Molecular Similarity Research Articles

Innovative virtual screening of PD-L1 inhibitors: the synergy of molecular similarity, neural networks and GNINA docking.

Aims: Immune checkpoint inhibitors targeting PD-L1 are crucial in cancer research for preventing cancer cells from evading the immune system.Materials & methods: This study developed a screening model combining ANN, molecular similarity, and GNINA 1.0 docking to target PD-L1. A database of 2044 substances was compiled from patents.Results: For molecular similarity, the AVALON emerged as the most effective fingerprint, demonstrating an AUC-ROC of 0.963. The ANN model outperformed the Random Forest andSupport Vector Classifier in cross-validation and external validation, achieving an average precision of 0.851 and an F1 score of 0.790. GNINA 1.0 was validated through redocking and retrospective control, achieving an AUC of 0.975.Conclusions: From 15235 DrugBank compounds, 22 candidates were shortlisted. Among which (3S)-1-(4-acetylphenyl)-5-oxopyrrolidine-3-carboxylic acid emerged as the most promising.

Kinetic insights into double-branched acyclic ether: Methyl tert-butyl ether and 2,2-dimethoxypropane

This study presents the first kinetic mechanism for methyl tert-butyl ether (MTBE) containing low-temperature chemistry, as well as the first mechanism for 2,2-dimethoxypropane (DMP). The mechanisms have been validated against ignition delay time experiments conducted in a high-pressure shock tube and rapid compression machine. The rapid compression machine conditions were set to 20 and 40 bar for MTBE, and 10 and 20 bar for DMP in a temperature range of 584 to 946 K. Shock tube experiments have been performed for DMP at 20 and 40 bar for stoichiometric and fuel-lean conditions in air at temperatures ranging from 913 to 1173 K. A pronounced negative temperature coefficient regime with two-stage ignition has been observed for both fuels. The developed mechanism consists of reaction rate constants that were primarily modeled in analogy to iso-octane and dimethoxymethane, and calculated thermodata on the G4//B3LYP-D3BJ/def2-TZVP level of theory. Simulations have been performed to analyze the fuel oxidation at different temperatures. Over the full temperature range, H-atom abstraction occurs mainly on the α-side for DMP and on the β-side for MTBE. At low temperatures, both fuels isomerize to the peroxy radical. The dominant MTBE radicals then tend to produce cyclic ether, while the DMP radicals react with O2, enabling significant chain branching and explaining the higher reactivity of DMP. With rising temperature, β-scission of the fuel radicals and unimolecular elimination reactions start to dominate the oxidation process.Novelty and Significance StatementThe novelty of this research is the first observation of a two-stage ignition of methyl-tert butyl ether (MTBE) in an RCM and a discussion of its fundamental ignition chemistry, which is based on a developed detailed kinetic mechanism. In addition, 2,2-dimethoxypropane (DMP) has been investigated experimentally and theoretically to explain the difference in reactivity to MTBE despite their strong molecular similarity. The experiments include RCM and shock tube experiments. The kinetic model is based on rate constant analogies and newly calculated thermo data on the G4//B3LYP-D3BJ/def2-TZVP level of theory. This work is significant, as MTBE is still a widely used octane booster and the developed model could help to improve engine simulations. Furthermore, the findings of DMP provide insights into future fuel design.

PROTAC-DB 3.0: an updated database of PROTACs with extended pharmacokinetic parameters.

Proteolysis-targeting chimera (PROTAC) is an emerging therapeutic technology that leverages the ubiquitin-proteasome system to target protein degradation. Due to its event-driven mechanistic characteristics, PROTAC has the potential to regulate traditionally non-druggable targets. Recently, AI-aided drug design has accelerated the development of PROTAC drugs. However, the rational design of PROTACs remains a considerable challenge. Here, we present an updated online database, PROTAC-DB 3.0. In this third version, we have expanded the database to include 6111 PROTACs (87% increase compared to the 2.0 version). Additionally, the database now contains 569 warheads (small molecules targeting the protein), 2753 linkers, and 107 E3 ligands (small molecules recruiting E3 ligases). The number of target-PROTAC-E3 ternary complex structures has also increased to 959. Recognizing the importance of druggability in PROTAC design, we have incorporated pharmacokinetic data to PROTAC-DB 3.0. To enhance user experience, we have added features for sorting based on molecular similarity and literature publication date. PROTAC-DB 3.0 is accessible at http://cadd.zju.edu.cn/protacdb/.

Molecular similarities between the genes for Trypanosoma cruzi microtubule-associated proteins, mammalian interferons, and TRIMs

Initial studies using bioinformatics analysis revealed DNA sequence similarities between Trypanosoma cruzi GenBank® M21331, coding for Antigen 36 (Ag 36), and tripartite motif (TRIM) genes. TRIM40 showed 9.7% identity to GenBank M21331, and four additional TRIM genes had identities greater than 5.0%. TRIM37 showed a continuous stretch of identity of 12 nucleotides, that is, at least 25% longer than any of the other TRIMs. When we extended our analysis on the relationships of GenBank M21331 to further innate immune genes, using the Needleman-Wunsch (NW) algorithm for alignment, identities to human IFN-α, IFN-β, and IFN-γ genes of 13.6%, 12.6%, and 17.9%, respectively, were found. To determine the minimum number of genes coding for proteins closely related to Ag 36, a BLAST-p search was conducted with it versus the T. cruzi genome. The BLAST-p search revealed that T. cruzi GenBank M21331 had 14 gene sequences homologous to microtubule-associated protein (MAP) genes with 100% amino acid sequence identity. To verify the similarities in non-human genes, a study comparing TRIM21 region sequences among mammalian species to the comparable human TRIM21 region showed that related sequences were also present in 11 mammalian species. The MAP genes homologous to Ag 36 form a family of at least 14 genes which mimic human immune genes in the IFN and TRIM families. This mimicry is of gene sequences and not their protein products or epitopes. These results appear to be the first description of molecular mimicry of immune genes in humans by a protozoan parasite.

Selenium deficiency and T-2 toxin trigger ferroptosis in cartilage from Kashin-Beck diseases

Kashin-Beck disease (KBD) is a prevalent, endemic, and degenerative cartilage injury disorder, characterized by high rates of teratogenicity and disability. The etiology and pathogenesis of KBD are not fully understood, although research suggests that selenium deficiency and exposure to T-2 toxin are significant environmental risk factors. The initial pathological changes of KBD manifest as necrosis of deep chondrocytes, dedifferentiation of chondrocytes, excessive apoptosis of chondrocytes, and subsequent disruption of extracellular matrix metabolism. However, the precise pathogenic mechanisms of chondrocyte damage in KBD remain incompletely understood. Ferroptosis is auniqueform of programmed cell death triggered byiron-dependent lipid peroxide accumulation. It has been shown to contribute to cartilage damage and chondrocyte death in various osteoarticular conditions, particularly osteoarthritis (OA). Notably, KBD not only exhibits clinical and pathologicalsimilarities with OA, but also indicates a potential association with ferroptosis in morphological and molecular similarities. Additionally, the environmental risk factors T-2 toxin exposure and selenium deficiency are also significant contributors toferroptosis. Consequently, it is plausible to postulate that environmental risk factors may trigger ferroptosis, leading to the initiation of cartilage damage in KBD. Our hypothesis can be verified through both in vitro and in vivo experiments. Chondrocyte injury induced by ferroptosis may be a novel finding in KBD, which is important for clarifying its etiology and developing effective therapeutic strategies.

Are the chemical families still there? Formal structure of similarity of elements and its thermochemical domain

The periodic table organizes chemical elements into families based on their similarity, now understood through Quantum Mechanics. However, these families were inferred from limited compounds in the nineteenth century. Since then, the number of compounds has exponentially grown, leading to the discovery of new types unknown to pioneers. This situation prompts the question of whether these families can still be discerned from the amassed data, or if their recognition is confined to specific thermochemical domains. To address this inquiry, we conducted a comprehensive exploration by comparing formulae (1771–2015) as a proxy for chemical similarity. Our findings reveal that stoichiometry not only captures a significant portion of the trends observed within families but also unveils other intriguing features of the formal structure of chemical similarity. These patterns approach equivalence classes independent of thermochemical context and demonstrate high resilience. Temporal analysis demonstrates that, since approximately 1980, similarity is diminishing due to an increasing production of unique formulae for nearly all elements. Nevertheless, chemical families endure over time and they stand out as the most robust similarity patterns. Our analysis offers compelling evidence that any study will reach the same conclusions, provided there is a sufficient diversity in input compound data.

Medical device similarity analysis: a promising approach to medical device equivalence regulation

ABSTRACT Background This study aims to facilitate the identification of similar devices for both, the European Medical Device Regulation (MDR) and the US 510(k) equivalence pathway by leveraging existing data. Both are related to the regulatory pathway of read across for chemicals, where toxicological data from a known substance is transferred to one under investigation, as they aim to streamline the accreditation process for new devices and chemicals. Research design and methods This study employs latent semantic analysis to generate similarity values, harnessing the US Food and Drug Administration 510k-database, utilizing their ‘Device Descriptions’ and ‘Intended Use’ statements. Results For the representative inhaler cluster, similarity values up to 0.999 were generated for devices within a 510(k)-predicate tree, whereas values up to 0.124 were gathered for devices outside this group. Conclusion Traditionally, MDR equivalence involves manual review of many devices, which is laborious. However, our results suggest that the automated calculation of similarity coefficients streamlines this process, thus reducing regulatory effort, which can be beneficial for patients needing medical devices. Although this study is focused on the European perspective, it can find application within 510(k) equivalence regulation. The conceptual approach is reminiscent of chemical fingerprint similarity analysis employed in read-across.

In Vivo Models of Steroid-Induced Intraocular Hypertension

: Corticosteroids are widely utilized for their anti-inflammatory and immunosuppressive properties but often lead to ocular complications, including ocular hypertension. If untreated, ocular hypertension can progress to optic nerve atrophy and eventually result in steroid-induced glaucoma, which poses a risk of irreversible visual damage. Approximately 40% of individuals experience increased intraocular pressure after steroid use, and around 6% develop glaucoma. Although steroid-induced glaucoma is usually temporary and reversible if the treatment duration is under a year, prolonged exposure can cause permanent vision impairment. The pathogenesis of steroid-induced glaucoma is suggested to arise from increased outflow resistance of aqueous humor, primarily due to decreased expression of matrix metalloproteinases. This deficiency promotes the deposition of extracellular matrix and the dysfunction of trabecular meshwork cells. Additionally, modifications in the actin cytoskeleton increase the stiffness and alter the morphology of trabecular meshwork, further impeding aqueous humor outflow. Molecular changes, such as elevated expression of the MYOC gene, have also been implicated in restricting aqueous outflow. Various animal models, including rats, mice, primates, rabbits, cattle, sheep, cats, and dogs, have been developed to study steroid-induced glaucoma. These models exhibit pathological, pathophysiological, and molecular similarities to human disease, making them valuable for research. This review aims to summarize common animal models of steroid-induced ocular hypertension, discussing their advantages and limitations. The goal is to help researchers select appropriate models for future studies, thereby advancing the understanding of disease mechanisms and developing preventive strategies.

Carvacrol-loaded premixed calcium phosphate bone cements with exceptional osteogenic and antibacterial properties to heal infected bone defects

The healing of infected bone fractures represents a significant clinical challenge in orthopedic surgery. Calcium phosphate cements (CPCs) are attractive materials, highly applicable in bone healing due to their satisfactory biological properties and chemical similarity to bone minerals. However, manual mixing is often required before localized application of conventional CPCs, increasing the risk of infection. Moreover, their antibacterial properties are often insufficient for treating infected fractures. In this study, antimicrobial two-paste premixed CPCs loaded with carvacrol were developed. The influence of the carvacrol on the setting properties and mechanical strength of the cement was studied. In vitro studies demonstrated the biocompatibility, osteogenic potential, and broad-spectrum antimicrobial efficacy of the premixed bone cements, including effectiveness against gram-positive, gram-negative, and drug-resistant bacteria. Notably, in vivo studies revealed exceptional antimicrobial and osteogenic properties of the carvacrol-loaded cements, confirming the promising potential of the premixed cements for the healing of infected bone defects.

Molecular similarity: Theory, applications, and perspectives

Molecular similarity pervades much of our understanding and rationalization of chemistry. This has become particularly evident in the current data-intensive era of chemical research, with similarity measures serving as the backbone of many Machine Learning (ML) supervised and unsupervised procedures. Here, we present a discussion on the role of molecular similarity in drug design, chemical space exploration, chemical “art” generation, molecular representations, and many more. We also discuss more recent topics in molecular similarity, like the ability to efficiently compare large molecular libraries.

Tumor-agnostic cancer therapy using antibodies targeting oncofetal chondroitin sulfate

Molecular similarities between embryonic and malignant cells can be exploited to target tumors through specific signatures absent in healthy adult tissues. One such embryonic signature tumors express is oncofetal chondroitin sulfate (ofCS), which supports disease progression and dissemination in cancer. Here, we report the identification and characterization of phage display-derived antibody fragments recognizing two distinct ofCS epitopes. These antibody fragments show binding affinity to ofCS in the low nanomolar range across a broad selection of solid tumor types in vitro and in vivo with minimal binding to normal, inflamed, or benign tumor tissues. Anti-ofCS antibody drug conjugates and bispecific immune cell engagers based on these targeting moieties disrupt tumor progression in animal models of human and murine cancers. Thus, anti-ofCS antibody fragments hold promise for the development of broadly effective therapeutic and diagnostic applications targeting human malignancies.

Structural Optimization of Quinazolin-4-One Derivatives as Novel SARS-CoV-2 Mpro Inhibitors by Molecular Simulation

Background: Severe acute respiratory syndrome coronavirus 2 main protease (SARSCoV- 2 Mpro) has been shown to be an effective target for inhibiting novel coronaviruses, which can be used as a crucial breakthrough for developing drugs to treat the coronavirus disease 2019 (COVID-19). Methods: To design novel SARS-CoV-2 Mpro inhibitors, we conducted 3D-QSAR, molecular docking, and molecular dynamics (MD) simulation on 64 quinazolin-4-one derivatives. Results: Comparative molecular field analysis (CoMFA) model (q2 = 0.590, R2 = 0.962), comparative molecular similarity index analysis (CoMSIA) model (q2 = 0.628, R2 = 0.923), and external validation indicated that the stability, reliability, and prediction performance of our constructed model were excellent. We designed 8 inhibitors with stronger antiviral activities through the three-dimensional equipotential field. Molecular docking and MD simulation probed the interactions of compounds and SARS-CoV-2 Mpro. This indicated that amino acid residues, including Met165, Met49, and Cys145, were very important in combination with the compounds. The prediction results of ADME/T and Lipinski’s rule of five indicated that the new compounds had favorable drug-like and pharmacokinetic properties. Conclusion: This study provides new ideas for exploring new drugs against COVID-19

Accelerating drug discovery and repurposing by combining transcriptional signature connectivity with docking.

We present an in silico approach for drug discovery, dubbed connectivity enhanced structure activity relationship (ceSAR). Building on the landmark LINCS library of transcriptional signatures of drug-like molecules and gene knockdowns, ceSAR combines cheminformatic techniques with signature concordance analysis to connect small molecules and their targets and further assess their biophysical compatibility using molecular docking. Candidate compounds are first ranked in a target structure-independent manner, using chemical similarity to LINCS analogs that exhibit transcriptomic concordance with a target gene knockdown. Top candidates are subsequently rescored using docking simulations and machine learning-based consensus of the two approaches. Using extensive benchmarking, we show that ceSAR greatly reduces false-positive rates, while cutting run times by multiple orders of magnitude and further democratizing drug discovery pipelines. We further demonstrate the utility of ceSAR by identifying and experimentally validating inhibitors of BCL2A1, an important antiapoptotic target in melanoma and preterm birth-associated inflammation.

Chemical Doppelgangers in GALAH DR3: The Distinguishing Power of Neutron-capture Elements among Milky Way Disk Stars

The observed chemical diversity of Milky Way stars places important constraints on Galactic chemical evolution and the mixing processes that operate within the interstellar medium. Recent works have found that the chemical diversity of disk stars is low. For example, the Apache Point Observatory Galactic Evolution Experiment (APOGEE) “chemical doppelganger rate,” or the rate at which random pairs of field stars appear as chemically similar as stars born together, is high, and the chemical distributions of APOGEE stars in some Galactic populations are well-described by two-dimensional models. However, limited attention has been paid to the heavy elements (Z > 30) in this context. In this work, we probe the potential for neutron-capture elements to enhance the chemical diversity of stars by determining their effect on the chemical doppelganger rate. We measure the doppelganger rate in GALactic Archaeology with HERMES DR3, with abundances rederived using The Cannon, and find that considering the neutron-capture elements decreases the doppelganger rate from ∼2.2% to 0.4%, nearly a factor of 6, for stars with −0.1 < [Fe/H] < 0.1. While chemical similarity correlates with similarity in age and dynamics, including neutron-capture elements does not appear to select stars that are more similar in these characteristics. Our results highlight that the neutron-capture elements contain information that is distinct from that of the lighter elements and thus add at least one dimension to Milky Way abundance space. This work illustrates the importance of considering the neutron-capture elements when chemically characterizing stars and motivates ongoing work to improve their atomic data and measurements in spectroscopic surveys.

Exhaustive local chemical space exploration using a transformer model

How many near-neighbors does a molecule have? This fundamental question in chemistry is crucial for molecular optimization problems under the similarity principle assumption. Generative models can sample molecules from a vast chemical space but lack explicit knowledge about molecular similarity. Therefore, these models need guidance from reinforcement learning to sample a relevant similar chemical space. However, they still miss a mechanism to measure the coverage of a specific region of the chemical space. To overcome these limitations, a source-target molecular transformer model, regularized via a similarity kernel function, is proposed. Trained on a largest dataset of ≥200 billion molecular pairs, the model enforces a direct relationship between generating a target molecule and its similarity to a source molecule. Results indicate that the regularization term significantly improves the correlation between generation probability and molecular similarity, enabling exhaustive exploration of molecule near-neighborhoods.

A rapid and accurate fluorescent sensor array based on lanthanide metal-organic framework for identification and determination of perfluorinated compounds

Perfluorinated compounds (PFCs), as an important class of environmental pollutants, have chemical and structural similarities that make their detection a great technical challenge. This study synthesized three species of metal-organic frameworks (MOFs) using different lanthanide metal ions or organic ligands, which were integrated into a fluorescent sensor array. This innovative approach offers a straightforward, rapid, and precise detection strategy for PFCs. Different ionization properties and fluorinated hydrophobic tails of PFCs lead to different electrostatic attraction and hydrophobic effects between PFCs and sensing elements, which become the basis for differential sensing. Furthermore, the fluorescence signal is more convenient to collect, making the sensor array simple to complete the identification. Combined with pattern recognition methods, the array successfully identified seven kinds of PFCs and mixtures with a classification accuracy of 100 % and a detection limit as low as 51 nM. Finally, the utility of the sensor array in river water sample analysis was verified. The strategy provides an effective method for identifying and determining PFCs and offers new opportunities for developing sensor arrays based on lanthanide MOFs.

Bringing the Genomic Revolution to Comparative Oncology: Human and Dog Cancers.

Dogs are humanity's oldest friend, the first species we domesticated 20,000-40,000years ago. In this unequaled collaboration, dogs have inadvertently but serendipitously been molded into a potent human cancer model. Unlike many common model species, dogs are raised in the same environment as humans and present with spontaneous tumors with human-like comorbidities, immunocompetency, and heterogeneity. In breast, bladder, blood, and several pediatric cancers, in-depth profiling of dog and human tumors has established the benefits of the dog model. In addition to this clinical and molecular similarity, veterinary studies indicate that domestic dogs have relatively high tumor incidence rates. As a result, there are a plethora of data for analysis, the statistical power of which is bolstered by substantial breed-specific variability. As such, dog tumors provide a unique opportunity to interrogate the molecular factors underpinning cancer and facilitate the modeling of new therapeutic targets. This review discusses the emerging field of comparative oncology, how it complements human and rodent cancer studies, and where challenges remain, given the rapid proliferation of genomic resources. Increasingly, it appears that human's best friend is becoming an irreplaceable component of oncology research.

Efficient separation of vanadium and chromium by the complexation with sulfate ions in solvent extraction using EHEHPA

The significant chemical similarity between vanadium and chromium complicates the process of efficient extracting V(Ⅳ) from the solution containing Cr(Ⅲ) to prepare high-purity vanadyl sulfate electrolyte. In this study, the separation of vanadium and chromium with 2-ethylhexyl phosphoric acid-2-ethylhexyl ester (EHEHPA) was enhanced by increasing the concentration of SO42−. Under the extraction equilibrium pH of 2.5, the extraction of Cr(III) was suppressed by increasing the concentration of SO42− anions, which hardly affected the extraction efficiency of V(IV), achieving a separation factor as high as 5780.6 at SO42− concentration of 1.75 mol·L−1. Furthermore, after pretreatment of the water-leaching solution of sodium-roasted vanadium slag, extraction was carried out under the conditions of equilibrium pH of 1.8 and SO42− concentration of about 2.00 mol·L−1, and after stripping, the vanadyl sulfate electrolyte containing 2.12 mol·L−1 of vanadium and only 0.11 mg·L−1 of chromium was obtained. It was proved that Cr(Ⅲ) mainly extracted in the form of CrSO4+ into organic phase by one EHEHPA dimer as [CrSO4(H2O)]+ under higher SO42− concentrations (e.g., ≥1.50 mol·L−1), while Cr(Ⅲ) was extracted by two EHEHPA dimers as Cr3+ without SO42− in the solution. Based on the density functional theory, the complex structures of Cr(III) were optimized and the energy changes of Cr(III) extraction reactions were calculated, indicating the complexation between SO42− and Cr(III) under higher SO42− concentrations resulting in the inhibition of Cr(III) extraction, and thus enhancing the separation of vanadium and chromium.

Donepezil Nanoemulsion Induces a Torpor-like State with Reduced Toxicity in Nonhibernating Xenopus laevis Tadpoles.

Achieving a reversible decrease of metabolism and other physiological processes in the whole organism, as occurs in animals that experience torpor or hibernation, could contribute to increased survival after serious injury. Using a Bayesian network tool with transcriptomic data and chemical structure similarity assessments, we predicted that the Alzheimer's disease drug donepezil (DNP) could be a promising candidate for a small molecule drug that might induce a torpor-like state. This was confirmed in a screening study with Xenopus laevis tadpoles, a nonhibernator whole animal model. To improve the therapeutic performance of the drug and minimize its toxicity, we encapsulated DNP in a nanoemulsion formulated with low-toxicity materials. This formulation is composed of emulsified droplets <200 nm in diameter that contain 1.250 mM DNP, representing ≥95% encapsulation efficiency. The DNP nanoemulsion induced comparable torpor-like effects to those produced by the free drug in tadpoles, as indicated by reduced swimming motion, cardiac beating frequency, and oxygen consumption, but with an improved biodistribution. Use of the nanoemulsion resulted in a more controlled increase of DNP concentration in the whole organism compared to free DNP, and to a higher concentration in the brain, which reduced DNP toxicity and enabled induction of a longer torpor-like state that was fully reversible. These studies also demonstrate the potential use of Xenopus tadpoles as a high-throughput in vivo screen to assess the efficacy, biodistribution, and toxicity of drug-loaded nanocarriers.

Comparative Transcriptomes of Canine and Human Prostate Cancers Identify Mediators of Castration Resistance.

Prostate cancer continues to be one of the most lethal cancers in men. While androgen-deprivation therapy is initially effective in treating prostate cancer, most cases of advanced prostate cancer eventually progress to castration-resistant prostate cancer (CRPC), which is incurable. Similarly, the most aggressive form of prostatic carcinoma occurs in dogs that have been castrated. To identify molecular similarities between canine prostate cancer and human CRPC, we performed a comparative analysis of gene expression profiles. Through this transcriptomic analysis, we found that prostatic carcinoma in castrated dogs demonstrate an androgen indifferent phenotype, characterized by low androgen receptor and neuroendocrine associated genes. Notably, we identified two genes, ISG15 and AZGP1 that were consistently up- and downregulated, respectively, in both canine prostatic carcinoma and human CRPC. Additionally, we identified several other genes, including GPX3, S100P, and IFITM1, that exhibited similar expression patterns in both species. Protein-protein interaction network analysis demonstrated that these 5 genes were part of a larger network of interferon-induced genes, suggesting that they may act together in signaling pathways that are disrupted in prostate cancer. Accordingly, our findings suggest that the interferon pathway may play a role in the development and progression of CRPC in both dogs and humans and chart a new therapeutic approach.