International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh.
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh.
Molecules. 2022 Mar 17;27(6):1936. doi: 10.3390/molecules27061936.
species account for the second-leading cause of deaths due to diarrheal diseases among children of less than 5 years of age. The emergence of multi-drug-resistant isolates and the lack of availability of vaccines have led to the pertinence in the efforts made for the development of new therapeutic strategies against shigellosis. Consequently, designing small-interfering RNA (siRNA) candidates against such infectious agents represents a novel approach to propose new therapeutic candidates to curb the rampant rise of anti-microbial resistance in such pathogens. In this study, we analyzed 264 conserved sequences from 15 different conserved virulence genes of sp., through extensive rational validation using a plethora of first-generation and second-generation computational algorithms for siRNA designing. Fifty-eight siRNA candidates were obtained by using the first-generation algorithms, out of which only 38 siRNA candidates complied with the second-generation rules of siRNA designing. Further computational validation showed that 16 siRNA candidates were found to have a substantial functional efficiency, out of which 11 siRNA candidates were found to be non-immunogenic. Finally, three siRNA candidates exhibited a sterically feasible three-dimensional structure as exhibited by parameters of nucleic acid geometry such as: the probability of wrong sugar puckers, bad backbone confirmations, bad bonds, and bad angles being within the accepted threshold for stable tertiary structure. Although the findings of our study require further wet-lab validation and optimization for therapeutic use in the treatment of shigellosis, the computationally validated siRNA candidates are expected to suppress the expression of the virulence genes, namely: IpgD (siRNA 9) and OspB (siRNA 15 and siRNA 17) and thus act as a prospective tool in the RNA interference (RNAi) pathway. However, the findings of our study require further wet-lab validation and optimization for regular therapeutic use for treatment of shigellosis.
志贺氏菌属是导致 5 岁以下儿童腹泻病死亡的第二大主要原因。多药耐药株的出现和疫苗的缺乏，使得针对志贺氏菌病开发新治疗策略的努力变得至关重要。因此，针对这些感染性病原体设计小干扰 RNA（siRNA）候选物代表了提出新的治疗候选物以遏制此类病原体中抗微生物耐药性猖獗的新方法。在这项研究中，我们通过广泛使用第一代和第二代计算算法进行 siRNA 设计的合理性验证，分析了来自 15 个不同保守毒力基因的 264 个保守序列。使用第一代算法获得了 58 个 siRNA 候选物，其中只有 38 个 siRNA 候选物符合 siRNA 设计的第二代规则。进一步的计算验证表明，有 16 个 siRNA 候选物具有显著的功能效率，其中 11 个 siRNA 候选物是非免疫原性的。最后，有三个 siRNA 候选物表现出可行的三维结构，这是由核酸几何参数表现出来的，例如：错糖凸起的概率、不良的骨架确认、不良的键和不良的角度都在稳定三级结构的可接受阈值内。虽然我们的研究结果需要进一步的湿实验室验证和优化，以用于治疗志贺氏菌病的治疗，但经过计算验证的 siRNA 候选物有望抑制毒力基因的表达，即：IpgD（siRNA9）和 OspB（siRNA15 和 siRNA17），并因此成为 RNA 干扰（RNAi）途径的有前途的工具。然而，我们的研究结果需要进一步的湿实验室验证和优化，以用于治疗志贺氏菌病的常规治疗。
