Добавил:
Sekretar
kiopkiopkiop18@yandex.ru
t.me/Prokururor I Вовсе не секретарь, но почту проверяю
Опубликованный материал нарушает ваши авторские права? Сообщите нам.
Вуз:
Предмет:
Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5435_Библиотеки_им_академика_М_И_Перельмана
.pdf
[60] Spyrakis, F., & Cavasotto, C. N. Open challenges in structure-based virtual screening: Receptor
modeling, target flexibility consideration and active site water molecules description. Archives of
Biochemistry and Biophysics, 2015, 583, 105–119. https://doi.org/10.1016/J.ABB.2015.08.002.
[61] Sharapova, A., Ol’khovich, M., Blokhina, S., & Perlovich, G. Physico-chemical characterization
antituberculosis thioacetazone: Vapor pressure, solubility and lipophilicity. Journal of Chemical
Thermodynamics, 2017, 108, 18–25. https://doi.org/10.1016/J.JCT.2016.12.034.
[62] Serrao, E., Odde, S., Ramkumar, K., & Neamati, N. Raltegravir, elvitegravir, and metoogravir: The
birth of “me-too” HIV-1 integrase inhibitors. Retrovirology, 2009, 6. https://doi.org/10.1186/1742-
4690-6-25.
[63] Srinivasan, S., Cui, H., Gao, Z., Liu, M., Lu, S., Mkandawire, W., Narykov, O., Sun, M., & Korkin,
D. Structural genomics of SARS-CoV-2 indicates evolutionary conserved functional regions of viral
proteins. Viruses, 2020, 12. https://doi.org/10.3390/V12040360.
[64] Williams, S. P., Kuyper, L. F., & Pearce, K. H. Recent applications of protein crystallography and
structure-guided drug design. Current Opinion in Chemical Biology, 2005, 9, 371–380. https://doi.
org/10.1016/J.CBPA.2005.06.007.
[65] Manghwar, H., Li, B., Ding, X., Hussain, A., Lindsey, K., Zhang, X., & Jin, S. CRISPR/Cas systems in
genome editing: Methodologies and tools for sgRNA design, off-target evaluation, and strategies to
mitigate off-target effects. Advanced Science (Weinh), 2020, 7. https://doi.org/10.1002/ADVS.
201902312.
[66] Gomez, K. Genomic analysis for the detection of bleeding and thrombotic disorders. Seminars in
Thrombosis and Hemostasis, 2021, 47, 174–182. https://doi.org/10.1055/S-0041-1722865.
[67] Teng, F., Li, J., Cui, T., Xu, K., Guo, L., Gao, Q., Feng, G., Chen, C., Han, D., Zhou, Q., & Li, W. Enhanced
mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds. Genome
Biology, 2019, 20. https://doi.org/10.1186/S13059-019-1620-8.
[68] Kadam, U. S., Shelake, R. M., Chavhan, R. L., & Suprasanna, P. Concerns regarding ‘off-target’
activity of genome editing endonucleases. Plant Physiology and Biochemistry, 2018, 131, 22–30.
https://doi.org/10.1016/j.plaphy.2018.03.027.
[69] Grabowski, M., Niedzialkowska, E., Zimmerman, M. D., & Minor, W. The impact of structural
genomics: The first quindecennial. Journal of Structural and Functional Genomics, 2016, 17.
https://doi.org/10.1007/S10969-016-9201-5.
[70] Erlandsen, H., Abola, E. E., & Stevens, R. C. Combining structural genomics and enzymology:
Completing the picture in metabolic pathways and enzyme active sites. Current Opinion in
Structural Biology, 2000, 10, 719–730. https://doi.org/10.1016/S0959-440X(00)00154-8.
[71] Wu, C. R., Yin, W. C., Jiang, Y., & Xu, H. E. Structure genomics of SARS-CoV-2 and its Omicron variant:
Drug design templates for COVID-19. Acta Pharmacologica Sinica, 2022, 43, 3021–3033. https://doi.
org/10.1038/S41401-021-00851-W.
[72] Siragusa, L., Cross, S., Baroni, M., Goracci, L., & Cruciani, G. BioGPS: Navigating biological space to
predict polypharmacology, off-targeting, and selectivity. Proteins, 2015, 83, 517–532. https://doi.
org/10.1002/PROT.24753.
[73] Fang, Z., Van Der Merwe, R. G., Warren, R. M., Schubert, W. D., & Gey Van Pittius, N. C. Assessing
the progress of Mycobacterium tuberculosis H37Rv structural genomics. Tuberculosis (Edinb), 2015,
95, 131–136. https://doi.org/10.1016/J.TUBE.2014.12.005.
[74] Ostrem, J. M. L., & Shokat, K. M. Direct small-molecule inhibitors of KRAS: From structural insights to
mechanism-based design. Nature Reviews Drug Discovery, 2016, 15, 771–785. https://doi.org/10.
1038/NRD.2016.139.
[75] Aoki, M., Das, D., Hayashi, H., Aoki-Ogata, H., Takamatsu, Y., Ghosh, A. K., & Mitsuya, H. Mechanism
of Darunavir (DRV)’s high genetic barrier to HIV-1 resistance: A key V32I substitution in protease
rarely occurs, but once it occurs, it predisposes HIV-1 to develop DRV resistance. mBio, 2018, 9.
https://doi.org/10.1128/MBIO.02425-17.
284 Anuradha Mehra et al.
https://t.me/med1917

[76] Moreira, W., Ngan, G. J. Y., Low, J. L., Poulsen, A., Chia, B. C. S., Ang, M. J. Y., Yap, A., Fulwood, J.,
Lakshmanan, U., Lim, J., Khoo, A. Y. T., Flotow, H., Hill, J., Raju, R. M., Rubin, E. J., & Dick, T. Target
mechanism-based whole-cell screening identifies bortezomib as an inhibitor of caseinolytic
protease in mycobacteria. mBio, 2015, 6, 1–13. https://doi.org/10.1128/MBIO.00253-15.
