Computationally Designed Peptides for Zika Virus Detection: An Incremental Construction Approach

Abstract

Herein, and in contrast to current production of anti-Zika virus antibodies, we propose a semi-combinatorial virtual strategy to select short peptides as biomimetic antibodies/binding agents for the detection of intact Zika virus (ZIKV) particles. The virtual approach was based on generating different docking cycles of tetra, penta, hexa, and heptapeptide libraries by maximizing the discrimination between the amino acid motif in the ZIKV and dengue virus (DENV) envelope protein glycosylation site. Eight peptides, two for each length (tetra, penta, hexa, and heptapeptide) were then synthesized and tested vs. intact ZIKV particles by using a direct enzyme linked immunosorbent assay (ELISA). As a reference, we employed a well-established anti-ZIKV antibody, the antibody 4G2. Three peptide-based assays had good detection limits with dynamic range starting from 105 copies/mL of intact ZIKV particles; this was one order magnitude lower than the other peptides or antibodies. These three peptides showed slight cross-reactivity against the three serotypes of DENV (DENV-1, -2, and -3) at a concentration of 106 copies/mL of intact virus particles, but the discrimination between the DENV and ZIKV was lost when the coating concentration was increased to 107 copies/mL of the virus. The sensitivity of the peptides was tested in the presence of two biological matrices, serum and urine diluted 1:10 and 1:1, respectively. The detection limits decreased about one order of magnitude for ZIKV detection in serum or urine, albeit still having for two of the three peptides tested a distinct analytical signal starting from 106 copies/mL, the concentration of ZIKV in acute infection.

Antiviral Peptides: Identification and Validation

“…Tetra, penta, hexa and heptapeptide libraries were docked using Open Eye Scientific Software against envelope protein of ZIKV; subsequently, eight peptides were selected. They were further tested by Direct ELISA and out of them, three were delineated with best performance for Zika detection (Mascini et al 2019). Another method is based on peptidomimetics which mimics the designed targets, prevents the interaction of proteins by competitive binding.…”

Peptide-Based Flavivirus Biosensors: From Cell Structure to Virological and Serological Detection Methods

“…Epitope arrangement may be impacted by the conformational epitope during its production and preparation. 98 Peptides fall into two categories: artificial/synthetic and natural. They are found in the human body as hormones, neurotransmitters, or immunomodulators.…”

“…However, due to its lower likelihood of allosteric changes, linear peptide during immunoassay may be a more practical and reproducible option than secondary or tertiary ones. Epitope arrangement may be impacted by the conformational epitope during its production and preparation …”

“…Given that ZIKV concentrations during infection can reach around 1 × 10 6 copies/mL, these peptides may be suitable for distinguishing between ZIKV and DENV at physiological levels. Despite the matrix impacting assay performance, detection limits were reduced by 1 order of magnitude, maintaining a distinct analytical signal starting at 10 6 copies/mL for two out of the three peptides tested …”

“…Despite the matrix impacting assay performance, detection limits were reduced by 1 order of magnitude, maintaining a distinct analytical signal starting at 10 6 copies/mL for two out of the three peptides tested. 98 Kim et al 120 explored potential peptide aptamers in their study, screening 25 candidates and selecting KRAVVSCAEA with the lowest energy and highest binding affinity to the envelope protein. Although the envelope protein is a primary target, certain conditions can enhance infection efficiency by inducing subneutralizing antibodies.…”