吡咯-咪唑聚酰胺的质子化状态研究

吡咯-咪唑聚酰胺分子是一类可自行透过细胞膜，进入细胞核，通过非共价氢键的作用高亲和力和高序列特异性与DNA小沟结合的药物分子，具有干预基因转录、调控基因表达的生物功能。研究表明，一个靶向雄激素反应元件的聚酰胺分子在对转移性去势抵抗性前列腺癌的药物——恩杂鲁胺产生耐药性的细胞模型和异种移植动物模型中都有着显著的抑制效果，在晚期前列腺癌的治疗中有着重大的应用前景，目前已经进入临床一期的研究中。

百分之九十以上的药物为弱酸/弱碱性分子，弱酸/弱碱性药物分子的质子化程度决定了其离子型、分子型药物的占比，直接关系到药物的溶解性、脂溶性等参数，可以预测药物在体内的吸收、分布、代谢和排除等药代动力学过程。吡咯-咪唑聚酰胺药物分子结构中包含羧酸、叔胺及N-甲基咪唑等可电离的基团，其质子化程度取决于自身的酸度解离常数和所处环境的pH值。故而准确测量聚酰胺分子的酸度解离常数对于揭示这类分子在生理环境中的具体存在形式和质子化程度有着重大意义。

测定酸度解离常数的常见手段包含：电化学滴定、紫外-可见光滴定，核磁共振、毛细管电泳法等。本文选用操作简单、准确性和重复性高的电位滴定法，测定聚酰胺分子的各个酸度解离常数，并且着重研究其N-甲基咪唑位点解离常数的序列特异性及分子构型特异性。然后通过对酸度解离常数与pH的函数计算，总结出在不同pH环境下聚酰胺分子的各种阳离子型、分子型、阴离子型之间的相互转化以及各物种的占比。进而推测在透过细胞膜，进入细胞核的过程生物中，聚酰胺分子的物种分布及比例。对后续指导聚酰胺分子的临床用药及递送方法、揭示其作用机制、研究其药代动力学性质等提供了新的参考思路。

Pyrrole-imidazole polyamides are a class of small molecules that penetrate cell membrane, access cell nucleus, and bind to the minor groove of DNA via non-covalent hydrogen bonds in high affinities and sequence specificities. They possess various biological functions, such as inhibiting gene transcription and manipulating gene expression. As shown in recent studies, pyrrole-imidazole polyamides which target androgen reaction element are effective in the treatment of metastatic castration-resistant prostate cancer in Enzalutamide-resistant cell lines and xenograft animal models. A pyrrole-imidazole polyamide molecule, which targets promoter of Androgen Receptor (AR)-initiated signaling pathway of prostate cancer, has been developed as a drug candidate, and entered phase I of clinical research.

Over ninety percent of drugs are weak acids or bases. The protonation degree of weak acids/bases determinates the proportion of ionic and molecular species, which are directly related to the solubility and lipid distribution of drugs. Furthermore, the protonation degree can influence the absorption, distribution, metabolism and elimination of drugs in vivo. Pyrrole-imidazole polyamides contain several ionizable functional groups, including carboxylic acid, tertiary amine and N-methylimidazole. The protonation degree of polyamides can be reflected by acid dissociation constants and the pH values in solution. Therefore, the accurate measurement of the acidity dissociation constant of pyrrole-imidazole polyamides, especially the N-methylimidazole subgroup, is of great value to reveal the ionic forms and protonation degree in the physiological environment.

There are many methods to determinate the acid dissociation constants, such as potentiometric titration, UV-Visible spectrophotometry titration, nuclear magnetic resonance, capillary electrophoresis, among others. In this study, an easy-operating potentiometric titration was used to determine the acid dissociation constants of polyamides with high accuracy and reproducibility. In addition, the impact of peptide sequence and molecular shape on the dissociation constants of N-methylimidazole moieties was evaluated. Then by calculating the function of acid dissociation constant and pH, the mutual conversion between species (cationic, neutral and anionic) at different pH environments were presented. Moreover, the species distribution and proportion of polyamides in the process of penetrating cell membrane and accessing nucleus were summarized. This study provides a guidance of pharmacokinetic properties and delivery of polyamides, paving the road for biological applications of this class of powerful molecules

[1] MRKSIH M, WADE, WS, DWYER TJ, et al. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin [J]. Proc Natl Acad Sci U S A, 1992, 89(16): 7586-7590.

[2] COLL M, FREDERICK CA, WANG AH, et al. A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin [J]. Proc Natl Acad Sci U S A, 1987, 84(23): 8385-8389.

[3] KOPKA ML, YOON C, GOODSELL D, et al. The molecular origin of DNA-drug specificity in netropsin and distamycin [J]. Proc Natl Acad Sci U S A, 1985, 82(5): 1376-1380.

[4] KIELKOPF CL, BAIRD EE, DERVAN PB, et al. Structural basis for G.C recognition in the DNA minor groove [J]. Nat Struct Biol, 1998, 5(2): 104-109.

[5] WHITE S, SZEWCZYK JW, TURNER JM, et al. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands [J]. Nature, 1998, 391(6666): 468-471.

[6] DERVAN PB, EDELSON BS. Recognition of the DNA minor groove by pyrrole-imidazole polyamides [J]. Curr Opin Struct Bio, 2003, 13(3): 284-299.

[7] CHENOWETH DM, HARKI DA, DERVAN PB. Solution-phase synthesis of pyrrole-imidazole polyamides [J]. J Am Chem Soc, 2009, 131(20): 7175-7181.

[8] CHO J, PARKS ME, DERVAN PB. Cyclic polyamides for recognition in the minor groove of DNA [J]. Proc Natl Acad Sci U S A, 1995, 92(22): 10389-10392.

[9] MRKSICH M, DERVAN PB. Design of a covalent peptide heterodimer for sequence-specific recognition in the minor groove of double-helical DNA [J]. J Am Chem Soc, 1994, 116(8): 3663-3664.

[10] HECKEL A, DERVAN PB. U-pin polyamide motif for recognition of the DNA minor groove [J]. Chem Eur J, 2003, 9(14): 3353-3366.

[11] HIRATA A, NOKIHARA K, KAWAMOTO Y, et al. Structural evaluation of tandem hairpin pyrrole-imidazole polyamides recognizing human telomeres [J]. J Am Chem Soc, 2014, 136(32): 11546-11554.

[12] HAWKINS CA, CLAIRAC DRP, Dominey RN, et al. Controlling binding orientation in hairpin polyamide DNA complexes [J]. J Am Chem Soc, 2000, 122(22): 5235-5243.

[13] HIROSE Y, ASAMITSU S, BANDO T, et al. Control of forward/reverse orientation preference of cyclic pyrrole-imidazole polyamides [J]. J Am Chem Soc, 2019, 141(33): 13165-13170.

[14] XU L, WANG W, GOTTE D, et al. RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif [J]. Proc Natl Acad Sci U S A, 2016, 113(44): 12426-12431.

[15] JACOBS CS, DERVAN PB. Modifications at the C-terminus to improve pyrrole-imidazole polyamide activity in cell culture [J]. J Med Chem, 2009, 52(23): 7380-7388.

[16] DERVAN PB, EDELSON BS. Recognition of the DNA minor groove by pyrrole-imidazole polyamides [J]. Curr Opin Struct Bio, 2003, 13(3): 284-299.

[17] SIEGEL RL, MILLER KD, FUCHS HE, et al. Cancer statistics, 2021 [J]. CA-Cancer J Clin, 2021, 71(1): 7-33.

[18] 邓波, 胡自力. 去势抵抗性前列腺癌药物治疗的研究现状和进展 [J]. 世界最新医学信息文摘, 2020, 20(32): 160-161.

[19] NICKOLS NG, DERVAN PB. Suppression of androgen receptor-mediated gene expression by a sequence-specific DNA-binding polyamide [J]. Proc Natl Acad Sci U S A, 2007, 104(25): 10418-10423.

[20] Yang F, Nickols NG, Li BC, et al. Antitumor activity of a pyrrole-imidazole polyamide [J]. Proc Natl Acad Sci U S A, 2013, 110(5): 1863-1868.

[21] Yang F, Nickols NG, Li BC, et al. Animal toxicity of hairpin pyrrole-imidazole polyamides varies with the turn unit [J]. J Med Chem, 2013, 56(18): 7449-7457.

[22] HARGROVE AE, MARTINEZ TF, HARE AA, et al. Tumor repression of VCaP xenografts by a pyrrole-imidazole polyamide [J]. PLoS One, 2015, 10(11): e0143161.

[23] KURMIS AA, YANG F, WELCH TR, et al. A Pyrrole-imidazole polyamide is active against Enzalutamide-resistant prostate cancer [J]. Cancer Res, 2017, 77(9): 2207-2212.

[24] KURMIS AA, DERVAN PB. Sequence specific suppression of androgen receptor-DNA binding in vivo by a Py-Im polyamide [J]. Nucleic Acids Res, 2019, 47(8): 3828-3835.

[25] DICKINSON LA, GULIZIA RJ, TRAUGER JW, et al. Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands [J]. Proc Natl Acad Sci U S A, 1998, 95(22): 12890-12895.

[26] MATSUDA H, FUKUDA N, UENO T, et al. Transcriptional inhibition of progressive renal disease by gene silencing pyrrole-imidazole polyamide targeting of the transforming growth factor-beta1 promoter [J]. Kidney Int, 2011, 79(1): 46-56.

[27] MATSUDA H, FUKUDA N, UENO T, et al. Development of gene silencing pyrrole-imidazole polyamide targeting the TGF-beta1 promoter for treatment of progressive renal diseases [J]. J Am Soc Nephrol, 2006, 17(2): 422-432.

[28] YAO EH, FUKUDA N, UENO T, et al. Novel gene silencer pyrrole-imidazole polyamide targeting lectin-like oxidized low-density lipoprotein receptor-1 attenuates restenosis of the artery after injury [J]. Hypertension, 2008, 52(1): 86-92.

