Protein tunnels are essential in transporting small molecules into the active sites of enzymes. Tunnels' geometrical and physico-chemical properties influence the transport process. The tunnels are attractive hot spots for protein engineering and drug development. However, studying the ligand binding and unbinding using experimental techniques is challenging, while in silico methods come with their limitations, especially in the case of resource-demanding virtual screening pipelines. Caver Web 1.2 is a new version of the web server combining the capabilities for the detection of protein tunnels with the calculation of the ligand trajectories. The new version of the Caver Web server was expanded with the ability to fetch novel ligands from the Integrated Database of Small Molecules and with the fully automated virtual screening pipeline allowing for the fast evaluation of the predefined set of over 4,300 currently approved drugs. The virtual screening pipeline is accompanied by a comprehensive user interface, making it a viable service for the broader spectrum of companies and the academic user community. The web server is freely available for academic use at https://loschmidt.chemi.muni.cz/caverweb.

Faculty of Information Technology Brno University of Technology Brno Czech Republic

Institute of Organic Chemistry and Biochemistry of the CAS Prague Czech Republic

International Clinical Research Center St Anne's University Hospital Brno Brno Czech Republic

Loschmidt Laboratories Department of Experimental Biology and RECETOX Masaryk University Brno Czech Republic

Zobrazit více v PubMed

Wagner B.K., Schreiber S.L. The Power of Sophisticated Phenotypic Screening and Modern Mechanism-of-Action Methods. Cell Chem Biol. 2016;23(1):3–9. doi: 10.1016/j.chembiol.2015.11.008. PubMed DOI PMC

Zheng W., Thorne N., McKew J.C. Phenotypic Screens as a Renewed Approach for Drug Discovery. Drug Discov Today. 2013;18(21):1067–1073. doi: 10.1016/j.drudis.2013.07.001. PubMed DOI PMC

Jumper J., Evans R., Pritzel A., Green T., Figurnov M., Ronneberger O., et al. Highly Accurate Protein Structure Prediction with AlphaFold. Nature. 2021;596(7873):583–589. doi: 10.1038/s41586-021-03819-2. PubMed DOI PMC

Eder J., Sedrani R., Wiesmann C. The Discovery of First-in-Class Drugs: Origins and Evolution. Nat Rev Drug Discov. 2014;13(8):577–587. doi: 10.1038/nrd4336. PubMed DOI

An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature2012, 489 (7414), 57–74. 10.1038/nature11247. PubMed PMC

Kim M.-S., Pinto S.M., Getnet D., Nirujogi R.S., Manda S.S., Chaerkady R., et al. A Draft Map of the Human Proteome. Nature. 2014;509(7502):575–581. doi: 10.1038/nature13302. PubMed DOI PMC

Geiger T., Wehner A., Schaab C., Cox J., Mann M. Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins. Mol Cell Proteomics. 2012;11(3) doi: 10.1074/mcp.M111.014050. PubMed DOI PMC

Wilhelm M., Schlegl J., Hahne H., Gholami A.M., Lieberenz M., Savitski M.M., et al. Mass-Spectrometry-Based Draft of the Human Proteome. Nature. 2014;509(7502):582–587. doi: 10.1038/nature13319. PubMed DOI

Uhlén M., Fagerberg L., Hallström B.M., Lindskog C., Oksvold P., Mardinoglu A., et al. Tissue-Based Map of the Human Proteome. Science. 2015 doi: 10.1126/science.1260419. PubMed DOI

DiMasi J.A., Grabowski H.G., Hansen R.W. Innovation in the Pharmaceutical Industry: New Estimates of R&D Costs. J Health Econ. 2016;47:20–33. doi: 10.1016/j.jhealeco.2016.01.012. PubMed DOI

Karamehic J., Ridic O., Ridic G., Jukic T., Coric J., Subasic D., et al. Financial Aspects and the Future of the Pharmaceutical Industry in the United States of America. Mater Sociomed. 2013;25(4):286–290. doi: 10.5455/msm.2013.25.286-290. PubMed DOI PMC

