Structural Investigation and Molecular Modeling Studies of Strobilurin-Based Fungicides Active against the Rice Blast Pathogen Pyricularia oryzae

The increasing emergence of fungicide-resistant pathogens requires urgent solutions for crop disease management. Here, we describe a structural investigation of new fungicides obtained by combining strobilurin and succinate dehydrogenase inhibitor pharmacophores. We identified compounds endowed with very good activity against wild-type Pyricularia oryzae, combined in some cases with promising activity against strobilurin-resistant strains. The first three-dimensional model of P. oryzae cytochrome bc1 complex containing azoxystrobin as a ligand was developed. The model was validated with a set of commercially available strobilurins, and it well explains both the resistance mechanism to strobilurins mediated by the mutation G143A and the activity of metyltetraprole against strobilurin-resistant strains. The obtained results shed light on the key recognition determinants of strobilurin-like derivatives in the cytochrome bc1 active site and will guide the further rational design of new fungicides able to overcome resistance caused by G143A mutation in the rice blast pathogen.

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Characterization of the Mycobacterium tuberculosis H37Rv alkyl hydroperoxidase AhpC points to the importance of ionic interactions in oligomerization and activity

Biochemical Journal ◽

10.1042/bj3540209 ◽

2001 ◽

Vol 354 (1) ◽

pp. 209-215 ◽

Cited By ~ 17

Author(s):

Radha CHAUHAN ◽

Shekhar C. MANDE

Keyword(s):

Mycobacterium Tuberculosis ◽

Conformational Changes ◽

Three Dimensional ◽

Enteric Bacteria ◽

Enzymic Activity ◽

Ionic Interactions ◽

Three Dimensional Model ◽

Mycobacterium Tuberculosis H37rv ◽

Resistant Strains ◽

Alkyl Hydroperoxidase

An alkyl hydroperoxidase (AhpC) has been found frequently to be overexpressed in isoniazid-resistant strains of Mycobacterium tuberculosis. These strains have an inactivated katG gene encoding a catalase peroxidase, which might render mycobacteria susceptible to the toxic peroxide radicals, thus leading to the concomitant overexpression of the AhpC. Although the overexpressed AhpC in isoniazid-resistant strains of M. tuberculosis may not directly participate in isoniazid action, AhpC might still assist M. tuberculosis in combating oxidative damage in the absence of the catalase. Here we have attempted to characterize the AhpC protein biochemically and report its functional and oligomerization properties. The alkyl hydroperoxidase of M. tuberculosis is unique in many ways compared with its well-characterized homologues from enteric bacteria. We show that AhpC is a decameric protein, composed of five identical dimers held together by ionic interactions. Dimerization of individual subunits takes place through an intersubunit disulphide linkage. The ionic interactions play a significant role in enzymic activity of the AhpC protein. The UV absorption spectrum and three-dimensional model of AhpC suggest that interesting conformational changes may take place during oxidation and reduction of the intersubunit disulphide linkage. In the absence of the partner AhpF subunit in M. tuberculosis, the mycobacterial AhpC might use small-molecule reagents, such as mycothiol, for completing its enzymic cycle.

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Dynamic inelastic analyses of a bridge structure

Bulletin of the Seismological Society of America ◽

10.1785/bssa0710020517 ◽

1981 ◽

Vol 71 (2) ◽

pp. 517-530

Author(s):

A. G. Gillies ◽

R. Shepherd

Keyword(s):

Equations Of Motion ◽

Resistance Mechanism ◽

Three Dimensional ◽

Time History ◽

Bridge Structure ◽

Three Dimensional Model ◽

Earthquake Excitation ◽

Plastic Yield ◽

Analysis Technique ◽

Bridge Structures

abstract The necessity for framed structures to be capable of dissipating significant amounts of energy inelastically under severe earthquake excitation is generally acknowledged. Bridge structures differ from buildings in their seismic lateral resistance mechanism in so far as they generally possess a small number of clearly identifiable potential zones in which plastic yield can occur and consequently tend to be amenable to postelastic studies. This paper presents the application of an analysis technique in which the response time history of a bridge structure, treated as a three-dimensional frame, is determined by direct integration of the equations of motion with allowances incorporated for inelastic member behavior. Aspects studied include the differences in responses predicted using a nonlinear three-dimensional model rather than a planar frame idealization and the effect of unequal span lengths or torsional vibrations.

