Multi-targeted natural products evaluation based on biological activity prediction with pass

Current Pharmaceutical Design

Volumn 16, Issue 15, 2010, Pages 1703-1717

  Lagunin, Alexey ^a   Filimonov, Dmitry ^a   Poroikov, Vladimir ^a  

^a INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

Author keywords

Biological activity spectra prediction; Computational evaluation; Drug drug interaction; Marine sponge alkaloids; Multitargeted action; Natural products; Pass; St John's Wort; Triterpenoids

Indexed keywords

AAPTAMINE; ACETYLSALICYLIC ACID; ALKALOID; AMPHOTERICIN; BETULIN; BETULIN BIS HEMIPHTHALATE; CINNAMIC ACID; CYTOTOXIC AGENT; ERYTHROMYCIN; FLUOXETINE; HALITULIN; HYPERFORIN; HYPERICIN; HYPERICUM PERFORATUM EXTRACT; HYPERIN; METHYMYCIN; MITOGEN ACTIVATED PROTEIN KINASE INHIBITOR; MOTUPORAMINE; NATURAL PRODUCT; NORTOSEPTIN; NYSTATIN; PROTEIN KINASE INHIBITOR; PYRIDOACRYDINE; PYRINODEMIN; QUERCETIN; QUERCITRIN; RUTOSIDE; TRITERPENOID; UNCLASSIFIED DRUG; UNINDEXED DRUG; VASODILATOR AGENT; BIOLOGICAL PRODUCT; PLANT MEDICINAL PRODUCT; TRITERPENE;

AMINOTRANSFERASE BLOOD LEVEL; ARTICLE; BIOLOGICAL ACTIVITY; BRONCHOSPASM; CHEMICAL STRUCTURE; CHOLESTATIC HEPATITIS; COMPUTER AIDED DESIGN; COMPUTER MODEL; COMPUTER PROGRAM; DEPRESSION; DIZZINESS; EYE IRRITATION; FATIGUE; GASTROINTESTINAL SYMPTOM; HEADACHE; HEPATITIS; HUMAN; HYPERCHOLESTEROLEMIA; HYPERICUM PERFORATUM; HYPERTHERMIA; INFLAMMATION; INSOMNIA; LIVER PROTECTION; NEUROTOXICITY; NONHUMAN; PAIN; PASS; PEPTIC ULCER; PERIPHERAL VASCULAR DISEASE; PHARMAEXPERT; PHOTOPHOBIA; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PSYCHOSEXUAL DISORDER; RESTLESSNESS; SEBORRHEA; SIDE EFFECT; SKIN INJURY; SKIN IRRITATION; SKIN MANIFESTATION; SYNTHESIS; TREMOR; TUMOR; VALIDATION PROCESS; VERTIGO; XEROSTOMIA; ANIMAL; CHEMISTRY; DRUG DEVELOPMENT; DRUG EFFECT; DRUG INTERACTION; HYPERICUM; METHODOLOGY; REVIEW; SPONGE (PORIFERA); STRUCTURE ACTIVITY RELATION;

ALKALOIDS; ANIMALS; BIOLOGICAL PRODUCTS; DRUG DISCOVERY; DRUG INTERACTIONS; HYPERICUM; PLANT PREPARATIONS; PORIFERA; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; TRITERPENES;

EID: 78049518795     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/138161210791164063     Document Type: Article

References (80)

