Chemical parameters influencing fine-tuning in the binding of macrolide antibiotics to the ribosomal tunnel

In comparison to existing structural, biochemical, and therapeutical data, the crystal structures of large ribosomal subunit from the eubacterial pathogen model Deinococcus radiodurans in complex with the 14-membered macrolides erythromycylamine, RU69874, and the 16-membered macrolide josamycin, highlighted the similarities and differences in macrolides binding to the ribosomal tunnel. The three compounds occupy the macrolide binding pocket with their desosamine or mycaminose aminosugar, the C4-C7 edge of the macrolactone ring and the cladinose sugar sharing similar positions and orientations, although the latter, known to be unnecessary for antibiotic activity, displays fewer contacts. The macrolactone ring displays altogether few contacts with the ribosome and can, therefore, tilt in order to optimize its interaction with the 23S rRNA. In addition to their contacts with nucleotides of domain V of the 23S RNA, erythromycylamine and RU69874 interact with domain II nucleotide U790, and RU69874 also reaches van der Waals distance from A752, in a fashion similar to that observed for the ketolides telithromycin and cethromycin. The variability in the sequences and consequently the diversity of the conformations of macrolide binding pockets in various bacterial species can explain the drug's altered level of effectiveness on different organisms and is thus an important factor in structure-based drug design.

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Phylogenetic Sequence Variations in Bacterial rRNA Affect Species-Specific Susceptibility to Drugs Targeting Protein Synthesis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01398-10 ◽

2011 ◽

Vol 55 (9) ◽

pp. 4096-4102 ◽

Cited By ~ 6

Author(s):

Subramanian Akshay ◽

Mihai Bertea ◽

Sven N. Hobbie ◽

Björn Oettinghaus ◽

Dimitri Shcherbakov ◽

...

Keyword(s):

Binding Pocket ◽

Drug Susceptibility ◽

Drug Binding ◽

23S Rrna ◽

Content Type ◽

Sequence Variations ◽

Binding Pockets ◽

Species Specific ◽

Peptidyltransferase Center ◽

A Site

ABSTRACTAntibiotics targeting the bacterial ribosome typically bind to highly conserved rRNA regions with only minor phylogenetic sequence variations. It is unclear whether these sequence variations affect antibiotic susceptibility or resistance development. To address this question, we have investigated the drug binding pockets of aminoglycosides and macrolides/ketolides. The binding site of aminoglycosides is located within helix 44 of the 16S rRNA (A site); macrolides/ketolides bind to domain V of the 23S rRNA (peptidyltransferase center). We have used mutagenesis of rRNA sequences inMycobacterium smegmatisribosomes to reconstruct the different bacterial drug binding sites and to study the effects of rRNA sequence variations on drug activity. Our results provide a rationale for differences in species-specific drug susceptibility patterns and species-specific resistance phenotypes associated with mutational alterations in the drug binding pocket.

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23S rRNA 2058A→G Alteration Mediates Ketolide Resistance in Combination with Deletion in L22

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00767-06 ◽

2006 ◽

Vol 50 (11) ◽

pp. 3816-3823 ◽

Cited By ~ 25

Author(s):

Rita Berisio ◽

Natascia Corti ◽

Peter Pfister ◽

Ada Yonath ◽

Erik C. Böttger

Keyword(s):

Mycobacterium Smegmatis ◽

Deinococcus Radiodurans ◽

Weak Interactions ◽

Ribosomal Subunit ◽

Drug Binding ◽

23S Rrna ◽

Large Ribosomal Subunit ◽

Drug Binding Site ◽

Nascent Chain ◽

Carbamate Group

ABSTRACT Resistance to macrolides and ketolides occurs mainly via alterations in RNA moieties of the drug-binding site. Using an A2058G mutant of Mycobacterium smegmatis, additional telithromycin resistance was acquired via deletion of 15 residues from protein L22. Molecular modeling, based on the crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with telithromycin, shows that the telithromycin carbamate group is located in the proximity of the tip of the L22 hairpin-loop, allowing for weak interactions between them. These weak interactions may become more important once the loss of A2058 interactions destabilizes drug binding, presumably resulting in a shift of the drug toward the other side of the tunnel, namely, to the vicinity of L22. Hence, the deletion of 15 residues from L22 may further destabilize telithromycin binding and confer telithromycin resistance. Such deletions may also lead to notable differences in the tunnel outline, as well as to an increase of its diameter to a size, allowing the progression of the nascent chain.

