Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.

Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very short period of time. These proteins are essentially characterized by their inherent structural disorder, encoded mainly by their amino acid sequences. The profound abundance of IDPs and intrinsically disordered regions (IDRs) in the biological world delineates their deep-rooted functionality. IDPs and IDRs convey such extensive functionality through their unique dynamic nature, which enables them to carry out huge number of multifaceted biomolecular interactions and make them "interaction hub" of the cellular systems. Additionally, with such widespread functions, their misfunctioning is also intimately associated with multiple diseases. Thus, understanding the dynamic heterogeneity of various IDPs along with their interactions with respective binding partners is an important field with immense potentials in biomolecular research. In this context, molecular docking-based computational approaches have proven to be remarkable in case of ordered proteins. Molecular docking methods essentially model the biomolecular interactions in both structural and energetic terms and use this information to characterize the putative interactions between the two participant molecules. However, direct applications of the conventional docking methods to study IDPs are largely limited by their structural heterogeneity and demands for unique IDP-centric strategies. Thus, in this chapter, we have presented an overview of current methodologies for successful docking operations involving IDPs and IDRs. These specialized methods majorly include the ensemble-based and fragment-based approaches with their own benefits and limitations. More recently, artificial intelligence and machine learning-assisted approaches are also used to significantly reduce the complexity and computational burden associated with various docking applications. Thus, this chapter aims to provide a comprehensive summary of major challenges and recent advancements of molecular docking approaches in the IDP field for their better utilization and greater applicability.Asp (D).

Increased platelet-leucocyte complexes do not result in coagulation activation in plateletpheresis donors.

BACKGROUND: Although plateletpheresis donation is commonly accepted as a safe procedure, its influence on platelet function, coagulation system and fibrinolysis is not completely elucidated. OBJECTIVES: In this study, we tried to assess the effects of plateletpheresis on donor's hemostasis system by measuring platelet activation, development of platelet-leukocyte aggregates, and coagulation activation. STUDY DESIGN: Prospective observational study. METHODS: We used flow cytometry to determine the levels of platelet-monocyte complexes (PMC) and platelet-neutrophil complexes (PNC). sP-selectin and prothrombin fragment (PF) 1 + 2 values were determined by ELISA. RESULTS: The PMC levels increased significantly seven days after apheresis in comparison with just after apheresis and 24 h after apheresis (p < 0.05). The PNC levels increased significantly seven days after apheresis compared to immediately after apheresis (p < 0.05). sP-selectin values decreased significantly immediately after apheresis (p < 0.05). While sP-selectin values increased seven days after apheresis in comparison with immediately after apheresis and 24 h after apheresis, but there were not statistically significant differences for sP-selectin levels (p > 0.05). PF1 + 2 levels decreased significantly immediately after apheresis compared to pre-apheresis (p < 0.05) and increased 24 h after apheresis and seven days after apheresis, but these differences were not statistically significant. CONCLUSION: We concluded that plateletpheresis affects platelet activation but does not cause any change in coagulation activation.

tRNA-derived fragment tRF-30 propels diabetes-induced retinal microvascular complications by regulating STAT3 signaling.

Transfer RNA-derived fragments (tRFs) represent a novel class of non-coding RNA transcripts that possess specific biological functions. However, the involvement of tRFs in retinal microvascular diseases remains poorly understood. In this study, we aimed to reveal whether modulation of tRF-30 expression could attenuate pathological retinal neovascular diseases. Our findings demonstrate a significant upregulation of tRF-30 expression levels in both in vivo models of diabetic retinopathy (DR) and in vitro endothelial sprouting models. Conversely, inhibition of tRF-30 expression suppressed the formation of abnormal neovascularization in the retina in vivo, while reducing the proliferation and migration activity of retinal vascular endothelial cells in vitro. We also found that tRF-30 modulates retinal neovascularization through the tRF-30/TRIB3/signal transducer and activated transcription 3 signaling pathway. Furthermore, we validated a significant upregulation of tRF-30 expression levels in the vitreous humor of DR patients, with high levels of both validity and specificity in diagnostic testing. Collectively, our findings highlight a pro-angiogenic role for tRF-30 in DR. Intervening in the tRF-30 signaling pathway may represent a promising prevention and treatment strategy for retinal angiogenesis.

PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models.

SMILES-based generative models are amongst the most robust and successful recent methods used to augment drug design. They are typically used for complete de novo generation, however, scaffold decoration and fragment linking applications are sometimes desirable which requires a different grammar, architecture, training dataset and therefore, re-training of a new model. In this work, we describe a simple procedure to conduct constrained molecule generation with a SMILES-based generative model to extend applicability to scaffold decoration and fragment linking by providing SMILES prompts, without the need for re-training. In combination with reinforcement learning, we show that pre-trained, decoder-only models adapt to these applications quickly and can further optimize molecule generation towards a specified objective. We compare the performance of this approach to a variety of orthogonal approaches and show that performance is comparable or better. For convenience, we provide an easy-to-use python package to facilitate model sampling which can be found on GitHub and the Python Package Index.Scientific contributionThis novel method extends an autoregressive chemical language model to scaffold decoration and fragment linking scenarios. This doesn't require re-training, the use of a bespoke grammar, or curation of a custom dataset, as commonly required by other approaches.

Differences in coagulation responses to vascular injury between uninterrupted dabigatran and apixaban - a clinical prospective randomized study.

BACKGROUND: The coagulation response during vascular injury with uninterrupted administration of direct oral anticoagulants (DOACs) has not been elucidated. OBJECTIVE: Our aim was to evaluate differences in coagulation responses after vascular injury between uninterrupted direct thrombin inhibitor and direct factor Xa inhibitor recipients. METHODS: Patients scheduled for catheter ablation for atrial fibrillation were randomly assigned to receive dabigatran or apixaban in this prospective, randomized, comparative, parallel-group study. Venous blood was collected three times: 180 minutes after taking the anticoagulant on the day before the procedure, before vascular punctures of the ablation procedure, and 10-15 minutes after the start of vascular punctures. RESULTS: Forty-two patients were enrolled. The prothrombin fragment 1+2 (F1+2) level, the primary endpoint, was much larger after vascular puncture in the uninterrupted dabigatran recipients (median: 83 pmol/L; interquartile range: 56-133 pmol/L) than in the uninterrupted apixaban recipients (median: 1 pmol/L; interquartile range: -3-19 pmol/L; P < 0.001). Antithrombin levels decreased after vascular puncture in dabigatran recipients, and both protein C and antithrombin levels decreased after vascular puncture in apixaban recipients. CONCLUSIONS: Unlike uninterrupted apixaban, uninterrupted dabigatran does not inhibit thrombin generation in response to vascular injury.

Fragment-based discovery of small molecule inhibitors of the HDGFRP2 PWWP domain.

The PWWP domain of hepatoma-derived growth factor-related protein 2 (HDGFRP2) recognizes methylated histones to initiate the recruitment of homologous recombination repair proteins to damaged silent genes. The combined depletion of HDGFRP2 and its paralog PSIP1 effectively impedes the onset and progression of diffuse intrinsic pontine glioma (DIPG). Here, we discovered varenicline and 4-(4-bromo-1H-pyrazol-3-yl) pyridine (BPP) as inhibitors of the HDGFRP2 PWWP domain through a fragment-based screening method. The complex crystal structures reveal that both Varenicline and BPP engage with the aromatic cage of the HDGFRP2 PWWP domain, albeit via unique binding mechanisms. Notably, BPP represents the first single-digit micromolar inhibitor of the HDGFRP2 PWWP domain with a high ligand efficiency. As a dual inhibitor targeting both HDGFRP2 and PSIP1 PWWP domains, BPP offers an exceptional foundation for further optimization into a chemical tool to dissect the synergetic function of HDGFRP2 and PSIP1 in DIPG pathogenesis.

Intracellular tau fragment droplets serve as seeds for tau fibrils.

Intracellular tau aggregation requires a local protein concentration increase, referred to as "droplets". However, the cellular mechanism for droplet formation is poorly understood. Here, we expressed OptoTau, a P301L mutant tau fused with CRY2olig, a light-sensitive protein that can form homo-oligomers. Under blue light exposure, OptoTau increased tau phosphorylation and was sequestered in aggresomes. Suppressing aggresome formation by nocodazole formed tau granular clusters in the cytoplasm. The granular clusters disappeared by discontinuing blue light exposure or 1,6-hexanediol treatment suggesting that intracellular tau droplet formation requires microtubule collapse. Expressing OptoTau-ΔN, a species of N-terminal cleaved tau observed in the Alzheimer's disease brain, formed 1,6-hexanediol and detergent-resistant tau clusters in the cytoplasm with blue light stimulation. These intracellular stable tau clusters acted as a seed for tau fibrils in vitro. These results suggest that tau droplet formation and N-terminal cleavage are necessary for neurofibrillary tangles formation in neurodegenerative diseases.

Endovascular Removal of Pulmonary Artery Bullet Embolus: Case Report and Literature Review.