1. th ed. Stockholm: Swedish Pharmaceutical Press 2004.
2. Kong DX, Li XJ, Zhang HY. Where is the hope for drug discovery? Let history tell the future. Drug Discov Today 2009; 14: 115-119.
3. Vaidya ADB, Devasagayam TPA. Current status of herbal drugs in India: an overview. J Clin Bioch Nutr 2007; 41: 1-11.
4. Domarew CA, Holt RR, Snitkoff GG. A study of Russian phytomedicine and commonly used herbal remedies. J Herbal Pharmacother 2002; 2: 31-48.
5. Ertl P, Roggo S, Schuffenhauer A. Natural product-likeness score and its application for prioritization of compound libraries. J Chem Inf Model 2008; 48: 68-74.
6. Newman DJ, Cragg GM. Natural products as sources of new drugs over the last 25 years. J Nat Prod 2007; 70: 461-477.
7. Harley AL. Natural products in drug discovery. Drug Discov Today 2008; 13: 894-901.
8. Morphy R, Rankovic Z. Designing multiple ligands - medicinal chemistry strategies and challenges. Cur Pharm Des 2009; 15: 586-600.
9. Rollinger JM, Langer T, Stuppner H. Strategies for efficient lead structure discovery from natural products. Curr Med Chem 2006; 13: 1491-1507.
10. Rollinger JM, Stuppner H, Langer T. Virtual screening for the discovery of bioactive natural products. In: Petersen F, Amstutz R, Eds. Progress in Drug Research. Series: Natural compounds as drugs. Vol. 1. Basel, Switzerland: Birkhäuser Verlag 2008; Vol. 65: pp. 212-249.
11. Ehrman TM, Barlow DJ, Hylands PJ. Phytochemical databases of Chinese herbal constituents and bioactive plant compounds with known target specificities. J Chem Inf Model 2007; 47: 254-63.
12. JM. Accessing target information by virtual parallel screening - The impact on natural product research. Phytochem Lett 2009; 2: 53-58.
13. Burov Yu V, Poroikov VV, Korolchenko LV. National system for registration and biological testing of chemical compounds: facilities for new drugs search. Bull Natl Cent Biol Active Compds (Rus) 1990; 1: 4-25.
14. Avidon VV. Criteria for the comparison of chemical structures and principles of construction of an information language for a logical information system for biologically active compounds. Pharm-Chem J (Rus) 1974; 8: 22-25.
15. Golender VE, Rozenblit AE. Computer Methods for Drug Design. Riga: Zinatne 1978.
16. Avidon VV, Arolovich VS, Kozlova SP, Piruzian LA. Statistical study of information file on biologically active compounds. II. Choice of decision rule for biological activity prediction. Pharm-Chem J (Rus) 1978; 12: 88-93.
17. Avidon VV, Arolovich VS, Kozlova SP, Piruzian LA. Statistical investigation of large volumes of data with respect to the biological activity of compounds III. Selection of a determinant for predicting biological activity. Pharm-Chem J (Rus) 1978; 12: 99-106.
18. Avidon VV, Arolovich VS, Blinova VG, Freidina AM. Statistical investigation of the data file on biologically active compounds. V. Allowance for the novelty of the chemical structure in the prediction of the biological activity by an improved method of substructural analysis. Pharm-Chem J (Rus) 1983; 17: 59-62.
19. Golender VE, Rosenblit AB. Logical and Combinatorial Algorithms for Drug Design, UK: Research Studies Press, Wiley & Sons 1983.
20. Poroikov VV, Filimonov DA, Boudunova AP. Comparison of the results of prediction of the spectra of biological activity of chemical compounds by experts and the PASS system. Automat Doc Math Linguist 1993; 27: 40-43.
21. Filimonov DA, Poroikov VV, Karaicheva EI, Kazarian RK, Budunova AP, Mikhailovskii EM, et al. Computer-aided prediction of biological activity spectra of chemical substances on the basis of their structural formulae: computerized system PASS. Exp Clin Pharmacol (Rus) 1995; 58: 56-62.
