Insights into Selectin Inhibitor Design from Endogenous Isomeric Ligands of SLea and SLex

Selectins interact with cell-surface glycans to promote the initial tethering and rolling of leukocytes, and these interactions are targets for designs of inhibitors to neutralize diseases related to excessive inflammatory responses in many cardiovascular and immune dysfunctions, as well as tumor markers in different cancers. The isomeric endogenous tetrasaccharides, sialyl Lewis X (sLex) and sialyl Lewis A (sLea), are minimal sugar structures required for selectin binding. Understanding their subtle structural variances and significant advanced binding strengths of sLea over sLex could benefit the rational designs for selectin inhibitors. Modeling based on the E-selectin-sLex crystal structure in the present study demonstrated that the N-acetyl group of GlcNAc in sLex could form steric hindrances in the E-selectin-sLex complex, but the hydroxy methylene group of GlcNAc in sLea at the same position allows for stronger binding interactions. The subsequent designed inhibitor with a synthetic accessible linker molecule that has no exo-cyclic moieties replacing GlcNAc displayed comparable dynamic and energetic binding features to sLea. The present study deciphered the clues from endogenous isomeric sLea and sLex and provided insights into designing selectin inhibitors with simplified synthesis.

[1]  R. Cummings.  “Stuck on sugars – how carbohydrates regulate cell adhesion, recognition, and signaling” , 2019, Glycoconjugate Journal.

[2]  Brian A. Gerwe,et al.  Chemoenzymatic synthesis of the sialyl Lewis X glycan and its derivatives. , 2010, Carbohydrate research.

[3]  P. Frenette,et al.  GMI-1070, a novel pan-selectin antagonist, reverses acute vascular occlusions in sickle cell mice. , 2010, Blood.

[4]  Karl Nicholas Kirschner,et al.  GLYCAM06: A generalizable biomolecular force field. Carbohydrates , 2008, J. Comput. Chem..

[5]  A. Wong,et al.  Selectins: An Important Family of Glycan-Binding Cell Adhesion Molecules in Ovarian Cancer , 2020, Cancers.

[6]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born , 2012, Journal of chemical theory and computation.

[7]  J. Chou,et al.  Accumulation of Tissue Factor into Developing Thrombi In Vivo Is Dependent upon Microparticle P-Selectin Glycoprotein Ligand 1 and Platelet P-Selectin , 2003, The Journal of experimental medicine.

[8]  M. Cybulsky,et al.  Getting to the site of inflammation: the leukocyte adhesion cascade updated , 2007, Nature Reviews Immunology.

[9]  Evan Bolton,et al.  Symbol Nomenclature for Graphical Representations of Glycans. , 2015, Glycobiology.

[10]  Jiangguo Lin,et al.  Flow-Enhanced Stability of Rolling Adhesion through E-Selectin. , 2016, Biophysical journal.

[11]  Q. Chao,et al.  Recent Progress in Chemo-Enzymatic Methods for the Synthesis of N-Glycans , 2020, Frontiers in Chemistry.

[12]  Joel B. Alderete,et al.  Rational Design of Novel Glycomimetic Peptides for E-Selectin Targeting , 2021, J. Chem. Inf. Model..

[13]  T. Keyes,et al.  Multiple branched adaptive steered molecular dynamics. , 2014, The Journal of chemical physics.

[14]  John S. Philo,et al.  Conformation of sLex Tetrasaccharide, Free in Solution and Bound to E-, P-, and L-Selectin†,‡ , 1997 .

[15]  Thong M. Cao,et al.  Stabilization of the Hinge Region of Human E-selectin Enhances Binding Affinity to Ligands Under Force , 2021, Cellular and Molecular Bioengineering.

[16]  H. Berendsen,et al.  ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS , 1977 .

[17]  P. Patel,et al.  Glycosylation: a hallmark of cancer? , 2016, Glycoconjugate Journal.

[18]  A. Walch,et al.  Monocytes, neutrophils, and platelets cooperate to initiate and propagate venous thrombosis in mice in vivo , 2012, The Journal of experimental medicine.

