In Vivo Targeting of Endogenous Proteins with Reactive Small Molecules

: Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder – nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.

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Computational study for suppression of CD25/IL-2 interaction

Biological Chemistry ◽

10.1515/hsz-2020-0326 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Moein Dehbashi ◽

Zohreh Hojati ◽

Majid Motovali-bashi ◽

Mazdak Ganjalikhani-Hakemi ◽

Akihiro Shimosaka ◽

...

Keyword(s):

Small Molecules ◽

Cancer Progression ◽

Immune Escape ◽

De Novo ◽

Computational Study ◽

Treg Cells ◽

Homology Search ◽

Small Interfering Rnas

AbstractCancer recurrence presents a huge challenge in cancer patient management. Immune escape is a key mechanism of cancer progression and metastatic dissemination. CD25 is expressed in regulatory T (Treg) cells including tumor-infiltrating Treg cells (TI-Tregs). These cells specially activate and reinforce immune escape mechanism of cancers. The suppression of CD25/IL-2 interaction would be useful against Treg cells activation and ultimately immune escape of cancer. Here, software, web servers and databases were used, at which in silico designed small interfering RNAs (siRNAs), de novo designed peptides and virtual screened small molecules against CD25 were introduced for the prospect of eliminating cancer immune escape and obtaining successful treatment. We obtained siRNAs with low off-target effects. Further, small molecules based on the binding homology search in ligand and receptor similarity were introduced. Finally, the critical amino acids on CD25 were targeted by a de novo designed peptide with disulfide bond. Hence we introduced computational-based antagonists to lay a foundation for further in vitro and in vivo studies.

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Peptide-tags for site-specific protein labelling in vitro and in vivo

Molecular BioSystems ◽

10.1039/c6mb00023a ◽

2016 ◽

Vol 12 (6) ◽

pp. 1731-1745 ◽

Cited By ~ 96

Author(s):

Jonathan Lotze ◽

Ulrike Reinhardt ◽

Oliver Seitz ◽

Annette G. Beck-Sickinger

Keyword(s):

Metal Ions ◽

Small Molecules ◽

Protein Localization ◽

Specific Protein ◽

Site Specific ◽

Protein Labelling ◽

Peptide Interactions ◽

Peptide Tags

Peptide-tag based labelling can be achieved by (i) enzymes (ii) recognition of metal ions or small molecules and (iii) peptide–peptide interactions and enables site-specific protein visualization to investigate protein localization and trafficking.

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Erratum: Corrigendum: Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature

Scientific Reports ◽

10.1038/srep40471 ◽

2017 ◽

Vol 7 (1) ◽

Author(s):

Paul E. Reyes-Gutiérrez ◽

Tomáš Kapal ◽

Blanka Klepetářová ◽

David Šaman ◽

Radek Pohl ◽

...

Keyword(s):

Small Molecules ◽

Cross Link ◽

Quadruplex Dna ◽

G Quadruplex ◽

Assignment Error

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A therapeutic combination of two small molecule toxin inhibitors provides pancontinental preclinical efficacy against viper snakebite

10.1101/2020.05.13.094599 ◽

2020 ◽

Cited By ~ 3

Author(s):

Laura-Oana Albulescu ◽

Chunfang Xie ◽

Stuart Ainsworth ◽

Jaffer Alsolaiss ◽

Edouard Crittenden ◽

...

Keyword(s):

Small Molecules ◽

Enzyme Inhibitors ◽

Interspecific Variation ◽

Medical Emergency ◽

Dual Inhibitor ◽

Mortality And Morbidity ◽

Venom Composition ◽

Inhibitor Combination

AbstractSnakebite is a medical emergency causing high mortality and morbidity in rural tropical communities that typically experience delayed access to unaffordable therapeutics. Viperid snakes are responsible for the majority of envenomings, but extensive interspecific variation in venom composition dictates that different antivenom treatments are used in different parts of the world, resulting in clinical and fiscal snakebite management challenges. Here, we show that a number of repurposed Phase 2-approved small molecules are capable of broadly neutralizing distinct viper venom bioactivities in vitro by inhibiting different enzymatic toxin families. Furthermore, using multiple in vivo models of envenoming, we demonstrate that a single dose of a rationally-selected dual inhibitor combination consisting of marimastat and varespladib prevents lethality caused by venom from the most medically-important vipers of Africa, South Asia and Central America. Our findings strongly support the translation of combinations of safe and affordable enzyme inhibitors as novel broad-spectrum therapeutics for snakebite.

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PET Imaging Radiotracers of Chemokine Receptors

Molecules ◽

10.3390/molecules26175174 ◽

2021 ◽

Vol 26 (17) ◽

pp. 5174

Author(s):

Santosh R. Alluri ◽

Yusuke Higashi ◽

Kun-Eek Kil

Keyword(s):

Small Molecules ◽

Chemokine Receptors ◽

Brain Disorders ◽

Infectious Agents ◽

Cardiovascular Research ◽

Critical Signal ◽

Inflammatory Reactions ◽

Positron Emission

Chemokines and chemokine receptors have been recognized as critical signal components that maintain the physiological functions of various cells, particularly the immune cells. The signals of chemokines/chemokine receptors guide various leukocytes to respond to inflammatory reactions and infectious agents. Many chemokine receptors play supportive roles in the differentiation, proliferation, angiogenesis, and metastasis of diverse tumor cells. In addition, the signaling functions of a few chemokine receptors are associated with cardiac, pulmonary, and brain disorders. Over the years, numerous promising molecules ranging from small molecules to short peptides and antibodies have been developed to study the role of chemokine receptors in healthy states and diseased states. These drug-like candidates are in turn exploited as radiolabeled probes for the imaging of chemokine receptors using noninvasive in vivo imaging, such as positron emission tomography (PET). Recent advances in the development of radiotracers for various chemokine receptors, particularly of CXCR4, CCR2, and CCR5, shed new light on chemokine-related cancer and cardiovascular research and the subsequent drug development. Here, we present the recent progress in PET radiotracer development for imaging of various chemokine receptors.

