Abstract
Background: The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery.
Objective: Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity.
Methods: We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space.
Results: The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces.
Conclusion: The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.
Keywords: Scoring function space, drug discovery, protein space, protein-ligand interactions, machine learning, systems biology.
[http://dx.doi.org/10.1007/978-1-4939-9752-7_17] [PMID: 31452111]
[PMID: 28641555]
[http://dx.doi.org/10.1021/ct4004228] [PMID: 24124403]
[http://dx.doi.org/10.1007/s10928-021-09790-9] [PMID: 34671863]
[http://dx.doi.org/10.2174/1875533XMTA5qNzU62] [PMID: 32895036]
[http://dx.doi.org/10.1021/acs.jctc.0c00355] [PMID: 32559068]
[http://dx.doi.org/10.2174/1875533XMTAy4MDQm4] [PMID: 31729287]
[http://dx.doi.org/10.1146/annurev-pharmtox-010716-104659] [PMID: 27814027]
[http://dx.doi.org/10.3389/fphys.2015.00366] [PMID: 26696900]
[http://dx.doi.org/10.1038/s41598-021-02282-3] [PMID: 34873190]
[http://dx.doi.org/10.1186/s12859-022-04663-5] [PMID: 35428180]
[http://dx.doi.org/10.1371/journal.pcbi.1009853] [PMID: 35143485]
[http://dx.doi.org/10.1002/(SICI)1098-1128(199601)16:1<3::AID-MED1>3.0.CO;2-6] [PMID: 8788213]
[http://dx.doi.org/10.1038/nature03192] [PMID: 15602547]
[http://dx.doi.org/10.1038/432823a]
[http://dx.doi.org/10.1038/nature03193] [PMID: 15602551]
[http://dx.doi.org/10.1038/nature03197] [PMID: 15602552]
[http://dx.doi.org/10.1038/nature03196] [PMID: 15602550]
[http://dx.doi.org/10.1038/225563a0] [PMID: 5411867]
[http://dx.doi.org/10.1073/pnas.0409772102] [PMID: 15705717]
[http://dx.doi.org/10.1016/j.cels.2021.05.017] [PMID: 34139171]
[http://dx.doi.org/10.1007/s10930-020-09939-4] [PMID: 33130957]
[http://dx.doi.org/10.1093/molbev/msaa215] [PMID: 32870983]
[http://dx.doi.org/10.1534/genetics.119.302764] [PMID: 32291354]
[http://dx.doi.org/10.1371/journal.pcbi.1005046] [PMID: 27736867]
[http://dx.doi.org/10.2174/156802606775193310] [PMID: 16454754]
[http://dx.doi.org/10.1021/ci2001428] [PMID: 21877753]
[http://dx.doi.org/10.1038/nbt1020] [PMID: 15470464]
[http://dx.doi.org/10.3390/ijms232213912] [PMID: 36430386]
[http://dx.doi.org/10.33011/livecoms.4.1.1497] [PMID: 36382113]
[http://dx.doi.org/10.1021/acs.jcim.2c00832] [PMID: 36341715]
[http://dx.doi.org/10.3389/fchem.2022.1012507] [PMID: 36339033]
[http://dx.doi.org/10.1038/s42004-022-00754-9] [PMID: 36320862]
[http://dx.doi.org/10.3389/fmolb.2022.1002535] [PMID: 36304919]
[http://dx.doi.org/10.1093/bioinformatics/btq112] [PMID: 20236947]
[http://dx.doi.org/10.1021/ci500091r] [PMID: 24528282]
[http://dx.doi.org/10.1007/978-3-319-24462-4_20]
[http://dx.doi.org/10.1371/journal.pone.0085678] [PMID: 24475049]
[http://dx.doi.org/10.3390/ijms21207648] [PMID: 33081086]
[http://dx.doi.org/10.1016/j.xphs.2020.10.015] [PMID: 33058896]
[http://dx.doi.org/10.1021/acs.chemrev.0c00534] [PMID: 33006893]
[http://dx.doi.org/10.3389/fimmu.2020.01304] [PMID: 32655572]
[http://dx.doi.org/10.1038/s41598-020-61860-z] [PMID: 32193447]
[http://dx.doi.org/10.1016/j.drudis.2020.03.003] [PMID: 32171918]
[PMID: 31598630]
[http://dx.doi.org/10.1016/j.bbagen.2020.129535] [PMID: 31954798]
[http://dx.doi.org/10.3389/fgene.2019.01243] [PMID: 31993067]
[http://dx.doi.org/10.1002/minf.201900095] [PMID: 31815371]
[http://dx.doi.org/10.1021/acsomega.9b01997] [PMID: 31592466]
[http://dx.doi.org/10.1158/2326-6066.CIR-19-0155] [PMID: 31515258]
[http://dx.doi.org/10.2174/0929867326666190620101637] [PMID: 31250750]
[http://dx.doi.org/10.2174/0929867327666200114114142] [PMID: 31942846]
[http://dx.doi.org/10.1371/journal.pcbi.1007970] [PMID: 32639954]
[http://dx.doi.org/10.1371/journal.pcbi.1008502] [PMID: 33284792]
[http://dx.doi.org/10.1371/journal.pcbi.1008247] [PMID: 33075050]
[http://dx.doi.org/10.1093/nar/gkaa1038] [PMID: 33211854]
[http://dx.doi.org/10.1107/S205225252000562X] [PMID: 32695409]
[http://dx.doi.org/10.1107/S2059798320014515] [PMID: 33263322]
[http://dx.doi.org/10.1016/j.jmb.2020.11.003] [PMID: 33186584]
[http://dx.doi.org/10.2174/138945008786949423] [PMID: 19128214]
[http://dx.doi.org/10.2174/1389450043490613] [PMID: 15011950]
[http://dx.doi.org/10.1016/j.bmcl.2020.127524] [PMID: 32890683]
[http://dx.doi.org/10.1038/nrd.2018.180] [PMID: 30410121]
[http://dx.doi.org/10.1016/j.toxicon.2005.07.018] [PMID: 16185738]
[http://dx.doi.org/10.1556/1886.2021.00020] [PMID: 34908533]
[http://dx.doi.org/10.1007/978-1-0716-1855-4_13] [PMID: 35298818]
[http://dx.doi.org/10.3389/fmolb.2021.787510] [PMID: 35071324]
[http://dx.doi.org/10.3389/fmolb.2021.724947] [PMID: 34466411]
[http://dx.doi.org/10.1016/j.drudis.2020.02.002] [PMID: 32068073]
[http://dx.doi.org/10.1007/s10930-020-09933-w] [PMID: 33098476]
[http://dx.doi.org/10.1038/s41388-020-01461-2] [PMID: 32939013]
[http://dx.doi.org/10.3390/molecules25153555] [PMID: 32759758]
[http://dx.doi.org/10.1016/j.drudis.2020.02.006] [PMID: 32084498]
[http://dx.doi.org/10.1016/j.sbi.2019.12.020] [PMID: 32006784]
[http://dx.doi.org/10.1107/S2052252519016993] [PMID: 32148843]
[http://dx.doi.org/10.3390/ijms20246195] [PMID: 31817979]
[http://dx.doi.org/10.3390/molecules24244451] [PMID: 31817305]
[http://dx.doi.org/10.1021/jm051197e] [PMID: 16722650]
[http://dx.doi.org/10.2174/092986711795029573] [PMID: 21366530]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_10] [PMID: 31452104]
[http://dx.doi.org/10.1021/acs.jcim.5b00559] [PMID: 26479676]
[http://dx.doi.org/10.1021/ci3001277] [PMID: 22587354]
[http://dx.doi.org/10.1021/ci049714+] [PMID: 15667143]
[PMID: 32881656]
[http://dx.doi.org/10.2174/0929867326666181203124102] [PMID: 30501591]
[http://dx.doi.org/10.2174/0929867325666180706101404] [PMID: 29984648]
[http://dx.doi.org/10.2174/0929867328666210113170222] [PMID: 33441063]
[http://dx.doi.org/10.2174/092986732742201105104417] [PMID: 33342397]
[http://dx.doi.org/10.2174/0929867327666201111144048] [PMID: 33176630]
[http://dx.doi.org/10.2174/0929867327666200831141337] [PMID: 32867630]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_13] [PMID: 31452107]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_12]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_3] [PMID: 31452097]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_9] [PMID: 31452103]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_11] [PMID: 31452105]