The current state of the literature for a bullet embolization to the heart and/or pulmonary vasculature indicates the occurrence is rare but could increase due to the rise in civilian low-kinetic-energy firearm acquisition and use. We present the case of an older teenage male who sustained a gunshot wound to the left flank. The bullet entered the iliac vein, travelled through the heart and lodged in the pulmonary artery. Successful relocation of the bullet to the internal iliac vein was performed by the interventional radiologist. This article highlights the advancement of interventional radiology as a successful non-invasive endovascular technique for bullet embolus removal.

Detection and Characterization of Methylated Circulating Tumor DNA in Gastric Cancer.

Gastric cancer is the fifth most common disease in the world and the fourth most common cause of death. It is diagnosed through esophagogastroduodenoscopy with biopsy; however, there are limitations in finding lesions in the early stages. Recently, research has been actively conducted to use liquid biopsy to diagnose various cancers, including gastric cancer. Various substances derived from cancer are reflected in the blood. By analyzing these substances, it was expected that not only the presence or absence of cancer but also the type of cancer can be diagnosed. However, the amount of these substances is extremely small, and even these have various variables depending on the characteristics of the individual or the characteristics of the cancer. To overcome these, we collected methylated DNA fragments using MeDIP and compared them with normal plasma to characterize gastric cancer tissue or patients' plasma. We attempted to diagnose gastric cancer using the characteristics of cancer reflected in the blood through the cancer tissue and patients' plasma. As a result, we confirmed that the consistency of common methylated fragments between tissue and plasma was approximately 41.2% and we found the possibility of diagnosing and characterizing cancer using the characteristics of the fragments through SFR and 5'end-motif analysis.

Cancer Antibody Engineering: Comparison of Mammalian, Yeast, Bacterial, Plants, Cell-free and Hybridoma Expression Systems.

BACKGROUND: Cancer is a significant issue worldwide. Generally, commercially available treatments, such as surgery, radiotherapy, and chemotherapy, are associated with undesirable complications. Hence, immunotherapy serves as a crucial alternative to those treatment options. OBJECTIVE: This modality is aimed to boost the immune system through the application of engineered antibodies, which can be produced using recombinant DNA technology. RESULTS: The discussion of the technologies leads to an introduction of the single-chain variable fragment (scFv). Thereafter, the advantages, disadvantages, and challenges associated with different expression systems, such as mammalian cells, yeast cells, bacterial cells, plant cells, and phage display were discussed comprehensively. CONCLUSION: Furthermore, conventional approaches such as hybridoma and modern approaches such as cell-free protein synthesis (CFPS) and simple colony assays are included. In short, this article has compiled evidence relating to each display system and may serve as a reference for those who aim to explore antibody engineering using one of the methods listed in this article.

Enzyme Cascade Amplification-Based Immunoassay Using Alkaline Phosphatase-Linked Single-Chain Variable Fragment Fusion Tracer and MnO2 Nanosheets for Detection of Deoxynivalenol in Corn Samples.

Deoxynivalenol (DON) is a common mycotoxin that contaminates cereals. Therefore, the development of sensitive and efficient detection methods for DON is essential to guarantee food safety and human health. In this study, an enzyme cascade amplification-based immunoassay (ECAIA) using a dual-functional alkaline phosphatase-linked single-chain fragment variable fusion tracer (scFv-ALP) and MnO2 nanosheets was established for DON detection. The scFv-ALP effectively catalyzes the hydrolysis of ascorbyl-2-phosphate (AAP) to produce ascorbic acid (AA). This AA subsequently interacts with MnO2 nanosheets to initiate a redox reaction that results in the loss of oxidizing properties of MnO2. In the absence of ALP, MnO2 nanosheets can oxidize 3,3',5,5'-tetramethylbenzidine (TMB) to produce the blue oxidized product of TMB, which exhibits a signal at a wavelength of 650 nm for quantitative analysis. After optimization, the ECAIA had a limit of detection of 0.45 ng/mL and a linear range of 1.2-35.41 ng/mL. The ECAIA exhibited good accuracy in recovery experiments and high selectivity for DON. Moreover, the detection results of the actual corn samples correlated well with those from high-performance liquid chromatography. Overall, the proposed ECAIA based on the scFv-ALP and MnO2 nanosheets was demonstrated as a reliable tool for the detection of DON in corn samples.

Identification of a Novel 16.8Kb Deletion of the α-Globin Gene Cluster by Third-Generation Sequencing.

α-thalassemia major (α-TM) often causes Hb Bart's (c4) hydrops fetalis and severe obstetric complications in the mother. Step-wise screening for couples at risk of having offspring(s) affected by α-TM is the efficient prevention method but some rare genotypes of thalassemia cannot be detected. A 32-year-old male with low HbA2 (2.4%) and mild anemia was performed real-time PCR-based multicolor melting curve analysis (MMCA) because his wife was -SEA deletion carrier. The result of multiplex ligation-dependent probe amplification (MLPA) suggested the existence of -SEA deletion in the proband. A novel deletion of the α-globin gene cluster was found using self-designed MLPA probes combined with longer PCR, which was further accurately described to be 16.8Kb (hg38, Chr16:1,65,236-1,82,113) deletion by the third-generation sequencing. A fragment ranging from 1,53,226 to 1,54,538(GRch38/hg38) was identified which suggested the existence of the homologous recombination event. The third-generation sequencing is accurate and efficient in obtaining accurate information for complex structural variations.

Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53.

Purpose: Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods: After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results: In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion: The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.

Wartime penetrating skull base trauma with unpredictable internal fragment ricochet and migration: illustrative case.

BACKGROUND: Transnasal transsphenoidal penetrating craniocerebral injury is very rare even in wartime. Cases with good outcomes are even less common. OBSERVATIONS: A 20-year-old male sustained multiple fragment wounds to his head and face from a landmine explosion. One metal fragment entered his right nostril, traversed the nasal septum and anterior sphenoid sinus, and ricocheted superiorly off the clivus. The fragment then traveled almost to the surface of the left parietal lobe. Subsequently, under its own weight, it migrated back down its original track. The patient suffered cerebrospinal fluid rhinorrhea, pneumocephalus, and right-sided hemiparesis. Digital subtraction angiography was followed by microscopic transnasal skull base reconstruction supplemented by external lumbar drainage. Follow-up brain computed tomogrpahy showed further metallic fragment migration through the ventricular system. The fragment was removed through a transcortical approach. The patient's neurological examination and brain magnetic resonance imaging results demonstrated good recovery. LESSONS: The absence of external signs of deep injuries does not exclude the presence of a penetrating craniocerebral injury. Metal fragments may undergo ricochet and internal migration in both the brain parenchyma and the ventricular system. Timely diagnosis including three-dimensional reconstruction of a projectile's trajectory may facilitate appropriate surgical planning in complex cases. Intraventricular fragment migration may necessitate microsurgical removal. https://thejns.org/doi/10.3171/CASE24128.

Streamlined two-step fragment analysis PCR and exome sequencing of RFC1 for diagnostic testing of suspected CANVAS patients.

Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) is caused by biallelic pathogenic expansions, or compound heterozygosity with other pathogenic variants in the RFC1 gene. CANVAS is estimated to be underdiagnosed, both because of the lack of formal diagnostic criteria and molecular challenges that translate to lesser access and high cost of routine testing. Our aim was to address the need for making CANVAS genetic testing routine, by designing a streamlined two-step PCR consisting of a short-allele screening PCR and a confirmatory PCR with fragment capillary electrophoresis detection. Exome sequencing of RFC1 was additionally foreseen to resolve potential compound heterozygosity cases. Specificity of our approach was evaluated using ataxia patients with known non-CANVAS diagnoses, and optimized using Southern blot confirmed CANVAS patients. We evaluated our approach by testing patients consecutively referred for clinically suspected CANVAS using first the two-step PCR, followed by exome sequencing. Our approach was able to accurately identify negative and confirm positive cases in prospectively collected suspected CANVAS patients presenting with at least three typical clinical signs. The proposed testing approach provides an alternative method able to clearly distinguish between CANVAS negative and positive cases and can be easily incorporated into the genetic diagnostic laboratory workflow.

Phacofragmentation of Posteriorly Dislocated Lens Fragments: Limbal versus Pars Plana Approach.

PURPOSE: To assess intra-operative complications and feasibility of removing crystalline lens fragments from the vitreous cavity through a limbal incision compared to a pars plana approach. DESIGN: Retrospective cohort study. SUBJECTS: 16 eyes underwent phacofragmentation via a limbal approach (Group A) and 9 eyes through a pars plana approach (Group B) at an academic center over a 10-year period. METHODS: We collected pre-operative, intra-operative, and post-operative data. We compared rates of intraoperative complications, including corneal wound burn, iris or capsular damage, retinal tears, and hemorrhage, and recorded post-operative BCVA and IOP measurements at the one-month post-operative appointment. We also compared rates of post-operative complications, including corneal edema, choroidal detachment, or retinal detachment. MAIN OUTCOME MEASURES: Primary outcomes of the study were the rates of intraoperative complications and the feasibility of crystalline lens removal with the limbal approach. We defined the latter outcome as the ability to complete lens removal without switching to the pars plana route. RESULTS: Mean BCVA for group A was 1.6, and for group B was 2.0 (p = .19). There was no significant difference between the two groups in the incidence of intraoperative complications, including corneal wound burn, iris damage, anterior capsular tear, iatrogenic retinal tear, or suprachoroidal hemorrhage (p > .99). There was no significant difference in the incidence of intra-operative vitreous hemorrhage (p = .36). Additionally, there was no significant difference in post-operative corneal edema (p = .27), choroidal detachment (p = .52), or retinal detachment (p > .99). The mean post-operative BCVA was 1.0 in group A and 1.0 in group B (p = .75). We completed all cases in group A using the limbal approach without switching to the pars plana route. CONCLUSION: Phacofragmentation through a limbal incision provides a feasible option for dropped nuclear fragment removal and is not associated with a higher risk of complications than the pars plana route.

Efficient generation of recombinant anti-HER2 scFv with high yield and purity using a simple method.

We developed a method to produce a soluble form of a single-chain fragment variable (scFv) targeting human epithelial growth factor receptor 2 (HER2) in Escherichia coli. By optimizing the orientations of the variable heavy (VH) and variable light (VL) domains and the His-tag, we identified the HL-His type antibody with the highest HER2-binding activity. Purification of HL-His yielded 40.7 mg from a 1 L culture, achieving >99% purity. The limit of detection was determined to be 2.9 ng, demonstrating high production yield, purity, and sensitivity. Moreover, we successfully labeled HER2+ cell lines with fluorescent dye-conjugated scFv, resulting in a significantly higher observed signal-to-background ratio, compared to that of HER2- cell lines. This highlights the potential of these fluorescent scFvs as valuable probes for HER2+ breast cancer diagnostics. Notably, the process for the complete scFv production was streamlined and required only 4-5 days. Additionally, the product maintained its activity after freeze storage, allowing for large-scale production and a wide range of practical applications.

hsp70 PCR-RFLP as an alternative tool to identify Sauroleishmania species.

Sauroleishmania spp. comprises one of the four Leishmania subgenera, which has been historically considered a non-pathogenic protozoan of reptiles. However, some strains appear to be transiently infective to mammals, and recent findings have detected these parasites in dogs and humans in areas where leishmaniasis is endemic. Herein, the digestion pattern of PCR-RFLP of the 234 bp-hsp70 fragment was evaluated as a simpler and cheaper tool to distinguish the Sauroleishmania species from the other Leishmania subgenera. As a result, the digestion of the 234 bp-hsp70 fragments with HaeIII produced a banding pattern specific to the four Sauroleishmania strains assessed. This technique could contribute to the identification of Leishmania parasites isolated from sandflies, reptiles, or even mammals in fieldworks as an alternative to the use of laborious and expensive methodologies.

Migration of Bullet Fragment 11 Years after Initial Gunshot Wound leads to Cervical Prevertebral Abscess: A Case Report.

Introduction: Literature showcases conflicting findings regarding the outcomes of ballistic fragment removal from the spine in gunshot wounds (GSW) patients. Further research in this area is needed to better comprehend the nuances of risks and benefits surrounding ballistic fragment removal from the spine in GSW patients. In this case report, we discuss the late-onset cervical prevertebral abscess which developed when a previously embedded bullet fragment migrated into the retropharyngeal space 11 years after an initial GSW. Case Report: A 29-year-old male sustained a gunshot wound to the face in 2011. He was stabilized with a posterior C3-C6 lateral mass instrumentation and fusion. There were no attempts to remove the bullet fragments. In 2023, the patient returned with worsening neck pain. Imaging demonstrated a retropharyngeal abscess with interval rotation of the ballistic fragment by 90°. An abscess was noted anterior to the cervical vertebrae with a freely mobile ballistic fragment within. Conclusion: This case highlights several questions: What is the criteria for radiographic surveillance of retained hardware? If there is documented movement, should this trigger further investigation? What complications can occur that warrant careful removal?

Backbone and methyl side-chain resonance assignments of the Fab fragment of adalimumab.

Adalimumab is a therapeutic monoclonal antibody developed to target human TNF an important mediator of immune-mediated inflammatory diseases such as rheumatoid arthritis, amongst others. The 48 kDa Fab fragment of adalimumab was produced in Escherichia coli using a single chain approach to allow complete isotopic incorporation of deuterium, carbon-13 and nitrogen-15 along with the protonated isoleucine-d, valine and leucine methyl groups. Here we report the near complete resonance assignment of the polypeptide backbone and the methyl groups of isoleucine, leucine and valine residues.