Ryan Dennis

Mr. Ryan Dennis

orcid

Research Focus & Metrics

Academic Career Length

1Year (2026-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
21 October 2026 in Preprints.org
Verified
Preprint
Open access
PDF file
MAMohammed Alshahrani
Mohammed Alshahrani
LTLucas Turano
Lucas Turano
BFBrandon Foley
Brandon Foley
RDRyan Dennis
Ryan Dennis
WGWill Gatlin
Will Gatlin
Gennady VerkhivkerGennady Verkhivker
Gennady Verkhivker
Broadly neutralizing antibodies targeting the silent face of the SARS-CoV-2 receptor-binding do-main (RBD) provide essential templates for pan-sarbecovirus therapeutics, yet the precise bio-physical mechanisms dictating their neutralization breadth, energetic propensities, and escape re-silience remain unresolved. By combining all-atom and coarse-grained molecular dynamics, systematic mutational scanning, rigorous MM-GBSA binding free energy analysis, and residue interaction network modeling we delineate the comparative structural, energetic, and allosteric signatures of Site V (CC25.4, CC25.43, CC25.56, 7D6, 6D6 ) and CR3022-site (Group 1: CC25.54, CC84.2, CC84.24) antibodies. We discover that these two classes by engaging spatially opposite faces of the RBD fold produce mutually exclusive energetic hotspot modules. Site V antibodies are anchored along a surface-exposed lateral ridge by residues R355, R357, R466, I468, F464, and K462, whereas CR3022-site antibodies engage a buried β-sheet-core module comprising R408, K378, C379, Y380, F377, and Q414. Remarkably, despite these distinct epitopes, both classes converge on an ultra-conserved paratope tyrosine triad (Y99, Y100, Y49), establishing a universal structural motif for silent-face recognition. Network centrality modeling demonstrates that Site V and CR3022-site antibodies modulate ACE2 receptor interface dynamics via distinct upstream allo-steric pathways that converge on shared RBM-loop relays at Y423, Y396, and F464. Crucially, in CR3022-site antibodies, binding free energy hotspots and allosteric communication hubs coincide directly within the structurally constrained β-sheet core. This enforces a dual-constraint mecha-nism where escape mutations inherently compromise viral fold integrity. Conversely, Site V binding hotspots and allosteric networks are structurally segregated, exposing cryptic allosteric liabilities where mutations at non-contact positions (F456, R509) dynamically rewire network communication to impair neutralization without altering static interface affinity. Furthermore, within-class resilience is governed by epitope architecture: focused antibodies (CC25.56, 6D6, CC25.54) concentrate binding energy into single dominant anchors vulnerable to point mutations, whereas broad antibodies (CC84.2, CC84.24, CC25.4, CC25.43) distribute binding energetics across multi-residue contact networks. These quantitative findings align directly with experimental neutralization data. The structural immutability of the β-sheet-core module provides a mechanistic explanation for why CR3022-site antibodies CC84.2 and CC84.24 retain activity against highly evasive Omicron sublineages BA.2.86 and JN.1. A complete absence of energetic or allosteric hotspots at major Class 1/2 escape loci explains the cross-variant breadth exhibited by both si-lent-face classes. By establishing how silent-face antibodies balance potency, breadth, and resili-ence, this work offers a predictive biophysical framework for tracking viral antigenic drift and designing durable, multi-epitope antibody cocktails.