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139. Ma’ayan, A., Schlessinger, A., Filizola, M., Sebra, R., Shi, L., Pandey, G., Itan, Y., Kenny, E.E. “AI + Omics are Bringing the Bench Closer to the Bedside” in The Frontiers of Medical Research (Science/AAAS, Washington, DC, 2023), p. 8-10. https://mshs.co/47uoRSN

138. Zilberg, G., Parpounas, A.K., Warren, A.L., Fiorillo, B., Provasi, D., Filizola, M., Wacker, D. “Structural Insights into the Unexpected Agonism of Tetracyclic Antidepressants at Serotonin Receptors 5-HT1eR and 5-HT1FR” bioRxiv Oct 7, 2023; https://doi.org/10.1101/2023.10.05.561100

137. Felt, K., Salas-Estrada, L., Stauffer, M., Guzzo, P.R., Xie, D., Huang, J., Filizola, M., Chakrapani, S. “Structural basis for partial agonism in 5-HT3A receptors” (2023) Nature Structural & Molecular Biology, in press.

136. Strauss, A., Gonzalez-Hernandez, A.J., Lee, J., Abreu, N., Selvakumar, P., Salas-Estrada, L., Kristt, M., Marx, D.C., Gilliland, K., Melancon, B.J., Filizola, M., Meyerson, J., Levitz, J. “Structural basis of allosteric modulation of metabotropic glutamate receptor activation and desensitization” bioRxiv 2023 Aug 14;2023.08.13.552748. doi: 10.1101/2023.08.13.552748. [PMID: 37645747]

135. Provasi, D. and Filizola, M.” Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques” bioRxiv 2023 Aug 7;2023.08.04.552065. doi: 10.1101/2023.08.04.552065. [PMID: 37609329]

134. Salas-Estrada, L., Provasi, D., Qui, X., Kaniskan, H.Ü., Huang, X.P., DiBerto, J.F., Ribeiro, J.M.L., Jin, J., Roth, B.L., Filizola, M. “De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework” bioRxiv  2023 Apr 26;2023.04.25.537995. doi: 10.1101/2023.04.25.537995. Journal of Chemical Information and Modeling (2023) Aug 28;63(16):5056-5065. [PMID: 37555591]

133. Ahn, D., Provasi, D., Duc, N.M., Xu, J., Salas-Estrada, L., Spasic,, Yun, M.W., Kang, J., Gim, D., Lee, J., Du, Y., Filizola, M., Chung, K.Y. “Gαs slow conformational transition upon GTP binding and a novel Gαs regulator” bioRxiv (2022) doi: https://doi.org/10.1101/2022.10.10.511514;  (2023); iScience Apr 8;26(5):106603. doi: 10.1016/j.isci.2023.106603. [PMID: 37128611 ]


132. Salas-Estrada, L., Fiorillo, B., Filizola, M. “Metadynamics Simulations Leveraged by Statistical Analyses and Artificial Intelligence-Based Tools to Inform the Discovery of G Protein-Coupled Receptor Ligands” (2022) Frontiers in Endocrinology, Section Cellular Endocrinology; 13:1099715. doi: 10.3389/fendo.2022.1099715 [PMID: 36619585]

131. Leitman, M.I., Muller, D., Miller, S., Hanss, B.G., Catron, T.F., Cooper, W.O., Filizola, M. “Implementation of an Online Reporting System to Identify Unprofessional Behaviors and Mistreatment Directed at Trainees at an Academic Medical Center” (2022) JAMA Netw Open; Dec 1;5(12):e2244661.  doi: 10.1001/jamanetworkopen.2022.44661

130. Sen, S., Spasic, A., Sinha, A., Wang, J., Bush, M., Li, J., Nešić, D., Zhou, Y., Angiulli, G., Morgan, P., Salas-Estrada, L., Takagi, J., Walz, T., Coller, B., Filizola, M. “Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonist of Integrin aVb3” (2022) Journal of Chemical Information and Modeling Oct 24. doi: 10.1021/acs.jcim.2c00999.


129. Filizola, M., Leitman I.M., Muller, D. “The future of medical, biomedical, and graduate medical education: We will reap what we sow” in The Frontiers of Medical Research (Science/AAAS, Washington, DC, 2021), p. 7-9. https://www.science.org/do/10.1126/resource.acx9648/full/icahn_booklet_2021_11_19.pdf

128. Fuchs, T.J., Kovatch, P., Bagiella, E., Darrow, B., Guttman-Yassky, E., Drayer, B., Fayad, Z.A., Cordon-Cardo, C., Bottinger, E., Filizola, M., Reich, D. “The advent of artificial intelligence in health care and its practical implementation” in The Frontiers of Medical Research (Science/AAAS, Washington, DC, 2021), p. 4-5. https://www.science.org/do/10.1126/resource.acx9648/full/icahn_booklet_2021_11_19.pdf

127. Kenny, P.J., Bhardwaj, N., Filizola, M., Stewart, A. “The future of therapeutic discovery: Pioneering new pathways to personalized medicine” in The Frontiers of Medical Research (Science/AAAS, Washington, DC, 2021), p. 31-33. https://www.science.org/do/10.1126/resource.acx9648/full/icahn_booklet_2021_11_19.pdf

126. Chakraborty, S., Diberto, J., Faouzi, A., Bernhard, S., Gutridge, A., Ramsey, S., Zhou, Y., Provasi, D., Nuthikattu, N., Jilakia, R., Nelson, M.N.F., Asher, W.B., Eans, S. O., Wilson, L.L., Chintala, S.M., Filizola, M., van Rijn, R.M., Margolis, E.B., Roth, B.L., McLaughlin, J.P., Che, T., Sames, D., Javitch, J.A., Majumdar, S. “A novel mitragynine analog with low efficacy mu-opioid receptor agonism displays antinociception with attenuated adverse effects” (2021) Journal of Medicinal Chemistry Sep 23;64(18):13873-13892. [PMID: 34505767]

