Academic Journal

Advances in Drug Discovery and Design using Computer-aided Molecular Modeling.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Advances in Drug Discovery and Design using Computer-aided Molecular Modeling.
Συγγραφείς: Singh K; Department of Pharmacology, Rajiv Academy for Pharmacy, Mathura Uttar Pradesh, India., Bhushan B; Department of Pharmacology, Institute of Pharmaceutical Research, GLA University, Mathura Uttar Pradesh, India., Singh B; Department of Pharmacy, B.S.A. College of Engineering & Technology, Mathura Uttar Pradesh India.
Πηγή: Current computer-aided drug design [Curr Comput Aided Drug Des] 2024; Vol. 20 (5), pp. 697-710.
Τύπος έκδοσης: Journal Article; Review
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Bentham Science Publishers Country of Publication: United Arab Emirates NLM ID: 101265750 Publication Model: Print Cited Medium: Internet ISSN: 1875-6697 (Electronic) Linking ISSN: 15734099 NLM ISO Abbreviation: Curr Comput Aided Drug Des Subsets: MEDLINE
Imprint Name(s): Original Publication: Sharjah, U.A.E. ; San Francisco, CA : Bentham Science Publishers, c2005-
Ιατρικοί όροι (MeSH): Drug Discovery*/methods , Drug Design*/methods , Computer-Aided Design* , Molecular Docking Simulation* , Quantitative Structure-Activity Relationship*, Humans ; Models, Molecular ; Algorithms
Περίληψη: Computer-aided molecular modeling is a rapidly emerging technology that is being used to accelerate the discovery and design of new drug therapies. It involves the use of computer algorithms and 3D structures of molecules to predict interactions between molecules and their behavior in the body. This has drastically improved the speed and accuracy of drug discovery and design. Additionally, computer-aided molecular modeling has the potential to reduce costs, increase the quality of data, and identify promising targets for drug development. Through the use of sophisticated methods, such as virtual screening, molecular docking, pharmacophore modeling, and quantitative structure-activity relationships, scientists can achieve higher levels of efficacy and safety for new drugs. Moreover, it can be used to understand the activity of known drugs and simplify the process of formulating, optimizing, and predicting the pharmacokinetics of new and existing drugs. In conclusion, computer-aided molecular modeling is an effective tool to rapidly progress drug discovery and design by predicting the interactions between molecules and anticipating the behavior of new drugs in the body.
(Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
References: Sliwoski G; Kothiwale S; Meiler J; Lowe EW; Computational methods in drug discovery. Pharmacol Rev 2014,66(1),334. (PMID: 10.1124/pr.112.007336)
Doman T.N.; McGovern S.L.; Witherbee B.J.; Kasten T.P.; Kurumbail R.; Stallings W.C.; Connolly D.T.; Shoichet B.K.; Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 2002,45(11),2213-2221. (PMID: 10.1021/jm010548w12014959)
Adelusi T.I.; Oyedele A.Q.K.; Boyenle I.D.; Ogunlana A.T.; Adeyemi R.O.; Ukachi C.D.; Idris M.O.; Olaoba O.T.; Adedotun I.O.; Kolawole O.E.; Xiaoxing Y.; Abdul-Hammed M.; Molecular modeling in drug discovery. Inform Med Unlocked, 2022,29,100880. (PMID: 10.1016/j.imu.2022.100880)
Du Toit A.; Outbreak of a novel coronavirus. Nat Rev Microbiol 2020,18(3),123-123. (PMID: 10.1038/s41579-020-0332-031988490)
Myers S.; Baker A.; Drug discovery—an operating model for a new era. Nat Biotechnol 2001,19(8),727-730. (PMID: 10.1038/9076511479559)
Manglik A.; Lin H.; Aryal D.K.; McCorvy J.D.; Dengler D.; Corder G.; Levit A.; Kling R.C.; Bernat V.; Hübner H.; Huang X.P.; Sassano M.F.; Giguère P.M.; Löber S.; Da Duan ; Scherrer G.; Kobilka B.K.; Gmeiner P.; Roth B.L.; Shoichet B.K.; Structure-based discovery of opioid analgesics with reduced side effects. Nature 2016,537(7619),185-190. (PMID: 10.1038/nature1911227533032)
Porter C.T.; Bartlett G.J.; Thornton J.M.; The catalytic site atlas: A resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004,32(90001),129D-133. (PMID: 10.1093/nar/gkh02814681376)
