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Kula S, Kalarus P, Kaźmierski Ł, Biernasiuk A, Krawczyk P. The Influence of the Functional Group on the Physicochemical and Biological Properties of New Phenanthro[9,10-d]-Imidazole Derivatives. Molecules 2024; 29:4703. [PMID: 39407631 PMCID: PMC11477550 DOI: 10.3390/molecules29194703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 09/27/2024] [Accepted: 09/29/2024] [Indexed: 10/20/2024] Open
Abstract
The search for safe, cheap, and repeatable diagnostic methods is a fundamental research goal. Currently, great hope is placed on fluorescence imaging. However, the development of this method mainly depends on efficient fluorescent probes. Designing and obtaining new probes with potential applications in fluorescence imaging is very difficult because compounds of this type must meet several requirements related to their properties. Therefore, this article attempted to obtain and study new phenanthro[9,10-d]-imidazole derivatives (PK1-PK3) with potential application as fluorescent probes for fluorescence imaging. The main goal of the work was to assess the effect of two functional groups (such as the formyl group (PK2) and rhodanine-3-acetic acid (PK3)) on selected physicochemical properties and possibilities of practical application of the considered compounds. The conducted studies proved that the influence of the functional group is significant, as it causes a bathochromic shift in both absorption and emission results (by the order PK1 < PK2 < PK3). Moreover, all compounds could stain live cells cultured in vitro. The staining efficiency was not affected by the cell line, thanks to which we obtained the correct staining of both mouse and human cell lines. PK3 was the most attractive of the tested compounds due to its staining potential of live cells and retention after fixation. Our results also showed some antibacterial and antifungal activity of the newly synthesized compounds (PK1-PK3). Among them, PK3 showed the highest antimicrobial effect, especially against Gram-positive bacteria.
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Affiliation(s)
- Slawomir Kula
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9 St., 40-007 Katowice, Poland;
| | - Paweł Kalarus
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia, Szkolna 9 St., 40-007 Katowice, Poland;
| | - Łukasz Kaźmierski
- Department of Oncology, Radiotherapy and Oncological, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, M. Curie Skłodowskiej 9, 85-094 Bydgoszcz, Poland;
| | - Anna Biernasiuk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Przemysław Krawczyk
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950 Bydgoszcz, Poland;
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2
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Lokhandwala J, Matlack JK, Smalley TB, Miner RE, Tran TH, Binning JM. Structural basis for FN3K-mediated protein deglycation. Structure 2024; 32:1711-1724.e5. [PMID: 39173621 PMCID: PMC11455621 DOI: 10.1016/j.str.2024.07.018] [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: 02/16/2024] [Revised: 06/05/2024] [Accepted: 07/28/2024] [Indexed: 08/24/2024]
Abstract
Protein glycation is a universal, non-enzymatic modification that occurs when a sugar covalently attaches to a primary amine. These spontaneous modifications may have deleterious or regulatory effects on protein function, and their removal is mediated by the conserved metabolic kinase fructosamine-3-kinase (FN3K). Despite its crucial role in protein repair, we currently have a poor understanding of how FN3K engages or phosphorylates its substrates. By integrating structural biology and biochemistry, we elucidated the catalytic mechanism for FN3K-mediated protein deglycation. Our work identifies key amino acids required for binding and phosphorylating glycated substrates and reveals the molecular basis of an evolutionarily conserved protein repair pathway. Additional structural-functional studies revealed unique structural features of human FN3K as well as differences in the dimerization behavior and regulation of FN3K family members. Our findings improve our understanding of the structure of FN3K and its catalytic mechanism, which opens new avenues for therapeutically targeting FN3K.
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Affiliation(s)
- Jameela Lokhandwala
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jenet K Matlack
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Tracess B Smalley
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robert E Miner
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Chemical Biology PhD Program, University of South Florida, Tampa, FL 33612, USA
| | - Timothy H Tran
- Chemical Biology Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jennifer M Binning
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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3
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Zhou Y, Jiang Y, Chen SJ. SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening. J Chem Theory Comput 2024. [PMID: 39150889 DOI: 10.1021/acs.jctc.4c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
The growing interest in RNA-targeted drugs underscores the need for computational modeling of interactions between RNA molecules and small compounds. Having a reliable scoring function for RNA-ligand interactions is essential for effective computational drug screening. An ideal scoring function should not only predict the native pose for ligand binding but also rank the affinity of the binding for different ligands. However, existing scoring functions are primarily designed to predict the native binding modes for a given RNA-ligand pair and have not been thoroughly assessed for virtual screening purposes. In this paper, we introduce SPRank, a combination of machine-learning and knowledge-based scoring functions developed through a weighted iterative approach, specifically designed to tackle both binding mode prediction and virtual screening challenges. Our approach incorporates third-party docking software, such as rDock and AutoDock Vina, to sample flexible ligands against an ensemble of RNA structures, capturing the conformational flexibility of both the RNA and the ligand. Through rigorous testing, SPRank demonstrates improved performance compared to the tested scoring functions across four test sets comprising 122, 42, 55, and 71 nucleic acid-ligand complexes. Furthermore, SPRank exhibits improved performance in virtual screening tests targeting the HIV-1 TAR ensemble, which highlights its advantage in drug discovery. These results underscore the advantages of SPRank as a potentially promising tool for the RNA-targeted drug design. The source code of SPRank and the data sets are freely accessible at https://github.com/Vfold-RNA/SPRank.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211-7010, United States
| | - Yangwei Jiang
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211-7010, United States
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri-Columbia, Columbia, Missouri 65211-7010, United States
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4
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Riaz R, Parveen S, Shafiq N, Ali A, Rashid M. Virtual screening, ADME prediction, drug-likeness, and molecular docking analysis of Fagonia indica chemical constituents against antidiabetic targets. Mol Divers 2024:10.1007/s11030-024-10897-7. [PMID: 39012565 DOI: 10.1007/s11030-024-10897-7] [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: 03/27/2024] [Accepted: 05/13/2024] [Indexed: 07/17/2024]
Abstract
Fagonia indica from Zygophyllaceae family is a medicinal specie with significant antidiabetic potential. The present study aimed to investigate the in vitro antidiabetic activity of Fagonia indica crude extract followed by an in silico screening of its phytoconstituents. For this purpose, crude extract of Fagonia indica was prepared and divided in three different parts, i.e., n-hexane, ethyl acetate, and methanolic fraction. Based on in vitro outcomes, the phytochemical substances of Fagonia indica were virtually screened through a literature survey and a screening library of compounds (1-13) was prepared. The clinical potential of these novel drug candidates was assessed by applying an ADME screening profile. Findings of SwissADME indicators (Absorption, Distribution, Metabolism, and Excretion) for the compounds (1-13) presented relatively optimal physicochemical characteristics, drug-likeness, and medicinal chemistry. The antidiabetic action of these leading drug candidates was optimized through molecular docking analysis against 3 different human pancreatic α-amylase macromolecular targets with (PDB ID 1B2Y), (PDB ID 3BAJ), and (PDB ID: 3OLI) by applying Virtual Docker (Molegro MVD). Metformin was taken as a reference standard for the sake of comparison. In vitro antidiabetic evaluation gave good results with promising α-amylase inhibitory action in the form of IC50 values, as for n-hexane extract = 206.3 µM, ethyl acetate = 41.64 µM, and methanolic extract = 9.61 µM. According to in silico outcomes, all 13 phytoconstituents possess the best binding affinity with successful MolDock scores ranging from - 97.2003 to - 65.6877 kcal/mol and show a great number of binding interactions than native drug metformin. Therefore, the current work concluded that the diabetic inhibition prospective of extract and the compounds of Fagonia indica may contribute to being investigated as a new class of antidiabetic drug or drug-like candidate for further studies.
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Affiliation(s)
- Rabia Riaz
- Synthetic & Natural Product Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic & Natural Product Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan
| | - Nusrat Shafiq
- Synthetic & Natural Product Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan.
| | - Awais Ali
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 2300, Pakistan
| | - Maryam Rashid
- Synthetic & Natural Product Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, 38000, Pakistan
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Li C, Shao X, Zhang S, Wang Y, Jin K, Yang P, Lu X, Fan X, Wang Y. scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network. Cell Rep Med 2024; 5:101568. [PMID: 38754419 PMCID: PMC11228399 DOI: 10.1016/j.xcrm.2024.101568] [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: 05/05/2023] [Revised: 12/27/2023] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
Abstract
Cells respond divergently to drugs due to the heterogeneity among cell populations. Thus, it is crucial to identify drug-responsive cell populations in order to accurately elucidate the mechanism of drug action, which is still a great challenge. Here, we address this problem with scRank, which employs a target-perturbed gene regulatory network to rank drug-responsive cell populations via in silico drug perturbations using untreated single-cell transcriptomic data. We benchmark scRank on simulated and real datasets, which shows the superior performance of scRank over existing methods. When applied to medulloblastoma and major depressive disorder datasets, scRank identifies drug-responsive cell types that are consistent with the literature. Moreover, scRank accurately uncovers the macrophage subpopulation responsive to tanshinone IIA and its potential targets in myocardial infarction, with experimental validation. In conclusion, scRank enables the inference of drug-responsive cell types using untreated single-cell data, thus providing insights into the cellular-level impacts of therapeutic interventions.
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Affiliation(s)
- Chengyu Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China.
| | - Shujing Zhang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Yingchao Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Kaiyu Jin
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China
| | - Penghui Yang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China
| | - Xiaoyan Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China; Jinhua Institute of Zhejiang University, Jinhua 321299, China; Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
| | - Yi Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314103, China.
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Binmujlli MA. Radiological and Molecular Analysis of Radioiodinated Anastrozole and Epirubicin as Innovative Radiopharmaceuticals Targeting Methylenetetrahydrofolate Dehydrogenase 2 in Solid Tumors. Pharmaceutics 2024; 16:616. [PMID: 38794278 PMCID: PMC11126143 DOI: 10.3390/pharmaceutics16050616] [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: 02/20/2024] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
In the dynamic field of radiopharmaceuticals, innovating targeted agents for cancer diagnosis and therapy is crucial. Our study enriches this evolving landscape by evaluating the potential of radioiodinated anastrozole ([125I]anastrozole) and radioiodinated epirubicin ([125I]epirubicin) as targeting agents against MTHFD2-driven tumors. MTHFD2, which is pivotal in one-carbon metabolism, is notably upregulated in various cancers, presenting a novel target for radiopharmaceutical application. Through molecular docking and 200 ns molecular dynamics (MD) simulations, we assess the binding efficiency and stability of [125I]anastrozole and [125I]epirubicin with MTHFD2. Molecular docking illustrates that [125I]epirubicin has a superior binding free energy (∆Gbind) of -41.25 kJ/mol compared to -39.07 kJ/mol for [125I]anastrozole and -38.53 kJ/mol for the control ligand, suggesting that it has a higher affinity for MTHFD2. MD simulations reinforce this, showing stable binding, as evidenced by root mean square deviation (RMSD) values within a narrow range, underscoring the structural integrity of the enzyme-ligand complexes. The root mean square fluctuation (RMSF) analysis indicates consistent dynamic behavior of the MTHFD2 complex upon binding with [125I]anastrozole and [125I]epirubicin akin to the control. The radius of gyration (RG) measurements of 16.90 Å for MTHFD2-[125I]anastrozole and 16.84 Å for MTHFD2-[125I]epirubicin confirm minimal structural disruption upon binding. The hydrogen bond analysis reveals averages of two and three stable hydrogen bonds for [125I]anastrozole and [125I]epirubicin complexes, respectively, highlighting crucial stabilizing interactions. The MM-PBSA calculations further endorse the thermodynamic favorability of these interactions, with binding free energies of -48.49 ± 0.11 kJ/mol for [125I]anastrozole and -43.8 kJ/mol for MTHFD2-. The significant contribution of Van der Waals and electrostatic interactions to the binding affinities of [125I]anastrozole and [125I]epirubicin, respectively, underscores their potential efficacy for targeted tumor imaging and therapy. These computational findings lay the groundwork for the future experimental validation of [125I]anastrozole and [125I]epirubicin as MTHFD2 inhibitors, heralding a notable advancement in precision oncology tools. The data necessitate subsequent in vitro and in vivo assays to corroborate these results.
