Importance of hydrogen-bonding interactions involving the side chain of Asp158 in the catalytic mechanism of papain

Abstract Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing Cα substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC50 value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the Cα substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand’s morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P1′ and P2′ may confer selectivity among MMPs and may aid in the search for novel lead compounds.

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A crystallographic study of the Toho-1 β-lactamase acylation mechanism

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314087920 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1207-C1207

Author(s):

Leighton Coates

Keyword(s):

Hydrogen Bonding ◽

Transition State ◽

Active Site ◽

Catalytic Mechanism ◽

Substrate Binding ◽

Ligand Complex ◽

Transition State Analog ◽

Hydrogen Bonding Interactions ◽

Active Site Region ◽

Neutron Crystallography

β-lactam antibiotics have been used effectively over several decades against many types of highly virulent bacteria. The predominant cause of resistance to these antibiotics in Gram-negative bacterial pathogens is the production of serine β-lactamase enzymes. A key aspect of the class A serine β-lactamase mechanism that remains unresolved and controversial is the identity of the residue acting as the catalytic base during the acylation reaction. Multiple mechanisms have been proposed for the formation of the acyl-enzyme intermediate that are predicated on understanding the protonation states and hydrogen-bonding interactions among the important residues involved in substrate binding and catalysis of these enzymes. For resolving a controversy of this nature surrounding the catalytic mechanism, neutron crystallography is a powerful complement to X-ray crystallography that can explicitly determine the location of deuterium atoms in proteins, thereby directly revealing the hydrogen-bonding interactions of important amino acid residues. Neutron crystallography was used to unambiguously reveal the ground-state active site protonation states and the resulting hydrogen-bonding network in two ligand-free Toho-1 β-lactamase mutants which provided remarkably clear pictures of the active site region prior to substrate binding and subsequent acylation [1,2] and an acylation transition-state analog, benzothiophene-2-boronic acid (BZB), which was also isotopically enriched with 11B. The neutron structure revealed the locations of all deuterium atoms in the active site region and clearly indicated that Glu166 is protonated in the BZB transition-state analog complex. As a result, the complete hydrogen-bonding pathway throughout the active site region could then deduced for this protein-ligand complex that mimics the acylation tetrahedral intermediate [3].

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Crystal structures and hydrogen bonding in the anhydrous tryptaminium salts of the isomeric (2,4-dichlorophenoxy)acetic and (3,5-dichlorophenoxy)acetic acids

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s205698901500907x ◽

2015 ◽

Vol 71 (6) ◽

pp. 671-674 ◽

Cited By ~ 2

Author(s):

Graham Smith ◽

Daniel E. Lynch

Keyword(s):

Hydrogen Bonding ◽

Chain Structure ◽

Side Chain ◽

The Third ◽

Hydrogen Bonding Interactions ◽

Graph Set ◽

Chain Conformations ◽

Dichlorophenoxy Acetic Acid ◽

Polymeric Structures ◽

Acetic Acids

The anhydrous salts of 2-(1H-indol-3-yl)ethanamine (tryptamine) with isomeric (2,4-dichlorophenoxy)acetic acid (2,4-D) and (3,5-dichlorophenoxy)acetic (3,5-D), both C10H13N2+·C8H5Cl2O3−[(I) and (II), respectively], have been determined and their one-dimensional hydrogen-bonded polymeric structures are described. In the crystal of (I), the aminium H atoms are involved in three separate inter-species N—H...O hydrogen-bonding interactions, two with carboxylate O-atom acceptors and the third in an asymmetric three-centre bidentate carboxylateO,O′chelate [graph setR12(4)]. The indole H atom forms an N—H...Ocarboxylatehydrogen bond, extending the chain structure along theb-axis direction. In (II), two of the three aminium H atoms are also involved in N—H...Ocarboxylatehydrogen bonds similar to (I) but with the third, a three-centre asymmetric interaction with carboxylate and phenoxy O atoms is found [graph setR12(5)]. The chain polymeric extension is also alongb. There are no π–π ring interactions in either of the structures. The aminium side-chain conformations differ significantly between the two structures, reflecting the conformational ambivalence of the tryptaminium cation, as found also in the benzoate salts.

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Crystal structure of ammonium (3,5-dichlorophenoxy)acetate hemihydrate

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989015016345 ◽

2015 ◽

Vol 71 (10) ◽

pp. o717-o718 ◽

Cited By ~ 2

Author(s):

Graham Smith

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Acetic Acid ◽

Water Molecule ◽

Rotation Axis ◽

Ammonium Cation ◽

Side Chain ◽

Hydrogen Bonding Interactions ◽

Hydrated Salt ◽

Dichlorophenoxy Acetic Acid

In the structure of the title hydrated salt, NH4+·C8H5Cl2O3−·0.5H2O, where the anion derives from (3,5-dichlorophenoxy)acetic acid, the ammonium cation is involved in extensive N—H...O hydrogen bonding with both carboxylate and ether O-atom acceptors giving sheet structures lying parallel to (100). The water molecule of solvation lies on a crystallographic twofold rotation axis and is involved in intra-sheet O—H...Ocarboxylatehydrogen-bonding interactions. In the anion, the oxoacetate side chain assumes anantiperiplanarconformation with the defining C—O—C—C torsion angle = −171.33 (15)°.

