新冠病毒在國際間快速的傳播及不斷的變異，已經成為了全球嚴重的公共衛生負擔，除了疫苗外我們還需要找到另一個有效預防或降低新冠病毒感染風險的方式。在小分子藥物的開發中，目前有Remdesivir、Favipiravir、Molnupiravir、Paxlovid等少數已核可藥物用於治療此疾病。因此本篇研究目的即是找到能抑制新冠病毒感染人類細胞的活性化合物，以利於後續抗新冠病毒藥物的開發。由於新冠病毒附著於人類細胞受體屬於RBD-ACE2蛋白質間交互作用力，藉由篩選1068種美國藥物食品管理局核准的藥物，已有文獻報導Ivermectin、Gramicidin巨環類藥物對於新冠病毒RBD附著於人類細胞受體ACE2有抑制效果。亦研究也指出巨環類化合物可以當作蛋白質間交互作用力抑制劑，因此我們認為巨環類化合物很有機會成為阻斷新冠病毒感染的活性化合物。本篇利用RBD-ACE2 Attachment Assay、Pseudovirus Neutralization Assay、Cytotoxicity從2560個不同的巨環類化合物中成功地篩選出1個全新的結構分子Mac734，對於人類細胞不具細胞毒性且擁有抑制新冠病毒主流變異株感染的效果，分別對Alpha (B.1.1.7)、Beta (B.1.351)、Delta (B.1.671.2)、Omicron (B.1.1.529)附著到人類細胞受體的EC50依序為22.2 M、10.3 M、9.5 M、5.4 M。未來可以根據此分子進行官能基的修飾，以利於抗新冠病毒藥物的開發。此外根據Mac734的結構，利用點擊化學快速合成一系列的結構類似物，且發現化合物5g能促進不同新冠病毒主流變異株感染人類細胞的效果。綜觀以上結果，本篇目前各別發現一個新冠病毒抑制劑與促進劑，日後皆有潛力成為研究抗新冠病毒感染的利器。

　Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a global public health burden. In addition to vaccines, effective prevention and reduction of SARS-CoV-2 associated risks are desired. Current development of small molecule drugs has yielded approved drugs such as Remdesivir, Favipiravir, Molnupiravir, and Paxlovid for the treatment of SARS-CoV-2. The purpose of this study is to identify new protein-protein interaction (PPI) inhibitor in the attachment of human cell receptor Angiotensin-Converting Enzyme 2 (ACE2) by SARS-CoV-2 Receptor Binding Domain (RBD) on the spike protein. By screening of 1068 FDA-approved drugs, previous study has identified macrocyclic drugs, such as Ivermectin and Gramicidin to exert an inhibitory effect on the attachment between RBD and ACE2. Moreover, numerous reports have leveraged macrocyclic scaffolds as PPI inhibitors. Herein, we used RBD-ACE2 attachment assay, pseudovirus neutralization assay, host cell cytotoxicity assay to successfully identify a new macrocyclic molecule Mac734. By click chemistry, we also synthesized a series of structural analogs, and surprisingly, found that analog 5g could promote the entry of SARS-CoV-2 variants during pseudovirus infection. In summary, this study has disclosed a new SARS-CoV-2 entry inhibitor and an enhancer, both of which are potential powerful tools for research on coronavirus pathogenesis.

