Skip to main content

Machine Learning and Computational Chemistry for the Endocannabinoid System

  • Protocol
  • First Online:
Endocannabinoid Signaling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2576))

Abstract

Computational methods in medicinal chemistry facilitate drug discovery and design. In particular, machine learning methodologies have recently gained increasing attention. This chapter provides a structured overview of the current state of computational chemistry and its applications for the interrogation of the endocannabinoid system (ECS), highlighting methods in structure-based drug design, virtual screening, ligand-based quantitative structure–activity relationship (QSAR) modeling, and de novo molecular design. We emphasize emerging methods in machine learning and anticipate a forecast of future opportunities of computational medicinal chemistry for the ECS.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Nicolaou CA, Brown N (2013) Multi-objective optimization methods in drug design. Drug Discov Today Technol 10:e427e435

    Article  Google Scholar 

  2. Lipinski C, Hopkins A (2004) Navigating chemical space for biology and medicine. Nature 432:855–861

    Article  CAS  PubMed  Google Scholar 

  3. Dobson CM et al (2004) Chemical space and biology. Nature 432:824–828

    Article  CAS  PubMed  Google Scholar 

  4. Schneider P et al (2020) Rethinking drug design in the artificial intelligence era. Nat Rev Drug Discov 19:353–364

    Article  CAS  PubMed  Google Scholar 

  5. Plowright AT et al (2012) Hypothesis driven drug design: improving quality and effectiveness of the design-make-test-analyse cycle. Drug Discov Today 17:56–62

    Article  CAS  PubMed  Google Scholar 

  6. Schneider G (2019) Mind and machine in drug design. Nat Mach Intell 1:128–130

    Article  Google Scholar 

  7. Jiménez-Luna J, Grisoni F, Weskamp N, Schneider G (2021) Artificial intelligence in drug discovery: recent advances and future perspectives. Expert Opin Drug Discovery 949-959

    Google Scholar 

  8. Maccarrone M (2020) New tools to interrogate endocannabinoid signalling, vol 76. Royal Society of Chemistry

    Book  Google Scholar 

  9. Cristino L, Bisogno T, Di Marzo V (2020) Cannabinoids and the expanded endocannabinoid system in neurological disorders. Nat Rev Neurol 16:9–29

    Article  PubMed  Google Scholar 

  10. Chicca A, Arena C, Manera C (2015) Beyond the direct activation of cannabinoid receptors: new strategies to modulate the endocannabinoid system in CNS-related diseases. Recent Patents on CNS Drug Discovery (Discontinued) 10:122–141

    Google Scholar 

  11. Maccarrone M (2020) Missing pieces to the endocannabinoid puzzle. Trends Mol Med 26:263–272

    Article  CAS  PubMed  Google Scholar 

  12. Bleicher KH, Böhm H-J, Müller K, Alanine AI (2003) Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov 2:369–378

    Article  CAS  PubMed  Google Scholar 

  13. Böhm H-J, Klebe G (1996) What can we learn from molecular recognition in protein–ligand complexes for the design of new drugs? Angew Chem Int Ed Engl 35:2588–2614

    Article  Google Scholar 

  14. Roberts NA et al (1990) Rational design of peptide-based hiv proteinase inhibitors. Science 248:358–361

    Article  CAS  PubMed  Google Scholar 

  15. Erickson J et al (1990) Design, activity, and 2.8 a° crystal structure of a c 2 symmetric inhibitor complexed to hiv-1 protease. Science 249:527–533

    Article  CAS  PubMed  Google Scholar 

  16. Böhm H-J (1993) A novel computational tool for automated structure-based drug design. J Mol Recognit 6:131–137

    Article  PubMed  Google Scholar 

  17. Böhm H-J, Schneider G et al (2003) Protein-ligand interactions from molecular recognition to drug design. Wiley-VCH GmbH