125. Pryce, K.D., Kang, H.J., Sakloth, F., Liu, Y., Khan, S., Toth, K., Kapoor, A., Nicolais, A., Che, T., Qin, L., Bertherat, F., Kaniskan, H.U., Jin, J., Cameron, M.D.,Roth, B.L., Zachariou, V., and Filizola, M.“Positive Allosteric Modulators of the m-Opioid Receptor Enhance the Antinociceptive Efficacy of Opioids but not their Adverse Effects” (2021) Neuropharmacology Sep 1;195:108673 [PMID: 34153316]

124. Jatiani, S.S., Christie, S., Leshchenko, V., Jain, R., Kapoor, A., Bisignano, P., Lee, C., Kaniskan, H.U., Edwards, D., Meng, F., Lagana, A., Youssef, Y., Wiestner, A., Alinari, L., Jin, J., Filizola, M., Aggarwal, A. K., Parekh, S. ““SOX11 Inhibitors Are Cytotoxic in Mantle Cell Lymphoma.” Clinical Cancer Research  (2021) Aug 15;27(16):4652-4663. [PMID: 34158358]

123. Thibado, J.K., Tano, J.Y., Lee, J. Salas-Estrada, L., Provasi, D., Strauss, A., Ribeiro, J.M.L., Xiang, G., Broichhagen, J., Filizola, M., Lohse, M.L., Levitz, J., “Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors” eLife (2021) Apr 21;10:e67027. [PMID: 33880992]

122. Nešić, D., Bush, M., Spasic, A., Li, J.,  Kamata, T., Handa, M., Filizola, M., Thomas Walz, T., Coller, B.S., “Electron Microscopy of the αIIbβ3–PT25-2 Fab Complex Identifies a Mechanism by Which PT25-2 Induces αIIbβ3 Ligand Binding” (2021) Blood Advances, 5(7):1781-1790. [PMID: 33760023]



121. Zhou, Y., Ramsey, S., Provasi, D., El Daibani, A., Appourchaux, K., Chakraborty, S., Kapoor, A., Che, T., Mazumdar, S., Filizola, M. “Predicted Mode of Binding to and Allosteric Modulation of the m-Opioid Receptor by Kratom’s Alkaloids with Reported Antinociception in Vivo” Biochemistry (2020) Dec 4. doi: 10.1021/acs.biochem.0c00658

120. Basak, , Kumar, A. Ramsey, S., Gibbs, E., Kapoor, A., Filizola, M., Chakrapani, S. “High-resolution structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition” https://www.biorxiv.org/content/10.1101/2020.03.30.016154v1;  Elife (2020) 9:e57870.

119. Ribeiro Lamim, J.M., Provasi, D., Filizola, M. “A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors” Journal of Chemical Physics (2020) 153(12):124105.

118. Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J.K.S., Aranda-García, D., Ramírez-Anguita, J.M., Stepniewski, T.M., Worp, N., Varela-Rial, A., Morales-Pastor, A., Lacruz, B.M., Pándy-Szekeres, G., Mayol, E., Giorgino, T., Carlsson, J., Deupi, X., Filipek, S., Filizola, M., Gómez-Tamayo, J.C., Gonzalez, A., Gutierrez-de-Teran, H., Jimenez, M., Jespers, W., Kapla, J., Kelashvili, G., Kolb, P., Latek, D., Marti-Solano, M., Matricon, P., Matsoukas, M.T., Miszta, P., Olivella, M., Perez-Benito, L., Provasi, D., Ríos, S., Rodríguez-Torrecillas, I., Sallander, J., Sztyler, A., Vasile, S., Weinstein, H., Zachariae, U., Hildebrand, P. W., De Fabritiis, G., Sanz, F., Gloriam, D.E., Cordomi, A., Guixà-González, R., Selent, J. “GPCRmd uncovers the dynamics of the 3D-GPCRome” (2020) Nature Methods (2020). https://doi.org/10.1038/s41592-020-0884-y

117. Kapoor, A., Provasi, D., Filizola, M. “Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ-Opioid Receptor” (2020) Molecular Pharmacology, mol.119.119339. doi: 10.1124/mol.119.119339.

116. Nesic, D., Zhang, Y., Spasic, A., Li, J., Provasi, D., Filizola, M., Walz, T., and Coller, B.S. “Cryo-Electron Microscopy Structure of the αIIbβ3-Abciximab Complex” (2020) Arteriosclerosis, Thrombosis, and Vascular Biology 40(3):624-637.



115. Hughes, T.E.T., Del Rosario, J.S., Kapoor, A., Yazici, A. T., Fluck, E.C., Filizola, M., Rohacs, T., Moiseenkova-Bell, V.Y. “Structure-based discovery of novel TRPV5 inhibitors” (2019) ELife ; pii: e49572. doi: 10.7554/eLife.49572.

114. Hu, X., Provasi, D., Filizola, M. “Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation.” bioRxiv 689612; doi: https://doi.org/10.1101/689612; (2019) Biophysical Journal, pii: S0006-3495(19)30854-9. doi: 10.1016/j.bpj.2019.10.007.

113. Ribeiro, JML & Filizola, M. “Insights from Molecular Dynamics Simulations of a Number of G-Protein Coupled Receptor Targets for the Treatment of Pain and Opioid Use Disorders” Frontiers in Molecular Neuroscience (2019) 12:207; doi: 10.3389/fnmol.2019.00207.

