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Journal of Computer Science and... 2022Generating molecules with desired properties is an important task in chemistry and pharmacy. An efficient method may have a positive impact on finding drugs to treat...
UNLABELLED
Generating molecules with desired properties is an important task in chemistry and pharmacy. An efficient method may have a positive impact on finding drugs to treat diseases like COVID-19. Data mining and artificial intelligence may be good ways to find an efficient method. Recently, both the generative models based on deep learning and the work based on genetic algorithms have made some progress in generating molecules and optimizing the molecule's properties. However, existing methods need to be improved in efficiency and performance. To solve these problems, we propose a method named the Chemical Genetic Algorithm for Large Molecular Space (CALM). Specifically, CALM employs a scalable and efficient molecular representation called molecular matrix. Then, we design corresponding crossover, mutation, and mask operators inspired by domain knowledge and previous studies. We apply our genetic algorithm to several tasks related to molecular property optimization and constraint molecular optimization. The results of these tasks show that our approach outperforms the other state-of-the-art deep learning and genetic algorithm methods, where the z tests performed on the results of several experiments show that our method is more than 99% likely to be significant. At the same time, based on the experimental results, we point out the insufficiency in the experimental evaluation standard which affects the fair evaluation of previous work.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s11390-021-0970-3.
PubMed: 36594005
DOI: 10.1007/s11390-021-0970-3 -
Biochemistry Apr 2020Messenger RNA degradation is an important component of overall gene expression. During the final step of eukaryotic mRNA degradation, exoribonuclease 1 (Xrn1) carries...
Messenger RNA degradation is an important component of overall gene expression. During the final step of eukaryotic mRNA degradation, exoribonuclease 1 (Xrn1) carries out 5' → 3' processive, hydrolytic degradation of RNA molecules using divalent metal ion catalysis. To initiate studies of the 5' → 3' RNA decay machinery in our lab, we expressed a C-terminally truncated version of Xrn1 and explored its enzymology using a second-generation, time-resolved fluorescence RNA degradation assay. Using this system, we quantitatively explored Xrn1's preference for 5'-monophosphorylated RNA substrates, its pH dependence, and the importance of active site mutations in the molecule's conserved catalytic core. Furthermore, we explore Xrn1's preference for RNAs containing a 5' single-stranded region both in an intermolecular hairpin structure and in an RNA-DNA hybrid duplex system. These results both expand and solidify our understanding of Xrn1, a centrally important enzyme whose biochemical properties have implications in numerous RNA degradation and processing pathways.
Topics: Exoribonucleases; Hydrogen-Ion Concentration; Models, Molecular; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 32251580
DOI: 10.1021/acs.biochem.9b01035 -
Journal of Orthopaedic Research :... May 2017Recent evidence suggests that common factor(s) or molecule(s) might regulate lipid and glucose metabolism, inflammation, and bone and cartilage degeneration. These... (Review)
Review
Recent evidence suggests that common factor(s) or molecule(s) might regulate lipid and glucose metabolism, inflammation, and bone and cartilage degeneration. These findings may be particularly relevant for cases of rheumatoid arthritis, in which chronic inflammation occurs in an autoimmune context and causes the degradation of articular joints as well as insulin resistance and cardiovascular complications. Candidates for this common regulatory system include signals mediated by peroxisome proliferator-activated regulator and its response factor, angiopoietin-like 4. The expression and bioactivity of angiopoietin-like 4, an adipocytokine that was originally reported to have an angiogenic function, have been detected not only in the vascular system and adipose tissue but also in rheumatoid joints. An essential role for angiopoietin-like 4 has been established in dyslipidemia, and recent reports indicate that it may modulate bone and cartilage catabolism in rheumatoid arthritis. The enhanced expression of angiopoietin-like 4 in rheumatoid arthritis may explain the occurrence of insulin resistance, cardiovascular risk, and joint destruction, thereby suggesting that this molecule could be a potential target for anti-rheumatoid arthritis strategies. This review describes recent research on the role of angiopoietin-like 4 in chronic inflammatory conditions and rheumatoid arthritis, as well as potential therapeutic candidates. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:939-943, 2017.
Topics: Angiopoietin-Like Protein 4; Angiopoietins; Arthritis, Rheumatoid; Chronic Disease; Humans; Inflammation; Insulin Resistance
PubMed: 28004425
DOI: 10.1002/jor.23507 -
PloS One 2021The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is a public health emergency of international concern. The spike glycoprotein (S protein) of...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is a public health emergency of international concern. The spike glycoprotein (S protein) of SARS-CoV-2 is a key target of antiviral drugs. Focusing on the existing S protein structure, molecular docking was used in this study to calculate the binding energy and interaction sites between 14 antiviral molecules with different structures and the SARS-CoV-2 S protein, and the potential drug candidates targeting the SARS-CoV-2 S protein were analyzed. Tizoxanide, dolutegravir, bictegravir, and arbidol were found to have high binding energies, and they effectively bind key sites of the S1 and S2 subunits, inhibiting the virus by causing conformational changes in S1 and S2 during the fusion of the S protein with host cells. Based on the interactions among the drug molecules, the S protein and the amino acid environment around the binding sites, rational structure-based optimization was performed using the molecular connection method and bioisosterism strategy to obtain Ti-2, BD-2, and Ar-3, which have much stronger binding ability to the S protein than the original molecules. This study provides valuable clues for identifying S protein inhibitor binding sites and the mechanism of the anti-SARS-CoV-2 effect as well as useful inspiration and help for the discovery and optimization of small molecule S protein inhibitors.
Topics: Antiviral Agents; COVID-19; Drug Design; Drug Discovery; Humans; Molecular Docking Simulation; SARS-CoV-2; Small Molecule Libraries; Spike Glycoprotein, Coronavirus; Virus Internalization; COVID-19 Drug Treatment
PubMed: 33493227
DOI: 10.1371/journal.pone.0245975 -
Journal of Chemical Information and... Mar 2023Cytochrome P450 enzymes aid in the elimination of a preponderance of small molecule drugs, but can generate reactive metabolites that may adversely react with protein...
Cytochrome P450 enzymes aid in the elimination of a preponderance of small molecule drugs, but can generate reactive metabolites that may adversely react with protein and DNA and prompt drug candidate attrition or market withdrawal. Previously developed models help understand how these enzymes modify molecule structure by predicting sites of metabolism or characterizing formation of metabolite-biomolecule adducts. However, the majority of reactive metabolites are formed by multiple metabolic steps, and understanding the progenitor molecule's network-level behavior necessitates an integrative approach that blends multiple site of metabolism and structure inference models. Our previously developed tool, XenoNet 1.0, generates metabolic networks, where nodes are molecules and weighted edges are metabolic transformations. We extend XenoNet with a bidirectional message passing neural network that integrates edge feature information and local network structure using edge-conditioned graph convolutions and jumping knowledge to predict the authenticity of inferred Phase I metabolite structures. Our model significantly outperformed prior work and algorithmic baselines on a data set of 311 networks and 6606 intermediates annotated using a chemically diverse set of 20 736 individual in vitro and in vivo reaction records accounting for 92.3% of all human Phase I metabolism in the Accelrys Metabolite Database. Cross-validated predictions resulted in area under the receiver operating characteristic curves of 88.5% and 87.6% for separating experimentally observed and unobserved metabolites at global and network levels, respectively. Further analysis verified robustness to networks of varying depth and breadth, accurate detection of metabolites, such as d,l-methamphetamine, that are experimentally observed or unobserved in different network contexts, extraction of important metabolic subnetworks, and identification of known bioactivation pathways, such as for nimesulide and terbinafine. By exploiting network structures, our approach accurately suggests unreported metabolites for experimental study and may rationalize modifications for avoiding deleterious pathways antecedent to reactive metabolite formation.
Topics: Humans; Neural Networks, Computer; Molecular Structure; Metabolic Networks and Pathways; Terbinafine
PubMed: 36926871
DOI: 10.1021/acs.jcim.2c01383 -
Molecules (Basel, Switzerland) Feb 2023For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer....
Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV-Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer).
For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule's 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV-Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule's charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO-LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.
Topics: Humans; Molecular Docking Simulation; Molecular Conformation; Molecular Dynamics Simulation; Spectroscopy, Fourier Transform Infrared; Spectrum Analysis, Raman; Static Electricity; Thermodynamics; Spectrophotometry, Ultraviolet; Pentoxyl; Quantum Theory
PubMed: 36903362
DOI: 10.3390/molecules28052116 -
Current Biology : CB Oct 1997Kinesin is a molecular-scale walking machine. New analyses of its mechanism indicate that each step along a microtubule consumes one ATP molecule, and that the binding... (Review)
Review
Kinesin is a molecular-scale walking machine. New analyses of its mechanism indicate that each step along a microtubule consumes one ATP molecule, and that the binding and cleavage of ATP precede detachment of the molecule's 'feet'. Directional walking ensues if ATP processing occurs preferentially on one foot.
Topics: Adenosine Triphosphatases; Adenosine Triphosphate; Kinesins; Microtubules
PubMed: 9368744
DOI: 10.1016/s0960-9822(06)00320-4 -
Accounts of Materials Research Dec 2022Photocatalytic conversion of small molecules (including HO, CO, N, CH, and benzene) into value-added chemicals or fuels (e.g., H, NH, C , etc.) is a promising strategy...
Photocatalytic conversion of small molecules (including HO, CO, N, CH, and benzene) into value-added chemicals or fuels (e.g., H, NH, C , etc.) is a promising strategy to cope with both the worldwide increasing energy demand and greenhouse gas emission in both energy sectors and chemical industry, thus paving an effective way to carbon neutrality. On the other hand, compared with conventionally thermo- or electrocatalytic processes, photoactivation can convert these very stable small molecules by the unexhausted solar energy, so leading to store solar energy in chemical bonds. Thus, it can effectively reduce the reliance on the nonrenewable fossil fuels and avoid the substantial emission of hazardous gases such as CO, NO , and so on while producing valued-added chemicals. For example, semiconductors can absorb solar light to split HO into H and O or convert CO to alcohols, which can then be used as zero or neutral carbon energy sources. Although many efforts have already been made on photocatalytic small molecule activation, the light-energy conversion efficiency is still rather moderate and the yield of aimed value-added chemicals cannot meet the requirement of large-scale application. The core for these artificial photocatalytic processes is to discover a novel photocatalyst with high efficiency, low cost, and excellent durability. Over the past two decades, the Tang group has discovered a few benchmark photocatalysts (such as dual-metal-loaded metal oxides, atomic photocatalysts, carbon-doped TiO, and polymer heterojunctions, etc.) and investigated them for photocatalytic conversion of the above-mentioned five robust molecules into value-added chemicals or liquid fuels. Besides, advanced photocatalytic reaction systems including batch and continuous flow membrane reactors have been studied. More importantly, the underlying reaction mechanism of these processes has been thoroughly analyzed using the state-of-the-art static and time-resolved spectroscopies. In this Account, we present the group's recent research progress in search of efficient photocatalysts for these small molecules' photoactivation. First, the strategies used in the group with respect to three key factors in photocatalysis, including light harvesting, charge separation, and reactant adsorption/product desorption, are comprehensively analyzed with the aim to provide a clear strategy for efficient photocatalyst design toward small and robust molecule photoactivation under ambient conditions. The application of in situ and operando techniques on charge carrier dynamics and reaction pathway analysis used in the group are next discussed. Finally, we point out the key challenges and future research directions toward each specific small molecule's photoactivation process.
PubMed: 36583010
DOI: 10.1021/accountsmr.2c00095 -
Biology of Reproduction Aug 2021Recent evidence indicates that niclosamide is an anti-cancer compound that is able to inhibit several signaling pathways. Although niclosamide has previously been...
Recent evidence indicates that niclosamide is an anti-cancer compound that is able to inhibit several signaling pathways. Although niclosamide has previously been identified by high-throughput screening platforms as a potential effective compound against several cancer types, no direct binding interactions with distinct biological molecule(s) has been established. The present study identifies key signal transduction mechanisms altered by niclosamide in ovarian cancer. Using affinity purification with a biotin-modified niclosamide derivative and mass spectrometry analysis, several RNA-binding proteins (RBPs) were identified. We chose the two RBPs, FXR1 and IGF2BP2, for further analysis. A significant correlation exists in which high-expression of FXR1 or IGF2BP2 is associated with reduced survival of ovarian cancer patients. Knockdown of FXR1 or IGF2BP2 in ovarian cancer cells resulted in significantly reduced cell viability, adhesion, and migration. Furthermore, FXR1 or IGF2BP2 deficient ovarian cancer cells exhibited reduced response to most doses of niclosamide showing greater cell viability than those with intact RBPs. These results suggest that FXR1 and IGF2BP2 are direct targets of niclosamide and could have critical activities that drive multiple oncogenic pathways in ovarian cancer.
Topics: Animals; Antineoplastic Agents; Cell Line, Tumor; Female; Humans; Mice; Niclosamide; Ovarian Neoplasms; RNA-Binding Proteins
PubMed: 33855343
DOI: 10.1093/biolre/ioab071 -
Annals of the American Thoracic Society Oct 2023It can be challenging for healthcare professionals (HCPs) to prescribe inhaled therapy for patients with chronic obstructive pulmonary disease (COPD) because of the... (Review)
Review
It can be challenging for healthcare professionals (HCPs) to prescribe inhaled therapy for patients with chronic obstructive pulmonary disease (COPD) because of the multiple individual and combinations of inhaled medications available in numerous delivery systems. Guidance on the selection of an inhaled delivery system has received limited attention compared with the emphasis on prescribing the class of the inhaled molecule(s). Although numerous recommendations and algorithms have been proposed to guide the selection of an inhaled delivery system for patients with COPD, no specific approach has been endorsed in COPD guidelines/strategies or by professional organizations. To provide recommendations for an inhaler selection strategy at initial and follow-up appointments, we examined the impact of patient errors using handheld inhalers on clinical outcomes and performed a focused narrative review to consider patient factors (continuity of the inhaled delivery system, cognitive function, manual function/dexterity, and peak inspiratory flow) when selecting an inhaled delivery system. On the basis of these findings, five questions are proposed for HCPs to consider in the initial selection of an inhaler delivery system and three questions to consider at follow-up. We propose that HCPs consider the inhaled medication delivery system as a unit and to match appropriate medication(s) with the unique features of the delivery system to individual patient factors. Assessment of inhaler technique and adherence together with patient outcomes/satisfaction at each visit is essential to determine whether the inhaled medication delivery system is providing benefits. Continued and repeated education on device features and correct technique is warranted to optimize efficacy.
Topics: Humans; Pulmonary Disease, Chronic Obstructive; Nebulizers and Vaporizers; Pharmaceutical Preparations; Patient Satisfaction; Administration, Inhalation; Bronchodilator Agents
PubMed: 37499210
DOI: 10.1513/AnnalsATS.202304-384CME