Arakaki A.K.; Zhang Y.; Skolnick J.; Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics 2004,20(7),1087-1096. (PMID: 10.1093/bioinformatics/bth04414764543)
Källberg M.; Wang H.; Wang S.; Peng J.; Wang Z.; Lu H.; Xu J.; Template-based protein structure modeling using the RaptorX web server. Nat Protoc 2012,7(8),1511-1522. (PMID: 10.1038/nprot.2012.08522814390)
Gupta R.; Srivastava D.; Sahu M.; Tiwari S.; Ambasta R.K.; Kumar P.; Artificial intelligence to deep learning: Machine intelligence approach for drug discovery. Mol Divers 2021,25(3),1315-1360. (PMID: 10.1007/s11030-021-10217-333844136)
Ejalonibu M.A.; Ogundare S.A.; Elrashedy A.A.; Ejalonibu M.A.; Lawal M.M.; Mhlongo N.N.; Kumalo H.M.; Drug discovery for Mycobacterium tuberculosis using structure-based computer- aided drug design approach. Int J Mol Sci 2021,22(24),13259. (PMID: 10.3390/ijms22241325934948055)
Bassani D.; Moro S.; Past, present, and future perspectives on computer-aided drug design methodologies. Molecules 2023,28(9),3906. (PMID: 10.3390/molecules2809390637175316)
Martin L.; Hutchens M.; Hawkins C.; Clinical trial cycle times continue to increase despite industry efforts. Nat Rev Drug Discov 2017,16(3),157-157. (PMID: 10.1038/nrd.2017.2128184041)
Mouchlis V.D.; Afantitis A.; Serra A.; Fratello M.; Papadiamantis A.G.; Aidinis V.; Lynch I.; Greco D.; Melagraki G.; Advances in de novo drug design: From conventional to machine learning methods. Int J Mol Sci 2021,22(4),1676. (PMID: 10.3390/ijms2204167633562347)
Petrović D.; Scott J.S.; Bodnarchuk M.S.; Lorthioir O.; Boyd S.; Hughes G.M.; Lane J.; Wu A.; Hargreaves D.; Robinson J.; Sadowski J.; Virtual screening in the cloud identifies potent and selective ROS1 kinase inhibitors. J Chem Inf Model 2022,62(16),3832-3843. (PMID: 10.1021/acs.jcim.2c0064435920716)
Gorgulla C.; Boeszoermenyi A.; Wang Z.F.; Fischer P.D.; Coote P.W.; Padmanabha Das K.M.; Malets Y.S.; Radchenko D.S.; Moroz Y.S.; Scott D.A.; Fackeldey K.; Hoffmann M.; Iavniuk I.; Wagner G.; Arthanari H.; An open-source drug discovery platform enables ultra-large virtual screens. Nature 2020,580(7805),663-668. (PMID: 10.1038/s41586-020-2117-z32152607)
Ooms F.; Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry. Curr Med Chem 2000,7(2),141-158. (PMID: 10.2174/092986700337531710637360)
Guha R.; The ups and downs of structure–activity landscapes. Chemoinformatics and Computational Chemical Biology Methods in Molecular Biology; Bajorath, J, Ed 2010,672,101-117. (PMID: 10.1007/978-1-60761-839-3_3)
Fu H.; Shao X.; Cai W.; Computer-aided design of molecular machines: Techniques, paradigms and difficulties. Phys Chem Chem Phys 2022,24(3),1286-1299. (PMID: 10.1039/D1CP04942A34951435)
Ferreira L.; dos Santos R.; Oliva G.; Andricopulo A.; Molecular docking and structure-based drug design strategies. Molecules 2015,20(7),13384-13421. (PMID: 10.3390/molecules20071338426205061)
Palazzesi F.; Pozzan A.; Deep learning applied to ligand-based de novo drug design. Artificial Intelligence in Drug Design Methods in Molecular Biology 2022,vol 2390,273-299. (PMID: 10.1007/978-1-0716-1787-8_12)
Yu W; Mackerell AD.; Computer-aided drug design methods., Methods Mol Biol, 2017, 1520, 85-106. (PMID: 10.1007/978-1-4939-6634-9_5)
Zhang Y.; Luo M.; Wu P.; Wu S.; Lee T.Y.; Bai C.; Application of computational biology and artificial intelligence in drug design. Int J Mol Sci 2022,23(21),13568. (PMID: 10.3390/ijms23211356836362355)
Pecina A.; Eyrilmez S.M.; Köprülüoğlu C.; Miriyala V.M.; Lepšík M.; Fanfrlík J.; Řezáč J.; Hobza P.; SQM/COSMO scoring function: Reliable quantum‐mechanical tool for sampling and ranking in structure‐based drug design. ChemPlusChem 2020,85(11),2362-2371. (PMID: 10.1002/cplu.20200012032609421)
Monteleone S.; Fedorov D.G.; Townsend-Nicholson A.; Southey M.; Bodkin M.; Heifetz A.; Hotspot identification and drug design of protein–protein interaction modulators using the fragment molecular orbital method. J Chem Inf Model 2022,62(16),3784-3799. (PMID: 10.1021/acs.jcim.2c0045735939049)
Tripathi A.; Bankaitis VA.; Molecular docking: From lock and key to combination lock. J Mol Med Clin Appl 2017,2(1),10.
