Patents and patent applications

  1. Therapy of RAS-dependent cancers
  2. Collagen receptor I-domain binding modulators
  3. Sulphonamide derivatives
  4. Novel compounds and their use in therapy
  5. Benzo (4,5) thieno (2,3-D) pyrimidin-4-ones and their use in therapy
  6. Crystalline vap-1 and uses thereof, patent no: US 7,499,847 B2
  7. Compounds and their use in therapy, patent no: US 7,524,853 B2
  8. Novel substituted thiophenepyrimidinone derivatives as inhibitors of 17β-hydroxysteroid dehydrogenase, patent no: EP1828197 (B1)

  9. Book Chapters (members of our research group are underlined)

  10. Postila PA, Kurkinen ST, Pentikäinen OT. Negative Image-Based Screening – Rigid Docking Using Cavity Information. Methods in Molecular Biology Series: "Protein-Ligand Interactions and Drug Design. 2266: 125-140.
  11. Pentikäinen OT, Postila PA. Negative Image-Based Rescoring – Using Cavity Information to Improve Docking Screening. Methods in Molecular Biology Series: "Protein-Ligand Interactions and Drug Design. 2266: 141-154.

  12. Research papers (members of our research group are underlined)

  13. Jokinen EM, Niemeläinen M, Kurkinen ST, Lehtonen JV, Lätti S, Postila PA, Pentikäinen OT, Niinivehmas S. Virtual Screening Strategy to Identify Retinoic Acid-Related Orphan Receptor γt Modulators. olecules. 28: 3420.
  14. Pathania S, Petrova-Szczasiuk K, Pentikäinen OT, Singh PK. Oxazolidinones: Are they only good for the discovery of antibiotics? A worm's eye view. Journal of Molecular Structure. In press
  15. 2022
  16. Jayaraj JM, Jothimani M, Palanisamy CP, Pentikäinen OT, Pannipara M, Al-Sehemi AG, Muthusamy K, Gopinath K. Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins. Bioinorganic Chemistry and Applications. 8635054.
  17. Małolepsza J, Marchwicka A, Serwa RA, Niinivehmas SP, Pentikäinen OT, Gendaszewska-Darmach E, Błazewska KM. Rational design, optimization, and biological evaluation of novel alpha-Phosphonopropionic acids as covalent inhibitors of Rab geranylgeranyl transferase. Journal of enzyme inhibition and medicinal chemistry, 37: 940-951.
  18. Kurkinen ST, Lehtonen JV, Pentikäinen OT, Postila PA. Optimization of cavity-based negative images to boost docking enrichment in virtual screening. Journal of Chemical Information and Modeling, 62: 1100-1112.
  19. Lätti S, Niinivehmas S, Pentikäinen OT. Sdfconf: Novel, Flexible, and Robust Molecular Data Management Tool. Journal of Chemical Information and Modeling, 62: 9-15.LINK

  20. 2021
  21. Pathania S, Pentikäinen OT, Singh PK. A holistic view on c-Kit in cancer: structure, signaling, pathophysiology and its inhibitors. BBA - Reviews on Cancer. 1876: 188631.
  22. Niinivehmas S, Pentikäinen OT. Coumarins as Tool Compounds to Aid the Discovery of Selective Function Modulators of Steroid Hormone Binding Proteins. Molecules, 26: 5142.
  23. Jokinen EM, Gopinath K, Kurkinen ST, Pentikäinen OT. Detection of binding sites on SARS-CoV-2 Spike protein receptor-binding domain by molecular dynamics simulations in mixed solvents.IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18: 1281-1289. Doi-page
  24. Juvonen RO, Ahinko M, Jokinen EM, Huuskonen J, Raunio H, Pentikäinen OT. Substrate Selectivity of Coumarin Derivatives by Human CYP1 Enzymes: In Vitro Enzyme Kinetics and In Silico Modeling. ACS Omega. 6, 11286-11296. Open Access
  25. Juvonen RO, Jokinen EM, Huuskonen J, Kärkkäinen O, Raunio H, Pentikäinen OT.Molecular docking and oxidation kinetics of 3-phenyl coumarin derivatives by human CYP2A13. Xenobiotica. 51: 1207-1216.