Abstract i
中文摘要 ii
目錄 iii
圖目錄 vi
圖譜目錄 vii
縮寫對照表 ix
第一章 緒論 1
1.1.1新冠病毒(SARS-CoV-2)的傳播方式、感染症狀、種類及影響 1
1.1.2 新冠病毒的感染機制與靶點 3
1.1.3 使新冠病毒進入的細胞受體 7
1.1.4 新冠病毒的結構與侵入細胞的方式 9
第二節 實驗設計與目的 12
1.2.1 疫苗、單株抗體、小分子藥物作為新冠病毒抑制劑的選擇 12
1.2.2 新冠病毒與人類細胞受體間的作用力是一種PPI 14
1.2.3 小分子藥物作為PPI抑制劑的困難點 15
1.2.4 熱點的發現使得小分子藥物有機會成為PPI抑制劑 16
1.2.5 新冠病毒受體結合域與人類細胞受體之間PPI的熱點 17
1.2.6 研究PPI的實驗方法 19
第二章 實驗結果與討論 30
2.1 初篩2560個不同的巨環類化合物對於野生型(wild type)新冠病毒RBD附著於人類細胞受體ACE2的冷光抑制率 30
2.2 篩選到10個活性化合物能夠抑制野生型新冠病毒RBD附著到人類細胞受體ACE2 33
2.3 使用RBD-ACE2 Attachment Assay可能會產生偽陽性的結果 35
2.4 篩選到1個病毒的進入抑制劑Mac734能夠抑制野生型新冠病毒附著到人類細胞受體ACE2 39
2.5 發現Mac734對於其他新冠病毒主流變異株附著到人類細胞受體ACE2皆有一定的抑制效果 43
2.6 利用點擊化學快速合成一系列Mac734的結構類似物 45
2.7 篩選到4個活性化合物能夠抑制野生型新冠病毒RBD附著到人類細胞受體ACE2 49
2.8 篩選到1個病毒的進入促進劑化合物5g能夠促進野生型新冠病毒附著到人類細胞ACE2 50
2.9 發現化合物5g對於其他病毒主流變異株附著到人類細胞受體ACE2都有一定的促進效果 52
第三章 結論 54
第四章 實驗步驟與光譜數據 57
第一節：儀器設備與藥品材料 57
第二節：生物實驗技術 60
第三節：化學合成步驟與光譜數據 62
4.3.1 化合物2之合成 63
General Procedure A : 疊氮化合物的合成 64
4.3.2 化合物4a之合成 65
4.3.3 化合物4b之合成 65
4.3.4 化合物4c之合成 66
4.3.5 化合物4d之合成 66
4.3.6 化合物4e之合成 67
4.3.7 化合物4f之合成 67
4.3.8 化合物4g之合成 68
4.3.9 化合物4h之合成 68
4.3.10 化合物4i之合成 69
General Procedure B : 銅催化疊氮化物-炔烴環加成反應 70
4.3.11 化合物5a之合成 71
4.3.12 化合物5b之合成 72
4.3.13 化合物5c之合成 73
4.3.14 化合物5d之合成 74
4.3.15 化合物5e之合成 76
4.3.16 化合物5f之合成 77
4.3.17 化合物5g之合成 78
4.3.18 化合物5h之合成 79
4.3.19 化合物5i之合成 81
4.3.20 化合物5j之合成 82
第五章 光譜資料 84
第一節 化合物之1H NMR、13C NMR光譜圖 85
第二節 化合物之HPLC光譜圖 118
第三節 化合物之HRMS光譜圖 124
第六章 參考文獻 130

(1) Comber, L.; E, O. M.; Drummond, L.; Carty, P. G.; Walsh, K. A.; De Gascun, C. F.; Connolly, M. A.; Smith, S. M.; O'Neill, M.; Ryan, M.; et al. Airborne transmission of SARS-CoV-2 via aerosols. Rev Med Virol 2021, 31 (3), e2184.
(2) Zou, L.; Ruan, F.; Huang, M.; Liang, L.; Huang, H.; Hong, Z.; Yu, J.; Kang, M.; Song, Y.; Xia, J.; et al. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N Engl J Med 2020, 382 (12), 1177-1179.
(3) Wang, D.; Hu, B.; Hu, C.; Zhu, F.; Liu, X.; Zhang, J.; Wang, B.; Xiang, H.; Cheng, Z.; Xiong, Y.; et al. Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA 2020, 323 (11), 1061-1069.
