Applications of protein engineering in pharmaceutical industry

doi:10.12211/2096-8280.2024-061

Abstract

Abstract:

Protein engineering carries out specific design and modification of proteins by means of directed evolution, semi-rational or rational design, computer-assisted design, and so on. The engineered proteins, with improved properties, have significant application value in food, medicine, fuel and material industries. In the field of pharmaceutical and chemical industry, engineered enzymes can serve as efficient biocatalysts for the synthesis of active pharmaceutical ingredients (API) and their intermediates, aligning with the concepts and principles of green chemistry and achieving green manufacturing. In terms of the biopharmaceutical industry, the engineering of peptide or protein modifying enzymes can boost the efficiency in preparing drug candidates, while engineered diagnostic enzymes can make detection more accurate and sensitive. Moreover, protein engineering can improve the bioactivities of biological drugs such as therapeutic enzymes and antibodies, increase drug stability and mitigate immunogenicity, improving the developability, safety and efficacy of drug. Here, we briefly review the tremendous progress of protein engineering, elucidate its importance in the research and development of chemically derived drugs and biologics, and provide examples of its applications. These application examples encompass the discovery of enzymes or antibodies, the process of protein engineering, and the subsequent economic advantages. We aim to showcase the practical implementation of protein engineering in the pharmaceutical industry and facilitate technology transfer, thereby fostering seamless integration between research, development, and industry. Furthermore, we discuss the challenges such as cost-effectiveness and market changes in the synthesis of API, and multi-objective optimization, long cycle and high risk in the discovery and development of biopharmaceuticals. Finally, we look forward to the prospects of protein engineering in pharmaceutical industry. In the future, the automated pipeline consisting artificial intelligence and self-driving laboratory will accelerate design-build-test-learn cycle, leading to rapid progress in molecular design and discovery.

Key words: protein engineering, biocatalysis, chemical pharmaceutical industry, biopharmaceutical industry, artificial intelligence

摘要：

蛋白质工程，通过定向进化、半理性或理性设计、计算机辅助设计等手段，实现对蛋白质特定功能的设计和改造，获得的工程化蛋白质在食品、医药、能源、材料等行业具有重要的应用价值。在医药化工领域，工程化酶可作为化学原料药及其中间体合成的高效生物催化剂，实现医药工业绿色制造。在生物制药领域，多肽或蛋白修饰酶的改造可显著提升候选药物的制备效率，诊断酶的改造则可以大幅增强检测的准确性和灵敏度。此外，蛋白质工程在提升治疗性酶和治疗性抗体等生物制剂的生物活性、增强药物稳定性、降低免疫原性等方面也发挥重要角色，从而提高药物的可开发性、安全性和有效性。因此，本文简要回顾了蛋白质工程的发展历程，具体阐述了其在化学原料药合成和生物制药两大产业中的一系列应用实例，旨在剖析蛋白质工程在科技成果转化及医药产业应用中存在的问题与挑战，并展望医药产业中蛋白质工程的未来发展方向，以期为促进产学研一体化发展提供借鉴。

关键词: 蛋白质工程, 生物催化, 医药化工, 生物制药, 人工智能

CLC Number:

Q816

Yanhua WEN, Hedong LIU, Chunlai CAO, Ruibo WU. Applications of protein engineering in pharmaceutical industry[J]. Synthetic Biology Journal, DOI: 10.12211/2096-8280.2024-061.

温艳华, 刘合栋, 曹春来, 巫瑞波. 蛋白质工程在医药产业中的应用[J]. 合成生物学, DOI: 10.12211/2096-8280.2024-061.

Figures/Tables 7

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酶	来源	蛋白质工程策略	应用	效益
转氨酶ATA-117	Arthrobacter sp.	底物游走、随机突变、ProSAR、理性设计	西格列汀酮→西格列汀^[54]	收率↑，产量↑ 生产成本↓，废料↓
转氨酶S6	Chromobacterium violaceum	底物游走、迭代饱和突变、随机突变	CGRP受体拮抗剂rimegepant中间体的合成^[61]	活性↑，转化率↑
酰基转移酶LovD	Aspergillus terreus	ProSAR、半理性设计	莫那可林J→辛伐他汀^{[68, 73]}	活性↑，稳定性↑ 反应步骤↓，有毒试剂↓，酰基供体用量↓
酮还原酶	Candida magnoliae	DNA shuffling	阿托伐他汀中间体羟基腈的合成^[76]	活性↑，稳定性↑，E因子↑，体积生产率↑
葡萄糖脱氢酶	Bacillus subtilis Bacillus megaterium
卤代醇脱卤酶	Agrobacterium sp.
酰胺酶Pa-Ami	Pantoea sp.	理性设计、通道改造	2-氯烟酰胺→2-氯烟酸^{[85, 89, 91]}	底物载量↑，转化率↑，时空收率↑
单胺氧化酶MAON	Aspergillus niger	随机突变、半理性设计	抗病毒药波塞普韦中间体的合成^[92]	活性↑，稳定性↑，收率↑ 原材料↓，用水量↓

