Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing.
We show that comprehensive sequence-function maps obtained by deep sequencing can be used to reprogram interaction specificity and to leapfrog over bottlenecks in affinity maturation by combining many individually small contributions not detectable in conventional approaches. We use this approach to optimize two computationally designed inhibitors against H1N1 influenza hemagglutinin and, in both cases, obtain variants with subnanomolar binding affinity. The most potent of these, a 51-residue protein, is broadly cross-reactive against all influenza group 1 hemagglutinins, including human H2, and neutralizes H1N1 viruses with a potency that rivals that of several human monoclonal antibodies, demonstrating that computational design followed by comprehensive energy landscape mapping can generate proteins with potential therapeutic utility.
Department of Biochemistry, University of Washington, Seattle, Washington, USA.
Timothy A
TA
Whitehead
Aaron
A
Chevalier
Yifan
Y
Song
Cyrille
C
Dreyfus
Sarel J
SJ
Fleishman
Cecilia
C
De Mattos
Chris A
CA
Myers
Hetunandan
H
Kamisetty
Patrick
P
Blair
Ian A
IA
Wilson
David
D
Baker
D000818:Animals; D000998:Antiviral Agents / Q000737:chemistry* / Q000494:pharmacology*; D002470:Cell Survival / Q000187:drug effects; D019295:Computational Biology; D004285:Dogs; D055808:Drug Discovery / Q000379:methods*; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry* / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D053118:Influenza A Virus, H1N1 Subtype / Q000187:drug effects* / Q000378:metabolism; D061985:Madin Darby Canine Kidney Cells; D008958:Models, Molecular; D009500:Neutralization Tests; D011485:Protein Binding; D055672:Static Electricity; D013816:Thermodynamics
D000998:Antiviral Agents; C543345:H1N1 virus hemagglutinin; D019267:Hemagglutinin Glycoproteins, Influenza Virus