scholarly journals The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4- benzoquinone and to FMN.

2021 ◽  
Author(s):  
Martin Alan Day ◽  
David Jarrom ◽  
Andrew J Christofferson ◽  
Antonio E Graziano ◽  
Ross Anderson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Furan Ring ◽  
Hydride Transfer ◽  
Binding Pocket ◽  
Phosphate Binding ◽  
Free Protein ◽  
E Coli ◽  
Nitrofuran Antibiotics ◽  
Dynamics Simulations

NfsA is a dimeric flavoprotein that catalyses the reduction of nitroaromatics and quinones by NADPH. This reduction is required for the activity of nitrofuran antibiotics. The crystal structure of free E. coli NfsA and several homologues have been determined previously, but there is no structure of the enzyme with ligands. We present here crystal structures of oxidised E. coli NfsA in the presence of several ligands, including the antibiotic nitrofurantoin. Nitrofurantoin binds with the furan ring, rather than the nitro group that is reduced, near the N5 of the FMN. Molecular dynamics simulations show that this orientation is only favourable in the oxidised enzyme, while potentiometry suggests that little semiquinone is formed in the free protein. This suggests that the reduction occurs by direct hydride transfer from FMNH- to nitrofurantoin bound in the reverse orientation to that in the crystal structure. We present a model of nitrofurantoin bound to reduced NfsA in a viable hydride transfer orientation. The substrate 1,4-benzoquinone and the product hydroquinone are positioned close to the FMN N5 in the respective crystal structures with NfsA, suitable for reaction, but are mobile within the active site. The structure with a second FMN, bound as a ligand, shows that a mobile loop in the free protein forms a phosphate-binding pocket. NfsA is specific for NADPH and a similar conformational change, forming a phosphate-binding pocket, is likely to also occur with the natural cofactor.

scholarly journals Crystal structure of the human NK1 tachykinin receptor

2018 ◽  
Vol 115 (52) ◽  
pp. 13264-13269 ◽  
Author(s):  
Jie Yin ◽  
Karen Chapman ◽  
Lindsay D. Clark ◽  
Zhenhua Shao ◽  
Dominika Borek ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substance P ◽  
Binding Pocket ◽  
Computational Docking ◽  
Tachykinin Receptor ◽  
Approved Drugs ◽  
Dynamics Simulations ◽  
Receptor Modulators ◽  
Further Development ◽  
G Protein Coupled

The NK1 tachykinin G-protein–coupled receptor (GPCR) binds substance P, the first neuropeptide to be discovered in mammals. Through activation of NK1R, substance P modulates a wide variety of physiological and disease processes including nociception, inflammation, and depression. Human NK1R (hNK1R) modulators have shown promise in clinical trials for migraine, depression, and emesis. However, the only currently approved drugs targeting hNK1R are inhibitors for chemotherapy-induced nausea and vomiting (CINV). To better understand the molecular basis of ligand recognition and selectivity, we solved the crystal structure of hNK1R bound to the inhibitor L760735, a close analog of the drug aprepitant. Our crystal structure reveals the basis for antagonist interaction in the deep and narrow orthosteric pocket of the receptor. We used our structure as a template for computational docking and molecular-dynamics simulations to dissect the energetic importance of binding pocket interactions and model the binding of aprepitant. The structure of hNK1R is a valuable tool in the further development of tachykinin receptor modulators for multiple clinical applications.

scholarly journals Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Nicholas Francia ◽  
Louise Price ◽  
Matteo Salvalaglio
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Large Scale ◽  
Lattice Energy ◽  
Racemic Mixture ◽  
Dynamics Simulations

<p>The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy calculations, which are known to significantly over-predict the number of plausible crystal structures. A valuable tool to reduce overprediction is to employ physics-based, dynamic simulations to coalesce lattice energy minima separated by small barriers into a smaller number of more stable geometries once thermal effects are introduced. Molecular dynamics simulations and enhanced sampling methods can be employed in this context to simulate crystal structures at finite temperature and pressure. </p><p>Here we demonstrate the applicability of approaches based on molecular dynamics to systematically process realistic CSP datasets containing several hundreds of crystal structures. The system investigated is ibuprofen, a conformationally flexible active pharmaceutical ingredient that crystallises both in enantiopure forms and as a racemic mixture. By introducing a hierarchical approach in the analysis of finite-temperature supercell configurations, we can post-process a dataset of 555 crystal structures, identifying 65% of the initial structures as labile, while maintaining all the experimentally known crystal structures in the final, reduced set. Moreover, the extensive nature of the initial dataset allows one to gain quantitative insight into the persistence and the propensity to transform of crystal structures containing common hydrogen-bonded intermolecular interaction motifs.</p>

scholarly journals Mutation of Tyr137 of the universalEscherichia colifimbrial adhesin FimH relaxes the tyrosine gate prior to mannose binding