酶	来源	蛋白质工程策略	应用	效益
转氨酶ATA-117	Arthrobacter sp.	底物游走、随机突变、ProSAR、理性设计	西格列汀酮→西格列汀^[54]	收率↑，产量↑ 生产成本↓，废料↓
转氨酶S6	Chromobacterium violaceum	底物游走、迭代饱和突变、随机突变	CGRP受体拮抗剂rimegepant中间体的合成^[61]	活性↑，转化率↑
酰基转移酶LovD	Aspergillus terreus	ProSAR、半理性设计	莫那可林J→辛伐他汀^{[68, 73]}	活性↑，稳定性↑ 反应步骤↓，有毒试剂↓，酰基供体用量↓
酮还原酶	Candida magnoliae	DNA shuffling	阿托伐他汀中间体羟基腈的合成^[76]	活性↑，稳定性↑，E因子↑，体积生产率↑
葡萄糖脱氢酶	Bacillus subtilis Bacillus megaterium
卤代醇脱卤酶	Agrobacterium sp.
酰胺酶Pa-Ami	Pantoea sp.	理性设计、通道改造	2-氯烟酰胺→2-氯烟酸^{[85, 89, 91]}	底物载量↑，转化率↑，时空收率↑
单胺氧化酶MAON	Aspergillus niger	随机突变、半理性设计	抗病毒药波塞普韦中间体的合成^[92]	活性↑，稳定性↑，收率↑ 原材料↓，用水量↓

酶/抗体	来源	蛋白质工程策略	应用	效益
青霉素G 酰化酶	Kluyvera cryocrescens	定向进化	胰岛素特定位置的保护和脱保护^[113]	位置选择性↑，催化活性↑
果糖肽氧化酶	Eupenicillium terrenum	理性设计、定点突变	糖尿病诊断^[118]	催化活性↑，催化特异性↑
纤维蛋白溶解酶	Homo sapiens	丙氨酸扫描^[151]、定点突变、理性设计	治疗急性心肌梗死的抗凝剂^{[127, 128]}	纤维蛋白特异性↑，耐受内源蛋白酶降解能力↑，半衰期↑
尿酸氧化酶	mammals	DNA shuffling	治疗高尿酸血症和痛风^[132]	活性↑，免疫原性↓，半衰期↑
尿酸氧化酶	Candida utilis	理性设计	治疗高尿酸血症和痛风的候选口服药物^[133]	胰酶和肠液稳定性↑，半衰期↑
纳米抗体K922	大羊驼免疫噬菌体文库筛选	DNA shuffling	减少大肠杆菌引起的仔猪腹泻^[138]	胃液和肠液稳定性↑

酶/抗体	来源	蛋白质工程策略	应用	效益
青霉素G 酰化酶	Kluyvera cryocrescens	定向进化	胰岛素特定位置的保护和脱保护^[113]	位置选择性↑，催化活性↑
果糖肽氧化酶	Eupenicillium terrenum	理性设计、定点突变	糖尿病诊断^[118]	催化活性↑，催化特异性↑
纤维蛋白溶解酶	Homo sapiens	丙氨酸扫描^[151]、定点突变、理性设计	治疗急性心肌梗死的抗凝剂^{[127, 128]}	纤维蛋白特异性↑，耐受内源蛋白酶降解能力↑，半衰期↑
尿酸氧化酶	mammals	DNA shuffling	治疗高尿酸血症和痛风^[132]	活性↑，免疫原性↓，半衰期↑
尿酸氧化酶	Candida utilis	理性设计	治疗高尿酸血症和痛风的候选口服药物^[133]	胰酶和肠液稳定性↑，半衰期↑
纳米抗体K922	大羊驼免疫噬菌体文库筛选	DNA shuffling	减少大肠杆菌引起的仔猪腹泻^[138]	胃液和肠液稳定性↑

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