Original articles
Lei Wang, Mary C. Casey, Sanjeev Kumar V. Vernekar, Rajkumar Lalji Sahani, Karen A. Kirby, Haijuan Du, Huanchun Zhang, Philip R. Tedbury, Jiashu Xie, Stefan G. Sarafianos, Zhengqiang Wang. Novel PF74-like small molecules targeting the HIV-1 capsid protein: Balance of potency and metabolic stability[J]. Acta Pharmaceutica Sinica B, 2021, 11(3): 810-822

Novel PF74-like small molecules targeting the HIV-1 capsid protein: Balance of potency and metabolic stability
Lei Wanga,d, Mary C. Caseyb, Sanjeev Kumar V. Vernekara, Rajkumar Lalji Sahania, Karen A. Kirbyc, Haijuan Duc, Huanchun Zhangc, Philip R. Tedburyc, Jiashu Xiea, Stefan G. Sarafianosc, Zhengqiang Wanga
a Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
b Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA;
c Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
d Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
Of all known small molecules targeting human immunodeficiency virus (HIV) capsid protein (CA), PF74 represents by far the best characterized chemotype, due to its ability to confer antiviral phenotypes in both early and late phases of viral replication. However, the prohibitively low metabolic stability renders PF74 a poor antiviral lead. We report herein our medicinal chemistry efforts toward identifying novel and metabolically stable small molecules targeting the PF74 binding site. Specifically, we replaced the inter-domain-interacting, electron-rich indole ring of PF74 with less electron-rich isosteres, including imidazolidine-2,4-dione, pyrimidine-2,4-dione, and benzamide, and identified four potent antiviral compounds (10, 19, 20 and 26) with markedly improved metabolic stability. Compared to PF74, analog 20 exhibited similar submicromolar potency, and much longer (51-fold) half-life in human liver microsomes (HLMs). Molecular docking corroborated that 20 binds to the PF74 binding site, and revealed distinct binding interactions conferred by the benzamide moiety. Collectively, our data support compound 20 as a promising antiviral lead.
Key words:    HIV-1    Capsid protein    PF74    Microsomal stability   
Received: 2020-06-17     Revised: 2020-07-08
DOI: 10.1016/j.apsb.2020.07.016
Funds: This research was supported by the National Institute of Allergy and Infectious Diseases, the National Institutes of Health, USA, grant number R01AI120860 (to Stefan G. Sarafianos and Zhengqiang Wang). We thank the Minnesota Supercomputing Institute (Minneapolis, MN, USA) for molecular modeling resources.
Corresponding author: Zhengqiang Wang     Email:wangx472@umn.edu
Author description:
PDF(KB) Free
Lei Wang
Mary C. Casey
Sanjeev Kumar V. Vernekar
Rajkumar Lalji Sahani
Karen A. Kirby
Haijuan Du
Huanchun Zhang
Philip R. Tedbury
Jiashu Xie
Stefan G. Sarafianos
Zhengqiang Wang

1. AIDSinfo. FDA-approved HIV medicines. March 2020. Available from: https://aidsinfo.nih.gov/understanding-hiv-aids/fact-sheets/21/ 58/fda-approved-hiv-medicines.
2. Ndung’u T, McCune JM, Deeks SG. Why and where an HIV cure is needed and how it might be achieved. Nature 2019;576:397-405.
3. Davenport MP, Khoury DS, Cromer D, Lewin SR, Kelleher AD, Kent SJ. Functional cure of HIV: the scale of the challenge. Nat Rev Immunol 2019;19:45-54.
4. Carnes SK, Sheehan JH, Aiken C. Inhibitors of the HIV-1 capsid, a target of opportunity. Curr Opin HIV AIDS 2018;13:359-65.
5. Thenin-Houssier S, Valente ST. HIV-1 capsid inhibitors as antiretroviral agents. Curr HIV Res 2016;14:270-82.
6. Zhang JY, Liu XY, de Clercq E. Capsid (CA) protein as a novel drug target: recent progress in the research of HIV-1 CA inhibitors. Mini Rev Med Chem 2009;9:510-8.
7. Ganser BK, Li S, Klishko VY, Finch JT, Sundquist WI. Assembly and analysis of conical models for the HIV-1 core. Science 1999;283: 80-3.
8. Li S, Hill CP, Sundquist WI, Finch JT. Image reconstructions of helical assemblies of the HIV-1 CA protein. Nature 2000;407:409-13.
9. Freed EO. HIV-1 assembly, release and maturation. Nat Rev Microbiol 2015;13:484-96.
10. Fassati A. Multiple roles of the capsid protein in the early steps of HIV-1 infection. Virus Res 2012;170:15-24.
11. Le Sage V, Mouland AJ, Valiente-Echeverria F. Roles of HIV-1 capsid in viral replication and immune evasion. Virus Res 2014;193:116-29.
12. Novikova M, Zhang Y, Freed EO, Peng K. Multiple roles of HIV-1 capsid during the virus replication cycle. Virol Sin 2019;34:119-34.
