LEE- Kimya Mühendisliği-Doktora

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http://hdl.handle.net/11527/19356

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Yazar "İnan, Tuğçe" ile LEE- Kimya Mühendisliği-Doktora'a göz atma
  • Öge
    Exploring allosteric mechanisms of chemokine receptor CXCR4 and implications in drug design
    (Graduate School, 2023-09-07) İnan, Tuğçe ; Levitas Kürkçüoğlu, Özge A. ; 506162009 ; Chemical Engineering
    Proteins work together with other proteins and bind to biomolecules and ions to perform crucial tasks in living organisms. The active site of a protein controls its functional activity, while ligand binding to its allosteric sites can trigger changes in its shape and adjust its activity. The active sites of the proteins induce vital activities. On the other hand, allosteric sites on which ligands are capable of binding promote their conformational changes, and in this way, fundamental properties of biomolecules can regulate. Therefore, targeting the allosteric sites of the protein is a progressive strategy for drug repurposing or design owing to low side effects compared to orthosteric site targeting. Several computational methods have been utilized to elucidate protein structures and explore new drug-binding regions. Elastic Network Models (ENMs) are valuable for defining collective dynamics and functions. Gaussian Network Model (GNM) is one of the ENMs, which describes the structure consisting of nodes assigned to amino acids and springs between nodes. Here, the amino acids involved in both high and low-frequency motions have a high potential as new allosteric drug binding sites. Another coarse-grained model, the residue network model (RNM), is constructed based on the contact topology. A protein complex comprises edges and nodes using the local interaction strengths of residues. The centrality measure of the betweenness of the network can detect the 'hub residues' having a high capacity to receive and send allosteric signals. These residues also promise plausible drug targets. This thesis begins with elastic network models to identify potential allosteric sites. GNM and RNM are applied to various protein structures. The dataset comprises the allosteric enzymes from the glycolytic pathway, belonging to parasites, bacteria, and humans; class A GPCRs; and the MainPro of SARS-CoV-2. Both models consistently capture the same regions as a potential allosteric site. Also, the Site Identification by Ligand Competitive Saturation (SILCS) approach is applied to GPCRs to determine the allosteric druggable pockets. Among the database, CXCR4 is selected for further docking and molecular dynamic studies. CXCR4 is a member of the CXC motif GPCR, and its ligand, CXCL12, is a chemokine protein. CXCR4/CXCL12 axis influences chemotaxis, particularly tumor cell proliferation and metastasis. CXCR4 gets attention with overexpression in cancer cells and is a coreceptor of HIV. Therefore, in this thesis, a systematic approach is used to explore allosteric binding sites to CXCR4. As a consequence of CXCR4 being found as a homodimer in cancer cells, monomer, and homodimer forms are individually studied. To begin with, the GNM and RIN are employed to discover the critical residues that can participate in allosteric regulations and further propose allosteric sites for CXCR4. Subsequently, the SILCS approach is applied for mapping both monomer and homodimer CXCR4 and revealing the druggability of the allosteric sites proposed. SILCS also indicates ring fragments on those sites, which gain to drug design. Mdpocket also identifies these pockets. The Allosigma web server is also utilized to determine free energy differences profiles of potential allosteric sites of interest. Following, FDA-approved and investigational drugs are docked using SP docking, the Glide module of Schrodinger, and calculate Prime MM/GBSA energies. Considering clinical importance and MM/GBSA energies, 41 ligands are investigated with 50 ns long molecular dynamics (MD) simulations and recalculated MM/GBSA energies. HIV protease inhibitors, antimalarial drugs, and anticancer agents, particularly against breast cancer, are subject to hit compounds. ZINC29238439, bemcentinib, and dibutyl-lumefantrine shine, with high binding free energies for monomer CXCR4. On the other hand, itraconazole, isavuconazonium, and brecanavir stand out among the hit compounds proposed for homodimer. Among the hit compounds, fulvestrant and lumefantrine are selected for 1 μs long MD studies due to biological relevancy with CXCR4. MD runs are performed using the NAMD program. According to the results, the dynamic behaviors of monomer and homodimer CXCR4 are different from each other. Also, allosteric behaviors and ligand effects are determined using essential dynamic analysis (EDA), dynamic cross-correlation map (DCCM), and gRINN, which supplies an energy interaction network.