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Side Chain Hydrogen-Bonding Interactions within Amyloid-like Fibrils Formed by the Low-Complexity Domain of FUS: Evidence from Solid State Nuclear Magnetic Resonance Spectroscopy

Biochemistry ◽

10.1021/acs.biochem.9b00892 ◽

2020 ◽

Vol 59 (4) ◽

pp. 364-378 ◽

Cited By ~ 4

Author(s):

Dylan T. Murray ◽

Robert Tycko

Keyword(s):

Nuclear Magnetic Resonance ◽

Hydrogen Bonding ◽

Solid State ◽

Magnetic Resonance ◽

Magnetic Resonance Spectroscopy ◽

Nuclear Magnetic Resonance Spectroscopy ◽

Low Complexity ◽

Side Chain ◽

Resonance Spectroscopy ◽

Hydrogen Bonding Interactions

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Binding energy and specificity in the catalytic mechanism of yeast aldose reductases

Biochemical Journal ◽

10.1042/bj3440101 ◽

1999 ◽

Vol 344 (1) ◽

pp. 101-107 ◽

Cited By ~ 3

Author(s):

Bernd NIDETZKY ◽

Peter MAYR ◽

Philipp HADWIGER ◽

Arnold E. STüTZ

Keyword(s):

Hydrogen Bonding ◽

Transition State ◽

Catalytic Mechanism ◽

Relative Proportion ◽

Binding Constants ◽

Stabilization Energy ◽

Binary Complex ◽

Hydrogen Bonding Interactions ◽

Transition State Stabilization ◽

Hydroxy Groups

Derivatives of D-xylose and D-glucose, in which the hydroxy groups at C-5, and C-5 and C-6 were replaced by fluorine, hydrogen and azide, were synthesized and used as substrates of the NAD(P)H-dependent aldehyde reduction catalysed by aldose reductases isolated from the yeasts Candida tenuis, C. intermedia and Cryptococcus flavus. Steady-state kinetic analysis showed that, in comparison with the parent aldoses, the derivatives were reduced with up to 3000-fold increased catalytic efficiencies (kcat/Km), reflecting apparent substrate binding constants (Km) decreased to as little as 1/250 and, for D-glucose derivatives, up to 5.5-fold increased maximum initial rates (kcat). The effects on Km mirror the relative proportion of free aldehyde that is available in aqueous solution for binding to the binary complex enzyme-NAD(P)H. The effects on kcat reflect non-productive binding of the pyranose ring of sugars; this occurs preferentially with the NADPH-dependent enzymes. No transition-state stabilization energy seems to be derived from hydrogen-bonding interactions between enzyme-NAD(P)H and positions C-5 and C-6 of the aldose. In contrast, unfavourable interactions with the C-6 group are used together with non-productive binding to bring about specificity (6-10 kJ/mol) in a series of D-aldoses and to prevent the reaction with poor substrates such as D-glucose. Azide introduced at C-5 or C-6 destabilizes the transition state of reduction of the corresponding hydrogen-substituted aldoses by approx. 4-9 kJ/mol. The total transition state stabilization energy derived from hydrogen bonds between hydroxy groups of the substrate and enzyme-NAD(P)H is similar for all yeast aldose reductases (yALRs), at approx. 12-17 kJ/mol. Three out of four yALRs manage on only hydrophobic enzyme-substrate interactions to achieve optimal kcat, whereas the NAD(P)H-dependent enzyme from C. intermedia requires additional, probably hydrogen-bonding, interactions with the substrate for efficient turnover.

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Structural view of the helicase reveals thatZika virususes a conserved mechanism for unwinding RNA

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x18003813 ◽

2018 ◽

Vol 74 (4) ◽

pp. 205-213 ◽

Cited By ~ 4

Author(s):

Lei Li ◽

Jin Wang ◽

Zhihui Jia ◽

Neil Shaw

Keyword(s):

Hydrogen Bonding ◽

High Resolution ◽

Crystal Structures ◽

Zika Virus ◽

Healthcare Professionals ◽

Neurological Complications ◽

Side Chain ◽

Hydrogen Bonding Interactions ◽

Solvent Molecules

Recent studies suggest a link between infection byZika virus(ZIKV) and the development of neurological complications. The lack of ZIKV-specific therapeutics has alarmed healthcare professionals worldwide. Here, crystal structures of apo and AMPPNP- and Mn2+-bound forms of the essential helicase of ZIKV refined to 1.78 and 1.3 Å resolution, respectively, are reported. The structures reveal a conserved trimodular topology of the helicase. ATP and Mn2+are tethered between two RecA-like domains by conserved hydrogen-bonding interactions. The binding of ligands induces the movement of backbone Cα and side-chain atoms. Numerous solvent molecules are observed in the vicinity of the AMPPNP, suggesting a role in catalysis. These high-resolution structures could be useful for the design of inhibitors targeting the helicase of ZIKV for the treatment of infections caused by ZIKV.

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