    Book  Google Scholar 

  18. Böhm H-J et al (2004) Fluorine in medicinal chemistry. Chembiochem 5:637–643

    Article  PubMed  Google Scholar 

  19. Kuhn B, Mohr P, Stahl M (2010) Intramolecular hydrogen bonding in medicinal chemistry. J Med Chem 53:2601–2611

    Article  CAS  PubMed  Google Scholar 

  20. Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist’s guide to molecular interactions. J Med Chem 53:5061–5084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hardegger LA, Kuhn B et al (2011) Systematic investigation of halogen bonding in protein– ligand interactions. Angew Chem Int Ed 50:314–318

    Google Scholar 

  22. S’ledz´ P, Caflisch A (2018) Protein structure-based drug design: from docking tomolecular dynamics. Curr Opin Struct Biol 48:93–102

    Article  Google Scholar 

  23. Drenth J (2007) Principles of protein X-ray crystallography. Springer

    Google Scholar 

  24. Renaud J-P et al (2018) Cryo-em in drug discovery: achievements, limitations and prospects. Nat Rev Drug Discov 17:471–492

    Article  CAS  PubMed  Google Scholar 

  25. Wüthrich K (1986) NMR with proteins and nucleic acids. Europhysics News 17:11–13

    Google Scholar 

  26. Müntener T, Joss D, Häussinger D, Hiller S (2022) Pseudocontact shifts in biomolecular NMR spectroscopy. Chem Rev 122:9422–9467

    Google Scholar 

  27. Müntener T, Böhm R, Atz K, Häussinger D, Hiller S (2020) NMR pseudocontact shifts in a symmetric protein homotrimer. J Biomol NMR 74:413–419

    Google Scholar 

  28. Hartmann J-B, Zahn M, Burmann IM, Bibow S, Hiller S (2018) Sequence- specific solution nmr assignments of the β-barrel insertase bama to monitor its conformational ensemble at the atomic level. J Am Chem Soc 140:11252–11260

    Google Scholar 

  29. Thonghin N, Kargas V, Clews J, Ford RC (2018) Cryo-electron microscopy of membrane proteins. Methods 147:176–186

    Article  CAS  PubMed  Google Scholar 

  30. Jumper J et al (2021) Highly accurate protein structure prediction with alphafold. Nature 596:583–589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Tunyasuvunakool K et al (2021) Highly accurate protein structure prediction for the human proteome. Nature 596:590–596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Hua T et al (2016) Crystal structure of the human cannabinoid receptor CB1. Cell 167:750–762

    Google Scholar 

  33. Shao Z et al (2016) High-resolution crystal structure of the human CB1 cannabinoid receptor. Nature 540:602–606

    Google Scholar 

  34. Shao Z et al (2019) Structure of an allosteric modulator bound to the CB1 cannabinoid receptor. Nat Chem Biol 15:1199–1205

    Google Scholar 

  35. Kumar KK et al (2019) Structure of a signaling cannabinoid receptor 1-g protein complex. Cell 176:448–458

    Article  PubMed Central  Google Scholar 

  36. Li X et al (2019) Crystal structure of the human cannabinoid receptor CB2. Cell 176:459–467

    Google Scholar 

  37. Xing C et al (2020) Cryo-em structure of the human cannabinoid receptor CB2-Gi signaling complex. Cell 180:645–654

    Google Scholar 

  38. Liao M, Cao E, Julius D, Cheng Y (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:107–112

    Google Scholar 

  39. Zubcevic L et al (2016) Cryo-electron microscopy structure of the TRPV2 ion channel. Nat Struct Mol Biol 23:180–186

    Google Scholar 

  40. Singh AK, McGoldrick LL, Sobolevsky AI (2018) Structure and gating mechanism of the transient receptor potential channel TRPV3. Nat Struct Mol Biol 25:805–813

    Google Scholar 

  41. Deng Z et al (2018) Cryo-em and x-ray structures of TRPV4 reveal insight into ion permeation and gating mechanisms. Nat Struct Mol Biol 25:252–260