22. Filimonov DA, Poroikov VV. PASS: computerized prediction of biological activity spectra for chemical substances. In: Bioactive Compound Design: Possibilities for Industrial Use. Oxford, UK: BIOS Scientific Publishers 1996; pp. 47-56.
23. Lagunin A, Stepanchikova A, Filimonov D, Poroikov V. PASS: prediction of activity spectra for biologically active substances. Bioinformatics 2000; 16: 747-748.
24. Stepanchikova AV, Lagunin AA, Filimonov DA, Poroikov VV. Prediction of biological activity spectra for substances: Evaluation on the diverse set of drugs-like structures. Cur Med Chem 2003; 10: 225-233.
25. Poroikov V, Filimonov D. PASS: Prediction of Biological Activity Spectra for Substances. In: Predictive Toxicology. Helma C, Ed. Boca Raton: Taylor & Francis 2005; pp. 459-478.
26. Filimonov DA, Poroikov VV. Probabilistic approach in activity prediction. In: Chemoinformatics Approaches to Virtual Screening. Varnek A, Tropsha A, Eds. Cambridge, UK: RSC Publishing 2008; pp. 182-216.
27. Lewi PJ. Spectral mapping, a technique for classifying biological activity profiles of chemical compounds. Arzneimittelforschung 1976; 26: 1295-1300.
28. Battistini A, Affabris E, Fiorucci G, Coccia EM, Romeo G, Marziali G, et al. Spectrum of biological activity of interferons. Annali dell'Istituto Superiore di Sanità 1990; 26: 227-253.
29. Gringorten JL, Sohi SS, Masson L. Activity spectra of Bacillus thuringiensis delta-endotoxins against eight insect cell lines. In Vitro Cell Dev Biol Anim 1999; 35: 299-303.
30. Fliri AF, Loging WT, Thadeio PF, Volkmann RA. Biological spectra analysis: linking biological activity profiles to molecular structure. Proc Natl Acad Sci USA 2005; 102: 261-266.
31. Rana A. Benzothiazoles: a new profile of biological activities. Indian J Pharm Sci 2007; 69: 10-17.
32. Anzali S, Barnickel G, Cezanne B, Krug M, Filimonov D, Poroikov V. Discriminating between drugs and nondrugs by Prediction of Activity Spectra for Substances (PASS). J Med Chem 2001; 44: 2432-7.
33. Gasteiger J. Handbooks of Cheminformatics: From Data to Knowledge. Weinheim: Wiley-VCH 2003.
34. Avidon VV, Pomerantsev IA, Rozenblit AB, Golender VE. Structure-activity relationship oriented languages for chemical structure representation. J Chem Inf Comput Sci 1982; 22: 207-214.
35. Todeschini R, Consonni V. Handbook of Molecular Descriptors. Weinheim: Wiley-VCH 2000.
36. Filimonov D, Poroikov V, Borodina Yu, Gloriozova T. Chemical similarity assessment through multilevel neighborhoods of atoms: definition and comparison with the other descriptors. J Chem Inf Comput Sci 1999; 39: 666-670.
37. Poroikov VV, Filimonov DA, Borodina Yu V, Lagunin AA, Kos A. Robustness of biological activity spectra predicting by computer program PASS for non-congeneric sets of chemical compounds. J Chem Inform Comput Sci 2000; 40: 1349-1355.
38. Poroikov VV, Filimonov DA, Ihlenfeldt WD, Gloriozova TA, Lagunin AA, Borodina Yu V, et al. PASS biological activity spectrum predictions in the enhanced open NCI database browser. J Chem Inform Comput Sci 2003; 43: 228-236.
39. Sadym A, Lagunin A, Filimonov D, Poroikov V. Prediction of biological activity spectra via Internet. SAR QSAR Environ Res 2003; 14: 339-347.
40. Geronikaki A, Druzhilovsky D, Zakharov A, Poroikov V. Computer-aided predictions for medicinal chemistry via Internet. SAR QSAR Environ Res 2008; 19: 27-38.
