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Development and Application of a Multi-Level Computational Approach for the Identification of Inhibitors of Mapk3 in Leishmania Martiniquensis and Leishmania Orientalis

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SSRN 2024年

作者： Kiriwan, Duangnapa Vieira, Tatiana F. Kumsiri, Nutnaree Sousa, Sergio F. Choowongkomon, Kiattawee Associate Laboratory i4HB—Institute for Health and Bioeconomy Faculdade de Medicina Universidade do Porto Porto Portugal LAQV/REQUIMTE BioSIM - Departamento de Biomedicina Faculdade de Medicina Universidade do Porto Porto Portugal Genetic Engineering and Bioinformatics program Kasetsart University 50 Ngam Wong Wan Road Chatuchak Bangkok10900 Thailand Center for Advanced Studies in Nanotechnology for Chemical Food and Agricultural Industries KU Institute for Advanced Studies Kasetsart University Bangkok10900 Thailand Department of Biochemistry Faculty of Science Kasetsart University 50 Ngam Wong Wan Road Chatuchak Bangkok10900 Thailand

Leishmania martiniquensis and Leishmania orientalis are two major species of parasites, associated to health problems in Thailand. Here, we focused on in silico strategies for the identification of inhibitors of the protein mitogen active protein kinase3 (MAPK3) in these two species. MAPK3 is a Ser/Thr protein kinase that plays an important role in the differentiation of amastigotes to promastigotes. This study describes a multi-level computational method for discovering new MAPK3 inhibitors with high potency. This approach involves creating 3D models of these protein targets through homology modelling, refined with molecular dynamics (MD) simulations, followed by protein-ligand docking validation for protocol validation, virtual screening of large molecular databases, followed by MD simulations on most promising protein-ligand complexes, and binding free energy calculations. This approach was applied to screen an in-house library of 8,000 tripeptides. The structure-based virtual screening results suggested nine tripeptides as promising inhibitors of MAPK3 for all the leishmania species considered. Four tripeptides were validated as very promising binders by the MD simulations and free energy calculations. Subsequent MAP Kinase 3 inhibition assay was performed. Our in vitro kinase assay demonstrated that the peptide WSY exhibited a significantly higher effectiveness in inhibiting MAPK3 compared to WHW at a concentration of 3.33 µM with percentages of 89.97±9.28% and 27.97±14.45%, *** optimized multi-level protocol can now be applied to other types of molecular databases to identify promising candidates targeting proteins LmrMAPK3 and LoMAPK3. © 2024, The Authors. All rights reserved.

关键词： Molecular dynamics

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Cellulose Microcrystalline: A Promising Ecofriendly Approach to Control Culex Quinquefasciatus Larvae

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SSRN 2023年

作者： de Souza, Sindoval Silva Gomes, Alex Rodrigues Batista Guimarães, Abraão Tiago Rodrigues, Aline Sueli de Lima de Matos, Letícia Paiva Mendonça, Juliana dos Santos Luz, Thiarlen Marinho da da Silva Matos, Stênio Gonçalves Safiur, M. Rahman Ragavendran, Chinnasamy Senthil-Nathan, Sengottayan Guru, Ajay Rakib, Md. Refat Jahan Mubarak, Nabisab Mujawar Mostafizur, Md. Rahman Rocha, Thiago Lopes Towfiqul Islam, Abu Reza Md. Malafaia, Guilherme Post-Graduation Program in Biotechnology and Biodiversity Federal University of Goiás GO Goiânia Brazil Laboratory of Toxicology Applied to the Environment Goiano Federal Institute Urutaí Campus. Rodovia Geraldo Silva Nascimento 25 km Zona Rural Urutaí GO Brazil Post-Graduation Program in Ecology Conservation and Biodiversity Federal University of Uberlândia MG Uberlândia Brazil Post-Graduation Program in Conservation of Cerrado Natural Resources Goiano Federal Institute Urutaí GO Brazil Department of Environmental Science and Disaster Management Noakhali Science and Technology University Noakhali3814 Bangladesh Saveetha University Tamil Nadu Chennai India Division of Biopesticides and Environmental Toxicology Sri Paramakalyani Centre for Excellence in Environmental Sciences Manonmaniam Sundaranar University Tirunelveli Tamil Nadu Alwarkurichi627 412 India Department of Cariology Saveetha Dental College and Hospitals SIMATS Tamil Nadu Chennai600 077 India Noakhali Science and Technology University Noakhali Bangladesh Petroleum and Chemical Engineering Faculty of Engineering Universiti Teknologi Brunei Bandar Seri BegawanBE1410 Brunei Jahangirnagar University Dhaka1342 Bangladesh Laboratory of Environmental Biotechnology and Ecotoxicology Institute of Tropical Pathology and Public Health Federal University of Goiás Goiás Goiânia Brazil Department of Disaster Management Begum Rokeya University Rangpur5400 Bangladesh

