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Zeng H, Zhang S, Nie H, Li J, Yang J, Zhuang Y, Huang Y, Zeng M. Identification of FTY720 and COH29 as novel topoisomerase I catalytic inhibitors by experimental and computational studies. Bioorg Chem 2024; 147:107412. [PMID: 38696845 DOI: 10.1016/j.bioorg.2024.107412] [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: 03/16/2024] [Revised: 04/17/2024] [Accepted: 04/27/2024] [Indexed: 05/04/2024]
Abstract
The development of novel topoisomerase I (TOP1) inhibitors is crucial for overcoming the drawbacks and limitations of current TOP1 poisons. Here, we identified two potential TOP1 inhibitors, namely, FTY720 (a sphingosine 1-phosphate antagonist) and COH29 (a ribonucleotide reductase inhibitor), through experimental screening of known active compounds. Biological experiments verified that FTY720 and COH29 were nonintercalative TOP1 catalytic inhibitors that did not induce the formation of DNA-TOP1 covalent complexes. Molecular docking revealed that FTY720 and COH29 interacted favorably with TOP1. Molecular dynamics simulations revealed that FTY720 and COH29 could affect the catalytic domain of TOP1, thus resulting in altered DNA-binding cavity size. The alanine scanning and interaction entropy identified Arg536 as a hotspot residue. In addition, the bioinformatics analysis predicted that FTY720 and COH29 could be effective in treating malignant breast tumors. Biological experiments verified their antitumor activities using MCF-7 breast cancer cells. Their combinatory effects with TOP1 poisons were also investigated. Further, FTY720 and COH29 were found to cause less DNA damage compared with TOP1 poisons. The findings provide reliable lead compounds for the development of novel TOP1 catalytic inhibitors and offer new insights into the potential clinical applications of FTY720 and COH29 in targeting TOP1.
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Affiliation(s)
- Huang Zeng
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China.
| | - Shengyuan Zhang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Hua Nie
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Junhao Li
- Department of Physics and Astronomy, Uppsala University, Lägerhyddsvägen 1, SE-75121 Uppsala, Sweden
| | - Jiunlong Yang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Yuanbei Zhuang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Yingjie Huang
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
| | - Miao Zeng
- Institute of Hakka Medicinal Bio-resources, Medical College, Jiaying University, Meizhou 514031, China
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2
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Fukumoto Y, Kyono R, Shibukawa Y, Tanaka YK, Suzuki N, Ogra Y. Differential molecular mechanisms of substrate recognition by selenium methyltransferases, INMT and TPMT, in selenium detoxification and excretion. J Biol Chem 2024; 300:105599. [PMID: 38159853 PMCID: PMC10844679 DOI: 10.1016/j.jbc.2023.105599] [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: 09/15/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
It is known that the recommended dietary allowance of selenium (Se) is dangerously close to its tolerable upper intake level. Se is detoxified and excreted in urine as trimethylselenonium ion (TMSe) when the amount ingested exceeds the nutritional level. Recently, we demonstrated that the production of TMSe requires two methyltransferases: thiopurine S-methyltransferase (TPMT) and indolethylamine N-methyltransferase (INMT). In this study, we investigated the substrate recognition mechanisms of INMT and TPMT in the Se-methylation reaction. Examination of the Se-methyltransferase activities of two paralogs of INMT, namely, nicotinamide N-methyltransferase and phenylethanolamine N-methyltransferase, revealed that only INMT exhibited Se-methyltransferase activity. Consistently, molecular dynamics simulations demonstrated that dimethylselenide was preferentially associated with the active center of INMT. Using the fragment molecular orbital method, we identified hydrophobic residues involved in the binding of dimethylselenide to the active center of INMT. The INMT-L164R mutation resulted in a deficiency in Se- and N-methyltransferase activities. Similarly, TPMT-R152, which occupies the same position as INMT-L164, played a crucial role in the Se-methyltransferase activity of TPMT. Our findings suggest that TPMT recognizes negatively charged substrates, whereas INMT recognizes electrically neutral substrates in the hydrophobic active center embedded within the protein. These observations explain the sequential requirement of the two methyltransferases in producing TMSe.
