TY - JOUR

T1 - Enhanced Binding Site Identification in Protein − Ligand Complexes with a Combined Blind Docking and Dipolar Electron Paramagnetic Resonance Approach

AU - Kolokolov, Mikhail

AU - Sannikova, Natalya

AU - Dementev, Sergei

AU - Podarov, Roman

AU - Zhdanova, Kseniya

AU - Bragina, Natal'ya

AU - Chubarov, Alexey

AU - Fedin, Matvey

AU - Krumkacheva, Olesya

PY - 2025/4/11

Y1 - 2025/4/11

N2 - Understanding protein-drug complex structures is crucial for elucidating therapeutic mechanisms and side effects. Blind docking facilitates site identification but is hindered by computational complexity and imprecise scoring, causing ambiguity. Dipolar electron paramagnetic resonance (EPR) provides spin-spin distances but struggles to determine relative positions within complexes. We present a novel approach combining GPU-accelerated blind docking with EPR distance constraints to enhance binding site detection. Our algorithm uses a single EPR distance distribution to filter and validate docking results. Ligand poses from blind docking are clustered, filtered by expected distances, and refined through focused docking. To illustrate our approach, we investigated human serum albumin binding with porphyrin-based photosensitizers used in photodynamic therapy. Combining docking and EPR, we identified possible binding sites, demonstrating that EPR data significantly reduce possible configurations and provide experimentally validated information. This strategy produces a detailed map of photoligand binding sites, revealing that binding may occur away from standard albumin sites and often involves multiple locations. Furthermore, it overcomes key limitations of fluorescence-based methods, which are prone to misinterpretation in albumin studies due to non one-to-one donor-acceptor relationships. By resolving ambiguities in both blind docking and EPR, our framework provides a versatile platform for investigating EPR-active ligands.

AB - Understanding protein-drug complex structures is crucial for elucidating therapeutic mechanisms and side effects. Blind docking facilitates site identification but is hindered by computational complexity and imprecise scoring, causing ambiguity. Dipolar electron paramagnetic resonance (EPR) provides spin-spin distances but struggles to determine relative positions within complexes. We present a novel approach combining GPU-accelerated blind docking with EPR distance constraints to enhance binding site detection. Our algorithm uses a single EPR distance distribution to filter and validate docking results. Ligand poses from blind docking are clustered, filtered by expected distances, and refined through focused docking. To illustrate our approach, we investigated human serum albumin binding with porphyrin-based photosensitizers used in photodynamic therapy. Combining docking and EPR, we identified possible binding sites, demonstrating that EPR data significantly reduce possible configurations and provide experimentally validated information. This strategy produces a detailed map of photoligand binding sites, revealing that binding may occur away from standard albumin sites and often involves multiple locations. Furthermore, it overcomes key limitations of fluorescence-based methods, which are prone to misinterpretation in albumin studies due to non one-to-one donor-acceptor relationships. By resolving ambiguities in both blind docking and EPR, our framework provides a versatile platform for investigating EPR-active ligands.

KW - Electron Spin Resonance Spectroscopy

KW - Ligands

KW - Binding Sites

KW - Humans

KW - Molecular Docking Simulation

KW - Serum Albumin, Human/chemistry

KW - Porphyrins/chemistry

KW - Protein Binding

KW - Photosensitizing Agents/chemistry

KW - Algorithms

UR - https://www.mendeley.com/catalogue/d9b250d1-7cd7-374e-a732-d5fdbca281b5/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-105002395537&origin=inward&txGid=836a79599bfdbb34838547818b52af0a

U2 - 10.1021/jacs.5c01274

DO - 10.1021/jacs.5c01274

M3 - Article

C2 - 40214089

VL - 147

SP - 13677

EP - 13687

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 16

ER -