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Affiliation(s)
- Mazen Abdulrahman Binmujlli
- Department of Internal Medicine, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh 11623, Saudi Arabia
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Nevskaya AA, Purgatorio R, Borisova TN, Varlamov AV, Anikina LV, Obydennik AY, Nevskaya EY, Niso M, Colabufo NA, Carrieri A, Catto M, de Candia M, Voskressensky LG, Altomare CD. Nature-Inspired 1-Phenylpyrrolo[2,1- a]isoquinoline Scaffold for Novel Antiproliferative Agents Circumventing P-Glycoprotein-Dependent Multidrug Resistance. Pharmaceuticals (Basel) 2024; 17:539. [PMID: 38675499 PMCID: PMC11054433 DOI: 10.3390/ph17040539] [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: 03/06/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Previous studies have shown that some lamellarin-resembling annelated azaheterocyclic carbaldehydes and related imino adducts, sharing the 1-phenyl-5,6-dihydropyrrolo[2,1-a]isoquinoline (1-Ph-DHPIQ) scaffold, are cytotoxic in some tumor cells and may reverse multidrug resistance (MDR) mediated by P-glycoprotein (P-gp). Herein, several novel substituted 1-Ph-DHPIQ derivatives were synthesized which carry carboxylate groups (COOH, COOEt), nitrile (CN) and Mannich bases (namely, morpholinomethyl derivatives) in the C2 position, as replacements of the already reported aldehyde group. They were evaluated for antiproliferative activity in four tumor cell lines (RD, HCT116, HeLa, A549) and for the ability of selectively inhibiting P-gp-mediated MDR. Lipophilicity descriptors and molecular docking calculations helped us in rationalizing the structure-activity relationships in the P-gp inhibition potency of the investigated 1-Ph-DHPIQs. As a main outcome, a morpholinomethyl Mannich base (8c) was disclosed which proved to be cytotoxic to all the tested tumor cell lines in the low micromolar range (IC50 < 20 μM) and to inhibit in vitro the efflux pumps P-gp and MRP1 responsible for MDR, with IC50s of 0.45 and 12.1 μM, respectively.
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Affiliation(s)
- Alisa A. Nevskaya
- Organic Chemistry Department, RUDN University, 6 Miklukho-Maklaya St, Moscow 117198, Russia; (A.A.N.); (A.V.V.); (A.Y.O.); (L.G.V.)
| | - Rosa Purgatorio
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (R.P.); (M.N.); (N.A.C.); (A.C.); (M.d.C.)
| | - Tatiana N. Borisova
- Organic Chemistry Department, RUDN University, 6 Miklukho-Maklaya St, Moscow 117198, Russia; (A.A.N.); (A.V.V.); (A.Y.O.); (L.G.V.)
| | - Alexey V. Varlamov
- Organic Chemistry Department, RUDN University, 6 Miklukho-Maklaya St, Moscow 117198, Russia; (A.A.N.); (A.V.V.); (A.Y.O.); (L.G.V.)
| | - Lada V. Anikina
- Institute of Physiologically Active Compounds of the FSBIS of the Federal Research Center for Problems of Chemical Physics and Medicinal Chemistry of the RAS, 1 SevernyiProezd, Chernogolovk 142432, Russia;
| | - Arina Yu. Obydennik
- Organic Chemistry Department, RUDN University, 6 Miklukho-Maklaya St, Moscow 117198, Russia; (A.A.N.); (A.V.V.); (A.Y.O.); (L.G.V.)
| | - Elena Yu. Nevskaya
- General and Inorganic Chemistry Department, RUDN University, 6 Miklukho-Maklaya St, Moscow 117198, Russia;
| | - Mauro Niso
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (R.P.); (M.N.); (N.A.C.); (A.C.); (M.d.C.)
| | - Nicola A. Colabufo
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (R.P.); (M.N.); (N.A.C.); (A.C.); (M.d.C.)
| | - Antonio Carrieri
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (R.P.); (M.N.); (N.A.C.); (A.C.); (M.d.C.)
| | - Marco Catto
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (R.P.); (M.N.); (N.A.C.); (A.C.); (M.d.C.)
| | - Modesto de Candia
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (R.P.); (M.N.); (N.A.C.); (A.C.); (M.d.C.)
| | - Leonid G. Voskressensky
- Organic Chemistry Department, RUDN University, 6 Miklukho-Maklaya St, Moscow 117198, Russia; (A.A.N.); (A.V.V.); (A.Y.O.); (L.G.V.)
| | - Cosimo D. Altomare
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; (R.P.); (M.N.); (N.A.C.); (A.C.); (M.d.C.)
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Samarelli F, Purgatorio R, Lopopolo G, Deruvo C, Catto M, Andresini M, Carrieri A, Nicolotti O, De Palma A, Miniero DV, de Candia M, Altomare CD. Novel 6-alkyl-bridged 4-arylalkylpiperazin-1-yl derivatives of azepino[4,3-b]indol-1(2H)-one as potent BChE-selective inhibitors showing protective effects against neurodegenerative insults. Eur J Med Chem 2024; 270:116353. [PMID: 38579622 DOI: 10.1016/j.ejmech.2024.116353] [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: 01/16/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]
Abstract
Due to the putative role of butyrylcholinesterase (BChE) in regulation of acetylcholine levels and functions in the late stages of the Alzheimer's disease (AD), the potential of selective inhibitors (BChEIs) has been envisaged as an alternative to administration of acetylcholinesterase inhibitors (AChEIs). Starting from our recent findings, herein the synthesis and in vitro evaluation of cholinesterase (ChE) inhibition of a novel series of some twenty 3,4,5,6-tetrahydroazepino[4,3-b]indol-1(2H)-one derivatives, bearing at the indole nitrogen diverse alkyl-bridged 4-arylalkylpiperazin-1-yl chains, are reported. The length of the spacers, as well as the type of arylalkyl group affected the enzyme inhibition potency and BChE/AChE selectivity. Two compounds, namely 14c (IC50 = 163 nM) and 14d (IC50 = 65 nM), bearing at the nitrogen atom in position 6 a n-pentyl- or n-heptyl-bridged 4-phenethylpiperazin-1-yl chains, respectively, proved to be highly potent mixed-type inhibitors of both equine and human BChE isoforms, showing more than two order magnitude of selectivity over AChE. The study of binding kinetics through surface plasmon resonance (SPR) highlighted differences in their BChE residence times (8 and 47 s for 14c and 14d, respectively). Moreover, 14c and 14d proved to hit other mechanisms known to trigger neurodegeneration underlying AD and other CNS disorders. Unlike 14c, compound 14d proved also capable of inhibiting by more than 60% the in vitro self-induced aggregation of neurotoxic amyloid-β (Aβ) peptide at 100 μM concentration. On the other hand, 14c was slightly better than 14d in counteracting, at 1 and 10 μM concentration, glutamate excitotoxicity, due to over-excitation of NMDA receptors, and hydrogen peroxide-induced oxidative stress assessed in neuroblastoma cell line SH-SY5Y. This paper is dedicated to Prof. Marcello Ferappi, former dean of the Faculty of Pharmacy of the University of Bari, in the occasion of his 90th birthday.
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Affiliation(s)
- Francesco Samarelli
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Rosa Purgatorio
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Gianfranco Lopopolo
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Caterina Deruvo
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Marco Catto
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Michael Andresini
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Antonio Carrieri
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Modesto de Candia
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy.
| | - Cosimo D Altomare
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125, Bari, Italy
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Nkungli NK, Fouegue ADT, Tasheh SN, Bine FK, Hassan AU, Ghogomu JN. In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study. Mol Divers 2024; 28:475-496. [PMID: 36622482 PMCID: PMC9838286 DOI: 10.1007/s11030-022-10594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The emergence of artemisinin-resistant variants of Plasmodium falciparum necessitates the urgent search for novel antimalarial drugs. In this regard, an in silico study to screen antimalarial drug candidates from a series of benzimidazole-thiosemicarbazone hybrid molecules with interesting antiplasmodial properties and explore their falcipain-2 (FP2) inhibitory potentials has been undertaken herein. FP2 is a key cysteine protease that degrades hemoglobin in Plasmodium falciparum and is an important biomolecular target in the development of antimalarial drugs. Pharmacokinetic properties, ADMET profiles, MM/GBSA-based binding free energies, reaction mechanisms, and associated barrier heights have been investigated. DFT, molecular dynamics simulation, molecular docking, and ONIOM methods were used. From the results obtained, four 4N-substituted derivatives of the hybrid molecule (E)-2-(1-(5-chloro-1H-benzo[d]imidazol-2-yl)ethylidene)hydrazine-1-carbothioamide (1A) denoted 1B, 1C, 1D, and 1E are drug-like and promising inhibitors of FP2, exhibiting remarkably small inhibitory constants (5.94 × 10-14 - 2.59 × 10-04 n M) and favorable binding free energies (-30.32 to -17.17 kcal/mol). Moreover, the ONIOM results have revealed that 1B and possibly 1C and 1D may act as covalent inhibitors of FP2. The rate-determining step of the thermodynamically favorable covalent binding mechanism occurs across a surmountable barrier height of 24.18 kcal/mol in water and 28.42 kcal/mol in diethyl ether. Our findings are useful for further experimental investigations on the antimalarial activities of the hybrid molecules studied.
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Affiliation(s)
- Nyiang Kennet Nkungli
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon.
| | - Aymard Didier Tamafo Fouegue
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Bertoua, P.O. Box 652, Bertoua, Cameroon
| | - Stanley Numbonui Tasheh
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Fritzgerald Kogge Bine
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Abrar Ul Hassan
- Department of Chemistry, University of Gujrat, Gujrat, 54400, PK, Pakistan
| | - Julius Numbonui Ghogomu
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
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10
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Alhawarri MB, Al-Thiabat MG, Dubey A, Tufail A, Fouad D, Alrimawi BH, Dayoob M. ADME profiling, molecular docking, DFT, and MEP analysis reveal cissamaline, cissamanine, and cissamdine from Cissampelos capensis L.f. as potential anti-Alzheimer's agents. RSC Adv 2024; 14:9878-9891. [PMID: 38528929 PMCID: PMC10961956 DOI: 10.1039/d4ra01070a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 03/17/2024] [Indexed: 03/27/2024] Open
Abstract
The current pharmacotherapies for Alzheimer's disease (AD) demonstrate limited efficacy and are associated with various side effects, highlighting the need for novel therapeutic agents. Natural products, particularly from medicinal plants, have emerged as a significant source of potential neuroprotective compounds. In this context, Cissampelos capensis L.f., renowned for its medicinal properties, has recently yielded three new proaporphine alkaloids; cissamaline, cissamanine, and cissamdine. Despite their promising bioactive profiles, the biological targets of these alkaloids in the context of AD have remained unexplored. This study undertakes a comprehensive in silico examination of the binding affinity and molecular interactions of these alkaloids with human protein targets implicated in AD. The drug likeness and ADME analyses indicate favorable pharmacokinetic profiles for these compounds, suggesting their potential efficacy in targeting the central nervous system. Molecular docking studies indicate that cissamaline, cissamanine, and cissamdine interact with key AD-associated proteins. These interactions are comparable to, or in some aspects slightly less potent than, those observed with established AD drugs, highlighting their potential as novel therapeutic agents for Alzheimer's disease. Crucially, Density Functional Theory (DFT) calculations offer deep insights into the electronic and energetic characteristics of these alkaloids. These calculations reveal distinct electronic properties, with differences in total energy, binding energy, HOMO-LUMO gaps, dipole moments, and electrophilicity indices. Such variations suggest unique reactivity profiles and molecular stability, pertinent to their pharmacological potential. Moreover, Molecular Electrostatic Potential (MEP) analyses provide visual representations of the electrostatic characteristics of these alkaloids. The analyses highlight areas prone to electrophilic and nucleophilic attacks, indicating their potential for specific biochemical interactions. This combination of DFT and MEP results elucidates the intricate electronic, energetic, and electrostatic properties of these compounds, underpinning their promise as AD therapeutic agents. The in silico findings of this study shed light on the promising potential of cissamaline, cissamanine, and cissamdine as agents for AD treatment. However, further in vitro and in vivo studies are necessary to validate these theoretical predictions and to understand the precise mechanisms through which these alkaloids may exert their therapeutic effects.