(4) Wu, F.; Zhao, S.; Yu, B.; Chen, Y. M.; Wang, W.; Song, Z. G.; Hu, Y.; Tao, Z. W.; Tian, J. H.; Pei, Y. Y.; et al. A new coronavirus associated with human respiratory disease in China. Nature 2020, 579 (7798), 265-269.
(5) Eckerle, L. D.; Becker, M. M.; Halpin, R. A.; Li, K.; Venter, E.; Lu, X.; Scherbakova, S.; Graham, R. L.; Baric, R. S.; Stockwell, T. B.; et al. Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing. PLoS Pathog 2010, 6 (5), e1000896.
(6) Aleem, A.; Akbar Samad, A. B.; Vaqar, S. Emerging Variants of SARS-CoV-2 And Novel Therapeutics Against Coronavirus (COVID-19). In StatPearls, 2023.
(7) Zhou, Y.; Wang, H.; Yang, L.; Wang, Q. Progress on COVID-19 Chemotherapeutics Discovery and Novel Technology. Molecules 2022, 27 (23).
(8) Gordon, D. E.; Jang, G. M.; Bouhaddou, M.; Xu, J.; Obernier, K.; White, K. M.; O'Meara, M. J.; Rezelj, V. V.; Guo, J. Z.; Swaney, D. L.; et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020, 583 (7816), 459-468.
(9) Khailany, R. A.; Safdar, M.; Ozaslan, M. Genomic characterization of a novel SARS-CoV-2. Gene Rep 2020, 19, 100682.
(10) Fehr, A. R.; Perlman, S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol 2015, 1282, 1-23.
(11) Naqvi, A. A. T.; Fatima, K.; Mohammad, T.; Fatima, U.; Singh, I. K.; Singh, A.; Atif, S. M.; Hariprasad, G.; Hasan, G. M.; Hassan, M. I. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochim Biophys Acta Mol Basis Dis 2020, 1866 (10), 165878.
(12) Yadav, R.; Chaudhary, J. K.; Jain, N.; Chaudhary, P. K.; Khanra, S.; Dhamija, P.; Sharma, A.; Kumar, A.; Handu, S. Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19. Cells 2021, 10 (4).
(13) Ullrich, S.; Nitsche, C. The SARS-CoV-2 main protease as drug target. Bioorg Med Chem Lett 2020, 30 (17), 127377.
(14) Baez-Santos, Y. M.; St John, S. E.; Mesecar, A. D. The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds. Antiviral Res 2015, 115, 21-38.
(15) He, J.; Hu, L.; Huang, X.; Wang, C.; Zhang, Z.; Wang, Y.; Zhang, D.; Ye, W. Potential of coronavirus 3C-like protease inhibitors for the development of new anti-SARS-CoV-2 drugs: Insights from structures of protease and inhibitors. Int J Antimicrob Agents 2020, 56 (2), 106055.
(16) Hillen, H. S.; Kokic, G.; Farnung, L.; Dienemann, C.; Tegunov, D.; Cramer, P. Structure of replicating SARS-CoV-2 polymerase. Nature 2020, 584 (7819), 154-156.
(17) Wang, M. Y.; Zhao, R.; Gao, L. J.; Gao, X. F.; Wang, D. P.; Cao, J. M. SARS-CoV-2: Structure, Biology, and Structure-Based Therapeutics Development. Front Cell Infect Microbiol 2020, 10, 587269.
(18) Gao, Y.; Yan, L.; Huang, Y.; Liu, F.; Zhao, Y.; Cao, L.; Wang, T.; Sun, Q.; Ming, Z.; Zhang, L.; et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science 2020, 368 (6492), 779-782.
(19) V'Kovski, P.; Kratzel, A.; Steiner, S.; Stalder, H.; Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 2021, 19 (3), 155-170.
(20) de Wit, E.; van Doremalen, N.; Falzarano, D.; Munster, V. J. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol 2016, 14 (8), 523-534.