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Role of Toll-Like Receptor 13 in Innate Immune Recognition of Group B Streptococci

Infection and Immunity ◽

10.1128/iai.02282-14 ◽

2014 ◽

Vol 82 (12) ◽

pp. 5013-5022 ◽

Cited By ~ 27

Author(s):

Giacomo Signorino ◽

Nastaran Mohammadi ◽

Francesco Patanè ◽

Marco Buscetta ◽

Mario Venza ◽

...

Keyword(s):

Bacterial Species ◽

Ribosomal Subunit ◽

23S Rrna ◽

Immune Recognition ◽

Toll Like Receptor ◽

Host Defenses ◽

Bacterial Rna ◽

Group B ◽

The Impact

ABSTRACTMurine Toll-like receptor 13 (TLR13), an endosomal receptor that is not present in humans, is activated by an unmethylated motif present in the large ribosomal subunit of bacterial RNA (23S rRNA). Little is known, however, of the impact of TLR13 on antibacterial host defenses. Here we examined the role of this receptor in the context of infection induced by the model pathogen group B streptococcus (GBS). To this end, we used bacterial strains masked from TLR13 recognition by virtue of constitutive expression of the ErmC methyltransferase, which results in dimethylation of the 23S rRNA motif at a critical adenine residue. We found that TLR13-mediated rRNA recognition was required for optimal induction of tumor necrosis factor alpha and nitrous oxide in dendritic cell and macrophage cultures stimulated with heat-killed bacteria or purified bacterial RNA. However, TLR13-dependent recognition was redundant when live bacteria were used as a stimulus. Moreover, masking bacterial rRNA from TLR13 recognition did not increase the ability of GBS to avoid host defenses and replicatein vivo. In contrast, increased susceptibility to infection was observed under conditions in which signaling by all endosomal TLRs was abolished, i.e., in mice with a loss-of-function mutation in the chaperone protein UNC93B1. Our data lend support to the conclusion that TLR13 participates in GBS recognition, although blockade of the function of this receptor can be compensated for by other endosomal TLRs. Lack of selective pressure by bacterial infections might explain the evolutionary loss of TLR13 in humans. However, further studies using different bacterial species are needed to prove this hypothesis.

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DeepBindPoc: a deep learning method to rank ligand binding pockets using molecular vector representation

PeerJ ◽

10.7717/peerj.8864 ◽

2020 ◽

Vol 8 ◽

pp. e8864

Author(s):

Haiping Zhang ◽

Konda Mani Saravanan ◽

Jinzhi Lin ◽

Linbu Liao ◽

Justin Tze-Yang Ng ◽

...

Keyword(s):

Deep Learning ◽

Ligand Binding ◽

Spatial Information ◽

Binding Pocket ◽

Learning Method ◽

Accurate Identification ◽

Data Set ◽

Structure Based Drug Design ◽

Binding Pockets ◽

High Level

Accurate identification of ligand-binding pockets in a protein is important for structure-based drug design. In recent years, several deep learning models were developed to learn important physical–chemical and spatial information to predict ligand-binding pockets in a protein. However, ranking the native ligand binding pockets from a pool of predicted pockets is still a hard task for computational molecular biologists using a single web-based tool. Hence, we believe, by using closer to real application data set as training and by providing ligand information, an enhanced model to identify accurate pockets can be obtained. In this article, we propose a new deep learning method called DeepBindPoc for identifying and ranking ligand-binding pockets in proteins. The model is built by using information about the binding pocket and associated ligand. We take advantage of the mol2vec tool to represent both the given ligand and pocket as vectors to construct a densely fully connected layer model. During the training, important features for pocket-ligand binding are automatically extracted and high-level information is preserved appropriately. DeepBindPoc demonstrated a strong complementary advantage for the detection of native-like pockets when combined with traditional popular methods, such as fpocket and P2Rank. The proposed method is extensively tested and validated with standard procedures on multiple datasets, including a dataset with G-protein Coupled receptors. The systematic testing and validation of our method suggest that DeepBindPoc is a valuable tool to rank near-native pockets for theoretically modeled protein with unknown experimental active site but have known ligand. The DeepBindPoc model described in this article is available at GitHub (https://github.com/haiping1010/DeepBindPoc) and the webserver is available at (http://cbblab.siat.ac.cn/DeepBindPoc/index.php).