  26. 2020
  27. Krishnasamy G, Jokinen EM, Kurkinen ST, Pentikäinen OT. Screening of natural products targeting SARS-CoV-2 -ACE2 receptor interface -A MixMD based HTVS pipeline. Frontiers in Chemistry. In Press
  28. Raunio H,Pentikäinen OT, Juvonen RO. Coumarin based profluorescent and fluorescent substrates for determining xenobiotic-metabolizing enzyme activities in vitro. International Journal of Molecular Sciences. Review. 21: 4708.
  29. Juvonen RO,Jokinen EM, Javaid A, Lehtonen M, Raunio H, Pentikäinen OT. Inhibition of human CYP1 enzymes by a classical inhibitor α-naphthoflavone and a novel inhibitor N-(3, 5- dichlorophenyl)cyclopropanecarboxamide - an in vitro and in silico study. Chemical Biology & Drug Design. 2020, 95: 520-533.
  30. Juvonen RO, Pentikäinen OT, Huuskonen J, Timonen J, Kärkkäinen O, Heikkinen A, Fashe M, Raunio H. In vitro sulfonation of 7-hydroxycoumarin derivatives in liver cytosol of human and six animal species. Xenobiotica. 2020, 50: 885-893.
  31. Juvonen RO, Heikkinen AT, Kärkkäinen O, Jehangir R, Huuskonen J, Troberg J, Raunio H, Pentikäinen OT, Finel M. In vitro glucuronidation of 7-hydroxycoumarin derivatives in intestine and liver microsomes of Beagle dogs. European Journal of Pharmaceutical Sciences. 2020, 141: 105118.
  32. Baster Z, Li L, Kukkurainen S, Chen J, Pentikäinen OT, Györffy B, Hytönen VP, Zhu H, Rajfur Z, Huang C. Cyanidin 3-glucoside binds to talin and modulates colon cancer cell adhesion and 3D growth. Faseb J. 2020, 34: 2227-2237.

  33. 2019
  34. Kurkinen S, Lätti S, Pentikäinen OT, Postila PA. Getting Docking into Shape Using Negative Image-Based Rescoring. Journal of Chemical Information and Modeling. 59: 3584-3599.
  35. Jokinen EM, Postila PA, Ahinko M, Niinivehmas S, Pentikäinen OT. Fragment- and Negative Image-Based Screening of Phosphodiesterase 10A Inhibitors. Chemical Biology & Drug Design. 94: 1799-1812.
  36. Ahinko M, Kurkinen S, Niinivehmas S, Pentikäinen OT, Postila PA. A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening. International Journal of Molecular Sciences. 20: e2779.

  37. 2018
  38. Ahinko M, Niinivehmas S, Jokinen E, Pentikäinen OT. Suitability of MMGBSA for the Selection of Correct Ligand Binding Modes from Docking Results. Chemical Biology & Drug Design. 93: 522-538.
  39. Juvonen RO, Ahinko M, Huuskonen J, Raunio H, Pentikäinen OT. Development of New Coumarin-Based Profluorescent Substrates for Human Cytochrome P450 Enzymes. Xenobiotica. 49: 1015-1024.
