Structure/Function Analysis of Truncated Amino-Terminal ACE2 Peptide Analogs That Bind to SARS-CoV-2 Spike Glycoprotein

Abstract

The global burden of the SARS-CoV-2 pandemic is thought to result from a high viral transmission rate. Here, we consider mechanisms that influence host cell–virus binding between the SARS-CoV-2 spike glycoprotein (SPG) and the human angiotensin-converting enzyme 2 (ACE2) with a series of peptides designed to mimic key ACE2 hot spots through adopting a helical conformation analogous to the N-terminal α1 helix of ACE2, the region experimentally shown to bind to the SARS-CoV-2 receptor-binding domain (RBD). The approach examines putative structure/function relations by assessing SPG binding affinity with surface plasmon resonance (SPR). A cyclic peptide (c[KFNHEAEDLFEKLM]) was characterized in an α-helical conformation with micromolar affinity (KD = 500 µM) to the SPG. Thus, stabilizing the helical structure of the 14-mer through cyclization improves binding to SPG by an order of magnitude. In addition, end-group peptide analog modifications and residue substitutions mediate SPG binding, with net charge playing an apparent role. Therefore, we surveyed reported viral variants, and a correlation of increased positive charge with increased virulence lends support to the hypothesis that charge is relevant to enhanced viral fusion. Overall, the structure/function relationship informs the importance of conformation and charge for virus-binding analog design.

Application of the Nicoya OpenSPR to Studies of Biomolecular Binding: A Review of the Literature from 2016 to 2022

“…SPR is a powerful tool for real-time, label-free measurement of binding affinity and kinetics, and the vast majority of papers citing the use of the OpenSPR fit neatly underneath this umbrella [ 3 , 5 , 7 , 9 , 15 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 ,…”

“…Several disease states emerge as common areas of study, with many researchers approaching the same problem with the same instrument in different ways. Three disease states frequently studied by OpenSPR users are Alzheimer’s disease [ 43 , 44 , 45 , 46 ], non-small cell lung cancer [ 47 , 48 , 49 , 50 , 51 ], and COVID-19 [ 34 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 ]. An overview of SPR research on these pathologies is included here, to demonstrate the versatility of the instrument on different kinds of biochemical systems, and to show some of the ways that researchers have used OpenSPR measurements of binding affinity and kinetics to solve critical research questions.…”

“…Researchers have used this technique to assess the binding affinity and kinetics of potential new therapeutics and affinity reagents, to study aggregation, to perform competition studies or inhibition assays, and other applications. OpenSPR has been leveraged to study diverse biochemical questions, including critical problems in human health such as Alzheimer’s disease (AD) [ 43 , 44 , 45 , 46 ], non-small cell lung cancer (NSCLC) [ 47 , 48 , 49 , 50 , 51 ], and COVID-19 [ 34 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 ]. This paper provides the first comprehensive review of the literature reporting the use of the OpenSPR.…”

Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers

“…Compared to unmodified L163, the L163 analogs exhibited enhanced stability against pH, plasma, and trypsin degradation. Furthermore, Mackin et al 76 conducted structural and functional analysis of ACE2 peptide analogs targeting the spike glycoprotein of SARS‐CoV‐2. They found that among the N‐terminal modifications of the peptide, succinimide acylation exhibited stronger binding affinity compared to the native ACE2 peptide.…”

Use of Antiandrogens as Therapeutic Agents in COVID-19 Patients

“…Targeting ACE2 was considered the obvious first-choice target for prophylactic and therapeutic interventions aiming to block virus accessibility to respiratory cells early on in infection [97,98]. Several strategies have been evaluated in vitro and in vivo with varied success, including decoy or soluble ACE2 molecules, pseudoligands with a high ACE2 affinity and blocking antibodies [67,99,100].…”