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Halobacterium cutirubrum ribosomes. Properties of the ribosomal proteins and ribonucleic acid

Biochemical Journal ◽

10.1042/bj1300103 ◽

1972 ◽

Vol 130 (1) ◽

pp. 103-110 ◽

Cited By ~ 51

Author(s):

L. P. Visentin ◽

C. Chow ◽

A. T. Matheson ◽

M. Yaguchi ◽

F. Rollin

Keyword(s):

Ribosomal Protein ◽

Ribosomal Proteins ◽

Soluble Fraction ◽

Ribosomal Subunit ◽

23S Rrna ◽

Core Particle ◽

Fractionation Procedure ◽

Additional Protein ◽

70S Ribosome ◽

Low Ionic Strength

1. The 30S ribosomal subunit of the extreme halophile Halobacterium cutirubrum is unstable and loses 75% of its ribosomal protein when the 70S ribosome is dissociated into the two subunits. A stable 30S subunit is obtained if the dissociation of the 70S particle is carried out in the presence of the soluble fraction. 2. A fractionation procedure was developed for the selective removal of groups of proteins from the 30S and 50S subunits. When the ribosomes, which are stable in 4m-K+ and 0.1m-Mg2+, were extracted with low-ionic-strength buffer 75–80% of the 30S proteins and 60–65% of the 50S proteins as well as the 5S rRNA were released. The proteins in this fraction are the most acidic of the H. cutirubrum ribosomal proteins. Further extraction with Li+–EDTA releases additional protein, leaving a core particle containing either 16S rRNA or 23S rRNA and about 5% of the total ribosomal protein. The amino acid composition, mobility on polyacrylamide gels at pH4.5 and 8.7, and the molecular-weight distribution of the various protein fractions were determined. 3. The s values of the rRNA are 5S, 16S and 23S. The C+G contents of the 16S and 23S rRNA were 56.1 and 58.8% respectively and these are higher than C+G contents of the corresponding Escherichia coli rRNA (53.8 and 54.1%).

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Ketolide Antimicrobial Activity Persists after Disruption of Interactions with Domain II of 23S rRNA

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.10.3677-3683.2004 ◽

2004 ◽

Vol 48 (10) ◽

pp. 3677-3683 ◽

Cited By ~ 20

Author(s):

Guy W. Novotny ◽

Lene Jakobsen ◽

Niels M. Andersen ◽

Jacob Poehlsgaard ◽

Stephen Douthwaite

Keyword(s):

Antimicrobial Activity ◽

Ribosomal Subunit ◽

23S Rrna ◽

Alkyl Aryl ◽

Interaction Sites ◽

Enhanced Resistance ◽

Low Levels ◽

Domain V ◽

Block Protein Synthesis ◽

Do So

ABSTRACT Ketolides are the latest derivatives developed from the macrolide erythromycin to improve antimicrobial activity. All macrolides and ketolides bind to the 50S ribosomal subunit, where they come into contact with adenosine 2058 (A2058) within domain V of the 23S rRNA and block protein synthesis. An additional interaction at nucleotide A752 in the rRNA domain II is made via the synthetic carbamate-alkyl-aryl substituent in the ketolides HMR3647 (telithromycin) and HMR3004, and this interaction contributes to their improved activities. Only a few macrolides, including tylosin, come into contact with domain II of the rRNA and do so via interactions with nucleotides G748 and A752. We have disrupted these macrolide-ketolide interaction sites in the rRNA to assess their relative importance for binding. Base substitutions at A752 were shown to confer low levels of resistance to telithromycin but not to HMR3004, while deletion of A752 confers low levels of resistance to both ketolides. Mutations at position 748 confer no resistance. Substitution of guanine at A2058 gives rise to the MLSB (macrolide, lincosamide, and streptogramin B) phenotype, which confers resistance to all the drugs. However, resistance to ketolides was abolished when the mutation at position 2058 was combined with a mutation in domain II of the same rRNA. In contrast, the same dual mutations in rRNAs conferred enhanced resistance to tylosin. Our results show that the domain II interactions of telithromycin and HMR3004 differ from each other and from those of tylosin. The data provide no indication that mutations within domain II, either alone or in combination with an A2058 mutation, can confer significant levels of telithromycin resistance.

