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Current Topics in Medicinal Chemistry

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ISSN (Print): 1568-0266
ISSN (Online): 1873-4294

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Review Article

OMICs Technologies for Natural Compounds-based Drug Development

Author(s): Abdullahi Tunde Aborode, Wireko Andrew Awuah*, Tatiana Mikhailova, Toufik Abdul- Rahman, Samantha Pavlock, Mrinmoy Kundu, Rohan Yarlagadda, Manas Pustake, Inês Filipa da Silva Correia, Qasim Mehmood, Parth Shah, Aashna Mehta, Shahzaib Ahmad, Abiola Asekun, Esther Patience Nansubuga, Shekinah Obinna Amaka, Anastasiia Dmytrivna Shkodina and Athanasios Alexiou*

Volume 22, Issue 21, 2022

Published on: 26 August, 2022

Page: [1751 - 1765] Pages: 15

DOI: 10.2174/1568026622666220726092034

Price: $65

Abstract

Compounds isolated from natural sources have been used for medicinal purposes for many centuries. Some metabolites of plants and microorganisms possess properties that would make them effective treatments against bacterial infection, inflammation, cancer, and an array of other medical conditions. In addition, natural compounds offer therapeutic approaches with lower toxicity compared to most synthetic analogues. However, it is challenging to identify and isolate potential drug candidates without specific information about structural specificity and limited knowledge of any specific physiological pathways in which they are involved. To solve this problem and find a way to efficiently utilize natural sources for the screening of compounds candidates, technologies, such as next-generation sequencing, bioinformatics techniques, and molecular analysis systems, should be adapted for screening many chemical compounds. Molecular techniques capable of performing analysis of large datasets, such as whole-genome sequencing and cellular protein expression profile, have become essential tools in drug discovery. OMICs, as genomics, proteomics, and metabolomics, are often used in targeted drug discovery, isolation, and characterization. This review summarizes technologies that are effective in natural source drug discovery and aid in a more precisely targeted pharmaceutical approach, including RNA interference or CRISPR technology. We strongly suggest that a multidisciplinary effort utilizing novel molecular tools to identify and isolate active compounds applicable for future drug discovery and production must be enhanced with all the available computational tools.

Keywords: Genomics, Proteomics, Metabolomics, Drugs development, Natural compounds, Bioinformatics.

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[1]
Goldrosen, M.H.; Straus, S.E. Complementary and alternative medicine: Assessing the evidence for immunological benefits. Nat. Rev. Immunol., 2004, 4(11), 912-921.
[http://dx.doi.org/10.1038/nri1486] [PMID: 15516970]
[2]
National Center for Complementary and Integrative Health. Complementary, alternative, or integrative health: What's in a name? Available form: https://nccih.nih.gov/health/integrative-health (Accessed on: December 14, 2021).
[3]
National Center for Complementary and Integrative Health. Natural doesn’t necessarily mean safer, or better., Available form: https://www.nccih.nih.gov/health/know-science/natural-doesnt-mean-better (Accessed on: December 16, 2021).
[4]
Gaynes, R. The discovery of penicillin—new insights after more than 75 years of clinical use. Emerg. Infect. Dis., 2017, 23(5), 849-853.
[http://dx.doi.org/10.3201/eid2305.161556]
[5]
Atanasov, A.G.; Zotchev, S.B.; Dirsch, V.M.; Supuran, C.T. Natural products in drug discovery: Advances and opportunities. Nat. Rev. Drug Discov., 2021, 20(3), 200-216.
[http://dx.doi.org/10.1038/s41573-020-00114-z] [PMID: 33510482]
[6]
Harvey, A. Natural products in drug discovery. Drug Discov. Today, 2008, 13(19-20), 894-901.
[http://dx.doi.org/10.1016/j.drudis.2008.07.004] [PMID: 18691670]
[7]
Scherlach, K.; Hertweck, C. Mining and unearthing hidden biosynthetic potential. Nat. Commun., 2021, 12(1), 3864.
[http://dx.doi.org/10.1038/s41467-021-24133-5]
[8]
Thomford, N.; Senthebane, D.; Rowe, A.; Munro, D.; Seele, P.; Maroyi, A.; Dzobo, K. Natural products for drug discovery in the 21st century: Innovations for novel drug discovery. Int. J. Mol. Sci., 2018, 19(6), 1578.
[http://dx.doi.org/10.3390/ijms19061578] [PMID: 29799486]
[9]
Hogeweg, P. The roots of bioinformatics in theoretical biology. PLOS Comput. Biol., 2011, 7(3), e1002021.
[http://dx.doi.org/10.1371/journal.pcbi.1002021] [PMID: 21483479]
[10]
Carriço, J.A.; Sabat, A.J.; Friedrich, A.W.; Ramirez, M. on behalf of the ESCMID Study Group. C. Bioinformatics in bacterial molecular epidemiology and public health: Databases, tools and the next-generation sequencing revolution. Euro Surveill., 2013, 18(4), 20382.
[http://dx.doi.org/10.2807/ese.18.04.20382-en] [PMID: 23369390]
[11]
Saeb, A.T.M.; Abouelhoda, M.; Selvaraju, M.; Althawadi, S.I.; Mutabagani, M.; Adil, M.; Al Hokail, A.; Tayeb, H.T. The use of next-generation sequencing in the identification of a fastidious pathogen: A lesson from a clinical setup. Evol. Bioinform. Online, 2017, 13, 1176934316686072.