IUCrJ ◽  
2017 ◽  
Vol 4 (1) ◽  
pp. 7-23 ◽  
Author(s):  
Said Rabbani ◽  
Eva-Maria Krammer ◽  
Goedele Roos ◽  
Adam Zalewski ◽  
Roland Preston ◽  
...  
Keyword(s):  
Ethylenediaminetetraacetic Acid ◽  
Hydrophobic Interactions ◽  
Binding Pocket ◽  
Lectin Domain ◽  
E Coli ◽  
Ligand Free ◽  
Mannose Binding ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Dynamics Simulations

The most prevalent diseases manifested byEscherichia coliare acute and recurrent bladder infections and chronic inflammatory bowel diseases such as Crohn's disease.E. coliclinical isolates express the FimH adhesin, which consists of a mannose-specific lectin domain connectedviaa pilin domain to the tip of type 1 pili. Although the isolated FimH lectin domain has affinities in the nanomolar range for all high-mannosidic glycans, differentiation between these glycans is based on their capacity to form predominantly hydrophobic interactions within the tyrosine gate at the entrance to the binding pocket. In this study, novel crystal structures of tyrosine-gate mutants of FimH, ligand-free or in complex with heptyl α-D-O-mannopyranoside or 4-biphenyl α-D-O-mannopyranoside, are combined with quantum-mechanical calculations and molecular-dynamics simulations. In the Y48A FimH crystal structure, a large increase in the dynamics of the alkyl chain of heptyl α-D-O-mannopyranoside attempts to compensate for the absence of the aromatic ring; however, the highly energetic and stringent mannose-binding pocket of wild-type FimH is largely maintained. The Y137A mutation, on the other hand, is the most detrimental to FimH affinity and specificity: (i) in the absence of ligand the FimH C-terminal residue Thr158 intrudes into the mannose-binding pocket and (ii) ethylenediaminetetraacetic acid interacts strongly with Glu50, Thr53 and Asn136, in spite of multiple dialysis and purification steps. Upon mutation, pre-ligand-binding relaxation of the backbone dihedral angles at position 137 in the tyrosine gate and their coupling to Tyr48viathe interiorly located Ile52 form the basis of the loss of affinity of the FimH adhesin in the Y137A mutant.

3′-Azidothymidine in the active site ofEscherichia colithymidine phosphorylase: the peculiarity of the binding on the basis of X-ray study

2014 ◽  
Vol 70 (4) ◽  
pp. 1155-1165 ◽  
Author(s):  
Vladimir Timofeev ◽  
Yulia Abramchik ◽  
Nadezda Zhukhlistova ◽  
Tatiana Muravieva ◽  
Ilya Fateev ◽  
...  
Keyword(s):  
Active Site ◽  
Thymidine Phosphorylase ◽  
Binding Pocket ◽  
Chemotherapeutic Agents ◽  
Nucleoside Analogues ◽  
Dimensional Structure ◽  
Phosphate Binding ◽  
X Ray ◽  
E Coli ◽  
Replacement Method

The structural study of complexes of thymidine phosphorylase (TP) with nucleoside analogues which inhibit its activity is of special interest because many of these compounds are used as chemotherapeutic agents. Determination of kinetic parameters showed that 3′-azido-3′-deoxythymidine (3′-azidothymidine; AZT), which is widely used for the treatment of human immunodeficiency virus, is a reversible noncompetitive inhibitor ofEscherichia colithymidine phosphorylase (TP). The three-dimensional structure ofE. coliTP complexed with AZT was solved by the molecular-replacement method and was refined at 1.52 Å resolution. Crystals for X-ray study were grown in microgravity by the counter-diffusion technique from a solution of the protein in phosphate buffer with ammonium sulfate as a precipitant. The AZT molecule was located with full occupancy in the electron-density maps in the nucleoside-binding pocket of TP, whereas the phosphate-binding pocket of the enzyme was occupied by phosphate (or sulfate) ion. The structure of the active-site cavity and conformational changes of the enzyme upon AZT binding are described in detail. It is found that the position of AZT differs remarkably from the positions of the pyrimidine bases and nucleoside analogues in other known complexes of pyrimidine phosphorylases, but coincides well with the position of 2′-fluoro-3′-azido-2′,3′-dideoxyuridine (N3FddU) in the recently investigated complex ofE. coliTP with this ligand (Timofeevet al., 2013). The peculiarities of the arrangement of N3FddU and 3′-azidothymidine in the nucleoside binding pocket of TP and correlations between the arrangement and inhibitory properties of these compounds are discussed.