[http://dx.doi.org/10.2174/1386207320666171121110019] [PMID: 29165067]
[http://dx.doi.org/10.2174/157489312803901063]
[PMID: 20214598]
[http://dx.doi.org/10.2174/138945010790711941] [PMID: 20210757]
[http://dx.doi.org/10.2174/157340908786786047]
[http://dx.doi.org/10.2174/1875533XMTEwBOTYhx] [PMID: 33109026]
[http://dx.doi.org/10.2174/1875533XMTA5rMDYp5] [PMID: 32787752]
[http://dx.doi.org/10.3390/molecules25122944] [PMID: 32604797]
[http://dx.doi.org/10.1021/acs.jproteome.0c00430] [PMID: 33090793]
[http://dx.doi.org/10.1016/j.scib.2020.10.018] [PMID: 33163253]
[http://dx.doi.org/10.1126/science.abb3405] [PMID: 32198291]
[http://dx.doi.org/10.1038/s41392-020-0178-y] [PMID: 32388537]
[http://dx.doi.org/10.1016/j.molstruc.2021.129979] [PMID: 33518801]
[http://dx.doi.org/10.2174/1381612826666201210092736] [PMID: 33302855]
[http://dx.doi.org/10.1073/pnas.2010470117] [PMID: 33051297]
[http://dx.doi.org/10.1021/acs.jproteome.0c00683] [PMID: 32960061]
[http://dx.doi.org/10.1016/j.ijbiomac.2020.08.166] [PMID: 32853604]
[http://dx.doi.org/10.2174/1386207323999200824115536] [PMID: 32838713]
[http://dx.doi.org/10.1016/j.molstruc.2020.128595] [PMID: 32834108]
[http://dx.doi.org/10.1080/07391102.2020.1804458] [PMID: 32772895]
[http://dx.doi.org/10.1016/j.ijantimicag.2020.106119] [PMID: 32738306]
[http://dx.doi.org/10.1166/jnn.2020.18955] [PMID: 32711596]
[http://dx.doi.org/10.1016/j.micpath.2020.104365] [PMID: 32619669]
[http://dx.doi.org/10.1016/j.ijantimicag.2020.106020]
[http://dx.doi.org/10.1080/07391102.2020.1760136] [PMID: 32329419]
[http://dx.doi.org/10.3390/ijms21113922] [PMID: 32486229]
[http://dx.doi.org/10.2174/18734286MTEx9NTUg2] [PMID: 33200697]
[http://dx.doi.org/10.1038/s41586-020-2575-3] [PMID: 32698190]
[http://dx.doi.org/10.1126/science.368.6496.1166] [PMID: 32527806]
[http://dx.doi.org/10.1002/cmdc.200700075] [PMID: 17694525]
[http://dx.doi.org/10.1016/j.aca.2013.07.003] [PMID: 23910962]
[http://dx.doi.org/10.1146/annurev-pharmtox-011613-135943] [PMID: 24016212]
[http://dx.doi.org/10.3390/molecules23040908] [PMID: 29662024]
[http://dx.doi.org/10.1038/s41598-019-43125-6] [PMID: 31118426]
[http://dx.doi.org/10.3390/ijms22157773] [PMID: 34360558]
[http://dx.doi.org/10.1038/s41586-021-03819-2] [PMID: 34265844]
[http://dx.doi.org/10.3390/ijms222312835] [PMID: 34884640]
[http://dx.doi.org/10.1371/journal.pcbi.1008753] [PMID: 33621244]
[http://dx.doi.org/10.3390/ijms22168831] [PMID: 34445537]
[http://dx.doi.org/10.1038/d41586-022-00997-5] [PMID: 35418629]
[http://dx.doi.org/10.1038/s41467-022-29268-7] [PMID: 35365602]
[http://dx.doi.org/10.1371/journal.pcbi.1009930] [PMID: 35333855]
[http://dx.doi.org/10.1073/pnas.2202107119] [PMID: 35235461]
[http://dx.doi.org/10.1038/s41467-022-28327-3] [PMID: 35181656]
[http://dx.doi.org/10.1016/j.sbi.2022.102329] [PMID: 35139457]
[http://dx.doi.org/10.3390/ijms22115553] [PMID: 34074028]
[http://dx.doi.org/10.1126/science.abj8754] [PMID: 34282049]
[http://dx.doi.org/10.1038/s41598-020-70026-w] [PMID: 32737414]