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Affiliation(s)
- Maram B Alhawarri
- Department of Pharmacy, Faculty of Pharmacy, Jadara University P.O.Box 733 Irbid 21110 Jordan
| | - Mohammad G Al-Thiabat
- School of Pharmaceutical Sciences, Universiti Sains Malaysia Gelugor 11800 Penang Malaysia
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences Chennai-600077 Tamil Nadu India
- Computational Chemistry and Drug Discovery Division Quanta Calculus Greater Noida-201310 Uttar Pradesh India
| | - Aisha Tufail
- Computational Chemistry and Drug Discovery Division Quanta Calculus Greater Noida-201310 Uttar Pradesh India
| | - Dania Fouad
- Faculty of Dentistry, Ibn Sina University for Medical and Pharmaceutical Sciences Baghdad Iraq
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11
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Szlapa-Kula A, Kula S, Kaźmierski Ł, Biernasiuk A, Krawczyk P. Can a Small Change in the Heterocyclic Substituent Significantly Impact the Physicochemical and Biological Properties of ( Z)-2-(5-Benzylidene-4-oxo-2-thioxothiazolidin-3-yl)acetic Acid Derivatives? SENSORS (BASEL, SWITZERLAND) 2024; 24:1524. [PMID: 38475060 DOI: 10.3390/s24051524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Rhodanine-3-acetic acid derivatives are attractive compounds with versatile effects. What is very important is that compounds of this type have many biological properties. They are tested, among others, as fluorescent probes for bioimaging and aldose reductase inhibitors. Rhodanine-3-acetic acid derivatives also have antibacterial, antifungal and anticancer activity. The presented work demonstrates that a slight change in the five-membered heterocyclic substituent significantly affects the properties of the compounds under consideration. Three rhodanine-3-acetic acid derivatives (A-1-A-3) were obtained in the Knoevenagel condensation reaction with good yields, ranging from 54% to 71%. High thermal stability of the tested compounds was also demonstrated above 240 °C. The absorption and emission maxima in polar and non-polar solvents were determined. Then, the possibility of using the considered derivatives for fluorescence bioimaging was checked. Compounds A-1 and A-2 were successfully used as fluorescent dyes of fixed cells of mammalian origin. In addition, biological activity tests against bacteria and fungi were carried out. Our results showed that A-1 and A-2 showed the most excellent antimicrobial activity among the newly synthesized compounds, especially against Gram-positive bacteria.
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Affiliation(s)
- Agata Szlapa-Kula
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9 St., 40-007 Katowice, Poland
| | - Slawomir Kula
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9 St., 40-007 Katowice, Poland
| | - Łukasz Kaźmierski
- Urology and Andrology, Department of Tissue Engineering, Collegium Medicum, Nicolaus Copernicus University, M. Curie Skłodowskiej 9, 85-094 Bydgoszcz, Poland
| | - Anna Biernasiuk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland
| | - Przemysław Krawczyk
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950 Bydgoszcz, Poland
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12
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Mteremko D, Chilongola J, Paluch AS, Chacha M. Ensemble-based virtual screening of African natural products to target human thymidylate synthase. J Mol Graph Model 2023; 125:108568. [PMID: 37591123 DOI: 10.1016/j.jmgm.2023.108568] [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: 04/19/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Human thymidylate synthase (hTS) is a validated drug target for chemotherapy. A virtual screening experiment was used to prioritize a list of compounds from African Natural Products Databases docked against the orthosteric binding pocket of hTS. Consensus scores of binding affinities from ensemble-based virtual screening, hydrated docking and MM-PBSA calculations ranked compounds NEA4433 and NEA4434 as the best candidates owing to binding affinity scores in the picomolar order, their excellent ADMET profiles and the good stability of the protein-ligand complexes formed. The current study demonstrates the role of water in small molecule binding to hTS in mediating protein-ligand interactions. Similarly, the robust ensemble docking (relaxed scheme complex) ranked NEA4433 and NEA4434 as the best candidates. Furthermore, the best candidates prioritized were shown to strongly interact with the same residues that interacted with hTS substrate and cofactor.
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Affiliation(s)
- Denis Mteremko
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
| | - Jaffu Chilongola
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Musa Chacha
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; Arusha Technical College, Arusha, Tanzania
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13
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Czarnota-Łydka K, Sudoł-Tałaj S, Kucwaj-Brysz K, Kurczab R, Satała G, de Candia M, Samarelli F, Altomare CD, Carocci A, Barbarossa A, Żesławska E, Głuch-Lutwin M, Mordyl B, Kubacka M, Wilczyńska-Zawal N, Jastrzębska-Więsek M, Partyka A, Khan N, Więcek M, Nitek W, Honkisz-Orzechowska E, Latacz G, Wesołowska A, Carrieri A, Handzlik J. Synthesis, computational and experimental pharmacological studies for (thio)ether-triazine 5-HT 6R ligands with noticeable action on AChE/BChE and chalcogen-dependent intrinsic activity in search for new class of drugs against Alzheimer's disease. Eur J Med Chem 2023; 259:115695. [PMID: 37567058 DOI: 10.1016/j.ejmech.2023.115695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Alzheimer's disease is becoming a growing problem increasing at a tremendous rate. Serotonin 5-HT6 receptors appear to be a particularly attractive target from a therapeutic perspective, due to their involvement not only in cognitive processes, but also in depression and psychosis. In this work, we present the synthesis and broad biological characterization of a new series of 18 compounds with a unique 1,3,5-triazine backbone, as potent 5-HT6 receptor ligands. The main aim of this research is to compare the biological activity of the newly synthesized sulfur derivatives with their oxygen analogues and their N-demethylated O- and S-metabolites obtained for the first time. Most of the new triazines displayed high affinity (Ki < 200 nM) and selectivity towards 5-HT6R, with respect to 5-HT2AR, 5-HT7R, and D2R, in the radioligand binding assays. For selected, active compounds crystallographic studies, functional bioassays, and ADME-Tox profile in vitro were performed. The exciting novelty is that the sulfur derivatives exhibit an agonistic mode of action contrary to all other compounds obtained to date in this chemical class herein and previously reported. Advanced computational studies indicated that this intriguing functional shift might be caused by presence of chalcogen bonds formed only by the sulfur atom. In addition, the N-demethylated derivatives have emerged highly potent antioxidants and, moreover, show a significant improvement in metabolic stability compared to the parent structures. The cholinesterase study present micromolar inhibitory AChE and BChE activity for both 5-HT6 agonist 19 and potent antagonist 5. Finally, the behavioral experiments of compound 19 demonstrated its antidepressant-like properties and slight ability to improve cognitive deficits, without inducing memory impairments by itself. Described pharmacological properties of both compounds (5 and 19) allow to give a design clue for the development of multitarget compounds with 5-HT6 (both agonist and antagonist)/AChE and/or BChE mechanism in the group of 1,3,5-triazine derivatives.
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Affiliation(s)
- Kinga Czarnota-Łydka
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland; Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, św. Łazarza 15, 31-530, Krakow, Poland.
| | - Sylwia Sudoł-Tałaj
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland; Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, św. Łazarza 15, 31-530, Krakow, Poland.
| | - Katarzyna Kucwaj-Brysz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
| | - Rafał Kurczab
- Maj Institute of Pharmacology Polish Academy of Sciences, Department of Medicinal Chemistry, Smętna 12, PL 31-343, Krakow, Poland.
| | - Grzegorz Satała
- Maj Institute of Pharmacology Polish Academy of Sciences, Department of Medicinal Chemistry, Smętna 12, PL 31-343, Krakow, Poland.
| | - Modesto de Candia
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy.
| | - Francesco Samarelli
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy.
| | - Cosimo Damiano Altomare
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy.
| | - Alessia Carocci
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy.
| | - Alexia Barbarossa
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy.
| | - Ewa Żesławska
- Pedagogical University of Krakow, Institute of Biology and Earth Sciences, Podchorążych 2, PL 30-084, Krakow, Poland.
| | - Monika Głuch-Lutwin
- Department of Pharmacobiology, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
| | - Barbara Mordyl
- Department of Pharmacobiology, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
| | - Monika Kubacka
- Department of Pharmacodynamics, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
| | - Natalia Wilczyńska-Zawal
- Department of Clinical Pharmacy, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Cracow, Poland.
| | - Magdalena Jastrzębska-Więsek
- Department of Clinical Pharmacy, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Cracow, Poland.
| | - Anna Partyka
- Department of Clinical Pharmacy, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Cracow, Poland.
| | - Nadia Khan
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland; Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, św. Łazarza 15, 31-530, Krakow, Poland; Department of Pathophysiology, Jagiellonian University, Medical College, Czysta 18, PL 30-688, Krakow, Poland.
| | - Małgorzata Więcek
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
| | - Wojciech Nitek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL 30-387, Krakow, Poland.
| | - Ewelina Honkisz-Orzechowska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
| | - Anna Wesołowska
- Department of Clinical Pharmacy, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Cracow, Poland.
| | - Antonio Carrieri
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125, Bari, Italy.
| | - Jadwiga Handzlik
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, PL 30-688, Krakow, Poland.
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14
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Hassan A, Akram W, Rizwana H, Aftab ZEH, Hanif S, Anjum T, Alwahibi MS. The Imperative Use of Bacillus Consortium and Quercetin Contributes to Suppress Fusarium Wilt Disease by Direct Antagonism and Induced Resistance. Microorganisms 2023; 11:2603. [PMID: 37894261 PMCID: PMC10609423 DOI: 10.3390/microorganisms11102603] [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: 09/20/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Fusarium wilt diseases severely influence the growth and productivity of numerous crop plants. The consortium of antagonistic rhizospheric Bacillus strains and quercetin were evaluated imperatively as a possible remedy to effectively manage the Fusarium wilt disease of tomato plants. The selection of Bacillus strains was made based on in-vitro antagonistic bioassays against Fusarium oxysporum f.sp. lycoprsici (FOL). Quercetin was selected after screening a library of phytochemicals during in-silico molecular docking analysis using tomato LysM receptor kinases "SILKY12" based on its dual role in symbiosis and plant defense responses. After the selection of test materials, pot trials were conducted where tomato plants were provided consortium of Bacillus strains as soil drenching and quercetin as a foliar spray in different concentrations. The combined application of consortium (Bacillus velezensis strain BS6, Bacillus thuringiensis strain BS7, Bacillus fortis strain BS9) and quercetin (1.0 mM) reduced the Fusarium wilt disease index up to 69%, also resulting in increased plant growth attributes. Likewise, the imperative application of the Bacillus consortium and quercetin (1.0 mM) significantly increased total phenolic contents and activities of the enzymes of the phenylpropanoid pathway. Non-targeted metabolomics analysis was performed to investigate the perturbation in metabolites. FOL pathogen negatively affected a range of metabolites including carbohydrates, amino acids, phenylpropanoids, and organic acids. Thereinto, combined treatment of Bacillus consortium and quercetin (1.0 mM) ameliorated the production of different metabolites in tomato plants. These findings prove the imperative use of Bacillus consortium and quercetin as an effective and sustainable remedy to manage Fusarium wilt disease of tomato plants and to promote the growth of tomato plants under pathogen stress conditions.