    Google Scholar 

  42. Paulsen CE, Armache J-P, Gao Y, Cheng Y, Julius D (2015) Structure of the TRPA1 ion channel suggests regulatory mechanisms. Nature 520:511–517

    Google Scholar 

  43. Yin Y et al (2018) Structure of the cold-and menthol-sensing ion channel TRPM8. Science 359:237–241

    Google Scholar 

  44. Labar G et al (2010) Crystal structure of the human monoacylglycerol lipase, a key actor in endocannabinoid signaling. Chembiochem 11:218–227

    Google Scholar 

  45. Li F, Fei X, Xu J, Ji C (2009) An unannotated α/β hydrolase superfamily member, ABHD6 differentially expressed among cancer cell lines. Mol Biol Rep 36:691–696

    Google Scholar 

  46. Mileni M et al (2008) Structure-guided inhibitor design for human FAAH by interspecies active site conversion. Proc Natl Acad Sci 105:12820–12824

    Google Scholar 

  47. Wiktor M et al (2017) Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis. Nat Commun 8:15952

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Magotti P et al (2015) Structure of human nape-pld: regulation of fatty-acid ethanolamide biosynthesis by bile acids. Structure (London, England: 1993) 23:598

    Google Scholar 

  49. Hough E et al (1989) High-resolution (1.5 a°) crystal structure of phospholipase c from bacillus cereus. Nature 338:357–360

    Article  CAS  PubMed  Google Scholar 

  50. Picot D, Loll PJ, Garavito RM (1994) The x-ray crystal structure of the membrane protein prostaglandin h 2 synthase-1. Nature 367:243–249

    Article  CAS  PubMed  Google Scholar 

  51. Gilbert NC et al (2020) Structural and mechanistic insights into 5-lipoxygenase inhibition by natural products. Nat Chem Biol 16:783–790

    Article  PubMed  PubMed Central  Google Scholar 

  52. Tresaugues L et al (2012) Crystal structure of the lipoxygenase domain of human arachidonate 12-lipoxygenase, 12s-type. Structure 20:1490–1497

    Google Scholar 

  53. Kobe MJ, Neau DB, Mitchell CE, Bartlett SG, Newcomer ME (2014) The structure of human 15-lipoxygenase-2 with a substrate mimic. J Biol Chem 289:8562–8569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Poulos TL, Finzel BC, Howard AJ (1986) Crystal structure of substrate-free pseudomonas putida cytochrome p-450. Biochemistry 25:5314–5322

    Article  CAS  PubMed  Google Scholar 

  55. Nolte RT et al (1998) Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-γ. Nature 395:137–143

    Article  CAS  PubMed  Google Scholar 

  56. Xu HE et al (2002) Structural basis for antagonist-mediated recruitment of nuclear co-repressors by PPAR α. Nature 415:813–817

    Google Scholar 

  57. Fyffe SA et al (2006) Recombinant human PPAR-β /δ ligand-binding domain is locked in an activated conformation by endogenous fatty acids. J Mol Biol 356:1005–1013

    Google Scholar 

  58. Hsu H-C et al (2017) The antinociceptive agent SBFI-26 binds to anandamide transporters fabp5 and fabp7 at two different sites. Biochemistry 56:3454–3462

    Google Scholar 

  59. Armstrong EH, Goswami D, Griffin PR, Noy N, Ortlund EA (2014) Structural basis for ligand regulation of the fatty acid-binding protein 5, peroxisome proliferator-activated receptor β /δ (FABP5-PPARβ /δ ) signaling pathway. J Biol Chem 289:14941–14954

    Google Scholar 

  60. Curry S, Mandelkow H, Brick P, Franks N (1998) Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites. Nat Struct Biol 5:827–835

    Article  CAS  PubMed  Google Scholar 

  61. Southworth DR, Agard DA (2011) Client-loading conformation of the HSP90 molecular chaperone revealed in the cryo-em structure of the human HSP90: hop complex. Mol Cell 42:771–781

    Google Scholar 

  62. Gorelik A, Gebai A, Illes K, Piomelli D, Nagar B (2018) Molecular mechanism of activation of the immunoregulatory amidase NAAA. Proc Natl Acad Sci 115:E10032–E10040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Muhammed MT, Aki-Yalcin E (2019) Homology modeling in drug discovery: overview, current applications, and future perspectives. Chem Biol Drug Des 93:12–20

    Article  CAS  PubMed  Google Scholar 

  64. Hillisch A, Pineda LF, Hilgenfeld R (2004) Utility of homology models in the drug discovery process. Drug Discov Today 9:659–669

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Montero C, Campillo NE, Goya P, Paèz JA (2005) Homology models of the cannabinoid CB1 and CB2 receptors. A docking analysis study. Eur J Med Chem 40:75–83

    Google Scholar 

  66. Munro S, Thomas KL, Abu-Shaar M (1993) Molecular characterization of a peripheral receptor for cannabinoids. Nature 365:61–65

    Article  CAS  PubMed  Google Scholar 

  67. Soethoudt M et al (2018) Selective photoaffinity probe that enables assessment of cannabinoid CB2 receptor expression and ligand engagement in human cells. J Am Chem Soc 140:6067–6075

    Google Scholar 

  68. Sarott RC et al (2020) Development of high-specificity fluorescent probes to enable cannabinoid type 2 receptor studies in living cells. J Am Chem Soc 142:16953–16964

    Article  CAS  PubMed  Google Scholar 

  69. Ouali Alami N et al (2018) Nf-κb activation in astrocytes drives a stage-specific beneficial neuroimmunological response in als. EMBO J 37:e98697

    Article  PubMed  PubMed Central  Google Scholar 

  70. Guba W, Nazaré M, Grether U (2020) Natural compounds and synthetic drugs to target type-2 cannabinoid (CB2) receptor. New tools to Interrogate Endocannabinoid Signaling 89–167

    Google Scholar 

  71. Haider A et al (2019) Structure–activity relationship studies of pyridine-based ligands and identification of a fluorinated derivative for positron emission tomography imaging of cannabinoid type 2 receptors. J Med Chem 62:11165–11181

    Article  CAS  PubMed  Google Scholar 

  72. Gazzi T et al (2019) Drug derived fluorescent probes for the specific visualization of cannabinoid type 2 receptor-a toolbox approach. ChemRxiv

    Google Scholar 

  73. Haider A et al (2020) Identification and preclinical development of a 2, 5, 6-trisubstituted fluorinated pyridine derivative as a radioligand for the positron emission tomography imaging of cannabinoid type 2 receptors. J Med Chem 63:10287–10306

    Article  CAS  PubMed  Google Scholar 

  74. Walters WP, Stahl MT, Murcko MA (1998) Virtual screening—an overview. Drug Discov Today 3:160–178

    Article  CAS  Google Scholar 

  75. Schneider G et al (2000) Virtual screening for bioactive molecules by evolutionary de novo design. Angew Chem Int Ed 39:4130–4133

    Article  CAS  Google Scholar 

  76. Cereto-Massagué A et al (2015) Molecular fingerprint similarity search in virtual screening. Methods 71:58–63

    Article  PubMed  Google Scholar 

  77. Schneider G, Neidhart W, Giller T, Schmid G (1999) “Scaffold-hopping” by topo- logicalpharmacophore search: a contribution to virtual screening. Angew Chem Int Ed 38:2894–2896

    Article  CAS  Google Scholar 

  78. Roche O et al (2002) Development of a virtual screening method for identification of “frequent hitters” in compound libraries. J Med Chem 45:137–142