(21) Breining, P.; Frolund, A. L.; Hojen, J. F.; Gunst, J. D.; Staerke, N. B.; Saedder, E.; Cases-Thomas, M.; Little, P.; Nielsen, L. P.; Sogaard, O. S.; et al. Camostat mesylate against SARS-CoV-2 and COVID-19-Rationale, dosing and safety. Basic Clin Pharmacol Toxicol 2021, 128 (2), 204-212.
(22) Tripathy, S.; Dassarma, B.; Roy, S.; Chabalala, H.; Matsabisa, M. G. A review on possible modes of action of chloroquine/hydroxychloroquine: repurposing against SAR-CoV-2 (COVID-19) pandemic. Int J Antimicrob Agents 2020, 56 (2), 106028.
(23) Lin, H. X. J.; Cho, S.; Meyyur Aravamudan, V.; Sanda, H. Y.; Palraj, R.; Molton, J. S.; Venkatachalam, I. Remdesivir in Coronavirus Disease 2019 (COVID-19) treatment: a review of evidence. Infection 2021, 49 (3), 401-410.
(24) Kabinger, F.; Stiller, C.; Schmitzova, J.; Dienemann, C.; Kokic, G.; Hillen, H. S.; Hobartner, C.; Cramer, P. Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nat Struct Mol Biol 2021, 28 (9), 740-746.
(25) Ghasemnejad-Berenji, M.; Pashapour, S. Favipiravir and COVID-19: A Simplified Summary. Drug Res (Stuttg) 2021, 71 (3), 166-170.
(26) Low, Z. Y.; Yip, A. J. W.; Lal, S. K. Repositioning Ivermectin for Covid-19 treatment: Molecular mechanisms of action against SARS-CoV-2 replication. Biochim Biophys Acta Mol Basis Dis 2022, 1868 (2), 166294.
(27) Zhao, L.; Li, S.; Zhong, W. Mechanism of Action of Small-Molecule Agents in Ongoing Clinical Trials for SARS-CoV-2: A Review. Front Pharmacol 2022, 13, 840639.
(28) Kuhn, J. H.; Li, W.; Choe, H.; Farzan, M. Angiotensin-converting enzyme 2: a functional receptor for SARS coronavirus. Cell Mol Life Sci 2004, 61 (21), 2738-2743.
(29) Li, W.; Moore, M. J.; Vasilieva, N.; Sui, J.; Wong, S. K.; Berne, M. A.; Somasundaran, M.; Sullivan, J. L.; Luzuriaga, K.; Greenough, T. C.; et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature 2003, 426 (6965), 450-454.
(30) Lu, R.; Zhao, X.; Li, J.; Niu, P.; Yang, B.; Wu, H.; Wang, W.; Song, H.; Huang, B.; Zhu, N.; et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 2020, 395 (10224), 565-574.
(31) Zhou, P.; Yang, X. L.; Wang, X. G.; Hu, B.; Zhang, L.; Zhang, W.; Si, H. R.; Zhu, Y.; Li, B.; Huang, C. L.; et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020, 579 (7798), 270-273.
(32) Shang, J.; Ye, G.; Shi, K.; Wan, Y.; Luo, C.; Aihara, H.; Geng, Q.; Auerbach, A.; Li, F. Structural basis of receptor recognition by SARS-CoV-2. Nature 2020, 581 (7807), 221-224.
(33) Walls, A. C.; Park, Y. J.; Tortorici, M. A.; Wall, A.; McGuire, A. T.; Veesler, D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 2020, 181 (2), 281-292 e286.
(34) Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Zhang, Q.; Shi, X.; Wang, Q.; Zhang, L.; et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 2020, 581 (7807), 215-220.
(35) Wang, Q.; Zhang, Y.; Wu, L.; Niu, S.; Song, C.; Zhang, Z.; Lu, G.; Qiao, C.; Hu, Y.; Yuen, K. Y.; et al. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell 2020, 181 (4), 894-904 e899.
(36) Asghari, A.; Naseri, M.; Safari, H.; Saboory, E.; Parsamanesh, N. The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options. DNA Cell Biol 2020, 39 (10), 1741-1753.
(37) Zhu, N.; Zhang, D.; Wang, W.; Li, X.; Yang, B.; Song, J.; Zhao, X.; Huang, B.; Shi, W.; Lu, R.; et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 2020, 382 (8), 727-733.
(38) Liu, D. X.; Liang, J. Q.; Fung, T. S. Human Coronavirus-229E, -OC43, -NL63, and -HKU1 (Coronaviridae). Encyclopedia of Virology 2021, 428-440.
(39) Su, S.; Wong, G.; Shi, W.; Liu, J.; Lai, A. C. K.; Zhou, J.; Liu, W.; Bi, Y.; Gao, G. F. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends Microbiol 2016, 24 (6), 490-502.
(40) He, Y.; Zheng, C. [Replication and transmission mechanisms of highly pathogenic human coronavirus]. Zhejiang Da Xue Xue Bao Yi Xue Ban 2020, 49 (3), 324-339.
(41) Lu, G.; Hu, Y.; Wang, Q.; Qi, J.; Gao, F.; Li, Y.; Zhang, Y.; Zhang, W.; Yuan, Y.; Bao, J.; et al. Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26. Nature 2013, 500 (7461), 227-231.
(42) Li, Z.; Tomlinson, A. C.; Wong, A. H.; Zhou, D.; Desforges, M.; Talbot, P. J.; Benlekbir, S.; Rubinstein, J. L.; Rini, J. M. The human coronavirus HCoV-229E S-protein structure and receptor binding. Elife 2019, 8.
(43) Castillo, G.; Mora-Diaz, J. C.; Breuer, M.; Singh, P.; Nelli, R. K.; Gimenez-Lirola, L. G. Molecular mechanisms of human coronavirus NL63 infection and replication. Virus Res 2023, 327, 199078.
(44) Kolb, A. F.; Hegyi, A.; Siddell, S. G. Identification of residues critical for the human coronavirus 229E receptor function of human aminopeptidase N. J Gen Virol 1997, 78 ( Pt 11), 2795-2802.
(45) Hulswit, R. J. G.; Lang, Y.; Bakkers, M. J. G.; Li, W.; Li, Z.; Schouten, A.; Ophorst, B.; van Kuppeveld, F. J. M.; Boons, G. J.; Bosch, B. J.; et al. Human coronaviruses OC43 and HKU1 bind to 9-O-acetylated sialic acids via a conserved receptor-binding site in spike protein domain A. Proc Natl Acad Sci U S A 2019, 116 (7), 2681-2690.
(46) Raj, V. S.; Mou, H.; Smits, S. L.; Dekkers, D. H.; Muller, M. A.; Dijkman, R.; Muth, D.; Demmers, J. A.; Zaki, A.; Fouchier, R. A.; et al. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature 2013, 495 (7440), 251-254.
(47) Abduljalil, J. M.; Abduljalil, B. M. Epidemiology, genome, and clinical features of the pandemic SARS-CoV-2: a recent view. New Microbes New Infect 2020, 35, 100672.
(48) Bai, Z.; Cao, Y.; Liu, W.; Li, J. The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation. Viruses 2021, 13 (6).
(49) Zhang, Z.; Nomura, N.; Muramoto, Y.; Ekimoto, T.; Uemura, T.; Liu, K.; Yui, M.; Kono, N.; Aoki, J.; Ikeguchi, M.; et al. Structure of SARS-CoV-2 membrane protein essential for virus assembly. Nat Commun 2022, 13 (1), 4399.
(50) Hulswit, R. J.; de Haan, C. A.; Bosch, B. J. Coronavirus Spike Protein and Tropism Changes. Adv Virus Res 2016, 96, 29-57.
(51) Reis, C. A.; Tauber, R.; Blanchard, V. Glycosylation is a key in SARS-CoV-2 infection. J Mol Med (Berl) 2021, 99 (8), 1023-1031.
(52) Hoffmann, M.; Kleine-Weber, H.; Pohlmann, S. A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells. Mol Cell 2020, 78 (4), 779-784 e775.
(53) Shang, J.; Wan, Y.; Luo, C.; Ye, G.; Geng, Q.; Auerbach, A.; Li, F. Cell entry mechanisms of SARS-CoV-2. Proc Natl Acad Sci U S A 2020, 117 (21), 11727-11734.
(54) Wettstein, L.; Knaff, P. M.; Kersten, C.; Muller, P.; Weil, T.; Conzelmann, C.; Muller, J. A.; Bruckner, M.; Hoffmann, M.; Pohlmann, S.; et al. Peptidomimetic inhibitors of TMPRSS2 block SARS-CoV-2 infection in cell culture. Commun Biol 2022, 5 (1), 681.
(55) Hoffmann, M.; Kleine-Weber, H.; Schroeder, S.; Kruger, N.; Herrler, T.; Erichsen, S.; Schiergens, T. S.; Herrler, G.; Wu, N. H.; Nitsche, A.; et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 2020, 181 (2), 271-280 e278.
(56) Glowacka, I.; Bertram, S.; Muller, M. A.; Allen, P.; Soilleux, E.; Pfefferle, S.; Steffen, I.; Tsegaye, T. S.; He, Y.; Gnirss, K.; et al. Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response. J Virol 2011, 85 (9), 4122-4134.
(57) Bestle, D.; Heindl, M. R.; Limburg, H.; Van Lam van, T.; Pilgram, O.; Moulton, H.; Stein, D. A.; Hardes, K.; Eickmann, M.; Dolnik, O.; et al. TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells. Life Sci Alliance 2020, 3 (9).
(58) Xu, Y.; Cole, D. K.; Lou, Z.; Liu, Y.; Qin, L.; Li, X.; Bai, Z.; Yuan, F.; Rao, Z.; Gao, G. F. Construct design, biophysical, and biochemical characterization of the fusion core from mouse hepatitis virus (a coronavirus) spike protein. Protein Expr Purif 2004, 38 (1), 116-122.
(59) Supekar, V. M.; Bruckmann, C.; Ingallinella, P.; Bianchi, E.; Pessi, A.; Carfi, A. Structure of a proteolytically resistant core from the severe acute respiratory syndrome coronavirus S2 fusion protein. Proc Natl Acad Sci U S A 2004, 101 (52), 17958-17963.
(60) Xia, S.; Liu, M.; Wang, C.; Xu, W.; Lan, Q.; Feng, S.; Qi, F.; Bao, L.; Du, L.; Liu, S.; et al. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res 2020, 30 (4), 343-355.
(61) Jiang, S.; Zhang, X.; Du, L. Therapeutic antibodies and fusion inhibitors targeting the spike protein of SARS-CoV-2. Expert Opin Ther Targets 2021, 25 (6), 415-421.
(62) Lamers, M. M.; Haagmans, B. L. SARS-CoV-2 pathogenesis. Nat Rev Microbiol 2022, 20 (5), 270-284.
(63) Mohseni Afshar, Z.; Barary, M.; Hosseinzadeh, R.; Alijanpour, A.; Hosseinzadeh, D.; Ebrahimpour, S.; Nazary, K.; Sio, T. T.; Sullman, M. J. M.; Carson-Chahhoud, K.; et al. Breakthrough SARS-CoV-2 infections after vaccination: a critical review. Hum Vaccin Immunother 2022, 18 (5), 2051412.
(64) Taylor, P. C.; Adams, A. C.; Hufford, M. M.; de la Torre, I.; Winthrop, K.; Gottlieb, R. L. Neutralizing monoclonal antibodies for treatment of COVID-19. Nat Rev Immunol 2021, 21 (6), 382-393.
(65) Casadevall, A.; Pirofski, L. A. The convalescent sera option for containing COVID-19. J Clin Invest 2020, 130 (4), 1545-1548.
(66) Harvey, W. T.; Carabelli, A. M.; Jackson, B.; Gupta, R. K.; Thomson, E. C.; Harrison, E. M.; Ludden, C.; Reeve, R.; Rambaut, A.; Consortium, C.-G. U.; et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 2021, 19 (7), 409-424.
(67) Rodrigues, L.; Bento Cunha, R.; Vassilevskaia, T.; Viveiros, M.; Cunha, C. Drug Repurposing for COVID-19: A Review and a Novel Strategy to Identify New Targets and Potential Drug Candidates. Molecules 2022, 27 (9).
(68) Hoshino, Y.; Lee, H.; Miura, Y. Interaction between synthetic particles and biomacromolecules: fundamental study of nonspecific interaction and design of nanoparticles that recognize target molecules. Polym J 2014, 46 (9), 537-545.
(69) Whitty, A.; Kumaravel, G. Between a rock and a hard place? Nat Chem Biol 2006, 2 (3), 112-118.
(70) Lo Conte, L.; Chothia, C.; Janin, J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999, 285 (5), 2177-2198.
(71) Fuller, J. C.; Burgoyne, N. J.; Jackson, R. M. Predicting druggable binding sites at the protein-protein interface. Drug Discov Today 2009, 14 (3-4), 155-161.
(72) Jones, S.; Thornton, J. M. Principles of protein-protein interactions. Proc Natl Acad Sci U S A 1996, 93 (1), 13-20.
(73) Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001, 46 (1-3), 3-26.
(74) Wells, J. A.; McClendon, C. L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450 (7172), 1001-1009.
(75) Clackson, T.; Wells, J. A. A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267 (5196), 383-386.
(76) Bogan, A. A.; Thorn, K. S. Anatomy of hot spots in protein interfaces. J Mol Biol 1998, 280 (1), 1-9.
(77) Scott, D. E.; Bayly, A. R.; Abell, C.; Skidmore, J. Small molecules, big targets: drug discovery faces the protein-protein interaction challenge. Nat Rev Drug Discov 2016, 15 (8), 533-550.
(78) Labbe, C. M.; Laconde, G.; Kuenemann, M. A.; Villoutreix, B. O.; Sperandio, O. iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions. Drug Discov Today 2013, 18 (19-20), 958-968.
(79) Arkin, M. R.; Wells, J. A. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 2004, 3 (4), 301-317.
(80) Rao, V. S.; Srinivas, K.; Sujini, G. N.; Kumar, G. N. Protein-protein interaction detection: methods and analysis. Int J Proteomics 2014, 2014, 147648.
(81) Uetz, P.; Giot, L.; Cagney, G.; Mansfield, T. A.; Judson, R. S.; Knight, J. R.; Lockshon, D.; Narayan, V.; Srinivasan, M.; Pochart, P.; et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403 (6770), 623-627.
(82) Fields, S.; Song, O. A novel genetic system to detect protein-protein interactions. Nature 1989, 340 (6230), 245-246.
(83) Adelmant, G.; Garg, B. K.; Tavares, M.; Card, J. D.; Marto, J. A. Tandem Affinity Purification and Mass Spectrometry (TAP-MS) for the Analysis of Protein Complexes. Curr Protoc Protein Sci 2019, 96 (1), e84.
(84) Rigaut, G.; Shevchenko, A.; Rutz, B.; Wilm, M.; Mann, M.; Seraphin, B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 1999, 17 (10), 1030-1032.
(85) Lin, J. S.; Lai, E. M. Protein-Protein Interactions: Co-Immunoprecipitation. Methods Mol Biol 2017, 1615, 211-219.
(86) Cooley, R.; Kara, N.; Hui, N. S.; Tart, J.; Roustan, C.; George, R.; Hancock, D. C.; Binkowski, B. F.; Wood, K. V.; Ismail, M.; et al. Development of a cell-free split-luciferase biochemical assay as a tool for screening for inhibitors of challenging protein-protein interaction targets. Wellcome Open Res 2020, 5, 20.
(87) England, C. G.; Ehlerding, E. B.; Cai, W. NanoLuc: A Small Luciferase Is Brightening Up the Field of Bioluminescence. Bioconjug Chem 2016, 27 (5), 1175-1187.
(88) Lee, R. K.; Li, T. N.; Chang, S. Y.; Chao, T. L.; Kuo, C. H.; Pan, M. Y.; Chiou, Y. T.; Liao, K. J.; Yang, Y.; Wu, Y. H.; et al. Identification of Entry Inhibitors against Delta and Omicron Variants of SARS-CoV-2. Int J Mol Sci 2022, 23 (7).
(89) Dougherty, P. G.; Qian, Z.; Pei, D. Macrocycles as protein-protein interaction inhibitors. Biochem J 2017, 474 (7), 1109-1125.
(90) Al-Wahaibi, L. H.; Mostafa, A.; Mostafa, Y. A.; Abou-Ghadir, O. F.; Abdelazeem, A. H.; Gouda, A. M.; Kutkat, O.; Abo Shama, N. M.; Shehata, M.; Gomaa, H. A. M.; et al. Discovery of novel oxazole-based macrocycles as anti-coronaviral agents targeting SARS-CoV-2 main protease. Bioorg Chem 2021, 116, 105363.
(91) Hein, C. D.; Liu, X. M.; Wang, D. Click chemistry, a powerful tool for pharmaceutical sciences. Pharm Res 2008, 25 (10), 2216-2230.
(92) Hein, J. E.; Fokin, V. V. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) and beyond: new reactivity of copper(I) acetylides. Chem Soc Rev 2010, 39 (4), 1302-1315.
(93) Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B. A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes. Angew Chem Int Ed Engl 2002, 41 (14), 2596-2599.
(94) Rabet, P. T.; Fumagalli, G.; Boyd, S.; Greaney, M. F. Benzylic C-H Azidation Using the Zhdankin Reagent and a Copper Photoredox Catalyst. Org Lett 2016, 18 (7), 1646-1649.
(95) Zeng, H. Y.; Tian, Q.; Shao, H. W. PEG 400 promoted nucleophilic substitution reaction of halides into organic azides under mild conditions. Green Chem Lett Rev 2011, 4 (3), 281-287.
(96) Muraca, A. C. A.; Raminelli, C. Exploring Possible Surrogates for Kobayashi's Aryne Precursors. ACS Omega 2020, 5 (5), 2440-2457.
(97) Maddani, M.; Prabhu, K. R. A chemoselective aerobic oxidation of benzylic azides catalyzed by molybdenum xanthate in an aqueous medium. Tetrahedron Lett 2008, 49 (29-30), 4526-4530.
(98) Bortolato, T.; Simionato, G.; Vayer, M.; Rosso, C.; Paoloni, L.; Benetti, E. M.; Sartorel, A.; Leboeuf, D.; Dell'Amico, L. The Rational Design of Reducing Organophotoredox Catalysts Unlocks Proton-Coupled Electron-Transfer and Atom Transfer Radical Polymerization Mechanisms. J Am Chem Soc 2023, 145 (3), 1835-1846.
(99) Lenstra, D. C.; Lenting, P. E.; Mecinovic, J. Sustainable organophosphorus-catalysed Staudinger reduction. Green Chem 2018, 20 (19), 4418-4422.
(100) Sakurai, K.; Snyder, T. M.; Liu, D. R. DNA-templated functional group transformations enable sequence-programmed synthesis using small-molecule reagents. J Am Chem Soc 2005, 127 (6), 1660-1661.