp. 1-38.

Статья

Zare Karizak A., Divsalar A., Leilabadi Asl A., Fateminasab F., Shityakov S., Saboury A.A. Molecular insights into the interaction of 5-fluorouracil and Fe3O4 nanoparticles with beta-casein: An experimental and theoretical study. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy. 2022. Vol. 267. No. Part. 2. pp. 120538.

Статья

Bencurova E., Shityakov S., Schaack D., Kaltdorf M., Sarukhanyan E., Hilgarth A., Rath C., Montenegro S., Roth G., Lopez D., Dandekar T. Nanocellulose Composites as Smart Devices With Chassis, Light-Directed DNA Storage, Engineered Electronic Properties, and Chip Integration. Frontiers in Bioengineering and Biotechnology. 2022. Vol. 10. pp. 869111.

Статья

El Azzouzi M., Azzaoui K., Warad I., Hammouti B., Shityakov S., Sabbahi R., Saoiabi S., Youssoufi M.H., Akartasse N., Jodeh S., Lamhamdi A., Zarrouk A. Moroccan, Mauritania, and senegalese gum Arabic variants as green corrosion inhibitors for mild steel in HCl: Weight loss, electrochemical, AFM and XPS studies. Journal of Molecular Liquids. 2022. Vol. 347. pp. 118354.

Статья

Forster C., Shityakov S., Scheper V., Lenarz T. Linking Cerebrovascular Dysfunction to Age-Related Hearing Loss and Alzheimer's Disease-Are Systemic Approaches for Diagnosis and Therapy Required?. Biomolecules. 2022. Vol. 12. No. 11. pp. 1717.

Статья

Fateminasab F., Bordbar A., Shityakov S., Asadi B., Zare Karizak A., Mohammadpoor-Baltork I., Saboury A.A. Modified beta-cyclodextrins: Rosmarinic acid inclusion complexes as functional food ingredients show improved operations (solubility, stability and antioxidant activity). Food Hydrocolloids. 2022. Vol. 131. pp. 107731.

Статья

Fareed M., Dutta K., Dandekar T., Tarabonda H., Skorb E.V., Shityakov S. In silico investigation of nonsynonymous single nucleotide polymorphisms in BCL2 apoptosis regulator gene to design novel protein-based drugs against cancer. Journal of Cellular Biochemistry. 2022. Vol. 123. No. 12. pp. 2044-2056.

Статья

Shityakov S., Chang J.P., Sun C.F., Guu D.T., Dandekar T., Su K.P. Supervised machine learning models and protein-protein interaction network analysis of gene expression profiles induced by omega-3 polyunsaturated fatty acids. Current Chinese Science. 2022. Vol. 2. No. 2. pp. 118-128.

Статья

Shafran Y., Hussein A.A., Beliaev N., Shevyrin V., Shityakov S., Beryozkina T., Bakulev V. Selective Synthesis of Azoloyl NH-1,2,3-Triazoles and Azolyl Diazoketones: Experimental and Computational Insights. ACS Omega. 2022. Vol. 7. No. 6. pp. 5008-5031.

Статья

Karnati S., Guntas G., Rajendran R., Shityakov S., Horing M., Liebisch G., Kosanovic D., Ergun S., Nagai M., Forster C. Quantitative Lipidomic Analysis of Takotsubo Syndrome Patients' Serum. Frontiers in Cardiovascular Medicine. 2022. Vol. 9. pp. 797154.

Статья

Fareed M., Ullah S., Aziz S., Johnsen T., Shityakov S. In-silico analysis of non-synonymous single nucleotide polymorphisms in human Beta-defensin type 1 gene reveals their impact on protein-ligand binding sites. Computational Biology and Chemistry. 2022. Vol. 98. pp. 107669.

Статья

Fareed M., Qasmi M., Aziz S., Volker E., Forster C., Shityakov S. The Role of Clusterin Transporter in the Pathogenesis of Alzheimer’s Disease at the Blood–Brain Barrier Interface: A Systematic Review. Biomolecules. 2022. Vol. 12. No. 10. pp. 1452.

Статья

Dutta K., Shityakov S., Zhu W., Khalifa I. High-risk meat and fish cooking methods of polycyclic aromatic hydrocarbons formation and its avoidance strategies. Food Control. 2022. Vol. 142. pp. 109253.

Статья

Shityakov S., Skorb E.V., Nosonovsky M. Topological bio-scaling analysis as a universal measure of protein folding. Royal Society Open Science. 2022. Vol. 9. No. 7. pp. 220160.

Статья

Esmaeilpour D., Broscheit J.A., Shityakov S. Cyclodextrin-Based Polymeric Materials Bound to Corona Protein for Theranostic Applications. International Journal of Molecular Sciences. 2022. Vol. 23. No. 21. pp. 13505.