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Affiliation(s)
- Ali Hassan
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Waheed Akram
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Humaira Rizwana
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Zill-E-Huma Aftab
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Sana Hanif
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Tehmina Anjum
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Mona S Alwahibi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
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15
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Loukili EH, Ouahabi S, Elbouzidi A, Taibi M, Yahyaoui MI, Asehraou A, Azougay A, Saleh A, Al Kamaly O, Parvez MK, El Guerrouj B, Touzani R, Ramdani M. Phytochemical Composition and Pharmacological Activities of Three Essential Oils Collected from Eastern Morocco (Origanum compactum, Salvia officinalis, and Syzygium aromaticum): A Comparative Study. PLANTS (BASEL, SWITZERLAND) 2023; 12:3376. [PMID: 37836118 PMCID: PMC10574104 DOI: 10.3390/plants12193376] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Abstract
Throughout history, essential oils have been employed for their pleasing scents and potential therapeutic benefits. These oils have shown promise in various areas, including aromatherapy, personal care products, natural remedies, and even as alternatives to traditional cleaning agents or pest control solutions. The study aimed to explore the chemical makeup, antioxidant, and antibacterial properties of Origanum compactum Benth., Salvia officinalis L., and Syzygium aromaticum (L.) Merr. et Perry. Initially, the composition of the three essential oils, O. compactum (HO), S. officinalis (HS), and S. aromaticum (HC) was analyzed using GC-MS technology, revealing significant differences in the identified compounds. α-thujone emerged as the predominant volatile component in the oils, making up 78.04% of the composition, followed by eugenol, which constituted 72.66% and 11.22% of the HC and HO oils, respectively. To gauge antioxidant capabilities, tests involving DPPH scavenging capacity and total antioxidant capacity were conducted. Antioxidant activity was determined through the phosphomolybdate test and the DPPH• radical scavenging activity, with the HO essential oil displaying significant scavenging capacity (IC50 of 0.12 ± 0.02 mg/mL), similar to ascorbic acid (IC50 of 0.26 ± 0.24 mg/mL). Similarly, the TAC assay for HO oil revealed an IC50 of 1086.81 ± 0.32 µM AAE/mg. Additionally, the oils' effectiveness against four bacterial strains, namely Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Listeria monocytogenes, and five fungi, Geotrichum candidum, Aspergillus niger, Saccharomyces cerevisiae, Candida glabrata, and Candida albicans, was tested in vitro. The examined essential oils generally exhibited limited antimicrobial effects, with the exception of HC oil, which demonstrated an exceptionally impressive level of antifungal activity. In order to clarify the antioxidant, antibacterial, and antifungal effects of the identified plant compounds, we employed computational methods, specifically molecular docking. This technique involved studying the interactions between these compounds and established protein targets associated with antioxidant, antibacterial, and antifungal activities.
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Affiliation(s)
- El Hassania Loukili
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Mohammed First University, Oujda 60000, Morocco;
| | - Safae Ouahabi
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
| | - Amine Elbouzidi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco;
| | - Mohamed Taibi
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Mohammed First University, Oujda 60000, Morocco;
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco;
| | - Meryem Idrissi Yahyaoui
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (M.I.Y.); (A.A.)
| | - Abdeslam Asehraou
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (M.I.Y.); (A.A.)
| | - Abdellah Azougay
- Laboratory of Applied Geosciences (LGA), Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco;
| | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (A.S.); (O.A.K.)
| | - Omkulthom Al Kamaly
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (A.S.); (O.A.K.)
| | - Mohammad Khalid Parvez
- Department of Pharmacognosy, College of Pharmacy King Saud University, P.O. Box 3660, Riyadh 11481, Saudi Arabia;
| | - Bouchra El Guerrouj
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Mohammed First University, Oujda 60000, Morocco;
| | - Rachid Touzani
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
| | - Mohammed Ramdani
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
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16
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Kurbanova M, Saravanan K, Ahmad S, Sadigova A, Askerov R, Magerramov A, Bakri YE. Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA. Appl Biochem Biotechnol 2023; 195:5338-5354. [PMID: 35195835 DOI: 10.1007/s12010-022-03849-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/11/2022] [Indexed: 11/02/2022]
Abstract
In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.
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Affiliation(s)
- Malahat Kurbanova
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan.
| | | | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Arzu Sadigova
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan
| | - Rizvan Askerov
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan
| | - Abel Magerramov
- Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Lenin prospect 76, Chelyabinsk, 454080, Russian Federation.
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Yunos NM, Wahab HA, Al-Thiabat MG, Sallehudin NJ, Jauri MH. In Vitro and In Silico Analysis of the Anticancer Effects of Eurycomanone and Eurycomalactone from Eurycoma longifolia. PLANTS (BASEL, SWITZERLAND) 2023; 12:2827. [PMID: 37570981 PMCID: PMC10421158 DOI: 10.3390/plants12152827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 08/13/2023]
Abstract
Eurycomanone and eurycomalactone are known quassinoids present in the roots and stems of Eurycoma longifolia. These compounds had been reported to have cytotoxic effects, however, their mechanism of action in a few cancer cell lines have yet to be elucidated. This study was aimed at investigating the anticancer effects and mechanisms of action of eurycomanone and eurycomalactone in cervical (HeLa), colorectal (HT29) and ovarian (A2780) cancer cell lines via Sulforhodamine B assay. Their mechanism of cell death was evaluated based on Hoechst 33342 assay and in silico molecular docking toward DHFR and TNF-α as putative protein targets. Eurycomanone and eurycomalactone exhibited in vitro anticancer effects manifesting IC50 values of 4.58 ± 0.090 µM and 1.60 ± 0.12 µM (HeLa), 1.22 ± 0.11 µM and 2.21 ± 0.049 µM (HT-29), and 1.37 ± 0.13 µM and 2.46 ± 0.081 µM (A2780), respectively. They induced apoptotic cancer cell death in dose- and time-dependent manners. Both eurycomanone and eurycomalactone were also predicted to have good inhibitory potential as demonstrated by the docking into TNF-α with binding affinity of -8.83 and -7.51 kcal/mol, respectively, as well as into DHFR with binding affinity results of -8.05 and -8.87 kcal/mol, respectively. These results support the evidence of eurycomanone and eurycomalactone as anticancer agents via apoptotic cell death mechanism that could be associated with TNF-α and DHFR inhibition as among possible protein targets.
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Affiliation(s)
- Nurhanan Murni Yunos
- Natural Products Division, Forest Research Institute Malaysia, Kepong 52109, Selangor, Malaysia; (N.J.S.); (M.H.J.)
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia;
| | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia;
| | - Mohammad G. Al-Thiabat
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia;
| | - Nor Jannah Sallehudin
- Natural Products Division, Forest Research Institute Malaysia, Kepong 52109, Selangor, Malaysia; (N.J.S.); (M.H.J.)
| | - Muhamad Haffiz Jauri
- Natural Products Division, Forest Research Institute Malaysia, Kepong 52109, Selangor, Malaysia; (N.J.S.); (M.H.J.)
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18
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Zsidó BZ, Bayarsaikhan B, Börzsei R, Szél V, Mohos V, Hetényi C. The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering. Int J Mol Sci 2023; 24:11784. [PMID: 37511543 PMCID: PMC10381018 DOI: 10.3390/ijms241411784] [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: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
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Affiliation(s)
- Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Bayartsetseg Bayarsaikhan
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Violetta Mohos
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
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Huang X, Liu Y, Wang Q, Rehman HM, Horváth D, Zhou S, Fu R, Zhang L, Szöllősi AG, Li Z. Brief literature review and comprehensive bioinformatics analytics unravel the potential mechanism of curcumin in the treatment of periodontitis. BMC Oral Health 2023; 23:469. [PMID: 37422651 PMCID: PMC10329799 DOI: 10.1186/s12903-023-03181-x] [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: 01/26/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
OBJECTIVE Periodontitis is a chronic oral disease prevalent worldwide, and natural products are recommended as adjunctive therapy due to their minor side effects. Curcumin, a widely used ancient compound, has been reported to possess therapeutic effects in periodontitis. However, the exact mechanism underlying its activity remains unclear. In this context, the present study aimed to conduct computational simulations to uncover the potential mechanism of action of Curcumin in the treatment of periodontitis. MATERIALS AND METHODS Single-cell analysis was conducted using a dataset (i.e., GSE164241) curated from the Gene Expression Omnibus (GEO) database through an R package "Seurat package." Bulk RNA sequencing data were curated from GSE10334 and GSE16134 and processed by R package "Limma." Then, the marker genes in the single-cell transcriptome and differentially expressed genes (DEGs) in the bulk transcriptome were integrated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were also carried out to reveal their functionalities. Key targets were mined from their protein-protein interaction (PPI) network topologically. Afterward, molecular docking was performed. The top-ranked pose was subjected to molecular dynamics simulations to investigate the stability of the docking result. RESULTS FOS, CXCL1, CXCL8, and IL1B, were filtered after a series of selected processes. The results of molecular modeling suggested that except for IL1B, the Vena Scores of the rest exceeded -5 kcal/mol. Furthermore, the molecular dynamic simulation indicated that the binding of the CXCL8-Curcumin complex was stable over the entire 100 ns simulation. CONCLUSION The present study unlocked the binding modes of CXCL1, FOS, and CXCL8 with the Curcumin molecule, which were relatively stable, especially for CXCL8, hindering its promising potential to serve as the critical targets of Curcumin in periodontitis treatment.
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Affiliation(s)
- Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Ying Liu
- Department of Cardiology, Sixth Medical Center, PLA General Hospital, Beijing, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, LahorePunjab, 54590 Pakistan
- Alnoorians Group of Institutes, 55-Elahi Bukhsh Park, Amir Road, Shad Bagh, Lahore, 54000 Pakistan
| | - Dorottya Horváth
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Shujing Zhou
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Rao Fu
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ling Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | | | - Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology and National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
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20
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Cao S, Ma H, Xu Z, Fang W, Huang J, Huang Y. Tiratricol, a thyroid hormone metabolite, has potent inhibitory activity against human dihydroorotate dehydrogenase. Chem Biol Drug Des 2023; 102:1-13. [PMID: 37088711 DOI: 10.1111/cbdd.14256] [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: 12/29/2022] [Revised: 03/25/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Human dihydroorotate dehydrogenase (hDHODH) is a promising drug target for many diseases including autoimmune diseases, cancer, and viral infection. To develop more novel and potent hDHODH inhibitors, we screened our in-house library of old drugs. We found that tiratricol (3,3',5-triiodothyroacetic acid), a thyroid hormone metabolite, has potent hDHODH inhibitory activity (IC50 : 0.754 ± 0.126 μM), and its precursor tetrac (3,3',5,5'-tetraiodothyroacetic acid) also shows a certain inhibitory activity against hDHODH (IC50 : 11.960 ± 1.453 μM). Enzyme kinetic analysis shows that tiratricol and tetrac are noncompetitive inhibitors versus CoQ0 , which is different from the positive control A771726. ThermoFMN assay, molecular docking and site-directed mutagenesis all indicate that tiratricol and tetrac interact with more key residues of hDHODH than A771726, especially some hydrophobic residues in Subsite 1. In conclusion, our experiment results indicate a potential new use for the old drug, tiratricol, and provide a novel chemical scaffold for the design of hDHODH inhibitors.
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Affiliation(s)
- Shuying Cao
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Hui Ma
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhaomin Xu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wenqing Fang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jin Huang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ying Huang
- Drug Inspection Technology, Guangdong Institute for Drug Control, Guangzhou, China
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21
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Jin S, Qian K, He L, Zhang Z. iORandLigandDB: A Website for Three-Dimensional Structure Prediction of Insect Odorant Receptors and Docking with Odorants. INSECTS 2023; 14:560. [PMID: 37367376 DOI: 10.3390/insects14060560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/28/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
The use of insect-specific odorants to control the behavior of insects has always been a hot spot in research on "green" control strategies of insects. However, it is generally time-consuming and laborious to explore insect-specific odorants with traditional reverse chemical ecology methods. Here, an insect odorant receptor (OR) and ligand database website (iORandLigandDB) was developed for the specific exploration of insect-specific odorants by using deep learning algorithms. The website provides a range of specific odorants before molecular biology experiments as well as the properties of ORs in closely related insects. At present, the existing three-dimensional structures of ORs in insects and the docking data with related odorants can be retrieved from the database and further analyzed.