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Phaseolin type and heat treatment influence the biochemistry of protein digestion in the rat intestine

British Journal Of Nutrition ◽

10.1017/s0007114507819179 ◽

2008 ◽

Vol 99 (3) ◽

pp. 531-539 ◽

Cited By ~ 11

Author(s):

Carlos A. Montoya ◽

Pascal Leterme ◽

Stephen Beebe ◽

Wolfgang B. Souffrant ◽

Daniel Mollé ◽

...

Keyword(s):

Heat Treatment ◽

Western Blotting ◽

Sole Source ◽

Protein Band ◽

Molecular Weights ◽

Endogenous Protein ◽

Anionic Trypsin ◽

Endogenous Proteins ◽

Protein Components

The study aimed to investigate thein vivodigestion ofPhaseolus vulgarisphaseolin types differing in their subunit pattern composition. Diets contained either casein as the sole source of protein or a mixture (1:1) of casein and pure Sanilac (S), Tendergreen (T) or Inca (I) phaseolin either unheated or heated. Rats were fed for 11 d with the experimental diets. Their ileal content and mucosa were collected and prepared for electrophoresis, Western blotting, densitometry and MS. Differences in digestion among native phaseolin types were observed for intact phaseolin at molecular weights (MW) of 47–50·5 kDa and for an undigested fragment at MW of 19–21·5 kDa in ileal digesta. In both cases, the concentration of these protein bands was lower for I phaseolin than for S or T phaseolin (P < 0·05). In the mucosa, the concentration of a protein band at MW of 20·5–21·5 kDa was lower for S phaseolin as compared to T or I phaseolin (P < 0·001). The presence of phaseolin subunits and their fragments was confirmed by Western blotting. MS analysis revealed the presence of undigested α and β subunit fragments from phaseolin and endogenous proteins (anionic trypsin I and pancreatic α-amylase) in ileal digesta. Thermal treatment improved digestion (P < 0·01), acting on both dietary and endogenous protein components. In conclusion, this study provides evidence for differences in intestinal digestion among phaseolin types, S phaseolin being more resistant and I phaseolin more susceptible. These differences were affected by the origin of the phaseolin subunit precursor. Heat treatment enhanced phaseolin digestion.

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Targeting the Respiratory Syncytial Virus N0-P Complex with Constrained α-Helical Peptides in Cells and Mice

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00717-20 ◽

2020 ◽

Vol 64 (10) ◽

Author(s):

Marie Galloux ◽

Nadège Gsponer ◽

Vanessa Gaillard ◽

Brice Fenner ◽

Thibaut Larcher ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Small Molecules ◽

Mechanisms Of Action ◽

Rsv Infection ◽

Macrocyclic Peptides ◽

Escape Mutants ◽

Severe Respiratory Infection ◽

Syncytial Virus

ABSTRACT Respiratory syncytial virus (RSV) is the main cause of severe respiratory infection in young children worldwide, and no therapies have been approved for the treatment of RSV infection. Data from recent clinical trials of fusion or L polymerase inhibitors for the treatment of RSV-infected patients revealed the emergence of escape mutants, highlighting the need for the discovery of inhibitors with novel mechanisms of action. Here we describe stapled peptides derived from the N terminus of the phosphoprotein (P) that act as replication inhibitors. We demonstrate that these peptides inhibit RSV replication in vitro and in vivo by preventing the formation of the N0-P complex. The present strategy provides a novel means of targeting RSV replication with constrained macrocyclic peptides or small molecules and is broadly applicable to other viruses of the Mononegavirales order.

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Targeting the TR4 nuclear receptor-mediated lncTASR/AXL signaling with tretinoin increases the sunitinib sensitivity to better suppress the RCC progression

Oncogene ◽

10.1038/s41388-019-0962-8 ◽

2019 ◽

Vol 39 (3) ◽

pp. 530-545 ◽

Cited By ~ 1

Author(s):

Hangchuan Shi ◽

Yin Sun ◽

Miao He ◽

Xiong Yang ◽

Michiaki Hamada ◽

...

Keyword(s):

Small Molecules ◽

Nuclear Receptor ◽

Preclinical Study ◽

First Line ◽

Novel Therapy ◽

Signaling Mechanism ◽

First Line Therapy ◽

Line Therapy ◽

The Stability

Abstract Renal cell carcinoma (RCC) is one of the most lethal urological tumors. Using sunitinib to improve the survival has become the first-line therapy for metastatic RCC patients. However, the occurrence of sunitinib resistance in the clinical application has curtailed its efficacy. Here we found TR4 nuclear receptor might alter the sunitinib resistance to RCC via altering the TR4/lncTASR/AXL signaling. Mechanism dissection revealed that TR4 could modulate lncTASR (ENST00000600671.1) expression via transcriptional regulation, which might then increase AXL protein expression via enhancing the stability of AXL mRNA to increase the sunitinib resistance in RCC. Human clinical surveys also linked the expression of TR4, lncTASR, and AXL to the RCC survival, and results from multiple RCC cell lines revealed that targeting this newly identified TR4-mediated signaling with small molecules, including tretinoin, metformin, or TR4-shRNAs, all led to increase the sunitinib sensitivity to better suppress the RCC progression, and our preclinical study using the in vivo mouse model further proved tretinoin had a better synergistic effect to increase sunitinib sensitivity to suppress RCC progression. Future successful clinical trials may help in the development of a novel therapy to better suppress the RCC progression.

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