Watermelon: setup and validation of an in silico fragment-based approach

References

• Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D. Multiple solvent crystal structures: probing binding sites, plasticity and hydration. J Mol Biol. 2006;357(5):1471–1482.
   PubMed Web of Science ®Google Scholar
• Mortier J, Dhakal P, Volkamer A. Truly target-focused pharmacophore modeling: a novel tool for mapping intermolecular surfaces. Molecules. 2018;23(8):1959.
   PubMed Web of Science ®Google Scholar
• Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable “hot spots” of proteins using Fourier domain correlation techniques. Bioinformatics. 2009;25(5):621–627.
   PubMed Web of Science ®Google Scholar
• Heider J, Kilian J, Garifulina A, Hering S, Langer T, Seidel T. Apo2ph4: a versatile workflow for the generation of receptor-based pharmacophore models for virtual screening. J Chem Inf Model. 2023;63(1):101–110.
   PubMed Web of Science ®Google Scholar
• Wolber G, Langer T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model. 2005;45(1):160–169.
   PubMed Web of Science ®Google Scholar
• Ung PMU, Ghanakota P, Graham SE, Lexa KW, Carlson HA. Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case. Biopolymers. 2016;105(1):21–34.
   PubMed Web of Science ®Google Scholar
• Graham SE, Smith RD, Carlson HA. Predicting displaceable water sites using mixed-solvent molecular dynamics. J Chem Inf Model. 2018;58(2):305–314.
   PubMed Web of Science ®Google Scholar
• Manera C, Tuccinardi T, Martinelli A. Indoles and related compounds as cannabinoid ligands. Mini Rev Med Chem. 2008;8(4):370–387.
   PubMed Web of Science ®Google Scholar
• Deng H, Li W. Monoacylglycerol lipase inhibitors: modulators for lipid metabolism in cancer malignancy, neurological and metabolic disorders. Acta Pharm Sin B. 2020;10(4):582–602.
   PubMed Web of Science ®Google Scholar
• Tuccinardi T, Granchi C, Rizzolio F, Caligiuri I, Battistello V, Toffoli G, Minutolo F, Macchia M, Martinelli A. Identification and characterization of a new reversible MAGL inhibitor. Bioorg Med Chem. 2014;22(13):3285–3291.
   PubMed Web of Science ®Google Scholar
• Galati S, Di Stefano M, Macchia M, Poli G, Tuccinardi T. MolBook UNIPI─create, manage, analyze, and share your chemical data for free. J Chem Inf Model. 2023;63(13):3977–3982.
   PubMed Web of Science ®Google Scholar
• Schalk-Hihi C, Schubert C, Alexander R, Bayoumy S, Clemente JC, Deckman I, DesJarlais RL, Dzordzorme KC, Flores CM, Grasberger B, et al. Crystal structure of a soluble form of human monoglyceride lipase in complex with an inhibitor at 1.35 Å resolution. Protein Sci. 2011;20(4):670–683.
   PubMed Web of Science ®Google Scholar
• Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res. 2000;28(1):235–242.
   PubMed Web of Science ®Google Scholar
• Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–2791.
   PubMed Web of Science ®Google Scholar
• Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem. 2005;26(16):1668–1688.
   PubMed Web of Science ®Google Scholar
• Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, et al. AmberTools. J Chem Inf Model. 2023;63(20):6183–6191.
   PubMed Web of Science ®Google Scholar
• Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25(9):1157–1174.
   PubMed Web of Science ®Google Scholar
• Jakalian A, Jack DB, Bayly CI. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem. 2002;23(16):1623–1641.
   PubMed Web of Science ®Google Scholar
• Wang J, Wang W, Kollman PA, Case DA. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model. 2006;25(2):247–260.
   PubMed Web of Science ®Google Scholar
• Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput. 2013;9(7):3084–3095.
   PubMed Web of Science ®Google Scholar
• Durrant JD, McCammon JA. BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model. 2011;29(6):888–893.
   PubMed Web of Science ®Google Scholar
• Poli G, Seidel T, Langer T. Conformational sampling of small molecules with iCon: performance assessment in comparison with OMEGA. Front Chem. 2018;6:229.