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Affiliation(s)
- Shuo Jin
- College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Kun Qian
- College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Lin He
- College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Zan Zhang
- College of Plant Protection, Southwest University, Chongqing 400716, China
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22
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Mohanty M, Mohanty PS. Molecular docking in organic, inorganic, and hybrid systems: a tutorial review. MONATSHEFTE FUR CHEMIE 2023; 154:1-25. [PMID: 37361694 PMCID: PMC10243279 DOI: 10.1007/s00706-023-03076-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023]
Abstract
Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA, RNA and a natural or synthetic organic/inorganic molecule (considered as a ligand). But the implementation of docking ideas to synthetic organic, inorganic, or hybrid systems is very limited with respect to their use as a receptor despite their huge popularity in different experimental systems. In this context, molecular docking can be an efficient computational tool for understanding the role of intermolecular interactions in hybrid systems that can help in designing materials on mesoscale for different applications. The current review focuses on the implementation of the docking method in organic, inorganic, and hybrid systems along with examples from different case studies. We describe different resources, including databases and tools required in the docking study and applications. The concept of docking techniques, types of docking models, and the role of different intermolecular interactions involved in the docking process to understand the binding mechanisms are explained. Finally, the challenges and limitations of dockings are also discussed in this review. Graphical abstract
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Affiliation(s)
- Madhuchhanda Mohanty
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India
| | - Priti S. Mohanty
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India
- School of Chemical Technology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India
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Yang C, Chen Y, Wu T, Gao Y, Liu X, Yang Y, Ling Y, Jia Y, Deng M, Wang J, Zhou Y. Discovery of N-(2-chloro-5-(3-(pyridin-4-yl)-1H-pyrazolo[3,4-b]pyridin-5-yl)pyridin-3-yl)-4-fluorobenzenesulfonamide (FD274) as a highly potent PI3K/mTOR dual inhibitor for the treatment of acute myeloid leukemia. Eur J Med Chem 2023; 258:115543. [PMID: 37329712 DOI: 10.1016/j.ejmech.2023.115543] [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: 04/14/2023] [Revised: 05/25/2023] [Accepted: 06/03/2023] [Indexed: 06/19/2023]
Abstract
PI3K-Akt-mTOR pathway is a highly activated signal transduction pathway in human hematological malignancies and has been validated as a promising target for acute myeloid leukemia (AML) therapy. Herein, we designed and synthesized a series of 7-azaindazole derivatives as potent PI3K/mTOR dual inhibitors based on our previously reported FD223. Among them, compound FD274 showed excellent dual PI3K/mTOR inhibitory activity, with IC50 values against PI3Kα/β/γ/δ and mTOR of 0.65 nM, 1.57 nM, 0.65 nM, 0.42 nM, and 2.03 nM, respectively, superior to compound FD223. Compared to the positive drug Dactolisib, FD274 exhibited significant anti-proliferation of AML cell lines (HL-60 and MOLM-16 with IC50 values of 0.092 μM and 0.084 μM, respectively) in vitro. Furthermore, FD274 demonstrated dose-dependent inhibition of tumor growth in the HL-60 xenograft model in vivo, with 91% inhibition of tumor growth at an intraperitoneal injection dose of 10 mg/kg and no observable toxicity. All of these results suggest that FD274 has potential for further development as a promising PI3K/mTOR targeted anti-AML drug candidate.
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Affiliation(s)
- Chengbin Yang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China; Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai, 201203, China
| | - Yi Chen
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tianze Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yunjian Gao
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xiaofeng Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yongtai Yang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yun Ling
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yu Jia
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Mingli Deng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Jianxin Wang
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery, Ministry of Education, Shanghai, 201203, China
| | - Yaming Zhou
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China.
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Ramlal A, Bhat I, Nautiyal A, Baweja P, Mehta S, Kumar V, Tripathi S, Mahto RK, Saini M, Mallikarjuna BP, Saluja S, Lal SK, Subramaniam S, Fawzy IM, Rajendran A. In silico analysis of angiotensin-converting enzyme inhibitory compounds obtained from soybean [ Glycine max (L.) Merr.]. Front Physiol 2023; 14:1172684. [PMID: 37324400 PMCID: PMC10264776 DOI: 10.3389/fphys.2023.1172684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Cardiovascular diseases (CVDs) are one of the major reasons for deaths globally. The renin-angiotensin-aldosterone system (RAAS) regulates body hypertension and fluid balance which causes CVD. Angiotensin-converting enzyme I (ACE I) is the central Zn-metallopeptidase component of the RAAS playing a crucial role in maintaining homeostasis of the cardiovascular system. The available drugs to treat CVD have many side effects, and thus, there is a need to explore phytocompounds and peptides to be utilized as alternative therapies. Soybean is a unique legume cum oilseed crop with an enriched source of proteins. Soybean extracts serve as a primary ingredient in many drug formulations against diabetes, obesity, and spinal cord-related disorders. Soy proteins and their products act against ACE I which may provide a new scope for the identification of potential scaffolds that can help in the design of safer and natural cardiovascular therapies. In this study, the molecular basis for selective inhibition of 34 soy phytomolecules (especially of beta-sitosterol, soyasaponin I, soyasaponin II, soyasaponin II methyl ester, dehydrosoyasaponin I, and phytic acid) was evaluated using in silico molecular docking approaches and dynamic simulations. Our results indicate that amongst the compounds, beta-sitosterol exhibited a potential inhibitory action against ACE I.
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Affiliation(s)
- Ayyagari Ramlal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, Penang, Malaysia
| | - Isha Bhat
- Department of Biosciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Aparna Nautiyal
- Department of Botany, Deshbandhu College, University of Delhi, New Delhi, India
| | - Pooja Baweja
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Sahil Mehta
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Vikash Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences and Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Shikha Tripathi
- ICAR- National Institute for Biotechnology, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Rohit Kumar Mahto
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Bingi Pujari Mallikarjuna
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), Regional Research Centre, Dharwad, Karnataka, India
| | - Shukla Saluja
- Department of Botany, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - S. K. Lal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Sreeramanan Subramaniam
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, Penang, Malaysia
- Chemical Centre Biology (CCB), Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
- Institute of Nano Optoelectronics Research and Technology, Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
| | - Iten M. Fawzy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt, Cairo, Egypt
| | - Ambika Rajendran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
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Eberhardt J, Forli S. WaterKit: Thermodynamic Profiling of Protein Hydration Sites. J Chem Theory Comput 2023; 19:2535-2556. [PMID: 37094087 PMCID: PMC10732097 DOI: 10.1021/acs.jctc.2c01087] [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] [Indexed: 04/26/2023]
Abstract
Water desolvation is one of the key components of the free energy of binding of small molecules to their receptors. Thus, understanding the energetic balance of solvation and desolvation resulting from individual water molecules can be crucial when estimating ligand binding, especially when evaluating different molecules and poses as done in High-Throughput Virtual Screening (HTVS). Over the most recent decades, several methods were developed to tackle this problem, ranging from fast approximate methods (usually empirical functions using either discrete atom-atom pairwise interactions or continuum solvent models) to more computationally expensive and accurate ones, mostly based on Molecular Dynamics (MD) simulations, such as Grid Inhomogeneous Solvation Theory (GIST) or Double Decoupling. On one hand, MD-based methods are prohibitive to use in HTVS to estimate the role of waters on the fly for each ligand. On the other hand, fast and approximate methods show an unsatisfactory level of accuracy, with low agreement with results obtained with the more expensive methods. Here we introduce WaterKit, a new grid-based sampling method with explicit water molecules to calculate thermodynamic properties using the GIST method. Our results show that the discrete placement of water molecules is successful in reproducing the position of crystallographic waters with very high accuracy, as well as providing thermodynamic estimates with accuracy comparable to more expensive MD simulations. Unlike these methods, WaterKit can be used to analyze specific regions on the protein surface, (such as the binding site of a receptor), without having to hydrate and simulate the whole receptor structure. The results show the feasibility of a general and fast method to compute thermodynamic properties of water molecules, making it well-suited to be integrated in high-throughput pipelines such as molecular docking.
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Affiliation(s)
- Jerome Eberhardt
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
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Shalayel MHF, Al-Mazaideh GM, Alanezi AA, Almuqati AF, Alotaibi M. Diosgenin and Monohydroxy Spirostanol from Prunus amygdalus var amara Seeds as Potential Suppressors of EGFR and HER2 Tyrosine Kinases: A Computational Approach. Pharmaceuticals (Basel) 2023; 16:704. [PMID: 37242487 PMCID: PMC10223344 DOI: 10.3390/ph16050704] [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: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Cancer continues to be leading cause of death globally, with nearly 7 million deaths per year. Despite significant progress in cancer research and treatment, there remain several challenges to overcome, including drug resistance, the presence of cancer stem cells, and high interstitial fluid pressure in tumors. To tackle these challenges, targeted therapy, specifically targeting HER2 (Human Epidermal Growth Factor Receptor 2) as well as EGFR (Epidermal Growth Factor Receptor), is considered a promising approach in cancer treatment. In recent years, phytocompounds have gained recognition as a potential source of chemopreventive and chemotherapeutic agents in tumor cancer treatment. Phytocompounds are compounds derived from medicinal plants that have the potential to treat and prevent cancer. This study aimed to investigate phytocompounds from Prunus amygdalus var amara seeds as inhibitors against EGFR and HER2 enzymes using in silico methods. In this study, fourteen phytocompounds were isolated from Prunus amygdalus var amara seeds and subjected to molecular docking studies to determine their ability to bind to EGFR and HER2 enzymes. The results showed that diosgenin and monohydroxy spirostanol exhibited binding energies comparable to those of the reference drugs, tak-285, and lapatinib. Furthermore, the drug-likeness and ADMET predictions, performed using the admetSAR 2.0 web-server tool, suggested that diosgenin and monohydroxy spirostanol have similar safety and ADMET properties as the reference drugs. To get deeper insight into the structural steadiness and flexibility of the complexes formed between these compounds and theEGFR and HER2 proteins, molecular dynamics simulations were performed for 100 ns. The results showed that the hit phytocompounds did not significantly affect the stability of the EGFR and HER2 proteins and were able to form stable interactions with the catalytic binding sites of the proteins. Additionally, the MM-PBSA analysis revealed that the binding free energy estimates for diosgenin and monohydroxy spirostanol is comparable to the reference drug, lapatinib. This study provides evidence that diosgenin and monohydroxy spirostanol may have the potential to act as dual suppressors of EGFR and HER2. Additional in vivo and in vitro research are needed to certify these results and assess their efficacy and safety as cancer therapy agents. The experimental data reported and these results are in agreement.
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Affiliation(s)
- Mohammed Helmy Faris Shalayel
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Ghassab M. Al-Mazaideh
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Abdulkareem A. Alanezi
- Department of Pharmaceutics, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Afaf F. Almuqati
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
| | - Meshal Alotaibi
- Department of Pharmacy Practice, College of Pharmacy, University of Hafr Al Batin, Hafr Al Batin 31991, Saudi Arabia
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Threat of respiratory syncytial virus infection knocking the door: a proposed potential drug candidate through molecular dynamics simulations, a future alternative. J Mol Model 2023; 29:91. [PMID: 36884131 DOI: 10.1007/s00894-023-05489-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/24/2023] [Indexed: 03/09/2023]
Abstract
The discovery of antiviral approaches to prevent or cure respiratory syncytial virus (RSV) infections is critical, particularly because RSV is one of the most common causes of infant respiratory problems. There is currently no approved vaccination available to treat RSV infections. FDA has approved the drug ribavirin, but it is not sufficient to treat RSV. This work aimed to find and study in silico anti-RSV drugs that target matrix protein and nucleoprotein. In this study, we have identified five drug candidates that had better binding energies than ribavirin. Garenoxacin appeared as top lead compounds between them. AutoDock Vina was used to execute molecular docking of a library of chosen chemicals. The high-score compound was then confirmed using the Maestro 12.3 module's molecular dynamics simulation and the binding energies derived using Prime/Molecular Mechanics Generalized Born Surface Area (Prime/MM-GBSA). Comparative molecular dynamics simulations revealed that garenoxacin has better stability and high residue contacts with high binding affinity than ribavirin. This study showed garenoxacin could prevent RSV infection better than ribavirin. In pursuing a more effective RSV control drug, additional research into these chemicals in vitro and in vivo is essential.
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Alhawarri MB, Dianita R, Rawa MSA, Nogawa T, Wahab HA. Potential Anti-Cholinesterase Activity of Bioactive Compounds Extracted from Cassia grandis L.f. and Cassia timoriensis DC. PLANTS (BASEL, SWITZERLAND) 2023; 12:344. [PMID: 36679057 PMCID: PMC9862305 DOI: 10.3390/plants12020344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Acetylcholinesterase (AChE) inhibitors remain the primary therapeutic drug that can alleviate Alzheimer's disease's (AD) symptoms. Several Cassia species have been shown to exert significant anti-AChE activity, which can be an alternative remedy for AD. Cassia timoriensis and Cassia grandis are potential plants with anti-AChE activity, but their phytochemical investigation is yet to be further conducted. The aims of this study were to identify the phytoconstituents of C. timoriensis and C. grandis and evaluate their inhibitory activity against AChE and butyrylcholinesterase (BChE). Two compounds were isolated for the first time from C. timoriensis: arachidyl arachidate (1) and luteolin (2). Five compounds were identified from C. grandis: β-sitosterol (3), stigmasterol (4), cinnamic acid (5), 4-hydroxycinnamic acid (6), and hydroxymethylfurfural (7). Compound 2 showed significant inhibition towards AChE (IC50: 20.47 ± 1.10 µM) and BChE (IC50: 46.15 ± 2.20 µM), followed by 5 (IC50: 40.5 ± 1.28 and 373.1 ± 16.4 µM) and 6 (IC50: 43.4 ± 0.61 and 409.17 ± 14.80 µM) against AChE and BChE, respectively. The other compounds exhibited poor to slightly moderate AChE inhibitory activity. Molecular docking revealed that 2 showed good binding affinity towards TcAChE (PDB ID: 1W6R) and HsBChE (PDB ID: 4BDS). It formed a hydrogen bond with TYR121 at the peripheral anionic site (PAS, 2.04 Å), along with hydrophobic interactions with the anionic site and PAS (TRP84 and TYR121, respectively). Additionally, 2 formed three H-bonds with the binding site residues: one bond with catalytic triad, HIS438 at distance 2.05 Å, and the other two H-bonds with GLY115 and GLU197 at distances of 2.74 Å and 2.19 Å, respectively. The evidence of molecular interactions of 2 may justify the relevance of C. timoriensis as a cholinesterase inhibitor, having more promising activity than C. grandis.
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Affiliation(s)
- Maram B. Alhawarri
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
- Faculty of Pharmacy, Jadara University, Irbid 21110, Jordan
| | - Roza Dianita
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
| | - Mira Syahfriena Amir Rawa
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
- USM-RIKEN Interdisciplinary Collaboration for Advanced Sciences (URICAS), Universiti Sains Malaysia, Gelugor 11800, Malaysia
| | - Toshihiko Nogawa
- USM-RIKEN Interdisciplinary Collaboration for Advanced Sciences (URICAS), Universiti Sains Malaysia, Gelugor 11800, Malaysia
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
- USM-RIKEN Interdisciplinary Collaboration for Advanced Sciences (URICAS), Universiti Sains Malaysia, Gelugor 11800, Malaysia
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Mteremko D, Chilongola J, Paluch AS, Chacha M. Targeting human thymidylate synthase: Ensemble-based virtual screening for drug repositioning and the role of water. J Mol Graph Model 2023; 118:108348. [PMID: 36257147 DOI: 10.1016/j.jmgm.2022.108348] [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: 06/07/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022]
Abstract
A drug repositioning computational approach was carried to search inhibitors for human thymidylate synthase. An ensemble-based virtual screening of FDA-approved drugs showed the drugs Imatinib, Lumacaftor and Naldemedine to be likely candidates for repurposing. The role of water in the drug-receptor interactions was revealed by the application of an extended AutoDock scoring function that included the water forcefield. The binding affinity scores when hydrated ligands were docked were improved in the drugs considered. Further binding free energy calculations based on the Molecular Mechanics Poisson-Boltzmann Surface Area method revealed that Imatinib, Lumacaftor and Naldemedine scored -130.7 ± 28.1, -210.6 ± 29.9 and -238.0 ± 25.4 kJ/mol, respectively, showing good binding affinity for the candidates considered. Overall, the analysis of the molecular dynamics trajectory of the receptor-drug complexes revealed stable structures for Imatinib, Lumacaftor and Naldemedine, for the entire simulation time.
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Affiliation(s)
- Denis Mteremko
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
| | - Jaffu Chilongola
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Musa Chacha
- The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; Arusha Technical College, Arusha, Tanzania
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Ahmmed F, Islam AU, Mukhrish YE, Bakri YE, Ahmad S, Ozeki Y, Kawsar SMA. Efficient Antibacterial/Antifungal Activities: Synthesis, Molecular Docking, Molecular Dynamics, Pharmacokinetic, and Binding Free Energy of Galactopyranoside Derivatives. Molecules 2022; 28:molecules28010219. [PMID: 36615413 PMCID: PMC9822152 DOI: 10.3390/molecules28010219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/13/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
The chemistry and biochemistry of carbohydrate esters are essential parts of biochemical and medicinal research. A group of methyl β-d-galactopyranoside (β-MGP, 1) derivatives was acylated with 3-bromobenzoyl chloride and 4-bromobenzoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to obtain 6-O-substitution products, which were subsequently converted into 2,3,4-tri-O-acyl derivatives with different aliphatic and aromatic substituents. Spectroscopic and elemental data exploration of these derivatives confirmed their chemical structures. In vitro biological experiments against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) revealed ascending antifungal and antibacterial activities compared with their antiviral activities. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) experiments were performed for two derivatives, 3 and 9, based on their antibacterial activities. Most of these derivatives showed >780% inhibition of fungal mycelial growth. Density functional theory (DFT) was used to calculate the chemical descriptors and thermodynamic properties, whereas molecular docking was performed against antibacterial drug targets, including PDB: 4QDI, 5A5E, 7D27, 1ZJI, 3K8E, and 2MRW, and antifungal drug targets, such as PDB: 1EA1 and 1AI9, to identify potential drug candidates for microbial pathogens. A 100 ns molecular dynamics simulation study revealed stable conformation and binding patterns in a stimulating environment by their uniform RMSD, RMSF, SASA, H-bond, and RoG profiles. In silico pharmacokinetic and quantitative structure−activity relationship (QSAR) calculations (pIC50 values 3.67~8.15) suggested that all the designed β-MGP derivatives exhibited promising results due to their improved kinetic properties with low aquatic and non-aquatic toxicities. These biological, structure−activity relationship (SAR) [lauroyl-(CH3(CH2)10CO-) group was found to have potential], and in silico computational studies revealed that the newly synthesized MGP derivatives are potential antibacterial/antifungal candidates and can serve as therapeutic targets for human and plant pathogens.
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Affiliation(s)
- Faez Ahmmed
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Anis Ul Islam
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Yousef E. Mukhrish
- Department of Chemistry, Faculty of Science, Jazan University, Jazan 45142, Saudi Arabia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Lenin Prospect 76, 454080 Chelyabinsk, Russia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Yokohama 236-0027, Japan
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
- Correspondence: ; Tel.: +88-01762717081
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Fenanir F, Semmeq A, Benguerba Y, Badawi M, Dziurla MA, Amira S, Laouer H. In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes. J Biomol Struct Dyn 2022; 40:11571-11586. [PMID: 34355673 DOI: 10.1080/07391102.2021.1960197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography-mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product-enzyme interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fares Fenanir
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
| | - Abderrahmane Semmeq
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France
| | - Yacine Benguerba
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS, Sétif, Algeria
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France.,IUT de Moselle-Est, Université de Lorraine, Saint-Avold, France
| | | | - Smain Amira
- Laboratory of Phytotherapy Applied to Chroniques Diseases, University Ferhat Abbas, Sétif, Algeria
| | - Hocine Laouer
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
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Anti-Alopecia Activity of Alkaloids Group from Noni Fruit against Dihydrotestosterone-Induced Male Rabbits and Its Molecular Mechanism: In Vivo and In Silico Studies. Pharmaceuticals (Basel) 2022; 15:ph15121557. [PMID: 36559008 PMCID: PMC9784383 DOI: 10.3390/ph15121557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Androgenic alopecia (AA) is a condition that most commonly affects adult men and is caused by an increase in the hormone dihydrotestosterone (DHT) in the hair follicles. Anti-alopecia drugs should be discovered for hair follicles to enter the anagen growth phase. Therefore, this study evaluated the hair growth-promoting activity of Noni fruit’s water, ethyl acetate, n-hexane fractions, and sub-fractions from the active fraction in the alopecia male white rabbit model. The Matias method was modified by inducing rabbits using DHT for 17 days, followed by topical application of Noni fruit solution for 21 days. Meanwhile, hair growth was evaluated by histological observation of the follicular density and the anagen/telogen (A/T) ratio in skin tissue. In the first stage, five groups of male white rabbits were studied to obtain the active fraction; DHT+Minoxidil as standard, DHT+vehicle (NaCMC 1%), DHT+FW, DHT+FEA, and DHT+FH. The FEA as the active fraction was followed by open-column chromatography separation (DCM:Methanol) with a gradient of 10% to produce sub-fractions. In the second stage, the six main sub-fraction groups of male rabbits studied were DHT+FEA-1 to DHT+FEA-6. The follicular density of groups FEA-3 was 78.00 ± 1.52 compared with 31.55 ± 1.64 and 80.12 ± 1.02 in the Vehicle and Minoxidil groups. Additionally, group FEA-3 showed large numbers of anagen follicles with an A/T ratio of 1.64/1 compared to the vehicle group of 1/1.50 and 1.39/1 for Minoxidil control. Group FEA-3 was identified by LC-MS/MS-QTOF, followed by molecular docking to the androgen receptor (PDB: 4K7A), causing alopecia. The results showed that three alkaloid compounds with skeleton piperazine and piperidine, namely (compounds 2 (−4.99 Kcal/mol), 3 (−4.60 Kcal/mol), and 4 (−4.57 Kcal/mol)) had a binding affinity similar to Minoxidil, with also has alkaloid skeleton piperidine−pyrimidine (−4.83 Kcal/mol). The dynamic behavior showed the stability of all androgen receptor compounds with good RMSD, SMSF, and SASA values after being studied with 100 ns molecular dynamics (MD) simulations. This study produced a common thread in discovering a class of alkaloid compounds as inhibitors of androgen receptors that cause alopecia.
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Lubeluzole Repositioning as Chemosensitizing Agent on Multidrug-Resistant Human Ovarian A2780/DX3 Cancer Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227870. [PMID: 36431971 PMCID: PMC9695310 DOI: 10.3390/molecules27227870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/19/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
In a previous paper, we demonstrated the synergistic action of the anti-ischemic lubeluzole (Lube S) on the cytotoxic activity of doxorubicin (Dox) and paclitaxel in human ovarian cancer A2780 and lung cancer A549 cells. In the present paper, we extended in vitro the study to the multi-drug-resistant A2780/DX3 cell line to verify the hypothesis that the Dox and Lube S drug association may potentiate the antitumor activity of this anticancer compound also in the context of drug resistance. We also evaluated some possible mechanisms underlying this activity. We analyzed the antiproliferative activity in different cancer cell lines. Furthermore, apoptosis, Dox accumulation, MDR1 downregulation, ROS, and NO production in A2780/DX3 cells were also evaluated. Our results confirm that Lube S improves Dox antiproliferative and apoptotic activities through different mechanisms of action, all of which may contribute to the final antitumor effect. Moderate stereoselectivity was found, with Lube S significantly more effective than its enantiomer (Lube R) and the corresponding racemate (Lube S/R). Docking simulation studies on the ABCB1 Cryo-EM structure supported the hypothesis that Lube S forms a stable MDR1-Dox-Lube S complex, which hampers the protein transmembrane domain flipping and blocks the efflux of Dox from resistant A2780/DX3 cells. In conclusion, our in vitro studies reinforce our previous hypothesis for repositioning the anti-ischemic Lube S as a potentiating agent in anticancer chemotherapy.
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Quantitative detection of urinary bladder cancer antigen via peptide-immobilized magnetic bead-based SERS probe. Anal Bioanal Chem 2022; 414:8289-8297. [DOI: 10.1007/s00216-022-04361-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/18/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022]
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Sahu SN, Satpathy SS, Pattnaik S, Mohanty C, Pattanayak SK. Boerhavia diffusa plant extract can be a new potent therapeutics against mutant nephrin protein responsible for type1 nephrotic syndrome: Insight into hydrate-ligand docking interactions and molecular dynamics simulation study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Zapevalova MV, Shchegravina ES, Fonareva IP, Salnikova DI, Sorokin DV, Scherbakov AM, Maleev AA, Ignatov SK, Grishin ID, Kuimov AN, Konovalova MV, Svirshchevskaya EV, Fedorov AY. Synthesis, Molecular Docking, In Vitro and In Vivo Studies of Novel Dimorpholinoquinazoline-Based Potential Inhibitors of PI3K/Akt/mTOR Pathway. Int J Mol Sci 2022; 23:ijms231810854. [PMID: 36142768 PMCID: PMC9503112 DOI: 10.3390/ijms231810854] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
A (series) range of potential dimorpholinoquinazoline-based inhibitors of the PI3K/Akt/mTOR cascade was synthesized. Several compounds exhibited cytotoxicity towards a panel of cancer cell lines in the low and sub-micromolar range. Compound 7c with the highest activity and moderate selectivity towards MCF7 cells which express the mutant type of PI3K was also tested for the ability to inhibit PI3K-(signaling pathway) downstream effectors and associated proteins. Compound 7c inhibited the phosphorylation of Akt, mTOR, and S6K at 125–250 nM. It also triggered PARP1 cleavage, ROS production, and cell death via several mechanisms. Inhibition of PI3Kα was observed at a concentration of 7b 50 µM and of 7c 500 µM and higher, that can indicate minority PI3Kα as a target among other kinases in the titled cascade for 7c. In vivo studies demonstrated an inhibition of tumor growth in the colorectal tumor model. According to the docking studies, the replacement of the triazine core in gedatolisib (8) by a quinazoline fragment, and incorporation of a (hetero)aromatic unit connected with the carbamide group via a flexible spacer, can result in more selective inhibition of the PI3Kα isoform.
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Affiliation(s)
- Maria V. Zapevalova
- Department of Organic Chemistry, Nizhny Novgorod State University, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia
| | - Ekaterina S. Shchegravina
- Department of Organic Chemistry, Nizhny Novgorod State University, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia
- N.D. Zelinsky Insitute of Organic Chemistry RAS, Leninsky Prospect 47, 119991 Moscow, Russia
- Correspondence: (E.S.S.); (A.Y.F.)
| | - Irina P. Fonareva
- Department of Organic Chemistry, Nizhny Novgorod State University, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia
| | - Diana I. Salnikova
- Department of Experimental Tumor Biology, Blokhin N.N. National Medical Research Center of Oncology, Kashirskoye Sh. 24, 115522 Moscow, Russia
| | - Danila V. Sorokin
- Department of Experimental Tumor Biology, Blokhin N.N. National Medical Research Center of Oncology, Kashirskoye Sh. 24, 115522 Moscow, Russia
| | - Alexander M. Scherbakov
- Department of Experimental Tumor Biology, Blokhin N.N. National Medical Research Center of Oncology, Kashirskoye Sh. 24, 115522 Moscow, Russia
| | - Alexander A. Maleev
- Department of Organic Chemistry, Nizhny Novgorod State University, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia
| | - Stanislav K. Ignatov
- Department of Organic Chemistry, Nizhny Novgorod State University, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia
| | - Ivan D. Grishin
- Department of Organic Chemistry, Nizhny Novgorod State University, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia
| | - Alexander N. Kuimov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye Gory, House 1, Building 40, 119992 Moscow, Russia
| | - Maryia V. Konovalova
- Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Elena V. Svirshchevskaya
- Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexey Yu. Fedorov
- Department of Organic Chemistry, Nizhny Novgorod State University, Gagarina Av. 23, 603950 Nizhny Novgorod, Russia
- N.D. Zelinsky Insitute of Organic Chemistry RAS, Leninsky Prospect 47, 119991 Moscow, Russia
- Correspondence: (E.S.S.); (A.Y.F.)
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In Silico Pharmacokinetic Profiling of the Identified Bioactive Metabolites of Pergularia tomentosa L. Latex Extract and In Vitro Cytotoxic Activity via the Induction of Caspase-Dependent Apoptosis with S-Phase Arrest. Pharmaceuticals (Basel) 2022; 15:ph15091132. [PMID: 36145353 PMCID: PMC9501251 DOI: 10.3390/ph15091132] [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] [Received: 08/14/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
The in vitro cytotoxic efficacy of plant latex from Pergularia tomentosa L. was studied using five human cancer cell lines: HeLa cells (cervical carcinoma cells), A-549 (lung carcinoma), Panc-1 (pancreatic carcinoma cells), MDA-MB-231 (metastatic mammary adenocarcinoma), and MRC-5 (lung fibroblast cell line) cells. The phytonutrient content of plant latex was identified using the liquid chromatography/mass spectra-quadrupole time of flight (LC/MS-QTOF) technique. In silico studies of polyphenols were carried out to clarify the potential mode of action of the plant latex’s constituents. The treatment of different tumor cell lines with different concentrations of plant latex revealed a potent efficacy on the human lung carcinoma cell line (A-549) (IC50 = 3.89 µg/mL) compared with that with vinblastine as a positive control (IC50 = 7.12 µg/mL). The effect of the potent concentration of plant latex on the A-549 cell line induced cell arrest, upregulated the expression of pre-apoptotic markers, and downregulated the expression of antiapoptotic markers. Seven identified polyphenols were selected for the in silico study. A docking assessment using the epidermal growth factor receptor kinase (EGFRk) and eltronib as a positive control showed a higher affinity for the enzyme receptor of the selected polyphenols, except for methyl orsellinate and ginkgotoxin. The ADMET assessment demonstrated the inhibitory effect of the polyphenols on CYP450, except for ouabagenin and xanthyletine. The selected polyphenols obey Lipinski’s drug-likeness with no significant toxicity effect. In conclusion, the plant latex of P. tomentosa L. showed cytotoxic activity on the A-549 cell line, and the selected polyphenols showed a promising prodrug agent with a low profile of toxicity in the study.
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Defois M, Rémondin C, Josselin B, Nauton L, Théry V, Anizon F, Ruchaud S, Giraud F, Moreau P. Synthesis and Kinase Inhibitory Potencies of Pyrazolo[3,4-g]isoquinolines. Molecules 2022; 27:molecules27175578. [PMID: 36080340 PMCID: PMC9457941 DOI: 10.3390/molecules27175578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/22/2022] [Accepted: 08/28/2022] [Indexed: 11/22/2022] Open
Abstract
A new series of pyrazolo[3,4-g]isoquinoline derivatives, diversely substituted at the 4- or 8-position, were synthesized. The results of the kinase inhibitory potency study demonstrated that the introduction of a bromine atom at the 8-position was detrimental to Haspin inhibition, while the introduction of an alkyl group at the 4-position led to a modification of the kinase inhibition profiles. Altogether, the results obtained demonstrated that new pyrazolo[3,4-g]isoquinolines represent a novel family of kinase inhibitors with various selectivity profiles.
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Affiliation(s)
- Mathilde Defois
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Chloé Rémondin
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Béatrice Josselin
- Sorbonne Université, CNRS, Plateforme de Criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Protein Phosphorylation and Human Diseases Unit, Station Biologique, Place Georges Teissier, F-29688 Roscoff, France
- Sorbonne Université/CNRS UMR8227, Station Biologique, Place Georges Teissier, CS90074, CEDEX, F-29688 Roscoff, France
| | - Lionel Nauton
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Vincent Théry
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Fabrice Anizon
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Sandrine Ruchaud
- Sorbonne Université/CNRS UMR8227, Station Biologique, Place Georges Teissier, CS90074, CEDEX, F-29688 Roscoff, France
| | - Francis Giraud
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
- Correspondence: (F.G.); (P.M.)
| | - Pascale Moreau
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
- Correspondence: (F.G.); (P.M.)
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Carocci A, Barbarossa A, Leuci R, Carrieri A, Brunetti L, Laghezza A, Catto M, Limongelli F, Chaves S, Tortorella P, Altomare CD, Santos MA, Loiodice F, Piemontese L. Novel Phenothiazine/Donepezil-like Hybrids Endowed with Antioxidant Activity for a Multi-Target Approach to the Therapy of Alzheimer’s Disease. Antioxidants (Basel) 2022; 11:antiox11091631. [PMID: 36139705 PMCID: PMC9495854 DOI: 10.3390/antiox11091631] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is a complex multi-factorial neurodegenerative disorder for which only few drugs (including donepezil, DPZ) are available as symptomatic treatments; thus, researchers are focusing on the development of innovative multi-target directed ligands (MTDLs), which could also alter the course of the disease. Among other pathological factors, oxidative stress has emerged as an important factor in AD that could affect several pathways involved in the onset and progression of the pathology. Herein, we propose a new series of hybrid molecules obtained by linking a phenothiazine moiety, known for its antioxidant properties, with N-benzylpiperidine or N-benzylpiperazine fragments, mimicking the core substructure of DPZ. The investigation of the resulting hybrids showed, in addition to their antioxidant properties, their activity against some AD-related targets, such as the inhibition of cholinesterases (both AChE and BChE) and in vitro Aβ1-40 aggregation, as well as the inhibition of the innovative target fatty acid amide hydrolase (FAAH). Furthermore, the drug-likeness properties of these compounds were assessed using cheminformatic tools. Compounds 11d and 12d showed the most interesting multi-target profiles, with all the assayed activities in the low micromolar range. In silico docking calculations supported the obtained results. Compound 13, on the other hand, while inactive in the DPPH assay, showed the best results in the in vitro antioxidant cell assays conducted on both HepG2 and SHSY-5Y cell lines. These results, paired with the low or absent cytotoxicity of these compounds at tested concentrations, allow us to aim our future research at the study of novel and effective drugs and pro-drugs with similar structural characteristics.
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Affiliation(s)
- Alessia Carocci
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
- Correspondence: (A.C.); (L.P.)
| | - Alexia Barbarossa
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Rosalba Leuci
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Antonio Carrieri
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Leonardo Brunetti
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Antonio Laghezza
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Marco Catto
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Francesco Limongelli
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Sílvia Chaves
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Paolo Tortorella
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Cosimo Damiano Altomare
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Maria Amélia Santos
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Fulvio Loiodice
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
| | - Luca Piemontese
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy
- Correspondence: (A.C.); (L.P.)
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Song M, Li Y, Gao R, Liu J, Huang Q. De novo design of DNA aptamers that target okadaic acid (OA) by docking-then-assembling of single nucleotides. Biosens Bioelectron 2022; 215:114562. [PMID: 35870338 DOI: 10.1016/j.bios.2022.114562] [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: 01/06/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022]
Abstract
Okadaic acid (OA) is a diarrhetic shellfish poison widespread in ocean, so its detection is of great significance to seafood safety. Because of good sensitivity and low cost, biosensors using nucleic-acid aptamers as the recognition molecules are emerging as an important detection tool. However, the traditional SELEX screening method for acquiring OA high-affinity aptamers is time- and resource-intensive. Alternatively, here we developed a de novo design method based on the 3D structure of a target molecule, such as OA. Without experimental screening, this method designs OA aptamers by a computational approach of docking-then-assembling (DTA) of single nucleotides (A, C, G and T) as: (1) determining the high-affinity nucleotide binding sites of the target molecule via saturated molecular docking; (2) assembling the bound nucleotides into binding units to the target molecule; (3) constructing full-length aptamers by introducing stabilizing units to connect these binding units. In this way, five OA aptamers were designed, and microscale thermophoresis (MST) experiments verified that their Kd values are in the range of 100-600 nM; and one of them (named 9CGAT_4_a) could specifically bind to OA with low affinities for the other three marine biotoxins. Therefore, this study provides high-affinity and specific aptamers for the development of OA biosensors, and presents a promising de novo design method applicable to other target molecules.
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Affiliation(s)
- Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuanyuan Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ruihua Gao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200438, China
| | - Jianping Liu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China; Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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Abstract
Background: PRMT5 is an epigenetics-related enzyme, which plays a critical role in cancer development. Hence PRMT5 inhibition has been validated as a promising therapeutic strategy. Methods & Results: We synthesized a series of methylpiperazinyl derivatives as novel PRMT5 inhibitors that were achieved by scaffold-hopping from EPZ015666 by virtual screening followed by rational drug design. Among all compounds 43g, bearing a thiourea linker, showed antitumor activity across multiple cancer cell lines and reduced the level of symmetric arginine dimethylation of SmD3 dose-dependently. Moreover, 43g selectively inhibited PRMT5 among protein arginine methyltransferase isoforms. Further proteomics analysis revealed that 43g remarkably reduced the global arginine dimethylation level in a cellular context. Conclusion: This work provides new chemical templates for future structural optimization of PRMT5-related cancer treatments.
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42
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Park S, Seok C. GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. J Chem Inf Model 2022; 62:3157-3168. [PMID: 35749367 DOI: 10.1021/acs.jcim.2c00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins interact with numerous water molecules to perform their physiological functions in biological organisms. Most water molecules act as solvent media; hence, their roles may be considered implicitly in theoretical treatments of protein structure and function. However, some water molecules interact intimately with proteins and require explicit treatment to understand their effects. Most physics-based computational methods are limited in their ability to accurately locate water molecules on protein surfaces because of inaccurate energy functions. Instead of relying on an energy function, this study attempts to learn the locations of water molecules from structural data. GalaxyWater-convolutional neural network (CNN) predicts water positions on protein chains, protein-protein interfaces, and protein-compound binding sites using a 3D-CNN model that is trained to generate a water score map on a given protein structure. The training data are compiled from high-resolution protein crystal structures resolved together with water molecules. GalaxyWater-CNN shows improved water prediction performance both in the coverage of crystal water molecules and in the accuracy of the predicted water positions when compared with previous energy-based methods. This method shows a superior performance in predicting water molecules that form hydrogen-bond networks precisely. The web service and the source code of this water prediction method are freely available at https://galaxy.seoklab.org/gwcnn and https://github.com/seoklab/GalaxyWater-CNN, respectively.
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Affiliation(s)
- Sangwoo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.,Galux Inc., Gwanak-gu, Seoul 08738, Republic of Korea
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43
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Design, synthesis, and biological evaluation of tetrahydroquinolinones and tetrahydroquinolines with anticancer activity. Sci Rep 2022; 12:9985. [PMID: 35705657 PMCID: PMC9200803 DOI: 10.1038/s41598-022-13867-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the most commonly diagnosed cancer in Europe and the United States and the second leading cause of cancer related mortality. A therapeutic strategy used for the treatment of CRC involves targeting the intracellular levels of reactive oxygen species (ROS). In this study, we synthesized a series of novel tetrahydroquinolinones and assessed their ability to inhibit CRC growth and proliferation by evoking cellular stress through ROS. Our results revealed that (2-oxo-4-phenyl-5,6,7,8-tetrahydroquinolin-8-yl) N-(3-fluorophenyl)carbamate (20d) exhibited in vitro antiproliferative activity at micromolar concentrations. The compound also suppressed colony formation and the migration of HCT-116 cells, as well as deregulated the expression of several proteins involved in cell proliferation and metastasis. Furthermore, 20d induced massive oxidative stress by disrupting the balance of cells survival resulting in autophagy via the PI3K/AKT/mTOR signaling pathway. These findings suggest that this tetrahydroquinolinone can be an ideal lead compound for drug discovery based on quinone derivatives.
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44
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Smith ST, Shub L, Meiler J. PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking. PLoS One 2022; 17:e0269072. [PMID: 35639743 PMCID: PMC9154094 DOI: 10.1371/journal.pone.0269072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/13/2022] [Indexed: 01/29/2023] Open
Abstract
Water molecules at the protein-small molecule interface often form hydrogen bonds with both the small molecule ligand and the protein, affecting the structural integrity and energetics of a binding event. The inclusion of these 'bridging waters' has been shown to improve the accuracy of predicted docked structures; however, due to increased computational costs, this step is typically omitted in ligand docking simulations. In this study, we introduce a resource-efficient, Rosetta-based protocol named "PlaceWaters" to predict the location of explicit interface bridging waters during a ligand docking simulation. In contrast to other explicit water methods, this protocol is independent of knowledge of number and location of crystallographic waters in homologous structures. We test this method on a diverse protein-small molecule benchmark set in comparison to other Rosetta-based protocols. Our results suggest that this coarse-grained, structure-based approach quickly and accurately predicts the location of bridging waters, improving our ability to computationally screen drug candidates.
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Affiliation(s)
- Shannon T. Smith
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Laura Shub
- Biomedical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Departments of Chemistry, Pharmacology, and Biomedical Informatics, Center for Structural Biology and Institute of Chemical Biology, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University Medical School, SAC, Leipzig, Germany
- * E-mail:
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Mteremko D, Shadrack DM, Ntie-Kang F, Chilongola J, Chacha M. Finding alternatives to 5-fluorouracil: application of ensemble-based virtual screening for drug repositioning against human thymidylate synthase. J Biomol Struct Dyn 2022:1-17. [PMID: 35538714 DOI: 10.1080/07391102.2022.2074140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
5-fluorouracil and analogs are used in the treatment of many solid tumours. However, there are many cases of resistance and high toxicity associated with 5-fluorouracil chemotherapy. Repurposing FDA drugs against human thymidylate synthase revealed a number of FDA drugs that have a potential to be further developed for the treatment of various cancers for which 5-fluorouracil and analogs have been used for chemotherapy. Four FDA drugs prioritized for further validation included Erismodegib, Irinotecan, Conivaptan and Ergotamine. The role of water in mediating drug interactions and its contribution to the total binding energy was also shown. MM-PBSA calculations revealed that the binding affinity was the lowest for the hTS-Ergotamine complex (-66.702 ± 1.807 kJ/mol) suggesting moderate inhibition despite a large energetic contribution from van der Waal interactions (-190.889 ± 1.027 kJ/mol).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Denis Mteremko
- Global Health and Biomedical Sciences, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | | | - Jaffu Chilongola
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Musa Chacha
- Global Health and Biomedical Sciences, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
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Ihara M, Tanaka K, Kai K, Hayashi H, Matsuda K. Competitive chrodrimanin B interactions with rat brain GABA A receptors revealed by radioligand binding assays. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 183:105074. [PMID: 35430068 DOI: 10.1016/j.pestbp.2022.105074] [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: 10/30/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Meroterpenoid compounds chrodrimanins produced by Talaromyces sp. YO-2 have been shown to act as competitive antagonists of silkworm larval GABAA receptors using electrophysiology, yet no further evidence has been provided to support such an action. We have investigated the actions of chrodrimanin B on rat brain GABAA receptors by binding assays with non-competitive ligand of GABAA receptors [3H]EBOB and competitive ligands [3H]gabazine and [3H]muscimol. Chrodrimanin B did not significantly affect the binding of [3H]EBOB while reducing the binding of [3H]gabazine and [3H]muscimol to the rat membrane preparations. Chrodrimanin B increased the dissociation constant Kd of [3H]gabazine and [3H]muscimol without significantly affecting the maximum binding, pointing to competitive interactions of chrodrimanin B with rat GABAA receptors in support of our previous observation that the compound acts as a competitive antagonist on the silkworm larval GABA receptor.
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Affiliation(s)
- Makoto Ihara
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Keiji Tanaka
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Kenji Kai
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Hideo Hayashi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Kazuhiko Matsuda
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University 3327-204 Nakamachi, Nara 631-8505, Japan; Agricultural Technology and Innovation Research Institute, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan.
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Liu C, Cai A, Li H, Deng N, Cho BP, Seeram NP, Ma H. Characterization of molecular interactions between cannabidiol and human plasma proteins (serum albumin and γ-globulin) by surface plasmon resonance, microcalorimetry, and molecular docking. J Pharm Biomed Anal 2022; 214:114750. [DOI: 10.1016/j.jpba.2022.114750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 01/22/2023]
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48
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Pan X, Wang H, Zhang Y, Wang X, Li C, Ji C, Zhang JZH. AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking. J Chem Inf Model 2022; 62:2499-2509. [PMID: 35452230 DOI: 10.1021/acs.jcim.1c01537] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The protein-ligand scoring function plays an important role in computer-aided drug discovery and is heavily used in virtual screening and lead optimization. In this study, we developed a new empirical protein-ligand scoring function with amino acid-specific interaction components for hydrogen bond, van der Waals, and electrostatic interactions. In addition, hydrophobic, π-stacking, π-cation, and metal-ligand interactions are also included in the new scoring function. To better evaluate the performance of the AA-Score, we generated several new test sets for evaluation of scoring, ranking, and docking performances, respectively. Extensive tests show that AA-Score performs well on scoring, docking, and ranking as compared to other widely used traditional scoring functions. The performance improvement of AA-Score benefits from the decomposition of individual interaction into amino acid-specific types. To facilitate applications, we developed an easy-to-use tool to analyze protein-ligand interaction fingerprint and predict binding affinity using the AA-Score. The source code and associated running examples can be found at https://github.com/xundrug/AA-Score-Tool.
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Affiliation(s)
- Xiaolin Pan
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Hao Wang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yueqing Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xingyu Wang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Cuiyu Li
- Advanced Computing East China Sub-center, Suma Technology Co., Ltd., Kunshan 215300, China
| | - Changge Ji
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, New York 10003, United States.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan Shanxi 030006, China
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Brunetti L, Leuci R, Carrieri A, Catto M, Occhineri S, Vinci G, Gambacorta L, Baltrukevich H, Chaves S, Laghezza A, Altomare CD, Tortorella P, Santos MA, Loiodice F, Piemontese L. Structure-based design of novel donepezil-like hybrids for a multi-target approach to the therapy of Alzheimer's disease. Eur J Med Chem 2022; 237:114358. [DOI: 10.1016/j.ejmech.2022.114358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 12/26/2022]
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Mastromarino M, Favia M, Schepetkin IA, Kirpotina LN, Trojan E, Niso M, Carrieri A, Leśkiewicz M, Regulska M, Darida M, Rossignolo F, Fontana S, Quinn MT, Basta-Kaim A, Leopoldo M, Lacivita E. Design, Synthesis, Biological Evaluation, and Computational Studies of Novel Ureidopropanamides as Formyl Peptide Receptor 2 (FPR2) Agonists to Target the Resolution of Inflammation in Central Nervous System Disorders. J Med Chem 2022; 65:5004-5028. [PMID: 35257581 PMCID: PMC9942528 DOI: 10.1021/acs.jmedchem.1c02203] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Formyl peptide receptor 2 (FPR2) agonists can boost the resolution of inflammation and can offer alternative approaches for the treatment of pathologies with underlying chronic neuroinflammation, including neurodegenerative disorders. Starting from the FPR2 agonist 2 previously identified in our laboratory and through fine-tuning of FPR2 potency and metabolic stability, we have identified a new series of ureidopropanamide derivatives endowed with a balanced combination of such properties. Computational studies provided insights into the key interactions of the new compounds for FPR2 activation. In mouse microglial N9 cells and in rat primary microglial cells stimulated with lipopolysaccharide, selected compounds inhibited the production of pro-inflammatory cytokines, counterbalanced the changes in mitochondrial function, and inhibited caspase-3 activity. Among the new agonists, (S)-11l stands out also for the ability to permeate the blood-brain barrier and to accumulate in the mouse brain in vivo, thus representing a valuable pharmacological tool for studies in vivo.
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Affiliation(s)
- Margherita Mastromarino
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona, 4, 70125 Bari, Italy
| | - Maria Favia
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona, 4, 70125 Bari, Italy
| | - Igor A Schepetkin
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, United States
| | - Lylia N Kirpotina
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, United States
| | - Ewa Trojan
- Laboratory of Immunoendocrinology, Department of Experimental Neuroendocrinology, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smȩtna St., 31-343 Kraków, Poland
| | - Mauro Niso
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona, 4, 70125 Bari, Italy
| | - Antonio Carrieri
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona, 4, 70125 Bari, Italy
| | - Monika Leśkiewicz
- Laboratory of Immunoendocrinology, Department of Experimental Neuroendocrinology, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smȩtna St., 31-343 Kraków, Poland
| | - Magdalena Regulska
- Laboratory of Immunoendocrinology, Department of Experimental Neuroendocrinology, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smȩtna St., 31-343 Kraków, Poland
| | | | | | - Stefano Fontana
- Aptuit Srl, an Evotec Company, Via A. Fleming, 4, 37135 Verona, Italy
| | - Mark T Quinn
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, United States
| | - Agnieszka Basta-Kaim
- Laboratory of Immunoendocrinology, Department of Experimental Neuroendocrinology, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smȩtna St., 31-343 Kraków, Poland
| | - Marcello Leopoldo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona, 4, 70125 Bari, Italy
| | - Enza Lacivita
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona, 4, 70125 Bari, Italy
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