  40. Rauhamäki S, Postila P, Lätti S, Niinivehmas S, Multamäki E, Liedl K, Pentikäinen OT. Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening. ACS Omega, 2018, 3: 6259–6266.OpenAccess
  41. Hopkins D, Envall T, Poikela N, Pentikäinen OT, Kankare M. Effect of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana. Scientific Reports, 2018, 8: 7577.Access
  42. Niinivehmas S, Postila PA, Rauhamäki S, Manivannan E, Kortet S, Ahinko M, Huuskonen P, Nyberg N., Koskimies P, Lätti S, Multamäki E, Juvonen RO, Raunio H, Pasanen M, Huuskonen J, Pentikäinen OT. Blocking oestradiol synthesis pathways with potent and selective coumarin derivatives. Journal of Enzyme Inhibition and Medicinal Chemistry. 2018, 33:743-754.Access
  43. Kurkinen S, Niinivehmas S, Ahinko M, Lätti S, Pentikäinen OT, Postila P. Improving Docking Performance Using Negative Image-Based Rescoring. Frontiers in Pharmacology. 2018, 9:260, Access.
  44. Rauhamäki S, Postila PA, Niinivehmas S, Kortet S, Schildt E, Pasanen Mi, Manivannan E, Ahinko M, Koskimies P, Nyberg N, Huuskonen P, Multamäki E, Pasanen Ma, Juvonen RO, Raunio H, Huuskonen J, Pentikäinen OT. Structure-Activity Relationship Analysis of 3-phenylcoumarin-Based Monoamine Oxidase B Inhibitors. Frontiers in Chemistry, 2018,
  45. Juvonen RO, Rauhamäki S, Kortet S, Niinivehmas S, Troberg J, Petsalo A, Huuskonen J, Raunio H, Finel M, Pentikäinen OT. Molecular Docking-Based Design and Development of a Highly Selective Probe Substrate for UDP-glucuronosyltransferase 1A10. Molecular Pharmaceutics. 2018, 15: 923-933.

  46. 2017
  47. Kaźmierczak, A; Kusy, D; Niinivehmas, S; Gmach, J; Joachimiak, Ł; Pentikäinen, OT; Gendaszewska-Darmach, E; Blazewska, K. Identification of the privileged position in the imidazo[1,2-a]pyridine ring of phosphonocarboxylates for development of Rab geranylgeranyl transferase (RGGT) inhibitors. Journal of Medicinal Chemistry, 2017, 60:8781-8800.
  48. Seppälä J, Bernardi RC, Haataja T, Hellman M, Pentikäinen OT, Schulten K, Permi P, Ylänne J, Pentikäinen U. Scientific Reports, 2017, 7: 4218.

  49. 2016
  50. Lätti S, Niinivehmas S, Pentikäinen OT. Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization. Journal of Cheminformatics, 2016, 8:45.
  51. Puurtinen M, Elo M, Jalasvuori M, Kahilainen A, Ketola T, Kotiaho JS, Monkkonen M, Pentikainen OT. Temperature-dependent mutational robustness can explain faster molecular evolution at warm temperatures, affecting speciation rate and global patterns of species diversity. Ecography 2016, 39, 1025-1033.
  52. Niinivehmas SP, Manivannan E, Rauhamäki S, Huuskonen J, Pentikäinen OT. Identification of estrogen receptor alpha ligands with virtual screening techniques. Journal of Molecular Graphics and Modeling. 2016, 64: 30-39.
  53. Yasuda T, Al Sazzad MA, Jäntti NZ, Pentikäinen OT, Slotte JP. The Influence of Hydrogen Bonding on Sphingomyelin/Colipid Interactions in Bilayer Membranes. Biophysical Journal. 2016, 110: 431-440.

  54. 2015
  55. Virtanen SI, Niinivehmas SP, Pentikäinen OT.. Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening. Journal of Molecular Graphics and Modeling. 2015, 62: 303-318.
  56. Niinivehmas SP, Salokas K, Lätti S, Raunio H, Pentikäinen OT. Ultrafast protein structure-based virtual screening with Panther. Journal of Computer-aided Molecular Discovery, 2015, 29: 989-1006.
  57. Shubina V, Niinivehmas S, Pentikäinen OT. Reliability of Virtual Screening Methods in Prediction of PDE4B-inhibitor activity. Current Drug Discovery Technologies, 12: 117-126.
