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Abstract：
BACKGROUND: The Integrase (IN) strand transfer inhibitor (INSTI), Dolutegravir (DTG), has been given the green light to form part of first-line combination antiretroviral therapy (cART) by the World Health Organization (WHO). DTG containing regimens have shown a high genetic barrier against HIV-1 isolates carrying specific resistance mutations when compared with other class of regimens.
METHODS: We evaluated the HIV-1 CRF02_AG IN gene sequences from Cameroon for the presence of resistance-associated mutations (RAMs) against INSTIs and naturally occurring polymorphisms (NOPs), using study sequences (n = 20) and (n = 287) sequences data derived from HIV Los Alamos National Laboratory database. The possible impact of NOPs on protein structure caused by HIV-1 CRF02_AG variations was addressed within the context of a 3D model of the HIV-1 IN complex and interaction analysis was performed using PyMol to validate DTG binding to the Wild type and seven mutant structures.
RESULTS: We observed 12.8% (37/287) sequences to contain RAMs, with only 1.0% (3/287) of the sequences having major INSTI RAMs: T66A, Q148H, R263K and N155H. Of these,11.8% (34/287) of the sequences contained five different IN accessory mutations; namely Q95K, T97A, G149A, E157Q and D232N. NOPs occurred at a frequency of 66% on the central core domain (CCD) position, 44% on the C-terminal domain (CTD) position and 35% of the N-terminal domain (NTD) position. The interaction analysis revealed that DTG bound to DNA, 2MG ions and DDE motif residues for T66A, T97A, Q148H, N155H and R263K comparable to the WT structure. Except for accessory mutant structure E157Q, only one MG contact was made with DTG, while DTG had no MG ion contacts and no DDE motif residue contacts for structure D232N.
CONCLUSIONS: Our analysis indicated that all RAM\'s that resulted in a change in the number of interactions with encompassing residues does not affect DTG binding, while accessory mutations E157Q and D232N could affect DTG binding leading to possible DTG resistance. However, further experimental validation is required to validate the in silico findings of our study.
METHODS: We evaluated the HIV-1 CRF02_AG IN gene sequences from Cameroon for the presence of resistance-associated mutations (RAMs) against INSTIs and naturally occurring polymorphisms (NOPs), using study sequences (n = 20) and (n = 287) sequences data derived from HIV Los Alamos National Laboratory database. The possible impact of NOPs on protein structure caused by HIV-1 CRF02_AG variations was addressed within the context of a 3D model of the HIV-1 IN complex and interaction analysis was performed using PyMol to validate DTG binding to the Wild type and seven mutant structures.
RESULTS: We observed 12.8% (37/287) sequences to contain RAMs, with only 1.0% (3/287) of the sequences having major INSTI RAMs: T66A, Q148H, R263K and N155H. Of these,11.8% (34/287) of the sequences contained five different IN accessory mutations; namely Q95K, T97A, G149A, E157Q and D232N. NOPs occurred at a frequency of 66% on the central core domain (CCD) position, 44% on the C-terminal domain (CTD) position and 35% of the N-terminal domain (NTD) position. The interaction analysis revealed that DTG bound to DNA, 2MG ions and DDE motif residues for T66A, T97A, Q148H, N155H and R263K comparable to the WT structure. Except for accessory mutant structure E157Q, only one MG contact was made with DTG, while DTG had no MG ion contacts and no DDE motif residue contacts for structure D232N.
CONCLUSIONS: Our analysis indicated that all RAM\'s that resulted in a change in the number of interactions with encompassing residues does not affect DTG binding, while accessory mutations E157Q and D232N could affect DTG binding leading to possible DTG resistance. However, further experimental validation is required to validate the in silico findings of our study.
摘要：
背景：整合酶（IN）链转移抑制剂（INSTI），Dolutegravir(DTG),已被世界卫生组织（WHO）批准成为一线联合抗逆转录病毒疗法（cART）的一部分。与其他类型的方案相比，含DTG的方案对携带特定抗性突变的HIV-1分离株具有高遗传屏障。
方法：我们评估了来自喀麦隆的HIV-1CRF02_AGIN基因序列是否存在针对INSTIs的抗性相关突变（RAM）和自然发生的多态性（NOP），使用研究序列（n=20）和（n=287）序列数据来自HIVLosAlamos国家实验室数据库。在HIV-1IN复合物的3D模型的背景下解决了由HIV-1CRF02_AG变异引起的NOP对蛋白质结构的可能影响,并且使用PyMol进行相互作用分析以验证DTG与野生型和七个突变体结构的结合。
结果：我们观察到12.8%(37/287)的序列含有RAM，只有1.0％（3/287）的序列具有主要的INSTIRAM：T66A，Q148H,R263K和N155H。其中,11.8%(34/287)的序列含有五种不同的IN辅助突变；即Q95K，T97A,G149A,E157Q和D232N。NOP在中央核心域（CCD）位置以66％的频率发生，44%位于C端结构域(CTD)位置和35%位于N端结构域(NTD)位置。相互作用分析表明DTG与DNA结合，T66A的2MG离子和DDE基序残基，T97A,Q148H,N155H和R263K与WT结构相当。除了附件突变体结构E157Q，只有一个MG触点与DTG接触，而DTG没有MG离子触点，也没有结构D232N的DDE基序残基触点。
结论：我们的分析表明，所有导致与包含残基相互作用数量变化的RAM都不影响DTG结合，而辅助突变E157Q和D232N可能影响DTG结合，导致可能的DTG抗性。然而,需要进一步的实验验证来验证我们研究的计算机模拟结果.
方法：我们评估了来自喀麦隆的HIV-1CRF02_AGIN基因序列是否存在针对INSTIs的抗性相关突变（RAM）和自然发生的多态性（NOP），使用研究序列（n=20）和（n=287）序列数据来自HIVLosAlamos国家实验室数据库。在HIV-1IN复合物的3D模型的背景下解决了由HIV-1CRF02_AG变异引起的NOP对蛋白质结构的可能影响,并且使用PyMol进行相互作用分析以验证DTG与野生型和七个突变体结构的结合。
结果：我们观察到12.8%(37/287)的序列含有RAM，只有1.0％（3/287）的序列具有主要的INSTIRAM：T66A，Q148H,R263K和N155H。其中,11.8%(34/287)的序列含有五种不同的IN辅助突变；即Q95K，T97A,G149A,E157Q和D232N。NOP在中央核心域（CCD）位置以66％的频率发生，44%位于C端结构域(CTD)位置和35%位于N端结构域(NTD)位置。相互作用分析表明DTG与DNA结合，T66A的2MG离子和DDE基序残基，T97A,Q148H,N155H和R263K与WT结构相当。除了附件突变体结构E157Q，只有一个MG触点与DTG接触，而DTG没有MG离子触点，也没有结构D232N的DDE基序残基触点。
结论：我们的分析表明，所有导致与包含残基相互作用数量变化的RAM都不影响DTG结合，而辅助突变E157Q和D232N可能影响DTG结合，导致可能的DTG抗性。然而,需要进一步的实验验证来验证我们研究的计算机模拟结果.
