In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein

Abstract

Aptamers are single-stranded, short DNA or RNA oligonucleotides that can specifically bind to various target molecules. To diagnose the infected cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in time, numerous conventional methods are applied for viral detection via the amplification and quantification of DNA or antibodies specific to antigens on the virus. Herein, we generated a large number of mutated aptamer sequences, derived from a known sequence of receptor-binding domain (RBD)-1C aptamer, specific to the RBD of SARS-CoV-2 spike protein (S protein). Structural similarity, molecular docking, and molecular dynamics (MD) were utilized to screen aptamers and characterize the detailed interactions between the selected aptamers and the S protein. We identified two mutated aptamers, namely, RBD-1CM1 and RBD-1CM2, which presented better docking results against the S protein compared with the RBD-1C aptamer. Through the MD simulation, we further confirmed that the RBD-1CM1 aptamer can form the most stable complex with the S protein based on the number of hydrogen bonds formed between the two biomolecules. Based on the experimental data of quartz crystal microbalance (QCM), the RBD-1CM1 aptamer could produce larger signals in mass change and exhibit an improved binding affinity to the S protein. Therefore, the RBD-1CM1 aptamer, which was selected from 1431 mutants, was the best potential candidate for the detection of SARS-CoV-2. The RBD-1CM1 aptamer can be an alternative biological element for the development of SARS-CoV-2 diagnostic testing.

Diagnostic and neutralizing aptamers technology against Sars-Cov-2

“…First, the majority of newly developed aptamers above for SARS-CoV-2 have not gone through in vivo or clinical sample testing. A small portion of aptamers only passed in silico simulation [13,27,35,39]. In real clinical samples, aptamers may not be well performed because of high renal clearance, toxicity, metabolic instability, non-specific immune activation, and high demand for chemical modifications, which impede the final approval for commercial use [33].…”

“…Its key feature, the Spike protein (S protein), is composed of three promoters and each has 2 domains, S1 and S2 [8,12]. S1 carries the receptor-binding domain (RBD, 319-541 residues) that binds to the human ACE2 receptor and is critically considered as an ideal drug target to block this binding site and subsequent infection actions, and the S2 domain is for virus-host membrane fusion [8,12,13]. Different variants are highly mutant, especially in the N-terminus domain and RBD of S protein.…”

“…First, Lin et al [13] ameliorate Song et al's aptamer products [25] into a more stable and selective aptamer, RBD-1CM1, using an in silico method. The computational selection involved structure similarity, docking, and MD simulations, which all pointed to the improved aptamer-spike protein interactions due to the increased hydrogen bond formation among 11 key amino acids in the spike protein.…”

OligoBinders: Bioengineered Soluble Amyloid-like Nanoparticles to Bind and Neutralize SARS-CoV-2

“…These reagents include antibodies, peptides, small molecules, and DNA aptamers. 8 , 9 However, except for antibodies, these molecules tend to exhibit moderate binding affinity.…”

“…The virus entry in host cells is mediated by the interaction between the receptor binding domain (RBD) from viral spike (S) protein and the cell surface angiotensin-converting enzyme 2 receptor (ACE2r) expressed by nasal ciliated cells, pneumocytes, exocrine pancreas, intestinal tract, seminal vesicle, epididymis, proximal renal tubules, heart muscle, and thyroid gland. − As the first step in the viral replication cycle, developing neutralizing agents that interfere with the S protein–ACE2r interaction has gained significant interest. These reagents include antibodies, peptides, small molecules, and DNA aptamers. , However, except for antibodies, these molecules tend to exhibit moderate binding affinity.…”