[http://dx.doi.org/10.1177/1176934316686072] [PMID: 28469373]
[12]
Santos, B.S.; Silva, L.C.N.; Silva, T.D. Application of omics technologies for evaluation of antibacterial mechanisms of action of plant-derived products: Mini review. Front. Microbiol., 2016, 7, 01466.
[http://dx.doi.org/10.3389/fmicb.2016.01466]
[13]
Renaud, J.P.; Chari, A.; Ciferri, C.; Liu, W.; Rémigy, H.W.; Stark, H.; Wiesmann, C. Cryo-EM in drug discovery: Achievements, limitations and prospects. Nat. Rev. Drug Discov., 2018, 17(7), 471-492.
[http://dx.doi.org/10.1038/nrd.2018.77] [PMID: 29880918]
[14]
Chan, H.C.S.; Shan, H.; Dahoun, T.; Vogel, H.; Yuan, S. Advancing drug discovery via artificial intelligence. Trends Pharmacol. Sci., 2019, 40(8), 592-604.
[http://dx.doi.org/10.1016/j.tips.2019.06.004] [PMID: 31320117]
[15]
Li, Z.; Lu, W.; Jia, S.; Yuan, H. Backbone-regulated cationic conjugated polymers for combating and monitoring pathogenic bacteria. ACS Appl. Polym. Mater., 2022, 4(1), 29-35.
[http://dx.doi.org/10.1021/acsapm.1c01672]
[16]
Li, Z.; Lu, W.; Jia, S.; Yuan, H.; Gao, L.H. Design and application of conjugated polymer nanomaterials for detection and inactivation of pathogenic microbes. ACS Appl. Bio Mater., 2021, 4(1), 370-386.
[http://dx.doi.org/10.1021/acsabm.0c01395] [PMID: 35014288]
[17]
Hieter, P.; Boguski, M. Functional genomics: It’s all how you read it. Science, 1997, 278(5338), 601-602.
[http://dx.doi.org/10.1126/science.278.5338.601] [PMID: 9381168]
[18]
Visscher, P.M.; Wray, N.R.; Zhang, Q.; Sklar, P.; McCarthy, M.I.; Brown, M.A.; Yang, J. 10 years of GWAS discovery: Biology, function, and translation. Am. J. Hum. Genet., 2017, 101(1), 5-22.
[http://dx.doi.org/10.1016/j.ajhg.2017.06.005] [PMID: 28686856]
[19]
Plenge, R.M.; Scolnick, E.M.; Altshuler, D. Validating therapeutic targets through human genetics. Nat. Rev. Drug Discov., 2013, 12(8), 581-594.
[http://dx.doi.org/10.1038/nrd4051]
[20]
Uenaka, T.; Satake, W.; Cha, P.C.; Hayakawa, H.; Baba, K.; Jiang, S.; Kobayashi, K.; Kanagawa, M.; Okada, Y.; Mochizuki, H.; Toda, T. In silico drug screening by using genome-wide association study data repurposed dabrafenib, an anti-melanoma drug, for Parkinson’s disease. Hum. Mol. Genet., 2018, 27(22), 3974-3985.
[http://dx.doi.org/10.1093/hmg/ddy279] [PMID: 30137437]
[21]
Yin, W.; Gao, C.; Xu, Y.; Li, B.; Ruderfer, D.M.; Chen, Y. Learning opportunities for drug repositioning via GWAS and PheWAS findings. AMIA Jt. Summits Transl. Sci. Proc., 2018, 2017, 237-246.
[22]
Cannon, M.E.; Mohlke, K.L. Deciphering the emerging complexities of molecular mechanisms at GWAS Loci. Am. J. Hum. Genet., 2018, 103(5), 637-653.
[http://dx.doi.org/10.1016/j.ajhg.2018.10.001] [PMID: 30388398]
[23]
Joehanes, R.; Zhang, X.; Huan, T. Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies. Genome Biol., 2017, 18(1), 16.
[http://dx.doi.org/10.1186/s13059-016-1142-6]
[24]
Elbashir, S.M.; Harborth, J.; Lendeckel, W.; Yalcin, A.; Weber, K.; Tuschl, T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 2001, 411(6836), 494-498.
[http://dx.doi.org/10.1038/35078107] [PMID: 11373684]
[25]
Hammond, S.M.; Bernstein, E.; Beach, D.; Hannon, G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature, 2000, 404(6775), 293-296.
[http://dx.doi.org/10.1038/35005107] [PMID: 10749213]
[26]
Brummelkamp, T.R.; Bernards, R.; Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science, 2002, 296(5567), 550-553.
[http://dx.doi.org/10.1126/science.1068999] [PMID: 11910072]
[27]
Jackson, A.L.; Bartz, S.R.; Schelter, J.; Kobayashi, S.V.; Burchard, J.; Mao, M.; Li, B.; Cavet, G.; Linsley, P.S. Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol., 2003, 21(6), 635-637.
[http://dx.doi.org/10.1038/nbt831] [PMID: 12754523]
[28]
LaFountaine, J.S.; Fathe, K.; Smyth, H.D.C. Delivery and therapeutic applications of gene editing technologies ZFNs, TALENs, and CRISPR/Cas9. Int. J. Pharm., 2015, 494(1), 180-194.
[http://dx.doi.org/10.1016/j.ijpharm.2015.08.029]
[29]
Carroll, D. Progress and prospects: Zinc-finger nucleases as gene therapy agents. Gene Ther., 2008, 15(22), 1463-1468.
[http://dx.doi.org/10.1038/gt.2008.145]
[30]
Li, T.; Huang, S.; Zhao, X.; Wright, D.A.; Carpenter, S.; Spalding, M.H.; Weeks, D.P.; Yang, B. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res., 2011, 39(14), 6315-6325.
