About the lab

Welcome to Molecular Recognition and Chemical Senses Lab! We study taste recognition and modulation using computational tools, cell-based and sensory evaluation techniques.

A major focus in our lab is the molecular recognition of taste and smell. We use computational methods to study the interactions of bitter, sweet and odorant molecules with their G-Protein coupled receptors (GPCRs). By combining in-silico methods with in-vivo sensory studies with human subjects, and in-vitro heterologous expression assays, we aim to make the connection between the molecular and the behavioral levels of chemosensation. We maintain the BitterDB and study the selectivity, promiscuity and evolution in ligand-receptor binding. Other interests include computer-aided drug discovery for metabolic disorders and cancer.

Funding from The Israeli Chief Scientist, Ministry of Health; The Israeli Chief Scientist, Ministry of Agriculture; and The Israel Science Foundation (ISF) is gratefully acknowledged.

We are hiring!

MSc, PHD and postdoc positions are available for exciting chemosensory-related 1) molecular modeling and 2) cell-based projects. Candidates with background in 1) programming, bioinformatics, chemoinformatics, computer-aided drug discovery or in 2) molecular biology and cell-based assays are encouraged to inquire at masha.niv@mail.huji.ac.il.

✔️ Chemosensation: molecules, receptors and recognition

✔️ GPCRs: modeling, interactions and activation

✔️ Protein Kinases: conformational dynamics, molecular recognition, inhibitors design

✔️ Peptides: structure, function and flexible docking

Selected recent publications
	Bitter or not? BitterPredict, a tool for predicting taste from chemical structure (Scientific Reports, 2017)
	Bitter taste receptors have significantly more agonists than antagonists compared to Family A GPCRs (Methods in Cell Biology, 2016)
	Promiscuity and selectivity of bitter molecules and their receptors (Bioorganic & medicinal chemistry, 2015)
	Schematic representation of the AnchorDock peptide docking protocol (Structure, 2015)
	The effect of bitter quinine on the expression of taste-related genes and behavarioal responses. Chicken was used as a minimalistic model of bitter taste system (Journal of Agricultural and Food Chemistry, 2014)
	Predicting GPCR promiscuity towards its ligands (Journal of Chemical Information and Modeling, 2013)
	BitterDB: a database of bitter compounds (Nucleic Acids Research, 2011)

✈️ Antonella won a JBC travel grant for presenting at a Keystone Symposia, February 2018 (English)

📰 BitterPredict article on PNAS Blog, October 2017 (English)

📻 Radio interview on bitter and sweet research, October 2017 (Hebrew)

📰 BitterPredict article on Ynet, October 2017 (Hebrew)

🍭 Exhibition on sugar, October 2017 (Hebrew)

🎥 Talk: “The Taste of Poisons and of Therapeutic Drugs: Who Cares and How to Predict it”, September 2017 (English)

🍗 Food design exhibition, March 2016 (Hebrew)

2018

  83. Ben Abu N, et al. (2018) The taste of KCl-what a difference a sugar makes. Food Chemistry.

  82. Qutob N, et al. (2018) RGS7 is recurrently mutated in melanoma and promotes migration and invasion of human cancer cells. Scientific Reports 8(1):653.

  81. Xue YA, et al. (2018) Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes. Frontiers in Molecular Biosciences 5:9.

  80. Di Pizio A, et al. (2018) Molecular features underlying selectivity in chicken bitter taste receptors. Frontiers in Molecular Biosciences 5:6.

2017

  79. Wu C, et al. (2017) Biomimetic Sensors for the Senses: Towards Better Understanding of Taste and Odor Sensation. Sensors 17:2881.

  78. Nissim I, et al. (2017) The taste of toxicity: A quantitative analysis of bitter and toxic molecules. IUBMB Life 69:938-946.

  77. Dagan-Wiener A, et al. (2017) Bitter or not? BitterPredict, a tool for predicting taste from chemical structure. Scientific Reports 7(1):12074.

  76. Di-Pizio A, et al. (2017) Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case. Scientific Reports 7(1):8223.

  75. Cheled-Shoval S, et al. (2017) From Cell to Beak: In-Vitro and In-Vivo Characterization of Chicken Bitter Taste Thresholds. Molecules 22(5):821.

  74. Oren T, et al. (2017) Recombinant ostreolysin induces brown fat-like phenotype in HIB-1B cells. Molecular Nutrition & Food Research 61(9).

  73. Dubovski N, et al. (2017) Bitter mouth-rinse affects emotions. Food Quality and Preference 60:154-164.

  72. Bahia MS, et al. (2017) Bitterness prediction in-silico: A step towards better drugs. International Journal of Pharmaceutics.