Vavra O., Filipovic J., Plhak J., Bednar D., Marques S.M., Brezovsky J., et al. CaverDock: A Molecular Docking-Based Tool to Analyse Ligand Transport through Protein Tunnels and Channels. Bioinformatics. 2019;35(23):4986–4993. doi: 10.1093/bioinformatics/btz386. PubMed DOI

Lee P.-H., Kuo K.-L., Chu P.-Y., Liu E.M., Lin J.-H. SLITHER: A Web Server for Generating Contiguous Conformations of Substrate Molecules Entering into Deep Active Sites of Proteins or Migrating through Channels in Membrane Transporters. Nucleic Acids Res. 2009;37(suppl_2):W559–W564. doi: 10.1093/nar/gkp359. PubMed DOI PMC

Devaurs D., Bouard L., Vaisset M., Zanon C., Al-Bluwi I., Iehl R., et al. MoMA-LigPath: A Web Server to Simulate Protein-Ligand Unbinding. Nucleic Acids Res. 2013;41(W1):W297–W302. doi: 10.1093/nar/gkt380. PubMed DOI PMC

Trott O., Olson A.J. AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J Comput Chem. 2010;31(2):455–461. doi: 10.1002/jcc.21334. PubMed DOI PMC

Slater O., Kontoyianni M. The Compromise of Virtual Screening and Its Impact on Drug Discovery. Expert Opin Drug Discov. 2019;14(7):619–637. doi: 10.1080/17460441.2019.1604677. PubMed DOI

Shoichet B.K. Virtual Screening of Chemical Libraries. Nature. 2004;432(7019):862–865. doi: 10.1038/nature03197. PubMed DOI PMC

Stourac J., Vavra O., Kokkonen P., Filipovic J., Pinto G., Brezovsky J., et al. Caver Web 1.0: Identification of Tunnels and Channels in Proteins and Analysis of Ligand Transport. Nucleic Acids Res. 2019;47(W1):W414–W422. doi: 10.1093/nar/gkz378. PubMed DOI PMC

Chovancova E., Pavelka A., Benes P., Strnad O., Brezovsky J., Kozlikova B., et al. 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Comput Biol. 2012;8(10):e1002708. PubMed PMC

Sterling T., Irwin J.J. ZINC 15 – Ligand Discovery for Everyone. J Chem Inf Model. 2015;55(11):2324–2337. doi: 10.1021/acs.jcim.5b00559. PubMed DOI PMC

Galgonek J., Vondrášek J. IDSM ChemWebRDF: SPARQLing Small-Molecule Datasets. J Cheminform. 2021;13(1):38. doi: 10.1186/s13321-021-00515-1. PubMed DOI PMC

Le Guilloux V., Schmidtke P., Tuffery P. Fpocket: An Open Source Platform for Ligand Pocket Detection. BMC Bioinf. 2009;10(1):168. doi: 10.1186/1471-2105-10-168. PubMed DOI PMC

Ribeiro A.J.M., Holliday G.L., Furnham N., Tyzack J.D., Ferris K., Thornton J.M. Mechanism and Catalytic Site Atlas (M-CSA): A Database of Enzyme Reaction Mechanisms and Active Sites. Nucleic Acids Res. 2018;46(D1):D618–D623. doi: 10.1093/nar/gkx1012. PubMed DOI PMC

UniProt Consortium, T. UniProt: The Universal Protein Knowledgebase. Nucleic Acids Research2018, 46 (5), 2699–2699. 10.1093/nar/gky092. PubMed PMC

Morris G.M., Huey R., Lindstrom W., Sanner M.F., Belew R.K., Goodsell D.S., et al. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. J Comput Chem. 2009;30(16):2785–2791. doi: 10.1002/jcc.21256. PubMed DOI PMC

Filipovič J., Vávra O., Plhák J., Bednář D., Marques S.M., Brezovský J., et al. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Trans Comput Biol Bioinf. 2020;17(5):1625–1638. doi: 10.1109/TCBB.2019.2907492. PubMed DOI

