Publications

MEDCHEM.fi

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)
   

Book Chapters

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.

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.

Research Papers

2024

• Moyano-Gómez P, Lehtonen JV, Pentikäinen OT, Postila PA. Building shape-focused pharmacophore models for effective docking ​screening. Journal of Cheminformatics. 16: 97. Open Access.
  

2023

• 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. Molecules. 28: 3420. Access.
  
• 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. 15; 135630.
  

2022

• 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. ​Access.
  
• 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. Access.
  
• 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. Access.
  
• Lätti S, Niinivehmas S, Pentikäinen OT. Sdfconf: Novel, Flexible, and Robust Molecular Data Management Tool. Journal of Chemical ​Information and Modeling, 62: 9-15. Access.
  

2021

• 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. Access.
  
• Niinivehmas S, Pentikäinen OT. Coumarins as Tool Compounds to Aid the Discovery of Selective Function Modulators of Steroid ​Hormone Binding Proteins. Molecules, 26: 5142. Access.
  
• 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. Access.
  
• 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
  
• 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. Access.
  

2020

• 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, 8, 589769. https://doi.org/10.3389/fchem.2020.589769
  
• 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. Access.
  
• 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. Access.
  
• 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. Access.
  
• 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. Access.
  
• 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. Access.
  

2019

• 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.
  
• 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.
  
• 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.
  

2018

• 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.
  
• 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.
  
• 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
  
• 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
  
• 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
  
• 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.
  
• 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, https://doi.org/10.3389/fchem.2018.00041
  
• 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.
  

2017

• 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.
  
• Seppälä J, Bernardi RC, Haataja T, Hellman M, Pentikäinen OT, Schulten K, Permi P, Ylänne J, Pentikäinen U. Scientific Reports, 2017, ​7: 4218.
  

2016

• 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.
  
• 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.
  
• 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.
  
• 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.
  

2015

• 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.
• 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.
• Shubina V, Niinivehmas S, Pentikäinen OT. Reliability of Virtual Screening Methods in Prediction of PDE4B-inhibitor activity. Current ​Drug Discovery Technologies, 12: 117-126.
• Raunio H, Kuusisto M, Juvonen RO, Pentikäinen OT. Modeling of interactions between xenobiotics and cytochrome P450 (CYP) ​enzymes. Frontiers in Pharmacology, 2015, 6:123

2014

• 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.
• 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.

2013

• 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
• 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
• 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

2012

• Ylilauri M, Pentikäinen OT. Structural Mechanism of N-Methyl-D-Aspartate Receptor Type 1 Partial Agonism. PLoS One, 2012, 7: ​e47604
  
• 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
• 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

2011

• 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.
• 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
  
• Niinivehmas SP*, Virtanen SI*, Lehtonen JV, Postila PA, Pentikäinen OT Comparison 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)
• 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.
• 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.

2010

• 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
  
• 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.
  
• 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.
• 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
• 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.
• 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.
  
• Postila P, Swanson GT, Pentikäinen OT. Exploring kainate receptor pharmacology using molecular dynamics simulations. ​Neuropharmacology, 2010, 58: 515-527.
  
• 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
• 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.
  

2009

• 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.
  
• 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.
  

2008

• 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
• 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.
  

2007

• 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.
• 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
• 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.
  
• 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.

2006

• 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.
• 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.
• 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.
• 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.
• 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.

2005

• 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!
  
• 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.

2004

• 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.
• 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.
• 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.
• 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.
• 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.

2003

• 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.
• Pentikäinen OT, Settimo L, Keinänen K, Johnson MS. Selective agonist binding of AMPA and kainate receptors, Biochemical ​Pharmacology, 2003, volume 66, pages: 2413-2425.
• Pentikäinen OT. Modeling of protein-ligand interactions: Integrin I-domains and ionotropic glutamate receptors. Ph.D.-thesis.

2002

• 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.
• 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.
• 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.
  
• 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.
• 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.
• 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.

2001

• 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.

2000

• 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.

1999

• 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.
• 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.
• 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.

1998

• 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.
  
• 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.