112. Li, J., Fukase, Y., Shang, Y., Zou, W., Munoz-Felix, J., Buitrago, L., van Agthoven, J., Zhang, X., Hara, R., Tanaka,Y., Okamoto, R.,  Yasui, T., Nakahata,  T., Imaeda, T., Aso, K.,  Zhou, Y., Locuson, C., Nesic, D., Duggan, M.,  Takagi, J., Vaughan, R., Walz, T., Hodivala-Dilke, K., Teitelbaum, S.L., Arnaout, A.M., Filizola, M., Foley, M.A., Coller, B.S. “Novel Pure αVβ3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations” ACS Pharmacology & Translational Science (2019) 2, 6, 387-401.

111. The PLUMED consortium. “A community effort to promote transparency and reproducibility in molecular simulations” (2019) Nature Methods  16(8):670-673 [PMID: 31363226].

110. Basak, S., Gicheru, Y., Kapoor, A., Mayer, M.L., Filizola, M. and Chakrapani, S. “Molecular mechanism of setron-mediated inhibition of full-length 5-HT3A receptor” (2019) Nature Communications 10(1): 3225 [PMID: 31324772]

109. Ribeiro, JML & Filizola, M. “Allostery in G Protein-Coupled Receptors Investigated by Molecular Dynamics Simulations” (2019) Current Opinion in Structural Biology  Volume 55: 121-128 [PMID: 31096158].

108.  Hu, X., Wang, Y., Hunkele, A., Provasi, D., Pasternak, G.W., Filizola, M. “Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis” (2019) PLOS Computational Biology, 15(1):e1006689  [PMID: 30677023].



107. Meral, D. , Provasi, D., Filizola, M. “An Efficient Strategy to Estimate Thermodynamics and Kinetics of G Protein-Coupled Receptor Activation Using Metadynamics and Maximum Caliber” bioRxiv; https://doi.org/10.1101/367888; (2018) Journal of Chemical Physics 149(22):224101 [PMID: 30553249].

106. Walsh, S., Mathiasen, S., Christensen, S.M., Fay, J.F., King, C., Provasi, D., Borrero, E., Rasmussen, S.G.F., Fung, J.J., Filizola, M., Hristova, K., Kobilka, B., Farrens, D.L., Stamou, D. “Single proteoliposome high content analysis reveals differences in the homo-oligomerization of GPCRs” (2018) Biophysical Journal 115(2):300-312. [PMID: 30021106]

105. Meral, D., Provasi, D., Prada-Gracia, D., Möller, J., Marino, K., Lohse, M.J., and Filizola, M. “Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations” (2018) Scientific Reports 8(1):7705 [PMID: 29769636]

104. Filizola, M. “Insights from Molecular Dynamics Simulations to Exploit New Trends for the Development of Improved Opioid Drugs” (2018) Neuroscience Letters, Feb 18. pii: S0304-3940(18)30119-8. doi: 10.1016/j.neulet.2018.02.037. [PMID: 29466721]

103. Hughes, T.E.T., Lodowski, D.T., Huynh, K.W., Yazici, A., Del Rosario, J., Kapoor, A., Bashak, S., Samanta, A., Han, X., Chakrapani, S., Zhou, Z.H., Filizola, M., Rohacs, T., Han, S., Moiseenkova-Bell, V.Y. “Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM ” (2018) Nature Structural & Molecular Biology, 25(1):53-60 [PMID: 29323279]

102. Marino, K.A. & Filizola, M. “Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations” (2018) “Methods in Molecular Biology”, 1705: 351-364. [PMID: 29188572]



101. Yano, H., Provasi, D., Sheng Cai, N., Filizola, M., Ferré, S., Javitch, J.A., “Development of novel biosensors to study receptor-mediated activation of Gs and Golf” (2017) Journal of Biological Chemistry Dec 8;292(49):19989-19998. [PMID: 29042444]

100. Kapoor, A., Martinez-Rosell, Provasi, D., de Fabritiis, G., and Filizola, M. “Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity” Scientific Reports, (2017) 7(1):11255. [PMID: 28900175]

99. Marino, K.A., Shang, Y., and Filizola, M. “Insights into the Function of Opioid Receptors from Molecular Dynamics Simulations of Available Crystal Structures” British Journal of Pharmacology (2017) Mar 7, doi: 10.1111/bph.13774. [PMID:28266020].

98. Zafar, H., Shang, Y., Li, J., David, G.A. III, Fernandez, J.P., Molina, H., Filizola, M., Coller, B.S. “αIIbβ3-Binding to a Fibrinogen Fragment Lacking the g-chain Dodecapeptide is Activation Dependent and EDTA-Inducible (2017) Blood Advances 1:417-428.



97. Crowley, R.S., Riley, A.P., Sherwood, A.M., Groer, C.E., Shivaperumal, N., Biscaia, M., Paton, K., Schneider, S., Provasi, D., Kivell, B.M., Filizola, M., and Prisinzano, T.E. “Synthetic Studies of Neoclerodane Diterpenes from Salvia divinorum: Identification of a Potent and Centrally Acting μ Opioid Analgesic with Reduced Abuse Liability” (2016) Journal of Medicinal Chemistry, 59(24):11027-11038 [PMID:27958743]

96. Marino, K., Prada-Gracia, D., Provasi, D., Filizola, M. “Impact of Lipid Composition and Receptor Conformation on the Spatio-Temporal Organization of mu-Opioid Receptors in a Multi-component Plasma Membrane Model” (2016) PLOS Computational Biology 12(12):e1005240 [PMID: 27959924].