scholarly journals Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures

RSC Advances ◽  
2020 ◽  
Vol 10 (14) ◽  
pp. 8435-8443
Author(s):  
Octav Caldararu ◽  
Majda Misini Ignjatović ◽  
Esko Oksanen ◽  
Ulf Ryde
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Water Structure ◽  
Protein Crystal ◽  
Local Clustering ◽  
Dynamics Simulations ◽  
Structure In Solution

Molecular dynamics simulations can reproduce the water structure around proteins in crystal structure only if a local clustering is performed.

scholarly journals Exploring New Crystal Structures of Glycine via Electric Field-Induced Structural Transformations with Molecular Dynamics Simulations

Processes ◽  
2019 ◽  
Vol 7 (5) ◽  
pp. 268 ◽  
Author(s):  
Pelin Su Bulutoglu ◽  
Conor Parks ◽  
Nandkishor K. Nere ◽  
Shailendra Bordawekar ◽  
Doraiswami Ramkrishna
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Solid State ◽  
Electric Field ◽  
Physical Properties ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Electric Fields ◽  
High Intensity ◽  
Dynamics Simulations

Being able to control polymorphism of a crystal is of great importance to many industries, including the pharmaceutical industry, since the crystal’s structure determines significant physical properties of a material. While there are many conventional methods used to control the final crystal structure that comes out of a crystallization unit, these methods fail to go beyond a few known structures that are kinetically accessible. Recent studies have shown that externally applied fields have the potential to effectively control polymorphism and to extend the set of observable polymorphs that are not accessible through conventional methods. This computational study focuses on the application of high-intensity dc electric fields (e-fields) to induce solid-state transformation of glycine crystals to obtain new polymorphs that have not been observed via experiments. Through molecular dynamics simulations of solid-state α -, β -, and γ -glycine crystals, it has been shown that the new polymorphs sustain their structures within 125 ns after the electric field has been turned off. It was also demonstrated that strength and direction of the electric field and the initial structure of the crystal are parameters that affect the resulting polymorph. Our results showed that application of high-intensity dc electric fields on solid-state crystals can be an effective crystal structure control method for the exploration of new crystal structures of known materials and to extend the range of physical properties a material can have.

scholarly journals Exploring the conformational space of a receptor for drug design: an ERα case study

2020 ◽  
Author(s):  
Melanie Schneider ◽  
Jean-Luc Pons ◽  
Gilles Labesse
Keyword(s):  
Molecular Dynamics ◽  
Drug Design ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Estrogen Receptor Alpha ◽  
Binding Pocket ◽  
Conformational Space ◽  
Toxicity Tests ◽  
Static Structure ◽  
Dynamics Simulations

ABSTRACTMotivationProtein flexibility is challenging for both experimentalists and modellers, especially in the field of drug design. Estrogen Receptor alpha (ERα) is an extensively studied Nuclear Receptor (NR) and a well-known therapeutic target with an important role in development and physiology. It is also a frequent off-target in standard toxicity tests for endocrine disruption. Here, we aim to evaluate the degree to which the conformational space and macromolecular flexibility of this well-characterized drug target can be described. Our approach exploits hundreds of crystallographic structures by means of molecular dynamics simulations and of virtual screening.ResultsThe analysis of hundreds of crystal structures confirms the presence of two main conformational states, known as ‘agonist’ and ‘antagonist’, that mainly differ by the orientation of the C-terminal helix H12 which serves to close the binding pocket. ERα also shows some loop flexibility, as well as variable side-chain orientations in its active site. We scrutinized the extent to which standard molecular dynamics simulations or crystallographic refinement as ensemble recapitulate most of the variability features seen by the array of available crystal structure. In parallel, we investigated on the kind and extent of flexibility that is required to achieve convincing docking for all high-affinity ERα ligands present in BindingDB. Using either only one conformation with a few side-chains set flexible, or static structure ensembles in parallel during docking led to good quality and similar pose predictions. These results suggest that the several hundreds of crystal structures already known can properly describe the whole conformational universe of ERα’s ligand binding domain. This opens the road for better drug design and affinity [email protected]

scholarly journals Pyridylpiperazine-based allosteric inhibitors of RND-type multidrug efflux pumps