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
| | - Rin Kyono
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yuka Shibukawa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yu-Ki Tanaka
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Noriyuki Suzuki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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Di Martino J, Arcieri M, Madeddu F, Pieroni M, Carotenuto G, Bottoni P, Botta L, Castrignanò T, Gabellone S, Saladino R. Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity. Int J Mol Sci 2023; 25:234. [PMID: 38203410 PMCID: PMC10778928 DOI: 10.3390/ijms25010234] [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: 10/30/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.
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Affiliation(s)
- Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Manuel Arcieri
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Francesco Madeddu
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Michele Pieroni
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Giovanni Carotenuto
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Paolo Bottoni
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Sofia Gabellone
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
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Aktaş E, Saygılı İ, Kahveci E, Tekbıyık Z, Özgentürk NÖ. Bioinformatic investigation of Nipah virus surface protein mutations: Molecular docking with Ephrin B2 receptor, molecular dynamics simulation, and structural impact analysis. Microbiol Immunol 2023; 67:501-513. [PMID: 37812043 DOI: 10.1111/1348-0421.13098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
The SARS-CoV-2 outbreak resulted in significant challenges and loss of life. The Nipah virus, known for its high infectivity and severity, was designated an emergency concern by the World Health Organization. To understand its mutations, the Nipah virus proteins were analyzed extensively, with a focus on the essential G and F proteins responsible for viral entry into host cells. Our bioinformatics analysis unveiled multiple mutations, including simultaneous mutations within a single sequence. Notably, the G273S mutation in the F protein was identified as a potential cause of structural damage, which carries significant implications for vaccine development. Comparing the docking scores of G and F proteins with the Ephrin B2 receptor, it was found that the Y228H mutation in the G protein and the D252G mutation in the F protein likely affect virus entry into host cells. Moreover, our investigation into stability and deformability highlighted the impact of the Y228H mutation in the G protein complex. Molecular dynamics simulations revealed increased flexibility and conformational changes in the G protein complex with the Y228H mutation compared with the known complex. Furthermore, evaluating the root mean square deviation variation demonstrated greater dynamic behavior in the G protein complex and the Ephrin B2 receptor complex. This comprehensive study provides valuable insights into Nipah virus mutations, their significance for vaccine development, and the importance of understanding protein complex behavior in drug discovery. The identified mutations, especially G273S and Y228H, hold crucial implications for future research and potential interventions against the Nipah virus.
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Affiliation(s)
- Emre Aktaş
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - İrem Saygılı
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Elif Kahveci
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Zeynep Tekbıyık
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Nehir Özdemir Özgentürk
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
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Eissa IH, Yousef RG, Elkady H, Elkaeed EB, Alsfouk AA, Husein DZ, Ibrahim IM, Radwan MM, Metwaly AM. A Theobromine Derivative with Anticancer Properties Targeting VEGFR-2: Semisynthesis, in silico and in vitro Studies. ChemistryOpen 2023; 12:e202300066. [PMID: 37803417 PMCID: PMC10558427 DOI: 10.1002/open.202300066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/23/2023] [Indexed: 10/08/2023] Open
Abstract
A computer-assisted drug design (CADD) approach was utilized to design a new acetamido-N-(para-fluorophenyl)benzamide) derivative of the naturally occurring alkaloid, theobromine, (T-1-APFPB), following the pharmacophoric features of VEGFR-2 inhibitors. The stability and reactivity of T-1-AFPB were assessed through density functional theory (DFT) calculations. Molecular docking assessments showed T-1-AFPB's potential to bind with and inhibit VEGFR-2. The precise binding of T-1-AFPB against VEGFR-2 with optimal energy was further confirmed through several molecular dynamics (MD) simulations, PLIP, MM-GBSA, and PCA studies. Then, T-1-AFPB (4-(2-(3,7-Dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-1-yl)acetamido)-N-(4-fluorophenyl)benzamide) was semi-synthesized and the in vitro assays showed its potential to inhibit VEGFR-2 with an IC50 value of 69 nM (sorafenib's IC50 was 56 nM) and to inhibit the growth of HepG2 and MCF-7 cancer cell lines with IC50 values of 2.24±0.02 and 3.26±0.02 μM, respectively. Moreover, T-1-AFPB displayed very high selectivity indices against normal Vero cell lines. Furthermore, T-1-AFPB induced early (from 0.72 to 19.12) and late (from 0.13 to 6.37) apoptosis in HepG2 cell lines. In conclusion, the combined computational and experimental approaches demonstrated the efficacy and safety of T-1-APFPB providing it as a promising lead VEGFR-2 inhibitor for further development aiming at cancer therapy.
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Affiliation(s)
- Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design DepartmentFaculty of Pharmacy (Boys)Al-Azhar UniversityCairo11884Egypt
| | - Reda G. Yousef
- Pharmaceutical Medicinal Chemistry & Drug Design DepartmentFaculty of Pharmacy (Boys)Al-Azhar UniversityCairo11884Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design DepartmentFaculty of Pharmacy (Boys)Al-Azhar UniversityCairo11884Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical SciencesCollege of PharmacyAlMaarefa UniversityRiyadh13713Saudi Arabia
| | - Aisha A. Alsfouk
- Department of Pharmaceutical SciencesCollege of PharmacyPrincess Nourah bint Abdulrahman UniversityP.O. Box 84428Riyadh11671Saudi Arabia
| | - Dalal Z. Husein
- Chemistry DepartmentFaculty of ScienceNew Valley UniversityEl-Kharja72511Egypt
| | | | - Mohamed M. Radwan
- National Center for Natural Products ResearchUniversity of MississippiMississippiMS 38677USA
- Department of PharmacognosyFaculty of PharmacyAlexandria UniversityAlexandriaEgypt
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants DepartmentFaculty of Pharmacy (Boys)Al-Azhar UniversityCairo11884Egypt
- Biopharmaceutical Products Research DepartmentGenetic Engineering and Biotechnology Research InstituteCity of Scientific Research and Technological Applications (SRTA-City)AlexandriaEgypt
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6
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Zare F, Solhjoo A, Sadeghpour H, Sakhteman A, Dehshahri A. Structure-based virtual screening, molecular docking, molecular dynamics simulation and MM/PBSA calculations towards identification of steroidal and non-steroidal selective glucocorticoid receptor modulators. J Biomol Struct Dyn 2023; 41:7640-7650. [PMID: 36134594 DOI: 10.1080/07391102.2022.2123392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Glucocorticoids have been used in the treatment of many diseases including inflammatory and autoimmune diseases. Despite the wide therapeutic effects of synthetic glucocorticoids, the use of these compounds has been limited due to side effects such as osteoporosis, immunodeficiency, and hyperglycaemia. To this end, extensive studies have been performed to discover new glucocorticoid modulators with the aim of increasing affinity for the receptor and thus less side effects. In the present work, structure-based virtual screening was used for the identification of novel potent compounds with glucocorticoid effects. The molecules derived from ZINC database were screened on account of structural similarity with some glucocorticoid agonists as the template. Subsequently, molecular docking was performed on 200 selected compounds to obtain the best steroidal and non-steroidal conformations. Three compounds, namely ZINC_000002083318, ZINC_000253697499 and ZINC_000003845653, were selected with the binding energies of -11.5, -10.5, and -9.5 kcal/mol, respectively. Molecular dynamic simulations on superior structures were accomplished with the glucocorticoid receptor. Additionally, root mean square deviations, root mean square fluctuation, radius of gyration, hydrogen bonds, and binding-free energy analysis showed the binding stability of the proposed compounds compared to budesonide as an approved drug. The results demonstrated that all the compounds had suitable binding stability compared to budesonide, while ZINC_000002083318 showed a tighter binding energy compared to the other compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fateme Zare
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Sadeghpour
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Dehshahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Santos JRC, Abreu PE, Marques JMC. Aggregation patterns of curcumin and piperine mixtures in different polar media. Phys Chem Chem Phys 2023; 25:19899-19910. [PMID: 37458414 DOI: 10.1039/d3cp00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
This work reports a thorough molecular dynamics investigation on the aggregation patterns of curcumin and piperine in water, ethanol and a mixture of both solvents. The low solubility of curcumin in water results in a rapid formation of very stable dimers for both keto and enol tautomers. In agreement with a higher solubility, piperine molecules move closer and farther apart several times during the simulation, which indicates the formation of a less stable dimer in water. In contrast, both curcumin and piperine are soluble in ethanol and, thus, dimers can hardly be formed in this media. In comparison with a pure-water solvent, a 30 : 70 mixture of ethanol and water significantly reduces the probability of formation of most dimers of curcumin and piperine molecules. The simulations show that larger clusters may be complex structures, but the formation of stacks (in the case of piperine and enol tautomer of curcumin) and cages (when the keto tautomer of curcumin is involved) are not rare. Furthermore, it is shown that each single molecule presents a certain degree of mobility in the cluster, especially on the surface, but without leading to dissociation.
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Affiliation(s)
- J R C Santos
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| | - P E Abreu
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| | - J M C Marques
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
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8
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Pieroni M, Madeddu F, Di Martino J, Arcieri M, Parisi V, Bottoni P, Castrignanò T. MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories. Int J Mol Sci 2023; 24:11671. [PMID: 37511429 PMCID: PMC10380688 DOI: 10.3390/ijms241411671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand-receptor binding interactions (lrbi) to be studied. In this study, we present MD-ligand-receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand-receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand-receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.
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Affiliation(s)
- Michele Pieroni
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Francesco Madeddu
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s.n.c., 01100 Viterbo, Italy
| | - Manuel Arcieri
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Valerio Parisi
- Department of Physics, "Sapienza" University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Paolo Bottoni
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s.n.c., 01100 Viterbo, Italy
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9
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Méndez-Álvarez D, Torres-Rojas MF, Lara-Ramirez EE, Marchat LA, Rivera G. Ligand-Based Virtual Screening, Molecular Docking, and Molecular Dynamic Simulations of New β-Estrogen Receptor Activators with Potential for Pharmacological Obesity Treatment. Molecules 2023; 28:molecules28114389. [PMID: 37298864 DOI: 10.3390/molecules28114389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Obesity is a pandemic and a serious health problem in developed and undeveloped countries. Activation of estrogen receptor beta (ERβ) has been shown to promote weight loss without modifying caloric intake, making it an attractive target for developing new drugs against obesity. This work aimed to predict new small molecules as potential ERβ activators. A ligand-based virtual screening of the ZINC15, PubChem, and Molport databases by substructure and similarity was carried out using the three-dimensional organization of known ligands as a reference. A molecular docking screening of FDA-approved drugs was also conducted as a repositioning strategy. Finally, selected compounds were evaluated by molecular dynamic simulations. Compounds 1 (-24.27 ± 0.34 kcal/mol), 2 (-23.33 ± 0.3 kcal/mol), and 6 (-29.55 ± 0.51 kcal/mol) showed the best stability on the active site in complex with ERβ with an RMSD < 3.3 Å. RMSF analysis showed that these compounds do not affect the fluctuation of the Cα of ERβ nor the compactness according to the radius of gyration. Finally, an in silico evaluation of ADMET showed they are safe molecules. These results suggest that new ERβ ligands could be promising molecules for obesity control.
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Affiliation(s)
- Domingo Méndez-Álvarez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Maria F Torres-Rojas
- Laboratorio de Biomedicina Molecular 2, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México 07320, Mexico
| | - Edgar E Lara-Ramirez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Laurence A Marchat
- Laboratorio de Biomedicina Molecular 2, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México 07320, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
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Nanoscale Iron-Based Metal-Organic Frameworks: Incorporation of Functionalized Drugs and Degradation in Biological Media. Int J Mol Sci 2023; 24:ijms24043362. [PMID: 36834775 PMCID: PMC9965190 DOI: 10.3390/ijms24043362] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Metal-organic frameworks (MOFs) attract growing interest in biomedical applications. Among thousands of MOF structures, the mesoporous iron(III) carboxylate MIL-100(Fe) (MIL stands for the Materials of Lavoisier Institute) is among the most studied MOF nanocarrier, owing to its high porosity, biodegradability, and lack of toxicity. Nanosized MIL-100(Fe) particles (nanoMOFs) readily coordinate with drugs leading to unprecedented payloads and controlled release. Here, we show how the functional groups of the challenging anticancer drug prednisolone influence their interactions with the nanoMOFs and their release in various media. Molecular modeling enabled predicting the strength of interactions between prednisolone-bearing or not phosphate or sulfate moieties (PP and PS, respectively) and the oxo-trimer of MIL-100(Fe) as well as understanding the pore filling of MIL-100(Fe). Noticeably, PP showed the strongest interactions (drug loading up to 30 wt %, encapsulation efficiency > 98%) and slowed down the nanoMOFs' degradation in simulated body fluid. This drug was shown to bind to the iron Lewis acid sites and was not displaced by other ions in the suspension media. On the contrary, PS was entrapped with lower efficiencies and was easily displaced by phosphates in the release media. Noticeably, the nanoMOFs maintained their size and faceted structures after drug loading and even after degradation in blood or serum after losing almost the totality of the constitutive trimesate ligands. Scanning electron microscopy with high annular dark field (STEM-HAADF) in conjunction with X-Ray energy-dispersive spectrometry (XEDS) was a powerful tool enabling the unraveling of the main elements to gain insights on the MOF structural evolution after drug loading and/or upon degradation.
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11
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Kulkarni S, Singh Y, Biharee A, Bhatia N, Monga V, Thareja S. Molecular docking, 3D-QSAR and simulation studies for identifying pharmacophoric features of indole derivatives as 17β-hydroxysteroid dehydrogenase type 5 (17β-HSD5) inhibitors. J Biomol Struct Dyn 2023; 41:12668-12685. [PMID: 36744535 DOI: 10.1080/07391102.2023.2175265] [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: 12/08/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023]
Abstract
Excess of androgens leads to various diseases such as Poly-Cystic Ovarian Syndrome, Prostate Cancer, Hirsutism, Obesity and Acne. 17β-Hydroxysteroid Dehydrogenase type 5 (17β-HSD5) converts androstenedione into testosterone peripherally, thereby significantly contributing to the development of these diseases. Indole-bearing scaffolds are reported as potential 17β-HSD5 inhibitors for the manifestation of diseases arising due to androgen excess. In the present work, we have extensively performed a combination of molecular docking, Gaussian field-based 3D-QSAR, Pharmacophore mapping and MD-simulation studies (100 ns) to identify the pharmacophoric features of indole-based compounds as potent 17β-HSD5 inhibitors. Molecular simulation studies of the most potent compound in the binding pocket of enzyme revealed that the compound 11 was stable in the binding pocket and showed good binding affinity through interactions with various residues of active site pocket. The Molecular mechanics Generalized Born surface area continuum solvation (MM/GBSA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations revealed that the compound 11 possessed a free binding energy of -36.36 kcal/mol and -7.00 kcal/mol, respectively, which was better as compared to reference compound Desmethyl indomethacin (DES). The developed pharmacophore will be helpful to design novel indole-based molecules as potent 17β-HSD5 inhibitors for the treatment of various androgenic disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swanand Kulkarni
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Yogesh Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Avadh Biharee
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Neha Bhatia
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab, India
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Pedron FN, Messias A, Zeida A, Roitberg AE, Estrin DA. Novel Lennard-Jones Parameters for Cysteine and Selenocysteine in the AMBER Force Field. J Chem Inf Model 2023; 63:595-604. [PMID: 36630702 DOI: 10.1021/acs.jcim.2c01104] [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: 01/13/2023]
Abstract
Cysteine is a common amino acid with a thiol group that plays a pivotal role in a variety of scenarios in redox biochemistry. In contrast, selenocysteine, the 21st amino acid, is only present in 25 human proteins. Classical force-field parameters for cysteine and selenocysteine are still scarce. In this context, we present a methodology to obtain Lennard-Jones parameters for cysteine and selenocysteine in different physiologically relevant oxidation and protonation states. The new force field parameters obtained in this work are available at https://github.com/MALBECC/AMBER-parameters-database. The parameters were adjusted to reproduce water radial distribution functions obtained by density functional theory ab initio molecular dynamics. We validated the results by evaluating the impact of the choice of parameters on the structure and dynamics in classical molecular dynamics simulations of representative proteins containing catalytic cysteine/selenocysteine residues. There are significant changes in protein structure and dynamics depending on the parameters choice, specifically affecting the residues close to the catalytic sites.
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Affiliation(s)
- Federico N Pedron
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Ari Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, 11800 Montevideo, Uruguay
| | - Adrián E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
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Madeddu F, Di Martino J, Pieroni M, Del Buono D, Bottoni P, Botta L, Castrignanò T, Saladino R. Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor. Int J Mol Sci 2022; 23:ijms232314652. [PMID: 36498979 PMCID: PMC9737192 DOI: 10.3390/ijms232314652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Human Topoisomerase I (hTop1p) is a ubiquitous enzyme that relaxes supercoiled DNA through a conserved mechanism involving transient breakage, rotation, and binding. Htop1p is the molecular target of the chemotherapeutic drug camptothecin (CPT). It causes the hTop1p-DNA complex to slow down the binding process and clash with the replicative machinery during the S phase of the cell cycle, forcing cells to activate the apoptotic response. This gives hTop1p a central role in cancer therapy. Recently, two artesunic acid derivatives (compounds c6 and c7) have been proposed as promising inhibitors of hTop1p with possible antitumor activity. We used several computational approaches to obtain in silico confirmations of the experimental data and to form a comprehensive dynamic description of the ligand-receptor system. We performed molecular docking analyses to verify the ability of the two new derivatives to access the enzyme-DNA interface, and a classical molecular dynamics simulation was performed to assess the capacity of the two compounds to maintain a stable binding pose over time. Finally, we calculated the noncovalent interactions between the two new derivatives and the hTop1p receptor in order to propose a possible inhibitory mechanism like that adopted by CPT.
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Affiliation(s)
- Francesco Madeddu
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Michele Pieroni
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Davide Del Buono
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Paolo Bottoni
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence:
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
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Novel inhibitors of the main protease enzyme of SARS-CoV-2 identified via molecular dynamics simulation-guided in vitro assay. Bioorg Chem 2021; 111:104862. [PMID: 33862474 PMCID: PMC8007184 DOI: 10.1016/j.bioorg.2021.104862] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/21/2021] [Indexed: 01/18/2023]
Abstract
For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, 3CLpro, which is critical for viral replication. We employ explicit solvent molecular dynamics simulations of about 150 compounds docked into 3CLpro’s binding site and that had emerged as good main protease ligands from our previous in silico screening of over 1.2 million compounds. By incoporating protein dynamics and applying a range of structural descriptors, such as the ability to form specific contacts with the catalytic dyad residues of 3CLpro and the structural fluctuations of the ligands in the binding site, we are able to further refine our compound selection. Fourteen compounds including estradiol shown to be the most promising based on our calculations were procured and screened against recombinant 3CLpro in a fluorescence assay. Eight of these compounds have significant activity in inhibiting the SARS-CoV-2 main protease. Among these are corilagin, a gallotannin, and lurasidone, an antipsychotic drug, which emerged as the most promising natural product and drug, respectively, and might thus be candidates for drug repurposing for the treatment of COVID-19. In addition, we also tested the inhibitory activity of testosterone, and our results reveal testosterone as possessing moderate inhibitory potency against the 3CLpro enzyme, which may thus provide an explanation why older men are more severely affected by COVID-19.
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