  58. Raunio H, Kuusisto M, Juvonen RO, Pentikäinen OT. Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes. Frontiers in Pharmacology, 2015, 6: 123.
  59. Juvonen RO, Kuusisto M, Fohrgrup C, Pitkänen MH, Nevalainen TJ, Auriola S, Raunio H, Pasanen M, Pentikäinen OT. Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarin via human CYP2A6 and its mouse and pig orthologous enzymes. Xenobiotica, 11: 1-11.

  60. 2014
  61. Sethi R, Seppälä J, Tossavainen H, Ylilauri M, Ruskamo S, Pentikäinen OT, Pentikäinen U, Permi P, Ylänne J. A Novel Structural Unit in the N-Terminal Region of Filamins. Journal of Biological Chemistry, 2014, 289: 8588-8598.
  62. Boratynski Z, Melo-Ferreira J, Berto S, Koskela E, Alves P, Pentikäinen O, Tarroso P, Ylilauri M, Mappes T. Molecular and ecological signs of mitochondrial adaptation: consequences for introgression? Heredity, 2014, 113: 277-286.
  63. 2013
  64. Ylilauri M, Pentikäinen OT. MMGBSA As a Tool To Understand the Binding Affinities of Filamin–Peptide Interactions. Journal of Chemical Information and Modeling, 2013, 53, 2626–33
  65. Ylilauri M, Mattila E, Nurminen EM, Käpylä J, Niinivehmas SP, Määttä JA, Pentikäinen U, Ivaska J, Pentikäinen OT. Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone. BBA - Protein and Proteomics, 2013, 1834: 1988-1997
  66. Maula T, Isaksson JE, García-Linares S, Niinivehmas S, Pentikäinen OT, Kurita M, Yamaguchi S, Yamamoto T, Katsumura S, Gavilanes JG, Martínez-del-Pozo Á, Slotte JP. 2NH and 3OH are crucial structural requirements in sphingomyelin for sticholysin II binding and pore formation in bilayer membranes, BBA - Biomembranes, 2013, 1828: 1390-95
  67. 2012
  68. Ylilauri M, Pentikäinen OT. Structural Mechanism of N-Methyl-D-Aspartate Receptor Type 1 Partial Agonism. PLoS One, 2012, 7: e47604
  69. Sergelius C, Niinivehmas S, Maula T, Kurita M, Yamaguchi S, Yamamoto T, Katsumura S, Pentikäinen OT, Slotte JP. Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus. Biochimica et Biophysica Acta - Biomembranes, 2012, 1818: 474-80
  70. Nissinen L, Koivunen J, Käpylä J, Salmela M, Nieminen J, Jokinen J, Sipilä K, Pihlavisto M, Pentikäinen OT, Marjamäki A, Heino J. Novel alpha2beta1 integrin inhibitors reveal that integrin binding to collagen under shear stress conditions does not require receptor preactivation. Journal of Biological Chemistry, 2012, 287: 44694-702
  71. 2011
  72. Koivunen JT, Nissinen L, Käpylä J, Jokinen J, Pihlavisto M, Marjamäki A, Heino J, Huuskonen J, Pentikäinen OT. Fluorescent small molecule probe to modulate and explore alpha2beta1 integrin function. Journal of the American Chemical Society, 2011, 133, 14558-14561.
  73. Koivunen JT, Nissinen L, Juhakoski A, Pihlavisto M, Marjamäki A, Huuskonen J, Pentikäinen OT.Blockage of Collagen Binding to Integrin alpha2beta1: Structure-activity Relationship of Protein-protein Interaction Inhibitors, Medicinal Chemistry Communications, 2011, 2:764-770.Journal page
  74. Niinivehmas SP*, Virtanen SI*, Lehtonen JV, Postila PA, Pentikäinen OTComparison of Virtual High-throughput Screening Methods for the Identification of Phosphodiesterase-5 Inhibitors, Journal of Chemical Information and Modeling, 2011, 51: 1353-1363.(*equal contribution)
  75. Postila PA, Ylilauri M, Pentikäinen OT Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations, Journal of Chemical Information and Modeling, 2011, 51:1037–1047.