[http://dx.doi.org/10.12659/AJCR.918927] [PMID: 31969553]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_1] [PMID: 31452095]
[PMID: 27686428]
[http://dx.doi.org/10.1002/jcc.26048] [PMID: 31410856]
[http://dx.doi.org/10.1186/s13321-021-00522-2] [PMID: 34108002]
[http://dx.doi.org/10.3390/molecules26237369] [PMID: 34885952]
[http://dx.doi.org/10.1021/ci300604z] [PMID: 23379370]
[http://dx.doi.org/10.1007/s10822-017-0081-y] [PMID: 29127581]
[http://dx.doi.org/10.1107/S0907444901013865] [PMID: 11679720]
[http://dx.doi.org/10.1016/S0006-291X(03)01431-1] [PMID: 12914785]
[http://dx.doi.org/10.1111/j.1432-1033.1997.0518a.x] [PMID: 9030780]
[http://dx.doi.org/10.1016/j.jsb.2007.04.009] [PMID: 17588773]
[http://dx.doi.org/10.1016/j.jsb.2007.07.012] [PMID: 17881248]
[PMID: 19499576]
[http://dx.doi.org/10.1021/acs.jcim.1c00203] [PMID: 34278794]
[http://dx.doi.org/10.1002/jcc.21256] [PMID: 19399780]
[http://dx.doi.org/10.1002/wcms.1225] [PMID: 27110292]
[http://dx.doi.org/10.1371/journal.pone.0155183] [PMID: 27171006]
[http://dx.doi.org/10.3390/molecules27061985] [PMID: 35335347]
[http://dx.doi.org/10.1016/j.csbj.2022.02.004] [PMID: 35317230]
[http://dx.doi.org/10.1021/acs.jcim.0c00545] [PMID: 32786511]
[http://dx.doi.org/10.3389/fchem.2021.750325] [PMID: 34778205]
[http://dx.doi.org/10.1080/07391102.2020.1798286] [PMID: 32741313]
[http://dx.doi.org/10.1021/acsomega.0c04808] [PMID: 33398250]
[http://dx.doi.org/10.1128/mbio.03705-21] [PMID: 35229634]
[http://dx.doi.org/10.1002/jmv.25985] [PMID: 32374457]
[http://dx.doi.org/10.1515/jbcpp-2020-0369] [PMID: 34265888]
[http://dx.doi.org/10.1016/j.isci.2021.102367] [PMID: 33817567]
[PMID: 33749547]
[http://dx.doi.org/10.3390/biom11020216] [PMID: 33557097]
[http://dx.doi.org/10.1016/j.virol.2022.04.005] [PMID: 35439707]
[http://dx.doi.org/10.1016/j.foodchem.2021.131594] [PMID: 34838409]
[PMID: 34950525]
[http://dx.doi.org/10.1080/14786419.2018.1519825] [PMID: 30449158]
[http://dx.doi.org/10.1016/j.antiviral.2019.104621] [PMID: 31634495]
[http://dx.doi.org/10.1021/jm0306430] [PMID: 15027865]
[http://dx.doi.org/10.1023/A:1011115820450] [PMID: 11394736]
[http://dx.doi.org/10.3390/ijms231911003] [PMID: 36232307]
[http://dx.doi.org/10.1093/nar/gkv1072] [PMID: 26481362]
[http://dx.doi.org/10.1038/s41586-020-2223-y] [PMID: 32272481]
[http://dx.doi.org/10.1186/s13321-015-0078-2] [PMID: 26101548]
[http://dx.doi.org/10.2174/092986711795029519] [PMID: 21366529]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_8] [PMID: 31452102]
[http://dx.doi.org/10.1007/978-1-4939-9752-7_2] [PMID: 31452096]
[http://dx.doi.org/10.2174/0929867328666210910141316] [PMID: 34514978]
[http://dx.doi.org/10.2174/0929867325666180622143548] [PMID: 29932031]
[http://dx.doi.org/10.2174/0929867323666160530144742] [PMID: 27237821]
[http://dx.doi.org/10.1016/j.molstruc.2021.131124] [PMID: 34305175]
[http://dx.doi.org/10.1016/j.molstruc.2021.131113] [PMID: 34305174]
[http://dx.doi.org/10.1016/j.molstruc.2021.130409] [PMID: 33840836]
[http://dx.doi.org/10.1016/j.molstruc.2020.129433] [PMID: 33071352]
[http://dx.doi.org/10.1038/s41592-021-01205-4] [PMID: 34316068]
![Wayfinder Image](/images/wayfinder.jpg)