Protein Allostery in Rational Drug Design

Discovery of Heparin Mimetic, Potent, and Selective Inhibitors of Human Clotting Factor XIIIa

Factor XIIIa (FXIIIa) is a cysteine transglutaminase that catalyzes the last step in the coagulation process. An anion-binding site inhibition of FXIIIa is a paradigm-shifting strategy that may offer key advantages of controlled inhibition. Such an approach is likely to lead to novel FXIIIa inhibitors that do not carry bleeding risks. We previously reported a flavonoid trimer-based allosteric inhibitor of FXIIIa with moderate potency and selectivity. To further advance this approach, we evaluated a series of 27 variably sulfonated heparin mimetics against human FXIIIa. Only 13 molecules exhibited inhibitory activity at the highest concentration tested with IC50 values of 2-286 μM. Specifically, inhibitor 16 demonstrated an IC50 value of 2.4 ± 0.5 μM in a bisubstrate, fluorescence-based trans-glutamination assay. It also demonstrated a significant selectivity over other clotting factors including thrombin, factor Xa, and factor XIa as well as other cysteine enzymes including papain and tissue transglutaminase 2. Inhibitor 16 did not affect the viability of three human cell lines at a concentration that is 5-fold its FXIIIa-IC50. The molecule had a very weak effect on the activated partial thromboplastin time of human plasma at a concentration of >700 μM, further supporting its functional selectivity. Importantly, molecule 16 inhibited FXIIIa-mediated polymerization of fibrin(ogen) in a concentration-dependent manner as shown by the gel electrophoresis experiment. Michaelis-Menten kinetics revealed that the molecule competes with the Gln-donor protein substrate, i.e., dimethylcasein, but not with the Lys-donor small substrate, i.e., dansylcadaverine. Molecular modeling studies revealed that this type of molecule likely binds to an anion-binding site comprising the basic amino acids of Lys54, Lys61, Lys73, Lys156, and Arg244 among others. Overall, our work puts forward a new anion-binding site, selective, nontoxic, sulfonated heparin mimetic FXIIIa inhibitor 16 for further development as an effective and safer anticoagulant.

Designing drugs and chemical probes with the dualsteric approach

Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.

Multi-Omics Analysis of the Anti-tumor Synergistic Mechanism and Potential Application of Immune Checkpoint Blockade Combined With Lenvatinib

The combination of immune-checkpoint blockade (ICB) and lenvatinib has demonstrated robust clinical effects that are superior to those of monotherapies, but the synergistic anti-tumor mechanisms remain unclear. Exploring the synergistic molecular mechanisms and early identifying potential application have key importance for clinical therapeutics. We firstly systematically reviewed published data of ICB in combination with lenvatinib for the treatment of cancer by meta-analysis. A subsequent bioinformatics analysis explored the mechanism of combined ICB and lenvatinib therapy in 33 cancer types. Transcriptomic analysis was conducted by RNA-seq, and genomic analysis was performed on gene mutations and copy-number alteration data. Tumor-related pathways and tumor immune micro-environment (TIME) were also investigated. The meta-analysis showed a 38.0% objective response rate (ORR) and 79% disease control rate (DCR) for ICB combined with lenvatinib. Multi-omics analysis revealed that ICB and lenvatinib target genes were highly expressed and showed driving alterations in six specific malignancies. Pathway-enrichment analysis found target genes were implicated in tumor development, angiogenesis, and immunoregulatory associated pathways. This study verified the potential synergistic mechanisms of ICB combined with lenvatinib at transcriptomics, genomics, protein, and cellular levels and recognized nine tumor types had ≥ 2 positive treatment-related molecular characteristics, which might benefit particularly from this combined strategy. The findings would help to provide clinical insights and theoretical basis for optimizing of targeted therapy-immunotherapy combinations, and for guiding individualized precision-medicine approaches for cancer treatment.

Drug discovery for enzymes

Enzymes are essential, physiological catalysts involved in all processes of life, including metabolism, cellular signaling and motility, as well as cell growth and division. They are attractive drug targets because of the presence of defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Understanding the reaction mechanisms of enzymes and the molecular mode of action of enzyme inhibitors is indispensable for the discovery and development of potent, efficacious, and safe novel drugs. The combination of classical concepts of enzymology with new experimental and data analysis methods opens new routes for drug discovery.