13. Campbell EM, Hope TJ. HIV-1 capsid: the multifaceted key player in HIV-1 infection. Nat Rev Microbiol 2015;13:471-83.
14. Gao D, Wu J, Wu YT, Du F, Aroh C, Yan N, et al. Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses. Science 2013;341:903-6.
15. Lahaye X, Satoh T, Gentili M, Cerboni S, Conrad C, Hurbain I, et al. The capsids of HIV-1 and HIV-2 determine immune detection of the viral cDNA by the innate sensor cGAS in dendritic cells. Immunity 2013;39:1132-42.
16. Ganser-Pornillos BK, Yeager M, Sundquist WI. The structural biology of HIV assembly. Curr Opin Struct Biol 2008;18:203-17.
17. Sundquist WI, Krausslich HG. HIV-1 assembly, budding, and maturation. Cold Spring Harb Perspect Med 2012;2:a006924.
18. Byeon IJ, Meng X, Jung J, Zhao G, Yang R, Ahn J, et al. Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell 2009;139:780-90.
19. Rankovic S, Ramalho R, Aiken C, Rousso I. PF74 reinforces the HIV-1 capsid to impair reverse transcription-induced uncoating. J Virol 2018;92: e00845-18.
20. Forshey BM, von Schwedler U, Sundquist WI, Aiken C. Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication. J Virol 2002;76:5667-77.
21. Yamashita M, Engelman AN. Capsid-dependent host factors in HIV-1 infection. Trends Microbiol 2017;25:741-55.
22. Sayah DM, Sokolskaja E, Berthoux L, Luban J. Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1. Nature 2004;430:569-73.
23. Stremlau M, Owens CM, Perron MJ, Kiessling M, Autissier P, Sodroski J. The cytoplasmic body component TRIM5a restricts HIV-1 infection in Old World monkeys. Nature 2004;427:848-53.
24. Achuthan V, Perreira JM, Sowd GA, Puray-Chavez M, McDougall WM, Paulucci-Holthauzen A, et al. Capsid-CPSF6 interaction licenses nuclear HIV-1 trafficking to sites of viral DNA integration. Cell Host Microbe 2018;24:392-404 e8.
25. Bejarano DA, Peng K, Laketa V, Borner K, Jost KL, Lucic B, et al. HIV-1 nuclear import in macrophages is regulated by CPSF6-capsid interactions at the nuclear pore complex. Elife 2019;8:e41800.
26. Woodward CL, Prakobwanakit S, Mosessian S, Chow SA. Integrase interacts with nucleoporin NUP153 to mediate the nuclear import of human immunodeficiency virus type 1. J Virol 2009;83:6522-33.
27. Matreyek KA, Yucel SS, Li X, Engelman A. Nucleoporin NUP153 phenylalanine-glycine motifs engage a common binding pocket within the HIV-1 capsid protein to mediate lentiviral infectivity. PLoS Pathog 2013;9:e1003693.
28. Buffone C, Martinez-Lopez A, Fricke T, Opp S, Severgnini M, Cifola I, et al. Nup153 unlocks the nuclear pore complex for HIV-1 nuclear translocation in nondividing cells. J Virol 2018;92: e00648-18.
29. Dharan A, Talley S, Tripathi A, Mamede JI, Majetschak M, Hope TJ, et al. KIF5B and Nup358 cooperatively mediate the nuclear import of HIV-1 during infection. PLoS Pathog 2016;12:e1005700.
30. Meehan AM, Saenz DT, Guevera R, Morrison JH, Peretz M, Fadel HJ, et al. A cyclophilin homology domain-independent role for Nup358 in HIV-1 infection. PLoS Pathog 2014;10:e1003969.
31. Fricke T, White TE, Schulte B, de Souza Aranha Vieira DA, Dharan A, Campbell EM, et al. MxB binds to the HIV-1 core and prevents the uncoating process of HIV-1. Retrovirology 2014;11:68.
32. Xu B, Pan Q, Liang C. Role of MxB in alpha interferon-mediated inhibition of HIV-1 infection. J Virol 2018;92: e00422-18.
33. Franke EK, Yuan HE, Luban J. Specific incorporation of cyclophilin A into HIV-1 virions. Nature 1994;372:359-62.
34. Thali M, Bukovsky A, Kondo E, Rosenwirth B, Walsh CT, Sodroski J, et al. Functional association of cyclophilin A with HIV-1 virions. Nature 1994;372:363-5.
35. Kim K, Dauphin A, Komurlu S, McCauley SM, Yurkovetskiy L, Carbone C, et al. Cyclophilin A protects HIV-1 from restriction by human TRIM5a. Nat Microbiol 2019;4:2044-51.
36. Gres AT, Kirby KA, KewalRamani VN, Tanner JJ, Pornillos O, Sarafianos SG. STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability. Science 2015;349:99-103.
37. Pornillos O, Ganser-Pornillos BK, Kelly BN, Hua Y, Whitby FG, Stout CD, et al. X-ray structures of the hexameric building block of the HIV capsid. Cell 2009;137:1282-92.
38. Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, et al. Mature HIV-1 capsid structure by cryo-electron microscopy and allatom molecular dynamics. Nature 2013;497:643-6.