95. Schneider, S., Provasi, D., Filizola, M. “How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State that Selectively Triggers G Protein-Signaling Pathways.” (2016) Biochemistry 55(46):6456-6466 [PMID: 27778501]

94. Wardman, J.H., Gomes, I., Bobeck, E.N., Stockert, J., Kapoor, A., Bisignano, P., Gupta, A., Mezei, M., Kumar, S., Filizola, M., Devi, L.A. “Identification of a small molecule ligand that activates the neuropeptide receptor GPR171 and increases food intake” (2016) Science Signaling 9(430):ra55. [PMID: 27245612]

93. Kruegel, A.C., Gassaway, M.M., Kapoor, A., Varadi, A., Majumdar, S., Filizola, M., Javitch, J.A., Sames, D. “Synthetic and Receptor Signaling Explorations of the Mitragyna Alkaloids: Mitragynine as an Atypical Molecular Framework for Opioid Receptor Modulators” (2016) Journal of the American Chemical Society 138(21):6754-64 [PMID:27192616]

92. Shang, Y., Yeatman, H.R., Provasi, D., Alt, A., Christopoulos, A.,  Canals, M., and Filizola, M. “Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors” (2016) ACS Chemical Biology11(5):1220-9 [PMID:26841170]



91. Bisignano, P., Burford, N.T., Shang, Y., Marlow, B., Livingston, K.E., Fenton, A.M., Rockwell,K., Budenholzer, L., Traynor, J., Gerritz, S.W., Alt, A., and Filizola, M. “Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the mu-Opioid Receptor” (2015) Journal of Chemical Information & Modeling 55(9):1836-43 [PMID:26347990]

90. Schneider, S., Provasi, D. & Filizola, M. “The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics” (2015) Methods in Molecular Biology, 1335:277-294 [PMID:26260607]

89. Shang, Y. and Filizola, M. “Opioid receptors: Structural and mechanistic insights into pharmacology and signaling” (2015) European Journal of Pharmacology, http://dx.doi.org/10.1016/j.ejphar.2015.05.012; [PMID: 25981301]

88. Burford, N., Livingston, K., Canals, M., Ryan, M., Budenholzer, L., Han, Y., Shang, Y., Herbst, J., O’Connell, J., Banks, M., Zhang, L., Filizola, M., Bassoni, D., Wehrman, T., Christopoulos, A., Traynor, J., Gerritz, S., Alt, A. “Discovery, Synthesis and Molecular Pharmacology of Selective Positive Allosteric Modulators of the δ-Opioid Receptor” (2015) Journal of Medicinal Chemistry 58(10:4220-4229[PMID: 25901762]

87. Buitrago, L., Rendon, A., Liang, Y., Turro, E., Simeoni, I., Negri, A., ThromboGenomics Consortium, Filizola, M., Ouwehand, W.H., Coller, B.S. “αIIbβ3 Variants Defined by Next Generation Sequencing: Predicting Variants Likely to Cause Glanzmann Thrombasthenia” (2015) Proceedings of the National Academy of Science USA, 112(15):E1898-907. [PMID:25827233]

86. G Protein-Coupled Receptors in Drug Discovery, Methods in Molecular Biology lab protocol series, Publisher: Springer; Editor: Marta Filizola; Sept. 14, 2015.

85. Provasi, D., Boz, M.B., Johnston, J.M., Filizola, M. “Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association” PLOS Computational Biology (2015) Mar 30;11(3):e1004148; [PMID: 25822938]


84. Li, J., Vootukuri, S., Shang, Y., Negri, A., Jiang, J.-K., Nedelman, M., Diacovo, T.G., Filizoljournalcovera, M., Thomas, C.J., Coller, B.S. “RUC-4: A Novel αIIbβ3 Antagonist for Pre-hospital Therapy of Myocardial Infarction” Arteriosclerosis, Thrombosis, and Vascular Biology (2014) Aug 21. pii: ATVBAHA.114.303724. [Epub ahead of print]; [PMID: 25147334]

83. Shang, Y., LeRouzic, V., Schneider, S., Bisignano, P., Pasternak, G.W., and Filizola, M. “Mechanistic Insights into the Allosteric Modulation of Opioid Receptors by Sodium Ions” Biochemistry (2014) Aug 12;53(31):5140-9. doi: 10.1021/bi5006915. Epub 2014 Jul 29.; [PMID:25073009]

82. Provasi, D., Negri, A., Coller, B.S., Filizola, M. “Talin-driven inside-out activation mechanism of platelet αIIbβ3 integrin probed by multi-microsecond, all-atom molecular dynamics simulations” PROTEINS: Structure, Function, and Bioinformatics (2014) DOI: 10.1002/prot.24540. [PMID:24677266]

81. Johnston, J.M. & Filizola, M. “Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptors” PLOS One (2014) DOI: 10.1371/journal.pone.0090694. [PMID: 24651466; PMCID: PMC3944890]

80. Jiang, J.-K. McCoy, J.G., Shen, M., LeClair, C., Huang, W., Negri, A., Li, J., Blue, R., Harrington, A., Naini,  S., David, G. III, Choi, W.-S., Volpi, E., Fernandez, J.,  Babayeva, M., Nedelman, M.A., Filizola, M., Coller, B.S., Thomas, C.G. “A novel class of ion displacement ligands as antagonists of the αIIbβ3 receptor that limit conformational reorganization of the receptor” Bioorganic & Medicinal Chemistry Letters (2014) 24(4):1148-53 [PMID: 24461295]

79. Ferré, S., Casadó, V., Devi, L.A., Filizola, M., Jokers, R., Lohse, M.J., Milligan, G., Pin, J.P., Guitart, X. “G Protein-Coupled Receptor Oligomerization Revisited: Functional And Pharmacological Perspectives” Pharmacological Reviews (2014) 66(2):413-34 [PMID: 24515647; PMCID: PMC3973609].

78. Johnston, J.M. and Filizola, M. “Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods” Advances in Experimental Medicine and Biology (2014) 796:95-125 [PMID: 24158803; PMCID: PMC4074508].