Статья

Dutta K., Elmezayen A., Al-Obaidi A., Zhu W., Morozova O., Shityakov S., Khalifa I. Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations. Journal of Molecular Structure. 2021. Vol. 1246. pp. 131113.

Статья

Esmaeilpour D., Shityakov S., Tamaddon A., Bordbar A. Comparative chemical examination of inclusion complexes formed with Beta-cyclodextrin derivatives and basic amino acids. Carbohydrate Polymers. 2021. Vol. 262. pp. 117868.

Учебник, учебное пособие

Rational drug design and testing applied to blood-brain barrier permeation and P-glycoprotein interaction of lead and test compounds as well as cyclodextrin-formulated drugs

Статья

Dutta K., Shityakov S., Khalifa I. New Trends in Bioremediation Technologies Toward Environment-Friendly Society: A Mini-Review. Frontiers in Bioengineering and Biotechnology. 2021. Vol. 9. pp. 666858.

Статья

Shityakov S., Hayashi K., Stork S., Scheper V., Lenarz T., Forster C. The conspicuous link between ear, brain and heart–could neurotrophin-treatment of age-related hearing loss help prevent alzheimer’s disease and associated amyloid cardiomyopathy?. Biomolecules. 2021. Vol. 11. No. 6. pp. 900.

Статья

Shityakov S., Skorb E.V., Forster C., Dandekar T. Scaffold Searching of FDA and EMA-Approved Drugs Identifies Lead Candidates for Drug Repurposing in Alzheimer’s Disease. Frontiers in Chemistry. 2021. Vol. 9. pp. 736509.

Автореферат

Rational drug design and testing applied to blood-brain barrier permeation and P-glycoprotein interaction of lead and test compounds as well as cyclodextrin-formulated drugs

Статья

Shityakov S., Bencurova E., Forster C., Dandekar T. Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. BMC Bioinformatics. 2020. Vol. 21. No. 1. pp. 132.

Статья

Sarukhanyan E., Shityakov S., Dandekar T. Rational drug design of Axl tyrosine kinase type I inhibitors as promising candidates against cancer. Frontiers in Chemistry. 2020. Vol. 7. pp. 920.

Статья

Hussein A.A., Al-Hadedi A.M., Mahrath A.J., Moustafa G.A., Almalki F.A., Shityakov S., Algazally M.E. Mechanistic investigations on Pinnick oxidation: a density functional theory study. Royal Society Open Science. 2020. Vol. 7. No. 2. pp. 191568.

Статья

Sun C.F., Chiu W.C., Chen P.C., Chang H.C., Guu T.W., Shityakov S., Miller A.H., Felger J.C., Chang J.P., Su K.P. Depression-free after Interferon-alpha exposure indicates less incidence of depressive disorder: A longitudinal study in Taiwan. Brain, Behavior, and Immunity. 2020. Vol. 88. pp. 125-131.

Статья

Esmaeilpour D., Hussein A.A., Almalki F.A., Shityakov S., Bordbar A. Probing inclusion complexes of 2-hydroxypropyl-beta-cyclodextrin with mono-amino mono-carboxylic acids: physicochemical specification, characterization and molecular modeling. Heliyon. 2020. Vol. 6. No. 4. pp. e03360.

Статья

Mammadova-Bach E., Gil-Pulido J., Sarukhanyan E., Burkard P., Shityakov S., Schonhart C., Stegner D., Remer K., Nurden P., Nurden A.T., Dandekar T., Nehez L., Dank M., Braun A., Mezzano D., Abrams S.I., Nieswandt B. Platelet glycoprotein VI promotes metastasis through interaction with cancer cell–derived galectin-3. Blood. 2020. Vol. 135. No. 14. pp. 1146-1160.

Учебник, учебное пособие

Molecular modeling and simulation of retroviral proteins and nanobiocomposites

Статья

Shityakov S., Bigdelian E., Hussein A.A., Hussain M.B., Tripathi Y.C., Khan M.U., Shariati M.A. Phytochemical and pharmacological attributes of piperine: A bioactive ingredient of black pepper. European Journal of Medicinal Chemistry. 2019. Vol. 176. pp. 149-161.

Статья

Hussein A.A., Almalki F.A., Alqahtani A.M., Shityakov S. Computational assessments of diastereoselective [4+2] cycloaddition and 1,3-borotopic shift of a dearomatized tertiary boronic ester intermediate: reactivities explained through transition-state distortion energies. RSC Advances. 2019. Vol. 9. No. 40. pp. 23148-23155.

Статья

Shityakov S., Roewer N., Foerster C.Y., Tran H.T., Cai W., Broscheit J.A. Investigation of Crystalline and Amorphous Forms of Aluminum and Its Alloys: Computational Modeling and Experiment. Nano. 2018. Vol. 13. No. 3. pp. 1850026.

Автореферат

Molecular modeling and simulation of retroviral proteins and nanobiocomposites