[77] Beygi, S., Fernandez-Pol, S., Duran, G., Wang, E. B., Stehr, H., Zehnder, J. L., Ramchurren, N., Fling,
S. P., Cheever, M. A., Weng, W. K., Kim, Y. H., & Khodadoust, M. S. Pembrolizumab in mycosis
fungoides with PD-L1 structural variants. Blood Advances, 2021, 5, 771–774. https://doi.org/10.1182/
BLOODADVANCES.2020002371.
[78] Buchanan, S., Sauder, J., & Harris, T. The promise of structural genomics in the discovery of new
antimicrobial agents. Current Pharmaceutical Design, 2002, 8, 1173–1188. https://doi.org/10.2174/
1381612023394809.
[79] Fissiha, W., & Kinde, M. Z. Anthelmintic resistance and its mechanism: A review. Infect Drug Resist,
2021, 14, 5403–5410. https://doi.org/10.2147/IDR.S332378.
[80] Barzegar, M., Afghan, M., Tarmahi, V., Behtari, M., Rahimi Khamaneh, S., & Raeisi, S. Ketogenic diet:
Overview, types, and possible anti-seizure mechanisms. Nutritional Neuroscience, 2021, 24,
307–316. https://doi.org/10.1080/1028415X.2019.1627769.
[81] Sun, H., Luo, G., Chen, D., & Xiang, Z. A comprehensive and system review for the pharmacological
mechanism of action of rhein, an active anthraquinone ingredient. Frontiers in Pharmacology, 2016,
7. https://doi.org/10.3389/FPHAR.2016.00247.
[82] Sutananta, W., CRAIG, D. Q. M., & Newton, J. M. An evaluation of the mechanisms of drug release
from glyceride bases. Journal of Pharmacy and Pharmacology, 1995, 47, 182–187. https://doi.org/10.
1111/J.2042-7158.1995.TB05775.X.
[83] Moravej, H., Moravej, Z., Yazdanparast, M., Heiat, M., Mirhosseini, A., Moosazadeh Moghaddam, M.,
& Mirnejad, R. Antimicrobial peptides: Features, action, and their resistance mechanisms in
bacteria. Microbial Drug Resistance, 2018, 24, 747–767. https://doi.org/10.1089/MDR.2017.0392.
[84] Chang, Y. M., Chen, C. K. M., Ko, T. P., Chang-Chien, M. W., & Wang, A. H. J. Structural analysis of the
antibiotic-recognition mechanism of MarR proteins. Acta Crystallographica Section D: Biological
Crystallography, 2013, 69, 1138–1149. https://doi.org/10.1107/S0907444913007117.
[85] Stevens, J. L. Future of toxicology – Mechanisms of toxicity and drug safety: Where do we go from
here? Chemical Research in Toxicology, 2006, 19, 1393–1401. https://doi.org/10.1021/TX060213N.
[86] Chen, P., Liu, J., Zeng, M., & Sang, H. Exploring the molecular mechanism of azole resistance in
Aspergillus fumigatus. Journal of Medical Mycology, 2020, 30. https://doi.org/10.1016/J.MYCMED.
2019.100915.
[87] Tao, Y., Lan, X., Zhang, Y., Qing, G., Wang, J., Xiao, Y., Chen, H., Liu, L., Liang, X. J., & Guo,
W. Navigations of the targeting pathway of nanomedicines toward tumor. Expert Opinion on Drug
Delivery, 2022, 19, 985–996. https://doi.org/10.1080/17425247.2022.2110064.
[88] Safar, M. E. Mechanism(s) of systolic blood pressure reduction and drug therapy in hypertension.
Hypertension, 2007, 50, 167–171. https://doi.org/10.1161/HYPERTENSIONAHA.107.088799.
[89] Sun, C., Chen, L., & Shen, Z. Mechanisms of gastrointestinal microflora on drug metabolism in
clinical practice. Saudi Pharmaceutical Journal, 2019, 27, 1146–1156. https://doi.org/10.1016/J.JSPS.
2019.09.011.
[90] Hou, Z., Liu, L., Wei, J., & Xu, B. Progress in the prevalence, classification and drug resistance
mechanisms of methicillin-resistant Staphylococcus aureus. Infection and Drug Resistance, 2023, 16,
3271–3292. https://doi.org/10.2147/IDR.S412308.
[91] Cowman, A. F. Mechanisms of drug resistance in malaria. Australian and New Zealand Journal of
Medicine, 1995, 25, 837–844. https://doi.org/10.1111/J.1445-5994.1995.TB02889.X.
[92] Chauhan, A., Kumar, M., Kumar, A., & Kanchan, K. Comprehensive review on mechanism of action,
resistance and evolution of antimycobacterial drugs. Life Sciences, 2021, 274. https://doi.org/10.
1016/J.LFS.2021.119301.
11 Role of structural genomics in drug discovery 285
https://t.me/med1917

[93] Zhang, X. W., Yang, Y. F., Qi, G. X., Zhai, F. H., Fei, T., Wang, J. H., Yu, Y. L., & Chen, S. Rapid and
accurate identification of cell phenotypes of different drug mechanisms by using single-cell
fluorescence images via deep learning. Analytical Chemistry, 2023, 95, 8113–8120. https://doi.org/
10.1021/ACS.ANALCHEM.3C01140.
[94] Borst, P., & Ouellette, M. New mechanisms of drug resistance in parasitic protozoa. Annual Review
of Microbiology, 1995, 49, 427–460. https://doi.org/10.1146/ANNUREV.MI.49.100195.002235.
[95] Pratama, M. Y., Pascut, D., Massi, M. N., & Tiribelli, C. The role of microRNA in the resistance to
treatment of hepatocellular carcinoma. Annals of Translational Medicine, 2019, 7, 577–577.
https://doi.org/10.21037/ATM.2019.09.142.