The growing use of synthetic chemical compounds/substances in vector control of mosquitoes, associated with their adverse effects on the environment and non-target organisms, has demanded the development of eco-friendly alternatives. In this context, this study aimed to evaluate the larvicidal action of different cellulose microcrystalline (CMs) concentrations and investigate their toxicity mechanisms in Culex quinquefasciatus fourth instar larvae as a model species. Probit analysis revealed that the median lethal concentrations (LC50) for 24 h and 36 h exposure were 100 and 58.29 mg/L, respectively. We also showed that such concentrations induced a redox imbalance in the larvae, marked by an increase in the production of reactive oxygen species (ROS) and thiobarbituric acid reactive substances (TBARS), as well as a reduction in the activity of superoxide dismutase (SOD) and catalase (CAT). Furthermore, different alterations in the external morphology of the larvae were associated with the ingestion of CMs. On the other hand, exposure of adult zebrafish (Danio rerio) to LC5024h and LC5036h for seven days did not induce any behavioral changes or alterations mutagenic, genotoxic, biochemical, or in the pro- and anti-inflammatory response. Thus, taken together, our study demonstrates for the first time that the use of CMs can constitute a promising strategy in the control of C. quinquefasciatus larvae, combining insecticidal efficiency with an "eco-friendly" approach in the fight against an important mosquito vector of several human diseases. © 2023, The Authors. All rights reserved.

关键词： Cellulose

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Digitizing microalgae production to support green process facing industry 4.0 era

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AIP Conference Proceedings 2023年第1期2667卷

作者： Rame Rame Purwanto Purwanto Sudarno Sudarno 1Doctoral Program of Environmental Science School of Postgraduate Studies Universitas Diponegoro Semarang 50241 Indonesia 2Center of Industrial Pollution Prevention Technology Jl. Ki Mangunsarkoro No. 6 Semarang 50241 Indonesia 3Department of Chemical Engineering Faculty of Engineering Universitas Diponegoro Semarang 50275 Indonesia 4Department of Environmental Engineering Faculty of Engineering Universitas Diponegoro Semarang 50275 Indonesia

The microalgae industry produces and processes microalgae such as Arthrospira platensis, Chlorella Vulgaris, and Haematococcus Pluvialis as raw materials. The product of the microalgae industry in Indonesia consists of raw materials, extract products, and retail products. The sales activity tends to rise, impacting the financial conditions of the industry in good condition. The potential of this business field is vast with open market demand so that the continuity of production and marketing of diversified products is still guaranteed. Problems and needs facing the Microalgae industry in Indonesia are the whole processes from upstream to downstream in the microalgae industry still manual. It replaced conventional methods with more efficient advanced green technologies that offer greater product quantity and low environmental impact. Literature reviews, observations in the industry, and interviews to evaluate development strategies to help the microalgae industry solves the problems in cultivation, drying techniques, standard fulfillment, and marketing by applying more efficient technology. Based on the analysis of conditions and opportunities, there are some critical aspects of microalgae industry development, namely the creation of an online monitoring application system of production pools that can be implemented in the field according to standards; construction design of encapsulation include spray drying. Moreover, a circular economy fulfills food safety standards such as halal certification, Hazard Analysis Critical Control Point, and Good Manufacturing Practice standards. Additionally, improvement of qualifications and competencies of reliable marketing personnel in the manufacture of marketing tools.

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Sustainable and integrated industrial wastewater treatment as a base of green industry 4.0

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AIP Conference Proceedings 2023年第1期2667卷

With the fast development of the global economy and population, there has been an increase in the amount of wastewater and industrial effluents being discharged into rivers and lakes, resulting in deterioration of water quality and a reduction in the availability of freshwater resources. A comprehensive discussion of the topic of Industrial Wastewater Treatment Integrated for Sustainable Green Industry 4.0, including the difficulties and possible solutions that may be encountered along the way, is provided in this article. According to the results of this study, industrial wastewater treatment that uses online/real-time water for quality monitoring and control has shown great promise in terms of quality monitoring and control when utilizing online/real-time water. Implementing such a system in industrial wastewater treatment may offer an early warning system for poor treatment while increasing the quantity and quality of the end product, both of which are desired outcomes.

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Charge density wave hampers exciton condensation in 1T−TiSe2

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Physical Review B 2019年第20期100卷 205423-205423页

作者： Chao Lian Zulfikhar A. Ali Bryan M. Wong Department of Chemical and Environmental Engineering Materials Science and Engineering Program and Department of Physics and Astronomy University of California-Riverside Riverside California 92521 USA

The Bose-Einstein condensation of excitons continues to garner immense attention as a prototypical example for observing emergent properties from many-body quantum effects. In particular, titanium diselenide (TiSe2) is a promising candidate for realizing exciton condensation and was experimentally observed only very recently [Kogar et al., science 358, 1314 (2017)]. Surprisingly, the condensate was experimentally characterized by a soft plasmon mode that only exists near the transition temperature Tc of the charge density wave (CDW). Here, we characterize and analyze the experimental spectra using linear-response time-dependent density functional theory and find that the soft mode can be attributed to interband electronic transitions. At the CDW state below Tc, the periodic lattice distortions hamper the spontaneous formation of the exciton by introducing a CDW gap. The band gap raises the soft mode and merges it into the regular plasmon. Our surprising results contradict previous simplistic analytical models commonly used in the scientific literature. In addition, we find that a finite electronic temperature Te introduces a dissipation channel and prevents the condensation above Tc. The combined effect of the CDW and Te explains the fragile temperature dependence of the exciton condensation. Taken together, our work provides the first ab initio atomic-level framework for rationalizing recent experiments and further manipulating exciton condensates in TiSe2.

关键词： Charge density waves Excitons Transition metal dichalcogenides Density functional approximations Time-dependent DFT

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Biochemical mechanisms and molecular interactions of vitamins in cancer therapy

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Cancer Pathogenesis and Therapy 2025年第1期3卷 3-15页

作者： Abdullahi T.Aborode Isreal A.Onifade Mercy M.Olorunshola Gladys O.Adenikinju Ibude J.Aruorivwooghene Adeboboye C.Femi Osasere Jude-Kelly Osayawe Abraham Osinuga Ebenezer A.Omojowolo Adekunle F.Adeoye Segun Olapade Ibroadhfrimed O.Acdoelaku Ogundepo D.Moyinoluwa Oluwatosin M.Adeyemo Godfred Y.Scott Ruth A.Ogbonna Emmanuel A.Fajemisin Omama Ehtasham Soyemi Toluwalashe Adetolase A.Bakre Ridwan O.Adesola Seto C.Ogunleye Nnenna R.Anyanwu Terungwa H.lorkula Department of Chemistry Mississippi State UniversityStarkvilleMS 39759USA Department of Biology University at AlbanyAlbanyNY 12222USA Department of Biological Sciences State University of New York at BinghantonBinghamtonNY 13902USA Department of Biological and Environmental Sciences University of Rhode IslandKingstonRI 02881USA Department of Biological Sciences University of Kansas Medical CenterKansasKS 66103USA Department of Microbiology Federal University of TechnologyAkure 340110Nigeria Department of Chemistry and Biochemistry Brigham Young UniversityProvoUT 84602USA 8 Department of Chemical and Biomolecular Engineering University of Nbraska-LincolnLincolnNE 68588USA9 Department of Chemistry University of AlbanyState University of New YorkAlbanyNY 12222USA Department of Mathematics and Statistics Georgia State UniversityAtlantaGA 30302USA Department of Chemistry University of LouisvilleLouisvilleKY 40208USA Department of Biochemistry Federal University of TechnologyAkure 340110Nigeria Deparment of Medical Diagnostics Kwame Nkrumah University of Science and TechnologyKumasi AK385Ghana Department of Research and Development Nasarawa State AIDS and STI Control ProgramNasarawaLafia 96210Nigeria Department of Integrative Biomedical Science University of Cape TownCape'Town 7701South Africa Department of Medicine and Surgery Karachi Medical and Dental CollegeKarachi 74700Pakistan Department of Medicine Lagos State University College of MedicineLagos 10010Nigeria Department of Veterinary Medicine Faculty of Veterinary MedicineUniversity of lbadanlbadan 200005Nigeria Faculty of Pharmaceutical Sciences University of JosPlateauJos 930003Nigeria