[http://dx.doi.org/10.1093/nar/gkr188] [PMID: 21459844]
[31]
Gaj, T.; Gersbach, C.A.; Barbas, C.F. III ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol., 2013, 31(7), 397-405.
[http://dx.doi.org/10.1016/j.tibtech.2013.04.004] [PMID: 23664777]
[32]
Miyaoka, Y.; Berman, J.R. Cooper, SB Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Sci. Rep., 2016, 6(1), 23549.
[http://dx.doi.org/10.1038/srep23549]
[33]
Qi, L.S.; Larson, M.H.; Gilbert, L.A.; Doudna, J.A.; Weissman, J.S.; Arkin, A.P.; Lim, W.A. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 2013, 152(5), 1173-1183.
[http://dx.doi.org/10.1016/j.cell.2013.02.022] [PMID: 23452860]
[34]
Kawai, K.; Negoro, R. Ichikawa, M Establishment of SLC15A1/PEPT1-knockout human-induced pluripotent stem cell line for intestinal drug absorption studies. Mol. Ther. Methods Clin. Dev., 2019, 17, 49-57.
[http://dx.doi.org/10.1016/j.omtm.2019.11.008]
[35]
Nakamoto, F.K.; Okamoto, S.; Mitsui, J. The pathogenesis linked to coenzyme Q10 insufficiency in iPSC-derived neurons from patients with multiple-system atrophy. Sci. Rep., 2018, 8(1), 14215.
[http://dx.doi.org/10.1038/s41598-018-32573-1]
[36]
Atanasov, A.G.; Waltenberger, B.; Pferschy-Wenzig, E.M.; Linder, T.; Wawrosch, C.; Uhrin, P.; Temml, V.; Wang, L.; Schwaiger, S.; Heiss, E.H.; Rollinger, J.M.; Schuster, D.; Breuss, J.M.; Bochkov, V.; Mihovilovic, M.D.; Kopp, B.; Bauer, R.; Dirsch, V.M.; Stuppner, H. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol. Adv., 2015, 33(8), 1582-1614.
[http://dx.doi.org/10.1016/j.biotechadv.2015.08.001] [PMID: 26281720]
[37]
Ulrich-Merzenich, G.S. Combination screening of synthetic drugs and plant derived natural products—Potential and challenges for drug development. Synergy, 2014, 1(1), 59-69.
[http://dx.doi.org/10.1016/j.synres.2014.07.011]
[38]
Martinet, L.; Naômé, A.; Deflandre, B.; Maciejewska, M.; Tellatin, D.; Tenconi, E.; Smargiasso, N.; de Pauw, E.; van Wezel, G.P.; Rigali, S. A single biosynthetic gene cluster is responsible for the production of bagremycin antibiotics and ferroverdin iron chelators. MBio, 2019, 10(4), e01230-e012319.
[http://dx.doi.org/10.1128/mBio.01230-19] [PMID: 31409675]
[39]
Keller, N.P. Fungal secondary metabolism: Regulation, function and drug discovery. Nat. Rev. Microbiol., 2019, 17(3), 167-180.
[http://dx.doi.org/10.1038/s41579-018-0121-1] [PMID: 30531948]
[40]
Albarano, L.; Esposito, R.; Ruocco, N.; Costantini, M. Genome mining as new challenge in natural products discovery. Mar. Drugs, 2020, 18(4), 199.
[http://dx.doi.org/10.3390/md18040199] [PMID: 32283638]
[41]
Lim, F.Y.; Sanchez, J.F.; Wang, C.C.C.; Keller, N.P. Toward awakening cryptic secondary metabolite gene clusters in filamentous fungi. Methods Enzymol., 2012, 517, 303-324.
[http://dx.doi.org/10.1016/B978-0-12-404634-4.00015-2] [PMID: 23084945]
[42]
Brierley, I. Macrolide-induced ribosomal frameshifting: A new route to antibiotic resistance. Mol. Cell, 2013, 52(5), 613-615.
[http://dx.doi.org/10.1016/j.molcel.2013.11.017] [PMID: 24332175]
[43]
Nah, J.H.; Kim, H.J.; Lee, H.N.; Lee, M.J.; Choi, S.S.; Kim, E.S. Identification and biotechnological application of novel regulatory genes involved in Streptomyces polyketide overproduction through reverse engineering strategy. BioMed Res. Int., 2013, 2013, 549737.
[http://dx.doi.org/10.1155/2013/549737] [PMID: 23555090]
[44]
Molnár, I.; Schupp, T.; Ono, M.; Zirkle, R.E.; Milnamow, M.; Nowak-Thompson, B.; Engel, N.; Toupet, C.; Stratmann, A.; Cyr, D.D.; Gorlach, J.; Mayo, J.M.; Hu, A.; Goff, S.; Schmid, J.; Ligon, J.M. The biosynthetic gene cluster for the microtubule-stabilizing agents epothilones A and B from Sorangium cellulosum So ce90. Chem. Biol., 2000, 7(2), 97-109.
[http://dx.doi.org/10.1016/S1074-5521(00)00075-2] [PMID: 10662695]
[45]
Chen, L.; Yue, Q.; Zhang, X. Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis. BMC Genomics, 2013, 14(1), 339.
[http://dx.doi.org/10.1186/1471-2164-14-339]
[46]
Saeb, A.T.M. Current Bioinformatics resources in combating infectious diseases. Bioinformation, 2018, 14(1), 031-035.
[http://dx.doi.org/10.6026/97320630014031] [PMID: 29497257]
[47]
Weinstock, G.M. Genomic approaches to studying the human microbiota. Nature, 2012, 489(7415), 250-256.
[http://dx.doi.org/10.1038/nature11553] [PMID: 22972298]
[48]
Petty, T.J.; Cordey, S.; Padioleau, I.; Docquier, M.; Turin, L.; Preynat-Seauve, O.; Zdobnov, E.M.; Kaiser, L. Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: A pilot study. J. Clin. Microbiol., 2014, 52(9), 3351-3361.
[http://dx.doi.org/10.1128/JCM.01389-14] [PMID: 25009045]
[49]
Kuroda, M.; Sekizuka, T.; Shinya, F.; Takeuchi, F.; Kanno, T.; Sata, T.; Asano, S. Detection of a possible bioterrorism agent, Francisella sp., in a clinical specimen by use of next-generation direct DNA sequencing. J. Clin. Microbiol., 2012, 50(5), 1810-1812.
[http://dx.doi.org/10.1128/JCM.06715-11] [PMID: 22337979]
[50]
Wilson, M.R.; Naccache, S.N.; Samayoa, E.; Biagtan, M.; Bashir, H.; Yu, G.; Salamat, S.M.; Somasekar, S.; Federman, S.; Miller, S.; Sokolic, R.; Garabedian, E.; Candotti, F.; Buckley, R.H.; Reed, K.D.; Meyer, T.L.; Seroogy, C.M.; Galloway, R.; Henderson, S.L.; Gern, J.E.; DeRisi, J.L.; Chiu, C.Y. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med., 2014, 370(25), 2408-2417.
[http://dx.doi.org/10.1056/NEJMoa1401268] [PMID: 24896819]
[51]
UK Health Security Agency. High consequence infectious diseases (HCID), Available form: https://www.gov.uk/guidance/high-consequence-infectious-diseases-hcid#definition-of-hcid (Accessed on: December 20, 2021).
[52]
Cosentino, S.; Voldby Larsen, M.; Møller Aarestrup, F.; Lund, O. PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data. PLoS One, 2013, 8(10), e77302.
[http://dx.doi.org/10.1371/journal.pone.0077302] [PMID: 24204795]
[53]
Schneider, Y.K. Bacterial natural product drug discovery for new antibiotics: Strategies for tackling the problem of antibiotic resistance by efficient bioprospecting. Antibiotics (Basel), 2021, 10(7), 842.
[http://dx.doi.org/10.3390/antibiotics10070842] [PMID: 34356763]
[54]
Wattam, A.R.; Abraham, D.; Dalay, O.; Disz, T.L.; Driscoll, T.; Gabbard, J.L.; Gillespie, J.J.; Gough, R.; Hix, D.; Kenyon, R.; Machi, D.; Mao, C.; Nordberg, E.K.; Olson, R.; Overbeek, R.; Pusch, G.D.; Shukla, M.; Schulman, J.; Stevens, R.L.; Sullivan, D.E.; Vonstein, V.; Warren, A.; Will, R.; Wilson, M.J.C.; Yoo, H.S.; Zhang, C.; Zhang, Y.; Sobral, B.W. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res., 2014, 42(D1), D581-D591.
[http://dx.doi.org/10.1093/nar/gkt1099] [PMID: 24225323]
[55]
Liu, B.; Pop, M. ARDB--antibiotic resistance genes database. Nucleic Acids Res., 2009, 37, D443-D447.
[http://dx.doi.org/10.1093/nar/gkn656] [PMID: 18832362]
[56]
McArthur, A.G.; Waglechner, N.; Nizam, F.; Yan, A.; Azad, M.A.; Baylay, A.J.; Bhullar, K.; Canova, M.J.; De Pascale, G.; Ejim, L.; Kalan, L.; King, A.M.; Koteva, K.; Morar, M.; Mulvey, M.R.; O’Brien, J.S.; Pawlowski, A.C.; Piddock, L.J.V.; Spanogiannopoulos, P.; Sutherland, A.D.; Tang, I.; Taylor, P.L.; Thaker, M.; Wang, W.; Yan, M.; Yu, T.; Wright, G.D. The comprehensive antibiotic resistance database. Antimicrob. Agents Chemother., 2013, 57(7), 3348-3357.
[http://dx.doi.org/10.1128/AAC.00419-13] [PMID: 23650175]
[57]
Zhang, M.M.; Qiao, Y.; Ang, E.L.; Zhao, H. Using natural products for drug discovery: The impact of the genomics era. Expert Opin. Drug Discov., 2017, 12(5), 475-487.
[http://dx.doi.org/10.1080/17460441.2017.1303478] [PMID: 28277838]
[58]
Chen, D.; Feng, J.; Huang, L.; Zhang, Q.; Wu, J.; Zhu, X.; Duan, Y.; Xu, Z. Identification and characterization of a new erythromycin biosynthetic gene cluster in Actinopolyspora erythraea YIM90600, a novel erythronolide-producing halophilic actinomycete isolated from salt field. PLoS One, 2014, 9(9), e108129-e108129.
[http://dx.doi.org/10.1371/journal.pone.0108129] [PMID: 25250723]
[59]
Yamanaka, K.; Reynolds, K.A.; Kersten, R.D.; Ryan, K.S.; Gonzalez, D.J.; Nizet, V.; Dorrestein, P.C.; Moore, B.S. Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc. Natl. Acad. Sci. USA, 2014, 111(5), 1957-1962.
[http://dx.doi.org/10.1073/pnas.1319584111] [PMID: 24449899]
[60]
Shao, Z.; Rao, G.; Li, C.; Abil, Z.; Luo, Y.; Zhao, H. Refactoring the silent spectinabilin gene cluster using a plug-and-play scaffold. ACS Synth. Biol., 2013, 2(11), 662-669.