  71. Cheled-Shoval SL, et al. (2017) Detecting thresholds for bitter, umami, and sweet tastants in broiler chicken using a 2-choice test method. Poultry science 96(1):2206-2218.

  70. Slutzki M, et al. (2017) AnchorDock for Blind Flexible Docking of Peptides to Proteins. Modeling Peptide-Protein Interactions: Methods and Protocols, 95-108.

2016

  69. Weintraub S, et al. (2016) Design and synthesis of novel protein kinase R (PKR) inhibitors. Molecular Diversity 20(4):805-819.

  68. Karaman R, et al. (2016) Probing the Binding Pocket of the Broadly Tuned Human Bitter Taste Receptor TAS2R14 by Chemical Modification of Cognate Agonists. Chemical Biology & Drug Design 88(1):66-75.

  67. Hariri BM, et al. (2016) In vitro effects of anthocyanidins on sinonasal epithelial nitric oxide production and bacterial physiology. American Journal of Rhinology & Allergy 30(4):261-268.

  66. Di Pizio A, et al. (2016) Comparing Class A GPCRs to bitter taste receptors: Structural motifs, ligand interactions and agonist-to-antagonist ratios. G Protein-Coupled Receptors: Signaling, Trafficking and Regulation, Methods in Cell Biology, ed Shukla AK), Vol 132, pp 401-427.

  65. Behrens M, et al. (2016) Structure-function of bitter taste receptors. Chemical Senses 41(4):382-383.

  64. Behrens M, et al. (2016) Bitter taste receptors, nature’s flexible sensors for changing chemical environments. Chemical Senses 41(9):E123-E124.

2015

  63. Di Pizio A & Niv MY (2015) Promiscuity of Bitter Taste Receptors. Chemical Senses 40(3):297-297.

  62. Di Pizio A & Niv MY (2015) Promiscuity and selectivity of bitter molecules and their receptors. Bioorganic & Medicinal Chemistry 23(14):4082-4091.

  61. Ben-Shimon A & Niv MY (2015) AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking. Structure 23(5):929-940.

  60. Arafeh R, et al. (2015) Recurrent inactivating RASA2 mutations in melanoma. Nature Genetics 47(12):1408-+.

2014

  59. Nowak S, Levit A, Niv MY, Meyerhof W, & Behrens M (2014) Activation properties of TAS2R14, a bitter taste receptor with an exceptional wide agonist spectrum. Chemical Senses 39(1):106-106.

  58. Li YD, et al. (2014) Aldehyde Recognition and Discrimination by Mammalian Odorant Receptors via Functional Group-Specific Hydration Chemistry. Acs Chemical Biology 9(11):2563-2571.

  57. Li Y, et al. (2014) Aldehyde recognition and discrimination by mammalian odorant receptors via functional group-specific hydration chemistry. Abstracts of Papers of the American Chemical Society 248.

  56. Levit A, et al. (2014) The bitter pill: clinical drugs that activate the human bitter taste receptor TAS2R14. Faseb Journal 28(3):1181-1197.

  55. Levit A, Beuming T, Krilov G, Sherman W, & Niv MY (2014) Predicting GPCR Promiscuity Using Binding Site Features. Journal of Chemical Information and Modeling 54(1):184-194.

  54. Kowalsman N & Niv MY (2014) GPCR & Company: Databases and Servers for GPCRs and Interacting Partners. G Protein-Coupled Receptors - Modeling and Simulation, Advances in Experimental Medicine and Biology, ed Filizola M), Vol 796, pp 185-204.

  53. Di Pizio A & Niv MY (2014) Computational Studies of Smell and Taste Receptors. Israel Journal of Chemistry 54(8-9):1205-1218.

  52. Cheled-Shoval SL, Behrens M, Meyerhof W, Niv MY, & Uni Z (2014) Perinatal Administration of a Bitter Tastant Influences Gene Expression in Chicken Palate and Duodenum. Journal of Agricultural and Food Chemistry 62(52):12512-12520.

  51. Chapnik N, Genzer Y, Ben-Shimon A, Niv MY, & Froy O (2014) AMPK-derived peptides reduce blood glucose levels but lead to fat retention in the liver of obese mice. Journal of Endocrinology 221(1):89-99.

  50. Behrens M, Nowak S, Levit A, Niv MY, & Meyerhof W (2014) Molecular dissection of human bitter taste receptor activation. Chemical Senses 39(1):77-77.

  49. Aizen J, Kowalsman N, Niv MY, & Levavi-Sivan B (2014) Characterization of tilapia (Oreochromis niloticus) gonadotropins by modeling and immunoneutralization. General and Comparative Endocrinology 207:28-33.