77. Scarabelli, G., Provasi, D., Negri, A., and Filizola, M. “Bioactive Conformations of Two Seminal Delta Opioid Receptor Penta-peptides Inferred from Free-Energy Profiles” Biopolymers (2014) 101(1):21-27  [PMID: 23564013; PMCID: PMC3812360]


76. Mondal, S., Johnston, J., Wang, H., Khelashvili, G., Filizola, M., Weinstein, H. “Membrane Driven Spatial Organization of GPCRs” Scientific Reports (2013) 3 (2909): 1-9 [PMID: 24105260; PMCID: PMC3793225].

75. Gomes, I., Fujita, W., Gupta, A., Saldanha, A.S., Negri, A., Pinello, C.E., Roberts, E., Filizola, M., Hodder, P., Devi, L.A. “Identification of a μOR-δOR heteromer-biased agonist with antinociceptive activity” Proceedings of the National Academy of Science USA (2013) Jul 16;110(29):12072-7. [PMID: 23818586; PMCID: PMC3718106]Picture1

74. G Protein-Coupled Receptors – Modeling and Simulation; Advances in Experimental Medicine and Biology series;  Publisher: Springer; 2013; Editor: Marta Filizola.

73. Negri, A., Rives, M.L., Caspers, M., Prisinzano, T.E., Javitch, J.A., Filizola, M. “Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening” Journal of Chemical Information and Modeling (2013) 53: 521-526 [PMID: 23461591; PMCID: PMC3702663]

72. Coudray, N., Valvo, S., Hu, M., Lasala, R., Kim, C., Vink, M., Zhou, M., Provasi, D., Filizola, M., Tao, J., Fang, J., Penczek, P.A., Ubarretxena-Belandia, I., Stokes, D.L. “Inward-Facing Conformation of the Zinc Transporter YiiP revealed by Cryo-electron Microscopy” Proceedings of the National Academy of Science USA (2013) 110(6):2140-2145 [PMID: 23341604; PMCID: PMC3568326]

71. Filizola, M. & Devi, L.A. “Grand Opening of Structure-Guided Design for Novel Opiates” Trends in Pharmacological Sciences (2013) 34(1):6-12 [PMID:23127545; PMCID: PMC3534797]


70. Negri, A., Li, J., Naini, S., Coller, B.S., Filizola, M. “Structure-Based Virtual Screening of Small-Molecule Antagonists of Platelet Integrin αIIbβ3 that Do Not Prime the Receptor to Bind Ligand” Journal of Computer-Aided Molecular Design (2012) 26 (9): 1005-1015 [PMID:22893377; PMCID: PMC3496400]

69. Johnston, J.M., Wang, H., Provasi, D., Filizola, M. “Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors.” PLOS Computational Biology (2012) 8(8):e1002649. [PMID:22916005; PMCID: PMC3420924]

68. Filizola, M. & Devi, L.A. “How opioid drugs bind to receptors” Nature (2012) 485: 314-317 [PMID: 22596150; PMCID: PMC3589518]

67. Zhu, J., Choi, W.-S., McCoy, J. G., Negri, A., Zhu, J., Naini, S., Li, J., Shen, M., Huang, W., Bougie, D., Rasmussen, M., Aster, R., Thomas, C. J.,  Filizola, M.,  Springer, T. A., Coller, B. S. “Structure-Guided Design of a High-Affinity Platelet Integrin αIIbβ3 Receptor Antagonist That Disrupts Mg2+ Binding to the MIDAS.” Science Translational Medicine (2012) 4: 125ra32 (Journal Cover Illustration). [PMID:22422993; PMCID: PMC3589518]

66. Provasi, D. and Filizola, M. “G Protein Coupled Receptors” In: Comprehensive Biophysics, Edward H. Egelman, editor, Vol. 9, Simulation and Modeling, Harel Weinstein. Oxford: Academic Press (2012) pp. 123-148.


65. Fribourg, M., Moreno, J.L., Holloway, T., Provasi, D., Baki, L., Mahajan, R., Park, G., Adney, S.K., Hatcher, C., Eltit, J.M., Ruta, J.D., Albizu, L., Li, Z., Umali, A., Shim, J., Fabiato, A., MacKerell, A.D. Jr., Brezina, V., Sealfon, S.C., Filizola, M., Gonzalez-Maeso, J., Logothetis, D.E. “Decoding the Signaling of a GPCR Heteromeric Complex Reveals a Unifying Mechanism of Action of Antipsychotic Drugs” Cell (2011) 147 (5):1011-1023 [PMID: 22118459; PMCID: PMC3255795]

64. Provasi, D., Camacho-Artacho, M., Negri, A., Mobarec, J.C., Filizola, M. “Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques.” PLOS Computational Biology (2011) 7(10):e1002193. [PMID: 22022248; PMCID: PMC3192824]

63. Johnston, J.M. and Filizola, M. “Showcasing Modern Molecular Dynamics Simulations of Membrane Proteins Through G Protein-Coupled Receptors” Current Opinion in Structural Biology (2011) 21(4):552-558 [PMID:21764295; PMCID: PMC3164745].

62.    Wang, H., Barreyro, L., Provasi, D., Djemil, I., Torres-Arancivia, C., Filizola, M., Ubarretxena-Belandia, I. “Molecular determinants and thermodynamics of the amyloid precursor protein transmembrane domain implicated in Alzheimer’s disease” Journal of Molecular Biology (2011); 408(5):879-895 [PMID:21440556; PMCID: PMC3082318]

61. Golebiewska, U., Johnston, J.M., Devi, L., Filizola, M., and Scarlata, S. “Differential Response to Morphine of the Oligomeric State of m-Opioid in the Presence of d-Opioid Receptors” Biochemistry (2011); 50(14):2829-37; [PMID: 21361347; PMCID: PMC3071705]

60. Johnston, J.M., Aburi, M., Provasi, D., Bortolato, A., Urizar, E., Lambert, N.A., Javitch, J.A., Filizola, M. “Making Structural Sense of Dimerization Interfaces of Delta Opioid Receptor Homodimers” Biochemistry (2011) 50(10):1682-90; [PMID: 21261298; PMCID: PMC3050604]

59. Johnston, J.M and Filizola M. “Investigating Mechanisms of Ligand Recognition, Activation, and Oligomerization in GPCRs Using Enhanced Molecular Dynamics Methods” In: G protein-coupled receptors: From structure to function, Chapter 21, Eds: Jesús Giraldo and Jean-Philippe Pin, The Royal Society of Chemistry (2011) 401-424.