[http://dx.doi.org/10.1021/sb400058n] [PMID: 23968564]
[61]
Liu, Y.; Tao, W.; Wen, S.; Li, Z.; Yang, A.; Deng, Z.; Sun, Y. In vitro CRISPR/Cas9 system for efficient targeted DNA editing. MBio, 2015, 6(6), e01714-e01715.
[http://dx.doi.org/10.1128/mBio.01714-15] [PMID: 26556277]
[62]
Kang, H.S.; Charlop-Powers, Z.; Brady, S.F. Multiplexed CRISPR/Cas9- and TAR-mediated promoter engineering of natural product biosynthetic gene clusters in yeast. ACS Synth. Biol., 2016, 5(9), 1002-1010.
[http://dx.doi.org/10.1021/acssynbio.6b00080] [PMID: 27197732]
[63]
Li, L.; Zheng, G.; Chen, J.; Ge, M.; Jiang, W.; Lu, Y. Multiplexed site-specific genome engineering for overproducing bioactive secondary metabolites in actinomycetes. Metab. Eng., 2017, 40, 80-92.
[http://dx.doi.org/10.1016/j.ymben.2017.01.004] [PMID: 28088540]
[64]
Jia, H.; Zhang, L.; Wang, T.; Han, J.; Tang, H.; Zhang, L. Development of a CRISPR/Cas9-mediated gene-editing tool in Streptomyces rimosus. Microbiology (Reading), 2017, 163(8), 1148-1155.
[http://dx.doi.org/10.1099/mic.0.000501] [PMID: 28742008]
[65]
Low, Z.J.; Pang, L.M.; Ding, Y. Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment. Sci. Rep., 2018, 8(1), 1594.
[http://dx.doi.org/10.1038/s41598-018-20018-8]
[66]
Mo, J.; Wang, S. Zhang, W Efficient editing DNA regions with high sequence identity in actinomycetal genomes by a CRISPR-Cas9 system. Synth. Syst. Biotechnol., 2019, 4(2), 86-91.
[http://dx.doi.org/10.1016/j.synbio.2019.02.004]
[67]
Greunke, C.; Duell, E.R.; D’Agostino, P.M.; Glöckle, A.; Lamm, K. Gulder, TAM Direct Pathway Cloning (DiPaC) to unlock natural product biosynthetic potential. Metab. Eng., 2018, 47, 334-345.
[http://dx.doi.org/10.1016/j.ymben.2018.03.010]
[68]
Deore, A.B.; Dhumane, J.R.; Wagh, R.; Sonawane, R. The stages of drug discovery and development process. Asian J. Pharmaceut. Res. Develop., 2019, 7(6), 62-67.
[http://dx.doi.org/10.22270/ajprd.v7i6.616]
[69]
Amiri-Dashatan, N.; Koushki, M.; Abbaszadeh, H-A.; Rostami-Nejad, M.; Rezaei-Tavirani, M. Proteomics applications in health: Biomarker and drug discovery and food industry. Iran. J. Pharm. Res., 2018, 17(4), 1523-1536.
[PMID: 30568709]
[70]
He, Q.Y.; Chiu, J.F. Proteomics in biomarker discovery and drug development. J. Cell. Biochem., 2003, 89(5), 868-886.
[http://dx.doi.org/10.1002/jcb.10576] [PMID: 12874822]
[71]
Hanash, S.M.; Madoz-Gurpide, J.; Misek, D.E. Identification of novel targets for cancer therapy using expression proteomics. Leukemia, 2002, 16(4), 478-485.
[http://dx.doi.org/10.1038/sj.leu.2402412] [PMID: 11960325]
[72]
Betts, J.C. Transcriptomics and proteomics: Tools for the identification of novel drug targets and vaccine candidates for tuberculosis. IUBMB Life, 2002, 53(4-5), 239-242.
[http://dx.doi.org/10.1080/15216540212651] [PMID: 12121002]
[73]
Cho, C.H.; Nuttall, M.E. Emerging techniques for the discovery and validation of therapeutic targets for skeletal diseases. Expert Opin. Ther. Targets, 2002, 6(6), 679-689.
[http://dx.doi.org/10.1517/14728222.6.6.679] [PMID: 12472380]
[74]
Lee, P.Y.; Chin, S.F.; Low, T.Y.; Jamal, R. Probing the colorectal cancer proteome for biomarkers: Current status and perspectives. J. Proteomics, 2019, 187, 93-105.
[http://dx.doi.org/10.1016/j.jprot.2018.06.014]
[75]
Swiatly, A.; Plewa, S.; Matysiak, J.; Kokot, Z.J. Mass spectrometry-based proteomics techniques and their application in ovarian cancer research. J. Ovarian Res., 2018, 11(1), 88.
[http://dx.doi.org/10.1186/s13048-018-0460-6]
[76]
Hughes, J.P.; Rees, S.; Kalindjian, S.B.; Philpott, K.L. Principles of early drug discovery. Br. J. Pharmacol., 2011, 162(6), 1239-1249.
[http://dx.doi.org/10.1111/j.1476-5381.2010.01127.x] [PMID: 21091654]
[77]
Guengerich, F.P. Mechanisms of drug toxicity and relevance to pharmaceutical development. Drug Metab. Pharmacokinet., 2011, 26(1), 3-14.