Maiti S.; Nazmeen A.; Banerjee A.; Significant impact of redox regulation of estrogen‐metabolizing proteins on cellular stress responses. Cell Biochem Funct 2023,41(4),461-477. (PMID: 10.1002/cbf.379637139830)
Zhou S.; Weiß R.G.; Cheng L.T.; Dzubiella J.; McCammon J.A.; Li B.; Variational implicit-solvent predictions of the dry–wet transition pathways for ligand–receptor binding and unbinding kinetics. Proc Natl Acad Sci USA 2019,116(30),14989-14994. (PMID: 10.1073/pnas.190271911631270236)
Śledź P.; Caflisch A.; Protein structure-based drug design: From docking to molecular dynamics. Curr Opin Struct Biol 2018,48,93-102. (PMID: 10.1016/j.sbi.2017.10.01029149726)
Lindorff-Larsen K.; Maragakis P.; Piana S.; Eastwood M.P.; Dror R.O.; Shaw D.E.; Systematic validation of protein force fields against experimental data. PLoS One 2012,7(2),e32131. (PMID: 10.1371/journal.pone.003213122384157)
Wang L.; Wu Y.; Deng Y.; Kim B.; Pierce L.; Krilov G.; Lupyan D.; Robinson S.; Dahlgren M.K.; Greenwood J.; Romero D.L.; Masse C.; Knight J.L.; Steinbrecher T.; Beuming T.; Damm W.; Harder E.; Sherman W.; Brewer M.; Wester R.; Murcko M.; Frye L.; Farid R.; Lin T.; Mobley D.L.; Jorgensen W.L.; Berne B.J.; Friesner R.A.; Abel R.; Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J Am Chem Soc 2015,137(7),2695-2703. (PMID: 10.1021/ja512751q25625324)
Caleman C.; van Maaren P.J.; Hong M.; Hub J.S.; Costa L.T.; van der Spoel D.; Force field benchmark of organic liquids: Density, enthalpy of vaporization, heat capacities, surface tension, isothermal compressibility, volumetric expansion coefficient, and dielectric constant. J Chem Theory Comput 2012,8(1),61-74. (PMID: 10.1021/ct200731v22241968)
Karunakar P.; P B S.; v K.; In silico modelling and virtual screening for identification of inhibitors for spore wall protein-5 in Nosema bombycis. J Biomol Struct Dyn 2022,40(4),1748-1763. (PMID: 10.1080/07391102.2020.183257933050775)
Hassan Baig M.; Ahmad K.; Roy S.; Mohammad Ashraf J.; Adil M.; Haris Siddiqui M.; Khan S.; Amjad Kamal M.; Provazník I.; Choi I.; Computer aided drug design: Success and limitations. Curr Pharm Des 2016,22(5),572-581. (PMID: 10.2174/138161282266615112500055026601966)
Seidel T.; Schuetz D.A.; Garon A.; Langer T.; The pharmacophore concept and its applications in computer-aided drug design. Progress in the Chemistry of Organic Natural Products 2019,110,99-141. (PMID: 10.1007/978-3-030-14632-0_4)
Yang D.; Zhou Q.; Labroska V.; Qin S.; Darbalaei S.; Wu Y.; Yuliantie E.; Xie L.; Tao H.; Cheng J.; Liu Q.; Zhao S.; Shui W.; Jiang Y.; Wang M.W.; G protein-coupled receptors: Structureand function-based drug discovery. Signal Transduct. Target Ther 2021,6(1),7. (PMID: 10.1038/s41392-020-00435-w33414387)
Morris G.M.; Lim-Wilby M.; Molecular docking. Methods Mol Biol 2008,443,365-382. (PMID: 10.1007/978-1-59745-177-2_19.18446297)
Shahin R.; Mansi I.; Swellmeen L.; Alwidyan T.; Al-Hashimi N.; Al-Qarar’h Y.; Shaheen O.; Ligand-based computer aided drug design reveals new tropomycin receptor kinase a (TrkA) inhibitors. J Mol Graph Model 2018,80,327-352. (PMID: 10.1016/j.jmgm.2018.01.00429454290)
Ballante F.; Kooistra A.J.; Kampen S.; de Graaf C.; Carlsson J.; Structure-based virtual screening for ligands of G protein-coupled receptors: What can molecular docking do for you? Pharmacol Rev 2021,73(4),527-565.