58. Zhu, J., Zhu, J., Negri, A., Provasi, D., Filizola, M., Coller, B.S., Springer, T.A. “The closed headpiece of integrin aIIbb3 and its complex with an aIIbb3-specific antagonist that does not induce opening” Blood (2010) 116 (23): 5050-5059 [PMID: 20679525].

57. Provasi, D., Johnston, J.M., Filizola, M. “Lessons from Free-Energy Simulations of delta-Opioid Receptor Homodimers Involving the Fourth Transmembrane Helix.” Biochemistry (2010) 49 (31): 6771–6776 [PMID: 20617813]

56. Khelashvili, G., Dorff, K., Shan, J., Camacho-Artacho, M., Skrabanek, L., Vroling, B., Bouvier, M., Devi, L., George, S.R., Javitch, J.A., Lohse, M.J., Milligan, G., Neubig, R., Palczewski, K., Parmentier, M., Pin, J.-P., Vriend, G.,  Campagne, F., Filizola, M. “GPCR-OKB: A database for G protein-coupled receptor oligomers.” Bioinformatics (2010) 26(14):1804-5 [PMID: 20501551]

55. Blue R, Li J, Steinberger J, Murcia M, Filizola M, Coller BS. “Effects of limiting extension at the aIIb genu on ligand binding to aIIbb3. Journal of Biological Chemistry (2010) 285(23):17604-13. [PMID: 20363746]

54. Provasi, D. & Filizola, M. “Putative Active States of a Prototypic G-Protein Coupled Receptor from Biased Molecular Dynamics.” Biophysical Journal (2010) 19(10):2347-2355. [PMID: 20483344]

53. Filizola, M. “Increasingly accurate dynamic molecular models of G-protein coupled receptor oligomers: Panacea or Pandora’s box for novel drug discovery?” Life Sciences (2010) 86:590-597. [PMID: 19465029]; [PMCID: PMC2848910]


52. Provasi, D., Bortolato A., Filizola, M. “Exploring Molecular Mechanisms of Ligand Recognition by Opioid Receptors with Metadynamics.” Biochemistry (2009), 48(42):10020-10029. [PMID: 19785461]; [PMCID: PMC2764813]

51. Mobarec, J.C., Sanchez, R., Filizola, M. “Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use?” Journal of Medicinal Chemistry (2009), 52 (16), 5207-5216. [PMID: 19627087]; [PMCID: PMC2891345]

50. Bortolato, A., Mobarec, J.C., Provasi, D., Filizola, M. “Progress in Elucidating the Structural and Dynamic Character of G-Protein Coupled Receptor Oligomers for Use in Drug Discovery” Current Pharmaceutical Design (2009), 15(35):4017-4025. [PMID: 20028319]

49. Blue, R., Kowalska, M.A., Hirsch, J., Murcia, M., Janczak, C., Harrington, A., Jirouskova, M., Li, J., Fuentes, R., Thornton, M.A., Filizola, M., Poncz, M., and Coller, B.S.”Structural and therapeutic insights from the species specificity and in vivo antithrombotic activity of a novel aIIb-specific aIIb3 antagonist” Blood (2009) 114(1):195-201. [PMID: 19414864]

48. Provasi, D., Murcia, M., Coller, B.S., and Filizola, M. “Targeted Molecular Dynamics Reveals Overall Common Conformational Changes Upon Hybrid Domain Swing-Out in beta3 Integrins.” PROTEINS: Structure, Function, and Bioinformatics (2009) 77(2):447-489. [PMID: 19455709]


47. Guo,W., Urizar, E., Kralikova,M., Mobarec,J.C., Shi, L., Filizola, M., Javitch, J.A. “Dopamine D2 Receptors Form Higher Order Oligomers at Physiological Expression Levels” The EMBO Journal, (2008), 27(17):2293-304. [PMID: 18668123]

46. Mobarec, J.C. & Filizola, M. “Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors” Expert Opinion on Drug Discovery (2008) 3:343-355. [PMID: 19672320]; [PMCID: PMC2764813]

45. González-Maeso, J., Ang, R., Yuen, T, Chan, P., Weisstaub, N.V., López-Giménez, J., Zhou, M., Okawa, Y., Callado, L.F., Milligan, G., Gingrich, J.A., Filizola, M., Meana, J.J., Sealfon, S.C. “Identification of a Novel Serotonin/Glutamate Receptor Complex Implicated in Psychosis” Nature (2008) 452:93-7. [PMID: 18297054]

44. Taylor, M. Fung, H.K., Rajgaria, R., Filizola, M., Weinstein, H., Floudas, C.A. “Mutations Affecting the Oligomerization Interface of G-Protein Coupled Receptors Revealed by a Novel De-novo Protein Design Framework.” Biophysical Journal (2008) 94:2470-81. [PMID: 18178645]; [PMCID: PMC2267121]

43. Murcia, M., Jirouskova, M., Li, J.H., Coller, B.S., Filizola, M. “Functional and computational studies of the LIgand-associated Metal Binding Site (LIMBS) of beta3 integrins” PROTEINS: Structure, Function, and Bioinformatics (2008) 71:1779-1791. [PMID: 18175315]