   PubMed Web of Science ®Google Scholar
• Tanchuk VY, Tanin VO, Vovk AI, Poda G. A new, improved hybrid scoring function for molecular docking and scoring based on AutoDock and AutoDock Vina. Chem Biol Drug Des. 2016;87(4):618–625.
   PubMed Web of Science ®Google Scholar
• Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem. 2004;47(7):1750–1759.
   PubMed Web of Science ®Google Scholar
• Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved protein-ligand docking using GOLD. Proteins. 2003;52(4):609–623.
   PubMed Web of Science ®Google Scholar
• Tietze S, Apostolakis J. GlamDock: development and validation of a new docking tool on several thousand protein-ligand complexes. J Chem Inf Model. 2007;47(4):1657–1672.
   PubMed Web of Science ®Google Scholar
• Korb O, Stützle T, Exner TE. Empirical scoring functions for advanced protein-ligand docking with PLANTS. J Chem Inf Model. 2009;49(1):84–96.
   PubMed Web of Science ®Google Scholar
• Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem. 2015;36(15):1132–1156.
   PubMed Web of Science ®Google Scholar
• OEDOCKING 4.3.0.3. OpenEye. Santa Fe (NM): Cadence Molecular Sciences, Inc., [accessed 2024 Apr 8]. http://www.eyesopen.com.
   Google Scholar
• Ruiz-Carmona S, Alvarez-Garcia D, Foloppe N, Garmendia-Doval AB, Juhos S, Schmidtke P, Barril X, Hubbard RE, Morley SD. rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLOS Comput Biol. 2014;10(4):e1003571.
   PubMed Web of Science ®Google Scholar
• Tuccinardi T, Poli G, Romboli V, Giordano A, Martinelli A. Extensive consensus docking evaluation for ligand pose prediction and virtual screening studies. J Chem Inf Model. 2014;54(10):2980–2986.
   PubMed Web of Science ®Google Scholar
• Granchi C, Lapillo M, Glasmacher S, Bononi G, Licari C, Poli G, El Boustani M, Caligiuri I, Rizzolio F, Gertsch J, et al. Optimization of a benzoylpiperidine class identifies a highly potent and ­selective reversible monoacylglycerol lipase (MAGL) inhibitor. J Med Chem. 2019;62(4):1932–1958.
   PubMed Web of Science ®Google Scholar
• Ferrario G, Baron G, Gado F, Della Vedova L, Bombardelli E, Carini M, D’Amato A, Aldini G, Altomare A. Polyphenols from thinned young apples: HPLC-HRMS profile and evaluation of their anti-oxidant and anti-inflammatory activities by proteomic studies. Antioxidants. 2022;11(8):1577.
   Web of Science ®Google Scholar
• Zygmunt PM, Ermund A, Movahed P, Andersson DA, Simonsen C, Jönsson BA, Blomgren A, Birnir B, Bevan S, Eschalier A, et al. Monoacylglycerols activate TRPV1–a link between phospholipase C and TRPV1. PLOS One. 2013;8(12):e81618.
   PubMed Web of Science ®Google Scholar
• Ikeda S, Sugiyama H, Tokuhara H, Murakami M, Nakamura M, Oguro Y, Aida J, Morishita N, Sogabe S, Dougan DR, et al. Design and synthesis of novel spiro derivatives as potent and reversible monoacylglycerol lipase (MAGL) inhibitors: bioisosteric transformation from 3-Oxo-3,4-dihydro-2 H -benzo [b] [1,4]oxazin-6-yl moiety. J Med Chem. 2021;64(15):11014–11044.
   PubMed Web of Science ®Google Scholar
• Jha V, Biagi M, Spinelli V, Di Stefano M, Macchia M, Minutolo F, Granchi C, Poli G, Tuccinardi T. Discovery of monoacylglycerol lipase (MAGL) inhibitors based on a pharmacophore-guided virtual screening study. Molecules. 2021;26(1):78.