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Fluorescent nanoparticle sensors with tailor-made recognition units and proximate fluorescent reporter groups

New Journal of Chemistry ◽

10.1039/c8nj01139g ◽

2018 ◽

Vol 42 (12) ◽

pp. 9377-9380 ◽

Cited By ~ 3

Author(s):

Xiaoyu Xing ◽

Yan Zhao

Keyword(s):

Molecular Imprinting ◽

Binding Pocket ◽

Fluorescent Sensors ◽

Covalent Modification ◽

Fluorescent Reporter ◽

Binding Pockets ◽

Fluorescent Nanoparticle

Molecular imprinting in micelles followed by covalent modification of the binding pocket yielded fluorescent sensors with precisely constructed binding pockets.

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Protein-Protein Interactions (PPIs) as an Alternative to Targeting the ATP Binding Site of Kinase

Advances in Medical Technologies and Clinical Practice - Applied Case Studies and Solutions in Molecular Docking-Based Drug Design ◽

10.4018/978-1-5225-0362-0.ch010 ◽

2016 ◽

pp. 249-277

Author(s):

Sailu Sarvagalla ◽

Mohane Selvaraj Coumar

Keyword(s):

Protein Interactions ◽

In Silico ◽

Rational Design ◽

Kinase Activity ◽

Hot Spot ◽

Binding Pocket ◽

Atp Binding ◽

Protein Protein Interactions ◽

Structure Based Drug Design ◽

Atp Binding Site

Most of the developed kinase inhibitor drugs are ATP competitive and suffer from drawbacks such as off-target kinase activity, development of resistance due to mutation in the ATP binding pocket and unfavorable intellectual property situations. Besides the ATP binding pocket, protein kinases have binding sites that are involved in Protein-Protein Interactions (PPIs); these PPIs directly or indirectly regulate the protein kinase activity. Of recent, small molecule inhibitors of PPIs are emerging as an alternative to ATP competitive agents. Rational design of inhibitors for kinase PPIs could be carried out using molecular modeling techniques. In silico tools available for the prediction of hot spot residues and cavities at the PPI sites and the means to utilize this information for the identification of inhibitors are discussed. Moreover, in silico studies to target the Aurora B-INCENP PPI sites are discussed in context. Overall, this chapter provides detailed in silico strategies that are available to the researchers for carrying out structure-based drug design of PPI inhibitors.

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Structure-based inhibitor design of mutant RAS proteins—a paradigm shift

Cancer and Metastasis Reviews ◽

10.1007/s10555-020-09914-6 ◽

2020 ◽

Vol 39 (4) ◽

pp. 1091-1105

Author(s):

Kinga Nyíri ◽

Gergely Koppány ◽

Beáta G. Vértessy

Keyword(s):

Covalent Modification ◽

Small Gtpase ◽

Drug Binding ◽

Ras Proteins ◽

Structure Based Drug Design ◽

Lung Cancers ◽

Long Time ◽

Binding Pockets ◽

Cancer Types ◽

Kras Protein

AbstractAs a member of small GTPase family, KRAS protein is a key physiological modulator of various cellular activities including proliferation. However, mutations of KRAS present in numerous cancer types, most frequently in pancreatic (> 60%), colorectal (> 40%), and lung cancers, drive oncogenic processes through overactivation of proliferation. The G12C mutation of KRAS protein is especially abundant in the case of these types of malignancies. Despite its key importance in human disease, KRAS was assumed to be non-druggable for a long time since the protein seemingly lacks potential drug-binding pockets except the nucleotide-binding site, which is difficult to be targeted due to the high affinity of KRAS for both GDP and GTP. Recently, a new approach broke the ice and provided evidence that upon covalent targeting of the G12C mutant KRAS, a highly dynamic pocket was revealed. This novel targeting is especially important since it serves with an inherent solution for drug selectivity. Based on these results, various structure-based drug design projects have been launched to develop selective KRAS mutant inhibitors. In addition to the covalent modification strategy mostly applicable for G12C mutation, different innovative solutions have been suggested for the other frequently occurring oncogenic G12 mutants. Here we summarize the latest advances of this field, provide perspectives for novel approaches, and highlight the special properties of KRAS, which might issue some new challenges.

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