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1.
Trends Biochem Sci ; 49(1): 52-67, 2024 01.
Article in English | MEDLINE | ID: mdl-37945409

ABSTRACT

Post-translational modifications (PTMs) add a major degree of complexity to the proteome and are essential controllers of protein homeostasis. Amongst the hundreds of PTMs identified, ubiquitin and ubiquitin-like (UBL) modifications are recognized as key regulators of cellular processes through their ability to affect protein-protein interactions, protein stability, and thus the functions of their protein targets. Here, we focus on the most recently identified UBL, ubiquitin-fold modifier 1 (UFM1), and the machinery responsible for its transfer to substrates (UFMylation) or its removal (deUFMylation). We first highlight the biochemical peculiarities of these processes, then we develop on how UFMylation and its machinery control various intertwined cellular processes and we highlight some of the outstanding research questions in this emerging field.


Subject(s)
Proteins , Ubiquitin , Ubiquitin/metabolism , Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Protein Processing, Post-Translational , Cell Communication
2.
EMBO J ; 41(18): e110596, 2022 09 15.
Article in English | MEDLINE | ID: mdl-35938214

ABSTRACT

Cells are constantly exposed to various chemical and physical stimuli. While much has been learned about the biochemical factors that regulate secretory trafficking from the endoplasmic reticulum (ER), much less is known about whether and how this trafficking is subject to regulation by mechanical signals. Here, we show that subjecting cells to mechanical strain both induces the formation of ER exit sites (ERES) and accelerates ER-to-Golgi trafficking. We found that cells with impaired ERES function were less capable of expanding their surface area when placed under mechanical stress and were more prone to develop plasma membrane defects when subjected to stretching. Thus, coupling of ERES function to mechanotransduction appears to confer resistance of cells to mechanical stress. Furthermore, we show that the coupling of mechanotransduction to ERES formation was mediated via a previously unappreciated ER-localized pool of the small GTPase Rac1. Mechanistically, we show that Rac1 interacts with the small GTPase Sar1 to drive budding of COPII carriers and stimulates ER-to-Golgi transport. This interaction therefore represents an unprecedented link between mechanical strain and export from the ER.


Subject(s)
Mechanotransduction, Cellular , Monomeric GTP-Binding Proteins , Biological Transport , COP-Coated Vesicles/metabolism , Endoplasmic Reticulum/metabolism , Golgi Apparatus/metabolism , Monomeric GTP-Binding Proteins/metabolism , Protein Transport/physiology
3.
J Biol Chem ; : 107575, 2024 Jul 14.
Article in English | MEDLINE | ID: mdl-39013537

ABSTRACT

Adaptation to shortage in free amino acids (AA) is mediated by two pathways, the integrated stress response (ISR) and the mechanistic target of rapamycin (mTOR). In response to reduced levels, primarily of leucine or arginine, mTOR in its complex 1 configuration (mTORC1) is suppressed leading to a decrease in translation initiation and elongation. The eIF2α kinase general control nonderepressible 2 (GCN2) is activated by uncharged tRNAs, leading to induction of the ISR in response to a broader range of AA shortage. ISR confers a reduced translation initiation, while promoting the selective synthesis of stress proteins, such as ATF4. To efficiently adapt to AA starvation, the two pathways are cross-regulated at multiple levels. Here we identified a new mechanism of ISR/mTORC1 crosstalk that optimizes survival under AA starvation, when mTORC1 is forced to remain active. mTORC1 activation during acute AA shortage, augmented ATF4 expression in a GCN2-dependent manner. Under these conditions, enhanced GCN2 activity was not dependent on tRNA sensing, inferring a different activation mechanism. We identified a labile physical interaction between GCN2 and mTOR that results in a phosphorylation of GCN2 on serine 230 by mTOR, which promotes GCN2 activity. When examined under prolonged AA starvation, GCN2 phosphorylation by mTOR promoted survival. Our data unveils an adaptive mechanism to AA starvation, when mTORC1 evades inhibition.

4.
Org Biomol Chem ; 22(19): 3848-3853, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38635230

ABSTRACT

Herein the first example of conversion of alcohols into carboxylic acids by use of the Dess-Martin Periodinane (DMP), which is otherwise routinely employed for the conversion to aldehydes, is reported. This methodology will have significant potential utility in the synthesis of cytidine analogues and other related biologically important molecules.