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Asp218 participates with Asp213 to bind a Ca2+ atom into the S1 subsite of aminopeptidase A: a key element for substrate specificity

Biochemical Journal ◽

10.1042/bj20080471 ◽

2008 ◽

Vol 416 (1) ◽

pp. 37-46 ◽

Cited By ~ 12

Author(s):

Cédric Claperon ◽

Raphael Rozenfeld ◽

Xavier Iturrioz ◽

Nicolas Inguimbert ◽

Mayumi Okada ◽

...

Keyword(s):

Rational Design ◽

Three Dimensional ◽

Antihypertensive Agents ◽

Three Dimensional Model ◽

Stimulatory Action ◽

Acidic Residues ◽

Aminopeptidase A ◽

Strict Specificity ◽

New Generation

APA (aminopeptidase A; EC 3.4.11.7) is a membrane-bound zinc metallopeptidase, also activated by Ca2+, involved in the formation of brain angiotensin III, which exerts a tonic stimulatory action on the central control of blood pressure in hypertensive animals. In the present study, in the three-dimensional model of the ectodomain of mouse APA, we docked the specific APA inhibitor glutamate phosphonate, in the presence of Ca2+. The model showed the presence of one Ca2+ atom in an hydrophilic pocket corresponding to the S1 subsite in which the lateral chain of the inhibitor is pointing. In this pocket, the Ca2+ atom was hexaco-ordinated with the acidic side chains of Asp213 and Asp218, the carbonyl group of Glu215 and three water molecules, one of them being engaged in a hydrogen bond with the negatively charged carboxylate side chain of the inhibitor. Mutagenic replacement of Asp213 and Asp218 with a conservative residue maintained the ability of mutated APAs to be activated by Ca2+. However, the replacement by a non-conservative residue abolished this property, demonstrating the crucial role of these residues in Ca2+ binding. We also showed the involvement of these residues in the strict specificity of APA in the presence of Ca2+ for N-terminal acidic residues from substrates or inhibitors, since mutagenic replacement of Asp213 and Asp218 induced a decrease of the inhibitory potencies of inhibitors homologous with acidic residues. Finally, this led to the rational design of a new potent APA inhibitor, NI926 (Ki=70 nM), which allowed us to precisely localize Asp213 at the entrance and Asp218 at the bottom of the S1 subsite. Taken together, these data provide new insight into the organization and functional role of the APA S1 subsite and will allow the design of pharmacophore of the inhibitor, helpful for the development of a new generation of APA inhibitors as central-acting antihypertensive agents.

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Three Dimensional Structure-Based Genetic Modifications of A Bacterial Cytochrome bc1 Complex

Photosynthesis: Mechanisms and Effects ◽

10.1007/978-94-011-3953-3_351 ◽

1998 ◽

pp. 1487-1492

Author(s):

Sevnur Mandaci ◽

A. Sami Saribas ◽

Fevzi Daldal

Keyword(s):

Three Dimensional ◽

Cytochrome Bc1 ◽

Dimensional Structure ◽

Bc1 Complex ◽

Cytochrome Bc1 Complex ◽

Three Dimensional Structure ◽

Genetic Modifications

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Overcoming drug-resistant malaria through rational drug design in cytochrome bc1

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314091931 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C806-C806

Author(s):

Michael Capper ◽

Paul O'Neill ◽

Giancarlo Biagini ◽

Samar Hasnain ◽

Svetlana Antonyuk

Keyword(s):