[29] KAWAMOTO Y, BANDO T, SUGIYAMA H. Sequence-specific DNA binding pyrrole-imidazole polyamides and their applications [J]. Bioorg Med Chem, 2018, 26(8): 1393-1411.

[30] KAWAMOTO Y, SASAKI A, CHANDRAN A, et al. Targeting 24 bp within telomere repeat sequences with tandem tetramer pyrrole-imidazole polyamide probes [J]. J Am Chem Soc, 2016, 138(42): 14100-14107.

[31] LI BC, MONTGOMERY DC, PUCKETT JW, et al. Synthesis of cyclic py-im polyamide libraries [J]. J Org Chem, 2013, 78(1): 124-133.

[32] CHENG Z, WANG W, WU CL, et al. Novel pyrrole-imidazole polyamide hoechst conjugate suppresses epstein-barr virus replication and virus-positive tumor growth [J]. J Med Chem, 2018, 61(15): 6674-6684.

[33] MORINAGA H, BANDO T, TAKAGAKI T, et al. Cysteine cyclic pyrrole-imidazole polyamide for sequence-specific recognition in the DNA minor groove [J]. J Am Chem Soc, 2011, 133(46): 18924-18930.

[34] SUENDERHAUF C, HAMMANN F, HUWYLER J. Computational prediction of blood-brain barrier permeability using decision tree induction [J]. Molecules, 2012, 17(9): 10429-10445.

[35] KERNS EH, DI L. Physicochemical profiling: overview of the screens [J]. Drug Discov Today Technol, 2004, 1(4): 343-348.

[36] AVDEEF A. Physicochemical profiling (solubility, permeability and charge state) [J]. Curr Top Med Chem, 2001, 1(4): 277-351.

[37] MANALLACK DT. The pKa distribution of drugs: application to drug discovery [J]. Perspect Med Chem, 2007: 25-38.

[38] HENDERSON LJ. Concerning the relationship between the strength of acids and their capacity to preserve neutrality [J]. Am J Physiol , 1908, 21(2): 173-179.

[39] SÖRENSON SSP. Enzymstudien. II: Mitteilung. Über die messung und die bedeutung der wasserstoffionenkoncentration bei enzymatischen prozessen. [J]. Biochemische Zeitschrift, 1909, 21: 131–200.

[40] HASSELBALCH KA. Die Berechnung der Wasserstoffzahl des blutes aus der freien und gebundenen kohlensäure desselben, und die sauerstoffbindung des blutes als funktion der wasserstoffzahl [J]. Biochemische Zeitschrift, 1916, 78: 112–144.

[41] REIJENGA J, VAN HA, VAN LA, et al. Development of methods for the determination of pKa values [J]. Anal Chem Insights, 2013, 8: 53-71.

[42] 张兰, 陈国南, 方禹之. 毛细管电泳-电化学检测法用于生物碱电离常数线性模型的研究 [J]. 化学学报, 2004, 62(10): 975-978.

[43] BEZENCON J, WITTWER MB, CUTTING B, et al. pKa determination by (1)H NMR spectroscopy - an old methodology revisited [J]. J Pharm Biomed Anal, 2014, 93: 147-155.

[44] QIANG Z, ADAMS C. Potentiometric determination of acid dissociation constants (pKa) for human and veterinary antibiotics [J]. Water Res, 2004, 38(12): 2874-2890.

[45] BELTRÁN JL, SANLI N, FONRODONA G, et al. Spectrophotometric, potentiometric and chromatographic pKa values of polyphenolic acids in water and acetonitrile–water media [J]. Analytica Chimica Acta, 2003, 484(2): 253-264.

[46] FANG LJ, YAO G, PAN Z, et al. Fully automated synthesis of DNA-binding py-im polyamides using a triphosgene coupling strategy [J]. Org Lett, 2015, 17(1): 158-161.

[47] CHENOWETH DM, HARKI DA, DERVAN PB. Oligomerization route to py-im polyamide macrocycles [J]. Org Lett, 2009, 11(16): 3590-3593.

[48] HEINRICH B, VAZQUEZ O. 4-methyltrityl-protected pyrrole and imidazole building blocks for solid phase synthesis of DNA-binding polyamides [J]. Org Lett, 2020, 22(2): 533-536.

[49] SANNA D, UGONE V, MICERA G, et al. Speciation in human blood of Metvan, a vanadium based potential anti-tumor drug [J]. Dalton Trans, 2017, 46(28): 8950-8967.

[50] CATALAN J, CLARAMUNT RM, ELGUERO J, et al. Basicity and acidity of azoles: the annelation effect in azoles [J]. J Am Chem Soc, 2002, 110(13): 4105-4111.

[51] HIDAKA T, PANDIAN GN, TANIGUCHI J, et al. Creation of a synthetic ligand for mitochondrial DNA sequence recognition and promoter-specific transcription suppression [J]. J Am Chem Soc, 2017, 139(25): 8444-8447.

[52] DOHERTY GJ, MCMAHON HT. Mechanisms of endocytosis [J]. Annu Rev Biochem, 2009, 78: 857-902.