  76. Nurminen EM, Pihlavisto M, Lázár L, Pentikäinen U, Fülöp F, Pentikäinen OT. Novel hydrazine molecules as tools to understand the flexibility of vascular adhesion protein-1 ligand-binding site . towards more selective inhibitors, Journal of Medicinal Chemistry, 2011, 54: 2143–2154.
  77. 2010
  78. Coleman SK, Möykkynen T, Hinkkuri S, Vaahtera L, Korpi ER, Pentikäinen OT, Keinänen K. Ligand-binding domain determines ER exit of AMPA receptors, Journal of Biological Chemistry, 2010, 285: 36032-36039
  79. Li C, Yu S, Nakamura F, Pentikäinen OT, Singh N, Yin S, Xin W, Sy M-S. Pro-prion binds filamin A facilitating its interaction with integrin beta1 and contributes to melanomagenesis, Journal of Biological Chemistry, 2010, 285: 30328-30339.
  80. Nurminen EM, Pihlavisto M, Lazar L, Szakonyi Z, Pentikäinen, U, Fulop, F, Pentikäinen, OT. Synthesis, in vitro activity, and three-dimensional quantitative structure-activity relationship of novel hydrazine inhibitors of human Vascular Adhesion Protein-1, Journal of Medicinal Chemistry, 2010, 53: 6301–6315.
  81. Nevo J, Mai A, Pellinen T, Pentikäinen OT, Heikkilä P, Lundin J, Joensuu H, Bono P, Ivaska J. Mammary derived growth inhibitor (MDGI) interacts with integrin alpha-subunits and suppresses integrin activity and invasion, Oncogene, 2010, 29: 6452-6463
  82. Virtanen SI, Pentikäinen OT. Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site. Journal of Chemical Information and Modeling, 2010, 50: 1005–1011.
  83. Playford MP*, Nurminen E*, Pentikäinen OT, Milgram S, Hartwig JH, Stossel TP, Nakamura F. The cystic fibrosis transmembrane conductance regulator interacts with multiple IG domains of filamin A. Journal of Biological Chemistry, 285: 17156-17165.
  84. Postila P, Swanson GT, Pentikäinen OT. Exploring kainate receptor pharmacology using molecular dynamics simulations. Neuropharmacology, 2010, 58: 515-527.
  85. Nissinen L*; Pentikäinen OT*, Jouppila A*, Käpylä J, Ojala M, Nieminen J, Lipsanen A, Lappalainen H, Eckes B, Johnson MS, Lassila R, Marjamäki A, Heino J. A small molecule inhibitor of integrin alpha2beta1 introduces a new strategy for antithrombotic therapy. Thrombosis and Haemostasis, 2010, 103: 387-397
  86. Lash-van Wyhe LL, Postila PA, Tsubone K, Sasaki M, Pentikäinen OT, Sakai R, Swanson GT. Pharmacological activity of C10-substituted analogs of the high-affinity kainate receptor agonist dysiherbaine. Neuropharmacology, 2010, 58: 640-649.
  87. 2009
  88. Nakamura F, Heikkinen O, Pentikäinen OT, Osborn TM, Kasza KE, Weitz DA, Kupiainen O, Permi P, Kilpeläinen I, Ylänne J, Hartwig JH, Stossel TP. Molecular Basis of Filamin A-FilGAP Interaction and Its Impairment in Congenital Disorders Associated with Filamin A Mutations, PLoS One, 2009;4(3):e4928.
  89. Frydenvang K, Lash LL, Naur P, Postila PA, Pickering DS, Smith CM, Gajhede M, Sasaki M, Sakai R, Pentikäinen OT, Swanson GT, Kastrup JS. Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high-affinity agonist dysiherbaine and the functional antagonist MSVIII-19, J. Biol. Chem. 2009, 284:14219-29.
  90. 2008
  91. Pentikäinen U, Pentikäinen OT, Mulholland AJ. Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations. Proteins: Structure, Function, and Bioinformatics, 2008, volume 70, pages: 498-508 DOI: 10.1002/prot.21540
  92. Lash LL, Sanders JM, Akiyama N, Shoji M, Postila P, Pentikäinen OT, Sasaki M, Sakai R, and Swanson GT. Novel analogs and stereoisomers of the marine toxin neodysiherbaine with specificity for kainate receptors. Journal of Pharmacology and Experimental Therapeutics, 2008, volume 324, pages: 484-496.
  93. 2007
  94. Dolman NP, More JCA, Alt A, Pentikäinen OT, Glasser CR, Bleakman D, Mayer ML, Collingridge GL, Jane DE. Synthesis and Pharmacological Characterization of N3-Substituted Willardiine Derivatives: Role of the Substituent at the 5-Position of the Uracil Ring in the Development of Highly Potent and Selective GLUK5 Kainate Receptor Antagonists, Journal of Medicinal Chemistry, 2007, volume 50, pages: 1558-1570.
  95. Käpylä J*, Pentikäinen OT*, Nyrönen T, Nissinen L, Lassander S, Jokinen J, Lahti M, Marjamäki A, Johnson MS, Heino J. A small molecule designed to target MIDAS in the alpha2I domain inhibits integrin function. Journal of Medicinal Chemistry, 2007, volume 50, pages: 2742-2746
  96. Lad Y, Kiema T, Jiang P, Pentikäinen OT, Coles CH, Campbell ID, Calderwood DA, Ylänne J. Structure of three tandem filamin domains reveals auto-inhibition of ligand binding. EMBO Journal, 2007, volume 26, pages: 3993-4004.
  97. Postila PA, Pentikäinen OT. Glutamate receptors: structure-function relationship and ligand discovery. CSC report on computational science in Finland 2006-2007, Eds: Sillanpää et al., 2007, pages: 105-108.
  98. 2006
  99. Messinger J, Hirvelä L, Husen B, Kangas L, Koskimies P, Pentikäinen O, Saarenketo P, Thole H. New inhibitors of 17beta-hydroxysteroid dehydrogenase type 1, 2006, Molecular and Cellular Endocrinology, 2006, volume 248, pages: 192-198.
  100. Pentikäinen U*, Settimo L*, Johnson MS and Pentikäinen OT. Subtype selectivity and flexibility of ionotropic Glutamate Receptors upon antagonist ligand binding. Organic & Biomolecular Chemistry, 2006, volume 4, pages: 1058-1070.
  101. Sanders JM, Pentikäinen OT, Settimo L, Pentikäinen U, Shoji M, Sasaki M, Sakai R, Johnson MS and Swanson GT. Determination of binding site residues responsible for the subunit selectivity of novel marine-derived compounds on kainate receptors. Molecular Pharmacology, 2006, volume 69, pages: 1849-1860.
  102. Marttila-Ichihara F, Smith DJ, Stolen C, Yegutkin G, Elima K, Mercier N, Merinen M, Kiviranta R, Pihlavisto M, Alaranta S, Pentikäinen U, Pentikäinen OT, Fülöp F, Jalkanen S and Salmi M. Vascular amine oxidases are needed for leukocyte extravasation into inflamed joints in vivo. Arthritis & Rheumatism, 2006, volume 54, pages: 2852-2862.
  103. Repo S, Paldanius TA, Hytönen VP, Nyholm TKM, Halling KK, Huuskonen J, Pentikäinen OT, Rissanen K, Slotte JP, Airenne TT, Salminen TA, Kulomaa MS and Johnson MS. Binding properties of HABA-type azo derivatives to avidin and avidin-related protein 4. Chemistry & Biology, 2006, volume 13, pages:1029-1039.
  104. 2005
  105. Sanders JM, Ito K, Settimo L, Pentikäinen OT, Shoji M, Sasaki M, Johnson MS, Sakai R, and Swanson GT. Divergent pharmacological activity of novel marine-derived excitatory amino acids on glutamate receptors, Journal of Pharmacology and Experimental Therapeutics, 2005, volume 314, pages: 1068-1078. See also cover caption!
  106. Riikonen R, Matilainen H, Rajala N, Pentikäinen O, Johnson M, Heino J and Oker-Blom C. Functional Display of an alpha2 Integrin-Specific Motif (RKK) on the Surface of Baculovirus Particles, Technology in Cancer Research and Treatment, 2005, volume 4, pages: 437-446.
  107. 2004
  108. Nymalm Y, Puranen S, Nyholm T, Käpylä J, Pentikäinen OT, Airenne TT, Kidron H, Kankare J, Johnson MS, Slotte JP, Johnson MS, Salminen TA. Structural changes in the alpha1I domain of the human integrin a1b1 upon peptide binding. Journal of Biological Chemistry, 2004, volume 279, pages: 7962-7970.
  109. Karisola P, Mikkola J, Kalkkinen N, Airenne KJ, Laitinen O, Repo S, Pentikäinen OT, Reunala T, Turjanmaa K, Johnson MS, Palosuo T, Kulomaa MS, Alenius H. Design of a pilot molecule with reduced allergenicity for immunotherapy of latex allergy by co-mutation of six amino acid residues on the conformational IgE epitopes of hevein (Hev b 6.02). Journal of Immunology, 2004, volume 172, pages: 2621-2628.
  110. Hytönen VP, Nyholm TKM, Pentikäinen OT, Vaarno J, Porkka EJ, Nordlund HR, Johnson MS, Slotte JP, Laitinen OH, Kulomaa MS. Chicken avidin related protein 4/5 shows superior heat stability when compared to avidin, Journal of Biological Chemistry, 2004, volume 279, pages: 9337-9343.
  111. Moretti L*, Pentikäinen OT*, Settimo L, Johnson MS. Model structures of the N-methyl-D-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligands, Journal of Structural Biology, 2004, volume 145, pages: 205-215.
  112. Lehtonen JV, Rantanen V-V, Still D-J, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Jussila A, Jaakkola J, Pentikäinen OT, Nyrönen T, Salminen TA, Gyllenberg M and Johnson MS. BODIL: a molecular modeling environment for structure-function analysis and drug discovery, Journal of Computer-Aided Molecular Design, 2004, volume 18, pages: 401-419.
  113. 2003
  114. Zhang W-M, Käpylä J, Puranen JS, Knight CG, Tiger CF, Pentikäinen OT, Johnson MS, Farndale RW, Heino J, Gullberg D. alpha11beta1 integrin recognizes the GFOGER sequence in interstitial collagens, Journal of Biological Chemistry, 2003, volume 278, pages: 7270-7277.
  115. Pentikäinen OT, Settimo L, Keinänen K, Johnson MS. Selective agonist binding of AMPA and kainate receptors, Biochemical Pharmacology, 2003, volume 66, pages: 2413-2425.
  116. Pentikäinen OT. Modeling of protein-ligand interactions: Integrin I-domains and ionotropic glutamate receptors. Ph.D.-thesis.
  117. 2002
  118. Ollila F, Pentikäinen OT, Forss S, Johnson MS, Slotte JP. Characterization of Bile Salt/Cyclodextrin Interactions Using Isothermal Titration Calorimetry. Langmuir, 2002, volume 17, pages 7107-7111.