39. Bhattacharya A, Alam SL, Fricke T, Zadrozny K, Sedzicki J, Taylor AB, et al. Structural basis of HIV-1 capsid recognition by PF74 and CPSF6. Proc Natl Acad Sci U S A 2014;111:18625-30.
40. Ning J, Zhong Z, Fischer DK, Harris G, Watkins SC, Ambrose Z, et al. Truncated CPSF6 forms higher-order complexes that bind and disrupt HIV-1 capsid. J Virol 2018;92: e00368-18.
41. Wu G, Zalloum WA, Meuser ME, Jing L, Kang D, Chen CH, et al. Discovery of phenylalanine derivatives as potent HIV-1 capsid inhibitors from click chemistry-based compound library. Eur J Med Chem 2018;158:478-92.
42. Xu JP, Francis AC, Meuser ME, Mankowski M, Ptak RG, Rashad AA, et al. Exploring modifications of an HIV-1 capsid inhibitor: design, synthesis, and mechanism of action. J Drug Des Res 2018;5:1070.
43. Vernekar SKV, Sahani RL, Casey MC, Kankanala J, Wang L, Kirby KA, et al. Toward structurally novel and metabolically stable HIV-1 capsid-targeting small molecules. Viruses 2020;12:452.
44. Wang L, Casey MC, Vernekar SKV, Do HT, Sahani RL, Kirby KA, et al. Chemical profiling of HIV-1 capsid-targeting antiviral PF74. Eur J Med Chem 2020;200:112427.
45. Sun L, Huang T, Dick A, Meuser ME, Zalloum WA, Chen CH, et al. Design, synthesis and structure—activity relationships of 4-phenyl-1H-1,2,3-triazole phenylalanine derivatives as novel HIV-1 capsid inhibitors with promising antiviral activities. Eur J Med Chem 2020; 190:112085.
46. Sun L, Dick A, Meuser ME, Huang T, Zalloum WA, Chen CH, et al. Design, synthesis, and mechanism study of benzenesulfonamidecontaining phenylalanine derivatives as novel HIV-1 capsid inhibitors with improved antiviral activities. J Med Chem 2020;63: 4790-810.
47. Lazzara PR, Moore TW. Scaffold-hopping as a strategy to address metabolic liabilities of aromatic compounds. RSC Med Chem 2020;11: 18-29.
48. Guengerich FP. Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. Chem Res Toxicol 2001; 14:611-50.
49. Kirchmair J, Goller AH, Lang D, Kunze J, Testa B, Wilson ID, et al. Predicting drug metabolism: experiment and/or computation?. Nat Rev Drug Discov 2015;14:387-404.
50. Xu LH, Liu HT, Murray BP, Callebaut C, Lee MS, Hong A, et al. Cobicistat (GS-9350): a potent and selective inhibitor of human CYP3A as a novel pharmacoenhancer. ACS Med Chem Lett 2010;1:209-13.
51. Zanger UM, Schwab M. Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacol Ther 2013;138:103-41.
52. Wacher VJ, Silverman JA, Zhang Y, Benet LZ. Role of P-glycoprotein and cytochrome P450 3A in limiting oral absorption of peptides and peptidomimetics. J Pharm Sci 1998;87:1322-30.
53. Xu L, Desai MC. Pharmacokinetic enhancers for HIV drugs. Curr Opin Invest Drugs 2009;10:775-86.
54. Cavallo G, Metrangolo P, Milani R, Pilati T, Priimagi A, Resnati G, et al. The halogen bond. Chem Rev 2016;116:2478-601.
55. Lo MC, Aulabaugh A, Jin G, Cowling R, Bard J, Malamas M, et al. Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery. Anal Biochem 2004;332:153-9.
56. Miyazaki Y, Doi N, Koma T, Adachi A, Nomaguchi M. Novel in vitro screening system based on differential scanning fluorimetry to search for small molecules against the disassembly or assembly of HIV-1 capsid protein. Front Microbiol 2017;8:1413.
57. Pantoliano MW, Petrella EC, Kwasnoski JD, Lobanov VS, Myslik J, Graf E, et al. High-density miniaturized thermal shift assays as a general strategy for drug discovery. J Biomol Screen 2001;6:429-40.
58. Adachi A, Gendelman HE, Koenig S, Folks T, Willey R, Rabson A, et al. Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. J Virol 1986;59:284-91.
59. Schrödinger. Schrödinger small-molecule drug discovery suite 2019-1. New York, NY, USA: Schrödinger LLC.; 2019.
60. Schrödinger. Schrödinger release 2019-1. New York, NY, USA: Maestro, Schrödinger LLC.; 2019.
61. Sastry GM, Adzhigirey M, Day T, Annabhimoju R, Sherman W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 2013;27: 221-34.
62. Jorgensen WL, Maxwell DS, TiradoRives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118:11225-36.
63. Schrödinger. Schrödinger release 2019-1. New York, NY, USA: LigPrep, Schrödinger LLC.; 2019.
64. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47: 1739-49.
Similar articles: