Assessment of a mechanism for reactive inhibition of carboxypeptidase A with QM/MM methods

Phoon, Lily; Burton, Neil A.

doi:10.1016/j.jmgm.2005.06.004

Cited by 7 publications

(6 citation statements)

References 19 publications

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“…The specificity of most MMPs is surprisingly similar, which makes it very difficult to design the much desired inhibitors that target individual MMPs, which are involved in cancer. Thus, the binding of inhibitors to various metalloproteases was investigated using QM/MM approaches since around the year 2000, e.g., for MMP1, MMP3, MMP9, carboxypeptidase A, and glutamate carboxypeptidase II [58][59][60][61][62][63][64][65][66][67]. A comparative study on MMP1-3, MMP8, MMP9, and MMP13 confirmed the good correlation of computed and experimental free binding energies of inhibitors, while a cross-docking matrix gave hints to rational design of more specific MMP inhibitors [68].…”

Section: Mechanisms Of Metalloproteasesmentioning

confidence: 82%

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Elsässer

Goettig

2021

IJMS

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Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.

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Section: Mechanisms Of Metalloproteasesmentioning

confidence: 82%

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Elsässer

Goettig

2021

IJMS

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“…The enzymatic reaction is perhaps best modeled using a hybrid quantum mechanical and molecular mechanical (QM/MM) method, − in which the enzyme active site is treated quantum mechanically while the remainder of the protein is modeled with a MM force field. Indeed, such QM/MM studies have been reported for CPA, but only for its inhibition. , …”

Section: Introductionmentioning

confidence: 99%

Quantum Mechanical/Molecular Mechanical and Density Functional Theory Studies of a Prototypical Zinc Peptidase (Carboxypeptidase A) Suggest a General Acid−General Base Mechanism

Guo

2009

J. Am. Chem. Soc.

114

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Carboxypeptidase A is a zinc containing enzyme which cleaves the C-terminal residue in a polypeptide substrate. Despite much experimental work, there is still a significant controversy concerning its catalytic mechanism. In this study, the carboxypeptidase A catalyzed hydrolysis of the hippuryl-L-Phe molecule (kcat=17.7±0.7 s−1) is investigated using both density functional theory and a hybrid quantum mechanical/molecular mechanical approach. The enzymatic reaction was found to proceed via a promoted-water pathway with Glu270 serving as the general base and general acid. Free-energy calculations indicate that the first nucleophilic addition step is rate-limiting, with a barrier of 17.9 kcal/mol. Besides activating the zinc-bound water nucleophile, the zinc cofactor also serves as an electrophilic catalyst that stabilizes the substrate carbonyl oxygen during the formation of the tetrahedral intermediate. In the Michaelis complex, Arg127, rather than Zn(II), is responsible for the polarization of the substrate carbonyl and it also serves as the oxyanion hole. As a result, its mutation leads to a higher free-energy barrier, in agreement with experimental observations.

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“…There is a relatively low barrier to cleavage of the peptide bond [10] following the formation of the tetrahedral intermediate and thus this step has not been modelled [12]. QM/MM methods have been used in previous studies to investigate the mechanism of inhibition of CPA [20]. Also, a QM/MM study of the mechanism of hydrolysis in a related zinc-based enzyme, thermolysin, has been published [21].…”

Section: Introductionmentioning

confidence: 99%