  119. Karisola P, Alenius H, Mikkola J, Kalkkinen N, Helin J, Pentikäinen OT, Repo S, Reunala T, Turjanmaa K, Johnson MS, Palosuo T, Kulomaa MS. The major conformational IgE-binding epitopes of hevein (Hev b6.02) are identified by a novel chimera-based allergen epitope mapping strategy. Journal of Biological Chemistry, 2002, volume 277, pages:22656-22661.
  120. Laitinen OH, Hytönen VP, Ahlroth MK, Pentikäinen OT, Gallagher C, Nordlund HR, Ovod V, Marttila AT, Porkka E, Heino S, Johnson MS, Airenne KJ, Kulomaa MS. Chicken avidin-related proteins show altered biotin-binding and physico-chemical properties as compared with avidin. Biochememical Journal, 2002, volume 363, pages: 609-617.
  121. Lampinen M, Settimo L, Pentikäinen OT, Jouppila A, Mottershead DG, Johnson MS, Keinänen K. Discrimination between agonists and antagonists by the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid-selective glutamate receptor. A mutation analysis of the ligand-binding domain of GluR-D subunit. Journal of Biological Chemistry, 2002, volume 277, pages: 41940-41947.
  122. Nymalm Y, Kravchuk Z, Salminen T, Chumanevich AA, Dubrovitsky AP, Kankare J, Pentikäinen O, Lehtonen J, Arosio P, Martsev S, Johnson MS. Antiferritin VL homodimer binds human spleen ferritin with high specificity. Journal of Structural Biology, 2002, volume 138, pages: 171-186.
  123. Jouppila A, Pentikäinen OT, Settimo L, Nyrönen T, Haapalahti J-P, Lampinen M, Mottershead D, Johnson MS, Keinänen K. Determinants of antagonist binding at the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor: Role of the conserved Arg-507 and Glu-727 residues. European Journal of Biochemistry, 2002, volume 269, pages: 6261-6270.
  124. 2001
  125. Tulla M, Pentikäinen OT, Viitasalo T, Käpylä J, Impola U, Nykvist P, Nissinen L, Johnson MS, Heino J. Selective binding of collagen subtypes by integrin alpha1I, alpha2I, and alpha10I domains. Journal of Biological Chemistry, 2001, volume 276, pages: 48206-48212.
  126. 2000
  127. Käpylä J, Ivaska J, Riikonen R, Nykvist P, Pentikäinen O, Johnson M, Heino J. Integrin alpha(2)I domain recognizes type I and type IV collagens by different mechanisms. Journal of Biological Chemistry, 2000, volume 275, pages: 3348-3354.
  128. 1999
  129. Ivaska J, Käpylä J, Pentikäinen O, Hoffrén AM, Hermonen J, Huttunen P, Johnson MS, Heino J. A peptide inhibiting the collagen binding function of integrin alpha2I domain. Journal of Biological Chemistry, 1999, volume 274, pages:3513-3521.
  130. Huhtala MT*, Pentikäinen OT*, Johnson MS. A dimeric ternary complex of FGFR [correction of FGFR1], heparin and FGF-1 leads to an 'electrostatic sandwich' model for heparin binding. Structure with Folding and Design, 1999, volume 15, pages: :699-709.
  131. Pentikäinen O, Hoffrén AM*, Ivaska J*, Käpylä J*, Nyrönen T*, Heino J, Johnson MS. "RKKH" peptides from the snake venom metalloproteinase of Bothrops jararaca bind near the metal ion-dependent adhesion site of the human integrin alpha(2) I-domain. Journal of Biological Chemistry, 1999, volume 274, pages: 31493-31505.
  132. 1998
  133. Lampinen M, Pentikäinen O, Johnson MS, Keinänen K. AMPA receptors and bacterial periplasmic amino acid-binding proteins share the ionic mechanism of ligand recognition. EMBO Journal, 1998, volume 17, pages: 4704-4711.
  134. Suoniemi A, Tanskanen J, Pentikäinen O, Johnson MS, Schulman AH. The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution. Molecular Biology and Evolution, 1998, volume 15, pages: 1135-1144.