Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Carbonic Anhydrase II Apo-Enzyme

From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system

Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.

Identification of the inhibition mechanism of carbonic anhydrase II by fructooligosaccharides

Polygonatum sibiricum (P. sibiricum), recognized as a precious nourishing Chinese traditional medicine, exhibits the pharmacological effect of anti-aging. In this work, we proposed a novel mechanism underlying this effect related to the less studied bioactive compounds fructooligosaccharides in P. sibiricum (PFOS) to identify the inhibition effect of the small glycosyl molecules on the age-related zinc metalloprotease carbonic anhydrase II (CA II). Molecular docking and molecular dynamics simulation were used to investigate the structural and energetic properties of the complex systems consisting of the CA II enzyme and two possible structures of PFOS molecules (PFOS-A and PFOS-B). The binding affinity of PFOS-A (-7.27 ± 1.02 kcal/mol) and PFOS-B (-8.09 ± 1.75 kcal/mol) shows the spontaneity of the binding process and the stability of the combination in the solvent. Based on the residue energy decomposition and nonbonded interactions analysis, the C-, D- and G-sheet fragments of the CA II were found to be crucial in binding process. Van der Waals interactions form on the hydrophobic surface of CAII mainly with 131PHE and 135VAL, while hydrogen bonds form on the hydrophilic surface mainly with 67ASN and 92GLN. The binding of PFOS results in the blocking of the zinc ions pocket and then inhibiting its catalytic activity, the stability of which has been further demonstrated by free energy landscape. These findings provide evidence of the effective inhibition of PFOS to CA II enzyme, which leads to a novel direction for exploring the mechanism of traditional Chinese medicine focused on small molecule fructooligosaccharides.

Strategies to improve the mass transfer in the CO2 capture process using immobilized carbonic anhydrase

High carbon dioxide (CO₂) concentration in the atmosphere urgently requires eco-friendly mitigation strategies. Carbonic anhydrase (CA) is a high-quality enzyme protein, available from a wide range of sources, which has an extremely high catalytic efficiency for the hydration of CO₂ compared with other catalytic CO₂ conversion systems. While free CA is costly and weakly stable, CA immobilization can significantly improve its stability and allow enzyme recycling. However, gaseous CO₂ is significantly different from traditional liquid substrates. Additionally, due to the presence of enzyme carriers, there is limited mass transfer between CO₂ and the active center of immobilized CA. Most of the available reviews provide an overview of the improvement in catalytic activity and stability of CA by different immobilization methods and substrates. However, they do not address the limited mass transfer between CO₂ and the active center of immobilized CA. Therefore, by focusing on the mass transfer process, this review presents CA immobilization strategies that are more efficient and of greater environmental tolerance by categorizing the methods of enhancing the mass transfer process at each stage of the enzymatic CO₂ capture reaction. Such improvements in this green and environmentally friendly biological carbon capture process can increase its efficiency for industrial applications.

On the Uses of PCA to Characterise Molecular Dynamics Simulations of Biological Macromolecules: Basics and Tips for an Effective Use

Principal Component Analysis (PCA) is a procedure widely used to examine data collected from molecular dynamics simulations of biological macromolecules. It allows for greatly reducing the dimensionality of their configurational space, facilitating further qualitative and quantitative analysis. Its simplicity and relatively low computational cost explain its extended use. However, a judicious implementation of PCA requires the knowledge of its theoretical grounds as well as its weaknesses and capabilities. In this article, we review these issues and discuss several strategies developed over the last years to mitigate the main PCA flaws and enhance the reproducibility of its results.

In the footsteps of an inhibitor unbinding from the active site of human carbonic anhydrase II

The crystal structure of human carbonic anhydrase (HCA) II bound to an inhibitor molecule, 6-hydroxy-2-thioxocoumarin (FC5), shows FC5 to be located in a hydrophobic pocket at the active site. The present work employs classical molecular dynamics (MD) simulation to follow the FC5 molecule for 1 μs as it unbinds from its binding location, adopts the path of substrate/product diffusion (path 1) to leave the active site at around 75 ns. It is then found to undergo repeated binding and unbinding at different locations on the surface of the enzyme in water. Several transient excursions through different regions of the enzyme are also observed prior to its exit from the active site. These transient paths are combined with functionally relevant cavities/channels to enlist five additional pathways (path 2-6). Pathways 1-6 are subsequently explored using steered MD and umbrella sampling simulations. A free energy barrier of 0.969 kcal mol^-1 is encountered along path 1, while barriers in the range of 0.57-2.84 kcal mol^-1 are obtained along paths 2, 4 and 5. We also analyze in detail the interaction between FC5 and the enzyme along each path as the former leaves the active site of HCA II. Our results indicate path 1 to be the major exit pathway for FC5, although competing contributions may also come from the paths 2, 4 and 5.Communicated by Ramaswamy H. Sarma.

Structural Characterization of Carbonic Anhydrase-Arylsulfonamide Complexes Using Ultraviolet Photodissociation Mass Spectrometry

Numerous mass spectrometry-based strategies ranging from hydrogen-deuterium exchange to ion mobility to native mass spectrometry have been developed to advance biophysical and structural characterization of protein conformations and determination of protein-ligand interactions. In this study, we focus on the use of ultraviolet photodissociation (UVPD) to examine the structure of human carbonic anhydrase II (hCAII) and its interactions with arylsulfonamide inhibitors. Carbonic anhydrase, which catalyzes the conversion of carbon dioxide to bicarbonate, has been the target of countless thermodynamic and kinetic studies owing to its well-characterized active site, binding cavity, and mechanism of inhibition by hundreds of ligands. Here, we showcase the application of UVPD for evaluating structural changes of hCAII upon ligand binding on the basis of variations in fragmentation of hCAII versus hCAII-arylsulfonamide complexes, particularly focusing on the hydrophobic pocket. To extend the coverage in the midregion of the protein sequence, a supercharging agent was added to the solutions to increase the charge states of the complexes. The three arylsulfonamides examined in this study largely shift the fragmentation patterns in similar ways, despite their differences in binding affinities.

Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle

In the design of high-affinity and enzyme isoform-selective inhibitors, we applied an approach of augmenting the substituents attached to the benzenesulfonamide scaffold in three ways, namely, substitutions at the 3,5- or 2,4,6-positions or expansion of the condensed ring system. The increased size of the substituents determined the spatial limitations of the active sites of the 12 catalytically active human carbonic anhydrase (CA) isoforms until no binding was observed because of the inability of the compounds to fit in the active site. This approach led to the discovery of high-affinity and high-selectivity compounds for the anticancer target CA IX and antiobesity target CA VB. The x-ray crystallographic structures of compounds bound to CA IX showed the positions of the bound compounds, whereas computational modeling confirmed that steric clashes prevent the binding of these compounds to other isoforms and thus avoid undesired side effects. Such an approach, based on the Lock-and-Key principle, could be used for the development of enzyme-specific drug candidate compounds.