41. Di Giorgio C, Delmas F, Filloux N, Robin M, Seferian L, Azas N, et al. In vitro activities of 7-substituted 9-chloro and 9-amino-2-methoxyacridines and their bis- and tetra-acridine complexes against Leishmania infantum. Antimicrob Agents Chemother 2003; 47: 174-180.
42. Delmas F, Di Giorgio C, Robin M, Azas N, Gasquet M, Detang C, et al. In vitro activities of position 2 substitution-bearing 6-nitro-and 6-aminobenzothiazoles and their corresponding anthranilic acid derivatives against Leishmania infantum and Trichomonas vaginalis. Antimicrob Agents and Chemother 2002; 46: 2588-2594.
43. Di Giorgio C, Delmas F, Ollivier E, Elias R, Balansard G, Timon-David P. In vitro activity of the beta-carboline alkaloids harmane, harmine, and harmaline toward parasites of the species Leishmania infantum. Exp Parasitol 2004; 106: 67-74.
44. Goel RK, Kumar V, Mahajan MP. Quinazolines revisited: search for novel anxiolytic and GABAergic agents. Bioorg Med Chem Lett 2005; 15: 2145-2148.
45. Geronikaki A, Babaev E, Dearden J, Dehaen W, Filimonov D, Galaeva I, et al. Design of new anxiolytics: from computer prediction to synthesis and biological evaluation. Bioorg Med Chem 2004; 12: 6559-6568.
46. Labanauskas L, Brukstus A, Udrenaite E, Bucinskaite V, Susvilo I, Urbelis G. Synthesis and anti-inflammatory activity of 1-acylaminoalkyl-3,4-dialkoxybenzene derivatives. Il Farmaco 2005; 60: 203-207.
47. Dolzhenko AV, Kolotova NV, Koz'minykh VO, Vasilyuk MV, Kotegov VP, Novoselova GN, et al. Substituted amides and hydrazides of dicarboxylic acids. Part 14. Synthesis and antimicrobial and antiinflammatory activity of 4-antipyrylamides, 2-thiazolylamides, and 1-triazolylamides of some dicarboxylic acids. Pharm Chem J 2003; 37: 149-151.
48. Lagunin AA, Gomazkov OA, Filimonov DA, Gureeva TA, Dilakyan EA, Kugaevskaya EV, et al. Computer-aided selection of potential antihypertensive compounds with dual mechanisms of action. J Med Chem 2003; 46: 3326-3332.
49. Geronikaki AA, Lagunin AA, Hadjipavlou-Litina DI, Elefteriou PT, Filimonov DA, Poroikov VV, et al. Computer-aided discovery of anti-inflammatory thiazolidinones with dual cyclooxygenase/ lipoxygenase inhibition. J Med Chem 2008; 51: 1601-1609.
50. Poroikov V, Lagunin A, Filimonov D. Pharmaexpert: diseases, targets and ligands - three in one. Proceedings of the 15th European symposium on structure-activity relationships (QSAR) and molecular modeling. Istanbul, Turkey, September 05-10, 2004. Sener EA, Yalcin I, Eds. Ankara (Turkey): CADD & D Society 2005; pp. 514-515.
51. Dembitsky VM, Gloriozova TA, Poroikov VV. Novel antitumor agents: marine sponge alkaloids, their synthetic analogues and derivatives. Mini-Rev Med Chem 2005; 5: 319-36.
52. Newman DJ. Natural products as leads to potential drugs: an old process or the new hope for drug discovery? J Med Chem 2008; 51: 2589-2599.
53. Flekhter OB, Karachurina LT, Poroikov VV, Nigmatullina LR, Baltina LA, Zarudii FC, et al. Synthesis of ether triterpenoides of lupan group and their hepatoprotective activity. Rus J Bioorg Chem 2000; 26: 215-223.
54. Rollinger JM, Schuster D, Danzl B, Schwaiger S, Markt P, Schmidtke M, et al. In silico target fishing for rationalized ligand discovery exemplified on constituents of Ruta graveolens. Planta Med 2009; 75: 195-204.
55. nd ed. New York: Academic Press 2002.
56. Weissman KJ. Polyketide biosynthesis: understanding and exploiting modularity. Phil Trans R Soc Lond 2004; 362: 2671-2690.
57. Zotchev SB, Stepanchikova AV, Sergeyko AP, Sobolev BN, Filimonov DA, Poroikov VV. Rational design of macrolides by virtual screening of combinatorial libraries generated through in silico manipulation of polyketide synthases. J Med Chem 2006; 49: 2077-87.