Forli S.; Huey R.; Pique M.E.; Sanner M.F.; Goodsell D.S.; Olson A.J.; Computational protein–ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc 2016,11(5),905-919. (PMID: 10.1038/nprot.2016.05127077332)
Blanes-Mira C.; Fernández-Aguado P.; de Andrés-López J.; Fernández-Carvajal A.; Ferrer-Montiel A.; Fernández-Ballester G.; Comprehensive survey of consensus docking for highthroughput virtual screening. Molecules 2022,28(1),175. (PMID: 10.3390/molecules2801017536615367)
Tahir ul Qamar M.; Zhu XT.; Chen LL; Alhussain L; Targetspecific machine learning scoring function improved structurebased virtual screening performance for SARS-CoV-2 drugs development. Int J Mol Sci 2022,23(19),11003.
Wu C; Liu Y; Yang Y; Zhang P; Zhong W; Wang Y; Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B 2020,10(5),766.
Rajasekaran R.; Chen Y.P.P.; Probing the structure of Leishmania major DHFR TS and structure based virtual screening of peptide library for the identification of anti-leishmanial leads. J Mol Model 2012,18(9),4089-4100. (PMID: 10.1007/s00894-012-1411-622527276)
Editorial (Hot Topic: Topological and electrotopological descriptors of molecules: Fundamental principles and applications to computer aided molecular design – Part II). Curr Comput Aided- Drug Des 2012,8(3),171. (PMID: 10.2174/157340912801619111)
Llinas del Torrent C.; Pérez-Benito L.; Tresadern G.; Computational drug design applied to the study of metabotropic glutamate receptors. Molecules 2019,24(6),1098. (PMID: 10.3390/molecules2406109830897742)
Barril X.; Hubbard R.E.; Morley S.D.; Virtual screening in structure- based drug discovery. Mini Rev Med Chem 2004,4(7),779-791. (PMID: 15379645)
Gao Y.; Zhou Z.; Zhang T.; Xue S.; Li K.; Jiang J.; Structurebased virtual screening towards the discovery of novel ULK1 inhibitors with anti-HCC activities. Molecules 2022,27(9),2627. (PMID: 10.3390/molecules2709262735565977)
Dong J.; Cao D.S.; Miao H.Y.; Liu S.; Deng B.C.; Yun Y.H.; Wang N.N.; Lu A.P.; Zeng W.B.; Chen A.F.; ChemDes: An integrated web-based platform for molecular descriptor and fingerprint computation. J Cheminform 2015,7(1),60. (PMID: 10.1186/s13321-015-0109-z26664458)
Vucicevic J.; Nikolic K.; Mitchell J.B.O.; Rational drug design of antineoplastic agents using 3D-QSAR, cheminformatic, and virtual screening approaches. Curr Med Chem 2019,26(21),3874-3889. (PMID: 10.2174/092986732466617071211541128707592)
Huynh L.; Neale C.; Pomès R.; Allen C.; Computational approaches to the rational design of nanoemulsions, polymeric micelles, and dendrimers for drug delivery. Nanomedicine 2012,8(1),20-36. (PMID: 10.1016/j.nano.2011.05.00621669300)
Zhang S.; Zhang J.; Gao P.; Sun L.; Song Y.; Kang D.; Liu X.; Zhan P.; Efficient drug discovery by rational lead hybridization based on crystallographic overlay. Drug Discov Today 2019,24(3),805-813. (PMID: 10.1016/j.drudis.2018.11.02130529326)
Testa A.; Hughes S.J.; Lucas X.; Wright J.E.; Ciulli A.; Structure‐ based design of a macrocyclic PROTAC. Angew Chem Int Ed 2020,59(4),1727-1734. (PMID: 10.1002/anie.20191439631746102)
Krüger D.M.; Evers A.; Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. ChemMedChem 2010,5(1),148-158. (PMID: 10.1002/cmdc.20090031419908272)
Rush T.S.; Grant J.A.; Mosyak L.; Nicholls A.; A shapebased 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J Med Chem 2005,48(5),1489-1495. (PMID: 10.1021/jm040163o15743191)
Razzaghi-Asl N.; Sepehri S.; Ebadi A.; Miri R.; Shahabipour S.; Effect of biomolecular conformation on docking simulation: A case study on a potent HIV-1 protease inhibitor. Iran J Pharm Res 2015,14(3),785-802. (PMID: 26330867)
Lin J.; Sahakian D.; de Morais S.; Xu J.; Polzer R.; Winter S.; The role of absorption, distribution, metabolism, excretion and toxicity in drug discovery. Curr Top Med Chem 2003,3(10),1125-1154. (PMID: 10.2174/156802603345209612769713)
Ansari S.; Azizian H.; Pedrood K.; Yavari A.; Mojtabavi S.; Faramarzi M.A.; Golshani S.; Hosseini S.; Biglar M.; Larijani B.; Rastegar H.; Hamedifar H.; Mohammadi-Khanaposhtani M.; Mahdavi M.; Design, synthesis, and α‐glucosidase‐inhibitory activity of phenoxy‐biscoumarin –N ‐phenylacetamide hybrids. Arch Pharm 2021,354(12),2100179. (PMID: 10.1002/ardp.20210017934467580)
Zhu Y.; Han Y.; Ma Y.; Yang P.; ADME/toxicity prediction and antitumor activity of novel nitrogenous heterocyclic compounds designed by computer targeting of alkylglycerone phosphate synthase. Oncol Lett 2018,16(2),1431-1438. (PMID: 10.3892/ol.2018.887330008821)
Rai H.; Barik A.; Singh Y.P.; Suresh A.; Singh L.; Singh G.; Nayak U.Y.; Dubey V.K.; Modi G.; Molecular docking, binding mode analysis, molecular dynamics, and prediction of ADMET/ toxicity properties of selective potential antiviral agents against SARS-CoV-2 main protease: an effort toward drug repurposing to combat COVID-19. Mol Divers 2021,25(3),1905-1927. (PMID: 10.1007/s11030-021-10188-533582935)
Parmar D.R.; Soni J.Y.; Guduru R.; Rayani R.H.; Kusurkar R.V.; Vala A.G.; Talukdar S.N.; Eissa I.H.; Metwaly A.M.; Khalil A.; Zunjar V.; Battula S.; Discovery of new anticancer thiourea- azetidine hybrids: design, synthesis, in vitro antiproliferative, SAR, in silico molecular docking against VEGFR-2, ADMET, toxicity, and DFT studies. Bioorg Chem 2021,115,105206. (PMID: 10.1016/j.bioorg.2021.10520634339975)
McKim J.; Building a tiered approach to in vitro predictive toxicity screening: A focus on assays with in vivo relevance. Comb Chem High Throughput Screen 2010,13(2),188-206. (PMID: 10.2174/13862071079059673620053163)
Alanazi M.M.; Elwan A.; Alsaif N.A.; Obaidullah A.J.; Alkahtani H.M.; Al-Mehizia A.A.; Alsubaie S.M.; Taghour M.S.; Eissa I.H.; Discovery of new 3-methylquinoxalines as potential anti- cancer agents and apoptosis inducers targeting VEGFR-2: design, synthesis, and in silico studies. J Enzyme Inhib Med Chem 2021,36(1),1732-1750. (PMID: 10.1080/14756366.2021.194559134325596)
Idris M.O.; Yekeen A.A.; Alakanse O.S.; Durojaye O.A.; Computer- aided screening for potential TMPRSS2 inhibitors: A combination of pharmacophore modeling, molecular docking and molecular dynamics simulation approaches. J Biomol Struct Dyn 2021,39(15),5638-5656. (PMID: 10.1080/07391102.2020.179234632672528)
Daoui O.; Nour H.; Abchir O.; Elkhattabi S.; Bakhouch M.; Chtita S.; A computer-aided drug design approach to explore novel type II inhibitors of c-Met receptor tyrosine kinase for cancer therapy: QSAR, molecular docking, ADMET and molecular dynamics simulations. J Biomol Struct Dyn 2023,41(16),7768-7785. (PMID: 10.1080/07391102.2022.212445636120976)
Tabeshpour J.; Sahebkar A.; Zirak M.R.; Zeinali M.; Hashemzaei M.; Rakhshani S.; Rakhshani S.; Computer-aided drug design and drug pharmacokinetic prediction: A mini-review. Curr Pharm Des 2018,24(26),3014-3019. (PMID: 10.2174/138161282466618090312342330179125)
Sodum N; Rao V; Cheruku SP; Kumar G; Sankhe R; Kishore A.; Amelioration of high-fat diet (HFD) + CCl4 induced NASH/NAFLD in CF-1 mice by activation of SIRT-1 using cinnamoyl sulfonamide hydroxamate derivatives: In-silico molecular modelling and in-vivo prediction. 3 Biotech 2022,12(7),147.
Rim K.T.; In silico prediction of toxicity and its applications for chemicals at work. Toxicol Environ Health Sci 2020,12(3),191-202. (PMID: 10.1007/s13530-020-00056-432421081)
Tripathy S.; Sahu S.K.; Azam M.A.; Jupudi S.; Computer-aided identification of lead compounds as Staphylococcal epidermidis FtsZ inhibitors using molecular docking, virtual screening, DFT analysis, and molecular dynamic simulation. J Mol Model 2019,25(12),360. (PMID: 10.1007/s00894-019-4238-631773394)
Krishnan S.R.; Bung N.; Vangala S.R.; Srinivasan R.; Bulusu G.; Roy A.; De novo structure-based drug design using deep learning. J Chem Inf Model 2022,62(21),5100-5109. (PMID: 10.1021/acs.jcim.1c0131934792338)
Lin Y.; Zhang Y.; Wang D.; Yang B.; Shen Y.Q.; Computer especially AI-assisted drug virtual screening and design in traditional Chinese medicine. Phytomedicine 2022,107,154481. (PMID: 10.1016/j.phymed.2022.15448136215788)
Congreve M.; Murray C.W.; Blundell T.L.; Keynote review: Structural biology and drug discovery. Drug Discov Today 2005,10(13),895-907. (PMID: 10.1016/S1359-6446(05)03484-715993809)
Hartenfeller M.; Schneider G.; De novo drug design. Chemoinformatics and Computational Chemical Biology Methods in Molecular Biology 2010,672,299-332. (PMID: 10.1007/978-1-60761-839-3_12)
Papadopoulos K.; Giblin K.A.; Janet J.P.; Patronov A.; Engkvist O.; De novo design with deep generative models based on 3D similarity scoring. Bioorg Med Chem 2021,44,116308. (PMID: 10.1016/j.bmc.2021.11630834280849)
Shulga D.A.; Ivanov N.N.; Palyulin V.A.; In silico structure-based approach for group efficiency estimation in fragment-based drug design using evaluation of fragment contributions. Molecules 2022,27(6),1985. (PMID: 10.3390/molecules2706198535335347)
Ullah A.; Khan A.; Al-Harrasi A.; Ullah K.; Shabbir A.; Threedimensional structure characterization and inhibition study of exfoliative toxin D from staphylococcus aureus. Front Pharmacol 2022,13(Feb),800970. (PMID: 10.3389/fphar.2022.80097035250557)
Wu K.; Bai H.; Chang Y.T.; Redler R.; McNally K.E.; Sheffler W.; Brunette T.J.; Hicks D.R.; Morgan T.E.; Stevens T.J.; Broerman A.; Goreshnik I.; DeWitt M.; Chow C.M.; Shen Y.; Stewart L.; Derivery E.; Silva D.A.; Bhabha G.; Ekiert D.C.; Baker D.; De novo design of modular peptide-binding proteins by superhelical matching. Nature 2023,616(7957),581-589. (PMID: 10.1038/s41586-023-05909-937020023)
Smith M.D.; Rao J.S.; Segelken E.; Cruz L.; Force-field induced bias in the structure of Aβ 21–30 : A comparison of OPLS, AMBER, CHARMM, and GROMOS force fields. J Chem Inf Model 2015,55(12),2587-2595. (PMID: 10.1021/acs.jcim.5b0030826629886)
Kiss G.; Röthlisberger D.; Baker D.; Houk K.N.; Evaluation and ranking of enzyme designs. Protein Sci 2010,19(9),1760-1773. (PMID: 10.1002/pro.46220665693)
Krieger E.; Joo K.; Lee J.; Lee J.; Raman S.; Thompson J.; Tyka M.; Baker D.; Karplus K.; Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins 2009,77(S9)(Suppl. 9),114-122. (PMID: 10.1002/prot.2257019768677)
Batool M.; Ahmad B.; Choi S.; A structure-based drug discovery paradigm. Int J Mol Sci 2019,20(11),2783. (PMID: 10.3390/ijms2011278331174387)
Emilien G.; Ponchon M.; Caldas C.; Isacson O.; Maloteaux J.M.; Impact of genomics on drug discovery and clinical medicine. QJM 2000,93(7),391-423. (PMID: 10.1093/qjmed/93.7.39110874050)
da Silva Rocha S.F.L.; Olanda C.G.; Fokoue H.H.; Sant’Anna C.M.R.; Virtual screening techniques in drug discovery: Review and recent applications. Curr Top Med Chem 2019,19(19),1751-1767. (PMID: 10.2174/156802661966619081610194831418662)
Trott O; Olson AJ; AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.. J Comput Chem 2009,31(2),455-461.
Hosseini M.; Chen W.; Xiao D.; Wang C.; Computational molecular docking and virtual screening revealed promising SARS-CoV- 2 drugs. Precis Clin Med 2021,4(1),1-16. (PMID: 10.1093/pcmedi/pbab00133842834)
Chen Z.; Li H.; Zhang Q.; Bao X.; Yu K.; Luo X.; Zhu W.; Jiang H.; Pharmacophore-based virtual screening versus dockingbased virtual screening: a benchmark comparison against eight targets. Acta Pharmacol Sin 2009,30(12),1694-1708. (PMID: 10.1038/aps.2009.15919935678)
Giordano D.; Biancaniello C.; Argenio M.A.; Facchiano A.; Drug design by pharmacophore and virtual screening approach. Pharmaceuticals 2022,15(5),646. (PMID: 10.3390/ph1505064635631472)
Van Drie J.H.; Computer-aided drug design: the next 20 years. J Comput Aided Mol Des 2007,21(10-11),591-601. (PMID: 10.1007/s10822-007-9142-y17989929)
León R.; Soto-Delgado J.; Montero E.; Vargas M.; Development of computational approaches with a fragment-based drug design strategy: In silico hsp90 inhibitors discovery. Int J Mol Sci 2021,22(24),13226. (PMID: 10.3390/ijms22241322634948022)
Michel M.; Homan E.J.; Wiita E.; Pedersen K.; Almlöf I.; Gustavsson A.L.; Lundbäck T.; Helleday T.; Warpman Berglund U.; In silico druggability assessment of the NUDIX hydrolase protein family as a workflow for target prioritization. Front Chem 2020,8,443. (PMID: 10.3389/fchem.2020.0044332548091)
Jäntschi L; Prediction of physico-chemical and biological properties with the help of mathematical descriptors 2000.
Jäntschi L.; Molecular descriptors family on structure activity relationships 1. Review of the methodology. Leonardo J Pract Technol 2005,4(6),76-98.
