Low Basicity as a Characteristic for Atypical Ligands of Serotonin Receptor 5-HT2

Serotonin receptors are extensively examined by academic and industrial researchers, due to their vital roles, which they play in the organism and constituting therefore important drug targets. Up to very recently, it was assumed that the basic nitrogen in compound structure is a necessary component to make it active within this receptor system. Such nitrogen interacts in its protonated form with the aspartic acid from the third transmembrane helix (D3x32) forming a hydrogen bond tightly fitting the ligand in the protein binding site. However, there are several recent studies that report strong serotonin receptor affinity also for compounds without a basic moiety in their structures. In the study, we carried out a comprehensive in silico analysis of the low-basicity phenomenon of the selected serotonin receptor ligands. We focused on the crystallized representatives of the proteins of 5-HT1B, 5-HT2A, 5-HT2B, and 5-HT2C receptors, and examined the problem both from the ligand- and structure-based perspectives. The study was performed for the native proteins, and for D3x32A mutants. The investigation resulted in the determination of nonstandard structural requirements for activity towards serotonin receptors, which can be used in the design of new nonbasic ligands.

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Increased release of serotonin from rat primary isolated adult cardiac myofibroblasts

Scientific Reports ◽

10.1038/s41598-021-99632-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Emiri Tarbit ◽

Indu Singh ◽

Jason Nigel Peart ◽

Svetlana Bivol ◽

Roselyn Barbara Rose’Meyer

Keyword(s):

Heart Failure ◽

Protein Expression ◽

Western Blot ◽

Serotonin Receptors ◽

Serotonin Receptor ◽

Cardiac Fibroblasts ◽

Cardiac Fibroblast ◽

Receptor Protein ◽

Receptor System ◽

Cardiac Myofibroblasts

AbstractElevated blood serotonin levels have been observed in patients with heart failure and serotonin has a role in pathological cardiac function. The serotonin receptor system was examined in adult rat isolated cardiac fibroblast and myofibroblast cells. This is one of the first studies that has investigated serotonin receptors and other proteins involved in the serotonin receptor system in rat cardiac fibroblast and myofibroblast cells. Rat primary cardiac fibroblasts were isolated and transformed into myofibroblasts using 5 ng/ml TGF-β1. Transformation of cells to myofibroblasts was confirmed with the presence of α-smooth muscle actin using Western blot. Serotonin metabolism and receptor protein expression was assessed using Western blot techniques and serotonin levels measured using ELISA. The 5-HT1A, 5-HT2A and 5-HT2B receptors were found to be present in both rat cardiac fibroblasts and myofibroblast cells, however no significance in protein expression between the two cell types was found (P > 0.05). In this study a significant increase in the serotonin transporter (SERT), tryptophan hydroxylase 1 and extracellular serotonin levels was observed in rat cardiac myofibroblasts when compared to fibroblasts (P < 0.05). These results suggest that serotonin levels may rise in parallel with cardiac myofibroblast populations and contribute to the pathogenesis of heart failure via serotonin receptors.

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In Silico Analysis of Effect of Non-synonymous SNPs associated with Permanent Neonatal Diabetes Mellitus on Stability and Structure of Human Insulin

10.1101/2020.09.01.278002 ◽

2020 ◽

Author(s):

Nishat Tabassum

Keyword(s):

Human Insulin ◽

Drug Targets ◽

In Silico Analysis ◽

Neonatal Diabetes ◽

Building Blocks ◽

Permanent Neonatal Diabetes ◽

The Impact ◽

Potential Drug Targets ◽

Analysis Determination

AbstractMotivationProteins are the building-blocks of life. However with the deluge of data on protein sequences and their association with diseases, it is imperative to use computational tools to aid experimental analysis. Determination of the impact of disease-causing SNPs on protein’s structure is crucial in discovering how a disease affects the functions on a fundamental level and thereafter, determining potential drug targets.ResultsSNPs associated with the genetic disease permanent neonatal diabetus mellitus (PNDM) were studied to determine their impact on human insulin. Out of 16 missense variants, eight were predicted to be deleterious. 6 of the SNPs resulted in high structural differences (RMSD > 0.9, H bonds > 35). Stability changes were also determined.

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Crystallographic approach to determination of active conformations of LCAPs

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314083028 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1697-C1697

Author(s):

Marek Glowka ◽

Malgorzata Szczesio ◽

Andrzej Olczak

Keyword(s):

