Application of Computational Biology and Artificial Intelligence in Drug Design.
artificial intelligence-aided drug design (AIDD)
computational biology
computer-aided drug design (CADD)
deep learning
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
05 Nov 2022
05 Nov 2022
Historique:
received:
08
10
2022
revised:
29
10
2022
accepted:
03
11
2022
entrez:
11
11
2022
pubmed:
12
11
2022
medline:
15
11
2022
Statut:
epublish
Résumé
Traditional drug design requires a great amount of research time and developmental expense. Booming computational approaches, including computational biology, computer-aided drug design, and artificial intelligence, have the potential to expedite the efficiency of drug discovery by minimizing the time and financial cost. In recent years, computational approaches are being widely used to improve the efficacy and effectiveness of drug discovery and pipeline, leading to the approval of plenty of new drugs for marketing. The present review emphasizes on the applications of these indispensable computational approaches in aiding target identification, lead discovery, and lead optimization. Some challenges of using these approaches for drug design are also discussed. Moreover, we propose a methodology for integrating various computational techniques into new drug discovery and design.
Identifiants
pubmed: 36362355
pii: ijms232113568
doi: 10.3390/ijms232113568
pmc: PMC9658956
pii:
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : National Natural Science Foundation of Youth Fund Project
ID : 22103066
Organisme : the 2021 Basic Research General Project of Shenzhen, China
ID : 20210316202830001
Organisme : the Warshel Institute for Computational Biology at the Chinese University of Hong Kong, Shenzhen
ID : C10120180043
Références
Nucleic Acids Res. 2016 Jan 4;44(D1):D1202-13
pubmed: 26400175
J Chem Inf Model. 2012 Nov 26;52(11):2864-75
pubmed: 23088335
J Chem Inf Model. 2009 Jun;49(6):1455-74
pubmed: 19476350
J Am Chem Soc. 2021 Oct 27;143(42):17646-17654
pubmed: 34648291
Nat Commun. 2018 Oct 18;9(1):4325
pubmed: 30337523
Nucleic Acids Res. 2019 Jan 8;47(D1):D1102-D1109
pubmed: 30371825
Acta Pharmacol Sin. 2020 Jan;41(1):138-144
pubmed: 31263275
Molecules. 2018 Aug 06;23(8):
pubmed: 30082644
Drug Discov Today. 2002 Oct 15;7(20):1047-55
pubmed: 12546894
Nucleic Acids Res. 2016 Jan 4;44(D1):D380-4
pubmed: 26590256
Chem Sci. 2019 Nov 18;11(2):577-586
pubmed: 32190274
Molecules. 2015 Jul 22;20(7):13384-421
pubmed: 26205061
Curr Opin Drug Discov Devel. 2006 May;9(3):370-9
pubmed: 16729734
J Med Chem. 2022 Jul 28;65(14):10001-10013
pubmed: 35786900
Chem Rev. 2014 Jan 8;114(1):493-537
pubmed: 24024775
Bioorg Med Chem. 2014 Jan 1;22(1):167-77
pubmed: 24332657
Mol Inform. 2016 Jan;35(1):3-14
pubmed: 27491648
J Chem Inf Model. 2007 Mar-Apr;47(2):342-53
pubmed: 17260980
Acc Chem Res. 2018 May 15;51(5):1281-1289
pubmed: 29715002
Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20550-5
pubmed: 22143769
J Chem Inf Model. 2009 Apr;49(4):913-24
pubmed: 19309119
Nucleic Acids Res. 2021 Jan 8;49(D1):D1388-D1395
pubmed: 33151290
Brief Bioinform. 2021 Sep 2;22(5):
pubmed: 33837771
Drug Discov Today. 2007 Sep;12(17-18):725-31
pubmed: 17826685
Future Med Chem. 2018 Nov;10(22):2641-2658
pubmed: 30499744
Proc Mach Learn Res. 2022 Jul;162:5777-5792
pubmed: 36193121
BMC Bioinformatics. 2020 Sep 16;21(Suppl 8):310
pubmed: 32938359
Curr Med Chem. 2012;19(25):4289-97
pubmed: 22830342
J Mol Model. 2003 Feb;9(1):47-57
pubmed: 12638011
Eur J Med Chem. 2016 Jun 30;116:36-45
pubmed: 27043269
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W223-8
pubmed: 18424800
Drug Discov Today Technol. 2004 Dec;1(4):337-41
pubmed: 24981612
Eur J Med Chem. 2015 Feb 16;91:4-14
pubmed: 25108504
J Comput Aided Mol Des. 2013 Mar;27(3):221-34
pubmed: 23579614
J Comput Chem. 2003 Oct;24(13):1549-62
pubmed: 12925999
Methods Biochem Anal. 2003;44:509-23
pubmed: 12647402
Int J Mol Sci. 2021 Feb 07;22(4):
pubmed: 33562347
PLoS Comput Biol. 2011 Feb;7(2):e1002002
pubmed: 21390201
Bioinformatics. 2019 Nov 1;35(22):4862-4865
pubmed: 31116374
Chem Rev. 2016 Jul 27;116(14):7898-936
pubmed: 27333362
J Chem Inf Model. 2022 May 23;62(10):2269-2279
pubmed: 35544331
J Chem Inf Model. 2021 Feb 22;61(2):621-630
pubmed: 33491455
Expert Opin Drug Discov. 2018 Jan;13(1):23-37
pubmed: 29139324
Virusdisease. 2021 Mar;32(1):29-37
pubmed: 33532517
J Chem Inf Model. 2005 Jan-Feb;45(1):160-9
pubmed: 15667141
Proteins. 2016 Jan;84(1):92-117
pubmed: 26531155
Nucleic Acids Res. 2016 Jan 4;44(D1):D1075-9
pubmed: 26481350
J Mol Model. 2006 Feb;12(3):366-72
pubmed: 16372175
Phys Chem Chem Phys. 2016 Oct 12;18(40):28281-28289
pubmed: 27711562
Curr Opin Struct Biol. 2022 Feb;72:135-144
pubmed: 34823138
J Comput Aided Mol Des. 2007 Oct-Nov;21(10-11):591-601
pubmed: 17989929
Comput Biol Chem. 2020 Dec;89:107372
pubmed: 32911432
Biomed Res Int. 2021 Jun 24;2021:8853056
pubmed: 34258282
Bioinformatics. 2010 Jan 1;26(1):46-52
pubmed: 19846440
Pharmaceuticals (Basel). 2022 Jan 04;15(1):
pubmed: 35056120
Nucleic Acids Res. 2016 Jul 8;44(W1):W430-5
pubmed: 27112573
J Chem Inf Model. 2012 Jul 23;52(7):1757-68
pubmed: 22587354
J Cheminform. 2021 Jun 9;13(1):43
pubmed: 34108002
J Chem Inf Model. 2017 Feb 27;57(2):355-364
pubmed: 28055196
J Mol Biol. 1997 Apr 4;267(3):727-48
pubmed: 9126849
Drug Discov Today. 2016 May;21(5):712-7
pubmed: 26891978
Curr Top Med Chem. 2018;18(12):998-1006
pubmed: 30101712
J Health Econ. 2016 May;47:20-33
pubmed: 26928437
Drug Des Devel Ther. 2017 Aug 31;11:2551-2564
pubmed: 28919707
Curr Opin Struct Biol. 2002 Apr;12(2):190-6
pubmed: 11959496
Proteins. 2014 Jul;82(7):1168-85
pubmed: 25050439
J Comput Chem. 2009 Dec;30(16):2785-91
pubmed: 19399780
J Clin Invest. 2000 Jan;105(1):3-7
pubmed: 10619854
Nat Methods. 2021 May;18(5):463-471
pubmed: 33963356
Curr Top Med Chem. 2007;7(10):1006-14
pubmed: 17508934
Nat Commun. 2022 Jun 7;13(1):3293
pubmed: 35672310
ACS Cent Sci. 2020 Jun 24;6(6):939-949
pubmed: 32607441
J Chem Inf Model. 2015 Nov 23;55(11):2411-20
pubmed: 26457994
FEBS Lett. 2006 Feb 20;580(5):1447-50
pubmed: 16460734
J Med Chem. 2007 Apr 19;50(8):1768-77
pubmed: 17367119
Brief Bioinform. 2021 Jul 20;22(4):
pubmed: 33140820
Int J Mol Sci. 2019 Mar 19;20(6):
pubmed: 30893780
Elife. 2021 Mar 29;10:
pubmed: 33779550
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
J Cheminform. 2020 May 29;12(1):38
pubmed: 33431013
Nature. 2020 Apr;580(7805):663-668
pubmed: 32152607
J Med Chem. 2004 Mar 25;47(7):1739-49
pubmed: 15027865
Sci China Life Sci. 2018 Oct;61(10):1191-1204
pubmed: 30054833
J Cell Biol. 2021 Apr 5;220(4):
pubmed: 33496723
Int J Gen Med. 2021 Jul 12;14:3295-3312
pubmed: 34285555
J Phys Chem B. 2020 Nov 12;124(45):10166-10172
pubmed: 33143418
Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19484-19489
pubmed: 31511421
Drug Discov Today. 2009 Jul;14(13-14):676-83
pubmed: 19422931
Front Pharmacol. 2018 Aug 22;9:923
pubmed: 30186166
J Chem Inf Model. 2012 Feb 27;52(2):360-72
pubmed: 22148551
Biomolecules. 2020 Apr 19;10(4):
pubmed: 32325877
J Med Chem. 2005 Oct 20;48(21):6679-89
pubmed: 16220984
BMC Mol Cell Biol. 2021 Jun 10;22(1):34
pubmed: 34112110
J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):161-8
pubmed: 18183356
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W609-14
pubmed: 20430828
J Struct Biol. 2008 Jan;161(1):31-42
pubmed: 17949996
Methods Mol Biol. 2017;1520:85-106
pubmed: 27873247
Nat Commun. 2022 Feb 21;13(1):973
pubmed: 35190542
Nature. 2004 Dec 16;432(7019):862-5
pubmed: 15602552
Eur J Med Chem. 2021 Nov 15;224:113705
pubmed: 34303871
J Med Chem. 2022 Jan 13;65(1):100-102
pubmed: 34913338
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W270-7
pubmed: 21624888
Drug Discov Today. 2017 Nov;22(11):1680-1685
pubmed: 28881183
Int J Mol Sci. 2019 Jun 06;20(11):
pubmed: 31174387
Chem Sci. 2021 Sep 9;12(41):13664-13675
pubmed: 34760151
Drug Discov Today Technol. 2004 Dec;1(3):203-7
pubmed: 24981486
Trends Pharmacol Sci. 2019 Nov;40(11):806-809
pubmed: 31629547
J Chem Inf Model. 2017 Jan 23;57(1):73-84
pubmed: 27983849
J Chem Theory Comput. 2013 Sep 10;9(9):3878-88
pubmed: 26592383
J Chem Theory Comput. 2015 Jul 14;11(7):3499-509
pubmed: 26190950
Expert Rev Clin Pharmacol. 2013 Mar;6(2):95-7
pubmed: 23473587
J Chem Inf Model. 2009 Mar;49(3):670-7
pubmed: 19434900
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Annu Rev Pharmacol Toxicol. 2020 Jan 6;60:51-71
pubmed: 31348870
Front Chem. 2019 Jul 11;7:498
pubmed: 31355188
Methods Mol Biol. 2021;2302:335-356
pubmed: 33877636
Drug Discov Today. 2021 Jun;26(6):1382-1393
pubmed: 33609779
Bioinformatics. 2005 Nov 15;21(22):4133-9
pubmed: 16174682
PeerJ. 2016 Feb 25;4:e1725
pubmed: 26966660
Nucleic Acids Res. 2022 Jan 7;50(D1):D439-D444
pubmed: 34791371
Expert Opin Drug Discov. 2015 May;10(5):449-61
pubmed: 25835573
Cancer Biol Med. 2022 Jun 15;19(6):
pubmed: 35699406
J Chem Inf Model. 2019 Mar 25;59(3):1182-1196
pubmed: 30785751
Proteins. 1992 Jul;13(3):206-22
pubmed: 1603810
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W582-9
pubmed: 20478829
Brief Bioinform. 2022 Jan 17;23(1):
pubmed: 34929743
J Phys Chem B. 2009 Dec 17;113(50):16226-36
pubmed: 19924840
Curr Med Chem. 2013;20(23):2839-60
pubmed: 23651302
Methods Mol Biol. 2019;1903:23-43
pubmed: 30547434
Chem Sci. 2020 Jan 23;11(9):2362-2368
pubmed: 34084397
J Comput Aided Mol Des. 2019 Feb;33(2):133-203
pubmed: 30506158
J Chem Inf Comput Sci. 1996 May-Jun;36(3):563-71
pubmed: 8690757
Curr Pharm Des. 2018;24(28):3347-3358
pubmed: 29879881
J Chem Inf Model. 2005 Jan-Feb;45(1):177-82
pubmed: 15667143
J Comput Chem. 2010 Jan 30;31(2):455-61
pubmed: 19499576
J Am Chem Soc. 2009 Jul 1;131(25):8732-3
pubmed: 19505099
Chemistry. 2016 Jun 27;22(27):9218-25
pubmed: 27225077
Biochim Biophys Acta. 2006 Nov;1764(11):1647-76
pubmed: 17049320
Protein Sci. 2002 Jul;11(7):1729-37
pubmed: 12070326
J Phys Chem B. 2010 Jul 8;114(26):8817-25
pubmed: 20550161
Brief Bioinform. 2019 Sep 27;20(5):1878-1912
pubmed: 30084866
Future Med Chem. 2015;7(17):2317-31
pubmed: 26599419
J Chem Inf Model. 2008 Sep;48(9):1773-91
pubmed: 18763758
Database (Oxford). 2014 Dec 23;2014:bau124
pubmed: 25539768
Brief Bioinform. 2021 Nov 5;22(6):
pubmed: 34423353
Nucleic Acids Res. 2016 Jan 4;44(D1):D1045-53
pubmed: 26481362
Curr Top Med Chem. 2014;14(16):1923-38
pubmed: 25262799
Curr Drug Targets Infect Disord. 2003 Mar;3(1):33-40
pubmed: 12570731
J Med Chem. 2018 Feb 8;61(3):638-649
pubmed: 28745501
Nucleic Acids Res. 2019 Jan 8;47(D1):D930-D940
pubmed: 30398643
Bioinformatics. 2013 Oct 15;29(20):2588-95
pubmed: 23975762
Methods Biochem Anal. 2003;44:547-57
pubmed: 12647404
Sci Adv. 2018 Jul 25;4(7):eaap7885
pubmed: 30050984
Sci Rep. 2018 Jun 14;8(1):9110
pubmed: 29904147
Proteins. 1999 Nov 1;37(2):228-41
pubmed: 10584068
Molecules. 2020 Jul 11;25(14):
pubmed: 32664504
Angew Chem Int Ed Engl. 2009;48(7):1198-229
pubmed: 19173328
Front Microbiol. 2017 Aug 23;8:1591
pubmed: 28878750
Curr Opin Struct Biol. 2001 Apr;11(2):236-42
pubmed: 11297934
J Comput Chem. 2008 Oct;29(13):2044-78
pubmed: 18623101
Proc Natl Acad Sci U S A. 2021 Jan 26;118(4):
pubmed: 33468660
AAPS J. 2012 Mar;14(1):133-41
pubmed: 22281989
Nucleic Acids Res. 2012 Jan;40(Database issue):D1100-7
pubmed: 21948594
Phys Chem Chem Phys. 2013 Jan 14;15(2):397-411
pubmed: 23172634
Trends Biochem Sci. 2015 Jan;40(1):49-57
pubmed: 25544475
Curr Top Med Chem. 2017;17(15):1709-1726
pubmed: 27848897
J Med Chem. 2022 Jul 14;65(13):9478-9492
pubmed: 35713420
J Am Chem Soc. 2005 Aug 10;127(31):10967-76
pubmed: 16076203
IEEE/ACM Trans Comput Biol Bioinform. 2022 Jul-Aug;19(4):2208-2218
pubmed: 33956632
J Phys Chem Lett. 2019 Dec 19;10(24):7740-7744
pubmed: 31747286
J Cheminform. 2019 Nov 21;11(1):71
pubmed: 33430971
Curr Pharm Des. 2004;10(9):1011-33
pubmed: 15078130
J Chem Inf Model. 2022 Nov 14;62(21):5100-5109
pubmed: 34792338
PLoS One. 2014 Dec 12;9(12):e114610
pubmed: 25502559
J Med Chem. 2021 Oct 14;64(19):14011-14027
pubmed: 34533311
J Cheminform. 2019 Jan 17;11(1):5
pubmed: 30656426
Curr Comput Aided Drug Des. 2011 Jun;7(2):146-57
pubmed: 21534921
J Chem Inf Model. 2020 Jan 27;60(1):77-91
pubmed: 31809029
Nucleic Acids Res. 2017 Jan 4;45(D1):D945-D954
pubmed: 27899562
J Med Chem. 2003 Jun 19;46(13):2765-73
pubmed: 12801239
J Chem Inf Model. 2013 Aug 26;53(8):2018-32
pubmed: 23834278
Med Res Rev. 2022 Mar;42(2):744-769
pubmed: 34697818
J Med Chem. 2014 Jun 26;57(12):4977-5010
pubmed: 24351051
Int J Mol Sci. 2019 Aug 01;20(15):
pubmed: 31375023
Brief Bioinform. 2009 Sep;10(5):579-91
pubmed: 19433475
Mol Inform. 2018 Jan;37(1-2):
pubmed: 29095571
J Chem Inf Model. 2020 Sep 28;60(9):4200-4215
pubmed: 32865404
J Chem Inf Model. 2020 Apr 27;60(4):2189-2198
pubmed: 32227880
In Silico Pharmacol. 2021 Mar 23;9(1):23
pubmed: 33854869
Molecules. 2018 Jul 30;23(8):
pubmed: 30061498
Curr Pharm Des. 2014;20(20):3281-92
pubmed: 23947650
Drug Discov Today Technol. 2019 Dec;32-33:55-63
pubmed: 33386095
Chem Biol Drug Des. 2006 May;67(5):370-2
pubmed: 16784462
Sci Rep. 2018 Mar 7;8(1):4163
pubmed: 29515203
Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):165-76
pubmed: 24419389
BMC Biol. 2011 Oct 28;9:71
pubmed: 22035460
Drug Discov Today. 2010 Jun;15(11-12):444-50
pubmed: 20362693
Curr Opin Struct Biol. 2018 Feb;48:93-102
pubmed: 29149726
Nat Rev Drug Discov. 2020 May;19(5):353-364
pubmed: 31801986
Nat Mach Intell. 2021 Dec;3(12):1040-1049
pubmed: 35187404
IEEE/ACM Trans Comput Biol Bioinform. 2022 Jan-Feb;19(1):407-417
pubmed: 33360998
Annu Rev Pharmacol Toxicol. 1997;37:71-90
pubmed: 9131247
Molecules. 2018 Oct 02;23(10):
pubmed: 30279331
J Am Chem Soc. 2021 Jul 28;143(29):11044-11051
pubmed: 34255502
Curr Top Med Chem. 2010;10(1):95-115
pubmed: 19929826
J Chem Inf Model. 2015 Nov 23;55(11):2324-37
pubmed: 26479676
Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6
pubmed: 18048412
Nat Rev Drug Discov. 2004 Nov;3(11):935-49
pubmed: 15520816
Curr Opin Pharmacol. 2010 Dec;10(6):738-44
pubmed: 20971684
J Chem Inf Model. 2021 Jan 25;61(1):36-45
pubmed: 33252229
J Cheminform. 2021 May 13;13(1):39
pubmed: 33985583
ACS Cent Sci. 2018 Jan 24;4(1):120-131
pubmed: 29392184
Molecules. 2020 Feb 18;25(4):
pubmed: 32085470
J Comput Aided Mol Des. 1995 Apr;9(2):113-30
pubmed: 7608743
Int J Mol Sci. 2010 Aug 18;11(8):3016-34
pubmed: 21152288
J Comput Chem. 2005 Jul 15;26(9):915-31
pubmed: 15841474
Signal Transduct Target Ther. 2020 May 21;5(1):72
pubmed: 32435053
Sci Rep. 2017 Nov 13;7(1):15451
pubmed: 29133831
J Chem Inf Model. 2019 Mar 25;59(3):945-946
pubmed: 30905159
Expert Opin Drug Discov. 2016;11(3):225-39
pubmed: 26814169
Pharmacol Rev. 2013 Dec 31;66(1):334-95
pubmed: 24381236
Phys Rev Lett. 2018 Apr 6;120(14):143001
pubmed: 29694129
Front Chem. 2018 May 29;6:188
pubmed: 29896472
Methods Mol Biol. 2021;2190:139-165
pubmed: 32804364
Br Med J (Clin Res Ed). 1983 Oct 29;287(6401):1299
pubmed: 6416376
Bioinformatics. 2017 Oct 01;33(19):3036-3042
pubmed: 28575181
J Comput Chem. 2018 Jun 5;39(15):917-924
pubmed: 29399815
J Cheminform. 2020 Feb 18;12(1):14
pubmed: 33430996
J Phys Chem B. 2011 Feb 10;115(5):1315-22
pubmed: 21175195
J Phys Chem B. 2017 Dec 21;121(50):11284-11291
pubmed: 29156125
Curr Pharm Des. 2007;13(14):1497-508
pubmed: 17504169
J Med Chem. 2005 Jul 14;48(14):4558-75
pubmed: 15999994
Bioorg Med Chem Lett. 2013 Feb 15;23(4):1056-62
pubmed: 23294700
Comb Chem High Throughput Screen. 2011 Dec;14(10):889-97
pubmed: 21843143
Drug Discov Today. 2018 Jun;23(6):1241-1250
pubmed: 29366762
ACS Cent Sci. 2018 Feb 28;4(2):268-276
pubmed: 29532027
Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082
pubmed: 29126136
Curr Comput Aided Drug Des. 2014;10(2):148-59
pubmed: 24724896
J Chem Inf Comput Sci. 1998 May-Jun;38(3):511-22
pubmed: 9611787
Curr Pharm Des. 2016;22(5):572-81
pubmed: 26601966
J Biomol Struct Dyn. 2019 Oct;37(16):4301-4311
pubmed: 30477412
J Biomol Struct Dyn. 2020 Feb;38(3):901-917
pubmed: 30938661
J Comput Aided Mol Des. 2002 Mar;16(3):151-66
pubmed: 12363215
J Am Chem Soc. 2007 May 23;129(20):6562-70
pubmed: 17461584
Curr Med Chem. 2021;28(15):2887-2942
pubmed: 32787752
J Med Chem. 2020 Aug 27;63(16):8749-8760
pubmed: 31408336
J Comput Chem. 2015 Jun 5;36(15):1132-56
pubmed: 25914306
Structure. 2012 Apr 4;20(4):628-40
pubmed: 22483110
Science. 2020 Dec 4;370(6521):
pubmed: 33060197
Eur J Med Chem. 2020 Jun 1;195:112290
pubmed: 32283295
Interdiscip Sci. 2019 Jun;11(2):320-328
pubmed: 30877639
Nat Biotechnol. 2019 Sep;37(9):1038-1040
pubmed: 31477924
Biochim Biophys Acta. 2012 Feb;1820(2):116-23
pubmed: 22155634