[19]  R. Hebbel.  Ischemia-reperfusion injury in sickle cell anemia: relationship to acute chest syndrome, endothelial dysfunction, arterial vasculopathy, and inflammatory pain. , 2014, Hematology/oncology clinics of North America.

[20]  R. Cummings,et al.  Convergent Synthesis of Sialyl LewisX- O-Core-1 Threonine. , 2018, The Journal of organic chemistry.

[21]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[22]  R. C. Preston,et al.  E-selectin ligand complexes adopt an extended high-affinity conformation , 2015, Journal of molecular cell biology.

[23]  D. Case,et al.  Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.

[24]  T. Okada,et al.  CSLEX (Sialyl Lewis X) is a useful tumor marker for monitoring of breast cancer patients. , 2011, Japanese journal of clinical oncology.

[25]  H. Reissig,et al.  Divalent Triazole‐Linked Carbohydrate Mimetics: Synthesis by Click Chemistry and Evaluation as Selectin Ligands , 2020, European Journal of Organic Chemistry.

[26]  Daniel R Roe,et al.  PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. , 2013, Journal of chemical theory and computation.

[27]  F. dall’Olio,et al.  Selectin Ligands Sialyl-Lewis a and Sialyl-Lewis x in Gastrointestinal Cancers , 2017, Biology.

[28]  Holger Gohlke,et al.  MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. , 2012, Journal of chemical theory and computation.

[29]  Xiaocong Wang,et al.  Insights into the Loop at the E-Selectin Binding Site: From Open to Close Conformation , 2020, J. Chem. Inf. Model..

[30]  Michael R. Tallack,et al.  Endothelial E-selectin inhibition improves acute myeloid leukaemia therapy by disrupting vascular niche-mediated chemoresistance , 2020, Nature Communications.

[31]  Tingjun Hou,et al.  Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking , 2011, J. Comput. Chem..

[32]  Klaus Schulten,et al.  3D implementation of the symbol nomenclature for graphical representation of glycans. , 2016, Glycobiology.

[33]  Keiichiro Sakuma,et al.  Selectin-Binding Assay by Flow Cytometry. , 2020, Methods in molecular biology.

[34]  B. Brooks,et al.  Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide , 1992, Biopolymers.

[35]  Amika Sood,et al.  Defining the Specificity of Carbohydrate-Protein Interactions by Quantifying Functional Group Contributions , 2018, J. Chem. Inf. Model..

[36]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[37]  Gungor Ozer,et al.  Adaptive steered molecular dynamics: validation of the selection criterion and benchmarking energetics in vacuum. , 2012, The Journal of chemical physics.

[38]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[39]  Evan Bolton,et al.  Updates to the Symbol Nomenclature For Glycans (SNFG) Guidelines. , 2019, Glycobiology.

[40]  Thomas J Boltje,et al.  Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research. , 2009, Nature chemistry.

[41]  M. Fukuda,et al.  Sulfated glycans control lymphocyte homing , 2012, Annals of the New York Academy of Sciences.

[42]  J. Harlan,et al.  The Role of Leukocyte and Endothelial Adhesion Molecules in Ischemia – Reperfusion Injury , 1997, Thrombosis and Haemostasis.

[43]  T. Lange,et al.  Systematic analysis of the human tumor cell binding to human vs. murine E- and P-selectin under static vs. dynamic conditions , 2020, Glycobiology.

[44]  M. Karplus,et al.  Method for estimating the configurational entropy of macromolecules , 1981 .

[45]  A. Beaudet,et al.  P-Selectin or Intercellular Adhesion Molecule (Icam)-1 Deficiency Substantially Protects against Atherosclerosis in Apolipoprotein E–Deficient Mice , 2000, The Journal of experimental medicine.

[46]  Rigoberto Hernandez,et al.  Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y. , 2010, Journal of chemical theory and computation.

[47]  P. Frenette,et al.  Complete identification of E-selectin ligands on neutrophils reveals distinct functions of PSGL-1, ESL-1, and CD44. , 2007, Immunity.