[96] Okombo, J., Kanai, M., Deni, I., & Fidock, D. A. Genomic and genetic approaches to studying
antimalarial drug resistance and plasmodium biology. Trends in Parasitology, 2021, 37, 476–492.
https://doi.org/10.1016/J.PT.2021.02.007.
[97] Zhang, Z., Li, X., Liu, H., Zamyadi, A., Guo, W., Wen, H., Gao, L., Nghiem, L. D., & Wang,
Q. Advancements in detection and removal of antibiotic resistance genes in sludge digestion: A
state-of-art review. Bioresource Technology, 2022, 344. https://doi.org/10.1016/J.BIORTECH.2021.
126197.
[98] Prasad, S., S., V. P., Abbas, H. S., & Kotakonda, M. Mechanisms of antimicrobial resistance:
highlights on current advance methods for detection of drug resistance and current pipeline
antitubercular agents. Current Pharmaceutical Biotechnology, 2022, 23, 1824–1836. https://doi.org/
10.2174/1389201023666220318104042.
[99] Blair, J. M. A., Webber, M. A., Baylay, A. J., Ogbolu, D. O., & Piddock, L. J. V. Molecular mechanisms of
antibiotic resistance. Nature Reviews Microbiology, 2015, 13, 42–51. https://doi.org/10.1038/
NRMICRO3380.
[100] Gholizadeh, Y., & Courvalin, P. Acquired and intrinsic glycopeptid e resistance in enterococci.
International Journal of Antimicrobial Agents, 2000, 16, 11–17. https://doi.org/10.1016/S0924-
8579(00)00300-9.
[101] Klopfleisch, R., Kohn, B., & Gruber, A. D. Mechanisms of tumour resistance against
chemotherapeutic agents in veterinary oncology. Veterinary Journal, 2016, 207, 63–72. https://doi.
org/10.1016/J.TVJL.2015.06.015.
[102] Lee, K., Yong, D., Jeong, S. H., & Chong, Y. Multidrug-resistant Acinetobacter spp.: Increasingly
problematic nosocomial pathogens. Yonsei Medical Journal, 2011, 52, 879–891. https://doi.org/10.
3349/YMJ.2011.52.6.879.
[103] Chee, Y. C., Pahnke, J., Bunte, R., Adsool, V. A., Madan, B., & Virshup, D. M. Intrinsic xenobiotic
resistance of the intestinal stem cell niche. Developmental Cell, 2018, 46, 681–695. https://doi.org/
10.1016/J.DEVCEL.2018.07.023.
[104] Balch, C., Huang, T. H. M., Brown, R., & Nephew, K. P. The epigenetics of ovarian cancer drug
resistance and resensitization. American Journal of Obstetrics and Gynecology, 2004, 191,
1552–1572. https://doi.org/10.1016/J.AJOG.2004.05.025.
[105] Goic-Barisic, I., Seruga Music, M., Kovacic, A., Tonkic, M., & Hrenovic, J. Pan drug-resistant
environmental isolate of Acinetobacter baumannii from Croatia. Microbial Drug Resistance, 2017, 23,
494–496. https://doi.org/10.1089/MDR.2016.0229.
[106] Madaci, L., Colle, J., Venton, G., Farnault, L., Loriod, B., & Costello, R. The contribution of single-cell
analysis of acute leukemia in the therapeutic strategy. Biomarker Research, 2021, 9. https://doi.org/
10.1186/S40364-021-00300-0.
[107] Ghilu, S., Morton, C. L., Vaseva, A. V., Zheng, S., Kurmasheva, R. T., & Houghton, P. J. Approaches to
identifying drug resistance mechanisms to clinically relevant treatments in childhood
rhabdomyosarcoma. Cancer Drug Resistance, 2022, 5, 80–89. https://doi.org/10.20517/CDR.
2021.112.
286 Anuradha Mehra et al.
https://t.me/med1917

[108] Singh, D., Khan, M. A., & Siddique, H. R. Specific targeting of cancer stem cells by immunotherapy: A
possible stratagem to restrain cancer recurrence and metastasis. Biochemical Pharmacology, 2022,
198. https://doi.org/10.1016/J.BCP.2022.114955.
[109] Menchón, S. A. The effect of intrinsic and acquired resistances on chemotherapy effectiveness. Acta
Biotheoretica, 2015, 63, 113–127. https://doi.org/10.1007/S10441-015-9248-X.
[110] Monaghan, A. E., & McEwan, I. J. A sting in the tail: The N-terminal domain of the androgen
receptor as a drug target. Asian Journal of Andrology, 2016, 18, 687–694. https://doi.org/10.4103/
1008-682X.181081.
[111] The Lancet: Personalised medicine in the UK. The Lancet, 2018, 391, e1. https://doi.org/10.1016/
S0140-6736(17)33261-0.
[112] Weitzel, J. N., Blazer, K. R., MacDonald, D. J., Culver, J. O., & Offit, K. Genetics, genomics, and cancer
risk assessment. CA: A Cancer Journal for Clinicians, 2011, n/a-n/a https://doi.org/10.3322/CAAC.
20128.
[113] Mooser, V. Genomik und personalisierte medizin. Praxis, 2014, 103, 567–571. https://doi.org/10.
1024/1661-8157/A001655.
[114] Fang, Y., Yao, Q., Chen, Z., Xiang, J., William, F. E., Gibbs, R. A., & Chen, C. Genetic and molecular
alterations in pancreatic cancer: Implications for personalized medicine. Medical Science Monitor,
2013, 19, 916–926. https://doi.org/10.12659/MSM.889636.
[115] Branco, I., & Choupina, A. Bioinformatics: New tools and applications in life science and
personalized medicine. Applied Microbiology and Biotechnology, 2021, 105, 937–951. https://doi.
org/10.1007/S00253-020-11056-2.
[116] Craig, S. P., & Eakin, A. E. Structure-based inhibitor design. Vitamins and Hormones, 2000, 58,
149–169. https://doi.org/10.1016/S0083-6729(00)58024-8.
