EFFECTS OF CCL2 CHEMOKINE MISSENSE MUTATIONS ON CCR5 RECEPTOR AFFINITY: A COMPUTATIONAL STUDY IN THE CONTEXT OF HIV INFECTION REGULATOR DISCOVERY



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Abstract

Introduction

HIV entry into host cells requires CD4 receptors and CCR5 co-receptors. Natural CCR5 ligands can inhibit HIV through steric blocking and receptor internalization. Although CCL2 is primarily a CCR2 ligand, emerging evidence suggests possible CCR5 interaction, challenging conventional views of chemokine specificity. Natural CCL2 missense mutations provide valuable insights into receptor interaction mechanisms and their potential role in HIV infection modulation, offering new perspectives on viral entry inhibition strategies.

Methods. The wild-type complex was modeled using AlphaFold Server with rigorous validation. From UniProt database, we selected 41 CCL2 mutations within predicted CCR5 binding sites based on structural analysis. For each variant, we generated mutant protein structures and complex models using FoldX algorithm in YASARA environment. We calculated binding energies, complex stability, and interaction energy parameters, while conducting detailed analysis of atomic contacts and hydrogen bonding patterns. Functional impact of mutations was assessed using PolyPhen-2 algorithm.

Results. Molecular modeling identified 35 CCL2 residues forming the comprehensive CCR5 interface. Five specific mutations (P78H, S57C, I28V, N29A, K79A) significantly enhanced CCR5 binding affinity, reducing interaction energy compared to wild type. P78H and S57C variants showed the strongest effects and were consistently predicted as "probably damaging". K79A demonstrated substantially improved binding while maintaining reasonable interfacial contacts. Detailed structural analysis revealed these mutations optimize the binding interface through strategic reorganization of molecular interactions and improved complementarity.

Discussion. Our findings demonstrate that specific natural CCL2 mutations can substantially enhance CCR5 binding affinity, revealing unexpected plasticity in chemokine-receptor recognition systems. The most impactful mutations suggest evolutionary mechanisms for modulating HIV entry pathways through natural genetic variation. These results provide structural insights into how sequence variations might influence viral pathogenesis through altered receptor specificity and binding kinetics.

Conclusion. This computational study identifies key CCL2 mutations that significantly enhance CCR5 binding, expanding our understanding of chemokine system flexibility and evolutionary adaptation. The results support further experimental investigation of natural CCL2 variants as potential modulators of HIV infection and contribute to fundamental knowledge of virus-host interactions at molecular level.

About the authors

Vladimir S. Davydenko

Saint Petersburg Pasteur Institute, St. Petersburg, Russia

Email: vladimir_david@mail.ru
ORCID iD: 0000-0003-0078-9681

Junior Researcher, Laboratory of Immunology and Virology of HIV Infection, PhD Student

Россия, Saint-Petersburg

Alexandr N. Schemelev

Saint Petersburg Pasteur Institute, St. Petersburg, Russia

Email: tvildorm@gmail.com
ORCID iD: 0000-0002-3139-3674

Junior Researcher, Laboratory of Immunology and Virology of HIV Infection

Россия, Saint-Petersburg

Yulia Vladimirovna Ostankova

Saint Petersburg Pasteur Institute, St. Petersburg, Russia

Email: shenna1@yandex.ru
ORCID iD: 0000-0003-2270-8897

PhD (Biology), Head of the Laboratory of immunology and Virology HIV Infection, Senior Researcher of the Laboratory of Molecular Immunology

Россия, Saint-Petersburg

E. V. Anufrieva

Saint Petersburg Pasteur Institute, St. Petersburg, Russia

Email: kate.an21@yandex.ru
ORCID iD: 0009-0002-1882-529X
SPIN-code: 5056-8485

Junior Researcher, Laboratory of Immunology and Virology HIV-Infection, Senior Researcher, Laboratory of Molecular Immunology

Россия, St. Petersburg

A. A. Totolian

Saint Petersburg Pasteur Institute, St. Petersburg, Russia

Author for correspondence.
Email: pasteur@pasteurorg.ru
ORCID iD: 0000-0003-4571-8799

PhD, MD (Medicine), Professor, RAS Full Member, Head of the Laboratory of Molecular Immunology; Director 

St. Petersburg

Россия

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