Single Point ◽

Rational Drug Design ◽

Complex Iii ◽

Cytochrome Bc1 ◽

Single Point Mutation ◽

Drug Resistant ◽

Cytochrome Bc1 Complex ◽

Phase I Clinical Trials ◽

Inner Mitochondrial Membrane ◽

Resistant Strains

Over three billion people live in regions affected by malaria and there are over one million deaths each year [1]. Malaria is caused by the Plasmodium parasite and various drugs are currently used in both treatment and prophylaxis but resistant strains are rapidly emerging. One of the most commonly used anti-malarial drugs is Atovaquone, a hydroxynapthoquinone that is currently used in combination with Proguanil and sold as Malarone™. Atovaquone targets cytochrome bc1 (Complex III, ubiquinol-cytochrome c oxidoreductase), a multi subunit electron transfer protein complex embedded in the inner mitochondrial membrane [2]. Drug resistance rises through a single point mutation in cytochrome b at the Qo site, one of two quinone binding sites. By visualising compounds bound to cytochrome bc1 through x-ray crystallography, it may be possible to modify the compounds to both bind stronger and more specifically. We have worked on compounds that recently failed phase I clinical trials due to cross-reactivity with human cytochrome bc1 [3]. Our structural studies have shown that these compounds appear to bind at the Qi site, which would overcome current drug-resistant strains. Further work here could produce a novel class of anti-malarial drug.

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Macrocyclic Tetramers—Structural Investigation of Peptide-Peptoid Hybrids

Molecules ◽

10.3390/molecules26154548 ◽

2021 ◽

Vol 26 (15) ◽

pp. 4548

Author(s):

Claudine Nicole Herlan ◽

Anna Sonnefeld ◽

Thomas Gloge ◽

Julian Brückel ◽

Luisa Chiara Schlee ◽

...

Keyword(s):

Amino Acids ◽

Nmr Spectroscopy ◽

Rational Design ◽

Structural Investigation ◽

Three Dimensional ◽

Dimensional Structure ◽

Proteolytic Degradation ◽

X Ray ◽

X Ray Scattering

Outstanding affinity and specificity are the main characteristics of peptides, rendering them interesting compounds for basic and medicinal research. However, their biological applicability is limited due to fast proteolytic degradation. The use of mimetic peptoids overcomes this disadvantage, though they lack stereochemical information at the α-carbon. Hybrids composed of amino acids and peptoid monomers combine the unique properties of both parent classes. Rigidification of the backbone increases the affinity towards various targets. However, only little is known about the spatial structure of such constrained hybrids. The determination of the three-dimensional structure is a key step for the identification of new targets as well as the rational design of bioactive compounds. Herein, we report the synthesis and the structural elucidation of novel tetrameric macrocycles. Measurements were taken in solid and solution states with the help of X-ray scattering and NMR spectroscopy. The investigations made will help to find diverse applications for this new, promising compound class.

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Macrocyclic Tetramers – Structural Investigation of Peptide-Peptoid Hybrids

10.20944/preprints202107.0196.v1 ◽

2021 ◽

Author(s):

Claudine Herlan ◽

Anna Sonnefeld ◽

Thomas Gloge ◽

Julian Brückel ◽

Luisa Schlee ◽

...

Keyword(s):

Nmr Spectroscopy ◽

Bioactive Compounds ◽

Rational Design ◽

Structural Investigation ◽

Three Dimensional ◽

Dimensional Structure ◽

X Ray ◽

Three Dimensional Structure ◽

X Ray Scattering

The determination of the three-dimensional structure is a key step for the identification of new targets as well as the rational design of bioactive compounds. Herein, we report the synthesis and the structural elucidation of novel tetrameric macrocycles. Measurements were taken in solid and solution states with the help of X-ray scattering and NMR spectroscopy. The investigations made will help to find diverse applications for this new, promising compound class.

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