Bolboacă S.D.; Jäntschi L.; Comparison of QSAR performances on carboquinone derivatives. ScientificWorldJournal 2009,9(10),1148-1166. (PMID: 10.1100/tsw.2009.13119838601)
Bolboacă S.D.; Jäntschi L.; Nano-quantitative structure-property relationship modeling on C42 fullerene isomers. J Chem 2016,2016,1-8. (PMID: 10.1155/2016/1791756)
Wang W.; He S.; Dong G.; Sheng C.; Nucleic-acid-based targeted degradation in drug discovery. J Med Chem 2022,65(15),10217-10232. (PMID: 10.1021/acs.jmedchem.2c0087535916496)
Diller D.J.; Swanson J.; Bayden A.S.; Jarosinski M.; Audie J.; Rational, computer-enabled peptide drug design: Principles, methods, applications and future directions. Future Med Chem 2015,7(16),2173-2193. (PMID: 10.4155/fmc.15.14226510691)
Dong D.; Xu Z.; Zhong W.; Peng S.; Parallelization of molecular docking: A review. Curr Top Med Chem 2018,18(12),1015-1028. (PMID: 10.2174/156802661866618082114521530129415)
Wadood A.; Ghufran M.; Hassan S.F.; Khan H.; Azam S.S.; Rashid U.; In silico identification of promiscuous scaffolds as potential inhibitors of 1-deoxy- D -xylulose 5-phosphate reductoisomerase for treatment of Falciparum malaria. Pharm Biol 2017,55(1),19-32. (PMID: 10.1080/13880209.2016.122577827650666)
Liu T.; Lu D.; Zhang H.; Zheng M.; Yang H.; Xu Y.; Luo C.; Zhu W.; Yu K.; Jiang H.; Applying high-performance computing in drug discovery and molecular simulation. Natl Sci Rev 2016,3(1),49-63. (PMID: 10.1093/nsr/nww00332288960)
Pérez B.; Antunes S.; Gonçalves L.M.; Domingos A.; Gomes J.R.B.; Gomes P.; Teixeira C.; Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina cysteine protease: in vitro evaluation, homology modeling and molecular docking studies. J Comput Aided Mol Des 2013,27(9),823-835. (PMID: 10.1007/s10822-013-9682-224129820)
Jiang Y.; Yang M.; Wang S.; Li X.; Sun Y.; Emerging role of deep learning‐based artificial intelligence in tumor pathology. Cancer Commun 2020,40(4),154-166. (PMID: 10.1002/cac2.1201232277744)
Huang W.; Zhang L.; Li Z.; Advances in computer-aided drug design for type 2 diabetes. Expert Opin Drug Discov 2022,17(5),461-472. (PMID: 10.1080/17460441.2022.204764435254188)
Usha T.; Shanmugarajan D.; Goyal A.K.; Kumar C.S.; Middha S.K.; Recent updates on computer-aided drug discovery: Time for a paradigm shift. Curr Top Med Chem 2018,17(30),3296-3307. (PMID: 10.2174/156802661866618010116365129295698)
Gurung A.B.; Ali M.A.; Lee J.; Farah M.A.; Al-Anazi K.M.; An updated review of computer-aided drug design and its application to COVID-19. Biomed Res Int 2021,2021,8853056.
Wang L.; Sarafianos S.G.; Wang Z.; Cutting into the substrate dominance: Pharmacophore and structure-based approaches toward inhibiting human immunodeficiency virus reverse transcriptaseassociated ribonuclease H. Acc Chem Res 2020,53(1),218-230. (PMID: 10.1021/acs.accounts.9b0045031880912)
Zeb A.; Park C.; Rampogu S.; Son M.; Lee G.; Lee K.W.; Structure- based drug designing recommends HDAC6 inhibitors to attenuate microtubule-associated tau-pathogenesis. ACS Chem Neurosci 2019,10(3),1326-1335. (PMID: 10.1021/acschemneuro.8b0040530407786)
Simon L.; Imane A.; Srinivasan K.K.; Pathak L.; Daoud I.; In silico drug-designing studies on flavanoids as anticolon cancer agents: Pharmacophore mapping, molecular docking, and monte carlo method-based QSAR modeling. Interdiscip Sci 2017,9(3),445-458. (PMID: 10.1007/s12539-016-0169-427059855)
Shen L.; Huang H.; Makriyannis A.; Fisher L.S.; Integrated ligand based pharmacophore model derived from diverse FAAH covalent ligand classes. Curr Computeraided Drug Des 2012,8(4),330-334. (PMID: 10.2174/15734091280351961522734710)
Kale A.; Kakde R.; Pawar S.; Jagtap V.; Dorugade R.; Importance of pharmacophore in designing anticonvulsant agents. CNS Neurol Disord Drug Targets 2023,22(4),500-511. (PMID: 10.2174/187152732166622040111552935366788)
Kesharwani R.K.; Singh D.V.; Misra K.; Computation-based virtual screening for designing novel antimalarial drugs by targeting falcipain-III: a structure-based drug designing approach. J Vector Borne Dis 2013,50(2),93-102. (PMID: 23995310)
Contributed Indexing: Keywords: Computer-aided molecular modeling; drug design optimization; molecular dynamics simulation; pharmacophore modeling.; quantitative structure-activity relationship (QSAR); virtual screening
Entry Date(s): Date Created: 20230915 Date Completed: 20240528 Latest Revision: 20240528
Update Code: 20260130
DOI: 10.2174/1573409920666230914123005
PMID: 37711101
Βάση Δεδομένων: MEDLINE
Περιγραφή
ISSN:1875-6697
DOI:10.2174/1573409920666230914123005