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Gianvincenzo PD, Leyes MF, Boonkam K, Puentes AF, Reyes SG, Nardi AN, Olivieri A, Pummarin S, Kamonsutthipaijit N, Amenitsch H, Ritacco H, D'Abramo M, Ortore MG, Boonla C, Moya SE. Supramolecular citrate poly allylamine hydrochloride nanoparticles for citrate delivery and calcium oxalate nanocrystal dissolution. J Colloid Interface Sci 2024; 669:667-678. [PMID: 38733878 DOI: 10.1016/j.jcis.2024.04.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024]
Abstract
HYPOTHESIS Renal calculi (kidney stones) are mainly made by calcium oxalate and can cause different complications including malfunction of the kidney. The most important urinary stone inhibitors are citrate molecules. Unfortunately, the amount of citrate reaching the kidney after oral ingestion is low. We hypothesized that nanoparticles of polyallylamine hydrochloride (CIT-PAH) carrying citrate ions could simultaneously deliver citrates while PAH would complex oxalate triggering dissolution and removal of CaOx nanocrystals. EXPERIMENTS We successfully prepared nanoparticles of citrate ions with polyallylamine hydrochloride (CIT-PAH), PAH with oxalate (OX-PAH) and characterize them by Small Angle X ray Scattering (SAXS), Transmission Electron Microscopy (TEM), Dynamic Light Scattering (DLS) and NMR. Dissolution of CaOx nanocrystals in presence of CIT-PAH have been followed with Wide Angle Xray Scattering (WAXS), DLS and Confocal Raman Microscopy. Raman spectroscopy was used to study the dissolution of crystals in synthetic urine samples. The release of citrate from CIT-PAH was followed by diffusion NMR. Molecular dynamics (MD) simulations were carried out to study the interaction of CIT and OX ions with PAH. FINDINGS CIT-PAH nanoparticles dissolves CaOx nanocrystals as shown by NMR, DLS, TEM and WAXS in water and by Raman spectroscopy in artificial human urine. WAXS and Raman show that the crystal structure of CaOx disappears in the presence of CIT-PAH. DLS shows that the time required for CaOX dissolution will depend on the concentration of CIT-PAH NPs. NMR proves that citrate ions are released from the CIT PAH NPs during CaOX dissolution, MD simulations showed that oxalates exhibit a stronger interaction for PAH than citrate, explaining the removal of oxalate ions and replacement of the citrate in the polymer nanoparticles.
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Affiliation(s)
- Paolo Di Gianvincenzo
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain
| | - Marcos Fernandez Leyes
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain; Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Kamonchat Boonkam
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 10330 Bangkok, Thailand
| | - Alejandro Fábrega Puentes
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain
| | - Santiago Gimenez Reyes
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain; Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | | | - Alessio Olivieri
- Chemistry Department, "La Sapienza" University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Siwanut Pummarin
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain; Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 10330 Bangkok, Thailand
| | | | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayergasse 9/V, Graz, Austria
| | - Hernan Ritacco
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Marco D'Abramo
- Chemistry Department, "La Sapienza" University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Maria Grazia Ortore
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona I-60131, Italy
| | - Chanchai Boonla
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 10330 Bangkok, Thailand
| | - Sergio E Moya
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Basque Research and Technological Alliance (BART), Paseo Miramón 182 C, 20014 San Sebastian, Spain.
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Fu W, Shentu C, Chen D, Qiu J, Zong C, Yu H, Zhang Y, Chen Y, Liu X, Xu T. Network pharmacology combined with affinity ultrafiltration to elucidate the potential compounds of Shaoyao Gancao Fuzi Decoction for the treatment of rheumatoid arthritis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118268. [PMID: 38677569 DOI: 10.1016/j.jep.2024.118268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/13/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Shaoyao Gancao Fuzi Decoction (SGFD), has been employed for thousands of years in the treatment of rheumatoid arthritis (RA) with remarkable clinical efficacy. However, the material basis underlying the effectiveness of SGFD still remains unclear. AIM OF THE REVIEW This study aims to elucidate the material basis of SGFD through the application of network pharmacology and biological affinity ultrafiltration. RESULTS UPLC-Q-TOF-MS/MS was employed to characterize the components in SGFD, the identified 145 chemical components were mainly categorized into alkaloids, flavonoids, triterpenoids, and monoterpenoids according to the structures. Network pharmacology method was utilized to identify potential targets and signaling pathways of SGFD in the RA treatment, and the anti-inflammatory and anti-RA effects of SGFD were validated through in vivo and in vitro experiments. Moreover, as the significant node in the pharmacology network, TNF-α, a classical therapeutic target in RA, was subsequent employed to screen the interacting compounds in SGFD via affinity ultrafiltration screening method, 6 active molecules (i.e.,glycyrrhizic acid, paeoniflorin, formononetin, isoliquiritigenin, benzoyl mesaconitine, and glycyrrhetinic acid) were exhibited significant interactions. Finally, the significant anti-inflammatory and anti-TNF-α effects of these compounds were validated at the cellular level. CONCLUSIONS In conclusion, this study comprehensively elucidates the pharmacodynamic material basis of SGFD, offering a practical reference model for the systematic investigation of traditional Chinese medicine formulas.
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Affiliation(s)
- Weiliang Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Chengyu Shentu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Dan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Junjie Qiu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China
| | - Chuhong Zong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Hengyuan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yiwei Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China
| | - Xuesong Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China.
| | - Tengfei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China.
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Deshpande H. Levoleucovorin inhibits LOXL2 (lysyl oxidase like-2) to control breast cancer proliferation: a repurposing approach. J Biomol Struct Dyn 2024; 42:5104-5113. [PMID: 37340696 DOI: 10.1080/07391102.2023.2224894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
Lysyl oxidase like-2 (LOXL2) belongs to copper dependent amine oxidase from the lysyl oxidase family and is associated with breast cancer metastasis This study used multi-stage computational screening and in vitro validations to repurpose FDA approved drugs targeting LOXL2 to control breast cancer progression.Molecular modeling techniques and high-throughput virtual-screening technique was employed to screen FDA-approved drug library for its avid binding to LOXL2.hLOXL2, MDA-MB231 and MCF 7 cells were used for in vitro.Collectively, this repurposing study identified levoleucovorin to bind the active site of LOXL2 protein to inhibit its activity. Further validation of levoleucovorin against LOXL2 activity is warranted toward repurposing levoleucovorin as a therapeutic agent for treating breast cancer patients. validations.Computational modeling of LOXL2 identified putative druggable region at the active site of LOXL2 protein. High-throughput virtual screening predicted levoleucovorin as a best lead drug candidate to have a favorable binding affinity for LOXL2 at its active site. Molecular dynamic simulation predicts levoleucovorin to bind stably and avidly to LOXL2 with favorable interactions. In vitro validations show levoleucovorin significantly inhibited hLOXL2 with and IC50 value of 68.81 μM. Levoleucovorin controlled cell proliferations in MDM-MB 231 and MCF-7 cells with GI50 values of 55.91 μM and 79.20 μM respectively. Further, a dose dependent inhibition of cancer cell migration was noted along with apoptosis induction in these cells with levoleucovorin treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hemali Deshpande
- Department of Anatomy, College of Medicine, King Khalid University, Abha, Asir, Kingdom of Saudi Arabia
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Erdogan T, Oguz Erdogan F. Probing some recent natural compounds from Phellinus baumii, Colletotrichum sp. and Ligustrum lucidum as heat shock protein 90 inhibitors. J Biomol Struct Dyn 2024; 42:5390-5401. [PMID: 37340683 DOI: 10.1080/07391102.2023.2226748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/11/2023] [Indexed: 06/22/2023]
Abstract
Heat shock protein 90 (HSP90) is one of the most attractive targets for research on cancer treatment, and nowadays, many studies carried out for the development of effective HSP90 inhibitors. In the current study, recently published ten natural compounds have been investigated using computer aided drug design (CADD) approach. The study consists of three parts; (1) density functional theory (DFT) calculations including geometry optimizations, vibrational analyses, and molecular electrostatic potential (MEP) map calculations, (2) molecular docking and molecular dynamics (MD) simulations, and (3) binding energy calculations. In DFT calculations, Becke three-parameter hybrid functional with Lee-Yang-Parr correlation functional (B3LYP) and 6-31 + G(d,p) basis set were used. After performing molecular docking calculations, top-scoring ligand-receptor complexes were subjected to MD simulations for 100 ns to investigate the stability of the ligand-receptor complexes and the interactions in more detail. Finally, in binding energy calculations molecular mechanics with Poisson-Boltzmann surface area (MM-PBSA) method was used. The results showed that five of the investigated ten natural compounds have higher binding affinity to HSP90α than that of reference drug Geldanamycin, and could be promising compounds for future studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taner Erdogan
- Department of Chemistry and Chemical Processing Technologies, Kocaeli Vocational School, Kocaeli University, Kocaeli, Turkey
| | - Fatma Oguz Erdogan
- Department of Chemistry and Chemical Processing Technologies, Kocaeli Vocational School, Kocaeli University, Kocaeli, Turkey
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Deng C, Wang X, Wang T, Liu W, Yuan X, Huang Y, Cao S. Virtual screening and molecular growth guide the design of inhibitors for the influenza virus drug-resistant mutant M2-V27A/S31N. J Biomol Struct Dyn 2024; 42:5253-5267. [PMID: 37424098 DOI: 10.1080/07391102.2023.2233026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
The influenza A virus matrix protein 2 (AM2) protein is a proton-gated, proton-selective ion channel essential for influenza replication that has been identified as an antiviral target. The drug-resistance of the M2-V27A/S31N strain, which has been growing more prevalent in recent years and has the potential to spread globally, prevents current amantadine inhibitors from having the desired impact. In this study, we compiled the most common influenza A virus strains from 2001-2020 from the U.S. National Center for Biotechnology Information database and hypothesized that M2-V27A/S31N would become a common strain. The lead compound ZINC299830590 was screened for M2-V27A/S31N in the ZINC15 database using a pharmacophore model and molecular descriptors. This lead compound was then optimized by molecular growth, which allowed us to identify important amino acid residues and create interactions with them to produce compound 4. Molecular dynamics simulation showed that the complex of compound 4 and M2-V27A/S31N had certain degrees of stability and flexibility. The binding free energy of compound 4 was calculated using the MM/PB(GB)SA method and totaled -106.525 kcal/mol. Finally, physicochemical and pharmacokinetic profiles were predicted using the Absorption, Distribution, Metabolism, Excretion, and Toxicity model, which indicated the good bioavailability of compound 4. These results provide the basis for further in vivo and in vitro studies to demonstrate that compound 4 is a promising drug candidate against M2-V27A/S31N.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Changyong Deng
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Xiaobo Wang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Tangle Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Wei Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Xiaolan Yuan
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Yan Huang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Shuang Cao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
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Diniz EADS, da Silva DP, Ferreira SDS, Fernandes-Pedrosa MDF, Vieira DS. Temperature effect in the inhibition of PLA 2 activity of Bothrops brazili venom by Rosmarinic and Chlorogenic acids, experimental and computational approaches. J Biomol Struct Dyn 2024; 42:5238-5252. [PMID: 37378497 DOI: 10.1080/07391102.2023.2226912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
Myotoxicity caused by snakebite envenoming emerges as one of the main problems of ophidic accidents as it is not well neutralized by the current serum therapy. A promising alternative is to search for efficient small molecule inhibitors that can act against multiple venom components. Phospholipase A2 (PLA2) is frequently found in snake venom and is usually associated with myotoxicity. Thus it represents an excellent target for the search of new treatments. This work reports the effect of temperature in the inhibition of catalytic properties of PLA2 from Bothrops brazili venom by Rosmarinic (RSM) and Chlorogenic (CHL) acids through experimental and computational approaches. Three temperatures were evaluated (25, 37 and 50 °C). In the experimental section, enzymatic assays showed that RSM is a better inhibitor in all three temperatures. At 50 °C, the inhibition efficiency decayed significantly for both acids. Docking studies revealed that both ligands bind to the hydrophobic channel of the protein dimer where the phospholipid binds in the catalytic process, interacting with several functional residues. In this context, RSM presents better interaction energies due to stronger interactions with chain B of the dimer. Molecular dynamics simulations showed that RSM can establish selective interactions with ARG112B of PLA2, which is located next to residues of the putative Membrane Disruption Site in PLA2-like structures. The affinity of RSM and CHL acids towards PLA2 is mainly driven by electrostatic interactions, especially salt bridge interactions established with residues ARG33B (for CHL) and ARG112B (RSM) and hydrogen bonds with residue ASP89A. The inability of CHL to establish a stable interaction with ARG112B was identified as the reason for its lower inhibition efficiency compared to RSM at the three temperatures. Furthermore, extensive structural analysis was performed to explain the lower inhibition efficiency at 50 °C for both ligands. The analysis performed in this work provides important information for the future design of new inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Diana Pontes da Silva
- Laboratory of Technology and Pharmaceutical Biotechnology (Tecbiofar), College of Pharmacy, Federal University of Rio Grande do Norte, Avenue General Gustavo Cordeiro de Farias, Petrópolis, Natal, Brazil
| | - Sarah de Sousa Ferreira
- Laboratory of Technology and Pharmaceutical Biotechnology (Tecbiofar), College of Pharmacy, Federal University of Rio Grande do Norte, Avenue General Gustavo Cordeiro de Farias, Petrópolis, Natal, Brazil
| | - Matheus de Freitas Fernandes-Pedrosa
- Laboratory of Technology and Pharmaceutical Biotechnology (Tecbiofar), College of Pharmacy, Federal University of Rio Grande do Norte, Avenue General Gustavo Cordeiro de Farias, Petrópolis, Natal, Brazil
| | - Davi Serradella Vieira
- Institute of Chemistry, Federal University of Rio Grande do Norte, Av Senador Salgado Filho, Natal-RN, Brazil
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Suh D, Arattu Thodika AR, Kim S, Nam K, Im W. CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. J Chem Theory Comput 2024. [PMID: 38856971 DOI: 10.1021/acs.jctc.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI QM/MM Interfacer, a web-based cyberinfrastructure designed to streamline the preparation of various QM/MM simulation inputs with ligand modification. The development of QM/MM Interfacer has been achieved through integration with existing CHARMM-GUI modules, such as PDB Reader and Manipulator, Solution Builder, and Membrane Builder. In addition, new functionalities have been developed to facilitate the one-stop preparation of QM/MM systems and enable interactive and intuitive ligand modifications and QM atom selections. QM/MM Interfacer offers support for a range of semiempirical QM methods, including AM1(+/d), PM3(+/PDDG), MNDO(+/d, +/PDDG), PM6, RM1, and SCC-DFTB, tailored for both AMBER and CHARMM. A nontrivial setup related to ligand modification, link-atom insertion, and charge distribution is automatized through intuitive user interfaces. To illustrate the robustness of QM/MM Interfacer, we conducted QM/MM simulations of three enzyme-substrate systems: dihydrofolate reductase, insulin receptor kinase, and oligosaccharyltransferase. In addition, we have created three tutorial videos about building these systems, which can be found at https://www.charmm-gui.org/demo/qmi. QM/MM Interfacer is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for hybrid QM/MM simulations.
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Affiliation(s)
- Donghyuk Suh
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Abdul Raafik Arattu Thodika
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Seonghoon Kim
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019-9800, United States
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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Duzgun Z, Korkmaz FD, Akgün E. FDI-6 inhibits VEGF-B expression in metastatic breast cancer: a combined in vitro and in silico study. Mol Divers 2024:10.1007/s11030-024-10891-z. [PMID: 38853176 DOI: 10.1007/s11030-024-10891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
Angiogenesis is the process by which new blood vessels are formed to meet the oxygen and nutrient needs of tissues. This process is vitally important in many physiological and pathological conditions such as tumor growth, metastasis, and chronic inflammation. Although the relationship of FDI-6 compound with FOXM1 protein is well known in the literature, its relationship with angiogenesis is not adequately elucidated. This study investigates the relationship of FDI-6 with angiogenesis and vascular endothelial growth factor B (VEGF-B) protein expression alterations. Furthermore, the study aims to elucidate the in silico interaction of FDI-6 with the VEGFR1 protein, a key player in initiating the angiogenic process, which is activated through its binding with VEGF-B. Our results demonstrate a significant effect of FDI-6 on cell viability. Specifically, we determined that the IC50 value of FDI-6 in HUVEC cells after 24 h of treatment is 24.2 μM, and in MDA-MB-231 cells after 24 h of application, it is 10.8 μM. These findings suggest that the cytotoxic effect of FDI-6 varies depending on the cell type. In wound healing experiments, FDI-6 significantly suppressed wound closure in MDA-MB-231 cells but did not show a similar effect in HUVEC cells. This finding suggests FDI-6 may have potential cell-type-specific effects. Molecular docking studies reveal that FDI-6 exhibits a stronger interaction with the VEGFR1 protein compared to its inhibitor, a novel interaction not previously reported in the literature. Molecular dynamic simulation results demonstrate a stable interaction between FDI-6 and VEGFR1. This interaction suggests that FDI-6 might modulate mechanisms associated with angiogenesis. Our Western blot analysis results show regulatory effects of FDI-6 on the expression of the VEGF-B protein. We encourage exploration of FDI-6 as a potential therapeutic agent in pathological processes related to angiogenesis. In conclusion, this study provides a detailed examination of the relationship between FDI-6 and both the molecular interactions and protein expressions of VEGF-B. Our findings support FDI-6 as a potential therapeutic agent in pathological processes associated with angiogenesis.
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Affiliation(s)
- Zekeriya Duzgun
- Department of Medical Biology, Faculty of Medicine, Giresun University, Giresun, Turkey.
| | | | - Egemen Akgün
- Department of Medical Biology, Faculty of Medicine, Giresun University, Giresun, Turkey
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Abdjan MI, Shafiq M, Nerukh D, Nur-E-Alam M, Ul-Haq Z. Exploring the mechanism of action of spirooxindoles as a class of CDK2 inhibitors: a structure-based computational approach. Phys Chem Chem Phys 2024; 26:16139-16152. [PMID: 38787638 DOI: 10.1039/d4cp00844h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Cyclin-dependent kinase 2 (CDK2) regulates cell cycle checkpoints in the synthesis and mitosis phases and plays a pivotal role in cancerous cell proliferation. The activation of CDK2, influenced by various protein signaling pathways, initiates the phosphorylation process. Due to its crucial role in carcinogenesis, CDK2 is a druggable hotspot target to suppress cancer cell proliferation. In this context, several studies have identified spirooxindoles as an effective class of CDK2 inhibitors. In the present study, three spirooxindoles (SOI1, SOI2, and SOI3) were studied to understand their inhibitory mechanism against CDK2 through a structure-based approach. Molecular docking and molecular dynamics (MD) simulations were performed to explore their interactions with CDK2 at the molecular level. The calculated binding free energy for the spirooxindole-based CDK2 inhibitors aligned well with experimental results regarding CDK2 inhibition. Energy decomposition (ED) analysis identified key binding residues, including I10, G11, T14, R36, F82, K89, L134, P155, T158, Y159, and T160, in the CDK2 active site and T-loop phosphorylation. Molecular mechanics (MM) energy was identified as the primary contributor to stabilizing inhibitor binding in the CDK2 protein structure. Furthermore, the analysis of binding affinity revealed that the inhibitor SOI1 binds more strongly to CDK2 compared to the other inhibitors under investigation. It demonstrated a robust interaction with the crucial residue T160 in the T-loop phosphorylation site, responsible for kinase activation. These insights into the inhibitory mechanism are anticipated to contribute to the development of potential CDK2 inhibitors using the spirooxindole scaffold.
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Affiliation(s)
- Muhammad Ikhlas Abdjan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Komplek Kampus C UNAIR, Jl. Mulyorejo, Surabaya, Indonesia
| | - Muhammad Shafiq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, B4 7ET, UK
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Kingdom of Saudi Arabia.
| | - Zaheer Ul-Haq
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
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Chen C, Lei Q, Geng W, Wang D, Gan X. Discovery of Novel Pyridazine Herbicides Targeting Phytoene Desaturase with Scaffold Hopping. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12425-12433. [PMID: 38781442 DOI: 10.1021/acs.jafc.3c09350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Phytoene desaturase (PDS) is a critical functional enzyme in blocking ζ-carotene biosynthesis and is one of the bleaching herbicide targets. At present, norflurazon (NRF) is the only commercial pyridazine herbicide targeting PDS. Therefore, developing new and diverse pyridazine herbicides targeting PDS is urgently required. In this study, diflufenican (BF) was used as the lead compound, and a scaffold-hopping strategy was employed to design and synthesize some pyridazine derivatives based on the action mode of BF and PDS. The preemergence herbicidal activity tests revealed that compound 6-chloro-N-(2,4-difluorophenyl)-3-(3-(trifluoromethyl)phenoxy)pyridazine-4-carboxamide (B1) with 2,4-diF substitution in the benzeneamino ring showed 100% inhibition rates against the roots and stems of Echinochloa crus-galli and Portulaca oleracea at 100 μg/mL, superior to the inhibition rates of BF. Meanwhile, compound B1 demonstrated excellent postemergence herbicidal activity against broadleaf weeds, which was similar to that of BF (inhibition rate of 100%) but superior to that of NRF. This indicated that 6-Cl in the pyridazine ring is the key group for postemergence herbicidal activity. In addition, compound B1 could induce downregulation of PDS gene expression, 15-cis-phytoene accumulation, and Y(II) deficiency and prevent photosynthesis. Therefore, B1 can be considered as a promising candidate for developing high-efficiency PDS inhibitors.
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Affiliation(s)
- Chao Chen
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
- State Key Laboratory of Functions and Applications of Medicinal Plants, Natural Products Research Center of Guizhou Province, Guizhou Medical University, Guiyang 550014, PR China
| | - Qiong Lei
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Wang Geng
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Daoping Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Natural Products Research Center of Guizhou Province, Guizhou Medical University, Guiyang 550014, PR China
| | - Xiuhai Gan
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
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11
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Kamsri B, Kamsri P, Punkvang A, Chimprasit A, Saparpakorn P, Hannongbua S, Spencer J, Oliveira ASF, Mulholland AJ, Pungpo P. Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations. Biochemistry 2024; 63:1493-1504. [PMID: 38742407 PMCID: PMC11154950 DOI: 10.1021/acs.biochem.4c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Abstract
DNA gyrases catalyze negative supercoiling of DNA, are essential for bacterial DNA replication, transcription, and recombination, and are important antibacterial targets in multiple pathogens, including Mycobacterium tuberculosis, which in 2021 caused >1.5 million deaths worldwide. DNA gyrase is a tetrameric (A2B2) protein formed from two subunit types: gyrase A (GyrA) carries the breakage-reunion active site, whereas gyrase B (GyrB) catalyzes ATP hydrolysis required for energy transduction and DNA translocation. The GyrB ATPase domains dimerize in the presence of ATP to trap the translocated DNA (T-DNA) segment as a first step in strand passage, for which hydrolysis of one of the two ATPs and release of the resulting inorganic phosphate is rate-limiting. Here, dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations of the dimeric 43 kDa N-terminal fragment of M. tuberculosis GyrB show how events at the ATPase site (dissociation/hydrolysis of bound nucleotides) are propagated through communication pathways to other functionally important regions of the GyrB ATPase domain. Specifically, our simulations identify two distinct pathways that respectively connect the GyrB ATPase site to the corynebacteria-specific C-loop, thought to interact with GyrA prior to DNA capture, and to the C-terminus of the GyrB transduction domain, which in turn contacts the C-terminal GyrB topoisomerase-primase (TOPRIM) domain responsible for interactions with GyrA and the centrally bound G-segment DNA. The connection between the ATPase site and the C-loop of dimeric GyrB is consistent with the unusual properties of M. tuberculosis DNA gyrase relative to those from other bacterial species.
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Affiliation(s)
- Bundit Kamsri
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Pharit Kamsri
- Division
of Chemistry, Faculty of Science, Nakhon
Phanom University, Nakhon
Phanom 48000, Thailand
| | - Auradee Punkvang
- Division
of Chemistry, Faculty of Science, Nakhon
Phanom University, Nakhon
Phanom 48000, Thailand
| | - Aunlika Chimprasit
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | | | - Supa Hannongbua
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Bangkok 10900, Thailand
| | - James Spencer
- School
of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K.
| | - A. Sofia F. Oliveira
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Pornpan Pungpo
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry,
Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
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12
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He G, Zheng Q, Wu J, Wu L, Geng Z, Jiang G, Huang H, Jiang X, Yu X. Discordant results between Xpert MTB/RIF assay and Bactec MGIT 960 culture system regarding the detection of rifampin-resistant Mycobacterium tuberculosis isolates in Wenzhou, China. Microbiol Spectr 2024; 12:e0385923. [PMID: 38738892 DOI: 10.1128/spectrum.03859-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/08/2024] [Indexed: 05/14/2024] Open
Abstract
This study aimed to assess the possible causes of discordant results between Xpert MTB/RIF (Xpert) and Bactec MGIT 960 Culture System (MGIT960) regarding rifampicin (RIF) susceptibility in Mycobacterium tuberculosis. Patients with previous RIF-resistant tuberculosis who were admitted to Wenzhou Central Hospital from January 2020 to December 2022 were enrolled. The isolates obtained from these patients were subjected to RIF susceptibility tests using Xpert and MGIT960, and the minimum inhibitory concentration (MIC) of RIF was determined by the MYCOTB MIC plate test. Additionally, molecular docking and molecular dynamics (MD) simulations were performed to evaluate the binding efficacy of rpoB and RIF based on rpoB mutations detected in the isolates with discordant RIF susceptibility results. A total of 28 isolates with discordant RIF susceptibility test results were detected, 15 of them were RIF susceptible with MICs ≤ 0.5 µg/mL. Twelve out of 15 isolates contained borderline RIF resistance-associated mutations [L430P (n = 6), H445N (n = 6)], 1 isolate had D435Y and Q429H double mutation, and the remaining 2 isolates had a silent (Q432Q) mutation. Compared with the affinity of RIF toward the wild type (WT) (-45.83 kcal/mol) by MD, its affinity toward L452P (-55.52 kcal/mol), D435Y (-47.39 kcal/mol), L430P (approximately -69.72 kcal/mol), H445N (-49.53 kcal/mol), and Q429H (-55.67 kcal/mol) increased. Borderline RIF resistance-associated mutations were the main cause for the discordant RIF susceptibility results between Xpert and MGIT960, and the mechanisms of the resistance need further investigated.IMPORTANCEThis study is aimed at assessing discordant results between Xpert MTB/RIF (Xpert) assay and Bactec MGIT 960 Culture System (MGIT960) regarding the detection of rifampicin (RIF)-resistant Mycobacterium tuberculosis isolates in Wenzhou, China. The discordant results of RIF between these two assays were mainly caused by borderline RIF resistance-associated mutations, subsequently by silent mutations of rpoB. Borderline RIF resistance- associated mutations detected in our study were demonstrated to not be affected by the affinity of rpoB and RIF by molecular dynamics, and the mechanism of resistance was needed to be clarified. For the discordant results of RIF by Xpert and MGIT960 that occurred, rpoB DNA sequencing was recommended to investigate its association with resistance to RIF.
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Affiliation(s)
- Guiqing He
- Department of Infectious Diseases, Wenzhou Central Hospital, The Dingli Clinical College of Wenzhou Medical University, The Second Affiliated Hospital of Shanghai University, Wenzhou, China
- Laboratory of Infectious Diseases, Wenzhou Central Hospital, The Dingli Clinical College of Wenzhou Medical University, The Second Affiliated Hospital of Shanghai University, Wenzhou, China
| | - Qingyong Zheng
- Laboratory of Infectious Diseases, Wenzhou Central Hospital, The Dingli Clinical College of Wenzhou Medical University, The Second Affiliated Hospital of Shanghai University, Wenzhou, China
| | - Jing Wu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Lianpeng Wu
- Department of Clinical Laboratory Medicine, Wenzhou Central Hospital, The Dingli Clinical College of Wenzhou Medical University, The Second Affiliated Hospital of Shanghai University, Wenzhou, China
| | - Zhi Geng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xiangao Jiang
- Department of Infectious Diseases, Wenzhou Central Hospital, The Dingli Clinical College of Wenzhou Medical University, The Second Affiliated Hospital of Shanghai University, Wenzhou, China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
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13
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Abdollahi-Najafabadi M, Farhadian S, Shareghi B, Asgharzadeh S. The investigation of the interaction determination between carbendazim and elastase, using both in vitro and in silico methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124586. [PMID: 38833886 DOI: 10.1016/j.saa.2024.124586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 05/28/2024] [Accepted: 06/01/2024] [Indexed: 06/06/2024]
Abstract
Pesticides, including fungicides, are one of the important groups of environmental toxins that affect human and animal health. Studies have shown that these compounds are considered chemical pollutants. Carbendazim is a systemic fungicide. Unfortunately, excessive use of carbendazim has caused environmental pollution all over the world. In this study, the effect of carbendazim on the enzyme elastase (secreted from the endocrine gland of the pancreas) has been investigated. In a study, the performance and reaction of carbendazim with elastase were investigated using spectroscopic techniques. The stability and structure of elastase enzymes were studied under the influence of carbendazim. The results of fluorescence emission and UV-visible absorption spectrum showed that in the presence of carbendazim, there is an increase in UV-Vis absorption and a decrease in the intensity of the intrinsic fluorescence emission in the protein spectrum. Additionally, a decrease in the thermal stability of elastase was observed in the presence of carbendazim. The stability and structure of elastase enzyme were investigated in the presence of carbendazim. The results revealed that the UV-Vis absorption increased due to the presence of carbendazim, as indicated by the hyperchromic spectrum at 220 and 280 nm peaks. Additionally, the intrinsic fluorescence emission in the protein spectrum decreased with increasing carbendazim concentration at three different temperatures (298, 303, and 313 K). Moreover, the study demonstrated that the TM decreased from 2.59 to 4.58 with the increase of carbendazim, suggesting a decrease in the stability of the elastase structure in response to the elevated carbendazim concentration. According to the results of the research, the interaction between elastase and carbendazim has occurred, and changes have been made in the enzyme under the influence of carbendazim. The formation of the complex between elastase and carbendazim was consistent with the results obtained from molecular simulation and confirmed the thermodynamic data.
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Affiliation(s)
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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14
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Boushehri S, Holey H, Brosz M, Gumbsch P, Pastewka L, Aponte-Santamaría C, Gräter F. O-glycans Expand Lubricin and Attenuate Its Viscosity and Shear Thinning. Biomacromolecules 2024. [PMID: 38815979 DOI: 10.1021/acs.biomac.3c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Lubricin, an intrinsically disordered glycoprotein, plays a pivotal role in facilitating smooth movement and ensuring the enduring functionality of synovial joints. The central domain of this protein serves as a source of this excellent lubrication and is characterized by its highly glycosylated, negatively charged, and disordered structure. However, the influence of O-glycans on the viscosity of lubricin remains unclear. In this study, we employ molecular dynamics simulations in the absence and presence of shear, along with continuum simulations, to elucidate the intricate interplay between O-glycans and lubricin and the impact of O-glycans on lubricin's conformational properties and viscosity. We found the presence of O-glycans to induce a more extended conformation in fragments of the disordered region of lubricin. These O-glycans contribute to a reduction in solution viscosity but at the same time weaken shear thinning at high shear rates, compared to nonglycosylated systems with the same density. This effect is attributed to the steric and electrostatic repulsion between the fragments, which prevents their conglomeration and structuring. Our computational study yields a mechanistic mechanism underlying previous experimental observations of lubricin and paves the way to a more rational understanding of its function in the synovial fluid.
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Affiliation(s)
- Saber Boushehri
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Hannes Holey
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
- Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, Freiburg 79110, Germany
| | - Matthias Brosz
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
| | - Peter Gumbsch
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
- Fraunhofer IWM, Wöhlerstraße 11, Freiburg 79108, Germany
| | - Lars Pastewka
- Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, Freiburg 79110, Germany
| | - Camilo Aponte-Santamaría
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
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15
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Stanevich V, Oyeniran O, Somani S. Modeling Chromatography Binding through Molecular Dynamics Simulations with Resin Fragments. J Phys Chem B 2024. [PMID: 38809811 DOI: 10.1021/acs.jpcb.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Accurate atomistic modeling of the interactions of a chromatography resin with a solute can inform the selection of purification conditions for a product, an important problem in the biotech and pharmaceutical industries. We present a molecular dynamics simulation-based approach for the qualitative prediction of interaction sites (specificity) and retention times (affinity) of a protein for a given chromatography resin. We mimicked the resin with an unrestrained ligand composed of the resin headgroup coupled with successively larger fragments of the agarose backbone. The interactions of the ligand with the protein are simulated in an explicit solvent using the Replica Exchange Molecular Dynamics enhanced sampling approach in conjunction with Hydrogen Mass Repartitioning (REMD-HMR). We computed the ligand interaction surface from the simulation trajectories and correlated the features of the interaction surface with experimentally determined retention times. The simulation and analysis protocol were first applied to a series of ubiquitin mutants for which retention times on Capto MMC resin are available. The ubiquitin simulations helped identify the optimal ligand that was used in subsequent simulations on six proteins for which Capto MMC elution times are available. For each of the six proteins, we computed the interaction surface and characterized it in terms of a range of simulation-averaged residue-level physicochemical descriptors. Modeling of the salt concentrations required for elution with respect to the descriptors resulted in a linear fit in terms of aromaphilicity and Kyte-Doolittle hydrophobicity that was robust to outliers, showed high correlation, and correctly ranked the protein elution order. The physics-based model building approach described here does not require a large experimental data set and can be readily applied to different resins and diverse biomolecules.
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Affiliation(s)
- Vitali Stanevich
- Protein Therapeutics API Development, Janssen Research & Development, LLC, a Johnson & Johnson company, Malvern, Pennsylvania 19355, United States
| | - Oluyemi Oyeniran
- Statistics and Decision Sciences, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
| | - Sandeep Somani
- In Silico Discovery, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
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16
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Yan Y, Xie X, Jiang W, Bao A, Deng Z, Wang D, Wang J, Li W, Tang X. Novel Pyrido[4,3- d]pyrimidine Derivatives as Potential Sterol 14α-Demethylase Inhibitors: Design, Synthesis, Inhibitory Activity, and Molecular Modeling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12260-12269. [PMID: 38759097 DOI: 10.1021/acs.jafc.3c09543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Thirty-four new pyrido[4,3-d]pyrimidine analogs were designed, synthesized, and characterized. The crystal structures for compounds 2c and 4f were measured by means of X-ray diffraction of single crystals. The bioassay results showed that most target compounds exhibited good fungicidal activities against Pyricularia oryzae, Rhizoctonia cerealis, Sclerotinia sclerotiorum, Botrytis cinerea, and Penicillium italicum at 16 μg/mL. Compounds 2l, 2m, 4f, and 4g possessed better fungicidal activities than the commercial fungicide epoxiconazole against B. cinerea. Their half maximal effective concentration (EC50) values were 0.191, 0.487, 0.369, 0.586, and 0.670 μg/mL, respectively. Furthermore, the inhibitory activities of the bioactive compounds were determined against sterol 14α-demethylase (CYP51). The results displayed that they had prominent activities. Compounds 2l, 2m, 4f, and 4g also showed better inhibitory activities than epoxiconazole against CYP51. Their half maximal inhibitory concentration (IC50) values were 0.219, 0.602, 0.422, 0.726, and 0.802 μg/mL, respectively. The results of molecular dynamics (MD) simulations exhibited that compounds 2l and 4f possessed a stronger affinity to CYP51 than epoxiconazole.
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Affiliation(s)
- Yingkun Yan
- School of Science, Xihua University, Chengdu 610039, PR China
| | - Xiansong Xie
- School of Science, Xihua University, Chengdu 610039, PR China
| | - Wenjing Jiang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, PR China
| | - Ailing Bao
- School of Science, Xihua University, Chengdu 610039, PR China
| | - Ziquan Deng
- School of Science, Xihua University, Chengdu 610039, PR China
| | - Deyuan Wang
- School of Science, Xihua University, Chengdu 610039, PR China
| | - Jingwen Wang
- School of Science, Xihua University, Chengdu 610039, PR China
| | - Weiyi Li
- School of Science, Xihua University, Chengdu 610039, PR China
| | - Xiaorong Tang
- School of Science, Xihua University, Chengdu 610039, PR China
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17
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Truong DT, Ho K, Nhi HTY, Nguyen VH, Dang TT, Nguyen MT. Imidazole[1,5-a]pyridine derivatives as EGFR tyrosine kinase inhibitors unraveled by umbrella sampling and steered molecular dynamics simulations. Sci Rep 2024; 14:12218. [PMID: 38806555 PMCID: PMC11133355 DOI: 10.1038/s41598-024-62743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
Although the use of the tyrosine kinase inhibitors (TKIs) has been proved that it can save live in a cancer treatment, the currently used drugs bring in many undesirable side-effects. Therefore, the search for new drugs and an evaluation of their efficiency are intensively carried out. Recently, a series of eighteen imidazole[1,5-a]pyridine derivatives were synthetized by us, and preliminary analyses pointed out their potential to be an important platform for pharmaceutical development owing to their promising actions as anticancer agents and enzyme (kinase, HIV-protease,…) inhibitors. In the present theoretical study, we further analyzed their efficiency in using a realistic scenario of computational drug design. Our protocol has been developed to not only observe the atomistic interaction between the EGFR protein and our 18 novel compounds using both umbrella sampling and steered molecular dynamics simulations, but also determine their absolute binding free energies. Calculated properties of the 18 novel compounds were in detail compared with those of two known drugs, erlotinib and osimertinib, currently used in cancer treatment. Inspiringly the simulation results promote three imidazole[1,5-a]pyridine derivatives as promising inhibitors into a further step of clinical trials.
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Affiliation(s)
- Duc Toan Truong
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Kiet Ho
- Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, 70000, Vietnam
| | - Huynh Thi Yen Nhi
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Van Ha Nguyen
- Faculty of Chemistry, VNU University of Science, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hoan Kiem, Hanoi, 11021, Vietnam
| | - Tuan Thanh Dang
- Faculty of Chemistry, VNU University of Science, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hoan Kiem, Hanoi, 11021, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
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18
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Şenel P, Faysal AA, Erdoğan T, Doğan M, Gölcü A. Quantitative study on a simple electrochemical dsDNA-pregabalin biosensor; multi-spectroscopic, molecular docking and modelling studies. J Pharm Biomed Anal 2024; 247:116261. [PMID: 38823224 DOI: 10.1016/j.jpba.2024.116261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/13/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Pregabalin (PGB) is a γ-aminobutyric acid (GABA) alkylated analog prescribed to treat neuropathic pain, fibromyalgia, and postherpetic neuralgia. Using analytical, spectroscopic methods and molecular docking and molecular dynamics (MD) simulations, a detailed experimental and theoretical investigation was conducted into the binding process and interactions between PGB and double-stranded fish sperm deoxyribonucleic acid (dsDNA). It was evident from the collected experimental results that PGB binds with ds-DNA. PGB attaches to dsDNA via minor groove binding, as demonstrated by the results of electrochemical studies, UV-Vis absorption spectroscopy, and replacement study with ethidium bromide and Hoechst-32588. PGB's binding constant (Kb) with dsDNA, as determined by the Benesi-Hildebrand plot, is 2.41×104 ± 0.30 at 298 K. The fluorescence investigation indicates that PGB and dsDNA have a binding stoichiometry (n) of 1.21 ± 0.09. Molecular docking simulations were used in the research to computational determination of the interactions between PGB and dsDNA. The findings demonstrated that minor groove binding was the mechanism by which PGB interacted with dsDNA. Based on the electrochemically responsive PGB-dsDNA biosensor, we developed a technique for low-concentration detection of PGB utilizing differential pulse voltammetry (DPV). The voltammetric analysis of the peak current decrease in the deoxyadenosine oxidation signals resulting from the association between PGB and dsDNA enabled a sensitive estimation of PGB in pH 4.80 acetate buffer. The deoxyguanosine oxidation signals exhibited a linear relationship between 2 and 16 μM PGB. The values for the limit of detection (LOD) and limit of quantitation (LOQ) were 0.57 μM and 1.91 μM, respectively.
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Affiliation(s)
- Pelin Şenel
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Istanbul, Turkiye
| | - Abdullah Al Faysal
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Istanbul, Turkiye
| | - Taner Erdoğan
- Kocaeli University, Kocaeli Vocational School, Department of Chemistry and Chemical Processing Technologies, Kocaeli, Turkiye
| | - Mustafa Doğan
- Istanbul Technical University, Faculty of Electrical-Electronics Engineering, Department of Control and Automation Engineering, Istanbul, Turkiye
| | - Ayşegül Gölcü
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Istanbul, Turkiye.
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19
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Liang JJ, Pitsillou E, Lau HLY, Mccubbery CP, Gan H, Hung A, Karagiannis TC. Utilization of the EpiMed Coronabank Chemical Collection to identify potential SARS-CoV-2 antivirals: in silico studies targeting the nsp14 ExoN domain and PL pro naphthalene binding site. J Mol Graph Model 2024; 131:108803. [PMID: 38815531 DOI: 10.1016/j.jmgm.2024.108803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome encodes 29 proteins including four structural, 16 nonstructural (nsps), and nine accessory proteins (https://epimedlab.org/sars-cov-2-proteome/). Many of these proteins contain potential targetable sites for the development of antivirals. Despite the widespread use of vaccinations, the emergence of variants necessitates the investigation of new therapeutics and antivirals. Here, the EpiMed Coronabank Chemical Collection (https://epimedlab.org/crl/) was utilized to investigate potential antivirals against the nsp14 exoribonuclease (ExoN) domain. Molecular docking was performed to evaluate the binding characteristics of our chemical library against the nsp14 ExoN site. Based on the initial screen, trisjuglone, ararobinol, corilagin, and naphthofluorescein were identified as potential lead compounds. Molecular dynamics (MD) simulations were subsequently performed, with the results highlighting the stability of the lead compounds in the nsp14 ExoN site. Protein-RNA docking revealed the potential for the lead compounds to disrupt the interaction with RNA when bound to the ExoN site. Moreover, hypericin, cyanidin-3-O-glucoside, and rutin were previously identified as lead compounds targeting the papain-like protease (PLpro) naphthalene binding site. Through performing MD simulations, the stability and interactions of lead compounds with PLpro were further examined. Overall, given the critical role of the exonuclease activity of nsp14 in ensuring viral fidelity and the multifunctional role of PLpro in viral pathobiology and replication, these nsps represent important targets for antiviral drug development. Our databases can be utilized for in silico studies, such as the ones performed here, and this approach can be applied to other potentially druggable SARS-CoV-2 protein targets.
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Affiliation(s)
- Julia J Liang
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia; Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Hannah L Y Lau
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cian P Mccubbery
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hockxuen Gan
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC, 3053, Australia; Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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20
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Ould Mohamed L, Abtouche S, Ghoualem Z, Assfeld X. Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling. J Mol Model 2024; 30:180. [PMID: 38780881 DOI: 10.1007/s00894-024-05963-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
CONTEXT In cellular environments, the reduction of disulfide bonds is pivotal for protein folding and synthesis. However, the intricate enzymatic mechanisms governing this process remain poorly understood. This study addresses this gap by investigating a disulfide bridge reduction reaction, serving as a model for comprehending electron and proton transfer in biological systems. Six potential mechanisms for reducing the dimethyl disulfide (DMDS) bridge through electron and proton capture were explored. Thermodynamic and kinetic analyses elucidated the sequence of proton and electron addition. MD-PMM, a method that combines molecular dynamics simulations and quantum-chemical calculations, was employed to compute the redox potential of the mechanism. This research provides valuable insights into the mechanisms and redox potentials involved in disulfide bridge reduction within proteins, offering an understanding of phenomena that are challenging to explore experimentally. METHODS All calculations used the Gaussian 09 software package at the MP2/6-311 + g(d,p) theory level. Visualization of the molecular orbitals and electron densities was conducted using Gaussview6. Molecular dynamics simulations were performed using GROMACS with the CHARMM36 force field. The PyMM program (Python Program for QM/MM Simulations Based on the Perturbed Matrix Method) is used to apply the Perturbed Matrix Method to MD simulations.
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Affiliation(s)
- Lina Ould Mohamed
- Laboratoire de Physico Chimie Théorique Et Chimie Informatique, LPCTCI, Faculté de Chimie, USTHB, 16111, Algiers, Algeria
| | - Soraya Abtouche
- Laboratoire de Physico Chimie Théorique Et Chimie Informatique, LPCTCI, Faculté de Chimie, USTHB, 16111, Algiers, Algeria.
| | - Zeyneb Ghoualem
- Laboratoire de Physico Chimie Théorique Et Chimie Informatique, LPCTCI, Faculté de Chimie, USTHB, 16111, Algiers, Algeria
| | - Xavier Assfeld
- Physique et Chimie Théoriques, UMR 7019, Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506, Vandoeuvre Lès Nancy Cedex, France
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21
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Sepali C, Gómez S, Grifoni E, Giovannini T, Cappelli C. Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling. J Phys Chem B 2024; 128:5083-5091. [PMID: 38733374 DOI: 10.1021/acs.jpcb.4c01443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
Fully atomistic multiscale polarizable quantum mechanics (QM)/molecular mechanics (MM) approaches, combined with techniques to sample the solute-solvent phase space, constitute the most accurate method to compute spectral signals in aqueous solution. Conventional sampling strategies, such as classical molecular dynamics (MD), may encounter drawbacks when the conformational space is particularly complex, and transition barriers between conformers are high. This can lead to inaccurate sampling, which can potentially impact the accuracy of spectral calculations. For this reason, in this work, we compare classical MD with enhanced sampling techniques, i.e., replica exchange MD and metadynamics. In particular, we show how the different sampling techniques affect computed UV, electronic circular dichroism, nuclear magnetic resonance shielding, and optical rotatory dispersion of N-acetylproline-amide in aqueous solution. Such a system is a model peptide characterized by complex conformational variability. Calculated values suggest that spectral properties are influenced by solute conformers, relative population, and solvent effects; therefore, particular care needs to be paid for when choosing the sampling technique.
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Affiliation(s)
- Chiara Sepali
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Emanuele Grifoni
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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22
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Bao A, Jiang W, Xie X, Wang D, Deng Z, Wang J, Li W, Tang X, Yan Y. Design, Synthesis, Bioactive Evaluation, and Molecular Dynamics Simulation of Novel 4 H-Pyrano[3,2- c]pyridine Analogues as Potential Sterol 14α-Demethylase (CYP51) Inhibitors. J Med Chem 2024; 67:7954-7972. [PMID: 38703119 DOI: 10.1021/acs.jmedchem.4c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
To discover potential sterol 14α-demethylase (CYP51) inhibitors, thirty-four unreported 4H-pyrano[3,2-c]pyridine derivatives were designed and synthesized. The assay results indicated that most compounds displayed significant fungicidal activity against Sclerotinia sclerotiorum, Colletotrichum lagenarium, Botrytis cinerea, Penicillium digitatum, and Fusarium oxysporum at 16 μg/mL. The half maximal effective concentration (EC50) values of compounds 7a, 7b, and 7f against B. cinerea were 0.326, 0.530, and 0.610, respectively. Namely, they had better antifungal activity than epoxiconazole (EC50 = 0.670 μg/mL). Meanwhile, their half maximal inhibitory concentration (IC50) values against CYP51 were 0.377, 0.611, and 0.748 μg/mL, respectively, representing that they also possessed better inhibitory activities than epoxiconazole (IC50 = 0.802 μg/mL). The fluorescent quenching tests of proteins showed that 7a and 7b had similar quenching patterns to epoxiconazole. The molecular dynamics simulations indicated that the binding free energy of 7a and epoxiconazole to CYP51 was -35.4 and -27.6 kcal/mol, respectively.
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Affiliation(s)
- Ailing Bao
- School of Science, Xihua University, Chengdu 610039, China
| | - Wenjing Jiang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiansong Xie
- School of Science, Xihua University, Chengdu 610039, China
| | - Deyuan Wang
- School of Science, Xihua University, Chengdu 610039, China
| | - Ziquan Deng
- School of Science, Xihua University, Chengdu 610039, China
| | - Jingwen Wang
- School of Science, Xihua University, Chengdu 610039, China
| | - Weiyi Li
- School of Science, Xihua University, Chengdu 610039, China
| | - Xiaorong Tang
- School of Science, Xihua University, Chengdu 610039, China
| | - Yingkun Yan
- School of Science, Xihua University, Chengdu 610039, China
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23
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Fang L, Jin J, Zhang Z, Yu S, Tian C, Luo F, Long M, Zuo H, Lou S. Antidote-controlled DNA aptamer modulates human factor IXa activity. Bioorg Chem 2024; 148:107463. [PMID: 38776649 DOI: 10.1016/j.bioorg.2024.107463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Thrombosis leads to elevated mortality rates and substantial medical expenses worldwide. Human factor IXa (HFIXa) protease is pivotal in tissue factor (TF)-mediated thrombin generation, and represents a promising target for anticoagulant therapy. We herein isolated novel DNA aptamers that specifically bind to HFIXa through systematic evolution of ligands by exponential enrichment (SELEX) method. We identified two distinct aptamers, seq 5 and seq 11, which demonstrated high binding affinity to HFIXa (Kd = 74.07 ± 2.53 nM, and 4.93 ± 0.15 nM, respectively). Computer software was used for conformational simulation and kinetic analysis of DNA aptamers and HFIXa binding. These aptamers dose-dependently prolonged activated partial thromboplastin time (aPTT) in plasma. We further rationally optimized the aptamers by truncation and site-directed mutation, and generated the truncated forms (Seq 5-1t, Seq 11-1t) and truncated-mutated forms (Seq 5-2tm, Seq 11-2tm). They also showed good anticoagulant effects. The rationally and structurally designed antidotes (seq 5-2b and seq 11-2b) were competitively bound to the DNA aptamers and effectively reversed the anticoagulant effect. This strategy provides DNA aptamer drug-antidote pair with effective anticoagulation and rapid reversal, developing advanced therapies by safe, regulatable aptamer drug-antidote pair.
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Affiliation(s)
- Liang Fang
- Department of Hematology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jin Jin
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhe Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Shuang Yu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cheng Tian
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Fukang Luo
- Department of Laboratory Medicine, The Ninth People's Hospital of Chongqing, Chongqing 400700, China
| | - Mengfei Long
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Hua Zuo
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Shifeng Lou
- Department of Hematology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
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24
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Blanford J, Zhai Z, Baer MD, Guo G, Liu H, Liu Q, Raugei S, Shanklin J. Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1. SCIENCE ADVANCES 2024; 10:eadn0895. [PMID: 38758793 PMCID: PMC11100557 DOI: 10.1126/sciadv.adn0895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
SUCROSE-NON-FERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), a central plant metabolic sensor kinase, phosphorylates its target proteins, triggering a global shift from anabolism to catabolism. Molecular modeling revealed that upon binding of KIN10 to GEMINIVIRUS REP-INTERACTING KINASE1 (GRIK1), KIN10's activation T-loop reorients into GRIK1's active site, enabling its phosphorylation and activation. Trehalose 6-phosphate (T6P) is a proxy for cellular sugar status and a potent inhibitor of SnRK1. T6P binds to KIN10, a SnRK1 catalytic subunit, weakening its affinity for GRIK1. Here, we investigate the molecular details of T6P inhibition of KIN10. Molecular dynamics simulations and in vitro phosphorylation assays identified and validated the T6P binding site on KIN10. Under high-sugar conditions, T6P binds to KIN10, blocking the reorientation of its activation loop and preventing its phosphorylation and activation by GRIK1. Under these conditions, SnRK1 maintains only basal activity levels, minimizing phosphorylation of its target proteins, thereby facilitating a general shift from catabolism to anabolism.
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Affiliation(s)
- Jantana Blanford
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Zhiyang Zhai
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Marcel D. Baer
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gongrui Guo
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hui Liu
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Qun Liu
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - John Shanklin
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA
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25
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de Lima Menezes G, Sales Bezerra K, Nobre Oliveira JI, Fontenele Araújo J, Soares Galvão D, Alves da Silva R, Vogel Saivish M, Laino Fulco U. Quantum mechanics insights into melatonin and analogs binding to melatonin MT 1 and MT 2 receptors. Sci Rep 2024; 14:10922. [PMID: 38740789 DOI: 10.1038/s41598-024-59786-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Melatonin receptors MT1 and MT2 are G protein-coupled receptors that mediate the effects of melatonin, a hormone involved in circadian rhythms and other physiological functions. Understanding the molecular interactions between these receptors and their ligands is crucial for developing novel therapeutic agents. In this study, we used molecular docking, molecular dynamics simulations, and quantum mechanics calculation to investigate the binding modes and affinities of three ligands: melatonin (MLT), ramelteon (RMT), and 2-phenylmelatonin (2-PMT) with both receptors. Based on the results, we identified key amino acids that contributed to the receptor-ligand interactions, such as Gln181/194, Phe179/192, and Asn162/175, which are conserved in both receptors. Additionally, we described new meaningful interactions with Gly108/Gly121, Val111/Val124, and Val191/Val204. Our results provide insights into receptor-ligand recognition's structural and energetic determinants and suggest potential strategies for designing more optimized molecules. This study enhances our understanding of receptor-ligand interactions and offers implications for future drug development.
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Affiliation(s)
- Gabriela de Lima Menezes
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-400, Brazil
| | - Katyanna Sales Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
- Applied Physics Department, University of Campinas, Campinas, São Paulo, 13083-859, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
| | - John Fontenele Araújo
- Departamento de Fisiologia e Comportamento, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil
| | - Douglas Soares Galvão
- Applied Physics Department, University of Campinas, Campinas, São Paulo, 13083-859, Brazil
| | - Roosevelt Alves da Silva
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí, GO, 75801-615, Brazil
| | - Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José Do Rio Preto, São José Do Rio, Preto, SP, 15090-000, Brazil
- Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Brazilian Biosciences National Laboratory, Campinas, SP, 13083-100, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande no Norte, Natal, RN, 59072-970, Brazil.
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-400, Brazil.
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26
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Saeedimasine M, Rahmani R, Lyubartsev AP. Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. J Chem Inf Model 2024; 64:3799-3811. [PMID: 38623916 PMCID: PMC11094735 DOI: 10.1021/acs.jcim.3c01606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.
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Affiliation(s)
- Marzieh Saeedimasine
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Roja Rahmani
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Alexander P. Lyubartsev
- Department of Materials and Environmental
Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
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27
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Junior DBC, Lacerda PS, de Pilla Varotti F, Leite FHA. Towards development of new antimalarial compounds through in silico and in vitro assays. Comput Biol Chem 2024; 111:108093. [PMID: 38772047 DOI: 10.1016/j.compbiolchem.2024.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/17/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Malaria is one of most widespread infectious disease in world. The antimalarial therapy presents a series of limitations, such as toxicity and the emergence of resistance, which makes the search for new drugs urgent. Thus, it becomes necessary to explore essential and exclusive therapeutic targets of the parasite to achieve selective inhibition. Enoyl-ACP reductase is an enzyme of the type II fatty acid biosynthetic pathway and is responsible for the rate-limiting step in the fatty acid elongation cycle. In this work, we use hierarchical virtual screening and drug repositioning strategies to prioritize compounds for phenotypic assays and molecular dynamics studies. The molecules were tested against chloroquine-resistant W2 strain of Plasmodium falciparum (EC50 between 330.05 and 13.92 µM). Nitrofurantoin was the best antimalarial activity at low micromolar range (EC50 = 13.92 µM). However, a hit compound against malaria must have a biological activity value below 1 µM. A large number of molecules present problems with permeability in biological membranes and reaching an effective concentration in their target's microenvironment. Nitrofurantoin derivatives with inclusions of groups which confer increased lipid solubility (methyl groups, halogens and substituted and unsubstituted aromatic rings) have been proposed. These derivatives were pulled through the lipid bilayer in molecular dynamics simulations. Molecules 14, 18 and 21 presented lower free energy values than nitrofurantoin when crossing the lipid bilayer.
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Affiliation(s)
| | - Pedro Sousa Lacerda
- Laboratório de Bioinformática e Modelagem Molecular, Universidade Federal da Bahia, Brazil
| | | | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil; Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Brazil; Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Brazil.
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28
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Truong DT, Ho K, Pham DQH, Chwastyk M, Nguyen-Minh T, Nguyen MT. Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics. Sci Rep 2024; 14:10475. [PMID: 38714683 PMCID: PMC11076533 DOI: 10.1038/s41598-024-59899-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/16/2024] [Indexed: 05/10/2024] Open
Abstract
To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.
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Affiliation(s)
- Duc Toan Truong
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Kiet Ho
- Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, 70000, Vietnam
| | | | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Thai Nguyen-Minh
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
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29
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Ferreira NCDS, Viviani LG, Lima LM, do Amaral AT, Romano JVP, Fortunato AL, Soares RF, Alberto AVP, Coelho Neto JA, Alves LA. A Hybrid Approach Combining Shape-Based and Docking Methods to Identify Novel Potential P2X7 Antagonists from Natural Product Databases. Pharmaceuticals (Basel) 2024; 17:592. [PMID: 38794162 PMCID: PMC11123696 DOI: 10.3390/ph17050592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 05/26/2024] Open
Abstract
P2X7 is an ATP-activated purinergic receptor implicated in pro-inflammatory responses. It is associated with the development of several diseases, including inflammatory and neurodegenerative conditions. Although several P2X7 receptor antagonists have recently been reported in the literature, none of them is approved for clinical use. However, the structure of the known antagonists can serve as a scaffold for discovering effective compounds in clinical therapy. This study aimed to propose an improved virtual screening methodology for the identification of novel potential P2X7 receptor antagonists from natural products through the combination of shape-based and docking approaches. First, a shape-based screening was performed based on the structure of JNJ-47965567, a P2X7 antagonist, using two natural product compound databases, MEGx (~5.8 × 103 compounds) and NATx (~32 × 103 compounds). Then, the compounds selected by the proposed shape-based model, with Shape-Tanimoto score values ranging between 0.624 and 0.799, were filtered for drug-like properties. Finally, the compounds that met the drug-like filter criteria were docked into the P2X7 allosteric binding site, using the docking programs GOLD and DockThor. The docking poses with the best score values were submitted to careful visual inspection of the P2X7 allosteric binding site. Based on our established visual inspection criteria, four compounds from the MEGx database and four from the NATx database were finally selected as potential P2X7 receptor antagonists. The selected compounds are structurally different from known P2X7 antagonists, have drug-like properties, and are predicted to interact with key P2X7 allosteric binding pocket residues, including F88, F92, F95, F103, M105, F108, Y295, Y298, and I310. Therefore, the combination of shape-based screening and docking approaches proposed in our study has proven useful in selecting potential novel P2X7 antagonist candidates from natural-product-derived compounds databases. This approach could also be useful for selecting potential inhibitors/antagonists of other receptors and/or biological targets.
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Affiliation(s)
- Natiele Carla da Silva Ferreira
- Laboratory of Cellular Communication, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil; (N.C.d.S.F.); (L.M.L.); (J.V.P.R.); (A.L.F.); (A.V.P.A.)
| | - Lucas Gasparello Viviani
- Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil; (L.G.V.); (A.T.d.A.)
| | - Lauro Miranda Lima
- Laboratory of Cellular Communication, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil; (N.C.d.S.F.); (L.M.L.); (J.V.P.R.); (A.L.F.); (A.V.P.A.)
| | | | - João Victor Paiva Romano
- Laboratory of Cellular Communication, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil; (N.C.d.S.F.); (L.M.L.); (J.V.P.R.); (A.L.F.); (A.V.P.A.)
- Laboratory of Immunobiotechnology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
| | - Anderson Lage Fortunato
- Laboratory of Cellular Communication, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil; (N.C.d.S.F.); (L.M.L.); (J.V.P.R.); (A.L.F.); (A.V.P.A.)
| | - Rafael Ferreira Soares
- Laboratory of Applied Genomics and Bioinnovations, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil;
| | - Anael Viana Pinto Alberto
- Laboratory of Cellular Communication, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil; (N.C.d.S.F.); (L.M.L.); (J.V.P.R.); (A.L.F.); (A.V.P.A.)
| | - Jose Aguiar Coelho Neto
- National Institute of Industrial Property, Rio de Janeiro 20090-910, Brazil;
- Tijuca Campus, Veiga de Almeida University, Rio de Janeiro 20271-020, Brazil
| | - Luiz Anastacio Alves
- Laboratory of Cellular Communication, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Brazil; (N.C.d.S.F.); (L.M.L.); (J.V.P.R.); (A.L.F.); (A.V.P.A.)
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Xu J, Li T, Huang WE, Zhou NY. Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene. Appl Environ Microbiol 2024:e0143623. [PMID: 38709097 DOI: 10.1128/aem.01436-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems.IMPORTANCEAs a result of human activities, various nitroaromatic pollutants continue to enter the biosphere with poor degradability, and dioxygenation is an important kickoff step to remove toxic nitro-groups and convert them into degradable products. The biodegradation of many nitroarenes has been reported over the decades; however, many others still lack corresponding enzymes to initiate their degradation. Although rieske non-heme dioxygenase family enzymes play extraordinarily important roles in the aerobic biodegradation of various nitroaromatic pollutants, prediction of their substrate specificity is difficult. This work greatly improved the catalytic activity of dioxygenase against 2,4-dichloronitrobenzene by computer-aided semi-rational design, paving a new way for the evolution strategy of nitroarene dioxygenase. This study highlights the potential for using enzyme structure-function information with computational pre-screening methods to rapidly tailor the catalytic functions of enzymes toward poorly biodegradable contaminants.
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Affiliation(s)
- Jia Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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31
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Zeng J, Qian Y. Adaptive lambda schemes for efficient relative binding free energy calculation. J Comput Chem 2024; 45:855-862. [PMID: 38153254 DOI: 10.1002/jcc.27287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/13/2023] [Accepted: 12/03/2023] [Indexed: 12/29/2023]
Abstract
The relative free energy perturbation (RFEP) calculation is one of the most theoretically sound computational chemistry approaches for the binding affinity prediction. However, its application is often hindered by the complexity of the calculation choices and the requirement of expertise in the field. Improper lambda scheme of RFEP may result in deviations from an accurate description of the perturbation process and is prone to erroneous affinity predictions. To address such challenges, an automated adaptive lambda method is proposed where the adaptive lambda schemes are obtained through a split-and-merge algorithm based on the pilot runs. The newly established workflow along with a series of improvements to the perturbation settings increases the consistency of the RFEP calculation results. Comparing the pilot and adaptive lambda schemes, the latter demonstrated improvements in convergence and reproducibility and lowered the mean unsigned error and the root-mean-square error. Overall, the adaptive lambda method is a reliable and robust choice to predict small molecule relative binding free energy and can be capitalized to benefit routine RFEP calculations for drug discovery projects.
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Affiliation(s)
- Jin Zeng
- AIxplorerBio Biotech Co., Ltd., Jiaxing, Zhejiang Province, China
| | - Yue Qian
- Viva Biotech (Shanghai) Ltd., Shanghai, China
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32
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Mukhametgalieva A, Mir SA, Shaihutdinova Z, Masson P. Human Plasma Butyrylcholinesterase Hydrolyzes Atropine: Kinetic and Molecular Modeling Studies. Molecules 2024; 29:2140. [PMID: 38731631 PMCID: PMC11085540 DOI: 10.3390/molecules29092140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
The participation of butyrylcholinesterase (BChE) in the degradation of atropine has been recurrently addressed for more than 70 years. However, no conclusive answer has been provided for the human enzyme so far. In the present work, a steady-state kinetic analysis performed by spectrophotometry showed that highly purified human plasma BChE tetramer slowly hydrolyzes atropine at pH 7.0 and 25 °C. The affinity of atropine for the enzyme is weak, and the observed kinetic rates versus the atropine concentration was of the first order: the maximum atropine concentration in essays was much less than Km. Thus, the bimolecular rate constant was found to be kcat/Km = 7.7 × 104 M-1 min-1. Rough estimates of catalytic parameters provided slow kcat < 40 min-1 and high Km = 0.3-3.3 mM. Then, using a specific organophosphoryl agent, echothiophate, the time-dependent irreversible inhibition profiles of BChE for hydrolysis of atropine and the standard substrate butyrylthiocholine (BTC) were investigated. This established that both substrates are hydrolyzed at the same site, i.e., S198, as for all substrates of this enzyme. Lastly, molecular docking provided evidence that both atropine isomers bind to the active center of BChE. However, free energy perturbations yielded by the Bennett Acceptance Ratio method suggest that the L-atropine isomer is the most reactive enantiomer. In conclusion, the results provided evidence that plasma BChE slowly hydrolyzes atropine but should have no significant role in its metabolism under current conditions of medical use and even under administration of the highest possible doses of this antimuscarinic drug.
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Affiliation(s)
- Aliya Mukhametgalieva
- Laboratory of Biochemical Neuropharmacology, Kazan Federal University, Kremlevskaya Str. 18, 420008 Kazan, Russia; (A.M.); (Z.S.)
| | - Showkat Ahmad Mir
- School of Life Sciences, Sambalpur University, Jyotivihar, Burla 768019, India;
| | - Zukhra Shaihutdinova
- Laboratory of Biochemical Neuropharmacology, Kazan Federal University, Kremlevskaya Str. 18, 420008 Kazan, Russia; (A.M.); (Z.S.)
| | - Patrick Masson
- Laboratory of Biochemical Neuropharmacology, Kazan Federal University, Kremlevskaya Str. 18, 420008 Kazan, Russia; (A.M.); (Z.S.)
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Kladova OA, Tyugashev TE, Miroshnikov AA, Novopashina DS, Kuznetsov NA, Kuznetsova AA. SNP-Associated Substitutions of Amino Acid Residues in the dNTP Selection Subdomain Decrease Polβ Polymerase Activity. Biomolecules 2024; 14:547. [PMID: 38785954 PMCID: PMC11117729 DOI: 10.3390/biom14050547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
In the cell, DNA polymerase β (Polβ) is involved in many processes aimed at maintaining genome stability and is considered the main repair DNA polymerase participating in base excision repair (BER). Polβ can fill DNA gaps formed by other DNA repair enzymes. Single-nucleotide polymorphisms (SNPs) in the POLB gene can affect the enzymatic properties of the resulting protein, owing to possible amino acid substitutions. For many SNP-associated Polβ variants, an association with cancer, owing to changes in polymerase activity and fidelity, has been shown. In this work, kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring polymorphic variants G274R, G290C, and R333W. Previously, the amino acid substitutions at these positions have been found in various types of tumors, implying a specific role of Gly-274, Gly-290, and Arg-333 in Polβ functioning. All three polymorphic variants had reduced polymerase activity. Two substitutions-G274R and R333W-led to the almost complete disappearance of gap-filling and primer elongation activities, a decrease in the deoxynucleotide triphosphate-binding ability, and a lower polymerization constant, due to alterations of local contacts near the replaced amino acid residues. Thus, variants G274R, G290C, and R333W may be implicated in an elevated level of unrepaired DNA damage.
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Affiliation(s)
- Olga A. Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
| | - Timofey E. Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
| | | | - Daria S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
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Nardi AN, Olivieri A, D'Abramo M, Amadei A. A Theoretical-Computational Study of Phosphodiester Bond Cleavage Kinetics as a Function of the Temperature. Chemphyschem 2024; 25:e202300952. [PMID: 38372713 DOI: 10.1002/cphc.202300952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/20/2024]
Abstract
The hydrolysis of the phosphodiester bond is an important chemical reaction involved in several biological processes. Here, we study the cleavage of this bond by means of a theoretical-computational method in a model system, the dineopentyl phosphate. By such an approach, we reconstructed the kinetics and related thermodynamics of this chemical reaction along an isochore. In particular, we evaluated the kinetic constants of all the reaction steps within a wide range of temperatures, mostly corresponding to conditions where no experimental measures are available due to the extremely slow kinetics. Our results, in good agreement with the experimental data, show the robustness of our theoretical-computational methodology which can be easily extended to more complex systems.
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Affiliation(s)
| | - Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Andrea Amadei
- Department of Technological and Chemical Sciences, Tor Vergata University of Rome, Italy
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Meher RK, Mir SA, Singh K, Mukerjee N, Nayak B, Kumer A, Zughaibi TA, Khan MS, Tabrez S. Decoding dynamic interactions between EGFR-TKD and DAC through computational and experimental approaches: A novel breakthrough in lung melanoma treatment. J Cell Mol Med 2024; 28:e18263. [PMID: 38685671 PMCID: PMC11058330 DOI: 10.1111/jcmm.18263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/22/2024] [Accepted: 02/04/2024] [Indexed: 05/02/2024] Open
Abstract
In the quest for effective lung cancer treatments, the potential of 3,6-diaminoacridine-9-carbonitrile (DAC) has emerged as a game changer. While DAC's efficacy against glioblastoma is well documented, its role in combating lung cancer has remained largely untapped. This study focuses on CTX-1, exploring its interaction with the pivotal EGFR-TKD protein, a crucial target in lung cancer therapeutics. A meticulous molecular docking analysis revealed that CTX-1 exhibits a noteworthy binding affinity of -7.9 kcal/mol, challenging Erlotinib, a conventional lung cancer medication, which displayed a binding affinity of -7.3 kcal/mol. For a deeper understanding of CTX-1's molecular mechanics, this study employed rigorous 100-ns molecular dynamics simulations, demonstrating CTX-1's remarkable stability in comparison with erlotinib. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method further corroborated these results, with CTX-1 showing a free binding energy of -105.976 ± 1.916 kJ/mol. The true prowess of CTX-1 was tested against diverse lung cancer cell lines, including A549, Hop-62 and H-1299. CTX-1 not only significantly outperformed erlotinib in anticancer activity but also exhibited a spectrum of therapeutic effects. It effectively diminished cancer cell viability, induced DNA damage, halted cell cycle progression, generated reactive oxygen species (ROS), impaired mitochondrial transmembrane potential, instigated apoptosis and successfully inhibited EGFR-TKD. This study not only underscores the potential of CTX-1 a formidable contender in lung cancer treatment but also marks a paradigm shift in oncological therapeutics, offering new horizons in the fight against this formidable disease.
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Affiliation(s)
| | | | - Kritika Singh
- Offenburg University of Applied SciencesOffenburgGermany
| | - Nobendu Mukerjee
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical SciencesChennaiIndia
- Department of Health SciencesNovel Global Community Educational FoundationHebershamNew South WalesAustralia
| | - Binata Nayak
- School of Life SciencesSambalpur UniversityBurlaOdishaIndia
| | - Ajoy Kumer
- Department of ChemistryCollege of Arts and Sciences, IUBAT‐International University of Business Agriculture and TechnologyDhakaBangladesh
| | - Torki A. Zughaibi
- King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical SciencesKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Mohd Shahnawaz Khan
- Department of BiochemistryCollege of Science, King Saud UniversityRiyadhSaudi Arabia
| | - Shams Tabrez
- King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical SciencesKing Abdulaziz UniversityJeddahSaudi Arabia
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36
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Qais FA, Furkan M, Altaf M, Ahmad I, Khan RH. Exploring the mechanism of interaction of glipizide with DNA: Combined in vitro and bioinformatics approach. Int J Biol Macromol 2024; 267:131573. [PMID: 38614188 DOI: 10.1016/j.ijbiomac.2024.131573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
DNA, vital for biological processes, encodes hereditary data for protein synthesis, shaping cell structure and function. Since revealing its structure, DNA has become a target for various therapeutically vital molecules, spanning antidiabetic to anticancer drugs. These agents engage with DNA-associated proteins, DNA-RNA hybrids, or bind directly to the DNA helix, triggering diverse downstream effects. These interactions disrupt vital enzymes and proteins essential for maintaining cell structure and function. Analysing drug-DNA interactions has significantly advanced our understanding of drug mechanisms. Glipizide, an antidiabetic drug, is known to cause DNA damage in adipocytes. However, its extract mechanism of DNA interaction is unknown. This study delves into the interaction between glipizide and DNA utilizing various biophysical tools and computational technique to gain insights into the interaction mechanism. Analysis of UV-visible and fluorescence data reveals the formation of complex between DNA and glipizide. The binding affinity of glipizide to DNA was of moderate strength. Examination of thermodynamic parameters at different temperatures suggests that the binding was entropically spontaneous and energetically favourable. Various experiments such as thermal melting assays, viscosity measurement, and dye displacement assays confirmed the minor grove nature of binding of glipizide with DNA. Molecular dynamics studies confirmed the glipizide forms stable complex with DNA when simulated by mimicking the physiological conditions. The binding was mainly favoured by hydrogen bonds and glipizide slightly reduced nucleotide fluctuations of DNA. The study deciphers the mechanism of interaction of glipizide with DNA at molecular levels.
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Affiliation(s)
- Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Furkan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Mohammad Altaf
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, 11451 Riyadh, Saudi Arabia
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP, India.
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37
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Abdullah KM, Sharma G, Qais FA, Khan I, Takkar S, Kaushal JB, Kanchan RK, Sarwar T, Chakravarti B, Siddiqui JA. Hydroxychloroquine interaction with phosphoinositide 3-kinase modulates prostate cancer growth in bone microenvironment: In vitro and molecular dynamics based approach. Int J Biol Macromol 2024; 266:130912. [PMID: 38513896 DOI: 10.1016/j.ijbiomac.2024.130912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Patients with advanced prostate cancer (PCa) are more likely to develop bone metastases. Tumor cells thrive in the bone microenvironment, interacting with osteoblasts and osteoclasts. Given the PI3K/AKT pathway's metastatic potential and signal integration's ability to modulate cell fates in PCa development, drugs targeting this system have great therapeutic promise. Hydroxychloroquine (HCQ) is an anti-malarial medication commonly used to treat clinical conditions such as rheumatology and infectious disorders. We explored the anti-neoplastic effect of HCQ on PC3 and C4-2B cell lines in the bone microenvironment. Interestingly, HCQ treatment substantially decreases the viability, proliferation, and migration potential of PCa cells in the bone microenvironment. HCQ induces apoptosis and cell cycle arrest, even in the presence of osteoblast-secreted factors. Mechanistically, HCQ inhibited the activity of the PI3K/AKT signaling pathway, which ultimately regulates the proliferation and migration of PCa cells in the bone. The binding energy for docking HCQ with PI3K was -6.7 kcal/mol, and the complex was stabilized by hydrogen bonds, hydrophobic forces, and van der Waals forces. Molecular simulations further validated the structural integrity of the HCQ-PI3K complex without altering PI3K's secondary structure. Our findings underscore the efficacy of HCQ as a potential therapeutic agent in treating PCa.
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Affiliation(s)
- K M Abdullah
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha NE-68198, USA
| | - Gunjan Sharma
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha NE-68198, USA
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Imran Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha NE-68198, USA
| | - Simran Takkar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha NE-68198, USA
| | - Jyoti B Kaushal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha NE-68198, USA
| | - Ranjana K Kanchan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha NE-68198, USA
| | - Tarique Sarwar
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, 51452, Saudi Arabia
| | - Bandana Chakravarti
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha NE-68198, USA.
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38
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Meher RK, Mir SA, Anisetti SS. In silico and in vitro investigation of dual targeting Prima-1 MET as precision therapeutic against lungs cancer. J Biomol Struct Dyn 2024; 42:4169-4184. [PMID: 37272907 DOI: 10.1080/07391102.2023.2219323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
This study emphasizes the explorations of binding of Prima-1MET with two targets, p53 a tumor suppressor protein, and tyrosine kinase of epidermal growth factor receptor. In silico investigations reveal that Prima-1MET showed robust binding with both targets. Molecular docking simulations demonstrated the binding affinity of Prima-1MET with p53 and tyrosine kinase was found to be -38.601 kJ/mol and -38.976 kJ/mol. In addition, the stability of Prima-1MET was explored by molecular dynamics simulation. Prima-1MET attains stability in the binding site of the respective protein till the simulation period is over. Moreover, the free binding energy ΔGbind was calculated by the molecular mechanics Poisson Boltzmann surface area method. The ΔGbind of Prima-1MET with tyrosine kinase was found to be -58.585 ± 0.327 kJ/mol and with p53 it was -35.910 ± 0.335 kJ/mol. Next, cytotoxicity of the Prima-1MET was evaluated using multiple cancer cell lines and the IC50 value were ranging between 4.5 and 30 μM. The cell death was identified by apoptosis assay. Further, the p53 and tyrosine kinase expression was monitored using immunofluorescence techniques, it was found Prima-1MET induces the expression of p53 protein and mimics the level of tyrosine kinase oncogenic target. Also, reactive oxygen species (ROS) and membrane potential activity of Prima-1MET was evaluated by using a lung cancer cell line. A significant decrease in intracellular ROS was observed and resulted in disruption of mitochondrial transmembrane potential. This study uncovers the underlying mechanism of Prima-1MET and could be helpful to design further leads against lung cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rajesh Kumar Meher
- Advance Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Department of Biotechnology and Bioinformatics, Sambalpur University, Burla, Odisha, India
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Sacramento MMA, Oliveira MB, Gomes JRB, Borges J, Freedman BR, Mooney DJ, Rodrigues JMM, Mano JF. Natural Polymer-Polyphenol Bioadhesive Coacervate with Stable Wet Adhesion, Antibacterial Activity, and On-Demand Detachment. Adv Healthc Mater 2024; 13:e2304587. [PMID: 38334308 DOI: 10.1002/adhm.202304587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Indexed: 02/10/2024]
Abstract
Medical adhesives are emerging as an important clinical tool as adjuvants for sutures and staples in wound closure and healing and in the achievement of hemostasis. However, clinical adhesives combining cytocompatibility, as well as strong and stable adhesion in physiological conditions, are still in demand. Herein, a mussel-inspired strategy is explored to produce adhesive coacervates using tannic acid (TA) and methacrylate pullulan (PUL-MA). TA|PUL-MA coacervates mainly comprise van der Waals forces and hydrophobic interactions. The methacrylic groups in the PUL backbone increase the number of interactions in the adhesives matrix, resulting in enhanced cohesion and adhesion strength (72.7 Jm-2), compared to the non-methacrylated coacervate. The adhesive properties are kept in physiologic-mimetic solutions (72.8 Jm-2) for 72 h. The photopolymerization of TA|PUL-MA enables the on-demand detachment of the adhesive. The poor cytocompatibility associated with the use of phenolic groups is here circumvented by mixing reactive oxygen species-degrading enzyme in the adhesive coacervate. This addition does not hamper the adhesive character of the materials, nor their anti-microbial or hemostatic properties. This affordable and straightforward methodology, together with the tailorable adhesivity even in wet environments, high cytocompatibility, and anti-bacterial activity, enables foresee TA|PUL-MA as a promising ready-to-use bioadhesive for biomedical applications.
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Affiliation(s)
- Margarida M A Sacramento
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Mariana B Oliveira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - José R B Gomes
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João Borges
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Benjamin R Freedman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
- Department of Orthopaedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - David J Mooney
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
| | - João M M Rodrigues
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João F Mano
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
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Abudurexiti A, Abdurahman A, Zhang R, Zhong Y, Lei Y, Qi S, Hou W, Ma X. Screening of α-Glucosidase Inhibitors in Cichorium glandulosum Boiss. et Huet Extracts and Study of Interaction Mechanisms. ACS OMEGA 2024; 9:19401-19417. [PMID: 38708260 PMCID: PMC11064185 DOI: 10.1021/acsomega.4c00699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 05/07/2024]
Abstract
Cichorium glandulosum Boiss. et Huet (CGB) extract has an α-glucosidase inhibitory effect (IC50 = 59.34 ± 0.07 μg/mL, positive control drug acarbose IC50 = 126.1 ± 0.02 μg/mL), but the precise enzyme inhibitors implicated in this process are not known. The screening of α-glucosidase inhibitors in CGB extracts was conducted by bioaffinity ultrafiltration, and six potential inhibitors (quercetin, lactucin, 3-O-methylquercetin, hyperoside, lactucopicrin, and isochlorogenic acid B) were screened as the precise inhibitors. The binding rate calculations and evaluation of enzyme inhibitory effects showed that lactucin and lactucopicrin exhibited the greatest inhibitory activities. Next, the inhibiting effects of the active components of CGB, lactucin and lactucopicrin, on α-glucosidase and their mechanisms were investigated through α-glucosidase activity assay, enzyme kinetics, multispectral analysis, and molecular docking simulation. The findings demonstrated that lactucin (IC50 = 52.76 ± 0.21 μM) and lactucopicrin (IC50 = 17.71 ± 0.64 μM) exhibited more inhibitory effects on α-glucosidase in comparison to acarbose (positive drug, IC50 = 195.2 ± 0.30 μM). Enzyme kinetic research revealed that lactucin inhibits α-glucosidase through a noncompetitive inhibition mechanism, while lactucopicrin inhibits it through a competitive inhibition mechanism. The fluorescence results suggested that lactucin and lactucopicrin effectively reduce the fluorescence of α-glucosidase by creating lactucin-α-glucosidase and lactucopicrin-α-glucosidase complexes through static quenching. Furthermore, the circular dichroism (CD) and Fourier transform infrared spectroscopy (FT-IR) analyses revealed that the interaction between lactucin or lactucopicrin and α-glucosidase resulted in a modification of the α-glucosidase's conformation. The findings from molecular docking and molecular dynamics simulations offer further confirmation that lactucopicrin has a robust binding affinity for certain residues located within the active cavity of α-glucosidase. Furthermore, it has a greater affinity for α-glucosidase compared to lactucin. The results validate the suppressive impact of lactucin and lactucopicrin on α-glucosidase and elucidate their underlying processes. Additionally, they serve as a foundation for the structural alteration of sesquiterpene derived from CGB, with the intention of using it for the management of diabetic mellitus.
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Affiliation(s)
| | | | - Rui Zhang
- School of Pharmacy, Xin Jiang Medical University, Urumqi 830054, China
| | - Yewei Zhong
- School of Pharmacy, Xin Jiang Medical University, Urumqi 830054, China
| | - Yi Lei
- School of Pharmacy, Xin Jiang Medical University, Urumqi 830054, China
| | - Shuwen Qi
- School of Pharmacy, Xin Jiang Medical University, Urumqi 830054, China
| | - Wenhui Hou
- School of Pharmacy, Xin Jiang Medical University, Urumqi 830054, China
| | - Xiaoli Ma
- School of Pharmacy, Xin Jiang Medical University, Urumqi 830054, China
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Chen X, Lu Z, Xiao J, Xia W, Pan Y, Xia H, Chen YH, Zhang H. Small-Molecule Inhibitors of TIPE3 Protein Identified through Deep Learning Suppress Cancer Cell Growth In Vitro. Cells 2024; 13:771. [PMID: 38727307 PMCID: PMC11082981 DOI: 10.3390/cells13090771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Tumor necrosis factor-α-induced protein 8-like 3 (TNFAIP8L3 or TIPE3) functions as a transfer protein for lipid second messengers. TIPE3 is highly upregulated in several human cancers and has been established to significantly promote tumor cell proliferation, migration, and invasion and inhibit the apoptosis of cancer cells. Thus, inhibiting the function of TIPE3 is expected to be an effective strategy against cancer. The advancement of artificial intelligence (AI)-driven drug development has recently invigorated research in anti-cancer drug development. In this work, we incorporated DFCNN, Autodock Vina docking, DeepBindBC, MD, and metadynamics to efficiently identify inhibitors of TIPE3 from a ZINC compound dataset. Six potential candidates were selected for further experimental study to validate their anti-tumor activity. Among these, three small-molecule compounds (K784-8160, E745-0011, and 7238-1516) showed significant anti-tumor activity in vitro, leading to reduced tumor cell viability, proliferation, and migration and enhanced apoptotic tumor cell death. Notably, E745-0011 and 7238-1516 exhibited selective cytotoxicity toward tumor cells with high TIPE3 expression while having little or no effect on normal human cells or tumor cells with low TIPE3 expression. A molecular docking analysis further supported their interactions with TIPE3, highlighting hydrophobic interactions and their shared interaction residues and offering insights for designing more effective inhibitors. Taken together, this work demonstrates the feasibility of incorporating deep learning and MD simulations in virtual drug screening and provides inhibitors with significant potential for anti-cancer drug development against TIPE3-.
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Affiliation(s)
- Xiaodie Chen
- Center for Cancer Immunology, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (X.C.); (Z.L.); (H.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Lu
- Center for Cancer Immunology, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (X.C.); (Z.L.); (H.X.)
| | - Jin Xiao
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (J.X.); (W.X.); (Y.P.)
| | - Wei Xia
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (J.X.); (W.X.); (Y.P.)
| | - Yi Pan
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (J.X.); (W.X.); (Y.P.)
| | - Houjun Xia
- Center for Cancer Immunology, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (X.C.); (Z.L.); (H.X.)
- Faculty of Pharmaceutical Sciences, Shenzhen University of Advanced Technology, Shenzhen 518055, China
| | - Youhai H. Chen
- Center for Cancer Immunology, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (X.C.); (Z.L.); (H.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Faculty of Pharmaceutical Sciences, Shenzhen University of Advanced Technology, Shenzhen 518055, China
| | - Haiping Zhang
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (J.X.); (W.X.); (Y.P.)
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42
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Peinado RDS, Saivish MV, Menezes GDL, Fulco UL, da Silva RA, Korostov K, Eberle RJ, Melo PA, Nogueira ML, Pacca CC, Arni RK, Coronado MA. The search for an antiviral lead molecule to combat the neglected emerging Oropouche virus. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100238. [PMID: 38745914 PMCID: PMC11090880 DOI: 10.1016/j.crmicr.2024.100238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Oropouche virus (OROV) is a member of the Peribunyaviridae family and the causative agent of a dengue-like febrile illness transmitted by mosquitoes. Although mild symptoms generally occur, complications such as encephalitis and meningitis may develop. A lack of proper diagnosis, makes it a potential candidate for new epidemics and outbreaks like other known arboviruses such as Dengue, Yellow Fever and Zika virus. The study of natural molecules as potential antiviral compounds is a promising alternative for antiviral therapies. Wedelolactone (WDL) has been demonstrated to inhibit some viral proteins and virus replication, making it useful to target a wide range of viruses. In this study, we report the in silico effects of WDL on the OROV N-terminal polymerase and its potential inhibitory effects on several steps of viral infection in mammalian cells in vitro, which revealed that WDL indeed acts as a potential inhibitor molecule against OROV infection.
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Affiliation(s)
- Rafaela dos Santos Peinado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP 15054-000, Brazil
| | - Marielena Vogel Saivish
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-100, Brazil
| | - Gabriela de Lima Menezes
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil
| | - Umberto Laino Fulco
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil
| | | | - Karolina Korostov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
| | - Raphael Josef Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf 40225, Germany
| | - Paulo A. Melo
- Departamento de Farmacologia Básica e Clínica - ICB, CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Maurício Lacerda Nogueira
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
- Sealy Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Carolina Colombelli Pacca
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP 15090-000, Brazil
| | - Raghuvir Krishnaswamy Arni
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP 15054-000, Brazil
| | - Mônika Aparecida Coronado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP 15054-000, Brazil
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich 52428, Germany
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Huang Y, Wan XW, Du YT, Feng Y, Yang LS, Liu YB, Chen T, Zhu Z, Xu YT, Wang CC. Norcantharidin Enhances the Antitumor Effect of 5-Fluorouracil by Inducing Apoptosis of Cervical Cancer Cells: Network Pharmacology, Molecular Docking, and Experimental Validation. Curr Issues Mol Biol 2024; 46:3906-3918. [PMID: 38785510 PMCID: PMC11120450 DOI: 10.3390/cimb46050242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
The high recurrence rate of cervical cancer is a leading cause of cancer deaths in women. 5-Fluorouracil (5-FU) is an antitumor drug used to treat many types of cancer, but its diminishing effectiveness and side effects limit its use. Norcantharidin (NCTD), a demethylated derivative of cantharidin, exhibits various biological activities. Here, we investigated whether NCTD could potentiate 5-FU to induce cervical cancer cell death. To assess the cell viability and synergistic effects of the drugs, cell counting kit-8 and colony formation assays were performed using HR-HPV-positive cervical cancer cell lines. Annexin V-FITC/PI staining and TUNEL assays were performed to confirm the induction of apoptosis. The synergistic effect of NCTD on the antitumor activity of 5-FU was analyzed using network pharmacology, molecular docking, and molecular dynamics simulations. Apoptosis-related proteins were examined using immunoblotting. The combination of NCTD and 5-FU was synergistic in cervical cancer cell lines. Network pharmacological analysis identified 10 common targets of NCTD and 5-FU for cervical cancer treatment. Molecular docking showed the strong binding affinity of both compounds with CA12, CASP9, and PTGS1. Molecular dynamics simulations showed that the complex system of both drugs with caspase-9 could be in a stable state. NCTD enhanced 5-FU-mediated cytotoxicity by activating apoptosis-related proteins. NCTD acts synergistically with 5-FU to inhibit cervical cancer cell proliferation. NCTD enhances 5-FU-induced apoptosis in cervical cancer cell lines via the caspase-dependent pathway.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Cheng-Cheng Wang
- GuiZhou University Medical College, Guiyang 550025, China; (Y.H.); (X.-W.W.); (Y.-T.D.); (Y.F.); (L.-S.Y.); (Y.-B.L.); (T.C.); (Z.Z.); (Y.-T.X.)
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44
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Zhang F, Zhang W, Yuwono JA, Wexler D, Fan Y, Zou J, Liang G, Sun L, Guo Z. Catalytic role of in-situ formed C-N species for enhanced Li 2CO 3 decomposition. Nat Commun 2024; 15:3393. [PMID: 38649349 PMCID: PMC11035688 DOI: 10.1038/s41467-024-47629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Sluggish kinetics of the CO2 reduction/evolution reactions lead to the accumulation of Li2CO3 residuals and thus possible catalyst deactivation, which hinders the long-term cycling stability of Li-CO2 batteries. Apart from catalyst design, constructing a fluorinated solid-electrolyte interphase is a conventional strategy to minimize parasitic reactions and prolong cycle life. However, the catalytic effects of solid-electrolyte interphase components have been overlooked and remain unclear. Herein, we systematically regulate the compositions of solid-electrolyte interphase via tuning electrolyte solvation structures, anion coordination, and binding free energy between Li ion and anion. The cells exhibit distinct improvement in cycling performance with increasing content of C-N species in solid-electrolyte interphase layers. The enhancement originates from a catalytic effect towards accelerating the Li2CO3 formation/decomposition kinetics. Theoretical analysis reveals that C-N species provide strong adsorption sites and promote charge transfer from interface to *CO22- during discharge, and from Li2CO3 to C-N species during charge, thereby building a bidirectional fast-reacting bridge for CO2 reduction/evolution reactions. This finding enables us to design a C-N rich solid-electrolyte interphase via dual-salt electrolytes, improving cycle life of Li-CO2 batteries to twice that using traditional electrolytes. Our work provides an insight into interfacial design by tuning of catalytic properties towards CO2 reduction/evolution reactions.
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Affiliation(s)
- Fangli Zhang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia
- Institute for Superconducting & Electronic Materials, University of Wollongong, Faculty of Engineering and Information Science, Wollongong, NSW, 2500, Australia
| | - Wenchao Zhang
- School of Metallurgy and Environment, Central South University, Changsha, 410083, China.
- Chinese National Engineering Research Centre for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China.
| | - Jodie A Yuwono
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - David Wexler
- Institute for Superconducting & Electronic Materials, University of Wollongong, Faculty of Engineering and Information Science, Wollongong, NSW, 2500, Australia
| | - Yameng Fan
- Institute for Superconducting & Electronic Materials, University of Wollongong, Faculty of Engineering and Information Science, Wollongong, NSW, 2500, Australia
| | - Jinshuo Zou
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Gemeng Liang
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Liang Sun
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Zaiping Guo
- School of Chemical Engineering, The University of Adelaide, Adelaide, SA, 5005, Australia.
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45
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Wang TH, Shao HP, Zhao BQ, Zhai HL. Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain. J Chem Inf Model 2024; 64:3503-3523. [PMID: 38517012 DOI: 10.1021/acs.jcim.3c01730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continuously emerge, an increasing number of mutations are accumulating in the Spike protein receptor-binding domain (RBD) region. Through sequence analysis of various Variants of Concern (VOC), we identified that they predominantly fall within the ο lineage although recent variants introduce any novel mutations in the RBD. Molecular dynamics simulations were employed to compute the binding free energy of these variants with human Angiotensin-converting enzyme 2 (ACE2). Structurally, the binding interface of the ο RBD displays a strong positive charge, complementing the negatively charged binding interface of ACE2, resulting in a significant enhancement in the electrostatic potential energy for the ο variants. Although the increased potential energy is partially offset by the rise in polar solvation free energy, enhanced electrostatic potential contributes to the long-range recognition between the ο variant's RBD and ACE2. We also conducted simulations of glycosylated ACE2-RBD proteins. The newly emerged ο (JN.1) variant has added a glycosylation site at N-354@RBD, which significantly weakened its binding affinity with ACE2. Further, our interaction studies with three monoclonal antibodies across multiple SARS-CoV-2 strains revealed a diminished neutralization efficacy against the ο variants, primarily attributed to the electrostatic repulsion between the antibodies and RBD interface. Considering the characteristics of the ο variant and the trajectory of emerging strains, we propose that newly developed antibodies against SARS-CoV-2 RBD should have surfaces rich in negative potential and, postbinding, exhibit strong van der Waals interactions. These findings provide invaluable guidance for the formulation of future therapeutic strategies.
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Affiliation(s)
- Tian Hua Wang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hai Ping Shao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Bing Qiang Zhao
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
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46
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Wang J, Ren T, Sun G, Zhang N, Zhao L, Zhong R. Mechanism of AGT-Mediated Repair of dG-dC Cross-Links in the Drug Resistance to Chloroethylnitrosoureas: Molecular Docking, MD Simulation, and ONIOM (QM/MM) Investigation. J Chem Inf Model 2024; 64:3411-3429. [PMID: 38511939 DOI: 10.1021/acs.jcim.3c01958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Chloroethylnitrosoureas (CENUs) are important chemotherapies applied in the treatment of cancer. They exert anticancer activity by inducing DNA interstrand cross-links (ICLs) via the formation of two O6-alkylguanine intermediates, O6-chloroethylguanine (O6-ClEtG) and N1,O6-ethanoguanine (N1,O6-EtG). However, O6-alkylguanine-DNA alkyltransferase (AGT), a DNA-repair enzyme, can restore the O6-alkylguanine damages and thereby obstruct the formation of ICLs (dG-dC cross-link). In this study, the inhibitory mechanism of ICL formation was investigated to elucidate the drug resistance of CENUs mediated by AGT in detail. Based on the structures of the substrate-enzyme complexes obtained from docking and MD simulations, two ONIOM (QM/MM) models with different sizes of the QM region were constructed. The model with a larger QM region, which included the substrate (O6-ClEtG or N1,O6-EtG), a water molecule, and five residues (Tyr114, Cys145, His146, Lys165, and Glu172) in the active pocket of AGT, accurately described the repairing reaction and generated the results coinciding with the experimental outcomes. The repair process consists of two sequential steps: hydrogen transfer to form a thiolate anion on Cys145 and alkyl transfer from the O6 site of guanine (the rate-limiting step). The repair of N1,O6-EtG was more favorable than that of O6-ClEtG from both kinetics and thermodynamics aspects. Moreover, the comparison of the repairing process with the formation of dG-dC cross-link and the inhibition of AGT by O6-benzylguanine (O6-BG) showed that the presence of AGT could effectively interrupt the formation of ICLs leading to drug resistance, and the inhibition of AGT by O6-BG that was energetically more favorable than the repair of O6-ClEtG could not prevent the repair of N1,O6-EtG. Therefore, it is necessary to completely eliminate AGT activity before CENUs medication to enhance the chemotherapeutic effectiveness. This work provides reasonable explanations for the supposed mechanism of AGT-mediated drug resistance of CENUs and will assist in the development of novel CENU chemotherapies and their medication strategies.
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Affiliation(s)
- Jiaojiao Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Ting Ren
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Na Zhang
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
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47
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Li J, Amador C, Wilson MR. Computational predictions of interfacial tension, surface tension, and surfactant adsorption isotherms. Phys Chem Chem Phys 2024; 26:12107-12120. [PMID: 38587476 DOI: 10.1039/d3cp06170a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
All-atom (AA) molecular dynamics (MD) simulations are employed to predict interfacial tensions (IFT) and surface tensions (ST) of both ionic and non-ionic surfactants. The general AMBER force field (GAFF) and variants are examined in terms of their performance in predicting accurate IFT/ST, γ, values for chosen water models, together with the hydration free energy, ΔGhyd, and density, ρ, predictions for organic bulk phases. A strong correlation is observed between the quality of ρ and γ predictions. Based on the results, the GAFF-LIPID force field, which provides improved ρ predictions is selected for simulating surfactant tail groups. Good γ predictions are obtained with GAFF/GAFF-LIPID parameters and the TIP3P water model for IFT simulations at a water-triolein interface, and for GAFF/GAFF-LIPID parameters together with the OPC4 water model for ST simulations at a water-vacuum interface. Using a combined molecular dynamics-molecular thermodynamics theory (MD-MTT) framework, a mole fraction of C12E6 molecule of 1.477 × 10-6 (from the experimental critical micelle concentration, CMC) gives a simulated surface excess concentration, ΓMAX, of 76 C12E6 molecules at a 36 nm2 water-vacuum surface (3.5 × 10-10 mol cm-2), which corresponds to a simulated ST of 35 mN m-1. The results compare favourably with an experimental ΓMAX of C12E6 of 3.7 × 10-10 mol cm-2 (80 surfactants for a 36 nm2 surface) and experimental ST of C12E6 of 32 mN m-1 at the CMC.
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Affiliation(s)
- Jing Li
- Department of Chemistry, Durham University, Stockton Road, Durham, DH1 3LE, UK.
| | - Carlos Amador
- Newcastle Innovation Centre, Procter & Gamble Ltd, Newcastle Upon Tyne, NE12 9BZ, UK
| | - Mark R Wilson
- Department of Chemistry, Durham University, Stockton Road, Durham, DH1 3LE, UK.
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48
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Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem 2024; 7:84. [PMID: 38609430 PMCID: PMC11015012 DOI: 10.1038/s42004-024-01161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.
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Affiliation(s)
- Pedro D Manrique
- Physics Department, George Washington University, Washington, 20052, DC, USA.
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - César A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Rama K Kinthada
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Liam Herndon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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49
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Kladova OA, Tyugashev TE, Yakimov DV, Mikushina ES, Novopashina DS, Kuznetsov NA, Kuznetsova AA. The Impact of SNP-Induced Amino Acid Substitutions L19P and G66R in the dRP-Lyase Domain of Human DNA Polymerase β on Enzyme Activities. Int J Mol Sci 2024; 25:4182. [PMID: 38673769 PMCID: PMC11050361 DOI: 10.3390/ijms25084182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Base excision repair (BER), which involves the sequential activity of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases, is one of the enzymatic systems that preserve the integrity of the genome. Normal BER is effective, but due to single-nucleotide polymorphisms (SNPs), the enzymes themselves-whose main function is to identify and eliminate damaged bases-can undergo amino acid changes. One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA. SNPs can significantly affect the catalytic activity of an enzyme by causing an amino acid substitution. In this work, pre-steady-state kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring variants of Polβ that have the substitutions L19P and G66R in the dRP-lyase domain. Despite the substantial distance between the dRP-lyase domain and the nucleotidyltransferase active site, it was found that the capacity to form a complex with DNA and with an incoming dNTP is significantly altered by these substitutions. Therefore, the lower activity of the tested polymorphic variants may be associated with a greater number of unrepaired DNA lesions.
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Affiliation(s)
- Olga A. Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Timofey E. Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Denis V. Yakimov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena S. Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Daria S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (N.A.K.)
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50
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Summa CM, Langford DP, Dinshaw SH, Webb J, Rick SW. Calculations of Absolute Free Energies, Enthalpies, and Entropies for Drug Binding. J Chem Theory Comput 2024; 20:2812-2819. [PMID: 38538531 DOI: 10.1021/acs.jctc.4c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Computer simulation methods can aid in the rational design of drugs aimed at a specific target, typically a protein. The affinity of a drug for its target is given by the free energy of binding. Binding can be further characterized by the enthalpy and entropy changes in the process. Methods exist to determine exact free energies, enthalpies, and entropies that are dependent only on the quality of the potential model and adequate sampling of conformational degrees of freedom. Entropy and enthalpy are roughly an order of magnitude more difficult to calculate than the free energy. This project combines a replica exchange method for enhanced sampling, designed to be efficient for protein-sized systems, with free energy calculations. This approach, replica exchange with dynamical scaling (REDS), uses two conventional simulations at different temperatures so that the entropy can be found from the temperature dependence of the free energy. A third replica is placed between them, with a modified Hamiltonian that allows it to span the temperature range of the conventional replicas. REDS provides temperature-dependent data and aids in sampling. It is applied to the bromodomain-containing protein 4 (BRD4) system. We find that for the force fields used, the free energies are accurate but the entropies and enthalpies are not, with the entropic contribution being too positive. Reproducing the entropy and enthalpy of binding appears to be a more stringent test of the force fields than reproducing the free energy.
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Affiliation(s)
- Christopher M Summa
- Department of Computer Science, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Dillon P Langford
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Sam H Dinshaw
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Jennifer Webb
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
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