5.
J Chem Inf Model ; 64(3): 905-917, 2024 Feb 12.
Article in English | MEDLINE | ID: mdl-38282538

ABSTRACT

Inositol-requiring enzyme 1 (IRE1) is a transmembrane sensor that is part of a trio of sensors responsible for controlling the unfolded protein response within the endoplasmic reticulum (ER). Upon the accumulation of unfolded or misfolded proteins in the ER, IRE1 becomes activated and initiates the cleavage of a 26-nucleotide intron from human X-box-containing protein 1 (XBP1). The cleavage is mediated by the RtcB ligase enzyme, which splices together two exons, resulting in the formation of the spliced isoform XBP1s. The XBP1s isoform activates the transcription of genes involved in ER-associated degradation to maintain cellular homeostasis. The catalytic activity of RtcB is controlled by the phosphorylation and dephosphorylation of three tyrosine residues (Y306, Y316, and Y475), which are regulated by the ABL1 tyrosine kinase and PTP1B phosphatase, respectively. This study focuses on investigating the mechanism by which the PTP1B phosphatase activates the RtcB ligase using a range of advanced in silico methods. Protein-protein docking identified key interacting residues between RtcB and PTP1B. Notably, the phosphorylated Tyr306 formed hydrogen bonds and salt bridge interactions with the "gatekeeper" residues Arg47 and Lys120 of the inactive PTP1B. Classical molecular dynamics simulation emphasized the crucial role of Asp181 in the activation of PTP1B, driving the conformational change from an open to a closed state of the WPD-loop. Furthermore, QM/MM-MD simulations provided insights into the free energy landscape of the dephosphorylation reaction mechanism of RtcB, which is mediated by the PTP1B phosphatase.


Subject(s)
Ligases , Phosphoric Monoester Hydrolases , Humans , Ligases/metabolism , Phosphoric Monoester Hydrolases/metabolism , Protein Serine-Threonine Kinases/metabolism , Phosphorylation , Protein Isoforms/metabolism , Protein Tyrosine Phosphatase, Non-Receptor Type 1/metabolism
6.
Cell Mol Life Sci ; 80(12): 352, 2023 Nov 07.
Article in English | MEDLINE | ID: mdl-37935993

ABSTRACT

To be functional, some RNAs require a processing step involving splicing events. Each splicing event necessitates an RNA ligation step. RNA ligation is a process that can be achieved with various intermediaries such as self-catalysing RNAs, 5'-3' and 3'-5' RNA ligases. While several types of RNA ligation mechanisms occur in human, RtcB is the only 3'-5' RNA ligase identified in human cells to date. RtcB RNA ligation activity is well known to be essential for the splicing of XBP1, an essential transcription factor of the unfolded protein response; as well as for the maturation of specific intron-containing tRNAs. As such, RtcB is a core factor in protein synthesis and homeostasis. Taking advantage of the high homology between RtcB orthologues in archaea, bacteria and eukaryotes, this review will provide an introduction to the structure of RtcB and the mechanism of 3'-5' RNA ligation. This analysis is followed by a description of the mechanisms regulating RtcB activity and localisation, its known partners and its various functions from bacteria to human with a specific focus on human cancer.


Subject(s)
RNA Ligase (ATP) , Transcription Factors , Humans , RNA Ligase (ATP)/genetics , RNA Ligase (ATP)/chemistry , RNA Ligase (ATP)/metabolism , Transcription Factors/metabolism , RNA/metabolism , Unfolded Protein Response , RNA, Transfer/genetics , RNA, Transfer/metabolism , RNA Splicing/genetics
7.
Nucleic Acids Res ; 50(16): 9072-9082, 2022 09 09.
Article in English | MEDLINE | ID: mdl-35979954

ABSTRACT

The static and dynamic structures of DNA duplexes affected by 5S-Tg (Tg, Thymine glycol) epimers were studied using MD simulations and Markov State Models (MSMs) analysis. The results show that the 5S,6S-Tg base caused little perturbation to the helix, and the base-flipping barrier was determined to be 4.4 kcal mol-1 through the use of enhanced sampling meta-eABF calculations, comparable to 5.4 kcal mol-1 of the corresponding thymine flipping. Two conformations with the different hydrogen bond structures between 5S,6R-Tg and A19 were identified in several independent MD trajectories. The 5S,6R-Tg:O6HO6•••N1:A19 hydrogen bond is present in the high-energy conformation displaying a clear helical distortion, and near barrier-free Tg base flipping. The low-energy conformation always maintains Watson-Crick base pairing between 5S,6R-Tg and A19, and 5S-Tg base flipping is accompanied by a small barrier of ca. 2.0 KBT (T = 298 K). The same conformations are observed in the MSMs analysis. Moreover, the transition path and metastable structures of the damaged base flipping are for the first time verified through MSMs analysis. The data clearly show that the epimers have completely different influence on the stability of the DNA duplex, thus implying different enzymatic mechanisms for DNA repair.


Subject(s)
DNA Repair , DNA , Base Pairing , DNA/chemistry , DNA Damage , Hydrogen Bonding , Nucleic Acid Conformation , Thermodynamics
8.
Reprod Health ; 21(1): 14, 2024 Jan 29.
Article in English | MEDLINE | ID: mdl-38287426

ABSTRACT

BACKGROUND: In 2021, Uganda's neonatal mortality rate was approximately 19 deaths per 1000 live births, with an estimated stillbirth rate of 15.1 per 1000 total births. Data are critical for indicating areas where deaths occur and why, hence driving improvements. Many countries rely on surveys like Demographic and Health Surveys (DHS), which face challenges with respondents' misinterpretation of questions. However, little is documented about this in Uganda. Cognitive interviews aim to improve questionnaires and assess participants' comprehension of items. Through cognitive interviews we explored women's interpretations of questions on pregnancy and pregnancy outcomes. METHODS: In November 2021, we conducted cognitive interviews with 20 women in Iganga Mayuge health and demographic surveillance system site in eastern Uganda. We adapted the reproductive section of the DHS VIII women's questionnaire, purposively selected questions and used concurrent verbal probing. Participants had secondary school education and were English speaking. Cognition was measured through comparing instructions in the DHS interviewers' manual to participants' responses and researcher's knowledge. A qualitative descriptive approach to analysis was undertaken. RESULTS: We report findings under the cognitive aspect of comprehension. Some questions were correctly understood, especially those with less technical terms or without multiple sections. Most participants struggled with questions asking whether the woman has her living biological children residing with her or not. Indeed, some thought it referred to how many living children they had. There were comprehension difficulties with long questions like 210 that asks about miscarriages, newborn deaths, and stillbirths together. Participants had varying meanings for miscarriages, while many misinterpreted stillbirth, not linking it to gestational age. Furthermore, even amongst educated women some survey questions were misunderstood. CONCLUSIONS: Population surveys may misclassify, over or under report events around pregnancy and pregnancy outcomes. Interviewers should begin with a standard definition of key terms and ensure respondents understand these. Questions can be simplified through breaking up long sentences, while interviewer training should be modified to ensure they thoroughly understand key terms. We recommend cognitive interviews while developing survey tools, beyond basic pre-testing. Improving respondents' comprehension and thus response accuracy will increase reporting and data quality.


Subject(s)
Abortion, Spontaneous , Stillbirth , Pregnancy , Infant, Newborn , Child , Female , Humans , Stillbirth/epidemiology , Uganda/epidemiology , Abortion, Spontaneous/epidemiology , Surveys and Questionnaires , Cognition
9.
J Chem Inf Model ; 63(5): 1578-1591, 2023 03 13.
Article in English | MEDLINE | ID: mdl-36802593