    Article  CAS  PubMed  Google Scholar 

  79. Singh J et al (2003) Successful shape-based virtual screening: the discovery of a potent inhibitor of the type uclid receptor kinase (tβ ri). Bioorg Med Chem Lett 13:4355–4359

    Article  CAS  PubMed  Google Scholar 

  80. Schneider G, Böhm H-J (2002) Virtual screening and fast automated docking methods. Drug Discov Today 7:64–70

    Article  CAS  PubMed  Google Scholar 

  81. Tanrikulu Y, Schneider G (2008) Pseudoreceptor models in drug design: bridging ligand-and receptor-based virtual screening. Nat Rev Drug Discov 7:667–677

    Article  CAS  PubMed  Google Scholar 

  82. Cheng T, Li Q, Zhou Z, Wang Y, Bryant SH (2012) Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J 14:133–141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Schneider G (2010) Virtual screening: an endless staircase? Nat Rev Drug Discov 9:273–276

    Article  CAS  PubMed  Google Scholar 

  84. Schneider P, Schneider G (2003) Collection of bioactive reference compounds for focused library design. QSAR Comb Sci 22:713–718

    Article  CAS  Google Scholar 

  85. Schneider G, Schneider P, Renner S (2006) Scaffold-hopping: how far can you jump? QSAR Comb Sci 25:1162–1171

    Article  CAS  Google Scholar 

  86. Reutlinger M et al (2013) Chemically advanced template search (CATS) for scaffold-hopping and prospective target prediction for ‘orphan’ molecules. Mol inform 32:133

    Google Scholar 

  87. Lyu J et al (2019) Ultra-large library docking for discovering new chemotypes. Nature 566:224–229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Rupp M et al (2010) From machine learning to natural product derivatives that selectively activate transcription factor PPARγ. ChemMedChem: Chemistry Enabling Drug Des Discov 5:191–194

    Google Scholar 

  89. Derksen S, Rau O, Schneider P, Schubert-Zsilavecz M, Schneider G (2006) Virtual screening for PPAR modulators using a probabilistic neural network. ChemMedChem: Chemistry Enabling Drug Des Discov 1:1346–1350

    Google Scholar 

  90. Wang H, Duffy RA, Boykow GC, Chackalamannil S, Madison VS (2008) Identification of novel cannabinoid CB1 receptor antagonists by using virtual screening with a pharmacophore model. J Med Chem 51:2439–2446

    Google Scholar 

  91. Foloppe N et al (2009) Discovery and functional evaluation of diverse novel human CB1 receptor ligands. Bioorg Med Chem Lett 19:4183–4190

    Google Scholar 

  92. Markt P et al (2009) Discovery of novel CB2 receptor ligands by a pharmacophore- based virtual screening workflow. J Med Chem 52:369–378

    Google Scholar 

  93. Jha V et al (2021) Discovery of monoacylglycerol lipase (MAGL) inhibitors based on a pharmacophore-guided virtual screening study. Molecules 26:78

    Google Scholar 

  94. Saario SM, Poso A, Juvonen RO, Järvinen T, Salo-Ahen OM (2006) Fatty acid amide hydrolase inhibitors from virtual screening of the endocannabinoid system. J Med Chem 49:4650–4656

    Article  CAS  PubMed  Google Scholar 

  95. Zhao D-S, Wang H-Y, Lian Z-H, Han D-X, Jin X (2011) Pharmacophore modeling and virtual screening for the discovery of new fatty acid amide hydrolase inhibitors. Acta Pharm Sin B 1:27–35

    Article  CAS  Google Scholar 

  96. Grisoni F et al (2018) Scaffold hopping from natural products to synthetic mimetics by holistic molecular similarity. Commun Chem 1:44

    Article  Google Scholar 

  97. Markt P et al (2008) Discovery of novel PPAR ligands by a virtual screening approach based on pharmacophore modeling, 3D shape, and electrostatic similarity screening. J Med Chem 51:6303–6317

    Google Scholar 

  98. Tanrikulu Y et al (2009) Structure-based pharmacophore screening for natural-product-derived PPAR-γ agonists. Chembiochem 10:75–78

    Google Scholar 

  99. Salo OM et al (2005) Virtual screening of novel CB2 ligands using a comparative model of the human cannabinoid CB2 receptor. J Med Chem 48:7166–7171

    Google Scholar 

  100. Chen J-Z, Wang J, Xie X-Q (2007) Gpcr structure-based virtual screening approach for CB2 antagonist search. J Chem Inf Model 47:1626–1637

    Google Scholar 

  101. Renault N et al (2013) Virtual screening of CB2 receptor agonists from uclidea network and high-throughput docking: structural insights into agonist-modulated GPCR features. Chem Biol Drug Des 81:442–454

    Google Scholar 

  102. Poli G et al (2019) Computationally driven discovery of phenyl (piperazin-1-yl) methanone derivatives as reversible monoacylglycerol lipase (MAGL) inhibitors. J Enzyme Inhib Med Chem 34:589–596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Bowman AL, Makriyannis A (2011) Approximating protein flexibility through dynamic pharmacophore models: application to fatty acid amide hydrolase (FAAH). J Chem Inf Model 51:3247–3253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Loo JS et al (2019) Ligand discrimination during virtual screening of the CB1 cannabinoid receptor crystal structures following cross-docking and microsecond molecular dynamics simulations. RSC Adv 9:15949–15956

    Google Scholar 

  105. Salam NK et al (2008) Novel PPAR-gamma agonists identified from a natural product library: a virtual screening, induced-fit docking and biological assay study. Chem Biol Drug Des 71:57–70

    Google Scholar 

  106. Afzal O et al (2014) Docking based virtual screening and molecular dynamics study to identify potential monoacylglycerol lipase inhibitors. Bioorg Med Chem Lett 24:3986–3996

    Article  CAS  PubMed  Google Scholar 

  107. Cherkasov A et al (2014) QSAR modeling: where have you been? Where are you going to? J Med Chem 57:4977–5010

    Google Scholar 

  108. Hansch C, Maloney PP, Fujita T, Muir RM (1962) Correlation of biological activity of phenoxyacetic acids with uclide substituent constants and partition coefficients. Nature 194:178–180

    Article  CAS  Google Scholar 

  109. Muratov EN et al (2020) QSAR without borders. Chem Soc Rev 49:3525–3564

    Google Scholar 

  110. Shoombuatong W et al (2017) Towards the revival of interpretable QSAR models. In: Advances in QSAR modeling. Springer, pp 3–55

    Google Scholar 

  111. Fichera M, Cruciani G, Bianchi A, Musumarra G (2000) A 3D-QSAR study on the structural requirements for binding to CB1 and CB2 cannabinoid receptors. J Med Chem 43:2300–2309

    Google Scholar 

  112. Chen J-Z et al (2006) 3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtypes CB1 and CB2. A combined NMR and COMFA approach. J Med Chem 49:625–636

    Google Scholar 

  113. Durdagi S et al (2007) The application of 3D-QSAR studies for novel cannabinoid ligands substituted at the c1 ‘position of the alkyl side chain on the structural requirements for binding to cannabinoid receptors CB1 and CB2. J Med Chem 50:2875–2885

    Google Scholar 

  114. De Freitas GB, da Silva LL, Romeiro NC, Fraga CA (2009) Development of comfa and comsia models of affinity and selectivity for indole ligands of cannabinoid CB1 and CB2 receptors. Eur J Med Chem 44:2482–2496

    Google Scholar 

  115. Ma C, Wang L, Yang P, Myint KZ, Xie X-Q, Licabeds II (2013) Modeling of ligand selectivity for g-protein-coupled cannabinoid receptors. J Chem Inf Model 53:11–26

    Article  PubMed  PubMed Central  Google Scholar 

  116. De Simone A et al (2017) Design, synthesis, structure–activity relationship studies, and three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling of a series of o-biphenyl carbamates as dual modulators of dopamine d3 receptor and fatty acid amide hydrolase. J Med Chem 60:2287–2304

    Google Scholar 

  117. Lorca M et al (2019) Three-dimensional quantitative structure-activity relationships (3D-QSAR) on a series of piperazine-carboxamides fatty acid amide hydrolase (FAAH) inhibitors as a useful tool for the design of new cannabinoid ligands. Int J Mol Sci 20:2510

    Google Scholar 

  118. Bian Y et al (2019) Prediction of orthosteric and allosteric regulations on cannabinoid receptors using supervised machine learning classifiers. Mol Pharm 16:2605–2615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Da’adoosh, B et al (2019) Discovering highly selective and diverse PPAR-delta agonists by ligand based machine learning and structural modeling. Sci Rep 9:1106

    Google Scholar 

  120. Wang Z, Chen J, Hong H (2021) Developing QSAR models with defined applicability domains on PPARγ binding affinity using large data sets and machine learning algorithms. Environ Sci Technol 55:6857–6866

    Google Scholar 

  121. Valsecchi C et al (2020) Predicting molecular activity on nuclear receptors by multitask neural networks. J Chemom e3325

    Google Scholar 

  122. Bronstein MM, Bruna J, Cohen T, Velicˇkovic´ (2021) Geometric deep learning: grids, groups, graphs, geodesics, and gauges. arXiv:2104.13478

    Google Scholar 

  123. Atz K, Grisoni F, Schneider G (2021) Geometric deep learning on molecular representations. Nat Mach Intell 3:1023–1032

    Article  Google Scholar 

  124. Isert C, Atz K, Jiménez-Luna J, Schneider G (2022) QMugs: quantum mechanical properties of drug-like molecules. Scientific Data 9:273

    Google Scholar 

  125. Atz K, Isert C, Böcker MNA, Jiménez-Luna J, Schneider G (2022) Δ-Quantum machine learning for medicinal chemistry. Phys Chem Chem Phys 24:10775–10783

    Google Scholar 

  126. Gainza P et al (2020) Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning. Nat Methods 17:184–192

    Article  CAS  PubMed  Google Scholar 

  127. Smidt TE, Geiger M, Miller BK (2021) Finding symmetry breaking order parameters with euclidean neural networks. Phys Rev Res 3:L012002

    Google Scholar 

  128. Brooks WH, Guida WC, Daniel KG (2011) The significance of chirality in drug design and development. Curr Top Med Chem 11:760–770

    Article  PubMed  Google Scholar 

  129. LaPlante SR et al (2011) Assessing atropisomer axial chirality in drug discovery and development. J Med Chem 54:7005–7022

    Article  CAS  PubMed  Google Scholar 

  130. Weiland KJ et al (2019) Mechanical stabilization of helical chirality in a macro-cyclic oligothiophene. J Am Chem Soc 141:2104–2110

    Google Scholar 

  131. Schneider G, Fechner U (2005) Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 4:649–663

    Article  CAS  PubMed  Google Scholar 

  132. Böhm H-J (1992) Ludi: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 6:593–606

    Article  PubMed  Google Scholar 

  133. Böhm H-J (1992) The computer program ludi: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des 6:61–78

    Article  PubMed  Google Scholar 

  134. Böhm H-J (1998) Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des 12:309–309

    Google Scholar 

  135. Schneider G, Wrede P (1998) Artificial neural networks for computer-based molecular design. Prog Biophys Mol Biol 70:175–222

    Article  CAS  PubMed  Google Scholar 

  136. Schneider G, Lee M-L, Stahl M, Schneider P (2000) De Novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J Comput Aided Mol Des 14:487–494

    Article  CAS  PubMed  Google Scholar 

  137. Schneider G, Clark DE (2019) Automated de novo drug design: are we nearly there yet? Angew Chem Int Ed 58:10792–10803

    Article  CAS  Google Scholar 

  138. Fechner U, Schneider G (2006) Flux (1): a virtual synthesis scheme for fragment-based de novo design. J Chem Inf Model 46:699–707

    Article  CAS  PubMed  Google Scholar 

  139. Patel H, Bodkin MJ, Chen B, Gillet VJ (2009) Knowledge-based approach to de novo design using reaction vectors. J Chem Inf Model 49:1163–1184

    Article  CAS  PubMed  Google Scholar 

  140. Lessel U, Wellenzohn B, Lilienthal M, Claussen H (2009) Searching fragment spaces with feature trees. J Chem Inf Model 49:270–279

    Article  CAS  PubMed  Google Scholar 

  141. Hartenfeller M et al (2012) Dogs: reaction-driven de novo design of bioactive compounds. PLoS Comput Biol 8:e1002380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Mauser H, Stahl M (2007) Chemical fragment spaces for de novo design. J Chem Inf Model 47:318–324

    Article  CAS  PubMed  Google Scholar 

  143. Chevillard F et al (2018) Binding-site compatible fragment growing applied to the design of β 2-adrenergic receptor ligands. J Med Chem 61:1118–1129

    Article  CAS  PubMed  Google Scholar 

  144. Loving K, Alberts I, Sherman W (2010) Computational approaches for fragment-based and de novo design. Curr Top Med Chem 10:14–32

    Google Scholar 

  145. Pegg SC-H, Haresco JJ, Kuntz ID (2001) A genetic algorithm for structure- based de novo design. J Comput Aided Mol Des 15:911–933

    Article  CAS  PubMed  Google Scholar 

  146. Wong WW, Burkowski FJ (2009) A constructive approach for discovering new drug leads: using a kernel methodology for the inverse-QSAR problem. J Chem 1:4

    Google Scholar 

  147. Miyao T, Kaneko H, Funatsu K (2014) Ring-system-based exhaustive structure generation for inverse-QSPR/QSAR. Mol Inform 33:764–778

    Google Scholar 

  148. Skinnider MA, Stacey RG, Wishart DS, Foster LJ (2021) Chemical language models enable navigation in sparsely populated chemical space. Nat Mach Intell 3:759–770

    Article  Google Scholar 

  149. Segler MH, Kogej T, Tyrchan C, Waller MP (2018) Generating focused molecule libraries for drug discovery with recurrent neural networks. ACS Central Sci 4:120–131

    Article  CAS  Google Scholar 

  150. Skalic M, Jiménez J, Sabbadin D, De Fabritiis G (2019) Shape-based generative modeling for de novo drug design. J Chem Inf Model 59:1205–1214

    Article  CAS  PubMed  Google Scholar 

  151. Merk D, Friedrich L, Grisoni F, Schneider G (2018) De novo design of bioactive small molecules by artificial intelligence. Mol Infor 37:1700153

    Article  Google Scholar 

  152. Grisoni F et al (2021) Combining generative artificial intelligence and on-chip synthesis for de novo drug design. Sci Adv 7:eabg3338

    Google Scholar 

Download references

Acknowledgments

This research was supported by the Swiss National Science Foundation (SNSF, grant no. 205321 182176) and the ETH RETHINK initiative.

Conflict of Interest

G.S. is a cofounder of inSili.com LLC, Zurich, and a consultant to the pharmaceutical industry. W.G. and U.G. are employees of F. Hoffmann-La Roche Ltd.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Uwe Grether .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Atz, K., Guba, W., Grether, U., Schneider, G. (2023). Machine Learning and Computational Chemistry for the Endocannabinoid System. In: Maccarrone, M. (eds) Endocannabinoid Signaling. Methods in Molecular Biology, vol 2576. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2728-0_39

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2728-0_39

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2727-3

  • Online ISBN: 978-1-0716-2728-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics