Developing novel Lin28 inhibitors by computer aided drug design.

Lin28 is a key regulator of cancer stem cell gene network that promotes therapy-resistant tumor progression in various tumors. However, no Lin28 inhibitor has been approved to treat cancer patients, urging exploration of novel compounds as candidates to be tested for clinical trials. In this contribution, we applied computer-aided drug design (CADD) in combination with quantitative biochemical and biological assays.

[The Influence of Antithrombotic Therapy on the Risk Factors for Cardiovascular Complications in Patients With Coronary Artery Disease And Diabetes Mellitus. Emphasis on Hypercoagulation].

Comorbid diabetes mellitus (DM) in patients with ischemic heart disease (IHD) is a serious factor that significantly impairs the life prognosis and increases the risk of cardiovascular complications (CVC) as well as the likelihood of death. The residual risk of developing CVC in such patients is largely determined by the high thrombotic status, that is associated with hypercoagulation characteristic of DM. Hypercoagulation causes activation of both platelet and coagulation pathways, which leads to an increased susceptibility to thrombosis.

Blood matters: the hematological signatures of Coronavirus infection.

Recent developments have broadened our perception of SARS-CoV-2, indicating its capability to affect the body systemically beyond its initial recognition as a mere respiratory pathogen. However, the pathways of its widespread are not well understood. Employing a dual-modality approach, we integrated findings from a Murine Hepatitis Virus (MHV) infection model with corroborative clinical data to investigate the pervasive reach of Coronaviruses.

Targeting eIF4G1-dependent translation in melanoma.

Elevated expression of components of eIF4F translation initiation complex has been documented in cancer, resulting in enhanced translation of mRNAs encoding pro-tumorigenic factors, including oncogenic proteins. We previously identified SBI-756, a small molecule that interferes with the eIF4F assembly and overcomes melanoma resistance to BRAF inhibitors. SBI-756 enhanced anti-tumor immunity in pancreatic cancer and was effective in the treatment of diffuse large B cell lymphoma.

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein.

The CACHE challenges are a series of prospective benchmarking exercises to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE challenge in which 23 computational teams each selected up to 100 commercially available compounds that they predicted would bind to the WDR domain of the Parkinson's disease target LRRK2, a domain with no known ligand and only an apo structure in the PDB. The lack of known binding data and presumably low druggability of the target is a challenge to computational hit finding methods.

Bridge-Dependent Donor-Metal-Acceptor-Metal-Donor (D-M-A-M-D) Systems: From Charge Transfer to Electron Transfer in Dioxolene-Ge-Diimine Complexes.

Synthesis and structural characterization of a family of germanium-dioxolene complexes with ditopic N-donor ligands (L-L) (L=1,2-bis(pyridin-2-ylmethylene)hydrazine L=1,6-bis-(pyridin-2-yl)-2,5-diaza-1,5-hexadiene, L=N,N-bis(pyridin-2-ylmethylene)-1,4-benzenediamine, L=N,N-bis(pyridin-2-ylmethylene)-(biphenyl)-4,4-diamine, L=2,2'-azopyridine) is reported. The reaction of germanium bis-catecholate with bridging ligands L - L, differing by the nature of the linker between pyridine sites gives rise to dinuclear digermanium complexes (36CatGe)L (36Cat=dianion of 3,6-di-tert-butylcatechol) 1-4 of DMAMD type (donor-metal-acceptor-metal-donor) with a charge transfer in the UV-Vis region. In opposite, the interaction of the 36CatGe with 2,2'-azopyridine (L) results in the two-electron transfer from the donor 36Cat ligands to the azopyridine bridge forming stable open-shell complex 5 [(36SQ)(36CatGe)](L) (36SQ=radical-anionic semiquinonate ligand).

screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations.

The Critical Assessment of Computational Hit-Finding Experiments (CACHE) Challenge series is focused on identifying small molecule inhibitors of protein targets using computational methods. Each challenge contains two phases, hit-finding and follow-up optimization, each of which is followed by experimental validation of the computational predictions. For the CACHE Challenge #1, the Leucine-Rich Repeat Kinase 2 (LRRK2) WD40 Repeat (WDR) domain was selected as the target for hit-finding and optimization.

Pharmacokinetics Profiler (PhaKinPro): Model Development, Validation, and Implementation as a Web Tool for Triaging Compounds with Undesired Pharmacokinetics Profiles.

Computational models that predict pharmacokinetic properties are critical to deprioritize drug candidates that emerge as hits in high-throughput screening campaigns. We collected, curated, and integrated a database of compounds tested in 12 major end points comprising over 10,000 unique molecules. We then employed these data to build and validate binary quantitative structure-activity relationship (QSAR) models.

Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.

FOXA1 is a pioneer transcription factor that is frequently mutated in prostate, breast, bladder, and salivary gland malignancies. Indeed, metastatic castration-resistant prostate cancer (mCRPC) commonly harbour FOXA1 mutations with a prevalence of 35%. However, despite the frequent recurrence of FOXA1 mutations in prostate cancer, the mechanisms by which FOXA1 variants drive its oncogenic effects are still unclear.

PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs.

Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than those of a small molecule drug, we explored a combination of computational chemistry and deep learning strategies to forecast PROTAC activity and enable automated design. A new method named PROTACable was developed for the de novo design of PROTACs, which includes a robust 3-D modeling workflow to model PROTAC ternary complexes using a library of E3 ligase and linker and an SE(3)-equivariant graph transformer network to predict the activity of newly designed PROTACs.

Luminescent Er based single molecule magnets with fluorinated alkoxide or aryloxide ligands.

We report the synthesis, structures, and magnetic and luminescence properties of a series of new mono- and dinuclear Er complexes derived from sterically demanding aryloxide and fluorinated alkoxide ligands: [4-Bu-2,6-(PhCH)CHO]Er(THF) (1), [(CF)CO]Er(MeSiOH) (2), [(CF)CO]Er[(MeSi)NH] (3), [(CF)CO]Er(CHCH) (4), [(CF)CO]Er(-MeNCHCH) (5) and {[Ph(CF)CO]Er(μ-OC(CF)Ph)} (6). In compounds 1, 2, and 4, the Er ion is four-coordinated and adopts a distorted trigonal pyramidal geometry, while in 3, 5, and 6, the coordination geometry of Er is impacted by the presence of several relatively short Er⋯F distances, making them rather 6-coordinated. All compounds behave as field-induced Single Molecule Magnets (SMMs) and exhibit an Er characteristic near infrared (NIR) emission associated with the I → I transition with a remarkably long lifetime going up to 73 μs, which makes them multifunctional luminescent SMMs.

Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR.

Quantitative structure-activity relationship (QSAR) modelling, an approach that was introduced 60 years ago, is widely used in computer-aided drug design. In recent years, progress in artificial intelligence techniques, such as deep learning, the rapid growth of databases of molecules for virtual screening and dramatic improvements in computational power have supported the emergence of a new field of QSAR applications that we term 'deep QSAR'. Marking a decade from the pioneering applications of deep QSAR to tasks involved in small-molecule drug discovery, we herein describe key advances in the field, including deep generative and reinforcement learning approaches in molecular design, deep learning models for synthetic planning and the application of deep QSAR models in structure-based virtual screening.

Self-assembly of a metal-organic cage-like structure bearing cofacial redox-active bis-(-semiquinone) copper(II) units.

Ditopic di--quinone with a resorcinol bridge exhibits the ability to self-assemble in a reaction with copper, giving a cage-like binuclear complex that, due to the cofacially placed metal ions, is capable of encapsulation of different solvent molecules as guest ligands. Notably, the geometry of the internal cavity of this complex adjusts depending on the coordinating properties of the encapsulated molecule (mono- or bidentate). A feature of this species is that the cage-forming units are copper(II) bis-semiquinonate moieties, capable of undergoing ligand-centered redox transformations.

Population Genomics of Two Closely Related Anhydrobiotic Midges Reveals Differences in Adaptation to Extreme Desiccation.

The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process is protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs).

A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants.

Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (). Our lead direct-acting antiviral (DAA), , is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro.

Dependency of Tamoxifen Sensitive and Resistant ER Breast Cancer Cells on Semaphorin 3C (SEMA3C) for Growth.

Estrogen receptor positive (ER) breast cancer (BCa) accounts for the highest proportion of breast cancer-related deaths. While endocrine therapy is highly effective for this subpopulation, endocrine resistance remains a major challenge and the identification of novel targets is urgently needed. Previously, we have shown that Semaphorin 3C (SEMA3C) is an autocrine growth factor that drives the growth and treatment resistance of various cancers, but its role in breast cancer progression and endocrine resistance is poorly understood.

Novel Inhibitors of androgen receptor's DNA binding domain identified using an ultra-large virtual screening.

Androgen receptor (AR) inhibition remains the primary strategy to combat the progression of prostate cancer (PC). However, all clinically used AR inhibitors target the ligand-binding domain (LBD), which is highly susceptible to truncations through splicing or mutations that confer drug resistance. Thus, there exists an urgent need for AR inhibitors with novel modes of action.

PurificationDB: database of purification conditions for proteins.

The isolation of proteins of interest from cell lysates is an integral step to study protein structure and function. Liquid chromatography is a technique commonly used for protein purification, where the separation is performed by exploiting the differences in physical and chemical characteristics of proteins. The complex nature of proteins requires researchers to carefully choose buffers that maintain stability and activity of the protein while also allowing for appropriate interaction with chromatography columns.

Novel Rigidochromic and Anti-Kasha Dual Emission Fluorophores Based on D-π-A Dyads as the Promising Materials for Potential Applications Ranging from Optoelectronics and Optical Sensing to Biophotonics and Medicine.

Today we see an increasing demand for new fluorescent materials exhibiting various sensory abilities due to their broad applicability ranging from the construction of flexible devices to bioimaging. In this paper, we report on the new fluorescent pigments AntTCNE, PyrTCNE, and PerTCNE which consist of 3-5 fused aromatic rings substituted with tricyanoethylene fragments forming D-π-A diad. Our studies reveal that all three compounds exhibit pronounced rigidochromic properties, i.

In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm.

Improving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media.