[http://dx.doi.org/10.2133/dmpk.DMPK-10-RV-062] [PMID: 20978361]
[78]
Steiner, S.; Aicher, L.; Raymackers, J.; Meheus, L.; Esquer-Blasco, R.; Anderson, N.L.; Cordier, A. Cyclosporine A decreases the protein level of the calcium-binding protein calbindin-D 28kDa in rat kidney. Biochem. Pharmacol., 1996, 51(3), 253-258.
[http://dx.doi.org/10.1016/0006-2952(95)02131-0] [PMID: 8573191]
[79]
Aicher, L.; Wahl, D.; Arce, A.; Grenet, O.; Steiner, S. New insights into cyclosporine A nephrotoxicity by proteome analysis. Electrophoresis, 1998, 19(11), 1998-2003.
[http://dx.doi.org/10.1002/elps.1150191118] [PMID: 9740060]
[80]
Aicher, L.; Meier, G.; Norcross, A.J.; Jakubowski, J.; Del Carmen Varela, M.; Cordier, A.; Steiner, S. Decrease in kidney calbindin-d 28kda as a possible mechanism mediating cyclosporine A- and FK-506-induced calciuria and tubular mineralization. Biochem. Pharmacol., 1997, 53(5), 723-731.
[http://dx.doi.org/10.1016/S0006-2952(96)00772-1] [PMID: 9113092]
[81]
Newman, D.J.; Cragg, G.M.; Snader, K.M. Natural products as sources of new drugs over the period 1981-2002. J. Nat. Prod., 2003, 66(7), 1022-1037.
[http://dx.doi.org/10.1021/np030096l] [PMID: 12880330]
[82]
Li, Z.H.; Alex, D.; Siu, S.O.; Chu, I.K.; Renn, J.; Winkler, C.; Lou, S.; Tsui, S.K.W.; Zhao, H.Y.; Yan, W.R.; Mahady, G.B.; Li, G.H.; Kwan, Y.W.; Wang, Y.T.; Lee, S.M.Y. Combined in vivo imaging and omics approaches reveal metabolism of icaritin and its glycosides in Zebrafish larvae. Mol. Biosyst., 2011, 7(7), 2128-2138.
[http://dx.doi.org/10.1039/c1mb00001b] [PMID: 21445457]
[83]
Hung, M.W.; Zhang, Z.J.; Li, S.; Lei, B.; Yuan, S.; Cui, G.Z.; Man Hoi, P.; Chan, K.; Lee, S.M.Y. From omics to drug metabolism and high content screen of natural product in zebrafish: A new model for discovery of neuroactive compound. Evid. Based Complement. Alternat. Med., 2012, 2012, 605303.
[http://dx.doi.org/10.1155/2012/605303] [PMID: 22919414]
[84]
McFedries, A.; Schwaid, A.; Saghatelian, A. Methods for the elucidation of protein-small molecule interactions. Chem. Biol., 2013, 20, 667-673.
[http://dx.doi.org/10.1016/j.chembiol.2013.04.008]
[85]
Schirle, M.; Bantscheff, M.; Kuster, B. Mass spectrometry-based proteomics in preclinical drug discovery. Chem. Biol., 2012, 19(1), 72-84.
[http://dx.doi.org/10.1016/j.chembiol.2012.01.002] [PMID: 22284356]
[86]
Lomenick, B.; Hao, R.; Jonai, N.; Chin, R.M.; Aghajan, M.; Warburton, S.; Wang, J.; Wu, R.P.; Gomez, F.; Loo, J.A.; Wohlschlegel, J.A.; Vondriska, T.M.; Pelletier, J.; Herschman, H.R.; Clardy, J.; Clarke, C.F.; Huang, J. Target identification using drug affinity responsive target stability (DARTS). Proc. Natl. Acad. Sci. USA, 2009, 106(51), 21984-21989.
[http://dx.doi.org/10.1073/pnas.0910040106] [PMID: 19995983]
[87]
Lomenick, B.; Olsen, R.W.; Huang, J. Identification of direct protein targets of small molecules. ACS Chem. Biol., 2011, 6(1), 34-46.
[http://dx.doi.org/10.1021/cb100294v] [PMID: 21077692]
[88]
Dejonghe, W.; Russinova, E. Target identification strategies in plant chemical biology. Front. Plant Sci., 2014, 5, 352.
[http://dx.doi.org/10.3389/fpls.2014.00352] [PMID: 25104953]
[89]
West, G.M.; Tucker, C.L.; Xu, T.; Park, S.K.; Han, X.; Yates, J.R., III; Fitzgerald, M.C. Quantitative proteomics approach for identifying protein–drug interactions in complex mixtures using protein stability measurements. Proc. Natl. Acad. Sci. USA, 2010, 107(20), 9078-9082.
[http://dx.doi.org/10.1073/pnas.1000148107] [PMID: 20439767]
[90]
Singhal, N.; Kumar, M.; Kanaujia, P.K.; Virdi, J.S. MALDI-TOF mass spectrometry: An emerging technology for microbial identification and diagnosis (Review). Front. Microbiol., 2015, 2015, 00791.
[http://dx.doi.org/10.3389/fmicb.2015.00791]
[91]
Lambert, C.; Cubedo, J.; Padró, T.; Vilahur, G.; López-Bernal, S.; Rocha, M.; Hernández-Mijares, A.; Badimon, L. Effects of a carob-pod-derived sweetener on glucose metabolism. Nutrients, 2018, 10(3), 271.
[http://dx.doi.org/10.3390/nu10030271] [PMID: 29495516]
[92]
Lee, S.Y.; Kim, G.T.; Roh, S.H.; Song, J.S.; Kim, H.J.; Hong, S.S.; Kwon, S.W.; Park, J.H. Proteomic analysis of the anti-cancer effect of 20S-ginsenoside Rg3 in human colon cancer cell lines. Biosci. Biotechnol. Biochem., 2009, 73(4), 811-816.