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Coline Plé ◽  
Heng-Keat Tam ◽  
Anais Vieira Da Cruz ◽  
Nina Compagne ◽  
Juan-Carlos Jiménez-Castellanos ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Efflux Pump ◽  
Binding Pocket ◽  
Multidrug Efflux ◽  
Allosteric Inhibitors ◽  
E Coli ◽  
Multidrug Efflux Pumps ◽  
Proton Relay ◽  
Rnd Transporter ◽  
Dynamics Simulations

AbstractEfflux transporters of the RND family confer resistance to multiple antibiotics in Gram-negative bacteria. Here, we identify and chemically optimize pyridylpiperazine-based compounds that potentiate antibiotic activity in E. coli through inhibition of its primary RND transporter, AcrAB-TolC. Characterisation of resistant E. coli mutants and structural biology analyses indicate that the compounds bind to a unique site on the transmembrane domain of the AcrB L protomer, lined by key catalytic residues involved in proton relay. Molecular dynamics simulations suggest that the inhibitors access this binding pocket from the cytoplasm via a channel exclusively present in the AcrB L protomer. Thus, our work unveils a class of allosteric efflux-pump inhibitors that likely act by preventing the functional catalytic cycle of the RND pump.

scholarly journals Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase (ppnP) revealed a Cupin fold

2021 ◽  
Author(s):  
Yan Wen ◽  
Xiaojia Li ◽  
Wenting Guo ◽  
Baixing Wu
Keyword(s):  
Crystal Structures ◽  
Purine Nucleoside Phosphorylase ◽  
Binding Pocket ◽  
Purine Nucleoside ◽  
Structural Basis ◽  
Nucleoside Phosphorylase ◽  
E Coli ◽  
New Class ◽  
Nucleoside Phosphorylases ◽  
Pocket Formation

Nucleotides metabolism is a fundamental process in all organisms. Two families of nucleoside phosphorylases (NP) that catalyze the phosphorolytic cleavage of the glycosidic bond in nucleosides have been found, including the trimeric or hexameric NP-I and dimeric NP-II family enzymes. Recently studies revealed another class of NP protein in E. coli named Pyrimidine/purine nucleoside phosphorylase (ppnP), which can catalyze the phosphorolysis of diverse nucleosides and yield D-ribose 1-phosphate and the respective free bases. Here, we solve the crystal structures of ppnP from E. coli and the other three species. Our studies revealed that the structure of ppnP belongs to the Rlmc-like cupin fold and showed as a rigid dimeric conformation. Detail analysis revealed a potential nucleoside binding pocket full of hydrophobic residues. And the residues involved in the dimer and pocket formation are all well conserved in bacteria. Since the cupin fold is a large superfamily in the biosynthesis of natural products, our studies provide the structural basis for understanding and the directed evolution of NP proteins.

scholarly journals Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Nicholas Francia ◽  
Louise Price ◽  
Matteo Salvalaglio
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Crystal Structures ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Large Scale ◽  
Lattice Energy ◽  
Racemic Mixture ◽  
Dynamics Simulations

<p>The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy calculations, which are known to significantly over-predict the number of plausible crystal structures. A valuable tool to reduce overprediction is to employ physics-based, dynamic simulations to coalesce lattice energy minima separated by small barriers into a smaller number of more stable geometries once thermal effects are introduced. Molecular dynamics simulations and enhanced sampling methods can be employed in this context to simulate crystal structures at finite temperature and pressure. </p><p>Here we demonstrate the applicability of approaches based on molecular dynamics to systematically process realistic CSP datasets containing several hundreds of crystal structures. The system investigated is ibuprofen, a conformationally flexible active pharmaceutical ingredient that crystallises both in enantiopure forms and as a racemic mixture. By introducing a hierarchical approach in the analysis of finite-temperature supercell configurations, we can post-process a dataset of 555 crystal structures, identifying 65% of the initial structures as labile, while maintaining all the experimentally known crystal structures in the final, reduced set. Moreover, the extensive nature of the initial dataset allows one to gain quantitative insight into the persistence and the propensity to transform of crystal structures containing common hydrogen-bonded intermolecular interaction motifs.</p>

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