Kim S., Thiessen P.A., Bolton E.E., Chen J., Fu G., Gindulyte A., et al. PubChem Substance and Compound Databases. Nucleic Acids Res. 2016;44(D1):D1202–D1213. doi: 10.1093/nar/gkv951. PubMed DOI PMC

Gaulton A., Bellis L.J., Bento A.P., Chambers J., Davies M., Hersey A., et al. ChEMBL: A Large-Scale Bioactivity Database for Drug Discovery. Nucleic Acids Res. 2012;40(D1):D1100–D1107. doi: 10.1093/nar/gkr777. PubMed DOI PMC

Degtyarenko K., de Matos P., Ennis M., Hastings J., Zbinden M., McNaught A., et al. A Database and Ontology for Chemical Entities of Biological Interest. Nucleic Acids Res. 2008;36(suppl_1):D344–D350. doi: 10.1093/nar/gkm791. PubMed DOI PMC

PyMOL | pymol.org. https://pymol.org/2/ (accessed 2022-06-30).

Yang J., Cui B., Sun S., Shi T., Zheng S., Bi Y., et al. Phenotype-Genotype Correlation in Eight Chinese 17α-Hydroxylase/17,20 Lyase-Deficiency Patients with Five Novel Mutations of CYP17A1 Gene. The Journal of Clinical Endocrinology & Metabolism. 2006;91(9):3619–3625. doi: 10.1210/jc.2005-2283. PubMed DOI

Gong Y., Qin F., Li W.-J., Li L.-Y., He P., Zhou X.-J. Cytochrome P450 Family 17 Subfamily A Member 1 Mutation Causes Severe Pseudohermaphroditism: A Case Report. World J Clin Cases. 2022;10(11):3553–3560. doi: 10.12998/wjcc.v10.i11.3553. PubMed DOI PMC

Wang M., Wang H., Zhao H., Li L., Liu M., Liu F., et al. Prevalence of CYP17A1 Gene Mutations in 17α-Hydroxylase Deficiency in the Chinese Han Population. Clin Hypertens. 2019;25(1):23. doi: 10.1186/s40885-019-0128-6. PubMed DOI PMC

Mula-Abed W.-A.-S., Pambinezhuth F.B., Al-Kindi M.K., Al-Busaidi N.B., Al-Muslahi H.N., Al-Lamki M.A. Congenital Adrenal Hyperplasia Due to 17-Alpha-Hydoxylase/17,20-Lyase Deficiency Presenting with Hypertension and Pseudohermaphroditism: First Case Report from Oman. Oman Med J. 2014;29(1):55–59. doi: 10.5001/omj.2014.12. PubMed DOI PMC

Costa-Santos M., Kater C.E., Auchus R.J., Brazilian Congenital Adrenal Hyperplasia Multicenter Study Group Two Prevalent CYP17 Mutations and Genotype-Phenotype Correlations in 24 Brazilian Patients with 17-Hydroxylase Deficiency. J Clin Endocrinol Metab. 2004;89(1):49–60. doi: 10.1210/jc.2003-031021. PubMed DOI

Acién P., Acién M. Disorders of Sex Development: Classification, Review, and Impact on Fertility. J Clin Med. 2020;9(11):3555. doi: 10.3390/jcm9113555. PubMed DOI PMC

Kostin V.A., Zolottsev V.A., Kuzikov A.V., Masamrekh R.A., Shumyantseva V.V., Veselovsky A.V., et al. Oxazolinyl Derivatives of [17(20)E]-21-Norpregnene Differing in the Structure of A and B Rings. Facile Synthesis and Inhibition of CYP17A1 Catalytic Activity. Steroids. 2016;115:114–122. doi: 10.1016/j.steroids.2016.06.002. PubMed DOI

Bonomo S., Hansen C.H., Petrunak E.M., Scott E.E., Styrishave B., Jørgensen F.S., et al. Promising Tools in Prostate Cancer Research: Selective Non-Steroidal Cytochrome P450 17A1 Inhibitors. Sci Rep. 2016;6:29468. doi: 10.1038/srep29468. PubMed DOI PMC

Mostaghel E.A., Marck B.T., Plymate S.R., Vessella R.L., Balk S., Matsumoto A.M., et al. Resistance to CYP17A1 Inhibition with Abiraterone in Castration-Resistant Prostate Cancer: Induction of Steroidogenesis and Androgen Receptor Splice Variants. Clin Cancer Res. 2011;17(18):5913–5925. doi: 10.1158/1078-0432.CCR-11-0728. PubMed DOI PMC

Cheong E.J.Y., Nair P.C., Neo R.W.Y., Tu H.T., Lin F., Chiong E., et al. Slow-, Tight-Binding Inhibition of CYP17A1 by Abiraterone Redefines Its Kinetic Selectivity and Dosing Regimen. J Pharmacol Exp Ther. 2020;374(3):438–451. doi: 10.1124/jpet.120.265868. PubMed DOI PMC

Storbeck K.-H., Swart P., Africander D., Conradie R., Louw R., Swart A.C. 16α-Hydroxyprogesterone: Origin, Biosynthesis and Receptor Interaction. Mol Cell Endocrinol. 2011;336(1–2):92–101. doi: 10.1016/j.mce.2010.11.016. PubMed DOI

DeVore N.M., Scott E.E. Structures of Cytochrome P450 17A1 with Prostate Cancer Drugs Abiraterone and TOK-001. Nature. 2012;482(7383):116–119. doi: 10.1038/nature10743. PubMed DOI PMC

Vasaitis T.S., Bruno R.D., Njar V.C.O. CYP17 Inhibitors for Prostate Cancer Therapy. J Steroid Biochem Mol Biol. 2011;125(1–2):23–31. doi: 10.1016/j.jsbmb.2010.11.005. PubMed DOI PMC

Enzyme Tunnels and Gates As Relevant Targets in Drug Design - Marques - 2017 - Medicinal Research Reviews - Wiley Online Library. https://onlinelibrary.wiley.com/doi/full/10.1002/med.21430 (accessed 2022-08-04). PubMed

Fernández-Cancio M., Camats N., Flück C.E., Zalewski A., Dick B., Frey B.M., et al. Mechanism of the Dual Activities of Human CYP17A1 and Binding to Anti-Prostate Cancer Drug Abiraterone Revealed by a Novel V366M Mutation Causing 17,20 Lyase Deficiency. Pharmaceuticals (Basel) 2018;11(2):E37. doi: 10.3390/ph11020037. PubMed DOI PMC

Eil C. Ketoconazole Binds to the Human Androgen Receptor. Horm Metab Res. 1992;24(8):367–370. doi: 10.1055/s-2007-1003337. PubMed DOI

Liu Y., Denisov I., Gregory M., Sligar S.G., Kincaid J.R. Importance of Asparagine 202 in Manipulating Active Site Structure and Substrate Preference for Human CYP17A1. Biochemistry. 2022;61(7):583–594. doi: 10.1021/acs.biochem.2c00023. PubMed DOI PMC

Varothai S., Bergfeld W.F. Androgenetic Alopecia: An Evidence-Based Treatment Update. Am J Clin Dermatol. 2014;15(3):217–230. doi: 10.1007/s40257-014-0077-5. PubMed DOI

Finasteride for Prostate Cancer Prevention - NCI. https://www.cancer.gov/types/prostate/research/finasteride-reduces-low-grade (accessed 2022-08-04).

Zink, C. Dictionary of Obstetrics and Gynecology; Walter de Gruyter, 2011.

Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning - ScienceDirect. https://www.sciencedirect.com/science/article/pii/S2001037021002245 (accessed 2022-08-04). PubMed PMC

In silico investigation of cholesterol-lowering drugs to find potential inhibitors of dehydrosqualene synthase in Staphylococcus aureus