[http://dx.doi.org/10.1271/bbb.80637] [PMID: 19352032]
[93]
Sela, I.; Yaskolka Meir, A.; Brandis, A.; Krajmalnik-Brown, R.; Zeibich, L.; Chang, D.; Dirks, B.; Tsaban, G.; Kaplan, A.; Rinott, E.; Zelicha, H.; Arinos, S.; Ceglarek, U.; Isermann, B.; Lapidot, M.; Green, R.; Shai, I. Wolffia globosa–Mankai plant-based protein contains bioactive vitamin B12 and is well absorbed in humans. Nutrients, 2020, 12(10), 3067.
[http://dx.doi.org/10.3390/nu12103067] [PMID: 33049929]
[94]
Wang, J.; Tan, X.F.; Nguyen, V.S.; Yang, P.; Zhou, J.; Gao, M.; Li, Z.; Lim, T.K.; He, Y.; Ong, C.S.; Lay, Y.; Zhang, J.; Zhu, G.; Lai, S.L.; Ghosh, D.; Mok, Y.K.; Shen, H.M.; Lin, Q. A quantitative chemical proteomics approach to profile the specific cellular targets of andrographolide, a promising anticancer agent that suppresses tumor metastasis. Mol. Cell. Proteomics, 2014, 13(3), 876-886.
[http://dx.doi.org/10.1074/mcp.M113.029793] [PMID: 24445406]
[95]
Hail, M.E.; Elliott, B.; Anderson, A. High-throughput analysis of oligonucleotides using automated electrospray ionization mass spectrometry. Am. Biotechnol. Lab., 2004, 22, 12-14.
[96]
Sinha, R.; Sharma, B.; Dangi, A.K.; Shukla, P. Recent metabolomics and gene editing approaches for synthesis of microbial secondary metabolites for drug discovery and development. World J. Microbiol. Biotechnol., 2019, 35(11), 166.
[http://dx.doi.org/10.1007/s11274-019-2746-2] [PMID: 31641867]
[97]
Harvey, A.L.; Edrada-Ebel, R.; Quinn, R.J. The re-emergence of natural products for drug discovery in the genomics era. Nat. Rev. Drug Discov., 2015, 14(2), 111-129.
[http://dx.doi.org/10.1038/nrd4510] [PMID: 25614221]
[98]
Wolfender, J.L.; Nuzillard, J.M.; van der Hooft, J.J.J.; Renault, J.H.; Bertrand, S. Accelerating metabolite identification in natural product research: Toward an ideal combination of liquid chromatography–high-resolution tandem mass spectrometry and nmr profiling, in silico databases, and chemometrics. Anal. Chem., 2019, 91(1), 704-742.
[http://dx.doi.org/10.1021/acs.analchem.8b05112] [PMID: 30453740]
[99]
Stuart, K.A.; Welsh, K.; Walker, M.C.; Edrada-Ebel, R. Metabolomic tools used in marine natural product drug discovery. Expert Opin. Drug Discov., 2020, 15(4), 499-522.
[http://dx.doi.org/10.1080/17460441.2020.1722636] [PMID: 32026730]
[100]
Allard, P.M.; Genta-Jouve, G.; Wolfender, J.L. Deep metabolome annotation in natural products research: Towards a virtuous cycle in metabolite identification. Curr. Opin. Chem. Biol., 2017, 36, 40-49.
[http://dx.doi.org/10.1016/j.cbpa.2016.12.022] [PMID: 28088695]
[101]
Allard, P.M.; Bisson, J.; Azzollini, A.; Pauli, G.F.; Cordell, G.A.; Wolfender, J.L. Pharmacognosy in the digital era: Shifting to contextualized metabolomics. Curr. Opin. Biotechnol., 2018, 54, 57-64.
[http://dx.doi.org/10.1016/j.copbio.2018.02.010] [PMID: 29499476]
[102]
Hubert, J.; Nuzillard, J.M.; Renault, J.H. Dereplication strategies in natural product research: How many tools and methodologies behind the same concept? Phytochem. Rev., 2017, 16(1), 55-95.
[http://dx.doi.org/10.1007/s11101-015-9448-7]
[103]
Liu, X.; Locasale, J.W. Metabolomics: A primer. Trends Biochem. Sci., 2017, 42(4), 274-284.
[http://dx.doi.org/10.1016/j.tibs.2017.01.004] [PMID: 28196646]
[104]
Smyth, M.S.; Martin, J.H. x Ray crystallography. Mol. Pathol., 2000, 53(1), 8-14.
[http://dx.doi.org/10.1136/mp.53.1.8] [PMID: 10884915]
[105]
Zheng, H.; Hou, J.; Zimmerman, M.D.; Wlodawer, A.; Minor, W. The future of crystallography in drug discovery. Expert Opin. Drug Discov., 2014, 9(2), 125-137.
[http://dx.doi.org/10.1517/17460441.2014.872623] [PMID: 24372145]
[106]
Wyss, D.F.; Wang, Y.S.; Eaton, H.L.; Strickland, C.; Voigt, J.H.; Zhu, Z.; Stamford, A.W. Combining NMR and X-ray crystallography in fragment-based drug discovery: Discovery of highly potent and selective BACE-1 inhibitors. Top. Curr. Chem., 2011, 317, 83-114.
[http://dx.doi.org/10.1007/128_2011_183] [PMID: 21647837]
[107]
Paul, D.; Sanap, G.; Shenoy, S.; Kalyane, D.; Kalia, K.; Tekade, R.K. Artificial intelligence in drug discovery and development. Drug Discov. Today, 2021, 26(1), 80-93.
[http://dx.doi.org/10.1016/j.drudis.2020.10.010] [PMID: 33099022]
[108]
Sharma, R.; Shrivastava, S.; Singh, S.K.; Kumar, A.; Singh, A.K.; Saxena, S. Deep-AVPpred: Artificial intelligence driven discovery of peptide drugs for viral infections. IEEE J. Biomed. Health Inform., 2021, 2021, 3130825.
[http://dx.doi.org/10.1109/JBHI.2021.3130825] [PMID: 34822333]
[109]
Kennedy, K.; Cal, R.; Casey, R.; Lopez, C.; Adelfio, A.; Molloy, B.; Wall, A.M.; Holton, T.A.; Khaldi, N. The anti‐ageing effects of a natural peptide discovered by artificial intelligence. Int. J. Cosmet. Sci., 2020, 42(4), 388-398.
[http://dx.doi.org/10.1111/ics.12635] [PMID: 32453870]
[110]
Keshavarzi Arshadi, A.; Salem, M.; Collins, J.; Yuan, J.S.; Chakrabarti, D. DeepMalaria: Artificial intelligence driven discovery of potent antiplasmodials: Original research. Front. Pharmacol., 2020, 2020, 01526.
[http://dx.doi.org/10.3389/fphar.2019.01526]
[111]
Gray, A.I.; Igoli, J.O.; Edrada-Ebel, R. Natural products isolation in modern drug discovery programs. Methods Mol. Biol., 2012, 864, 515-534.
[http://dx.doi.org/10.1007/978-1-61779-624-1_20] [PMID: 22367910]
[112]
Surur, A.S.; Fekadu, A.; Makonnen, E.; Hailu, A. Challenges and opportunities for drug discovery in developing countries: The example of cutaneous leishmaniasis. ACS Med. Chem. Lett., 2020, 11(11), 2058-2062.
[http://dx.doi.org/10.1021/acsmedchemlett.0c00446] [PMID: 33214808]
[113]
Romano, J.D.; Tatonetti, N.P. Informatics and computational methods in natural product drug discovery: A review and perspectives. Front. Genet., 2019, 2019, 00368.
[http://dx.doi.org/10.3389/fgene.2019.00368]
[114]
Bioinformatics, X.X.; Discovery, D. Curr. Top. Med. Chem., 2017, 17(15), 1709-1726.
[http://dx.doi.org/10.2174/1568026617666161116143440] [PMID: 27848897]
[115]
Dalpé, G.; Joly, Y. Opportunities and challenges provided by cloud repositories for bioinformatics-enabled drug discovery. Drug Dev. Res., 2014, 75(6), 393-401.
[http://dx.doi.org/10.1002/ddr.21211] [PMID: 25195583]
[116]
Henrich, C.J.; Beutler, J.A. Matching the power of high throughput screening to the chemical diversity of natural products. Nat. Prod. Rep., 2013, 30(10), 1284-1298.
[http://dx.doi.org/10.1039/c3np70052f] [PMID: 23925671]
[117]
Li, F.S.; Weng, J.K. Demystifying traditional herbal medicine with modern approach. Nat. Plants, 2017, 3(8), 17109.
[http://dx.doi.org/10.1038/nplants.2017.109] [PMID: 28758992]
[118]
Kellie, J.F.; Sikorski, T.W.; An, B.; Chen, Z.; Moghieb, A.H.; Busz, M.G.; Szapacs, M.E.; Angel, T.E. A new era for proteomics. Bioanalysis, 2019, 11(19), 1731-1735.
[http://dx.doi.org/10.4155/bio-2019-0191] [PMID: 31617394]
[119]
Perkins, R.C. Making the case for functional proteomics. Methods Mol. Biol., 2019, 1871, 1-40.
[http://dx.doi.org/10.1007/978-1-4939-8814-3_1] [PMID: 30276729]
[120]
Angel, T.E.; Aryal, U.K.; Hengel, S.M.; Baker, E.S.; Kelly, R.T.; Robinson, E.W.; Smith, R.D. Mass spectrometry-based proteomics: Existing capabilities and future directions. Chem. Soc. Rev., 2012, 41(10), 3912-3928.
[http://dx.doi.org/10.1039/c2cs15331a] [PMID: 22498958]
[121]
Woollard, P.M.; Mehta, N.A.L.; Vamathevan, J.J.; Van Horn, S.; Bonde, B.K.; Dow, D.J. The application of next-generation sequencing technologies to drug discovery and development. Drug Discov. Today, 2011, 16(11), 512-519.
[http://dx.doi.org/10.1016/j.drudis.2011.03.006]
[122]
Kabadi, A.; McDonnell, E.; Frank, C.L.; Drowley, L. Applications of functional genomics for drug discovery. SLAS Discov., 2020, 25(8), 823-842.
[http://dx.doi.org/10.1177/2472555220902092]
[123]
Rask-Andersen, M.; Masuram, S.; Schiöth, H.B. The druggable genome: Evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication. Annu. Rev. Pharmacol. Toxicol., 2014, 54(1), 9-26.
[http://dx.doi.org/10.1146/annurev-pharmtox-011613-135943] [PMID: 24016212]
[124]
Ricke, D.O.; Wang, S.; Cai, R.; Cohen, D. Genomic approaches to drug discovery. Curr. Opin. Chem. Biol., 2006, 10(4), 303-308.
[http://dx.doi.org/10.1016/j.cbpa.2006.06.024] [PMID: 16822705]

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