58. Sergeyko AP, Stepanchikova AV, Sobolev BN, Zotchev SB, Filimonov DA, Lagunin AA, et al. Computer-aided design of polyketides with the required properties. Biomed Chem (Rus) 2007; 53: 522-531.
59. Buckingham J. Dictionary of Natural Products. UK: Chapman & Hall/CRC 2007.
60. th ed. London: Elsevier 2006.
61. Kostrubsky VE, Strom SC, Hanson J, Urda E, Rose K, Burliegh J, et al. Evaluation of hepatotoxic potential of drugs by inhibition of bile-acid transport in cultured primary human hepatocytes and intact rats. Toxicol Sci 2003; 76: 220-228.
62. Di Carlo G, Borrelli F, Ernst E, Izzo AA. St John's wort: Prozac from the plant kingdom. Trends Pharmacol Sci 2001; 22: 292-297.
63. Erdelmeier CAJ, Koch E, Hoerr R. Hypericum perforatum - St. John's Wort chemical, pharmacological and clinical aspects. Stud Nat Prod Chem 2000; 22: 643-716.
64. Kurkin VA. Pharmacognosy. Samara, Russia: SSU 2007.
65. Smelcerovic A, Spiteller M, Ligon AP, Smelcerovic Z, Raabe N. Essential oil composition of Hypericum L. species from Southeastern Serbia and their chemotaxonomy. Biochem Syst Ecol 2007; 35: 99-113.
66. Radusiene J, Judzentiene A, Bernotiene G. Essential oil composition and variability of Hypericum perforatum L. growing in Lithuania. Biochem Syst Ecol 2005; 33: 113-124.
67. Poroikov VV, Filimonov DA. How to acquire new biological activities in old compounds by computer prediction. J Comput-Aid Mol Des 2002; 16: 819-824.
68. Pogrebnyak AV, Poroikov VV, Staryh VV, Konovalov DA. Computer assisted analysis of antitumor activity of sesquiterpene lactones from the family of Asteraceae. Plant Res (Rus) 1998; 34: 61-64.
69. Dembitsky VM, Levitsky DO, Gloriozova TA, Poroikov VV. Acetylenic aquatic anticancer agents and related compounds. Nat Prod Commun 2006; 1: 773-812.
70. Sergeiko AP, Poroikov VV, Hanus LO, Dembitsky VM. Cyclobutane-containing alkaloids: origin, synthesis, and biological activities. Open Med Chem J 2008, 2: 26-37.
71. Dembitsky VM, Gloriozova TA, Poroikov VV. Natural peroxy antincancer agents. Mini-Rev Med Chem 2007; 7: 571-589.
72. Devillers J, Dore JC, Guyot M, Poroikov V, Gloriozova T, Lagunin A, et al. Prediction of biological activity profiles of cyanobacterial secondary metabolites. SAR QSAR Environ Res 2007; 18: 629-643.
73. Goel RK, Lagunin AA, Poroikov VV. PASS - assisted exploration of new therapeutic potential of natural products. Med Chem Res 2010; in press.
74. Phillipson JD. Phytochemistry and pharmacognosy. Phytochemistry 2007; 68: 2960-2972.
75. Sardari S, Shokrgozar MA, Ghavami G. Cheminformatics based selection and cytotoxic effects of herbal extracts. Toxicol in Vitro 2009; 23: 1412-1421.
76. Pors K, Goldberg FW, Leamon CP, Rigby AC, Snyder SA, Falconer RA. The changing landscape of cancer drug discovery: a challenge to the medicinal chemist of tomorrow. Drug Discov Today 2009; 14: 1045-1050.
77. Filimonov DA, Zakharov AV, Lagunin AA, Poroikov VV. QNA based "Star Track" QSAR approach. SAR QSAR Environ Res 2009; 20: 679-709.
78. Koborova ON, Filimonov DA, Zakharov AV, Lagunin AA, Ivanov SM, Kel A, et al. In silico method for identification of promising anticancer drug targets. SAR QSAR Environ Res 2009; 20: 755-766.
79. Kel A, Voss N, Valeev T, Stegmaier P, Kel-Margoulis O, Wingender E. ExPlain: finding upstream drug targets in disease gene regulatory networks. SAR QSAR Environ Res 2008; 19: 481-494.
80. Lopez A, Parsons AB, Nislow C, Giaever G, Boone C. Chemical-genetic approaches for exploring the mode of action of natural products. Prog Drug Res 2008; 66(237): 239-271.