[117] Graham, B. S., Gilman, M. S. A., & McLellan, J. S. Structure-based vaccine antigen design. Annual
Review of Medicine, 2019, 70, 91–104. https://doi.org/10.1146/ANNUREV-MED-121217-094234.
[118] Mitrasinovic, P. M. Progress in structure-based design of EGFR inhibitors. Current Drug Targets,
2013, 14, 817–829. https://doi.org/10.2174/1389450111314070009.
[119] Kuntz, I. D. Structure-based strategies for drug design and discovery. Science, 1979 1992, 257,
1078–1082. https://doi.org/10.1126/SCIENCE.257.5073.1078.
[120] Katz, A., & Caufield, C. Structure-based design approaches to cell wall biosynthesis inhibitors.
Current Pharmaceutical Design, 2005, 9, 857–866. https://doi.org/10.2174/1381612033455305.
[121] Tomlinson, S., Malmstrom, R., & Watowich, S. New approaches to structure-based discovery of
dengue protease inhibitors. Infectious Disorders – Drug Targets, 2012, 9, 327–343. https://doi.org/
10.2174/1871526510909030327.
[122] Grandits, M., & Ecker, G. F. Ligand- and structure-based approaches for transmembrane transporter
modeling. Curr Drug Res Rev, 2023, 15. https://doi.org/10.2174/2589977515666230508123041.
[123] Ferreira, R., & Andricopulo, A. Structure-based drug design to overcome drug resistance:
Challenges and opportunities. Current Pharmaceutical Design, 2014, 20, 687–693. https://doi.org/
10.2174/138161282005140214161949.
[124] Brady, R., & Cameron, A. Structure-based approaches to the development of novel anti-malarials.
Current Drug Targets, 2005, 5, 137–149. https://doi.org/10.2174/1389450043490587.
[125] Philippon, A., Jacquier, H., Ruppé, E., & Labia, R. Structure-based classification of class A beta-
lactamases, an update. Current Research in Translational Medicine, 2019, 67, 115–122. https://doi.
org/10.1016/J.RETRAM.2019.05.003.
[126] Tran-Nguyen, V. K., Simeon, S., Junaid, M., & Ballester, P. J. Structure-based virtual screening for
PDL1 dimerizers: Evaluating generic scoring functions. Current Research in Structural Biology, 2022,
4, 206–210. https://doi.org/10.1016/J.CRSTBI.2022.06.002.
11 Role of structural genomics in drug discovery 287
https://t.me/med1917

[127] Powers, R. A., & Shoichet, B. K. Structure-based approach for binding site identification on AmpC
β-lactamase. Journal of Medicinal Chemistry, 2002, 45, 3222–3234. https://doi.org/10.1021/
JM020002P.
[128] Klepsch, F., Vasanthanathan, P., & Ecker, G. F. Ligand and structure-based classification models for
prediction of P-glycoprotein inhibitors. Journal of Chemical Information and Modeling, 2014, 54,
218–229. https://doi.org/10.1021/CI400289J.
[129] Bhaskar, B. V., Babu, T. M. C., Rammohan, A., Zheng, G. Y., Zyryanov, G. V., & Gu, W. Structure-based
virtual screening of pseudomonas aeruginosa lpxa inhibitors using pharmacophore-based
approach. Biomolecules, 2020, 10. https://doi.org/10.3390/BIOM10020266.
[130] Gayatri, S. K., Chhabra, V., Kumar, H., & Sobhia, M. E. Identification of prospective covalent
inhibitors for SARS-CoV-2 main protease using structure-based approach. Journal of Biomolecular
Structure and Dynamics, 2022. https://doi.org/10.1080/07391102.2022.2129453.
[131] Hassan, M., Awan, F. M., Naz, A., Deandrés-Galiana, E. J., Alvarez, O., Cernea, A., Fernández-Brillet, L.,
Fernández-Martínez, J. L., & Kloczkowski, A. Innovations in genomics and big data analytics for
personalized medicine and health care: A review. International Journal of Molecular Sciences, 2022,
23. https://doi.org/10.3390/IJMS23094645.
[132] Marchevsky, A. M., Walts, A. E., & Wick, M. R. Pathology in the era of “Personalized Medicine”: The
need to learn how to integrate multivariate immunohistochemical and “omics” data with
clinicopathologic information in a clinically relevant way”. Annals of Diagnostic Pathology, 2019, 43.
https://doi.org/10.1016/J.ANNDIAGPATH.2019.151410.
[133] Bem, A. E., Velikova, N., Pellicer, M. T., Baarlen, P. V., Marina, A., & Wells, J. M. Bacterial histidine
kinases as novel antibacterial drug targets. ACS Chemical Biology, 2015, 10, 213–224. https://doi.
org/10.1021/CB5007135.
[134] Xu, C., Zhou, T., Kuroda, M., & Rosen, B. P. Metalloid resistance mechanisms in prokaryotes. Journal
of Biochemistry, 1998, 123, 16–23. https://doi.org/10.1093/oxfordjournals.jbchem.a021904.
[135] Acar, J. F., & Moulin, G. Antimicrobial resistance: A complex issue. OIE Revue Scientifique Et
Technique, 2012, 31, 23–31. https://doi.org/10.20506/rst.31.1.2098.
[136] Marloye, M., Berger, G., Gelbcke, M., & Dufrasne, F. A survey of the mechanisms of action of
anticancer transition metal complexes. Future Medicinal Chemistry, 2016, 8, 2263–2286. https://doi.
org/10.4155/FMC-2016-0153.
[137] Xie, L., Ge, X., Tan, H., Xie, L., Zhang, Y., Hart, T., Yang, X., & Bourne, P. E. Towards structural systems
pharmacology to study complex diseases and personalized medicine. PLOS Computational Biology,
2014, 10. https://doi.org/10.1371/JOURNAL.PCBI.1003554.
[138] Cleland, K., Marcantonio, T. L., Hunt, M. E., & Jozkowski, K. N. “It prevents a fertilized egg from
attaching . . . and causes a miscarriage of the baby”: A qualitative assessment of how people
understand the mechanism of action of emergency contraceptive pills. Contraception, 2021, 103,
408–413. https://doi.org/10.1016/J.CONTRACEPTION.2021.01.009.
[139] Howe, A. C., & Soupir, M. L. Antimicrobial resistance in integrated agroecosystems: State of the
science and future opportunities. Journal of Environmental Quality, 2021, 50, 1255–1265. https://doi.
org/10.1002/JEQ2.20289.
[140] Aronica, E., Bauer, S., Bozzi, Y., Caleo, M., Dingledine, R., Gorter, J. A., Henshall, D. C., Kaufer, D., Koh,
S., Löscher, W., Louboutin, J. P., Mishto, M., Norwood, B. A., Palma, E., Poulter, M. O., Terrone, G.,
Vezzani, A., & Kaminski, R. M. Neuroinflammatory targets and treatments for epilepsy validated in
experimental models. Epilepsia, 2017, 58, 27–38. https://doi.org/10.1111/EPI.13783.
[141] Sreedurgalakshmi, K., Srikar, R., & Rajkumari, R. CRISPR-Cas deployment in non-small cell lung
cancer for target screening, validations, and discoveries. Cancer Gene Therapy, 2021, 28, 566– 580.
https://doi.org/10.1038/S41417-020-00256-7.
[142] Hollis, T. Crystallization of protein-DNA complexes. 2007, 225–237. https://doi.org/10.1007/978-1-
59745-209-0_11.
288 Anuradha Mehra et al.
https://t.me/med1917

[143] Liu, J., Zhang, B., Zhang, P., Zhao, K., Lu, Z., Wei, H., Zheng, Z., Yang, R., & Yu, Y. Protein
crystallization-mediated self-strengthening of high-performance printable conducting
organohydrogels. ACS Nano, 2022, 16, 17998–18008. https://doi.org/10.1021/ACSNANO.2C07823.
[144] DeLucas, L. J., Hamrick, D., Cosenza, L., Nagy, L., McCombs, D., Bray, T., Chait, A., Stoops, B.,
Belgovskiy, A., William Wilson, W., Parham, M., & Chernov, N. Protein crystallization: Virtual
screening and optimization. Progress in Biophysics and Molecular Biology, 2005, 88, 285–309.
https://doi.org/10.1016/J.PBIOMOLBIO.2004.07.008.
[145] Ke, A., & Doudna, J. A. Crystallization of RNA and RNA-protein complexes. Methods, 2004, 34,
408–414. https://doi.org/10.1016/J.YMETH.2004.03.027.
[146] Dörner, K., Martin-Garcia, J. M., Kupitz, C., Gong, Z., Mallet, T. C., Chen, L., Wachter, R. M., &
Fromme, P. Characterization of protein nanocrystals based on the reversibility of crystallization.
Crystal Growth & Design, 2016, 16, 3838–3845. https://doi.org/10.1021/ACS.CGD.6B00384.
[147] Wallace, E., Dranow, D., Laible, P. D., Christensen, J., & Nollert, P. Monoolein lipid phases as
incorporation and enrichment materials for membrane protein crystallization. PLoS One, 2011, 6.
https://doi.org/10.1371/JOURNAL.PONE.0024488.
[148] Maurer, A., Tanaka, M., Ozawa, T., & Fleischer, S. Purification and crystallization of the calcium
binding protein of sarcoplasmic reticulum from skeletal muscle. Proceedings of the National
Academy of Sciences, 1985, 82, 4036–4040. https://doi.org/10.1073/PNAS.82.12.4036.
[149] Friedmann, D., Messick, T., & Marmorstein, R. Crystallization of macromolecules. Current Protocols
in Protein Science, 2011, 1. https://doi.org/10.1002/0471140864.PS1704S66.
[150] Phillips, K., & De la Peña, A. H. The combined use of the thermofluor assay and thermoQ analytical
software for the determination of protein stability and buffer optimization as an aid in protein
crystallization. Current Protocols in Molecular Biology, 2011. https://doi.org/10.1002/0471142727.
MB1028S94.
[151] Saikrishnan, K., Jeyakanthan, J., Venkatesh, J., Acharya, N., Purnapatre, K., Sekar, K., Varshney, U., &
Vijayan, M. Crystallization and preliminary X-ray studies of the single-stranded DNA-binding protein
from Mycobacterium tuberculosis. Acta Crystallographica Section D: Biological Crystallography, 2002,
58, 327–329. https://doi.org/10.1107/S090744490102008X.
[152] Sundaresan, R., Samen, U., & Ponnuraj, K. Expression, purification, crystallization and preliminary
X-ray diffraction studies of the human keratin 4-binding domain of serine-rich repeat protein 1 from
Streptococcus agalactiae. Acta Crystallographica Section F: Structural Biology and Crystallization
Communications, 2011, 67, 1582–1585. https://doi.org/10.1107/S1744309111040413.
[153] Borko, L., Kostan, J., Zahradníkova, A., Pevala, V., Gasperík, J., Hostinova, E., Urbanikova, L., Djinovic-
Carugo, K., Bauerova-Hlinkova, V., & Sevcík, J. Human cardiac ryanodine receptor: Preparation,
crystallization and preliminary X-ray analysis of the N-terminal region. Protein & Peptide Letters,
2013, 20, 1211–1216. https://doi.org/10.2174/0929866511320110004.
[154] Kuang, Q., Purhonen, P., & Hebert, H. Two-dimensional crystallization procedure, from protein
expression to sample preparation. BioMed Research International, 2015, 2015. https://doi.org/10.
1155/2015/693869.
[155] Derewenda, Z. S. The use of recombinant methods and molecular engineering in protein
crystallization. Methods, 2004, 34, 354–363. https://doi.org/10.1016/J.YMETH.2004.03.024.
[156] Messick, T., & Marmorstein, R. Crystallization of macromolecules. Current Protocols in Protein
Science, 2003, 34. https://doi.org/10.1002/0471140864.PS1704S34.
[157] Pamula, F., Mühle, J., Blanc, A., Nehmé, R., Edwards, P. C., Tate, C. G., & Tsai, C. J. Strategic screening
and characterization of the visual GPCR-mini-g protein signaling complex for successful
crystallization. Journal of Visualized Experiments, 2020, 2020. https://doi.org/10.3791/60747.
[158] Page, R., & Stevens, R. C. Crystallization data mining in structural genomics: Using positive and
negative results to optimize protein crystallization screens. Methods, 2004, 34, 373–389. https://doi.
org/10.1016/J.YMETH.2004.03.026.
11 Role of structural genomics in drug discovery 289
https://t.me/med1917

[159] Patching, S. G. Solid-state NMR structures of integral membrane proteins. Molecular Membrane
Biology, 2015, 32, 156–178. https://doi.org/10.3109/09687688.2016.1139754.
[160] Evans, D. R. H., Romero, J. K., & Westoby, M. Chapter 9 concentration of proteins and removal of
solutes. Methods in Enzymology, 2009, 463, 97–120. https://doi.org/10.1016/S0076-6879(09)63009-3.
[161] Jithesh, P. V., & Scaria, V. From genomes to genomic medicine: Enabling personalized and precision
medicine in the Middle East. Personalized Medicine, 2017, 14, 377–382. https://doi.org/10.2217/PME-
2017-0048.
[162] Prokop, J. W., May, T., Strong, K., Bilinovich, S. M., Bupp, C., Rajasekaran, S., Worthey, E. A., & Lazar,
J. Genome sequencing in the clinic: The past, present, and future of genomic medicine.
Physiological Genomics, 2018, 50, 563–579. https://doi.org/10.1152/PHYSIOLGENOMICS.00046.2018.
[163] Nakagawa, H., & Fujita, M. Whole genome sequencing analysis for cancer genomics and precision
medicine. Cancer Science, 2018, 109, 513–522. https://doi.org/10.1111/CAS.13505.
[164] Feero, W. G., & Guttmacher, A. E. Genomics, personalized medicine, and pediatrics. Academic
Pediatrics, 2014, 14, 14–22. https://doi.org/10.1016/J.ACAP.2013.06.008.
[165] Offit, K. Personalized medicine: New genomics, old lessons. Human Genetics, 2011, 130, 3–14.
https://doi.org/10.1007/S00439-011-1028-3.
[166] Sonis, S. T. Genomics, personalized medicine, and supportive cancer care. American Society of
Clinical Oncology Educational Book, 2015, 9–16. https://doi.org/10.14694/EDBOOK_AM.2015.35.9.
[167] Kurnat-Thoma, E. L. Genetics and genomics: The scientific drivers of personalized medicine. Annual
Review of Nursing Research, 2011, 29, 27–54. https://doi.org/10.1891/0739-6686.29.27.
[168] Blix, A. Personalized medicine, genomics, and pharmacogenomics: A primer for nurses. Clinical
Journal of Oncology Nursing, 2014, 18, 437–441. https://doi.org/10.1188/14.CJON.437-441.
[169] Neuhaus, D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful.
Progress in Nuclear Magnetic Resonance Spectroscopy, 2022, 130–131, 60–103. https://doi.org/10.
1016/J.PNMRS.2022.07.001.
[170] Schmidt-Krey, I., & Rubinstein, J. L. Electron cryomicroscopy of membrane proteins: Specimen
preparation for two-dimensional crystals and single particles. Micron, 2011, 42, 107–116. https://doi.
org/10.1016/J.MICRON.2010.07.004.
[171] Maslennikov, I., Kefala, G., Johnson, C., Riek, R., Choe, S., & Kwiatkowski, W. NMR spectroscopic and
analytical ultracentrifuge analysis of membrane protein detergent complexes. BMC Structural
Biology, 2007, 7. https://doi.org/10.1186/1472-6807-7-74.
[172] Nannenga, B. L., & Gonen, T. Protein structure determination by MicroED. Current Opinion in
Structural Biology, 2014, 27, 24–31. https://doi.org/10.1016/J.SBI.2014.03.004.
[173] Maslennikov, I., Krupa, M., Dickson, C., Esquivies, L., Blain, K., Kefala, G., Choe, S., & Kwiatkowski,
W. Characterization of protein detergent complexes by NMR, light scattering, and analytical
ultracentrifugation. Journal of Structural and Functional Genomics, 2009, 10, 25–35. https://doi.org/
10.1007/S10969-009-9061-3.
[174] Costa, T. R. D., Ignatiou, A., & Orlova, E. V. Structural analysis of protein complexes by cryo electron
microscopy. Methods in Molecular Biology, 2017, 1615, 377–413. https://doi.org/10.1007/978-1-4939-
7033-9_28.
[175] Acosta, D., Das, T., & Eliezer, D. Probing IDP interactions with membranes by fluorescence
spectroscopy. Methods in Molecular Biology, 2020, 2141, 555–567. https://doi.org/10.1007/978-1-
0716-0524-0_28.
[176] Kim, D., Echelmeier, A., Cruz Villarreal, J., Gandhi, S., Quintana, S., Egatz-Gomez, A., & Ros, A. Electric
triggering for enhanced control of droplet generation. Analytical Chemistry, 2019, 91, 9792–9799.
https://doi.org/10.1021/ACS.ANALCHEM.9B01449.
[177] Morrison, K. A., Doekhie, A., Neville, G. M., Price, G. J., Whitley, P., Doutch, J., & Edler, K. J. Ab initio
reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs. BBA
Advances, 2022, 2. https://doi.org/10.1016/J.BBADVA.2021.100033.
290 Anuradha Mehra et al.
https://t.me/med1917

[178] Nam, K. H. Polysaccharide-based injection matrix for serial crystallography. International Journal of
Molecular Sciences, 2020, 21. https://doi.org/10.3390/IJMS21093332.
[179] Keller, B. O., & Li, L. Three-layer matrix/sample preparation method for MALDI MS analysis of low
nanomolar protein samples. Journal of the American Society for Mass Spectrometry, 2006, 17,
780–785. https://doi.org/10.1016/J.JASMS.2006.02.012.
[180] Hattne, J., Reyes, F. E., Nannenga, B. L., Shi, D., De La Cruz, M. J., Leslie, A. G. W., & Gonen,
T. MicroED data collection and processing. Acta Crystallographica Section A: Foundations and
Advances, 2015, 71, 353–360. https://doi.org/10.1107/S2053273315010669.
[181] Mathaes, R., Hildebrandt, C., Winter, G., Engert, J., & Besheer, A. Quality control of protein crystal
suspensions using microflow imaging and flow cytometry. Journal of Pharmaceutical Sciences, 2013,
102, 3860–3866. https://doi.org/10.1002/JPS.23677.
[182] Januliene, D., & Moeller, A. Single-particle Cryo-EM of membrane proteins. Methods in Molecular
Biology, 2021, 2302, 153–178. https://doi.org/10.1007/978-1-0716-1394-8_9.
[183] Yuan, X., Zhu, Y., Ruiz-Carrillo, D., & Kadowaki, T. Evolutionary history of metazoan TMEM16 family.
Molecular Phylogenetics and Evolution, 2022, 177. https://doi.org/10.1016/J.YMPEV.2022.107595.
[184] Hennig, J., & Sattler, M. The dynamic duo: Combining NMR and small angle scattering in structural
biology. Protein Science, 2014, 23, 669–682. https://doi.org/10.1002/PRO.2467.
[185] Shaw Stewart, P., & Mueller-Dieckmann, J. Automation in biological crystallization. Acta
Crystallographica Section F: Structural Biology Communications, 2014, 70, 686–696. https://doi.org/
10.1107/S2053230X14011601.
[186] Ruggiero, A., Smaldone, G., Squeglia, F., & Berisio, R. Enhanced crystallizability by protein
engineering approaches: A general overview. Protein & Peptide Letters, 2012, 19, 732–742.
https://doi.org/10.2174/092986612800793172.
[187] Kim, J., & Ng, H. L. Screening and identifying membrane proteins favorable for crystallization.
Current Protocols in Protein Science, 2017, 90, 29.19.1–29.19.10 https://doi.org/10.1002/CPPS.40.
[188] Liu, X., Sitsel, O., Wang, K., & Gourdon, P. Overproduction of PIB-type ATPases. Methods in
Molecular Biology, 2016, 1377, 29–36. https://doi.org/10.1007/978-1-4939-3179-8_5.
[189] Zhang, X., Shi, L., Shu, S., Wang, Y., Zhao, K., Xu, N., Liu, S., & Roepstorff, P. An improved method of
sample preparation on AnchorChip™ targets for MALDI-MS and MS/MS and its application in the
liver proteome project. Proteomics, 2007, 7, 2340–2349. https://doi.org/10.1002/PMIC.200600184.
[190] Ravelli, R. B. G., Haselmann-Weiss, U., McGeehan, J. E., McCarthy, A. A., Marquez, J. A., Antony, C.,
Frangakis, A. S., & Stranzl, G. Plastic-embedded protein crystals. Journal of Synchrotron Radiation,
2007, 14, 128–132. https://doi.org/10.1107/S0909049506043111.
[191] Hajiani, S., Ghassempour, A., & Shokri, B. Protein ion yield enhancement in matrix-assisted laser
desorption/ionization mass spectrometry after sample and matrix low-pressure glow discharge
plasma irradiation. Rapid Communications in Mass Spectrometry, 2021, 35. https://doi.org/10.1002/
RCM.8964.
[192] Adrian, M., Dubochet, J., Fuller, S. D., & Harris, J. R. Cryo-negative staining. Micron, 1998, 29,
145–160. https://doi.org/10.1016/S0968-4328(97)00068-1.
[193] Yu, G., Li, K., & Jiang, W. Antibody-based affinity cryo-EM grid. Methods, 2016, 100, 16–24.
https://doi.org/10.1016/J.YMETH.2016.01.010.
[194] Danelius, E., & Gonen, T. Protein and small molecule structure determination by the Cryo-EM
method MicroED. Methods in Molecular Biology, 2021, 2305, 323–342. https://doi.org/10.1007/978-1-
0716-1406-8_16.
[195] Gupta, M. N., Alam, A., & Hasnain, S. E. Protein promiscuity in drug discovery, drug-repurposing
and antibiotic resistance. Biochimie, 2020, 175, 50–57. https://doi.org/10.1016/J.BIOCHI.2020.05.004.
[196] Schmidt, D. Antiepileptic drug discovery: Does mechanism of action matter? Epilepsy and Behavior,
2011, 21, 342–343. https://doi.org/10.1016/J.YEBEH.2011.03.037.
11 Role of structural genomics in drug discovery 291
https://t.me/med1917

[197] Gadakh, B., & Aerschot, A. Renaissance in antibiotic discovery: Some novel approaches for finding
drugs to treat bad bugs. Current Medicinal Chemistry, 2015, 22, 2140–2158. https://doi.org/10.2174/
0929867322666150319115828.
[198] De Beer, T., Wells, G., Burger, P., Joubert, F., Marechal, E., Birkholtz, L., & Louw, A. Antimalarial drug
discovery: In silico structural biology and rational drug design. Infectious Disorders – Drug Targets,
2012, 9, 304–318. https://doi.org/10.2174/1871526510909030304.
[199] Brtz-Oesterhelt, H., & Sass, P. Postgenomic strategies in antibacterial drug discovery. Future
Microbiology, 2010, 5, 1553–1579. https://doi.org/10.2217/FMB.10.119.
[200] Yu, Y., Jiang, X. X., & Li, J. C. Biomarker discovery for tuberculosis using metabolomics. Frontiers in
Molecular Biosciences, 2023, 10. https://doi.org/10.3389/FMOLB.2023.1099654.
[201] Nicola, G., & Abagyan, R. Structure-based approaches to antibiotic drug discovery. Current
Protocols in Microbiology, 2009. https://doi.org/10.1002/9780471729259.MC1702S12.
[202] Holton, S. J., Weiss, M. S., & Tucker, P. A. Matthias Wilmanns: Structure-based approaches to drug
discovery against tuberculosis. Current Protocols in Protein Science, 2007, 8, 365–375. https://doi.
org/10.2174/138920307781369445.
[203] Langer, T., & Hoffmann, R. Virtual screening an effective tool for lead structure discovery. Current
Pharmaceutical Design, 2005, 7, 509–527. https://doi.org/10.2174/1381612013397861.
[204] Cavasotto, C. N., & Phatak, S. S. Homology modeling in drug discovery: Current trends and
applications. Drug Discovery Today, 2009, 14, 676–683. https://doi.org/10.1016/J.DRUDIS.2009.
04.006.
[205] Reddy, V. B., Yusop, A., Jaafar, Z., Madhavi, J., Madhavi, V., & Madhavi, G. Advances in drug
discovery: Impact of genomics and role of analytical instrumentation. Current Drug Discovery
Technology, 2016, 13, 211–224. https://doi.org/10.2174/1570163813666160930122643.
[206] Freiberg, C., & Brötz-Oesterhelt, H. Functional genomics in antibacterial drug discovery. Drug
Discovery Today, 2005, 10, 927–935. https://doi.org/10.1016/S1359-6446(05)03474-4.
[207] Ruiz-Garcia, A., Bermejo, M., Moss, A., & Casabo, V. G. Pharmacokinetics in drug discovery. Journal
of Pharmaceutical Sciences, 2008, 97, 654–690. https://doi.org/10.1002/JPS.21009.
[208] Rabinowitz, J. D., Purdy, J. G., Vastag, L., Shenk, T., & Koyuncu, E. Metabolomics in drug target
discovery. Cold Spring Harbor Symposia on Quantitative Biology, 2011, 76, 235–246. https://doi.org/
10.1101/SQB.2011.76.010694.
[209] Kim, D., Hwang, H. Y., & Kwon, H. J. Targeting autophagy in disease: Recent advances in drug
discovery. Expert Opinion Drug Discovery, 2020, 15, 1045–1064. https://doi.org/10.1080/17460441.
2020.1773429.
[210] Jani, M., & Azad, R. K. Discovery of mosaic genomic islands in Pseudomonas spp. Archives of
Microbiology, 2021, 203, 2735–2742. https://doi.org/10.1007/S00203-021-02253-2.
[211] Buysse, J. The role of genomics in antibacterial target discovery. Current Medicinal Chemistry, 2012,
8, 1713–1726. https://doi.org/10.2174/0929867013371699.
[212] Hill, J. A., & Cowen, L. E. Using combination therapy to thwart drug resistance. Future Microbiology,
2015, 10, 1719–1726. https://doi.org/10.2217/FMB.15.68.
[213] Sekyere, J. O., & Asante, J. Emerging mechanisms of antimicrobial resistance in bacteria and fungi:
Advances in the era of genomics. Future Microbiology, 2018, 13, 241–262. https://doi.org/10.2217/
FMB-2017-0172.
[214] Wiederhold, N. P. Antifungal resistance: Current trends and future strategies to combat. Infection
and Drug Resistance, 2017, 10, 249–259. https://doi.org/10.2147/IDR.S124918.
[215] Gupta, R., Srivastava, D., Sahu, M., Tiwari, S., Ambasta, R. K., & Kumar, P. Artificial intelligence to
deep learning: Machine intelligence approach for drug discovery. Molecular Diversity, 2021, 25,
1315–1360. https://doi.org/10.1007/S11030-021-10217-3.
292 Anuradha Mehra et al.
https://t.me/med1917

[216] Gao, M., & Shang, X. Identification of associations between lncRNA and drug resistance based on
deep learning and attention mechanism. Frontiers in Microbiology, 2023, 14. https://doi.org/10.
3389/FMICB.2023.1147778.
[217] Lahiri, S., Kazmirski, S., Kern, G., & Sanyal, G. Applications of biophysical tools to target-based
discovery of novel antibacterial leads. Current Drug Targets, 2012, 13, 388–408. https://doi.org/10.
2174/138945012799424660.
[218] Koui, Y., Himeno, M., Mori, Y., Nakano, Y., Saijou, E., Tanimizu, N., Kamiya, Y., Anzai, H., Maeda, N.,
Wang, L., Yamada, T., Sakai, Y., Nakato, R., Miyajima, A., & Kido, T. Development of human iPSC-
derived quiescent hepatic stellate cell-like cells for drug discovery and in vitro disease modeling.
Stem Cell Reports, 2021, 16, 3050–3063. https://doi.org/10.1016/J.STEMCR.2021.11.002.
[219] Clark, P. G. K., Dixon, D. J., & Brennan, P. E. Development of chemical probes for the bromodomains
of BRD7 and BRD9. Drug Discovery Today Technology, 2016, 19, 73–80. https://doi.org/10.1016/J.
DDTEC.2016.05.002.
[220] El-Hossary, E. M., Abdel-Halim, M., Ibrahim, E. S., Pimentel-Elardo, S. M., Nodwell, J. R., Handoussa,
H., Abdelwahab, M. F., Holzgrabe, U., & Abdelmohsen, U. R. Natural products repertoire of the red
sea. Marine Drugs, 2020, 18. https://doi.org/10.3390/MD18090457.
11 Role of structural genomics in drug discovery 293
https://t.me/med1917
Соседние файлы в папке Библиотека им академика М.И. Перельмана