   Web of Science ®Google Scholar
• He Y, Schild M, Grether U, Benz J, Leibrock L, Heer D, Topp A, Collin L, Kuhn B, Wittwer M, et al. Development of high brain-penetrant and reversible monoacylglycerol lipase PET tracers for neuroimaging. J Med Chem. 2022;65(3):2191–2207.
   PubMed Web of Science ®Google Scholar
• Aida J, Fushimi M, Kusumoto T, Sugiyama H, Arimura N, Ikeda S, Sasaki M, Sogabe S, Aoyama K, Koike T. Design, synthesis, and evaluation of piperazinyl pyrrolidin-2-ones as a novel series of reversible monoacylglycerol lipase inhibitors. J Med Chem. 2018;61(20):9205–9217.
   PubMed Web of Science ®Google Scholar
• Poli G, Martinelli A, Tuccinardi T. Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies. J Enzyme Inhib Med Chem. 2016;31(suppl 2):167–173.
   PubMedGoogle Scholar
• Russo Spena C, De Stefano L, Poli G, Granchi C, El Boustani M, Ecca F, Grassi G, Grassi M, Canzonieri V, Giordano A, et al. Virtual screening identifies a PIN1 inhibitor with possible antiovarian cancer effects. J Cell Physiol. 2019;234(9):15708–15716.
   PubMed Web of Science ®Google Scholar
• Chiarelli LR, Mori M, Barlocco D, Beretta G, Gelain A, Pini E, Porcino M, Mori G, Stelitano G, Costantino L, et al. Discovery and development of novel salicylate synthase (MbtI) furanic inhibitors as antitubercular agents. Eur J Med Chem. 2018;155:754–763.
   PubMed Web of Science ®Google Scholar
• Poli G, Giuntini N, Martinelli A, Tuccinardi T. Application of a FLAP-consensus docking mixed strategy for the identification of new fatty acid amide hydrolase inhibitors. J Chem Inf Model. 2015;55(3):667–675.
   PubMed Web of Science ®Google Scholar
• Lapillo M, Salis B, Palazzolo S, Poli G, Granchi C, Minutolo F, Rotondo R, Caligiuri I, Canzonieri V, Tuccinardi T, et al. First-of-its-kind STARD 3 inhibitor: in silico identification and biological evaluation as anticancer agent. ACS Med Chem Lett. 2019;10(4):475–480.
   PubMed Web of Science ®Google Scholar
• Galati S, Sainas S, Giorgis M, Boschi D, Lolli ML, Ortore G, Poli G, Tuccinardi T. Identification of human dihydroorotate dehydrogenase inhibitor by a pharmacophore-based virtual screening study. Molecules. 2022;27(12):3660.
   PubMed Web of Science ®Google Scholar
• Granchi C, Rizzolio F, Palazzolo S, Carmignani S, Macchia M, Saccomanni G, Manera C, Martinelli A, Minutolo F, Tuccinardi T. Structural optimization of 4-chlorobenzoylpiperidine derivatives for the development of potent, reversible, and selective monoacylglycerol lipase (MAGL) inhibitors. J Med Chem. 2016;59(22):10299–10314.
   PubMed Web of Science ®Google Scholar
• Yamamoto M, Kensler TW, Motohashi H. The KEAP1-NRF2 system: a thiol-based sensor-effector apparatus for maintaining redox homeostasis. Physiol Rev. 2018;98(3):1169–1203.
   PubMed Web of Science ®Google Scholar
• Della Vedova L, Ferrario G, Gado F, Altomare A, Carini M, Morazzoni P, Aldini G, Baron G. Liquid chromatography–high-resolution mass spectrometry (LC-HRMS) profiling of commercial enocianina and evaluation of their antioxidant and anti-inflammatory activity. Antioxidants. 2022;11(6):1187.
   Web of Science ®Google Scholar
• Zhao Q, He Z, Chen N, Cho YY, Zhu F, Lu C, Ma WY, Bode AM, Dong Z. 2-Arachidonoylglycerol stimulates activator protein-1-dependent transcriptional activity and enhances epidermal growth factor-induced cell transformation in JB6 P + cells. J Biol Chem. 2005;280(29):26735–26742.
   PubMed Web of Science ®Google Scholar