Earlier

  48. Cohen-Kutner M, et al. (2013) Thioredoxin-mimetic peptides (TXM) reverse auranofin induced apoptosis and restore insulin secretion in insulinoma cells. Biochemical Pharmacology 85(7):977-990.

  47. Born S, Levit A, Niv MY, Meyerhof W, & Behrens M (2013) The Human Bitter Taste Receptor TAS2R10 Is Tailored to Accommodate Numerous Diverse Ligands. Journal of Neuroscience 33(1):201-213.

  46. Ben-Shimon A, Shalev DE, & Niv MY (2013) Protonation States in Molecular Dynamics Simulations of Peptide Folding and Binding. Current Pharmaceutical Design 19(23):4173-4181.

  45. Wiener A, Shudler M, Levit A, & Niv MY (2012) BitterDB: a database of bitter compounds. Nucleic Acids Research 40(D1):D413-D419.

  44. Gorinski N, et al. (2012) Computational and Experimental Analysis of the Transmembrane Domain ⁴⁄₅ Dimerization Interface of the Serotonin 5-HT1A Receptor. Molecular Pharmacology 82(3):448-463.

  43. Chapnik N, Levit A, Niv MY, & Froy O (2012) Expression and Structure/Function Relationships of Human Defensin 5. Applied Biochemistry and Biotechnology 166(7):1703-1710.

  42. Aizen J, et al. (2012) Experimental and computational study of inter- and intra-species specificity of gonadotropins for various gonadotropin receptors. Molecular and Cellular Endocrinology 364(1-2):89-100.

  41. Tal-Gan Y, et al. (2011) Backbone Cyclic Peptide Inhibitors of Protein Kinase B (PKB/Akt). Journal of Medicinal Chemistry 54(14):5154-5164.

  40. Levit A, Yarnitzky T, Wiener A, Meidan R, & Niv MY (2011) Modeling of Human Prokineticin Receptors: Interactions with Novel Small-Molecule Binders and Potential Off-Target Drugs. Plos One 6(11).

  39. Levit A, et al. (2011) Iterative in-silico and in-vitro tools for exploration of bitterness. Chemical Senses 36(1):E45-E45.

  38. Born S, et al. (2011) Identification of agonist interaction sites in the human bitter taste receptor hTAS2R10 through in silico model-guided mutagenesis. Chemical Senses 36(1):E44-E45.

  37. Ben-Shimon A & Niv MY (2011) Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping. Plos Computational Biology 7(11).

  36. Behrens M, et al. (2011) Bitter taste receptors of mammals. Chemical Senses 36(1):E5-E6.

  35. Yarnitzky T, Levit A, & Niv MY (2010) Homology modeling of G-protein-coupled receptors with X-ray structures on the rise. Current Opinion in Drug Discovery & Development 13(3):317-325.

  34. Cheng S & Niv MY (2010) Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation. Journal of Chemical Information and Modeling 50(9):1602-1610.

  33. Brockhoff A, Behrens M, Niv MY, & Meyerhof W (2010) Structural requirements of bitter taste receptor activation. Proceedings of the National Academy of Sciences of the United States of America 107(24):11110-11115.

  32. Shudler M & Niv MY (2009) BlockMaster: Partitioning Protein Kinase Structures Using Normal-Mode Analysis. Journal of Physical Chemistry A 113(26):7528-7534.

  31. Rubinstein M & Niv MY (2009) Peptidic Modulators of Protein-Protein Interactions: Progress and Challenges in Computational Design. Biopolymers 91(7):505-513.

  30. Niv MY, et al. (2009) Rational redesign of neutral endopeptidase binding to merlin and moesin proteins. Protein Science 18(5):1042-1050.

  29. Skrabanek L & Niv MY (2008) Scan2S: Increasing the precision of PROSITE pattern motifs using secondary structure constraints. Proteins-Structure Function and Bioinformatics 72(4):1138-1147.

  28. Qvit N, et al. (2008) Synthesis of a novel macrocyclic library: Discovery of an IGF-IR inhibitor. Journal of Combinatorial Chemistry 10(2):256-266.

  27. Niv MY, Skrabanek L, Roberts RJ, Scheraga HA, & Weinstein H (2008) Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S - a novel motif scan algorithm with optional secondary structure constraints. Proteins-Structure Function and Bioinformatics 71(2):631-640.

  26. Niv MY & Filizola M (2008) Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis. Proteins-Structure Function and Bioinformatics 71(2):575-586.

