Engineering Antiviral Agents via Surface Plasmon Resonance

Summary

The present protocol describes new tools for SPR binding assays to examine CV-N binding to HA, S glycoprotein, related hybrid-type glycans, and high-mannose oligosaccharides. SPR is used to determine the K_D for binding either dimeric or monomeric CV-N to these glycans.

Abstract

Surface plasmon resonance (SPR) is used to measure hemagglutinin (HA) binding to domain-swapped Cyanovirin-N (CV-N) dimer and to monitor interactions between mannosylated peptides and CV-N's high-affinity binding site. Virus envelope spikes gp120, HA, and Ebola glycoprotein (GP) 1,2 have been reported to bind both high- and low-affinity binding sites on dimeric CVN2. Dimannosylated HA peptide is also bound at the two low-affinity binding sites to an engineered molecule of CVN2, which is bearing a high-affinity site for the respective ligand and mutated to replace a stabilizing disulfide bond in the carbohydrate-binding pocket, thus confirming multivalent binding. HA binding is shown to one high-affinity binding site of pseudo-antibody CVN2 at a dissociation constant (K_D) of 275 nM that further neutralizes human immunodeficiency virus type 1 (HIV-1) through oligomerization. Correlating the number of disulfide bridges in domain-swapped CVN2, which are decreased from 4 to 2 by substituting cystines into polar residue pairs of glutamic acid and arginine, results in reduced binding affinity to HA. Among the strongest interactions, Ebola GP1,2 is bound by CVN2 with two high-affinity binding sites in the lower nanomolar range using the envelope glycan without a transmembrane domain. In the present study, binding of the multispecific monomeric CV-N to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein is measured at K_D = 18.6 µM as compared with nanomolar K_D to those other virus spikes, and via its receptor-binding domain in the mid-µ-molar range.

Introduction

Tetherin-associated antiviral activity is induced by interferon-α, and it comprises protein-based tethers, that leads to the retention of fully formed virions on infected cell surfaces¹. The necessity for tetherin glycosylation in the inhibition of virus release remains uncertain, implying the importance of glycosylation patterns on recombinantly expressed glycans for in vitro studies^1,2, which depends on the conformation of (in the case of influenza virus) surface-expressed influenza hemagglutinin HA^3,4. It has be....

Protocol

For the present study, a CVN-small ubiquitin-like modifier (SUMO) fusion protein has been used in enzyme-linked immunosorbent assays instead of CV-N and is suitable for cell-based assays. Recombinant full-length influenza A virus HA H3 protein is obtained commercially (see Table of Materials) or expressed in mammalian HEK293 cell lines and baculovirus-infected insect cells according to standard protocols¹². Wuhan-1 spike protein is expressed in mammalian HEK293 cells. The synthesi.......

Discussion

CV-N's binding affinity is correlated with the number of functional binding sites [2H on domains B, and 2L on domain(s) A when engineered as domain-swapped dimer]. A variant with an altered binding affinity (CVN2L0-V2, a homodimeric stable fold of CV-N comprising a disulfide bridge knock-out) is expressed in E. coli, purified, and positively tested for binding to HA-protein (H3N2) using SPR¹⁰, and shows a conformational change upon binding HA with either H or L carbohydrate-binding si.......

Materials

Name	Company	Catalog Number	Comments
Äkta primeplus	Cytiva
Amicon tubes	Merck	C7715
Ampillicin	Sigma-Aldrich	A5354
Beckmann Coulter Cooler Allegra X-30R centrifuge	Beckman Coulter	B06320
Cell spreader	Sigma-Aldrich	HS86655	silver stainless steel, bar L 33 mm
Custom DNA Oligos	Sigma-Aldrich	OLIGO
Custom Gensynthesis	GenScript	#1390661	cloning vector: pET27b(+)
Cytiva HBS-EP+ Buffer 10, 4x50mL	Thermo Scientific	50-105-5354
Dionex UlitMate 3000	Thermo Scientific	IQLAAAGABHFAPBMBFB
Dpn I restriction enzyme (10 U/μL)	Fisher Scientific	ER1701
DTT	Merck	DTT-RO
EDC	Merck	39391
EDTA	Merck	E9884
Eppendorf Safe-Lock Tubes	Eppendorf	30120086
Eppendorf Safe-Lock Tubes	Eppendorf	30120094
Eppendorf Minispin and MiniSpin Plus personal microcentrifuge	Sigma-Aldrich	Z606235
Ethanol	Merck	51976
Ethanolamine HCl	Merck	E6133
Falcon 50mL Conical Centrifuge Tubes	Fisher Scientific	14-432-22
Falcon 14 mL Round Bottom Polystyrene Test Tube, with Snap Cap, Sterile, 25/Pack	Corning	352057
Glucose	Merck	G8270
Glycine HCl	Merck	55097
HA H3 protein	Abcam	ab69751
HEPES	Merck	H3375
His-select Ni2+	Merck	H0537
Imidazole	Merck	I2399
IPTG	Merck	I6758
Kanamycin A	Sigma-Aldrich	K1377
Kromasil 300-5-C4	Nouryon
LB agar	Merck	52062
LB agar	Merck	19344
LB Lennox	Merck	L3022
Lysozyme	Merck	10837059001
Magnesium chloride	Merck	M8266
Magnesium sulfate	Merck	M7506
NaH2P04	Merck	S0751
NanoDrop UV-Vis2000c spectrophotometer	Thermo Scientific	ND2000CLAPTOP
NaOH	Merck	S5881
NHS	Merck	130672
NZ amine (casein hydrolysate)	Merck	C0626
PBS	Merck	806552
PD MidiTrap G-10	Sigma-Aldrich	GE28-9180-11
Peptone	Merck	70171
pET11a	Merck Millipore (Novagen)	69436
PMSF	Merck	PMSF-RO
QIAprep Spin Miniprep Kit (1000)	Qiagen	27106X4
Reichert Software Package Autolink1-1-9	Reichert
Reichert SPR SR7500DC Dual Channel System	Reichert
Scrubber2-2012-09-04 for data analysis	Reichert
SDS	Merck	11667289001
Site-directed mutagenesis kit incl pUC18 control plasmid	Stratagene	#200518
Sodim chloride	Merck	S9888
Sodium acetate.Trihydrate	Merck	236500
SPR sensor chip C19RBDHC30M	XanTec bioanalytics	SCR C19RBDHC30M
SPR sensor chip CMD500D	XanTec bioanalytics	SCR CMD500D
Sterilin Standard 90mm Petri Dishes	Thermo Scientific	101R20
TBS	Merck	T5912	10x, solution
Triton-X100	Merck	T8787
Tryptone	Merck	93657
Tween20	Merck	P1379
Vortex-Genie 2 Mixer	Merck	Z258423
X-gal	Merck	XGAL-RO
XL1-Blue Supercompetent Cells	Stratagene	#200236
Yeast extract	Merck	Y1625