42. Niv, M.Y., Filizola, M. “Influence of Oligomerization on the Dynamics of G-Protein Coupled Receptors as Assessed by Normal Mode Analysis.PROTEINS: Structure, Function, and Bioinformatics (2008) 71:575-586. [PMID: 17963239]; [PMCID: PMC3489929]


41. Skrabanek, L., Murcia, M., Bouvier, M., Devi, L., George, S.R., Lohse, M.J., Milligan, G., Neubig, R., Palczewski, K., Parmentier, M., Pin, J.P., Vriend, G., Javitch, J.A., Campagne, F., Filizola, M. “Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base.” BMC Bioinformatics (2007) 8:177. [PMID: 17537266]

40. Pin, J.-P., Neubig, R., Bouvier, M., Devi, L., Filizola, M., Javitch, J.A., Lohse, M.J., Milligan, G., Palczewski, K., Parmentier, M., Spedding, M. “International Union of Basic and Clinical Pharmacology. LXVII. Recommendations for the Recognition and Nomenclature of G Protein-Coupled Receptor Heteromultimers.” Pharmacological Reviews (2007) 59:5-13. [PMID: 17329545]


39. Filizola, M., Wang, S.X., Weinstein, H. “Dynamic Models of G-Protein Coupled Receptors Dimers: Indications of Asymmetry in the Rhodopsin Dimer from Molecular Dynamics Simulations in a POPC Bilayer.” Journal of Computer-Aided Molecular Design (2006) 20(7-8):405-16. [PMID: 17089205]

38. Niv, M.Y., Skrabanek, L., Filizola, M., Weinstein, H. “Modeling activated states of GPCRs: the rhodopsin template” Journal of Computer-Aided Molecular Design (2006) 20(7-8):437-48. [PMID: 17103019];[PMCID: PMC4030242]

37. Mezei, M. & Filizola, M. “TRAJELIX: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations.” Journal of Computer-Aided Molecular Design (2006) 20: 97-107. [PMID: 16783601]


36. Guo, W., Shi, L., Filizola, M., Weinstein, H., Javitch, J.A. “Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation” Proceedings of the National Academy of Science (2005) 102(48):17495-17500. [PMID: 16301531]

35. Filizola, M., Weinstein, H. “The structure and dynamics of GPCR oligomers: A new focus in models of cell signaling mechanisms and drug design.” Current Opinion in Drug Discovery & Development (2005) 8(5):577-84. [PMID: 16159019]

34. Filizola M. & Weinstein, H. “The study of G-protein coupled receptor oligomerization with computational modeling and bioinformatics.” FEBS Journal (2005) 272, 2926-2938. [PMID: 15955053]

33. Filizola, M., Guo, W., Javitch, J.A., Weinstein, H. “Oligomerization domains of G-protein Coupled Receptors: Insights into the structural basis of GPCR association”. In: Contemporary Clinical Neuroscience: The G Protein-Coupled Receptor Handbook, Ed: L.A. Devi, Humana Press Inc., Totowa, NJ, (2005) Chapter 11, pp. 243-265.[pdf]


32. Filizola, M., Hassan, S.A., Artoni, A., Coller, B.S., Weinstein, H. “Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3” Journal of Biological Chemistry (2004) 279(23), 24624-24630. [PMID: 15056669]


31. Filizola, M., Visiers, I., Skrabanek, L., Campagne, F. and Weinstein H. “Functional mechanisms of GPCRs in a structural context.” In Molecular Neuropharmacology: Strategies and Methods, Eds., A. Schousboe and H. Bräuner-Osborne, Humana Press Inc., Totowa, NJ, (2003) Chapter 13, pp.235-266.[pdf]


30. Filizola, M., Olmea, O., Weinstein, H. “Prediction of heterodimerization interfaces of G-protein coupled receptors with a new subtractive correlated mutation method” Protein Engineering (2002) 15, 881-885. [PMID: 12538907]

29. Filizola, M. and Weinstein, H. “Structural models for dimerization of G-protein coupled receptors: The opioid receptor homodimers” Biopolymers (Peptide Science) (2002) 66, 317-325.  [PMID: 12539260]

28. Filizola, M. & Harris, D.H. “Molecular determinants of recognition and activation at GABAA/benzodiazepine receptors” International Journal of Quantum Chemistry (2002) 88, 56-64.[pdf]

27. Filizola, M. & Perez, J.J. “Assessment of the bioactive conformation of the vasoactive intestinal peptide (VIP) by computational methods” International Journal of Quantum Chemistry (2002) 88, 201-210.[pdf]


26. Filizola, M., Tasso, S.M., Loew, G.H., Villar, H.O., “Global physicochemical properties as activity discriminants for the mGluR1 subtype of metabotropic glutamate receptors” Journal of Computational Chemistry (2001) 22 (16), 2018-2027.[pdf]

25. Filizola, M., Villar, H.O., Loew, G.H. “Differentiation of delta, mu, and kappa opioid receptor agonists based on pharmacophore development and computed physicochemical properties” Journal of Computer Aided Molecular Design (2001) 15(4), 297-307. [PMID: 11349813]

24. Filizola, M., Villar, H.O., Loew, G.H. “Molecular determinants of non-specific recognition of delta, mu, and kappa opioid receptors” Bioorganic Medicinal Chemistry (2001) 9(1), 69-76. [PMID: 11197347]


23. Filizola, M., Harris, D.H., Loew, G.H. “Development of a 3D pharmacophore for non-specific ligand recognition of alpha1, alpha2, alpha3, alpha5, and alpha6 containing GABAA/benzodiazepine receptors” Bioorganic Medicinal Chemistry (2000) 8 (7), 1799-1807. [PMID: 10976528]

22. Filizola, M. & Loew, G.H. “Probing the role of protein environment in Compound I formation of Chloroperoxidase (CPO)” Journal of American Chemical Society (2000) 122, 3599-3605.[pdf]

21. Corcho, F., Filizola, M., Perez, J.J. “Evaluation of the iterative simulated annealing technique in conformational search of peptides” Chemical Physics Letters (2000) 319, 65-70.[pdf]

20. Filizola, M., Harris, D.L., Loew, G.H. “Benzodiazepine-induced hyperphagia: Development and assessment of a 3D pharmacophore by computational methods” Journal of Biomolecular Structure & Dynamics (2000) 17 (5): 769-778. (Journal Cover Illustration). [PMID: 10798522]

19. Filizola, M. & Loew, G.H. “Role of protein environment in horseradish peroxidase Compound I formation: Molecular dynamics simulations of horseradish peroxidase-HOOH complex” Journal of American Chemical Society (2000) 122 (1): 18-25.[pdf]

18. Perez, J.J., Filizola, M., Corcho, F., “Docking of peptide T onto the D1 domain of CD4 receptor” Journal of Biomolecular Structure & Dynamics (2000) 17 (4): 1-9. [PMID: 10698109]


17. Filizola, M., Laakkonen, L., Loew, G.H. “3D modeling, ligand binding and activation studies of the cloned mouse delta, mu, and kappa opioid receptors” Protein Engineering (1999) 12 (11): 927-942. [PMID: 10585498]

16. Filizola, M., Cartení-Farina, M., Perez, J.J. “Molecular modeling study of the differential ligand-receptor interaction at the delta, mu, and kappa opioid receptors” Journal of Computer Aided Molecular Design (1999) 13:397-407. [PMID: 10425604]

15. Corcho, F.J., Filizola, M., Perez, J.J. “Assessment of the bioactive conformation of the farnesyltransferase protein binding recognition motif by computational methods” Journal of Biomolecular Structure & Dynamics (1999) 16: 1043-1052. [PMID: 10333174]

14. Filizola, M., Cartení-Farina, M., Perez, J.J. “Modeling of the 3D structure of rhodopsin using a de novo approach to build G-protein coupled receptors” Journal of Physical Chemistry (1999) 103: 2520-2527.[pdf]


13. Filizola, M., Llorens, O., Cartenì-Farina, M., Perez, J.J. “New insights into the conformational requirements of B2 bradykinin antagonism” Bioorganic Medicinal Chemistry (1998) 6: 1491-1500. [PMID: 9801820]

12. Filizola, M., Perez, J.J., Cartení-Farina, M. “Bundle: A program for building the transmembrane domains of G-protein coupled receptors” Journal of Computer Aided Molecular Design (1998) 12:111-118. [PMID: 9690171]

11. Perez, J.J., Filizola, M., Cartení-Farina, M. “A general procedure for building the transmembrane domains of G-protein coupled receptors” Journal of Mathematical Chemistry (1998) 23: 229-238.

10. Filizola, M., Centeno, N.B., Cartení-Farina, M. Perez, J.J., “Conformational analysis of the highly potent Bradykinin antagonist Hoe-140 by means of two different computational methods” Journal of Biomolecular Structure & Dynamics (1998), 15 (4): 639-652. [PMID: 9514242]

9. Llorens, O., Filizola, M., Spisani, S., Marastoni, M., Herranz, C., Perez, J.J “Amygdalin binds to the CD4 receptor as suggested from molecular modeling studies” Bioorganic Medicinal Chemistry Letters (1998), 8: 781-786. [PMID: 9871541]

8. Filizola, M., Rosell, G., Guerrero, A., Perez, J.J., “Conformational requirements for inhibition of the pheromone catabolism in Spodoptera littoralis” QSAR (1998) 17: 205-210.[pdf]

7. Llorens, O., Centeno, N.B., Filizola, M., Spisani, S., Marastoni, M., Calafell, M., Herranz, C., Perez, J.J. “A proposed bioactive form of peptide T and the design of peptidomimetics” Letters in Peptide Science (1998), 5:179–182.[pdf]


6. Filizola, M., Perez, J.J., Palomer, A., Mauleón, D., “Comparative molecular modeling study of the three dimensional structures of prostaglandin endoperoxide H2 synthase 1 and 2 (COX-1 and COX-2)” Journal of Molecular Graphics (1997), 15: 290-300. [PMID: 9640560]

5. Filizola, M., Cartení-Farina, M., Perez, J.J. “Conformational study of vasoactive intestinal peptide (VIP) by computational methods”, Journal of Peptide Research (1997), 50: 55-64. [PMID: 9273888]

4. Filizola, M., Centeno, N., Perez, J. J. “Computational study of the conformational domains of peptideT” Journal of Peptide Science, (1997), 3: 85-92. [PMID: 9230473]


3. Saviano, M., Rossi, F., Filizola, M., Di Blasio, B., Pedone, C.”[Aib5,6-D-Ala8]cyclolinopeptide A grown from a benzene/acetonitrile mixture” Acta Crystallographica Sect.C (1995) C51, Part4: 663-666. [PMID: 7619339]

2. Saviano, M., Rossi, F., Filizola, M., Isernia, C., Di Blasio, B., Benedetti, E., Pedone, C., Siemion, Z., Pedyczak, A. “Bioactive peptides: conformational studies of [Tyr4]cyclolinopeptide A” Biopolymers (1995), 36: 453-460. [PMID: 7578940]

1. Zanotti, G., Rossi, F., Saviano, M., Tancredi, T., Saviano, G., Maione, A., Filizola, M., Di Blasio, B., Pedone, C. “A potent cyclolinopeptide A analogue: solid state and solution conformation of cyclo[Pro-Phe-Phe-Ala-Glu(otBu)]2” Journal of American Chemical Society (1995), 117: 8651-8658.[pdf]