Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.

Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure–function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca2+ removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca2+ removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.

To investigate natural inhibitors against tobacco mosaic virus (TMV) from plants, 10 known beta-carboline alkaloids and one quassinoid have been isolated from MeOH extract of the wood of Picrasma quassioides Benn. These compounds were screened for their inhibitory activities against tobacco mosaic virus (TMV). The activity of each compound against TMV infection and replication was tested using a half-leaf assay method, a leaf-disk method, and Western blotting analyses. All of the beta-carboline alkaloids showed moderate anti-TMV activities and exhibited synergistic effects when combined with the quassinoid nigakilactone B (11). To our knowledge, this is the first report on anti-TMV activity of beta-carbolines and their synergistic effects against TMV when combined with a quassinoid.

Two new quassinoids, javanicolide E (1) and javanicolide F (2), along with fifteen known C-20 quassinoids were isolated from the seeds of Brucea javanica (L.) Merr. The antitobacco mosaic virus (TMV) activity of these quassinoids was screened by the conventional half-leaf and leaf-disk method along with Western blot analysis. All of the seventeen quassinoids showed potent anti-TMV activity. Among them, eight compounds, brusatol (3), bruceine B (4), bruceoside B (5), yadanzioside I (6), yadanzioside L (7), bruceine D (8), yadanziolide A (9), and aglycone of yadanziolide D (17), showed strong antiviral activities, with IC(50) values in the range of 3.42-5.66 microM, and were much more effective than the positive control, ningnanmycin (IC(50) = 117.3 microM). The antiviral structure-activity relationships of quassinoids against TMV were also discussed.