ABSTRACT

Exotoxin A (ETA) is an extracellular secreted toxin and a single-chain polypeptide with A and B fragments that is produced by Pseudomonas aeruginosa. It catalyzes the ADP-ribosylation of a post-translationally modified histidine (diphthamide) on eukaryotic elongation factor 2 (eEF2), which results in the inactivation of the latter and the inhibition of protein biosynthesis. Studies show that the imidazole ring of diphthamide plays an important role in the ADP-ribosylation catalyzed by the toxin. In this work, we employ different in silico molecular dynamics (MD) simulation approaches to understand the role of diphthamide versus unmodified histidine in eEF2 on the interaction with ETA. Crystal structures of the eEF2-ETA complexes with three different ligands NAD+, ADP-ribose, and ßTAD were selected and compared in the diphthamide and histidine containing systems. The study shows that NAD+ bound to ETA remains very stable in comparison with other ligands, enabling the transfer of ADP-ribose to the N3 atom of the diphthamide imidazole ring in eEF2 during ribosylation. We also show that unmodified histidine in eEF2 has a negative impact on ETA binding and is not a suitable target for the attachment of ADP-ribose. Analyzing of radius of gyration and COM distances for NAD+, ßTAD, and ADP-ribose complexes revealed that unmodified His affects the structure and destabilizes the complex with all different ligands throughout the MD simulations.


Subject(s)
Histidine , Molecular Dynamics Simulation , Peptide Elongation Factor 2/chemistry , Histidine/chemistry , NAD/metabolism , Adenosine Diphosphate Ribose/metabolism , Pseudomonas aeruginosa , Pseudomonas aeruginosa Exotoxin A
10.
BMC Public Health ; 23(1): 1581, 2023 08 18.
Article in English | MEDLINE | ID: mdl-37596665

ABSTRACT

BACKGROUND: In 2021, Uganda had an estimated 25,855 stillbirths and 32,037 newborn deaths. Many Adverse Pregnancy Outcomes (APOs) go unreported despite causing profound grief and other mental health effects. This study explored psychosocial effects of APOs and their influence on reporting these events during surveys and surveillance settings in Uganda. METHODS: A qualitative cross-sectional study was conducted in September 2021 in Iganga Mayuge health and demographic surveillance system site, eastern Uganda. Narratives were held with 44 women who had experienced an APO (miscarriage, stillbirth or neonatal death) and 7 men whose spouses had undergone the same. Respondents were purposively selected and the sample size premised on the need for diverse respondents. Reflexive thematic analysis was undertaken, supported by NVivo software. RESULTS: 60.8% of respondents had experienced neonatal deaths, 27.4% stillbirths, 11.8% miscarriages and almost half had multiple APOs. Theme one on psychosocial effects showed that both women and men suffered disbelief, depression, shame and thoughts of self-harm. In theme two on reactions to interviews, most respondents were reminded about their loss. Indeed, some women cried and a few requested termination of the interview. However, many said they eventually felt better, especially where interviewers comforted and advised them. In theme three about why people consent to such interviews, it was due to the respondents' need for sensitization on causes of pregnancy loss and danger signs, plus the expectation that the interview would lead to improved health services. Theme four on suggestions for improving interviews highlighted respondents' requests for a comforting and encouraging approach by interviewers. CONCLUSION: Psychosocial effects of APOs may influence respondents' interest and ability to effectively engage in an interview. Findings suggest that a multi-pronged approach, including interviewer training in identifying and dealing responsively with grieving respondents, and meeting needs for health information and professional counselling could improve reporting of APOs in surveys and surveillance settings. More so, participants need to understand the purpose of the interview and have realistic expectations.


Subject(s)
Abortion, Spontaneous , Perinatal Death , Male , Infant, Newborn , Pregnancy , Female , Humans , Abortion, Spontaneous/epidemiology , Pregnancy Outcome , Stillbirth/epidemiology , Cross-Sectional Studies , Uganda/epidemiology , Surveys and Questionnaires
11.
Proc Natl Acad Sci U S A ; 117(10): 5376-5385, 2020 03 10.
Article in English | MEDLINE | ID: mdl-32098846

ABSTRACT

The mannose-6-phosphate isomerase (Mpi) locus in Semibalanus balanoides has been studied as a candidate gene for balancing selection for more than two decades. Previous work has shown that Mpi allozyme genotypes (fast and slow) have different frequencies across Atlantic intertidal zones due to selection on postsettlement survival (i.e., allele zonation). We present the complete gene sequence of the Mpi locus and quantify nucleotide polymorphism in S. balanoides, as well as divergence to its sister taxon Semibalanus cariosus We show that the slow allozyme contains a derived charge-altering amino acid polymorphism, and both allozyme classes correspond to two haplogroups with multiple internal haplotypes. The locus shows several footprints of balancing selection around the fast/slow site: an enrichment of positive Tajima's D for nonsynonymous mutations, an excess of polymorphism, and a spike in the levels of silent polymorphism relative to silent divergence, as well as a site frequency spectrum enriched for midfrequency mutations. We observe other departures from neutrality across the locus in both coding and noncoding regions. These include a nonsynonymous trans-species polymorphism and a recent mutation under selection within the fast haplogroup. The latter suggests ongoing allelic replacement of functionally relevant amino acid variants. Moreover, predicted models of Mpi protein structure provide insight into the functional significance of the putatively selected amino acid polymorphisms. While footprints of selection are widespread across the range of S. balanoides, our data show that intertidal zonation patterns are variable across both spatial and temporal scales. These data provide further evidence for heterogeneous selection on Mpi.


Subject(s)
Mannose-6-Phosphate Isomerase/genetics , Selection, Genetic , Thoracica/enzymology , Thoracica/genetics , Alleles , Animals , Genetic Loci , Genotype , Isoenzymes/chemistry , Isoenzymes/genetics , Mannose-6-Phosphate Isomerase/chemistry , Mutation , Polymorphism, Genetic
12.
Genet Med ; 24(7): 1567-1582, 2022 07.
Article in English | MEDLINE | ID: mdl-35482014

ABSTRACT

PURPOSE: Diphthamide is a post-translationally modified histidine essential for messenger RNA translation and ribosomal protein synthesis. We present evidence for DPH5 as a novel cause of embryonic lethality and profound neurodevelopmental delays (NDDs). METHODS: Molecular testing was performed using exome or genome sequencing. A targeted Dph5 knockin mouse (C57BL/6Ncrl-Dph5em1Mbp/Mmucd) was created for a DPH5 p.His260Arg homozygous variant identified in 1 family. Adenosine diphosphate-ribosylation assays in DPH5-knockout human and yeast cells and in silico modeling were performed for the identified DPH5 potential pathogenic variants. RESULTS: DPH5 variants p.His260Arg (homozygous), p.Asn110Ser and p.Arg207Ter (heterozygous), and p.Asn174LysfsTer10 (homozygous) were identified in 3 unrelated families with distinct overlapping craniofacial features, profound NDDs, multisystem abnormalities, and miscarriages. Dph5 p.His260Arg homozygous knockin was embryonically lethal with only 1 subviable mouse exhibiting impaired growth, craniofacial dysmorphology, and multisystem dysfunction recapitulating the human phenotype. Adenosine diphosphate-ribosylation assays showed absent to decreased function in DPH5-knockout human and yeast cells. In silico modeling of the variants showed altered DPH5 structure and disruption of its interaction with eEF2. CONCLUSION: We provide strong clinical, biochemical, and functional evidence for DPH5 as a novel cause of embryonic lethality or profound NDDs with multisystem involvement and expand diphthamide-deficiency syndromes and ribosomopathies.


Subject(s)
Methyltransferases , Neurodevelopmental Disorders , Adenosine Diphosphate/metabolism , Animals , Histidine/analogs & derivatives , Histidine/metabolism , Humans , Methyltransferases/genetics , Mice , Mice, Inbred C57BL , Neurodevelopmental Disorders/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Syndrome
13.
Am J Pathol ; 191(8): 1398-1411, 2021 08.
Article in English | MEDLINE | ID: mdl-34111430

ABSTRACT

Bronchiolitis obliterans syndrome, a common form of chronic lung allograft dysfunction, is the major limitation to long-term survival after lung transplantation. The histologic correlate is progressive, fibrotic occlusion of small airways, obliterative bronchiolitis lesions, which ultimately lead to organ failure. The molecular composition of these lesions is unknown. In this sutdy, the protein composition of the lesions in explanted lungs from four end-stage bronchiolitis obliterans syndrome patients was analyzed using laser-capture microdissection and optimized sample preparation protocols for mass spectrometry. Immunohistochemistry and immunofluorescence were used to determine the spatial distribution of commonly identified proteins on the tissue level, and protein signatures for 14 obliterative bronchiolitis lesions were established. A set of 39 proteins, identified in >75% of lesions, included distinct structural proteins (collagen types IV and VI) and cellular components (actins, vimentin, and tryptase). Each respective lesion exhibited a unique composition of proteins (on average, n = 66 proteins), thereby mirroring the morphologic variation of the lesions. Antibody-based staining confirmed these mass spectrometry-based findings. The 14 analyzed obliterative bronchiolitis lesions showed variations in their protein content, but also common features. This study provides molecular and morphologic insights into the development of chronic rejection after lung transplantation. The protein patterns in the lesions were correlated to pathways of extracellular matrix organization, tissue development, and wound healing processes.


Subject(s)
Bronchiolitis Obliterans/metabolism , Bronchiolitis Obliterans/pathology , Lung/pathology , Transplants/metabolism , Transplants/pathology , Airway Remodeling , Humans , Laser Capture Microdissection , Lung Transplantation , Proteome
14.
J Chem Inf Model ; 62(2): 386-398, 2022 01 24.
Article in English | MEDLINE | ID: mdl-34994562

ABSTRACT

Damaged or mismatched DNA bases are normally thought to be able to flip out of the helical stack, providing enzymes with access to the faulty genetic information otherwise hidden inside the helix. Thymine glycol (Tg) is one of the most common products of nucleic acid damage. However, the static and dynamic structures of DNA duplexes affected by 5R-Tg epimers are still not clearly understood, including the ability of these to undergo spontaneous base flipping. Structural effects of the 5R-Tg epimers on the duplex DNA are herein studied using molecular dynamics together with reliable DFT based calculations. In comparison with the corresponding intact DNA, the cis-5R,6S-Tg epimer base causes little perturbation to the duplex DNA, and a barrier of 4.9 kcal mol-1 is obtained by meta-eABF for cis-5R,6S-Tg base flipping out of the duplex DNA, comparable to the 5.4 kcal mol-1 obtained for the corresponding thymine flipping in intact DNA. For the trans-5R,6R-Tg epimer, three stable local structures were identified, of which the most stable disrupts the Watson-Crick hydrogen-bonded G5/C20 base pair, leading to conformational distortion of the duplex. Interestingly, the relative barrier height of the 5R-Tg flipping is only 1.0 kcal mol-1 for one of these trans-5R,6R-Tg epimers. Water bridge interactions were identified to be essential for 5R-Tg flipping. The study clearly demonstrates the occurrence of partial trans-5R,6R-Tg epimer flipping in solution.


Subject(s)
DNA , Thymine , Base Pairing , DNA/chemistry , DNA Damage , Nucleic Acid Conformation , Thermodynamics , Thymine/analogs & derivatives , Thymine/chemistry
15.
J Chem Inf Model ; 62(17): 4247-4260, 2022 09 12.
Article in English | MEDLINE | ID: mdl-35960929

ABSTRACT

A range of in silico methodologies were herein employed to study the unconventional XBP1 mRNA cleavage mechanism performed by the unfolded protein response (UPR) mediator Inositol Requiring Enzyme 1α (IRE1). Using Protein-RNA molecular docking along with a series of extensive restrained/unrestrained atomistic molecular dynamics (MD) simulations, the dynamical behavior of the system was evaluated and a reliable model of the IRE1/XBP1 mRNA complex was constructed. From a series of well-converged quantum mechanics molecular mechanics well-tempered metadynamics (QM/MM WT-MetaD) simulations using the Grimme dispersion interaction corrected semiempirical parametrization method 6 level of theory (PM6-D3) and the AMBER14SB-OL3 force field, the free energy profile of the cleavage mechanism was determined, along with intermediates and transition state structures. The results show two distinct reaction paths based on general acid-general base type mechanisms, with different activation energies that perfectly match observations from experimental mutagenesis data. The study brings unique atomistic insights into the cleavage mechanism of XBP1 mRNA by IRE1 and clarifies the roles of the catalytic residues H910 and Y892. Increased understanding of the details in UPR signaling can assist in the development of new therapeutic agents for its modulation.


Subject(s)
Inositol , Ribonucleases , Endoribonucleases/genetics , Molecular Docking Simulation , Protein Serine-Threonine Kinases/genetics , RNA, Messenger/genetics , Ribonucleases/metabolism
16.
J Chem Inf Model ; 62(12): 2999-3007, 2022 06 27.
Article in English | MEDLINE | ID: mdl-35699524

ABSTRACT

Peptides are an important modality in drug discovery. While current peptide optimization focuses predominantly on the small number of natural and commercially available non-natural amino acids, the chemical spaces available for small molecule drug discovery are in the billions of molecules. In the present study, we describe the development of a large virtual library of readily synthesizable non-natural amino acids that can power the virtual screening protocols and aid in peptide optimization. To that end, we enumerated nearly 380 thousand amino acids and demonstrated their vast chemical diversity compared to the 20 natural and commercial residues. Furthermore, we selected a diverse ten thousand amino acid subset to validate our virtual screening workflow on the Keap1-Neh2 complex model system. Through in silico mutations of Neh2 peptide residues to those from the virtual library, our docking-based protocol identified a number of possible solutions with a significantly higher predicted affinity toward the Keap1 protein. This protocol demonstrates that the non-natural amino acid chemical space can be massively extended and virtually screened with a reasonable computational cost.


Subject(s)
Amino Acids , NF-E2-Related Factor 2 , Amino Acids/chemistry , Drug Discovery/methods , Kelch-Like ECH-Associated Protein 1 , Molecular Docking Simulation , Peptides/chemistry
17.
BMC Pregnancy Childbirth ; 22(1): 292, 2022 Apr 06.
Article in English | MEDLINE | ID: mdl-35387593

ABSTRACT

BACKGROUND: Globally, approximately 6,700 newborn deaths and 5,400 stillbirths occur daily. The true figure is likely higher, with under reporting of adverse pregnancy outcomes (APOs) noted. Decision-making in health is influenced by various factors, including one's social networks. We sought to understand APOs disclosure within social networks in Uganda, Ghana, Guinea-Bissau and Bangladesh and how this could improve formal reporting of APOs in surveys.  METHODS: A qualitative, exploratory multi-country study was conducted within four health and demographic surveillance system sites. 16 focus group discussions were held with 147 women aged 15-49 years, who had participated in a recent household survey. Thematic analysis, with both deductive and inductive elements, using three pre-defined themes of Sender, Message and Receiver was done using NVivo software. RESULTS: Disclosure of APOs was a community concern, with news often shared with people around the bereaved for different reasons, including making sense of what happened and decision-making roles of receivers. Social networks responded with comfort, providing emotional, in-kind and financial support. Key decision makers included men, spiritual and traditional leaders. Non-disclosure was usually to avoid rumors in cases of induced abortions, or after a previous bad experience with health workers, who were frequently excluded from disclosure, except for instances where a woman sought advice on APOs. CONCLUSIONS: Communities must understand why they should report APOs and to whom. Efforts to improve APOs reporting could be guided by diffusion of innovation theory, for instance for community entry and sensitization before the survey, since it highlights how information can be disseminated through community role models. In this case, these gatekeepers we identified could promote reporting of APOs. The stage at which a person is in decision-making, what kind of adopter they are and their take on the benefits and other attributes of reporting are important. In moving beyond survey reporting to getting better routine data, the theory would be applicable too. Health workers should demonstrate a more comforting and supportive response to APOs as the social networks do, which could encourage more bereaved women to inform them and seek care.


Subject(s)
Disclosure , Pregnancy Outcome , Adolescent , Adult , Female , Humans , Infant, Newborn , Male , Middle Aged , Pregnancy , Qualitative Research , Social Networking , Surveys and Questionnaires , Young Adult
18.
Biochem J ; 478(15): 2953-2975, 2021 08 13.
Article in English | MEDLINE | ID: mdl-34375386

ABSTRACT

The Unfolded Protein response is an adaptive pathway triggered upon alteration of endoplasmic reticulum (ER) homeostasis. It is transduced by three major ER stress sensors, among which the Inositol Requiring Enzyme 1 (IRE1) is the most evolutionarily conserved. IRE1 is an ER-resident type I transmembrane protein exhibiting an ER luminal domain that senses the protein folding status and a catalytic kinase and RNase cytosolic domain. In recent years, IRE1 has emerged as a relevant therapeutic target in various diseases including degenerative, inflammatory and metabolic pathologies and cancer. As such several drugs altering IRE1 activity were developed that target either catalytic activity and showed some efficacy in preclinical pathological mouse models. In this review, we describe the different drugs identified to target IRE1 activity as well as their mode of action from a structural perspective, thereby identifying common and different modes of action. Based on this information we discuss on how new IRE1-targeting drugs could be developed that outperform the currently available molecules.


Subject(s)
Endoplasmic Reticulum Stress/physiology , Endoplasmic Reticulum/metabolism , Endoribonucleases/metabolism , Homeostasis/physiology , Protein Serine-Threonine Kinases/metabolism , Unfolded Protein Response/physiology , Animals , Endoplasmic Reticulum/drug effects , Endoribonucleases/antagonists & inhibitors , Endoribonucleases/chemistry , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Homeostasis/drug effects , Humans , Protein Folding/drug effects , Protein Serine-Threonine Kinases/antagonists & inhibitors , Protein Serine-Threonine Kinases/chemistry , Signal Transduction/drug effects , Signal Transduction/physiology , Unfolded Protein Response/drug effects
19.
Nucleic Acids Res ; 48(12): 6471-6480, 2020 07 09.
Article in English | MEDLINE | ID: mdl-32442296

ABSTRACT

Despite their great success in recognizing small molecules in vitro, nucleic acid aptamers are rarely used in clinical settings. This is partially due to the lack of structure-based mechanistic information. In this work, atomistic molecular dynamics simulations are used to study the static and dynamic supramolecular structures relevant to the process of the wild-type (wt) nucleic acid aptamer recognition and binding of ATP. The effects brought about by mutation of key residues in the recognition site are also explored. The simulations reveal that the aptamer displays a high degree of rigidity and is structurally very little affected by the binding of ATP. Interaction energy decomposition shows that dispersion forces from π-stacking between ATP and the G6 and A23 nucleobases in the aptamer binding site plays a more important role in stabilizing the supramolecular complex, compared to hydrogen-bond interaction between ATP and G22. Moreover, metadynamics simulations show that during the association process, water molecules act as essential bridges connecting ATP with G22, which favors the dynamic stability of the complex. The calculations carried out on three mutated aptamer structures confirm the crucial role of the hydrogen bonds and π-stacking interactions for the binding affinity of the ATP nucleic acid aptamer.


Subject(s)
Adenosine Triphosphate/chemistry , Aptamers, Nucleotide/chemistry , Molecular Dynamics Simulation , Aptamers, Nucleotide/genetics , Base Pairing , Hydrogen Bonding , Mutation
20.
Acta Paediatr ; 111(3): 653-666, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34813675

ABSTRACT

AIM: To investigate both quantitatively and qualitatively the differences between participation in team-based visits (TBVs) and perceived needs for TBVs from the perspectives of healthcare professionals, in the context of the Swedish 3-tier national Child Healthcare programme. METHODS: A study-specific questionnaire, including multiple-choice questions with fixed and free-text response options, was developed, and used. To capture healthcare professionals' experiences and find explanations for the quantitative results in qualitative data, a convergent parallel mixed-methods study design was used. Descriptive statistics and McNemar's test were used to analyse the quantitative data, and content analysis was used to analyse the qualitative data. RESULTS: Healthcare professionals perceived the need for TBVs in the Swedish Child Healthcare Services (CHS) to a high extent. The largest difference between the perceived need for TBVs and experienced TBVs was for indications associated with psychosocial problems. The quantitative findings were explored by the qualitative findings. Both individual and organisational factors influenced TBVs. CONCLUSION: Perceived needs for TBVs in Swedish CHS exceed its existence. Healthcare professionals require TBVs delivered by interprofessional teams, in line with proportionate universalism. Accordingly, organisational structures (e.g. colocation and clear instructions on how to distribute TBVs) and human resources (e.g. psychologists and social worker) are needed.


Subject(s)
Child Health Services , Patient Care Team , Attitude of Health Personnel , Child , Health Personnel , Humans , Qualitative Research , Sweden
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