Generating a mirror-image monobody targeting MCP-1 via TRAP display and chemical protein synthesis

Biologically produced protein drugs are generally susceptible to degradation by proteases and often exhibit immunogenicity. To address this issue, mirror-image peptide/protein binders consisting of D-amino acids have been developed so far through the mirror-image phage display technique. Here, we develop a mirror-image protein binder derived from a monobody, one of the promising protein scaffolds, utilizing two notable technologies: chemical protein synthesis and TRAP display, an improved version of mRNA display. A sequential workflow of initial screening followed by affinity maturation, facilitated by TRAP display, generates an L-monobody with high affinity (KD = 1.3 nM) against monocyte chemoattractant protein-1 (MCP-1) D-enantiomer. The chemically synthesized D-monobody demonstrates strong and specific binding to L-MCP-1 and exhibits pharmaceutically favorable properties such as proteolytic resistance, minimal immune response, and a potent inhibitory effect on MCP-1-induced cell migration. This study elevates the value of mirror-image peptide/protein binders as an alternative modality in drug discovery.

Network Pharmacology Research Indicates that Wu-Mei-Wan Treats Obesity by Inhibiting Th17 Cell Differentiation and Alleviating Metabolic Inflammation

BACKGROUND

Wu-Mei-Wan (WMW), a traditional Chinese medicine (TCM) formula, has a good effect on the treatment of obesity and has been proven helpful to promote the metabolism of adipose tissue. However, its underlying mechanism remains to be studied. This study aims to explore the potential pharmacological mechanism of WMW in the treatment of obesity.

METHODS

Network pharmacology was used to sort out the relationship between WMW putative targets and obesity-related drug targets or disease targets, which indicated the mechanism of WMW in treating obesity from two aspects of clinical drugs approved by the Food and Drug Administration (FDA) and obesity-related diseases. Databases such as Traditional Chinese Medicine Systems Pharmacology (TCMSP), PubChem, DrugBank, DisGeNET, and Genecards were used to collect information about targets. String platform was used to convert the data into gene symbol of "homo sapiens", and perform gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. With the Human Protein Reference Database (HPRD) as background data, Cytoscape 3.6.0 software was used to construct a new protein-protein interaction (PPI) network. Mechanism diagrams of key pathways were obtained from the KEGG database. AutoDock Vina software was used to conduct molecular docking verification.

RESULTS

The number of targets in the overlap between WMW putative targets and obesity-related drug targets accounted for more than 50% of the latter, and HTR3A, SLC6A4, and CYP3A4 were core targets. In obesity-related disease targets-WMW putative targets PPI network, the Th17 cell differentiation pathway, and the IL-17 signaling pathway were key pathways, and the 1st module and the 7th module were central function modules that were highly associated with immunity and inflammation. Molecular docking verified that STAT3, TGFB1, MMP9, AHR, IL1B, and CCL2 were core targets in the treatment of WMW on obesity.

CONCLUSION

WMW has similar effects on lipid and drug metabolism as the current obesity-related drugs, and is likely to treat obesity by inhibiting Th17 cell differentiation and alleviating metabolic inflammation.

Chemoenzymatic Semisynthesis of Proteins

Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.

Molecular basis of lateral force spectroscopy nano-diagnostics: computational unbinding of autism related chemokine MCP-1 from IgG antibody

Monocyte-chemoattractant protein-1 (MCP-1), also known as CCL2, is a potent chemoattractant of T cells and monocytes, involved in inflammatory and angio-proliferative brain and retinal diseases. Higher expression of MCP-1 is observed in metastatic tumors. Unusual levels of MCP-1 in the brain may be correlated with autism. Immunochemistry where atomic force microscope (AFM) tips functionalized with appropriate antibodies against MCP-1 are used could in principle support medical diagnostics. Useful signals from single molecule experiments may be generated if interaction forces are large enough. The chemokine-antibody unbinding force depends on a relative motion of the interacting fragments of the complex. In this paper the stability of the medically important MCP-1- immunoglobulin G antibody Fab fragment complex has been studied using steered molecular dynamics (SMD) computer simulations with the aim to model possible arrangements of nano-diagnostics experiments. Using SMD we confirm that molecular recognition in MCP1-IgG is based mainly on six pairs of residues: Glu39A - Arg98H, Lys56A - Asp52H, Asp65A - Arg32L, Asp68A - Arg32L, Thr32A - Glu55L, Gln61A - Tyr33H. The minimum external force required for mechanical dissociation of the complex depends on a direction of the force. The pulling of the MCP-1 antigen in the directions parallel to the antigen-antibody contact plane requires forces about 20 %–40 % lower than in the perpendicular one. Fortunately, these values are large enough that the fast lateral force spectroscopy may be used for effective nano-diagnostics purposes. We show that molecular modeling is a useful tool in planning AFM force spectroscopy experiments.

Figure

Structural basis for high selectivity of anti-CCL2 neutralizing antibody CNTO 888

Human CC chemokine ligand 2 (CCL2), also known as monocyte chemoattractant protein-1 (MCP-1), is a member of the β chemokine family whose actions are mediated through the G-protein-coupled receptor CCR2. Binding of CCL2 to its receptor CCR2 triggers calcium mobilization and chemotaxis. CCL2 is implicated in the pathogenesis of certain inflammatory diseases and cancer. CNTO 888, a neutralizing human anti-CCL2 antibody, was derived by antibody phage display. The antibody binds human CCL2 with high affinity (K(D)=22 pM) and inhibits CCL2 binding to its receptor. The crystal structure of the CNTO 888 Fab alone and in complex with the monomeric form of CCL2 (P8A variant) was determined at 2.6 Å and 2.8 Å resolution, respectively. CNTO 888 recognizes a conformational epitope encompassing residues 18-24 and 45-51 that overlaps the mapped receptor binding site. The epitope of CNTO 888 does not overlap with the dimerization site of CCL2, and thus its inhibitory activity is not expected to result from interference with the oligomeric state of CCL2. Comparison of the X-ray-determined epitopes of CNTO 888 and another CCL2-neutralizing antibody, 11K2, provides insight into the molecular basis of antibody selectivity and functional inhibition.