  25. Madsen KL, et al. (2008) Membrane localization is critical for activation of the PICK1BAR domain. Traffic 9(8):1327-1343.

  24. Mack E, et al. (2008) Prevention of insulin resistance and beta-cell loss by abrogating PKC epsilon-induced serine phosphorylation of muscle IRS-1 in Psammomys obesus. Diabetes-Metabolism Research and Reviews 24(7):577-584.

  23. Niv MY, Skrabanek L, Filizola M, & Weinstein H (2007) Modeling activated states of GPCRs: the rhodopsin template (vol 21, pg 419, 2007). Journal of Computer-Aided Molecular Design 21(7):419-419.

  22. Niv MY, et al. (2007) Topology of type II REases revisited; structural classes and the common conserved core. Nucleic Acids Research 35(7):2227-2237.

  21. Niv MY, Han D, Madsen K, Gether U, & Weinstein H (2007) Structural modeling and phenotypic characterization of the functional modulation produced by the interaction between the PDZ and BAR domains in PICK1. Biophysical Journal:219A-219A.

  20. Niv MY & Filizola M (2007) Dynamic models of G-protein coupled receptor oligomers: Insights from normal mode analysis. Biophysical Journal:379A-379A.

  19. Bargheer M, et al. (2007) Dynamics of electronic states and spin-flip for photodissociation of dihalogens in matrices: Experiment and semiclassical surface-hopping and quantum model Simulations for F-2 and CIF in solid Ar. Journal of Physical Chemistry A 111(38):9573-9585.

  18. Niv MY, Skrabanek L, Filizola M, & Weinstein H (2006) Modeling activated states of GPCRs: the rhodopsin template. Journal of Computer-Aided Molecular Design 20(7-8):437-448.

  17. Wexler ID, Niv MY, & Reuveni H (2005) Sequence-based protein kinase inhibition: applications for drug development. Biotechniques 39(4):575-576.

  16. Niv MY & Weinstein H (2005) Structural insights into phosphorylation-mediated regulation of PDZ domains interactions. Biophysical Journal 88(1):219A-219A.

  15. Niv MY & Weinstein H (2005) A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains. Journal of the American Chemical Society 127(40):14072-14079.

  14. Madsen KL, et al. (2005) Molecular determinants for the complex binding specificity of the PDZ domain in PICK1. Journal of Biological Chemistry 280(21):20539-20548.

  13. Beuming T, Skrabanek L, Niv MY, Mukherjee P, & Weinstein H (2005) PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics 21(6):827-828.

  12. Beuming T, et al. (2005) Specific PDZ-peptide interactions identified with PDZBase - a database of PDZ-domain mediated protein-protein interactions. Biophysical Journal 88(1):219A-219A.

  11. Qvit N, et al. (2004) NOVEL MACROCYCLIC LIBRARIES WITH SPATIAL DIVERSITY (SIBS): APPLICATION FOR THE DISCOVERY OF IGF-1R INHIBITOR. Journal of Peptide Science 10:95-95.

  10. Niv MY, et al. (2004) Sequence-based design of kinase inhibitors applicable for therapeutics and target identification. Journal of Biological Chemistry 279(2):1242-1255.

  9. Gerber RB, Niv MY, & Cohen A (2003) Ultrafast cage-induced spin flip processes in molecular photodissociation in matrices and clusters. Abstracts of Papers of the American Chemical Society 226:U429-U429.

  8. Bargheer M, Niv MY, Gerber RB, & Schwentner N (2002) Ultrafast solvent-induced spin-flip and nonadiabatic coupling: ClF in argon solids. Physical Review Letters 89(10).

  7. Cohen A, Niv MY, & Gerber RB (2001) Formation of novel rare-gas-containing molecules by molecular photodissociation in clusters. Faraday Discussions 118:269-280.

  6. Chaban G, et al. (2001) Photodissociation dynamics of molecular fluorine in an argon matrix induced by ultrashort laser pulses. Journal of Physical Chemistry A 105(12):2770-2782.

  5. Niv MY, Bargheer M, & Gerber RB (2000) Photodissociation and recombination of F-2 molecule in Ar-54 cluster: Nonadiabatic molecular dynamics simulations. Journal of Chemical Physics 113(16):6660-6672.

  4. Gerber RB, Korolkov MV, Manz J, Niv MY, & Schmidt B (2000) A reflection principle for the control of molecular photodissociation in solids: model simulation for F-2 in Ar. Chemical Physics Letters 327(1-2):76-84.

  3. Baumfalk R, Nahler NH, Buck U, Niv MY, & Gerber RB (2000) Photodissociation of HBr adsorbed on the surface and embedded in large Ar-n clusters. Journal of Chemical Physics 113(1):329-338.

