Skip to main content

AI-Driven Enhancements in Drug Screening and Optimization

  • Protocol
  • First Online:
Computational Drug Discovery and Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2714))

Abstract

The greatest challenge in drug discovery remains the high rate of attrition across the different phases of the process, which cost the industry billions of dollars every year. While all phases remain crucial to ensure pharmaceutical-level safety, quality, and efficacy of the end product, streamlining these efforts toward compounds with success potential is pivotal for a more efficient and cost-effective process. The use of artificial intelligence (AI) within the pharmaceutical industry aims at just this, and has applications in preclinical screening for biological activity, optimization of pharmacokinetic properties for improved drug formulation, early toxicity prediction which reduces attrition, and pre-emptively screening for genetic changes in the biological target to improve therapeutic longevity. Here, we present a series of in silico tools that address these applications in small molecule development and describe how they can be embedded within the current pharmaceutical development pipeline.

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

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
eBook
USD 139.00
Price excludes VAT (USA)
Hardcover Book
USD 179.99
Price excludes VAT (USA)

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Hutchinson L, Kirk R (2011) High drug attrition rates–where are we going wrong? Nat Rev Clin Oncol 8(4):189–190. https://doi.org/10.1038/nrclinonc.2011.34

    Article  PubMed  Google Scholar 

  2. Moreno L, Pearson AD (2013) How can attrition rates be reduced in cancer drug discovery? Expert Opin Drug Discov 8(4):363–368. https://doi.org/10.1517/17460441.2013.768984

    Article  CAS  PubMed  Google Scholar 

  3. Seyhan AA (2019) Lost in translation: the valley of death across preclinical and clinical divide – identification of problems and overcoming obstacles. Transl Med Commun 4(1):18. https://doi.org/10.1186/s41231-019-0050-7

    Article  Google Scholar 

  4. Pires DEV, Kaminskas LM, Ascher DB (2018) Prediction and optimization of pharmacokinetic and toxicity properties of the ligand. Methods Mol Biol 1762:271–284. https://doi.org/10.1007/978-1-4939-7756-7_14

    Article  CAS  PubMed  Google Scholar 

  5. Pires DEV, Portelli S, Rezende PM, Veloso WNP, Xavier JS, Karmakar M, Myung Y, Linhares JPV, Rodrigues CHM, Silk M, Ascher DB (2020) A comprehensive computational platform to guide drug development using graph-based signature methods. Methods Mol Biol 2112:91–106. https://doi.org/10.1007/978-1-0716-0270-6_7

    Article  CAS  PubMed  Google Scholar 

  6. Rodrigues CHM, Garg A, Keizer D, Pires DEV, Ascher DB (2022) CSM-peptides: a computational approach to rapid identification of therapeutic peptides. Protein Sci 31(10):e4442. https://doi.org/10.1002/pro.4442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminform 3:33. https://doi.org/10.1186/1758-2946-3-33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wu P, Clausen MH, Nielsen TE (2015) Allosteric small-molecule kinase inhibitors. Pharmacol Ther 156:59–68. https://doi.org/10.1016/j.pharmthera.2015.10.002

    Article  CAS  PubMed  Google Scholar 

  9. Jubb H, Blundell TL, Ascher DB (2015) Flexibility and small pockets at protein-protein interfaces: new insights into druggability. Prog Biophys Mol Biol 119(1):2–9. https://doi.org/10.1016/j.pbiomolbio.2015.01.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Jubb HC, Pandurangan AP, Turner MA, Ochoa-Montano B, Blundell TL, Ascher DB (2017) Mutations at protein-protein interfaces: small changes over big surfaces have large impacts on human health. Prog Biophys Mol Biol 128:3–13. https://doi.org/10.1016/j.pbiomolbio.2016.10.002

    Article  CAS  PubMed  Google Scholar 

  11. Al-Jarf R, de Sa AGC, Pires DEV, Ascher DB (2021) pdCSM-cancer: using graph-based signatures to identify small molecules with anticancer properties. J Chem Inf Model 61(7):3314–3322. https://doi.org/10.1021/acs.jcim.1c00168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Velloso JPL, Ascher DB, Pires DEV (2021) pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. Bioinform Adv 1(1):vbab031. https://doi.org/10.1093/bioadv/vbab031