Serotonin Receptor ◽

Antidepressant Drugs ◽

Terminal Group ◽

Aliphatic Chain ◽

Receptor Ligands ◽

Piperazine Ring ◽

Flexible Spacer ◽

Or Groups ◽

Conformational Freedom

Long-Chain Aryl-Piperazines (LCAPs) are well known serotonin receptor ligands used in several marketed antidepressant drugs. LCAPs consist of three structural units: a terminal group, an arylpiperazine at one N atom and an aliphatic chain (spacer) at the other N atom joining the two former units. Both the arylpiperazine and the terminal groups have rather rigid structures and thus their conformational freedom is limited. The opposite is true for the aliphatic spacer, which allows practically any orientation of the terminal group. The resulting diversity of conformations observed in the crystals of LCAPs is significant, which explains their affinity to many serotonin receptors. There is a vast literature on the subject and some qualitative observations were developed. However, due to the flexible spacer and diversity of the terminal groups, their usefulness is limited. Our X-ray (16 crystal structures) and affinity studies on almost sixty new LCAPs [1], together with the data from CSD, enable us to determine the common conformations of LCAPs and the relationships between structure, affinity and conformation. In the analysis, the following features were considered: (i) - axial/equatorial orientations of the substituents of the piperazine ring; (ii) –N1 protonation possible in the physiological environment; (iii) - a twist of the aryl ring; (iv) –the parity and the number of atoms in the spacer; (v) – the presence of heteroatoms or groups in the spacer; (vi) – the spatial position of the terminal group in relation to the piperazine ring.

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Living-Cell Diffracted X-ray Tracking Analysis Confirmed Internal Salt Bridge Is Critical for Ligand-Induced Twisting Motion of Serotonin Receptors

International Journal of Molecular Sciences ◽

10.3390/ijms22105285 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5285

Author(s):

Kazuhiro Mio ◽

Shoko Fujimura ◽

Masaki Ishihara ◽

Masahiro Kuramochi ◽

Hiroshi Sekiguchi ◽

...

Keyword(s):

Serotonin Receptors ◽

Serotonin Receptor ◽

Frame Rate ◽

Receptor Subtype ◽

Transmembrane Segment ◽

Hek 293 ◽

Gold Nanocrystals ◽

X Ray ◽

Time Dynamics ◽

Analytical Technique

Serotonin receptors play important roles in neuronal excitation, emotion, platelet aggregation, and vasoconstriction. The serotonin receptor subtype 2A (5-HT2AR) is a Gq-coupled GPCR, which activate phospholipase C. Although the structures and functions of 5-HT2ARs have been well studied, little has been known about their real-time dynamics. In this study, we analyzed the intramolecular motion of the 5-HT2AR in living cells using the diffracted X-ray tracking (DXT) technique. The DXT is a very precise single-molecular analytical technique, which tracks diffraction spots from the gold nanocrystals labeled on the protein surface. Trajectory analysis provides insight into protein dynamics. The 5-HT2ARs were transiently expressed in HEK 293 cells, and the gold nanocrystals were attached to the N-terminal introduced FLAG-tag via anti-FLAG antibodies. The motions were recorded with a frame rate of 100 μs per frame. A lifetime filtering technique demonstrated that the unliganded receptors contain high mobility population with clockwise twisting. This rotation was, however, abolished by either a full agonist α-methylserotonin or an inverse agonist ketanserin. Mutation analysis revealed that the “ionic lock” between the DRY motif in the third transmembrane segment and a negatively charged residue of the sixth transmembrane segment is essential for the torsional motion at the N-terminus of the receptor.

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In silico characterization and structural modeling of bacterial metalloprotease of family M4

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-020-00105-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Rajnee Hasan ◽

Md. Nazmul Haq Rony ◽

Rasel Ahmed

Keyword(s):

Drug Targets ◽

Active Sites ◽

Pathogenic Bacteria ◽

Tertiary Structure ◽

Transmembrane Helix ◽

Confidence Score ◽

Potential Drug ◽

Protein Protein Interaction ◽

Industrial Level ◽

Potential Drug Targets

Abstract Background The M4 family of metalloproteases is comprised of a large number of zinc-containing metalloproteases. A large number of these enzymes are important virulence factors of pathogenic bacteria and therefore potential drug targets. Whereas some enzymes have potential for biotechnological applications, the M4 family of metalloproteases is known almost exclusively from bacteria. The aim of the study was to identify the structure and properties of M4 metalloprotease proteins. Results A total of 31 protein sequences of M4 metalloprotease retrieved from UniProt representing different species of bacteria have been characterized for various physiochemical properties. They were thermostable, hydrophillic protein of a molecular mass ranging from 38 to 66 KDa. Correlation on the basis of both enzymes and respective genes has also been studied by phylogenetic tree. B. cereus M4 metalloprotease (PDB ID: 1NPC) was selected as a representative species for secondary and tertiary structures among the M4 metalloprotease proteins. The secondary structure displaying 11 helices (H1-H11) is involved in 15 helix-helix interactions, while 4 β-sheet motifs composed of 15 β-strands in PDBsum. Possible disulfide bridges were absent in most of the cases. The tertiary structure of B. cereus M4 metalloprotease was validated by QMEAN4 and SAVES server (Ramachandran plot, verify 3D, and ERRAT) which proved the stability, reliability, and consistency of the tertiary structure of the protein. Functional analysis was done in terms of membrane protein topology, disease-causing region prediction, proteolytic cleavage sites prediction, and network generation. Transmembrane helix prediction showed absence of transmembrane helix in protein. Protein-protein interaction networks demonstrated that bacillolysin of B. cereus interacted with ten other proteins in a high confidence score. Five disorder regions were identified. Active sites analysis showed the zinc-binding residues—His-143, His-147, and Glu-167, with Glu-144 acting as the catalytic residues. Conclusion Moreover, this theoretical overview will help researchers to get a details idea about the protein structure and it may also help to design enzymes with desirable characteristics for exploiting them at industrial level or potential drug targets.

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Role of some types of serotonin receptors in murine hypophyseal-testicular complex activation induced by the presence of a female

Problems of Endocrinology ◽

10.14341/probl11792 ◽

2003 ◽

Vol 49 (6) ◽

pp. 53-56

Author(s):

T. G. Amstislavskaya ◽

N. K. Popova

Keyword(s):

Serotonin Receptors ◽

Receptor Agonist ◽

Serotonin Receptor ◽

Receptive Female ◽

Plasma Testosterone ◽

Blood Levels ◽

Inhibitory Effects ◽

Sexual Activation ◽

Different Types

Placement of a sexually receptive female mouse behind a partition that prevents physical contacts, but permits it to see and smell caused an increase in the blood levels of testosterone in male mice. The selective 5-HTIA-serotonin receptor agonist 08-OH- DPAT (0.1 mg/kg) and the mixed 5-HTIA/IB agonist eltoprazine, 3.0 and 10.0 mg/kg, blocked the activating effect of female exposure on the male pituitary-testicular system. The 5-HT/-receptor agonist p-MPPI (0.2 mg/kg) prevented the inhibitory effects of 8-OH-DPATand eltoprazine. The 5-HT/B-receptor agonist CGS- 12066A (1.0 and 2.0 mg/kg) exerted no effect while the mixed 5-HTIB/2C-receptor agonist TFMPP (5.2 mg/kg) inhibited a female-induced increase in the levels of male blood testosterone. The 5-HT/-receptor agonist keranserin (1.0 and 2.0 mg/kg) prevented a female-induced increase in the levels of testosterone. The 5-HT3-receptor agonist ondansetron (0.05 and 0.1 mg/kg) elevated the baseline level of plasma testosterone, but blocked receptive female-induced activation of the male hypothalamic-pituitary-testicular system (HPTS). It is concluded that 5-HTIA-receptors are involved in the control of male sexual activation. At the same time different types and even subtypes of the same type of 5-HT-receptors produce varying inhibitory and activating effects on the receptive female-induced activation of HPTS. Blocking of the female-induced activation of HPTS seems to be realized by involving 5-HTu- and 5-HT2C-receptors and its activation occurs with the participation of 5-HT^- and 5- HT3-receptors.

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A successful use of a new shuttle cloning vector pA13 for the cloning of the bacteriocins BacSJ and acidocin 8912

Archives of Biological Sciences ◽

10.2298/abs1002231k ◽

2010 ◽

Vol 62 (2) ◽

pp. 231-243 ◽

Cited By ~ 1

Author(s):

Milan Kojic ◽

Jelena Lozo ◽

B. Jovcic ◽

Ivana Strahinic ◽

D. Fira ◽

...

Keyword(s):

In Silico Analysis ◽

Functional Expression ◽

Open Reading Frames ◽

Cloning Vector ◽

The Novel ◽

Genetic Manipulations ◽

Genes Encoding ◽

Editorial Decision ◽

Terminal Amino

The aim of this paper was to research the molecular cloning of genes encoding the novel bacteriocin BacSJ from Lactobacillus paracasei subsp. paracasei BGSJ2-8 by using a newly constructed shuttle cloning vector pA13. A new shuttle-cloning vector, pA13, was constructed and successfully introduced into Escherichia coli, Lactobacillus and Lactococcus strains, showing a high segregational and structural stability in all three hosts. The natural plasmid pSJ2-8 from L. paracasei subsp. paracasei BGSJ2-8 was cloned in the pA13 using BamHI, obtaining the construct pB5. Sequencing and in silico analysis of the pB5 revealed 15 open reading frames (ORF). Plasmid pSJ2-8 harbors the genes encoding the production of two bacteriocins, BacSJ and acidocin 8912. The combined N-terminal amino acid sequencing of BacSJ in combination with DNA sequencing of the bacSJ2-8 gene enabled the determination of the primary structure of a bacteriocin BacSJ. The production and functional expression of BacSJ in homologous and heterologous hosts suggest that bacSJ2-8 and bacSJ2-8i together with the genes encoding the ABC transporter and accessory protein are the minimal requirement for the production of BacSJ. Biochemical and genetic analyses showed that BacSJ belongs to the class II bacteriocins. The shuttle cloning vector pA13 could be used as a tool for genetic manipulations in lactobacilli and lactococci. withdrawn; due to a printing error. Link to the Editorial Decision <a href="http://dx.doi.org/10.2298/ABS1004251U">10.2298/ABS1004251U</a>

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