  2. Niv MY, Krylov AI, Gerber RB, & Buck U (1999) Photodissociation of HCl adsorbed on the surface of an Ar-12 cluster: Nonadiabatic molecular dynamics simulations. Journal of Chemical Physics 110(22):11047-11053.

  1. Niv MY, Krylov AI, & Gerber RB (1997) Photodissociation, electronic relaxation and recombination of HCl in Ar-n(HCl) clusters - Non-adiabatic molecular dynamics simulations. Faraday Discussions 108:243-254.

Education

• 🎓 PhD, Mentor: Prof. Benny Gerber (2001)
  Institute of Chemistry, The Hebrew University of Jerusalem, Israel

• 🎓 MSc via direct PHD program (1997)
  Institute of Chemistry, The Hebrew University of Jerusalem, Israel

• 🎓 BSc in Chemistry, cum laude (1994)
  The Hebrew University of Jerusalem, Israel

Current Positions

• 🎓 Vice Dean for Research (2017- )
  Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel

• 🎓 Associate Professor, tenured (2014- )
  Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel

Past Positions

• 🎓 Director of Biochemistry and Food Science BSc study program (2014-2017)
  Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel

• 🎓 Visiting scholar at UCSF, hosted by Prof. Brian Shoichet (2015 summer sabbatical)

• 🎓 Director of MSc study program in Biochemistry and Food Science (2014-2016)
  The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel

• 🎓 Senior Lecturer (2009-2014)
  The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel

• 🎓 Lecturer (2007-2009)
  The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Israel

• 🎓 Post-doctoral fellow in Computational Biomedicine (2003-2007)
  Weill Medical College of Cornell University, NY, US; Mentor: Prof. Harel Weinstein

• 💊 Bioinformatics and Molecular Modeling Group Leader (2000-2003)
  Keryx Biopharmaceuticals, Jerusalem, Israel

Teaching

• 👉 Introduction to Bioinformatics and Structural Biochemistry (71437)
• 👉 Methodology of Sensory Food Evaluation (71451)
• 👉 Laboratory in Sensory Food Evaluation (71450)
• 👉 New horizons in food and nutrition research (71479)

Distinctions and Awards

• Vigevani Visiting Professor to Italy (2017-2018)
• Women’s League for Israel Senior Lectureship in Nutrition (since 2011)
• Krill Prize for Excellence in Science from the Wolf Foundation (2010)
• Fritz Haber research award (1999)
• BSc honorary award (1993)
• DAAD scholarship (1992)
• Faculty of science dean` s list (1991)
• Elwing award for excellence in analytical chemistry (1991)

Recent international conferences

• Weurman Flavour Research Symposium, Graz, Austria (2017)
• ECRO meeting, Cambridge, UK (2017)
• Pangborn Sensory Science Symposium, Rhode Island, USA (2017)
• GLISTEN COST CM1027, Prague, Czech Republic, invited (2016)
• ECRO meeting, Athens, Greece, invited (2016)
• EupFI Lisbon, Portugal, invited (2016)
• EuroQSAR, Verona, Italy, Keynote (2016)
• ISQPB President’s meeting, Bergen, Norway, Keynote, declined (2016)
• ACHEMS annual meeting, Florida, US, invited (2015)
• 3DSig Boston, US, Keynote (2014)
• Nauta GPCR Medicinal Chemistry Symposium, Amsterdam, Netherlands, invited (2013)
• Cecam workshop, Lausanne, Switzerland, invited (2012)
• ISQPB President’s meeting, Cetraro, Italy, invited (2010)

Academic Activities

• 💊 Advisory board member for ScienceAbroad (2017- )
• 📰 Editorial Advisory Board Member (2015-2017)
  Journal of Agricultural and Food Chemistry
• 📰 Editorial Board Member (2014- )
  Scientific Reports, Nature publishing group
• 🎓 SAB member for international PhD school (Bavaria)
• 🍉 Academic chair of Food Innovation Forum, Israel (2016- )
• 💻 Member of Fritz Haber Center for Molecular Dynamics (2012- )
• 🎓 Member of Jerusalem Brain Community (2016- )
• 💊 Management committee member and WG leader in COST ACTION CM1027 (GLISTEN) (2013- )
• 💊 Management committee substitute member in COST ACTION CA15135 (Mu.Ta.Lig) (2016- )

Office Address: The Institute of Biochemistry, Food and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O.Box 12, Rehovot 76100, Israel

Tel: +972–(0)8–9489664

Email Address: masha.niv@mail.huji.ac.il