Recently,the potential role of vitamins in cancer therapy has attracted considerable research ***,the reported findings are inconsistent,with limited information on the biochemical and molecular interactions of different vitamins in various cancer ***,the presence of vitamin receptors in tumor cells suggests that vitamins play a significant role in the molecular and biochemical interactions in ***,studies on the efficacy of vitamin supplementation and dosage levels on tumor progression and mortality risk have yielded inconsistent ***,molecular and biochemical investigations have reported the function of vitamins in the proliferation,growth,and invasiveness of tumor cells,as well as in cell cycle arrest and inflammatory ***,different vitamins may regulate the cancer microenvironment by activating various molecular *** significantly affect immunological function,antioxidant defense,inflammation,and epigenetic control,and can improve treatment outcomes by affecting cell behavior and combating stress and DNA ***,further research is necessary to confirm the efficacy of vitamins,establish ideal dosages,and develop effective cancer prevention and treatment *** supplementation plans guided by medical knowledge are crucial to achieving optimal results in clinical and preclinical *** this review,we critically evaluated the effects of different vitamins on the risk and development of ***,we examined the potential of vitamin supplements to enhance the efficacy of drug therapy and counteract resistance mechanisms that often arise during cancer treatment.

关键词： Vitamins Cancer Biochemical Molecular interactions Therapy

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Machine learning framework to predict product distribution of lignocellulosic biomass pyrolysis

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Bioresource Technology 2025年

作者： Leonardo Voltolini Fernando Arrais Romero Dias Lima Carine Menezes Rebello Ivaldo Itabaiana Idelfonso B.R. Nogueira Argimiro Resende Secchi Maurício B. de Souza School of Chemistry EPQB Universidade Federal do Rio de Janeiro (UFRJ) P.O. Box 68542 Rio de Janeiro 21941-909 RJ Brazil Chemical Engineering Department Norwegian University of Science and Technology (NTNU) Trondheim 793101 Trøndelag Norway Chemical Engineering Program PEQ/COPPE Universidade Federal do Rio de Janeiro (UFRJ) PO Box 68502 Rio de Janeiro 21941-972 RJ Brazil

Machine learning methods have become a trend to model distinct chemical processes, as an alternative to complex first-principles models. Given the complexity of biomass pyrolysis mechanisms, these methods offer a promising approach but often face challenges regarding data scarcity and lack of interpretability. This study aims to develop an interpretable framework for modeling biomass pyrolysis using data from fixed-bed lignocellulosic biomass pyrolysis experiments. A mass change basis was proposed to construct machine learning models, including artificial neural network (ANN) and symbolic regression (SR) models. Feature importance was assessed using Shapley Additive Explanations (SHAP) and compared to Partial Least Squares (PLS) regression, with PLS consistently identifying the best features for symbolic regression. Both ANN and SR models showed similar accuracy, achieving coefficient of determination (R 2 ) greater than 0.85 across all phase products in the testing set. Additionally, an uncertainty assessment of SR parameters was conducted to improve model robustness ensuring prediction stability. SR models exhibited superior generalization capacity during extrapolation tests, achieving R 2 values above 0.9 for char and gas phases. For oil values exceeding 10 grams, the SR models struggled with generalization. Overall, the proposed framework provides a valuable tool for interpreting and modeling pyrolysis process data, enabling its use in the decision-making process.

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Electronic excitations of α−Fe2O3 heteroepitaxial films measured by resonant inelastic x-ray scattering at the Fe L edge

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Physical Review B 2022年第7期105卷 075101-075101页

作者： David S. Ellis Ru-Pan Wang Deniz Wong Jason K. Cooper Christian Schulz Yi-De Chuang Yifat Piekner Daniel A. Grave Markus Schleuning Dennis Friedrich Frank M. F. de Groot Avner Rothschild Department of Materials Science and Engineering Technion-Israel Institute of Technology Haifa 32000 Israel Department of Physics University of Hamburg Luruper Chaussee 149 22761 Hamburg Germany Dynamics and Transport in Quantum Materials Helmholtz-Zentrum Berlin für Materialen und Energie Albert-Einstein-Strasse 15 12489 Berlin Germany Chemical Sciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley California 94720 USA Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley California 94720 USA The Nancy & Stephen Grand Technion Energy Program (GTEP) Technion-Israel Institute of Technology Haifa 32000 Israel Department of Materials Engineering and Ilse Katz Institute for Nanoscale Science and Technology Ben Gurion University of the Negev Be'er Sheva 8410501 Israel Institute for Solar Fuels Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Hahn-Meitner-Platz 1 14109 Berlin Germany Department of Inorganic Chemistry and Catalysis Debye Institute of Nanomaterials Science Utrecht University Universiteitsweg 99 3584 CG Utrecht Netherlands

Resonant inelastic x-ray scattering (RIXS) spectra of hematite (α−Fe2O3) were measured at the Fe L3 edge for heteroepitaxial thin films which were undoped and doped with 1% Ti, Sn, or Zn, in the energy-loss range in excess of 1 eV to study electronic transitions. The spectra were measured for several momentum transfers q, conducted at both low temperature (T=14 K) and room temperature. While we cannot rule out dispersive features possibly owing to propagating excitations, the coarse envelopes of the general spectra did not appreciably change shape with q, implying that the bulk of the observed L-edge RIXS intensity originates from (mostly) nondispersive ligand field excitations. Summing the RIXS spectra over q and comparing the results at T=14 K to those at T=300 K revealed pronounced temperature effects, including an intensity change and energy shift of the ≈1.4 eV peak, a broadband intensity increase of the 3–4 eV range, and higher energy features. The q-summed spectra and their temperature dependencies are virtually identical for nearly all of the samples with different dopants, save for the temperature dependence of the Ti-doped sample's spectrum, which we attribute to being affected by a large number of free charge carriers. Comparing with magnetization measurements for different temperatures and dopings likewise did not show a clear correlation between the RIXS spectra and the magnetic ordering states. To clarify the excited states, we performed spin multiplet calculations which were in excellent agreement with the RIXS spectra over a wide energy range and provide detailed electronic descriptions of the excited states. The implications of these findings to the photoconversion efficiency of hematite photoanodes is discussed.

关键词： Electronic structure Energy materials Strongly correlated systems Crystal-field theory Energy-dispersive x-ray spectroscopy

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Fenofibrate ameliorates ocular surface inflammation in diabetic keratopathy

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The ocular surface 2025年 38卷 31-40页

作者： Hassan Mansoor Isabelle Xin Yu Lee Chang Liu Mingyi Yu Charmaine Jan Li Toh Victor Wei-Tsu Hsu Fengyi Liu Daqian Lu Thomas Chuen Lam Hong Chang Tan Lei Zhou Yu-Chi Liu Al Shifa Trust Eye Hospital Rawalpindi Pakistan. Tissue Engineering and Stem Cell Group Singapore Eye Research Institute Singapore. Lee Kong Chian School of Medicine Nanyang Technological University Singapore. University of Cambridge Girton College Cambridgeshire United Kingdom. Centre for Myopia Research School of Optometry The Hong Kong Polytechnic University Hong Kong. Centre for Myopia Research School of Optometry The Hong Kong Polytechnic University Hong Kong Centre for Eye and Vision Research (CEVR) 17W Hong Kong Science Park Hong Kong. Department of Endocrinology Singapore General Hospital Singapore. School of Optometry Department of Applied Biology and Chemical Technology Research Centre for SHARP Vision (RCSV) The Hong Kong Polytechnic University Hong Kong. Tissue Engineering and Stem Cell Group Singapore Eye Research Institute Singapore Cornea and Refractive Surgery Group Singapore Eye Research Institute Singapore Department of Cornea and External Eye Disease Singapore National Eye Centre Singapore Eye-Academic Clinical Program Duke-National University Singapore Graduate Medical School Singapore Department of Ophthalmology National Taiwan University Hospital Taiwan. Electronic address: liuchiy@***.

PURPOSE:To investigate the efficacy of oral fenofibrate in the amelioration of ocular surface inflammation in diabetes mellitus (DM). METHODS:In this open-label interventional study, 41 participants with type 2 DM received oral fenofibrate for 30 days. Forty age-matched healthy controls were recruited. Ocular surface objective and subjective assessment, in-vivo confocal microscopy (IVCM) imaging and quantification for corneal dendritic cells (DCs), epithelium and neuromas were performed. Tear inflammatory markers and proteomics were analyzed with enzyme-linked immunosorbent assay (ELISA) and Data Independent Acquisition experiments before and after treatment. RESULTS:Oral fenofibrate treatment significantly improved tear film breakup time (p=0.004), corneal staining evaluated with National Eye Institute-Corneal Fluorescein Staining scores (p=0.005), and ocular surface symptoms assessed with the Ocular Surface Disease Index scores (p=0.003), in DM patients. On IVCM, fenofibrate significantly reduced mean DC area (p=0.01) and mean DC density (p=0.02), while increasing mean DC elongation (p=0.004) and length (p=0.01), suggesting less DC activities. Fenofibrate also significantly increased corneal epithelial cell density (p=0.04). 192 tear proteins were significantly altered after treatment. Fenofibrate significantly up-regulated the expression of anti-inflammatory interleukin-1 receptor antagonist, while significantly reduced the concentrations of pro-inflammatory and inflammatory proteins, including tumour necrosis factor α, nuclear factor kappa B, complement 4B, cytochrome B5 Type A, and cytochrome B5 Type B (all p<0.05) in tears, via regulation of tricarboxylic acid cycle, oxidative phosphorylation and liver X receptor/retinoid X receptor activation. CONCLUSION:This first clinical trial demonstrated that oral fenofibrate ameliorates diabetic ocular surface inflammation, providing a novel therapeutic option for diabetic keratopathy.

关键词： Apoptosis Cornea Diabetes Fenofibrate Inflammation Ocular Surface

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A facile strategy for the preparation of end-capped and cross-linkable poly(propylene carbonate) with high performance

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Advanced Industrial and engineering Polymer Research 2019年第4期2卷 161-166页

作者： Song, Pengfei Ran, Baocheng Shang, Yingqi Kang, Li Chen, Yalun Sun, Luyi College of Chemistry and Chemical Engineering Gansu International Scientific and Technological Cooperation Base of Water-Retention Chemical Functional Materials Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education Key Laboratory of Eco-environmental Polymer Materials of Gansu Province Northwest Normal University Lanzhou730070 China Polymer Program Institute of Materials Science Department of Chemical & Biomolecular Engineering University of Connecticut StorrsCT06269 United States

Itaconic anhydride (IAn) was firstly used for the modification of poly(propylene carbonate) (PPC) by solution blending following with the direct heating treatment, producing end-capped and cross-linkable PPC (PECPPC) with high performance. The reaction of PPC with IAn was detailed investigated and the structure of PECPPC was identified by FTIR and 1H NMR. A facile strategy including end-capping and cross-linking can be developed to improve the performance of PPC. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) measurements revealed that the glass transition temperature (Tg) and thermal decomposition temperature (Td) of PECPPCs are all much higher than those of PPC and increased with the increasing content of IAn. Tensile tests also showed the huge enhancement on the mechanical properties of PPC with the end-capping and cross-linking techniques, and the highest tensile strength of PECPPC4 is 37.5 MPa. Furthermore, ECPPC4 exhibits high hydrolysis rate in phosphate buffer solution (PBS) than that of PPC. It is demonstrated that the strategy with the combination of end-capping and cross-linking is efficient for the perfect modification of PPC with IAn. © 2019 Kingfa SCI. & TECH. CO., LTD.

关键词： Differential scanning calorimetry

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