    Article  PubMed  PubMed Central  Google Scholar 

  13. Zhou Y, Al-Jarf R, Alavi A, Nguyen TB, Rodrigues CHM, Pires DEV, Ascher DB (2022) kinCSM: using graph-based signatures to predict small molecule CDK2 inhibitors. Protein Sci 31(11):e4453. https://doi.org/10.1002/pro.4453

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Rodrigues CHM, Pires DEV, Ascher DB (2021) pdCSM-PPI: using graph-based signatures to identify protein-protein interaction inhibitors. J Chem Inf Model 61(11):5438–5445. https://doi.org/10.1021/acs.jcim.1c01135

    Article  CAS  PubMed  Google Scholar 

  15. Portelli S, Phelan JE, Ascher DB, Clark TG, Furnham N (2018) Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Sci Rep 8(1):15356. https://doi.org/10.1038/s41598-018-33370-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Karmakar M, Cicaloni V, Rodrigues CHM, Spiga O, Santucci A, Ascher DB (2022) HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase. Curr Res Struct Biol 4:271–277. https://doi.org/10.1016/j.crstbi.2022.08.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Karmakar M, Globan M, Fyfe JAM, Stinear TP, Johnson PDR, Holmes NE, Denholm JT, Ascher DB (2018) Analysis of a novel pncA mutation for susceptibility to pyrazinamide therapy. Am J Respir Crit Care Med 198(4):541–544. https://doi.org/10.1164/rccm.201712-2572LE

    Article  PubMed  PubMed Central  Google Scholar 

  18. Karmakar M, Rodrigues CHM, Holt KE, Dunstan SJ, Denholm J, Ascher DB (2019) Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. PLoS One 14(5):e0217169. https://doi.org/10.1371/journal.pone.0217169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Karmakar M, Rodrigues CHM, Horan K, Denholm JT, Ascher DB (2020) Structure guided prediction of Pyrazinamide resistance mutations in pncA. Sci Rep 10(1):1875. https://doi.org/10.1038/s41598-020-58635-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Vedithi SC, Malhotra S, Das M, Daniel S, Kishore N, George A, Arumugam S, Rajan L, Ebenezer M, Ascher DB, Arnold E, Blundell TL (2018) Structural implications of mutations conferring rifampin resistance in Mycobacterium leprae. Sci Rep 8(1):5016. https://doi.org/10.1038/s41598-018-23423-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Vedithi SC, Malhotra S, Skwark MJ, Munir A, Acebron-Garcia-De-Eulate M, Waman VP, Alsulami A, Ascher DB, Blundell TL (2020) HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae. Comput Struct Biotechnol J 18:3692–3704. https://doi.org/10.1016/j.csbj.2020.11.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhou Y, Portelli S, Pat M, Rodrigues CHM, Nguyen TB, Pires DEV, Ascher DB (2021) Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase. Comput Struct Biotechnol J 19:5381–5391. https://doi.org/10.1016/j.csbj.2021.09.016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Vedithi SC, Rodrigues CHM, Portelli S, Skwark MJ, Das M, Ascher DB, Blundell TL, Malhotra S (2020) Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae. Comput Struct Biotechnol J 18:271–286. https://doi.org/10.1016/j.csbj.2020.01.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Tunstall T, Portelli S, Phelan J, Clark TG, Ascher DB, Furnham N (2020) Combining structure and genomics to understand antimicrobial resistance. Comput Struct Biotechnol J 18:3377–3394. https://doi.org/10.1016/j.csbj.2020.10.017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Hnizda A, Fabry M, Moriyama T, Pachl P, Kugler M, Brinsa V, Ascher DB, Carroll WL, Novak P, Zaliova M, Trka J, Rezacova P, Yang JJ, Veverka V (2018) Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia 32(6):1393–1403. https://doi.org/10.1038/s41375-018-0073-5

    Article  CAS  PubMed  Google Scholar 

  26. Andrews KA, Ascher DB, Pires DEV, Barnes DR, Vialard L, Casey RT, Bradshaw N, Adlard J, Aylwin S, Brennan P, Brewer C, Cole T, Cook JA, Davidson R, Donaldson A, Fryer A, Greenhalgh L, Hodgson SV, Irving R, Lalloo F, McConachie M, McConnell VPM, Morrison PJ, Murday V, Park SM, Simpson HL, Snape K, Stewart S, Tomkins SE, Wallis Y, Izatt L, Goudie D, Lindsay RS, Perry CG, Woodward ER, Antoniou AC, Maher ER (2018) Tumour risks and genotype-phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes SDHB, SDHC and SDHD. J Med Genet 55(6):384–394. https://doi.org/10.1136/jmedgenet-2017-105127

    Article  CAS  PubMed  Google Scholar 

  27. Pires DE, Chen J, Blundell TL, Ascher DB (2016) In silico functional dissection of saturation mutagenesis: interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Sci Rep 6:19848. https://doi.org/10.1038/srep19848

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Portelli S, Myung Y, Furnham N, Vedithi SC, Pires DEV, Ascher DB (2020) Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Sci Rep 10(1):18120. https://doi.org/10.1038/s41598-020-74648-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Rodrigues CHM, Ascher DB (2022) CSM-potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. Nucleic Acids Res 50(W1):W204–W209. https://doi.org/10.1093/nar/gkac381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Williams NP, Rodrigues CHM, Truong J, Ascher DB, Holien JK (2023) DockNet: high-throughput protein-protein interface contact prediction. Bioinformatics 39(1). https://doi.org/10.1093/bioinformatics/btac797

  31. Blassel L, Zhukova A, Villabona-Arenas CJ, Atkins KE, Hue S, Gascuel O (2021) Drug resistance mutations in HIV: new bioinformatics approaches and challenges. Curr Opin Virol 51:56–64. https://doi.org/10.1016/j.coviro.2021.09.009

    Article  CAS  PubMed  Google Scholar 

  32. Munita JM, Arias CA (2016) Mechanisms of antibiotic resistance. Microbiol Spectr 4(2). https://doi.org/10.1128/microbiolspec.VMBF-0016-2015

  33. Cao X, Hou J, An Q, Assaraf YG, Wang X (2020) Towards the overcoming of anticancer drug resistance mediated by p53 mutations. Drug Resist Updat 49:100671. https://doi.org/10.1016/j.drup.2019.100671

    Article  PubMed  Google Scholar 

  34. Ascher DB, Wielens J, Nero TL, Doughty L, Morton CJ, Parker MW (2014) Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA. Sci Rep 4:4765. https://doi.org/10.1038/srep04765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Hawkey J, Ascher DB, Judd LM, Wick RR, Kostoulias X, Cleland H, Spelman DW, Padiglione A, Peleg AY, Holt KE (2018) Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. Microb Genom 4(3). https://doi.org/10.1099/mgen.0.000165

  36. Lai CY, Tsai IJ, Chiu PC, Ascher DB, Chien YH, Huang YH, Lin YL, Hwu WL, Lee NC (2021) A novel deep intronic variant strongly associates with Alkaptonuria. NPJ Genom Med 6(1):89. https://doi.org/10.1038/s41525-021-00252-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Portelli S, Olshansky M, Rodrigues CHM, D’Souza EN, Myung Y, Silk M, Alavi A, Pires DEV, Ascher DB (2020) Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nat Genet 52(10):999–1001. https://doi.org/10.1038/s41588-020-0693-3

    Article  CAS  PubMed  Google Scholar 

  38. Xavier JS, Moir M, Tegally H, Sitharam N, Abdool Karim W, San JE, Linhares J, Wilkinson E, Ascher DB, Baxter C, Pires DEV, de Oliveira T (2023) SARS-CoV-2 Africa dashboard for real-time COVID-19 information. Nat Microbiol 8(1):1–4. https://doi.org/10.1038/s41564-022-01276-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Jafri M, Wake NC, Ascher DB, Pires DE, Gentle D, Morris MR, Rattenberry E, Simpson MA, Trembath RC, Weber A, Woodward ER, Donaldson A, Blundell TL, Latif F, Maher ER (2015) Germline mutations in the CDKN2B tumor suppressor gene predispose to renal cell carcinoma. Cancer Discov 5(7):723–729. https://doi.org/10.1158/2159-8290.CD-14-1096

    Article  CAS  PubMed  Google Scholar 

  40. Boer JC, Pan Q, Holien JK, Nguyen TB, Ascher DB, Plebanski M (2022) A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility. Front Immunol 13:954435. https://doi.org/10.3389/fimmu.2022.954435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Casey RT, Ascher DB, Rattenberry E, Izatt L, Andrews KA, Simpson HL, Challis B, Park SM, Bulusu VR, Lalloo F, Pires DEV, West H, Clark GR, Smith PS, Whitworth J, Papathomas TG, Taniere P, Savisaar R, Hurst LD, Woodward ER, Maher ER (2017) SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity. Mol Genet Genomic Med 5(3):237–250. https://doi.org/10.1002/mgg3.279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Karmakar M, Ragonnet R, Ascher DB, Trauer JM, Denholm JT (2022) Estimating tuberculosis drug resistance amplification rates in high-burden settings. BMC Infect Dis 22(1):82. https://doi.org/10.1186/s12879-022-07067-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Karmakar M, Trauer JM, Ascher DB, Denholm JT (2019) Hyper transmission of Beijing lineage Mycobacterium tuberculosis: systematic review and meta-analysis. J Infect 79(6):572–581. https://doi.org/10.1016/j.jinf.2019.09.016

    Article  PubMed  Google Scholar 

  44. Holt KE, McAdam P, Thai PVK, Thuong NTT, Ha DTM, Lan NN, Lan NH, Nhu NTQ, Hai HT, Ha VTN, Thwaites G, Edwards DJ, Nath AP, Pham K, Ascher DB, Farrar J, Khor CC, Teo YY, Inouye M, Caws M, Dunstan SJ (2018) Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat Genet 50(6):849–856. https://doi.org/10.1038/s41588-018-0117-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Portelli S, Albanaz A, Pires DEV, Ascher DB (2022) Identifying the molecular drivers of ALS-implicated missense mutations. J Med Genet. https://doi.org/10.1136/jmg-2022-108798

  46. Portelli S, Barr L, de Sa AGC, Pires DEV, Ascher DB (2021) Distinguishing between PTEN clinical phenotypes through mutation analysis. Comput Struct Biotechnol J 19:3097–3109. https://doi.org/10.1016/j.csbj.2021.05.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Parthasarathy S, Ruggiero SM, Gelot A, Soardi FC, Ribeiro BFR, Pires DEV, Ascher DB, Schmitt A, Rambaud C, Represa A, Xie HM, Lusk L, Wilmarth O, McDonnell PP, Juarez OA, Grace AN, Buratti J, Mignot C, Gras D, Nava C, Pierce SR, Keren B, Kennedy BC, Pena SDJ, Helbig I, Cuddapah VA (2022) A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism. Am J Hum Genet 109(12):2253–2269. https://doi.org/10.1016/j.ajhg.2022.11.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Hildebrand JM, Kauppi M, Majewski IJ, Liu Z, Cox AJ, Miyake S, Petrie EJ, Silk MA, Li Z, Tanzer MC, Brumatti G, Young SN, Hall C, Garnish SE, Corbin J, Stutz MD, Di Rago L, Gangatirkar P, Josefsson EC, Rigbye K, Anderton H, Rickard JA, Tripaydonis A, Sheridan J, Scerri TS, Jackson VE, Czabotar PE, Zhang JG, Varghese L, Allison CC, Pellegrini M, Tannahill GM, Hatchell EC, Willson TA, Stockwell D, de Graaf CA, Collinge J, Hilton A, Silke N, Spall SK, Chau D, Athanasopoulos V, Metcalf D, Laxer RM, Bassuk AG, Darbro BW, Fiatarone Singh MA, Vlahovich N, Hughes D, Kozlovskaia M, Ascher DB, Warnatz K, Venhoff N, Thiel J, Biben C, Blum S, Reveille J, Hildebrand MS, Vinuesa CG, McCombe P, Brown MA, Kile BT, McLean C, Bahlo M, Masters SL, Nakano H, Ferguson PJ, Murphy JM, Alexander WS, Silke J (2020) A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction. Nat Commun 11(1):3150. https://doi.org/10.1038/s41467-020-16819-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Ascher DB, Spiga O, Sekelska M, Pires DEV, Bernini A, Tiezzi M, Kralovicova J, Borovska I, Soltysova A, Olsson B, Galderisi S, Cicaloni V, Ranganath L, Santucci A, Zatkova A (2019) Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. Eur J Hum Genet 27(6):888–902. https://doi.org/10.1038/s41431-019-0354-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Tichkule S, Myung Y, Naung MT, Ansell BRE, Guy AJ, Srivastava N, Mehra S, Caccio SM, Mueller I, Barry AE, van Oosterhout C, Pope B, Ascher DB, Jex AR (2022) VIVID: a web application for variant interpretation and visualization in multi-dimensional analyses. Mol Biol Evol 39(9). https://doi.org/10.1093/molbev/msac196

  51. Stephenson SEM, Costain G, LER B, Silk MA, Nguyen TB, Dong X, Alhuzaimi DE, Dowling JJ, Walker S, Amburgey K, Hayeems RZ, Rodan LH, Schwartz MA, Picker J, Lynch SA, Gupta A, Rasmussen KJ, Schimmenti LA, Klee EW, Niu Z, Agre KE, Chilton I, Chung WK, Revah-Politi A, PYB A, Griffith C, Racobaldo M, Raas-Rothschild A, Ben Zeev B, Barel O, Moutton S, Morice-Picard F, Carmignac V, Cornaton J, Marle N, Devinsky O, Stimach C, Wechsler SB, Hainline BE, Sapp K, Willems M, Bruel AL, Dias KR, Evans CA, Roscioli T, Sachdev R, Temple SEL, Zhu Y, Baker JJ, Scheffer IE, Gardiner FJ, Schneider AL, Muir AM, Mefford HC, Crunk A, Heise EM, Millan F, Monaghan KG, Person R, Rhodes L, Richards S, Wentzensen IM, Cogne B, Isidor B, Nizon M, Vincent M, Besnard T, Piton A, Marcelis C, Kato K, Koyama N, Ogi T, Goh ES, Richmond C, Amor DJ, Boyce JO, Morgan AT, Hildebrand MS, Kaspi A, Bahlo M, Friethriksdottir R, Katrinardottir H, Sulem P, Stefansson K, Bjornsson HT, Mandelstam S, Morleo M, Mariani M, Group TS, Scala M, Accogli A, Torella A, Capra V, Wallis M, Jansen S, Weisfisz Q, de Haan H, Sadedin S, Broad Center for Mendelian G, Lim SC, White SM, Ascher DB, Schenck A, Lockhart PJ, Christodoulou J, Tan TY (2022) Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome. Am J Hum Genet 109(4):601–617. https://doi.org/10.1016/j.ajhg.2022.03.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Pandurangan AP, Ascher DB, Thomas SE, Blundell TL (2017) Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance. Biochem Soc Trans 45(2):303–311. https://doi.org/10.1042/BST20160422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Nemethova M, Radvanszky J, Kadasi L, Ascher DB, Pires DE, Blundell TL, Porfirio B, Mannoni A, Santucci A, Milucci L, Sestini S, Biolcati G, Sorge F, Aurizi C, Aquaron R, Alsbou M, Lourenco CM, Ramadevi K, Ranganath LR, Gallagher JA, van Kan C, Hall AK, Olsson B, Sireau N, Ayoob H, Timmis OG, Sang KH, Genovese F, Imrich R, Rovensky J, Srinivasaraghavan R, Bharadwaj SK, Spiegel R, Zatkova A (2016) Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on ‘black bone disease’ in Italy. Eur J Hum Genet 24(1):66–72. https://doi.org/10.1038/ejhg.2015.60

    Article  CAS  PubMed  Google Scholar 

  54. Pires DE, Blundell TL, Ascher DB (2015) Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Res 43(Database issue):D387–D391. https://doi.org/10.1093/nar/gku966

    Article  CAS  PubMed  Google Scholar 

  55. Pires DE, Blundell TL, Ascher DB (2016) mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. Sci Rep 6:29575. https://doi.org/10.1038/srep29575

    Article  PubMed  PubMed Central  Google Scholar 

  56. Chang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW, Schomburg D (2015) BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res 43(Database issue):D439–D446. https://doi.org/10.1093/nar/gku1068

    Article  CAS  PubMed  Google Scholar 

  57. Copoiu L, Torres PHM, Ascher DB, Blundell TL, Malhotra S (2020) ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Res 48(D1):D368–D375. https://doi.org/10.1093/nar/gkz860

    Article  CAS  PubMed  Google Scholar 

  58. Pires DE, Ascher DB (2016) CSM-lig: a web server for assessing and comparing protein-small molecule affinities. Nucleic Acids Res 44(W1):W557–W561. https://doi.org/10.1093/nar/gkw390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Nguyen TB, Pires DEV, Ascher DB (2022) CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. Brief Bioinform 23(1). https://doi.org/10.1093/bib/bbab512

  60. Jubb HC, Higueruelo AP, Ochoa-Montano B, Pitt WR, Ascher DB, Blundell TL (2017) Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures. J Mol Biol 429(3):365–371. https://doi.org/10.1016/j.jmb.2016.12.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Eddershaw PJ, Beresford AP, Bayliss MK (2000) ADME/PK as part of a rational approach to drug discovery. Drug Discov Today 5(9):409–414. https://doi.org/10.1016/s1359-6446(00)01540-3

    Article  CAS  PubMed  Google Scholar 

  62. Li AP (2001) Screening for human ADME/Tox drug properties in drug discovery. Drug Discov Today 6(7):357–366. https://doi.org/10.1016/s1359-6446(01)01712-3

    Article  CAS  PubMed  Google Scholar 

  63. Lin J, Sahakian DC, de Morais SM, Xu JJ, Polzer RJ, Winter SM (2003) The role of absorption, distribution, metabolism, excretion and toxicity in drug discovery. Curr Top Med Chem 3(10):1125–1154. https://doi.org/10.2174/1568026033452096

    Article  PubMed  Google Scholar 

  64. Thompson TN (2000) Early ADME in support of drug discovery: the role of metabolic stability studies. Curr Drug Metab 1(3):215–241. https://doi.org/10.2174/1389200003339018

    Article  CAS  PubMed  Google Scholar 

  65. Kaminskas LM, Pires DEV, Ascher DB (2019) dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction. Sci Rep 9(1):15465. https://doi.org/10.1038/s41598-019-51789-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Pires DE, Blundell TL, Ascher DB (2015) pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem 58(9):4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. de Sa AGC, Long Y, Portelli S, Pires DEV, Ascher DB (2022) toxCSM: comprehensive prediction of small molecule toxicity profiles. Brief Bioinform 23(5). https://doi.org/10.1093/bib/bbac337

  68. Iftkhar S, de Sa AGC, Velloso JPL, Aljarf R, Pires DEV, Ascher DB (2022) cardioToxCSM: a web server for predicting cardiotoxicity of small molecules. J Chem Inf Model 62(20):4827–4836. https://doi.org/10.1021/acs.jcim.2c00822

    Article  CAS  PubMed  Google Scholar 

  69. Pires DEV, Stubbs KA, Mylne JS, Ascher DB (2022) cropCSM: designing safe and potent herbicides with graph-based signatures. Brief Bioinform 23(2). https://doi.org/10.1093/bib/bbac042

  70. Aljarf R, Tang S, Pires DEV, Ascher DB (2023) embryoTox: using graph-based signatures to predict the teratogenicity of small molecules. J Chem Inf Model. https://doi.org/10.1021/acs.jcim.2c00824

Download references

Funding

S.P. and D.B.A. were supported by an Investigator Grant from the National Health and Medical

Research Council (NHMRC) of Australia (GNT1174405 to D.B.A.). This research was supported in part by the Victorian Government’s Operational Infrastructure Support Program.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Stephanie Portelli or David B. Ascher .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2024 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

Serghini, A., Portelli, S., Ascher, D.B. (2024). AI-Driven Enhancements in Drug Screening and Optimization. In: Gore, M., Jagtap, U.B. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 2714. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3441-7_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3441-7_15

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3440-0

  • Online ISBN: 978-1-0716-3441-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics