We report here the investigation of a novel description of specificity in protein-ligand binding based on energy landscape theory. We define a new term, intrinsic specificity ratio (ISR), which describes the level of discrimination in binding free energies of the native basin for a protein-ligand complex from the weaker binding states of the same ligand. We discuss the relationship between the intrinsic specificity we defined here and the conventional definition of specificity. In a docking study of molecules with the enzyme COX-2, we demonstrate a statistical correspondence between ISR value and geometrical shapes of the small molecules binding to COX-2. We further observe that the known selective (nonselective) inhibitors of COX-2 have higher (lower) ISR values. We suggest that intrinsic specificity ratio may be a useful new criterion and a complement to affinity in drug screening and in searching for potential drug lead compounds.

Luminol-based electrochemiluminescence (ECL) can be readily excited by various reactive oxygen species (ROS) electrogenerated with an oxygen reduction reaction (ORR). However, the multiple active intermediates involved in the ORR catalyzed with complex nanomaterials lead to recognizing the role of ROS still elusive. Moreover, suffering from the absence of the direct electrochemical oxidation of luminol at the cathode and poor transformation efficiency of O2 to ROS, the weak cathodic ECL emission of luminol is often neglected. Herein, owing to the tunable coordination environment and structure-dependent catalytic feature, single-atom catalysts (SACs) are employed to uncover the relationship between the intrinsic ORR activity and ECL behavior. Interestingly, the traditionally negligible cathodic ECL of luminol is first boosted (ca. 70-fold) owing to the combination of electrochemical ORR catalyzed via SACs and chemical oxidation of luminol. The boosted cathodic ECL emission exhibits electron-transfer pathway-dependent response by adjusting the surrounding environment of the center metal atoms in a controlled way to selectively produce different active intermediates. This work bridges the relationship between ORR performance and ECL behavior, which will guide the development of an amplified sensing platform through rational tailoring of the ORR activity of SACs and potential-resolved ECL assays based on the high-efficiency cathodic ECL reported.

Interfacial electron engineering between noble metal and transition metal carbide is identified as a powerful strategy to improve the intrinsic activity of electrocatalytic oxygen reduction reaction (ORR). However, this short-range effect and the huge structural differences make it a significant challenge to obtain the desired electrocatalyst with atomically thin noble metal layers. Here, we demonstrated the combinatorial strategies to fabricate the heterostructure electrocatalyst of Mo 2 C-coupled Pd atomic layers (AL-Pd/ Mo 2 C) by precise control of metal−organic framework confinement and covalent interaction. Both atomic characterizations and density functional theory calculations uncovered that the strong electron effect imposed on Pd atomic layers has intensively regulated the electronic structures and d-band center and then optimized the reaction kinetics. Remarkably, AL-Pd/Mo 2 C showed the highest ORR electrochemical activity and stability, which delivered a mass activity of 2.055 A mg Pd −1 at 0.9 V, which is 22.1, 36.1, and 80.3 times higher than Pt/C, Pd/C, and Pd nanoparticles, respectively. The present work has developed a novel approach for atomically noble metal catalysts and provides new insights into interfacial electron regulation.

Abstract. The identification and application of druggable pockets of targets play a key role in in silico drug design, which is a fundamental step in structure-based drug design. Herein, some recent progresses and developments of the computational analysis of pockets have been covered. Also, the pockets at the proteinprotein interfaces (PPI) have been considered to further explore the pocket space for drug discovery. We have presented two case studies targeting the kinetic pockets generated by normal mode analysis and molecular dynamics method, respectively, in which we focus upon incorporating the pocket flexibility into the twodimensional virtual screening with both affinity and specificity. We applied the specificity and affinity (SPA) score to quantitatively estimate affinity and evaluate specificity using the intrinsic specificity ratio (ISR) as a quantitative criterion. In one of two cases, we also included some applications of pockets located at the dimer interfaces to emphasize the role of PPI in drug discovery. This review will attempt to summarize the current status of this pocket issue and will present some prospective avenues of further inquiry.

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Binding affinity and specificity are crucial for biomolecular recognition. Past studies have focused on binding affinity while the quantification of specificity has remained an elusive challenge. The conventional specificity measures the discrimination of the specific receptor against others for a ligand binding. It is difficult to explore all the possible competing receptors for the ligand. Here, we quantified the thermodynamic intrinsic specificity of discriminating the "native" binding mode against the "nonnative" binding modes. Intrinsic specificity is relatively easy to compute since one doesn't need to explore all the other receptors. We found that the thermodynamic intrinsic specificity correlates with the conventional specificity. This validates the statistical equivalence of conventional and intrinsic specificities for receptors at reasonable size. We also computationally quantified the residence time of a ligand on the receptor target as the kinetic specificity. We found that the kinetic specificity correlates with the thermodynamic intrinsic specificity and the binding affinity, suggesting the kinetics and the thermodynamics can be simultaneously optimized for biological activities. With the thermodynamic and kinetic specificities in addition to affinity, we carried out a drug screening test on the target cyclooxygenase-2 (COX-2). We showed that multidimensional (two-and three-dimensional) screening has higher capability than affinity alone to discriminate the drug target (COX-2) from the competitive receptor (COX-1), and the selective drugs from the non-selective drugs. Our work suggests a new way of multidimensional drug screening and target identification, which has significant potential applications for drug discovery and design.

We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

Thymopentin (TP5) triggers an immune response by contacting with T cells; however the molecular basis of how TP5 achieves this process remains incompletely understood. According to the main idea of immunomodulation, we suppose that it would be necessary for TP5 to form complex with human class II major histocompatibility complex DR molecules (HLA-DR) before TP5 interacts with T cells. The uptake of TP5 by EBV-transformed B cells expressing HLA-DR molecules and the histogram of fluorescence intensities were observed by using fluorescent- labeled TP5, testifying the direct binding of TP5 to HLA-DR. The binding specificity was confirmed by the inhibition with unlabeled TP5, suggesting the recognition of TP5 by HLA-DR. To confirm the interaction between TP5 and HLA-DR, the complex formation was predicted by using various modeling strategies including six groups of trials with different parameters, alanine substitutions of TP5, and the mutants of HLA-DR. The results demonstrated that TP5 and its alanine substitutions assumed distinct conformations when they bound to HLA-DR. The observation further showed that there was flexibility in how the peptide bound within the binding cleft. Also, the molecular analysis supplemented a newly important discovery to the effect of Val anchor on TP5 binding HLA-DR, and revealed the important effects of Glu11 and Asn62 on the recognition of TP5. These results demonstrated the capability of TP5 to associate with HLA-DR in living antigen presenting cells (APC), thereby providing a new and promising strategy to understand the immunomodulation mechanism induced by TP5 and to design potential immunoregulatory polypeptides.