蛋白质药物的分子设计
袁杰 靳征 苏冬梅 娄竞

沈阳三生制药有限责任公司，辽宁沈阳，110027；

摘要：随着 X 射线晶体学、核磁共振光谱学及生物信息学的发展，蛋白质分子结构测定速度加快，PDB 蛋白质结构数据库已收载 18 万个生物大分子晶体结构数据，为蛋白质药物分子设计提供基础。蛋白质药物分子设计基于蛋白质静态与动态结构分析及功能关联，现有策略包括提高活性、稳定性、特异性，降低免疫原性，延长体内半衰期等，方法有一级结构改造、化学修饰、翻译后修饰、融合蛋白等，且AI技术与生物信息学软件推动了改造后蛋白质结构预测与评价，助力新型药物开发。在设计优势方面，通过对半胱氨酸改造、优化分子内相互作用、降低蛋白酶水解敏感性等可提高药物稳定性；通过置换游离半胱氨酸、翻译后与化学修饰、突变表面氨基酸、增加短肽等能增加溶解性；借助糖基化修饰、聚乙二醇化修饰（分随机与定点修饰）、融合蛋白等可改善药代动力学性质；合理设计可改变蛋白质与相互作用分子的亲和力和特异性以改善生物学活性；通过人源化改造（嵌合抗体、改型抗体）、聚乙二醇化、改善溶液性质等能降低免疫原性。在现状上，2012-2021年FDA批准新药中蛋白质药物占比24.18%，2021年FDA、欧盟、日本批准新药中蛋白质药物或抗体类靶向药物占比均较高，未来药品需求将增长，审批改革与AI技术应用将推动蛋白质药物分子设计发展。

关键词：蛋白质药物分子设计；AI技术；FDA批准

参考文献

[1] Burley SK, Berman HM, Kleywegt GJ, et al. Protein Data Bank (PDB): the singele global maromolecular structure archive[J]. Methods in molecular biology, 2017,1607:627-641.

[2] Burley SK, Bhikadiya C, Bi C, et al. RCSB Protein Data Bank: celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D[J]. Protein science: a publication of the protein society, 2022, 31(1):187-208.

[3] Marshall SA, Lazar GA, Chirino AJ, et al. Rational design and engineering of therapeutic proteins[J]. Drug discovery today, 2003,8(5):212-221.

[4] Xia X, Kumru OS, Blaber SI, et al. Engineering a cysteine-free form of human fibroblast growth factor-1 for “second generation” therapeutic application[J]. Journal of pharmaceutical sciences, 2016, 105(4):1444-1453.

[5] Xia X, Longo LM, Blaber M. Mutation choice to eliminate buried free cysteines in protein therapeutics[J]. Joural of pharmaceutical sciences, 2015,104(2):566-576.

[6] Ishikawa M, lijima H, Statake-Ishikawa R, et al. The substitution of cysteine 17 of recombinant human G-CSF with alanine greatly enhanced its stability[J]. Cell structure and function, 1992,17(1):61-65.

[7] Ma H, O Fagain C, O’Kennedy R. Unravelling enhancement of antibody fragement stability-role of format structure and cysteine modification[J]. Journal of immunological methods, 2019,464:57-63.

[8] Filikov AV, Hayes RJ, Luo P, et al. Computational stabilization of human growth hormone[J]. Protein science: a publication of the protein society, 2002,11(6):1452-1461.

[9] Pipe SW, Kaufman RJ. Characterization of a genetically engineered inactivation-resistant coagulation factor VIIIa[J]. Proceedings of the national academy of sciences of the United States of America, 1997, 94(22):11851-11856.

[10] Du F, Kruziki MA, Zudock EJ, et al. Engineering an EGFR-binding Gp2 domain for increased hydrophilicity[J]. Biotechnology and bioengineering, 2019,116(3):526-535.

[11] Nautiyal K, Kibria MG, Akazawa-Ogawa Y, et al. Design and assessment of an active anti-epidermal growth factor receptor (EGFR) single chain variable fragement (ScFv) with improved solubility[J]. Biochemical and biophysical research communications, 2019,508(4): 1043-1049.

[12] Nautiyal K, Kuroda Y. A SEP tag enhances the expression, solubility and yield of recombinant TEV protease without altering its activity[J]. New biotechnology, 2018,42:77-84.

[13] Song K, Yoon IS, Kim NA, et al. Glycoengineering of interferon-β1a improves its biophysical and pharmacokinetic properties[J]. Plos one, 2014,9(5): e96967.

[14] Ibbotson T, Goa KL. Darbepoetin alfa[J]. Drugs, 2001,61(14):2097-2104.

[15] Locatelli F, Vecchio LD. Darbepoetin alfa. Amgen[J]. Current opinion in investigational drugs, 2001,2(8):1097-1104.

[16] Macdougall IC, Padhi D, Jang G. Pharmacology of darbepoetin alfa[J]. Nephrology, dialysis, transplantation, 2007,22(4): iv2-iv9.

[17] Cases A. Darbepoetin alfa: a noval erythropoiesis-stimulating protein[J]. Drugs of today, 2003,39(7):477-495.

[18] Joy MS. Darbepoetin alfa: a noval erythropoiesis-stimulating protein[J]. The annals of pharmacotherapy, 2002,36(7-8):1183-1192.

[19] Markham A. Ibalizumab: first global approval[J]. Drugs, 2018,78(7):781-785.

[20] Chahine EB, Durham SH. Ibalizumab: the first monoclonal antibody for the treatment of HIV-1 infection[J]. The annals of pharmacotherapy, 2021,55(2):230-239.

[21] Rizza RA, Bhatia R, Zeuli J, et al. Ibalizumab for the treatment of multidrug-resistant HIV-1 infection[J]. Drugs today, 2019,55(1):25-34.

[22] Song R, Oren DA, Franco D, et al. Strategic addition of an N-linked glycan to a monoclonal antibody improves its HIV-1 neutralizing activity[J]. Nature biotechnology, 2013,31(11):1047-1052.

[23] Toma J, Weinheimer SP, Stawiski E, et al. Loss of asparagine-linked glycosylation sites in variable region 5 of human immunodeficiency virus type 1 envelope is associated with resistance to CD4 antibody ibalizumab[J]. Journal of virology, 2011,85(8):3872-3880.

[24] Majjhoo A, Kumar A, Zdains M, et al. Comparison of two corticosteroid pre-infusion regiments for pegloticase in the United States: a retrospective analysis in community rheumatology practices[J]. Drugs – real world outcomes, 2019,6(4):165-171.

[25] Hershfield MS, Ganson NJ, Kelly SJ, et al. Induced and pre-existing anti-polyethylene glycol antibody in a trial of every 3-week dosing of pegloticase for refractory gout, including in organ transplant recipients[J]. Arthritis research & therapy, 2014,16(2): R63.

[26] Sherman MR, Saifer MG, Perez-Ruiz F. PEG-uricase in the management of treatment-resistant gout and hyperuricemia[J]. Advanced drug delivery reviews, 2008,60(1):59-68.

[27] Zhang C, Fan K, Luo H, et al. Characterization, efficacy, pharmacokinetics, and biodistribution of 5kDa mPEG modified tetrameric canine uricase variant[J]. International journal of pharmaceutics, 2012,430(1-2):307-317.

[28] Zhang C, Fan K, Ma X, et al. Impact of large aggregated uricases and PEG diol on accelerated blood clearance of PEGylated canine uricase[J]. Plos one, 2012,7(6): e39659.

[29] Li H, Huo J, Sun D, et al. Determination of PEGylation homogeneity of polyethylene glycol-modified canine uricase[J]. Electrophoresis, 2021,42(6):693-699.

[30] Molineux G. The design and development of pegfilgrastim (PEG-rmetHuG-CSF, Neulasta) [J]. Current pharmaceutical design, 2004,10(11):1235-1244.

[31] Crawford J. Once-per-cycle pegfilgrastim (Neulasta) for the management of chemotherapy-induced neutropenia[J]. Seminars in oncology, 2003,30(4 Suppl 13):24-30.

[32] Lee A, Scott LJ. Certolizumab pegol: a review in moderate to severe plaque psoriasis[J]. Biodrugs, 2020,34(2):235-244.

[33] Goel N, Stephens S. Certolizumab pegol[J]. Mabs, 2010,2(2):137-147.

[34] Deeks ED. Certolizumab pegol: a review in inflammatory autoimmune diseases[J]. Biodrugs, 2016,30(6):607-617.

[35] Acosta-Felquer ML, Rosa J, Soriano ER. An evidence-based review of certolizumab pegol in the treatment of active psoriatic arthritis: place in therapy[J]. Open access rheumatology, 2016,30(8):37-44.

[36] Mitoma H, Horiuchi T, Tsukamoto H, et al. Molecular mechanisms of action of anti-TNF-α agents – comparison among therapeutic TNF-α antagonists[J]. Cytokine, 2018,101(1):56-63.

[37] Gottlieb AB, Blauvelt A, Thaci D, et al. Certolizumab pegol for the treatment of chronic plaque psoriasis: results through 48 weeks from 2 phase 3, multicenter, randomized, double-blinded, placebo-controlled studies (CIMPASI-1 and CIMPASI-2) [J]. Journal of the American academy of dermatology, 2018,79(2):302-314.

[38] Lebwohl M, Blauvelt A, Paul C, et al. Certolizumab pegol for the treatment of chronic plaque psoriasis: result through 48 weeks of a phase 3, multicenter, randomized, double-blind, etanercept and placebo-controlled study (CIMPACT), 2018,79(2):266-276.

[39] Nikravesh FY, Shirkhani S, Bayat E, et al. Extension of human GCSF serum half-life by the fusion of albumin binding[J]. Scientific reports, 2022,12(1):667.

[40] Venkateswarlu D. Role of hydrophobic mutations on the binding affinity and stability of blood coagulation factor VIIIa: a computational molecular dynamics and free-energy analysis[J]. Biochemical and biophysical research communications, 2014,450(1):735-740.

[41] Clackson T, Ultsch MH, Wells JA, et al. Structural and functional analysis of the 1:1 growth hormone: receptor complex reveals the molecular basis for receptor affinity[J]. Journal of molecular biology, 1998,277(5):1111-1128.

[42] Campara M, Shord SS, Haaf CM. Single-dose rasburicase for tumour lysis syndrome in adults: weight-based approach[J]. Journal of clinical pharmacy and therapeutics, 2009,34(2):207-2013.

[43] Knoebel RW, Lo M, Crank CW. Evaluation of a low, weight-based dose of rasburicase in adult patients for the treatment or prophylaxis of tumor lysis syndrome[J]. Journal of oncology pharmacy practice, 2011,17(3):147-154.

[44] Tatay VS, Castilla JD, Ponce JM, et al. Rasburicase versus allopurinol in the treatment of hyperuricaemia in tumour lysis syndrome[J]. Randomized controlled trial, 2010,72(2):103-110.

[45] Allen KC, Champlain AH, Cotliar JA, et al. Risk of anaphylaxis with repeated courses of rasburicase: a research on adverse drug events and reports (RADAR) project[J]. Drug safety, 2015,38(2):183-187.

[46] Cheuk DK, Chiang AK, Chan GC, et al. Urate oxidase for the prevention and treatment of tumour lysis syndrome in children with cancer[J]. The cochrane database of systematic reviews, 2017,3(3): CD006945.

[47] Strand V, Balsa A, AI-Saleh J, et al. Immunogenicity of biologics in chronic inflammatory diseases: a systematic review[J]. Biodrugs, 2017,31(4):299-316.

[48] Gorovits B, Baltrukonis DJ, Bhattacharya I, et al. Immunoassay methods used in clinical studies for the detection of anti-drug antibodies to adalimumab and infliximab[J]. Clinical and experimental immunology, 2018,192(3):348-365.

[49] Padron IM, Garcia JG, Diaz RR, et al. Anti-drug antibodies anti-trastuzumab in the treatment of breast cancer[J]. Journal of oncology pharmacy practice, 2021,27(6):1354-1356.

[50] Richette P, Garay R. Novel drug discovery strategies for gout[J]. Expert opinion on drug discovery, 2013,8(2): 183-189.